1
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Santhanam B, Sluter M, Babu MM. Exploring GPCR signaling pathway networks as cancer therapeutic targets. Cell Genom 2024; 4:100560. [PMID: 38723606 PMCID: PMC11099381 DOI: 10.1016/j.xgen.2024.100560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 05/15/2024]
Abstract
GPCR signaling can contribute to establishing the tumor microenvironment and influence the progression and metabolism of tumors. Arora et al.1 describe a systems-level approach to investigate the patterns of co-expression of GPCR signaling pathway networks across diverse tumors and identify network components that correlate with patient-survival data across different cancer types.
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Affiliation(s)
- Balaji Santhanam
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN 38120, USA.
| | - Madison Sluter
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN 38120, USA.
| | - M Madan Babu
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN 38120, USA.
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2
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Lemke EA, Babu MM, Kriwacki RW, Mittag T, Pappu RV, Wright PE, Forman-Kay JD. Intrinsic disorder: A term to define the specific physicochemical characteristic of protein conformational heterogeneity. Mol Cell 2024; 84:1188-1190. [PMID: 38579677 DOI: 10.1016/j.molcel.2024.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 04/07/2024]
Abstract
In his commentary in this issue of Molecular Cell,1 Struhl reasons that the term "intrinsically disordered regions" represents a vague and confusing concept for protein function. However, the term "intrinsically disordered" highlights the important physicochemical characteristic of conformational heterogeneity. Thus, "intrinsically disordered" is the counterpart to the term "folded, " with neither term having specific functional implications.
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Affiliation(s)
- Edward A Lemke
- Biocenter, Johannes Gutenberg University, Hanns-Dieter-Hüsch Weg 17, 55128 Mainz, Germany; Institute for Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany.
| | - M Madan Babu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA; Center of Excellence for Data Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, USA.
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA.
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Julie D Forman-Kay
- Molecular Medicine Program, Hospital for Sick Children, Toronto ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto ON M5S 1A8, Canada.
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3
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Bell M, Lange S, Sejdiu BI, Ibanez J, Shi H, Sun X, Meng X, Nguyen P, Sutton M, Wagner J, Kc A, Langfitt D, Patil SL, Tan H, Pandey RV, Li Y, Yuan ZF, Anido AA, Ho M, Sheppard H, Vogel P, Yu J, Peng J, Chi H, Babu MM, Krenciute G, Gottschalk S. Modular chimeric cytokine receptors with leucine zippers enhance the antitumour activity of CAR T cells via JAK/STAT signalling. Nat Biomed Eng 2024; 8:380-396. [PMID: 38036617 DOI: 10.1038/s41551-023-01143-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 10/20/2023] [Indexed: 12/02/2023]
Abstract
The limited availability of cytokines in solid tumours hinders maintenance of the antitumour activity of chimeric antigen receptor (CAR) T cells. Cytokine receptor signalling pathways in CAR T cells can be activated by transgenic expression or injection of cytokines in the tumour, or by engineering the activation of cognate cytokine receptors. However, these strategies are constrained by toxicity arising from the activation of bystander cells, by the suboptimal biodistribution of the cytokines and by downregulation of the cognate receptor. Here we show that replacement of the extracellular domains of heterodimeric cytokine receptors in T cells with two leucine zipper motifs provides optimal Janus kinase/signal transducer and activator of transcription signalling. Such chimeric cytokine receptors, which can be generated for common γ-chain receptors, interleukin-10 and -12 receptors, enabled T cells to survive cytokine starvation without induction of autonomous cell growth, and augmented the effector function of CAR T cells in vitro in the setting of chronic antigen exposure and in human tumour xenografts in mice. As a modular design, leucine zippers can be used to generate constitutively active cytokine receptors in effector immune cells.
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Affiliation(s)
- Matthew Bell
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shannon Lange
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Besian I Sejdiu
- Center of Excellence for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jorge Ibanez
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hao Shi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiang Sun
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiaoxi Meng
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Phuong Nguyen
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Morgan Sutton
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jessica Wagner
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Anil Kc
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Deanna Langfitt
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sagar L Patil
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ram Vinay Pandey
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zuo-Fei Yuan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alejandro Allo Anido
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mitchell Ho
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Heather Sheppard
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter Vogel
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - M Madan Babu
- Center of Excellence for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Giedre Krenciute
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA.
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4
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Zoine JT, Immadisetty K, Ibanez-Vega J, Moore SE, Nevitt C, Thanekar U, Tian L, Karouni A, Chockley PJ, Arthur B, Sheppard H, Klco JM, Langfitt DM, Krenciute G, Gottschalk S, Babu MM, Velasquez MP. Peptide-scFv antigen recognition domains effectively confer CAR T cell multiantigen specificity. Cell Rep Med 2024; 5:101422. [PMID: 38350450 PMCID: PMC10897625 DOI: 10.1016/j.xcrm.2024.101422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/06/2023] [Accepted: 01/19/2024] [Indexed: 02/15/2024]
Abstract
The emergence of immune escape is a significant roadblock to developing effective chimeric antigen receptor (CAR) T cell therapies against hematological malignancies, including acute myeloid leukemia (AML). Here, we demonstrate feasibility of targeting two antigens simultaneously by combining a GRP78-specific peptide antigen recognition domain with a CD123-specific scFv to generate a peptide-scFv bispecific antigen recognition domain (78.123). To achieve this, we test linkers with varying length and flexibility and perform immunophenotypic and functional characterization. We demonstrate that bispecific CAR T cells successfully recognize and kill tumor cells that express GRP78, CD123, or both antigens and have improved antitumor activity compared to their monospecific counterparts when both antigens are expressed. Protein structure prediction suggests that linker length and compactness influence the functionality of the generated bispecific CARs. Thus, we present a bispecific CAR design strategy to prevent immune escape in AML that can be extended to other peptide-scFv combinations.
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Affiliation(s)
- Jaquelyn T Zoine
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kalyan Immadisetty
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Structural Biology and Center of Excellence for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jorge Ibanez-Vega
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sarah E Moore
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chris Nevitt
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Unmesha Thanekar
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Liqing Tian
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Abbas Karouni
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter J Chockley
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Bright Arthur
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Heather Sheppard
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Deanna M Langfitt
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Giedre Krenciute
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - M Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - M Paulina Velasquez
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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5
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Leslie BJ, Lang B, Babu MM. A genome-wide view of disordered proteins. Nat Biotechnol 2024; 42:32-34. [PMID: 37783848 DOI: 10.1038/s41587-023-01955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Affiliation(s)
- Benjamin J Leslie
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Benjamin Lang
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - M Madan Babu
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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6
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Li XH, Yu CWH, Gomez-Navarro N, Stancheva V, Zhu H, Murthy A, Wozny M, Malhotra K, Johnson CM, Blackledge M, Santhanam B, Liu W, Huang J, Freund SMV, Miller EA, Babu MM. Dynamic conformational changes of a tardigrade group-3 late embryogenesis abundant protein modulate membrane biophysical properties. PNAS Nexus 2024; 3:pgae006. [PMID: 38269070 PMCID: PMC10808001 DOI: 10.1093/pnasnexus/pgae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/26/2023] [Indexed: 01/26/2024]
Abstract
A number of intrinsically disordered proteins (IDPs) encoded in stress-tolerant organisms, such as tardigrade, can confer fitness advantage and abiotic stress tolerance when heterologously expressed. Tardigrade-specific disordered proteins including the cytosolic-abundant heat-soluble proteins are proposed to confer stress tolerance through vitrification or gelation, whereas evolutionarily conserved IDPs in tardigrades may contribute to stress tolerance through other biophysical mechanisms. In this study, we characterized the mechanism of action of an evolutionarily conserved, tardigrade IDP, HeLEA1, which belongs to the group-3 late embryogenesis abundant (LEA) protein family. HeLEA1 homologs are found across different kingdoms of life. HeLEA1 is intrinsically disordered in solution but shows a propensity for helical structure across its entire sequence. HeLEA1 interacts with negatively charged membranes via dynamic disorder-to-helical transition, mainly driven by electrostatic interactions. Membrane interaction of HeLEA1 is shown to ameliorate excess surface tension and lipid packing defects. HeLEA1 localizes to the mitochondrial matrix when expressed in yeast and interacts with model membranes mimicking inner mitochondrial membrane. Yeast expressing HeLEA1 shows enhanced tolerance to hyperosmotic stress under nonfermentative growth and increased mitochondrial membrane potential. Evolutionary analysis suggests that although HeLEA1 homologs have diverged their sequences to localize to different subcellular organelles, all homologs maintain a weak hydrophobic moment that is characteristic of weak and reversible membrane interaction. We suggest that such dynamic and weak protein-membrane interaction buffering alterations in lipid packing could be a conserved strategy for regulating membrane properties and represent a general biophysical solution for stress tolerance across the domains of life.
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Affiliation(s)
- Xiao-Han Li
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Conny W H Yu
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | | | - Hongni Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Andal Murthy
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Michael Wozny
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Ketan Malhotra
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Martin Blackledge
- Université Grenoble Alpes, CNRS, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Balaji Santhanam
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- Department of Structural Biology, Center of Excellence for Data-Driven Discovery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wei Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jinqing Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | | | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- Department of Structural Biology, Center of Excellence for Data-Driven Discovery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
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7
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Heydenreich FM, Marti-Solano M, Sandhu M, Kobilka BK, Bouvier M, Babu MM. Molecular determinants of ligand efficacy and potency in GPCR signaling. Science 2023; 382:eadh1859. [PMID: 38127743 PMCID: PMC7615523 DOI: 10.1126/science.adh1859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 11/07/2023] [Indexed: 12/23/2023]
Abstract
Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) bind to extracellular ligands and drugs and modulate intracellular responses through conformational changes. Despite their importance as drug targets, the molecular origins of pharmacological properties such as efficacy (maximum signaling response) and potency (the ligand concentration at half-maximal response) remain poorly understood for any ligand-receptor-signaling system. We used the prototypical adrenaline-β2 adrenergic receptor-G protein system to reveal how specific receptor residues decode and translate the information encoded in a ligand to mediate a signaling response. We present a data science framework to integrate pharmacological and structural data to uncover structural changes and allosteric networks relevant for ligand pharmacology. These methods can be tailored to study any ligand-receptor-signaling system, and the principles open possibilities for designing orthosteric and allosteric compounds with defined signaling properties.
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Affiliation(s)
- Franziska M. Heydenreich
- Department of Molecular and Cellular Physiology, Stanford University
School of Medicine, Stanford, CA, USA
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Biochemistry and Molecular Medicine, Institute for
Research in Immunology and Cancer, Université de Montréal, Montreal,
QC, Canada
| | - Maria Marti-Solano
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Pharmacology, University of Cambridge, Cambridge,
UK
| | - Manbir Sandhu
- Department of Pharmacology, University of Cambridge, Cambridge,
UK
| | - Brian K. Kobilka
- Department of Molecular and Cellular Physiology, Stanford University
School of Medicine, Stanford, CA, USA
| | - Michel Bouvier
- Department of Biochemistry and Molecular Medicine, Institute for
Research in Immunology and Cancer, Université de Montréal, Montreal,
QC, Canada
| | - M. Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Structural Biology and Center of Excellence for
Data-Driven Discovery, St. Jude Children’s Research Hospital, Memphis, TN,
USA
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8
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Casadio R, Babu MM. Editorial overview: Sequences and topology. Curr Opin Struct Biol 2023; 82:102677. [PMID: 37595511 DOI: 10.1016/j.sbi.2023.102677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Affiliation(s)
- Rita Casadio
- Biocomputing Group, University of Bologna, Italy.
| | - M Madan Babu
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA.
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9
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Tripathi S, Shirnekhi HK, Gorman SD, Chandra B, Baggett DW, Park CG, Somjee R, Lang B, Hosseini SMH, Pioso BJ, Li Y, Iacobucci I, Gao Q, Edmonson MN, Rice SV, Zhou X, Bollinger J, Mitrea DM, White MR, McGrail DJ, Jarosz DF, Yi SS, Babu MM, Mullighan CG, Zhang J, Sahni N, Kriwacki RW. Defining the condensate landscape of fusion oncoproteins. Nat Commun 2023; 14:6008. [PMID: 37770423 PMCID: PMC10539325 DOI: 10.1038/s41467-023-41655-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 09/13/2023] [Indexed: 09/30/2023] Open
Abstract
Fusion oncoproteins (FOs) arise from chromosomal translocations in ~17% of cancers and are often oncogenic drivers. Although some FOs can promote oncogenesis by undergoing liquid-liquid phase separation (LLPS) to form aberrant biomolecular condensates, the generality of this phenomenon is unknown. We explored this question by testing 166 FOs in HeLa cells and found that 58% formed condensates. The condensate-forming FOs displayed physicochemical features distinct from those of condensate-negative FOs and segregated into distinct feature-based groups that aligned with their sub-cellular localization and biological function. Using Machine Learning, we developed a predictor of FO condensation behavior, and discovered that 67% of ~3000 additional FOs likely form condensates, with 35% of those predicted to function by altering gene expression. 47% of the predicted condensate-negative FOs were associated with cell signaling functions, suggesting a functional dichotomy between condensate-positive and -negative FOs. Our Datasets and reagents are rich resources to interrogate FO condensation in the future.
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Affiliation(s)
- Swarnendu Tripathi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hazheen K Shirnekhi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott D Gorman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Arrakis Therapeutics, 830 Winter St, Waltham, MA, 02451, USA
| | - Bappaditya Chandra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David W Baggett
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheon-Gil Park
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ramiz Somjee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Rhodes College, Memphis, TN, USA
- Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - Benjamin Lang
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Seyed Mohammad Hadi Hosseini
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brittany J Pioso
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yongsheng Li
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qingsong Gao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael N Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen V Rice
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John Bollinger
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Diana M Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Dewpoint Therapeutics, 451 D Street, Suite 104, Boston, MA, 02210, USA
| | - Michael R White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- IDEXX Laboratories, Inc., One IDEXX Drive, Westbrook, ME, 04092, USA
| | - Daniel J McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - S Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Biomedical Engineering, and Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX, USA
| | - M Madan Babu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, USA.
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10
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Gunnarsson PA, Babu MM. Predicting evolutionary outcomes through the probability of accessing sequence variants. Sci Adv 2023; 9:eade2903. [PMID: 37506212 PMCID: PMC10381947 DOI: 10.1126/sciadv.ade2903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 06/27/2023] [Indexed: 07/30/2023]
Abstract
Natural selection can only operate on available genetic variation. Thus, determining the probability of accessing different sequence variants from a starting sequence can help predict evolutionary trajectories and outcomes. We define the concept of "variant accessibility" as the probability that a set of genotypes encoding a particular protein function will arise through mutations before subject to natural selection. This probability is shaped by the mutational biases of nucleotides and the structure of the genetic code. Using the influenza A virus as a model, we discuss how a more accessible but less fit variant can emerge as an adaptation rather than a more fit variant. We describe a genotype-accessibility landscape, complementary to the genotype-fitness landscape, that informs the likelihood of a starting sequence reaching different parts of genotype space. The proposed framework lays the foundation for predicting the emergence of adaptive genotypes in evolving systems such as viruses and tumors.
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Affiliation(s)
- P. Alexander Gunnarsson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Department of Structural Biology and Center of Excellence for Data-Driven Discovery, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - M. Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Department of Structural Biology and Center of Excellence for Data-Driven Discovery, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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11
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Polychronidou M, Hou J, Babu MM, Liberali P, Amit I, Deplancke B, Lahav G, Itzkovitz S, Mann M, Saez-Rodriguez J, Theis F, Eils R. Single-cell biology: what does the future hold? Mol Syst Biol 2023:e11799. [PMID: 37318792 DOI: 10.15252/msb.202311799] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/16/2023] Open
Affiliation(s)
| | | | - M Madan Babu
- Center for Data Driven Discovery, Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Ido Amit
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Bart Deplancke
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Galit Lahav
- Department of Systems Biology, Harvard Medical School, Boston, USA
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Matthias Mann
- Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Julio Saez-Rodriguez
- Faculty of Medicine, Heidelberg University Hospital, Heidelberg University, Heidelberg, Germany
| | | | - Roland Eils
- Berlin Institute of Health at Charité Universitätsmedizin Berlin, Berlin, Germany
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12
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Mészáros B, Park E, Malinverni D, Sejdiu BI, Immadisetty K, Sandhu M, Lang B, Babu MM. Recent breakthroughs in computational structural biology harnessing the power of sequences and structures. Curr Opin Struct Biol 2023; 80:102608. [PMID: 37182396 DOI: 10.1016/j.sbi.2023.102608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023]
Abstract
Recent advances in computational approaches and their integration into structural biology enable tackling increasingly complex questions. Here, we discuss several key areas, highlighting breakthroughs and remaining challenges. Theoretical modeling has provided tools to accurately predict and design protein structures on a scale currently difficult to achieve using experimental approaches. Molecular Dynamics simulations have become faster and more precise, delivering actionable information inaccessible by current experimental methods. Virtual screening workflows allow a high-throughput approach to discover ligands that bind and modulate protein function, while Machine Learning methods enable the design of proteins with new functionalities. Integrative structural biology combines several of these approaches, pushing the frontiers of structural and functional characterization to ever larger systems, advancing towards a complete understanding of the living cell. These breakthroughs will accelerate and significantly impact diverse areas of science.
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Affiliation(s)
- Bálint Mészáros
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Electa Park
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Duccio Malinverni
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/DucMalinverni
| | - Besian I Sejdiu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/bisejdiu
| | - Kalyan Immadisetty
- Department of Bone Marrow Transplantation & Cellular Therapy, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/k_immadisetty
| | - Manbir Sandhu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/M5andhu
| | - Benjamin Lang
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/langbnj
| | - M Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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13
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Malinverni D, Babu MM. Data-driven design of orthogonal protein-protein interactions. Sci Signal 2023; 16:eabm4484. [PMID: 36853962 DOI: 10.1126/scisignal.abm4484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Engineering protein-protein interactions to generate new functions presents a challenge with great potential for many applications, ranging from therapeutics to synthetic biology. To avoid unwanted cross-talk with preexisting protein interaction networks in a cell, the specificity and selectivity of newly engineered proteins must be controlled. Here, we developed a computational strategy that mimics gene duplication and the divergence of preexisting interacting protein pairs to design new interactions. We used the bacterial PhoQ-PhoP two-component system as a model system to demonstrate the feasibility of this strategy and validated the approach with known experimental results. The designed protein pairs are predicted to exclusively interact with each other and to be insulated from potential cross-talk with their native partners. Thus, our approach enables exploration of uncharted regions of the protein sequence space and the design of new interacting protein pairs.
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Affiliation(s)
- Duccio Malinverni
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.,Department of Structural Biology and Center of Excellence for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.,Department of Structural Biology and Center of Excellence for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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14
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Sandhu M, Cho A, Ma N, Mukhaleva E, Namkung Y, Lee S, Ghosh S, Lee JH, Gloriam DE, Laporte SA, Babu MM, Vaidehi N. Dynamic spatiotemporal determinants modulate GPCR:G protein coupling selectivity and promiscuity. Nat Commun 2022; 13:7428. [PMID: 36460632 PMCID: PMC9718833 DOI: 10.1038/s41467-022-34055-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/11/2022] [Indexed: 12/03/2022] Open
Abstract
Recent studies have shown that G protein coupled receptors (GPCRs) show selective and promiscuous coupling to different Gα protein subfamilies and yet the mechanisms of the range of coupling preferences remain unclear. Here, we use Molecular Dynamics (MD) simulations on ten GPCR:G protein complexes and show that the location (spatial) and duration (temporal) of intermolecular contacts at the GPCR:Gα protein interface play a critical role in how GPCRs selectively interact with G proteins. We identify that some GPCR:G protein interface contacts are common across Gα subfamilies and others specific to Gα subfamilies. Using large scale data analysis techniques on the MD simulation snapshots we derive a spatio-temporal code for contacts that confer G protein selective coupling and validated these contacts using G protein activation BRET assays. Our results demonstrate that promiscuous GPCRs show persistent sampling of the common contacts more than G protein specific contacts. These findings suggest that GPCRs maintain contact with G proteins through a common central interface, while the selectivity comes from G protein specific contacts at the periphery of the interface.
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Affiliation(s)
- Manbir Sandhu
- grid.410425.60000 0004 0421 8357Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010 USA ,grid.240871.80000 0001 0224 711XDepartment of Structural Biology, Center for Data Driven Discovery, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Aaron Cho
- grid.63984.300000 0000 9064 4811Department of Medicine, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1 Canada
| | - Ning Ma
- grid.410425.60000 0004 0421 8357Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010 USA
| | - Elizaveta Mukhaleva
- grid.410425.60000 0004 0421 8357Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010 USA ,grid.410425.60000 0004 0421 8357Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010 USA
| | - Yoon Namkung
- grid.63984.300000 0000 9064 4811Department of Medicine, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1 Canada
| | - Sangbae Lee
- grid.410425.60000 0004 0421 8357Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010 USA
| | - Soumadwip Ghosh
- grid.410425.60000 0004 0421 8357Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010 USA
| | - John H. Lee
- grid.410425.60000 0004 0421 8357Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010 USA
| | - David E. Gloriam
- grid.5254.60000 0001 0674 042XDepartment of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Stéphane A. Laporte
- grid.63984.300000 0000 9064 4811Department of Medicine, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1 Canada ,grid.14709.3b0000 0004 1936 8649Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6 Canada
| | - M. Madan Babu
- grid.240871.80000 0001 0224 711XDepartment of Structural Biology, Center for Data Driven Discovery, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA ,grid.42475.300000 0004 0605 769XMRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH UK
| | - Nagarajan Vaidehi
- grid.410425.60000 0004 0421 8357Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010 USA ,grid.410425.60000 0004 0421 8357Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010 USA
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15
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Eiamthong B, Meesawat P, Wongsatit T, Jitdee J, Sangsri R, Patchsung M, Aphicho K, Suraritdechachai S, Huguenin‐Dezot N, Tang S, Suginta W, Paosawatyanyong B, Babu MM, Chin JW, Pakotiprapha D, Bhanthumnavin W, Uttamapinant C. Inside Cover: Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio‐Functionalization of PET (Angew. Chem. Int. Ed. 37/2022). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/anie.202210188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Bhumrapee Eiamthong
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Piyachat Meesawat
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Thanakrit Wongsatit
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Jariya Jitdee
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Raweewan Sangsri
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Maturada Patchsung
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Kanokpol Aphicho
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Surased Suraritdechachai
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - Shan Tang
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Wipa Suginta
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - M. Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Worawan Bhanthumnavin
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
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16
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Eiamthong B, Meesawat P, Wongsatit T, Jitdee J, Sangsri R, Patchsung M, Aphicho K, Suraritdechachai S, Huguenin‐Dezot N, Tang S, Suginta W, Paosawatyanyong B, Babu MM, Chin JW, Pakotiprapha D, Bhanthumnavin W, Uttamapinant C. Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio‐Functionalization of PET. Angew Chem Int Ed Engl 2022; 61:e202203061. [PMID: 35656865 PMCID: PMC7613822 DOI: 10.1002/anie.202203061] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Indexed: 11/24/2022]
Abstract
We report a bioinformatic workflow and subsequent discovery of a new polyethylene terephthalate (PET) hydrolase, which we named MG8, from the human saliva metagenome. MG8 has robust PET plastic degradation activities under different temperature and salinity conditions, outperforming several naturally occurring and engineered hydrolases in degrading PET. Moreover, we genetically encoded 2,3-diaminopropionic acid (DAP) in place of the catalytic serine residue of MG8, thereby converting a PET hydrolase into a covalent binder for bio-functionalization of PET. We show that MG8(DAP), in conjunction with a split green fluorescent protein system, can be used to attach protein cargos to PET as well as other polyester plastics. The discovery of a highly active PET hydrolase from the human metagenome—currently an underexplored resource for industrial enzyme discovery—as well as the repurposing of such an enzyme into a plastic functionalization tool, should facilitate ongoing efforts to degrade and maximize reusability of PET.
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Affiliation(s)
- Bhumrapee Eiamthong
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Piyachat Meesawat
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Thanakrit Wongsatit
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Jariya Jitdee
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Raweewan Sangsri
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Maturada Patchsung
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Kanokpol Aphicho
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Surased Suraritdechachai
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - Shan Tang
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Wipa Suginta
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - M. Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Worawan Bhanthumnavin
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
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17
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Eiamthong B, Meesawat P, Wongsatit T, Jitdee J, Sangsri R, Patchsung M, Aphicho K, Suraritdechachai S, Huguenin‐Dezot N, Tang S, Suginta W, Paosawatyanyong B, Madan Babu M, Chin JW, Pakotiprapha D, Bhanthumnavin W, Uttamapinant C. Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio‐Functionalization of PET. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202210188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Bhumrapee Eiamthong
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Piyachat Meesawat
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Thanakrit Wongsatit
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Jariya Jitdee
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Raweewan Sangsri
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Maturada Patchsung
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Kanokpol Aphicho
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Surased Suraritdechachai
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - Shan Tang
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Wipa Suginta
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - M. Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Worawan Bhanthumnavin
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
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18
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Kleist AB, Jenjak S, Sente A, Laskowski LJ, Szpakowska M, Calkins MM, Anderson EI, McNally LM, Heukers R, Bobkov V, Peterson FC, Thomas MA, Chevigné A, Smit MJ, McCorvy JD, Babu MM, Volkman BF. Conformational selection guides β-arrestin recruitment at a biased G protein-coupled receptor. Science 2022; 377:222-228. [PMID: 35857540 PMCID: PMC9574477 DOI: 10.1126/science.abj4922] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
G protein-coupled receptors (GPCRs) recruit β-arrestins to coordinate diverse cellular processes, but the structural dynamics driving this process are poorly understood. Atypical chemokine receptors (ACKRs) are intrinsically biased GPCRs that engage β-arrestins but not G proteins, making them a model system for investigating the structural basis of β-arrestin recruitment. Here, we performed nuclear magnetic resonance (NMR) experiments on 13CH3-ε-methionine-labeled ACKR3, revealing that β-arrestin recruitment is associated with conformational exchange at key regions of the extracellular ligand-binding pocket and intracellular β-arrestin-coupling region. NMR studies of ACKR3 mutants defective in β-arrestin recruitment identified an allosteric hub in the receptor core that coordinates transitions among heterogeneously populated and selected conformational states. Our data suggest that conformational selection guides β-arrestin recruitment by tuning receptor dynamics at intracellular and extracellular regions.
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Affiliation(s)
- Andrew B Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Medical Scientist Training Program, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shawn Jenjak
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Andrija Sente
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Lauren J Laskowski
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Martyna Szpakowska
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), L-4354 Esch-sur-Alzette, Luxembourg
| | - Maggie M Calkins
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Emilie I Anderson
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Lisa M McNally
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Raimond Heukers
- Amsterdam Institute for Molecular and Life Sciences, Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit, 1081 HZ Amsterdam, Netherlands
| | - Vladimir Bobkov
- Amsterdam Institute for Molecular and Life Sciences, Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit, 1081 HZ Amsterdam, Netherlands
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monica A Thomas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Medical Scientist Training Program, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Andy Chevigné
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), L-4354 Esch-sur-Alzette, Luxembourg
| | - Martine J Smit
- Amsterdam Institute for Molecular and Life Sciences, Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit, 1081 HZ Amsterdam, Netherlands
| | - John D McCorvy
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - M Madan Babu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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19
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Eiamthong B, Meesawat P, Wongsatit T, Jitdee J, Sangsri R, Patchsung M, Aphicho K, Suraritdechachai S, Huguenin-Dezot N, Tang S, Suginta W, Paosawatyanyong B, Babu MM, Chin JW, Pakotiprapha D, Bhanthumnavin W, Uttamapinant C. Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio‐Functionalization of PET. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Bhumrapee Eiamthong
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering THAILAND
| | - Piyachat Meesawat
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering THAILAND
| | - Thanakrit Wongsatit
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering THAILAND
| | - Jariya Jitdee
- Chulalongkorn University Faculty of Science Chemistry THAILAND
| | | | - Maturada Patchsung
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | - Kanokpol Aphicho
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | - Surased Suraritdechachai
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | | | - Shan Tang
- MRC Laboratory of Molecular Biology Protein and nucleic acid chemistry UNITED KINGDOM
| | - Wipa Suginta
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | | | - M. Madan Babu
- St Jude Children's Research Hospital Department of Structural Biology Structural Biology UNITED STATES
| | - Jason W Chin
- MRC Laboratory of Molecular Biology Protein and nucleic acid chemistry UNITED KINGDOM
| | | | | | - Chayasith Uttamapinant
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering 555 Moo 1 PayupnaiWangchan Valley 21210 Rayong THAILAND
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20
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Umeda M, Ma J, Huang BJ, Hagiwara K, Westover T, Abdelhamed S, Barajas JM, Thomas ME, Walsh MP, Song G, Tian L, Liu Y, Chen X, Kolekar P, Tran Q, Foy SG, Maciaszek JL, Kleist AB, Leonti AR, Ju B, Easton J, Wu H, Valentine V, Valentine MB, Liu YC, Ries RE, Smith JL, Parganas E, Iacobucci I, Hiltenbrand R, Miller J, Myers JR, Rampersaud E, Rahbarinia D, Rusch M, Wu G, Inaba H, Wang YC, Alonzo TA, Downing JR, Mullighan CG, Pounds S, Babu MM, Zhang J, Rubnitz JE, Meshinchi S, Ma X, Klco JM. Integrated Genomic Analysis Identifies UBTF Tandem Duplications as a Recurrent Lesion in Pediatric Acute Myeloid Leukemia. Blood Cancer Discov 2022; 3:194-207. [PMID: 35176137 PMCID: PMC9780084 DOI: 10.1158/2643-3230.bcd-21-0160] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 08/27/2021] [Accepted: 01/24/2022] [Indexed: 01/21/2023] Open
Abstract
The genetics of relapsed pediatric acute myeloid leukemia (AML) has yet to be comprehensively defined. Here, we present the spectrum of genomic alterations in 136 relapsed pediatric AMLs. We identified recurrent exon 13 tandem duplications (TD) in upstream binding transcription factor (UBTF) in 9% of relapsed AML cases. UBTF-TD AMLs commonly have normal karyotype or trisomy 8 with cooccurring WT1 mutations or FLT3-ITD but not other known oncogenic fusions. These UBTF-TD events are stable during disease progression and are present in the founding clone. In addition, we observed that UBTF-TD AMLs account for approximately 4% of all de novo pediatric AMLs, are less common in adults, and are associated with poor outcomes and MRD positivity. Expression of UBTF-TD in primary hematopoietic cells is sufficient to enhance serial clonogenic activity and to drive a similar transcriptional program to UBTF-TD AMLs. Collectively, these clinical, genomic, and functional data establish UBTF-TD as a new recurrent mutation in AML. SIGNIFICANCE We defined the spectrum of mutations in relapsed pediatric AML and identified UBTF-TDs as a new recurrent genetic alteration. These duplications are more common in children and define a group of AMLs with intermediate-risk cytogenetic abnormalities, FLT3-ITD and WT1 alterations, and are associated with poor outcomes. See related commentary by Hasserjian and Nardi, p. 173. This article is highlighted in the In This Issue feature, p. 171.
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Affiliation(s)
- Masayuki Umeda
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Benjamin J. Huang
- Department of Pediatrics, University of California, Benioff Children's Hospital, San Francisco, California
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Juan M. Barajas
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Melvin E. Thomas
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael P. Walsh
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Pandurang Kolekar
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Quang Tran
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Scott G. Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jamie L. Maciaszek
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew B. Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Amanda R. Leonti
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Bengsheng Ju
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Huiyun Wu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | | | - Yen-Chun Liu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Rhonda E. Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jenny L. Smith
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Evan Parganas
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ryan Hiltenbrand
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jonathan Miller
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jason R. Myers
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Delaram Rahbarinia
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Todd A. Alonzo
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - James R. Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - M. Madan Babu
- Department of Structural Biology and the Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jeffrey E. Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jeffery M. Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
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21
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Pan M, Wright WC, Chapple RH, Zubair A, Sandhu M, Batchelder JE, Huddle BC, Low J, Blankenship KB, Wang Y, Gordon B, Archer P, Brady SW, Natarajan S, Posgai MJ, Schuetz J, Miller D, Kalathur R, Chen S, Connelly JP, Babu MM, Dyer MA, Pruett-Miller SM, Freeman BB, Chen T, Godley LA, Blanchard SC, Stewart E, Easton J, Geeleher P. The chemotherapeutic CX-5461 primarily targets TOP2B and exhibits selective activity in high-risk neuroblastoma. Nat Commun 2021; 12:6468. [PMID: 34753908 PMCID: PMC8578635 DOI: 10.1038/s41467-021-26640-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 10/13/2021] [Indexed: 12/26/2022] Open
Abstract
Survival in high-risk pediatric neuroblastoma has remained around 50% for the last 20 years, with immunotherapies and targeted therapies having had minimal impact. Here, we identify the small molecule CX-5461 as selectively cytotoxic to high-risk neuroblastoma and synergistic with low picomolar concentrations of topoisomerase I inhibitors in improving survival in vivo in orthotopic patient-derived xenograft neuroblastoma mouse models. CX-5461 recently progressed through phase I clinical trial as a first-in-human inhibitor of RNA-POL I. However, we also use a comprehensive panel of in vitro and in vivo assays to demonstrate that CX-5461 has been mischaracterized and that its primary target at pharmacologically relevant concentrations, is in fact topoisomerase II beta (TOP2B), not RNA-POL I. This is important because existing clinically approved chemotherapeutics have well-documented off-target interactions with TOP2B, which have previously been shown to cause both therapy-induced leukemia and cardiotoxicity-often-fatal adverse events, which can emerge several years after treatment. Thus, while we show that combination therapies involving CX-5461 have promising anti-tumor activity in vivo in neuroblastoma, our identification of TOP2B as the primary target of CX-5461 indicates unexpected safety concerns that should be examined in ongoing phase II clinical trials in adult patients before pursuing clinical studies in children.
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Affiliation(s)
- Min Pan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - William C Wright
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Richard H Chapple
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Asif Zubair
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Manbir Sandhu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jake E Batchelder
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Brandt C Huddle
- The Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Jonathan Low
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kaley B Blankenship
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yingzhe Wang
- Preclinical Pharmacokinetic Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Brittney Gordon
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Payton Archer
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Samuel W Brady
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Sivaraman Natarajan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Matthew J Posgai
- Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - John Schuetz
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Darcie Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Ravi Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Siquan Chen
- Cellular Screening Center, The University of Chicago, Chicago, IL, 60637, USA
| | - Jon Patrick Connelly
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - M Madan Babu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Burgess B Freeman
- Preclinical Pharmacokinetic Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Lucy A Godley
- Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Elizabeth Stewart
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Paul Geeleher
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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22
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Hauser AS, Kooistra AJ, Munk C, Heydenreich FM, Veprintsev DB, Bouvier M, Babu MM, Gloriam DE. GPCR activation mechanisms across classes and macro/microscales. Nat Struct Mol Biol 2021; 28:879-888. [PMID: 34759375 PMCID: PMC8580822 DOI: 10.1038/s41594-021-00674-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 09/22/2021] [Indexed: 12/27/2022]
Abstract
Two-thirds of human hormones and one-third of clinical drugs activate ~350 G-protein-coupled receptors (GPCR) belonging to four classes: A, B1, C and F. Whereas a model of activation has been described for class A, very little is known about the activation of the other classes, which differ by being activated by endogenous ligands bound mainly or entirely extracellularly. Here we show that, although they use the same structural scaffold and share several 'helix macroswitches', the GPCR classes differ in their 'residue microswitch' positions and contacts. We present molecular mechanistic maps of activation for each GPCR class and methods for contact analysis applicable for any functional determinants. This provides a superfamily residue-level rationale for conformational selection and allosteric communication by ligands and G proteins, laying the foundation for receptor-function studies and drugs with the desired modality.
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Affiliation(s)
- Alexander S Hauser
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Albert J Kooistra
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Christian Munk
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Data Tools Department, Novozymes A/S, Copenhagen, Denmark
| | - Franziska M Heydenreich
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biochemistry and Molecular Medicine, Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
- Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Dmitry B Veprintsev
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Nottingham, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Michel Bouvier
- Department of Biochemistry and Molecular Medicine, Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - M Madan Babu
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
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23
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Schlick T, Sundberg EJ, Schroeder SJ, Babu MM. Biophysicists' continued outstanding response to COVID-19. Biophys J 2021; 120:E1. [PMID: 34265250 PMCID: PMC8279538 DOI: 10.1016/j.bpj.2021.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 06/21/2021] [Indexed: 11/03/2022] Open
Affiliation(s)
- Tamar Schlick
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, New York.
| | - Eric J Sundberg
- Department of Biochemistry, Emory University, Atlanta, Georgia
| | - Susan J Schroeder
- Department of Chemistry and Biochemistry, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma
| | - M Madan Babu
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, Tennessee
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24
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Affiliation(s)
- Benjamin Lang
- Department of Structural Biology and the Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - M Madan Babu
- Department of Structural Biology and the Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA.
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25
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Sveidahl Johansen O, Ma T, Hansen JB, Markussen LK, Schreiber R, Reverte-Salisa L, Dong H, Christensen DP, Sun W, Gnad T, Karavaeva I, Nielsen TS, Kooijman S, Cero C, Dmytriyeva O, Shen Y, Razzoli M, O'Brien SL, Kuipers EN, Nielsen CH, Orchard W, Willemsen N, Jespersen NZ, Lundh M, Sustarsic EG, Hallgren CM, Frost M, McGonigle S, Isidor MS, Broholm C, Pedersen O, Hansen JB, Grarup N, Hansen T, Kjær A, Granneman JG, Babu MM, Calebiro D, Nielsen S, Rydén M, Soccio R, Rensen PCN, Treebak JT, Schwartz TW, Emanuelli B, Bartolomucci A, Pfeifer A, Zechner R, Scheele C, Mandrup S, Gerhart-Hines Z. Lipolysis drives expression of the constitutively active receptor GPR3 to induce adipose thermogenesis. Cell 2021; 184:3502-3518.e33. [PMID: 34048700 PMCID: PMC8238500 DOI: 10.1016/j.cell.2021.04.037] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 02/10/2021] [Accepted: 04/23/2021] [Indexed: 12/19/2022]
Abstract
Thermogenic adipocytes possess a therapeutically appealing, energy-expending capacity, which is canonically cold-induced by ligand-dependent activation of β-adrenergic G protein-coupled receptors (GPCRs). Here, we uncover an alternate paradigm of GPCR-mediated adipose thermogenesis through the constitutively active receptor, GPR3. We show that the N terminus of GPR3 confers intrinsic signaling activity, resulting in continuous Gs-coupling and cAMP production without an exogenous ligand. Thus, transcriptional induction of Gpr3 represents the regulatory parallel to ligand-binding of conventional GPCRs. Consequently, increasing Gpr3 expression in thermogenic adipocytes is alone sufficient to drive energy expenditure and counteract metabolic disease in mice. Gpr3 transcription is cold-stimulated by a lipolytic signal, and dietary fat potentiates GPR3-dependent thermogenesis to amplify the response to caloric excess. Moreover, we find GPR3 to be an essential, adrenergic-independent regulator of human brown adipocytes. Taken together, our findings reveal a noncanonical mechanism of GPCR control and thermogenic activation through the lipolysis-induced expression of constitutively active GPR3.
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Affiliation(s)
- Olivia Sveidahl Johansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Embark Biotech ApS, Copenhagen, Denmark; Center for Adipocyte Signaling, University of Southern Denmark, Odense, Denmark
| | - Tao Ma
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Embark Biotech ApS, Copenhagen, Denmark
| | - Jakob Bondo Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Embark Biotech ApS, Copenhagen, Denmark
| | - Lasse Kruse Markussen
- Center for Adipocyte Signaling, University of Southern Denmark, Odense, Denmark; Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Renate Schreiber
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Laia Reverte-Salisa
- Institute of Pharmacology and Toxicology, University Hospital, University of Bonn, Bonn, Germany
| | - Hua Dong
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | | - Wenfei Sun
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Thorsten Gnad
- Institute of Pharmacology and Toxicology, University Hospital, University of Bonn, Bonn, Germany
| | - Iuliia Karavaeva
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Svava Nielsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Sander Kooijman
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Cheryl Cero
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - Oksana Dmytriyeva
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Yachen Shen
- Institute for Diabetes, Obesity, and Metabolism, Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Maria Razzoli
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - Shannon L O'Brien
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Birmingham, UK; Institute of Pharmacology and Toxicology and Bio-Imaging Center, University of Würzburg, Würzburg, Germany
| | - Eline N Kuipers
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Carsten Haagen Nielsen
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Physiology, Nuclear Medicine & PET and Cluster for Molecular Imaging, Rigshospitalet, Copenhagen, Denmark
| | | | - Nienke Willemsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Naja Zenius Jespersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Centre of Inflammation and Metabolism and Centre for Physical Activity Research, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Morten Lundh
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Elahu Gosney Sustarsic
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Cecilie Mørch Hallgren
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Frost
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Seth McGonigle
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - Marie Sophie Isidor
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Christa Broholm
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Bo Hansen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Kjær
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Physiology, Nuclear Medicine & PET and Cluster for Molecular Imaging, Rigshospitalet, Copenhagen, Denmark
| | - James G Granneman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, UK; Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Davide Calebiro
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Birmingham, UK; Institute of Pharmacology and Toxicology and Bio-Imaging Center, University of Würzburg, Würzburg, Germany
| | - Søren Nielsen
- Centre of Inflammation and Metabolism and Centre for Physical Activity Research, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Mikael Rydén
- Department of Medicine (H7), Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Raymond Soccio
- Institute for Diabetes, Obesity, and Metabolism, Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Patrick C N Rensen
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Jonas Thue Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Thue Walter Schwartz
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Embark Biotech ApS, Copenhagen, Denmark
| | - Brice Emanuelli
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Alessandro Bartolomucci
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - Alexander Pfeifer
- Institute of Pharmacology and Toxicology, University Hospital, University of Bonn, Bonn, Germany
| | - Rudolf Zechner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Camilla Scheele
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Mandrup
- Center for Adipocyte Signaling, University of Southern Denmark, Odense, Denmark; Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Zachary Gerhart-Hines
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Embark Biotech ApS, Copenhagen, Denmark; Center for Adipocyte Signaling, University of Southern Denmark, Odense, Denmark.
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26
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Schlick T, Sundberg EJ, Schroeder SJ, Babu MM. Biophysicists' outstanding response to Covid-19. Biophys J 2021; 120:E1-E2. [PMID: 33689685 PMCID: PMC7931721 DOI: 10.1016/j.bpj.2021.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | | | - M Madan Babu
- St Jude Children's Research Hospital, Memphis, Tennessee
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27
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Lam SD, Babu MM, Lees J, Orengo CA. Biological impact of mutually exclusive exon switching. PLoS Comput Biol 2021; 17:e1008708. [PMID: 33651795 PMCID: PMC7954323 DOI: 10.1371/journal.pcbi.1008708] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 03/12/2021] [Accepted: 01/14/2021] [Indexed: 12/27/2022] Open
Abstract
Alternative splicing can expand the diversity of proteomes. Homologous mutually exclusive exons (MXEs) originate from the same ancestral exon and result in polypeptides with similar structural properties but altered sequence. Why would some genes switch homologous exons and what are their biological impact? Here, we analyse the extent of sequence, structural and functional variability in MXEs and report the first large scale, structure-based analysis of the biological impact of MXE events from different genomes. MXE-specific residues tend to map to single domains, are highly enriched in surface exposed residues and cluster at or near protein functional sites. Thus, MXE events are likely to maintain the protein fold, but alter specificity and selectivity of protein function. This comprehensive resource of MXE events and their annotations is available at: http://gene3d.biochem.ucl.ac.uk/mxemod/. These findings highlight how small, but significant changes at critical positions on a protein surface are exploited in evolution to alter function.
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Affiliation(s)
- Su Datt Lam
- Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, United Kingdom
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
- * E-mail: (SDL); (JL); (CO)
| | - M. Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Structural Biology and Center for Data Driven Discovery, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Jonathan Lees
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
- * E-mail: (SDL); (JL); (CO)
| | - Christine A. Orengo
- Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, United Kingdom
- * E-mail: (SDL); (JL); (CO)
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28
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Brouwers B, de Oliveira EM, Marti-Solano M, Monteiro FBF, Laurin SA, Keogh JM, Henning E, Bounds R, Daly CA, Houston S, Ayinampudi V, Wasiluk N, Clarke D, Plouffe B, Bouvier M, Babu MM, Farooqi IS, Mokrosiński J. Human MC4R variants affect endocytosis, trafficking and dimerization revealing multiple cellular mechanisms involved in weight regulation. Cell Rep 2021; 34:108862. [PMID: 33761344 PMCID: PMC7994375 DOI: 10.1016/j.celrep.2021.108862] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/29/2021] [Accepted: 02/19/2021] [Indexed: 12/13/2022] Open
Abstract
The Melanocortin-4 Receptor (MC4R) plays a pivotal role in energy homeostasis. We used human MC4R mutations associated with an increased or decreased risk of obesity to dissect mechanisms that regulate MC4R function. Most obesity-associated mutations impair trafficking to the plasma membrane (PM), whereas obesity-protecting mutations either accelerate recycling to the PM or decrease internalization, resulting in enhanced signaling. MC4R mutations that do not affect canonical Gαs protein-mediated signaling, previously considered to be non-pathogenic, nonetheless disrupt agonist-induced internalization, β-arrestin recruitment, and/or coupling to Gαs, establishing their causal role in severe obesity. Structural mapping reveals ligand-accessible sites by which MC4R couples to effectors and residues involved in the homodimerization of MC4R, which is disrupted by multiple obesity-associated mutations. Human genetic studies reveal that endocytosis, intracellular trafficking, and homodimerization regulate MC4R function to a level that is physiologically relevant, supporting the development of chaperones, agonists, and allosteric modulators of MC4R for weight loss therapy.
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Affiliation(s)
- Bas Brouwers
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Edson Mendes de Oliveira
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | | | - Fabiola B F Monteiro
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Suli-Anne Laurin
- Institute for Research in Immunology and Cancer, Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Julia M Keogh
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Elana Henning
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Rebecca Bounds
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Carole A Daly
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Shane Houston
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Vikram Ayinampudi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Natalia Wasiluk
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - David Clarke
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Bianca Plouffe
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Michel Bouvier
- Institute for Research in Immunology and Cancer, Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, UK; Department of Structural Biology and Center for Data Driven Discovery, St Jude Children's Research Hospital, Memphis, TN, USA
| | - I Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.
| | - Jacek Mokrosiński
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
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29
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Dishman AF, Tyler RC, Fox JC, Kleist AB, Prehoda KE, Babu MM, Peterson FC, Volkman BF. Evolution of fold switching in a metamorphic protein. Science 2021; 371:86-90. [PMID: 33384377 PMCID: PMC8017559 DOI: 10.1126/science.abd8700] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/11/2020] [Indexed: 12/14/2022]
Abstract
Metamorphic proteins switch between different folds, defying the protein folding paradigm. It is unclear how fold switching arises during evolution. With ancestral reconstruction and nuclear magnetic resonance, we studied the evolution of the metamorphic human protein XCL1, which has two distinct folds with different functions, making it an unusual member of the chemokine family, whose members generally adopt one conserved fold. XCL1 evolved from an ancestor with the chemokine fold. Evolution of a dimer interface, changes in structural constraints and molecular strain, and alteration of intramolecular protein contacts drove the evolution of metamorphosis. Then, XCL1 likely evolved to preferentially populate the noncanonical fold before reaching its modern-day near-equal population of folds. These discoveries illuminate how one sequence has evolved to encode multiple structures, revealing principles for protein design and engineering.
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Affiliation(s)
- Acacia F Dishman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
- Medical Scientist Training Program, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Robert C Tyler
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jamie C Fox
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Andrew B Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
- Medical Scientist Training Program, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Kenneth E Prehoda
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.
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30
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Stancheva VG, Li XH, Hutchings J, Gomez-Navarro N, Santhanam B, Babu MM, Zanetti G, Miller EA. Combinatorial multivalent interactions drive cooperative assembly of the COPII coat. J Cell Biol 2020; 219:e202007135. [PMID: 32997735 PMCID: PMC7594496 DOI: 10.1083/jcb.202007135] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 12/31/2022] Open
Abstract
Protein secretion is initiated at the endoplasmic reticulum by the COPII coat, which self-assembles to form vesicles. Here, we examine the mechanisms by which a cargo-bound inner coat layer recruits and is organized by an outer scaffolding layer to drive local assembly of a stable structure rigid enough to enforce membrane curvature. An intrinsically disordered region in the outer coat protein, Sec31, drives binding with an inner coat layer via multiple distinct interfaces, including a newly defined charge-based interaction. These interfaces combinatorially reinforce each other, suggesting coat oligomerization is driven by the cumulative effects of multivalent interactions. The Sec31 disordered region could be replaced by evolutionarily distant sequences, suggesting plasticity in the binding interfaces. Such a multimodal assembly platform provides an explanation for how cells build a powerful yet transient scaffold to direct vesicle traffic.
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Affiliation(s)
| | - Xiao-Han Li
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Joshua Hutchings
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK
| | | | | | | | - Giulia Zanetti
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK
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31
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Marti-Solano M, Crilly SE, Malinverni D, Munk C, Harris M, Pearce A, Quon T, Mackenzie AE, Wang X, Peng J, Tobin AB, Ladds G, Milligan G, Gloriam DE, Puthenveedu MA, Babu MM. Combinatorial expression of GPCR isoforms affects signalling and drug responses. Nature 2020; 587:650-656. [PMID: 33149304 PMCID: PMC7611127 DOI: 10.1038/s41586-020-2888-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 09/24/2020] [Indexed: 02/06/2023]
Abstract
G-protein-coupled receptors (GPCRs) are membrane proteins that modulate physiology across human tissues in response to extracellular signals. GPCR-mediated signalling can differ because of changes in the sequence1,2 or expression3 of the receptors, leading to signalling bias when comparing diverse physiological systems4. An underexplored source of such bias is the generation of functionally diverse GPCR isoforms with different patterns of expression across different tissues. Here we integrate data from human tissue-level transcriptomes, GPCR sequences and structures, proteomics, single-cell transcriptomics, population-wide genetic association studies and pharmacological experiments. We show how a single GPCR gene can diversify into several isoforms with distinct signalling properties, and how unique isoform combinations expressed in different tissues can generate distinct signalling states. Depending on their structural changes and expression patterns, some of the detected isoforms may influence cellular responses to drugs and represent new targets for developing drugs with improved tissue selectivity. Our findings highlight the need to move from a canonical to a context-specific view of GPCR signalling that considers how combinatorial expression of isoforms in a particular cell type, tissue or organism collectively influences receptor signalling and drug responses.
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Affiliation(s)
| | - Stephanie E Crilly
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Duccio Malinverni
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Structural Biology and Center for Data Driven Discovery, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Christian Munk
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Matthew Harris
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Abigail Pearce
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Tezz Quon
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Amanda E Mackenzie
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Biology, University of North Dakota, Grand Forks, ND, USA
| | - Junmin Peng
- Center for Proteomics and Metabolomics, St Jude Children's Research Hospital, Memphis, TN, USA
- Departments of Structural Biology and Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Andrew B Tobin
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Graeme Milligan
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Manojkumar A Puthenveedu
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, UK.
- Department of Structural Biology and Center for Data Driven Discovery, St Jude Children's Research Hospital, Memphis, TN, USA.
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32
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Jones EM, Lubock NB, Venkatakrishnan AJ, Wang J, Tseng AM, Paggi JM, Latorraca NR, Cancilla D, Satyadi M, Davis JE, Babu MM, Dror RO, Kosuri S. Structural and functional characterization of G protein-coupled receptors with deep mutational scanning. eLife 2020; 9:54895. [PMID: 33084570 PMCID: PMC7707821 DOI: 10.7554/elife.54895] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 10/16/2020] [Indexed: 01/14/2023] Open
Abstract
The >800 human G protein–coupled receptors (GPCRs) are responsible for transducing diverse chemical stimuli to alter cell state- and are the largest class of drug targets. Their myriad structural conformations and various modes of signaling make it challenging to understand their structure and function. Here, we developed a platform to characterize large libraries of GPCR variants in human cell lines with a barcoded transcriptional reporter of G protein signal transduction. We tested 7800 of 7828 possible single amino acid substitutions to the beta-2 adrenergic receptor (β2AR) at four concentrations of the agonist isoproterenol. We identified residues specifically important for β2AR signaling, mutations in the human population that are potentially loss of function, and residues that modulate basal activity. Using unsupervised learning, we identify residues critical for signaling, including all major structural motifs and molecular interfaces. We also find a previously uncharacterized structural latch spanning the first two extracellular loops that is highly conserved across Class A GPCRs and is conformationally rigid in both the inactive and active states of the receptor. More broadly, by linking deep mutational scanning with engineered transcriptional reporters, we establish a generalizable method for exploring pharmacogenomics, structure and function across broad classes of drug receptors.
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Affiliation(s)
- Eric M Jones
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Nathan B Lubock
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - A J Venkatakrishnan
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Jeffrey Wang
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Alex M Tseng
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Joseph M Paggi
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Naomi R Latorraca
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Daniel Cancilla
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Megan Satyadi
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Jessica E Davis
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Ron O Dror
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
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33
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Yu X, Nagai J, Marti-Solano M, Soto JS, Coppola G, Babu MM, Khakh BS. Context-Specific Striatal Astrocyte Molecular Responses Are Phenotypically Exploitable. Neuron 2020; 108:1146-1162.e10. [PMID: 33086039 DOI: 10.1016/j.neuron.2020.09.021] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 08/13/2020] [Accepted: 09/16/2020] [Indexed: 12/14/2022]
Abstract
Astrocytes tile the central nervous system and are widely implicated in brain diseases, but the molecular mechanisms by which astrocytes contribute to brain disorders remain incompletely explored. By performing astrocyte gene expression analyses following 14 experimental perturbations of relevance to the striatum, we discovered that striatal astrocytes mount context-specific molecular responses at the level of genes, pathways, and upstream regulators. Through data mining, we also identified astrocyte pathways in Huntington's disease (HD) that were reciprocally altered with respect to the activation of striatal astrocyte G protein-coupled receptor (GPCR) signaling. Furthermore, selective striatal astrocyte stimulation of the Gi-GPCR pathway in vivo corrected several HD-associated astrocytic, synaptic, and behavioral phenotypes, with accompanying improvement of HD-associated astrocyte signaling pathways, including those related to synaptogenesis and neuroimmune functions. Overall, our data show that astrocytes are malleable, using context-specific responses that can be dissected molecularly and used for phenotypic benefit in brain disorders.
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Affiliation(s)
- Xinzhu Yu
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1751, USA
| | - Jun Nagai
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1751, USA
| | - Maria Marti-Solano
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Joselyn S Soto
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1751, USA
| | - Giovanni Coppola
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1751, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1751, USA; Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1751, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK; Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Baljit S Khakh
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1751, USA; Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1751, USA.
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34
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Masuho I, Balaji S, Muntean BS, Skamangas NK, Chavali S, Tesmer JJG, Babu MM, Martemyanov KA. A Global Map of G Protein Signaling Regulation by RGS Proteins. Cell 2020; 183:503-521.e19. [PMID: 33007266 PMCID: PMC7572916 DOI: 10.1016/j.cell.2020.08.052] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 07/03/2020] [Accepted: 08/29/2020] [Indexed: 12/24/2022]
Abstract
The control over the extent and timing of G protein signaling is provided by the regulator of G protein signaling (RGS) proteins that deactivate G protein α subunits (Gα). Mammalian genomes encode 20 canonical RGS and 16 Gα genes with key roles in physiology and disease. To understand the principles governing the selectivity of Gα regulation by RGS, we examine the catalytic activity of all canonical human RGS proteins and their selectivity for a complete set of Gα substrates using real-time kinetic measurements in living cells. The data reveal rules governing RGS-Gα recognition, the structural basis of its selectivity, and provide principles for engineering RGS proteins with defined selectivity. The study also explores the evolution of RGS-Gα selectivity through ancestral reconstruction and demonstrates how naturally occurring non-synonymous variants in RGS alter signaling. These results provide a blueprint for decoding signaling selectivity and advance our understanding of molecular recognition principles. Systematic analysis reveals G protein selectivity of all canonical RGS proteins RGS proteins rely on selectivity bar codes for selective G protein recognition Transplantation of bar codes across RGS proteins switches their G protein preferences Natural variants, mutations, and evolution shape RGS selectivity
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Affiliation(s)
- Ikuo Masuho
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL 33458, USA
| | - Santhanam Balaji
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Departments of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Brian S Muntean
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL 33458, USA
| | - Nickolas K Skamangas
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL 33458, USA
| | - Sreenivas Chavali
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Karakambadi Road, Tirupati 517 507, India
| | - John J G Tesmer
- Departments of Biological Sciences and Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907-2054, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Departments of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kirill A Martemyanov
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL 33458, USA.
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35
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Abstract
Amino acid homorepeats, or homorepeats, are polypeptide segments found in proteins that contain stretches of identical amino acid residues. Although abnormal homorepeat expansions are linked to pathologies such as neurodegenerative diseases, homorepeats are prevalent in eukaryotic proteomes, suggesting that they are important for normal physiology. In this Review, we discuss recent advances in our understanding of the biological functions of homorepeats, which range from facilitating subcellular protein localization to mediating interactions between proteins across diverse cellular pathways. We explore how the functional diversity of homorepeat-containing proteins could be linked to the ability of homorepeats to adopt different structural conformations, an ability influenced by repeat composition, repeat length and the nature of flanking sequences. We conclude by highlighting how an understanding of homorepeats will help us better characterize and develop therapeutics against the human diseases to which they contribute.
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Affiliation(s)
- Sreenivas Chavali
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India.
| | - Anjali K Singh
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
| | - Balaji Santhanam
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA.
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36
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Heifetz A, Morao I, Babu MM, James T, Southey MWY, Fedorov DG, Aldeghi M, Bodkin MJ, Townsend-Nicholson A. Characterizing Interhelical Interactions of G-Protein Coupled Receptors with the Fragment Molecular Orbital Method. J Chem Theory Comput 2020; 16:2814-2824. [PMID: 32096994 PMCID: PMC7161079 DOI: 10.1021/acs.jctc.9b01136] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
G-protein coupled receptors (GPCRs) are the largest superfamily of membrane proteins, regulating almost every aspect of cellular activity and serving as key targets for drug discovery. We have identified an accurate and reliable computational method to characterize the strength and chemical nature of the interhelical interactions between the residues of transmembrane (TM) domains during different receptor activation states, something that cannot be characterized solely by visual inspection of structural information. Using the fragment molecular orbital (FMO) quantum mechanics method to analyze 35 crystal structures representing different branches of the class A GPCR family, we have identified 69 topologically equivalent TM residues that form a consensus network of 51 inter-TM interactions, providing novel results that are consistent with and help to rationalize experimental data. This discovery establishes a comprehensive picture of how defined molecular forces govern specific interhelical interactions which, in turn, support the structural stability, ligand binding, and activation of GPCRs.
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Affiliation(s)
- Alexander Heifetz
- Evotec
(U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
- Institute
of Structural & Molecular Biology, Research Department of Structural
& Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
- E-mail: (A.H.)
| | - Inaki Morao
- Evotec
(U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
- E-mail: (I.M.)
| | - M. Madan Babu
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Tim James
- Evotec
(U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | | | - Dmitri G. Fedorov
- CD-FMat,
National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Matteo Aldeghi
- Department
of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Michael J. Bodkin
- Evotec
(U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Andrea Townsend-Nicholson
- Institute
of Structural & Molecular Biology, Research Department of Structural
& Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
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37
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Li Y, McGrail DJ, Latysheva N, Yi S, Babu MM, Sahni N. Pathway perturbations in signaling networks: Linking genotype to phenotype. Semin Cell Dev Biol 2020; 99:3-11. [PMID: 29738884 PMCID: PMC6230320 DOI: 10.1016/j.semcdb.2018.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 03/29/2018] [Accepted: 05/04/2018] [Indexed: 02/07/2023]
Abstract
Genes and gene products interact with each other to form signal transduction networks in the cell. The interactome networks are under intricate regulation in physiological conditions, but could go awry upon genome instability caused by genetic mutations. In the past decade with next-generation sequencing technologies, an increasing number of genomic mutations have been identified in a variety of disease patients and healthy individuals. As functional and systematic studies on these mutations leap forward, they begin to reveal insights into cellular homeostasis and disease mechanisms. In this review, we discuss recent advances in the field of network biology and signaling pathway perturbations upon genomic changes, and highlight the success of various omics datasets in unraveling genotype-to-phenotype relationships.
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Affiliation(s)
- Yongsheng Li
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Natasha Latysheva
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Song Yi
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - M Madan Babu
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Nidhi Sahni
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA; Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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38
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Zhou Q, Yang D, Wu M, Guo Y, Guo W, Zhong L, Cai X, Dai A, Jang W, Shakhnovich EI, Liu ZJ, Stevens RC, Lambert NA, Babu MM, Wang MW, Zhao S. Common activation mechanism of class A GPCRs. eLife 2019; 8:e50279. [PMID: 31855179 PMCID: PMC6954041 DOI: 10.7554/elife.50279] [Citation(s) in RCA: 264] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/19/2019] [Indexed: 12/26/2022] Open
Abstract
Class A G-protein-coupled receptors (GPCRs) influence virtually every aspect of human physiology. Understanding receptor activation mechanism is critical for discovering novel therapeutics since about one-third of all marketed drugs target members of this family. GPCR activation is an allosteric process that couples agonist binding to G-protein recruitment, with the hallmark outward movement of transmembrane helix 6 (TM6). However, what leads to TM6 movement and the key residue level changes of this movement remain less well understood. Here, we report a framework to quantify conformational changes. By analyzing the conformational changes in 234 structures from 45 class A GPCRs, we discovered a common GPCR activation pathway comprising of 34 residue pairs and 35 residues. The pathway unifies previous findings into a common activation mechanism and strings together the scattered key motifs such as CWxP, DRY, Na+ pocket, NPxxY and PIF, thereby directly linking the bottom of ligand-binding pocket with G-protein coupling region. Site-directed mutagenesis experiments support this proposition and reveal that rational mutations of residues in this pathway can be used to obtain receptors that are constitutively active or inactive. The common activation pathway provides the mechanistic interpretation of constitutively activating, inactivating and disease mutations. As a module responsible for activation, the common pathway allows for decoupling of the evolution of the ligand binding site and G-protein-binding region. Such an architecture might have facilitated GPCRs to emerge as a highly successful family of proteins for signal transduction in nature.
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Affiliation(s)
- Qingtong Zhou
- iHuman InstituteShanghaiTech UniversityShanghaiChina
| | - Dehua Yang
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Meng Wu
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Yu Guo
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Wanjing Guo
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Li Zhong
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Xiaoqing Cai
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Antao Dai
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Wonjo Jang
- Department of Pharmacology and Toxicology, Medical College of GeorgiaAugusta UniversityAugustaUnited States
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Zhi-Jie Liu
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Raymond C Stevens
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of GeorgiaAugusta UniversityAugustaUnited States
| | - M Madan Babu
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Ming-Wei Wang
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- School of PharmacyFudan UniversityShanghaiChina
| | - Suwen Zhao
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
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39
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Masuho I, Chavali S, Muntean BS, Skamangas NK, Simonyan K, Patil DN, Kramer GM, Ozelius L, Babu MM, Martemyanov KA. Molecular Deconvolution Platform to Establish Disease Mechanisms by Surveying GPCR Signaling. Cell Rep 2019; 24:557-568.e5. [PMID: 30021154 PMCID: PMC6077248 DOI: 10.1016/j.celrep.2018.06.080] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 05/10/2018] [Accepted: 06/19/2018] [Indexed: 01/01/2023] Open
Abstract
Despite the wealth of genetic information available, mechanisms underlying pathological effects of disease-associated mutations in components of G protein-coupled receptor (GPCR) signaling cascades remain elusive. In this study, we developed a scalable approach for the functional analysis of clinical variants in GPCR pathways along with a complete analytical framework. We applied the strategy to evaluate an extensive set of dystonia-causing mutations in G protein Gαolf. Our quantitative analysis revealed diverse mechanisms by which pathogenic variants disrupt GPCR signaling, leading to a mechanism-based classification of dystonia. In light of significant clinical heterogeneity, the mechanistic analysis of individual disease-associated variants permits tailoring personalized intervention strategies, which makes it superior to the current phenotype-based approach. We propose that the platform developed in this study can be universally applied to evaluate disease mechanisms for conditions associated with genetic variation in all components of GPCR signaling. A scalable platform allows multidimensional analysis of GPCR signaling The approach is applied to dystonia-causing mutations in G protein Gαolf Pathogenic variants in Gαolf disrupt GPCR signaling by diverse mechanisms Mechanism-based disease classification could allow targeted therapies
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Affiliation(s)
- Ikuo Masuho
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL 33458, USA
| | - Sreenivas Chavali
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Brian S Muntean
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL 33458, USA
| | - Nickolas K Skamangas
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL 33458, USA
| | - Kristina Simonyan
- Department of Otolaryngology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA 02114, USA
| | - Dipak N Patil
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL 33458, USA
| | - Grant M Kramer
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL 33458, USA; Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Laurie Ozelius
- Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kirill A Martemyanov
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL 33458, USA.
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40
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Abstract
Molecular Systems Biology warmly welcomes its new academic Chief Editor, M. Madan Babu. Madan shared his thoughts on the evolution of the field and the importance of bridging disciplines to enable next generation systems biology.
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41
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Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, Orchard S, Ouzounis CA, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Promponas VJ, Ruch P, Rustici G, Romero P, Sarntivijai S, Saunders G, Schuler B, Sharan M, Shields DC, Sussman JL, Tedds JA, Tompa P, Turewicz M, Vondrasek J, Vranken WF, Wallace BA, Wichapong K, Tosatto SCE. An intrinsically disordered proteins community for ELIXIR. F1000Res 2019; 8. [PMID: 31824649 PMCID: PMC6880265 DOI: 10.12688/f1000research.20136.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/18/2019] [Indexed: 01/20/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled “An intrinsically disordered protein user community proposal for ELIXIR” held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders.
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Affiliation(s)
- Norman E Davey
- Division of Cancer Biology, Institute of Cancer Research, UK, London, SW3 6JB, UK
| | - M Madan Babu
- MRC Laboratory of Molecular Biology,, Cambridge, CB2 0QH, UK
| | - Martin Blackledge
- Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, 38000, France
| | - Alan Bridge
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | - Zsuzsanna Dosztanyi
- Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | | | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Isabella C Felli
- Department of Chemistry and CERM "Ugo Schiff", University of Florence, Florence, Italy
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
| | - John M Hancock
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Jen Harrow
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Desmond Higgins
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, D4, Ireland
| | - Cy M Jeffries
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Philippe Le Mercier
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Balint Mészáros
- Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Marco Necci
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
| | - Christos A Ouzounis
- BCPL-CPERI, Centre for Research & Technology Hellas (CERTH), Thessalonica, 57001, Greece
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
| | - Roberta Pierattelli
- Department of Chemistry and CERM "Ugo Schiff", University of Florence, Florence, Italy
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
| | - Patrick Ruch
- HES-SO/HEG and SIB Text Mining, Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Gabriella Rustici
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Pedro Romero
- University of Wisconsin-Madison, Madison, WI, 53706-1544, USA
| | | | - Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Malvika Sharan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Denis C Shields
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, D4, Ireland
| | - Joel L Sussman
- Department of Structural Biology and the Israel Structural Proteomics, Center (ISPC), Weizmann Institute of Science, Reḥovot, 7610001, Israel
| | | | - Peter Tompa
- VIB Center for Structural Biology (CSB), VIB Flemish Institute for Biotechnology, Brussels, 1050, Belgium
| | - Michael Turewicz
- Faculty of Medicine, Medizinisches Proteom-Center, Ruhr University Bochum, GesundheitsCampus 4, Bochum, 44801, Germany
| | - Jiri Vondrasek
- Institute of Organic Chemistry and Biochemistry, CAS, Prague, Czech Republic
| | - Wim F Vranken
- VUB/ULB Interuniversity Institute of Bioinformatics in Brussels and Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium
| | - Bonnie Ann Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1H 0HA, UK
| | - Kanin Wichapong
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
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42
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Abstract
Phase separation of soluble proteins into insoluble deposits is associated with numerous diseases. However, protein deposits can also function as membrane-less compartments for many cellular processes. What are the fitness costs and benefits of forming such deposits in different conditions? Using a model protein that phase-separates into deposits, we distinguish and quantify the fitness contribution due to the loss or gain of protein function and deposit formation in yeast. The environmental condition and the cellular demand for the protein function emerge as key determinants of fitness. Protein deposit formation can influence cell-to-cell variation in free protein abundance between individuals of a cell population (i.e., gene expression noise). This results in variable manifestation of protein function and a continuous range of phenotypes in a cell population, favoring survival of some individuals in certain environments. Thus, protein deposit formation by phase separation might be a mechanism to sense protein concentration in cells and to generate phenotypic variability. The selectable phenotypic variability, previously described for prions, could be a general property of proteins that can form phase-separated assemblies and may influence cell fitness.
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Affiliation(s)
- Natalia Sanchez de Groot
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK .,Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marc Torrent Burgas
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Ala Trusina
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - M Madan Babu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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43
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Abstract
![]()
Although gene fusions
are recognized as driver mutations in a wide
variety of cancers, the general molecular mechanisms underlying oncogenic
fusion proteins are insufficiently understood. Here, we employ large-scale
data integration and machine learning and (1) identify three functionally
distinct subgroups of gene fusions and their molecular signatures;
(2) characterize the cellular pathways rewired by fusion events across
different cancers; and (3) analyze the relative importance of over
100 structural, functional, and regulatory features of ∼2200
gene fusions. We report subgroups of fusions that likely act as driver
mutations and find that gene fusions disproportionately affect pathways
regulating cellular shape and movement. Although fusion proteins are
similar across different cancer types, they affect cancer type-specific
pathways. Key indicators of fusion-forming proteins include high and
nontissue specific expression, numerous splice sites, and higher centrality
in protein-interaction networks. Together, these findings provide
unifying and cancer type-specific trends across diverse oncogenic
fusion proteins.
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Affiliation(s)
- Natasha S Latysheva
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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44
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Wright SC, Kozielewicz P, Kowalski-Jahn M, Petersen J, Bowin CF, Slodkowicz G, Marti-Solano M, Rodríguez D, Hot B, Okashah N, Strakova K, Valnohova J, Babu MM, Lambert NA, Carlsson J, Schulte G. A conserved molecular switch in Class F receptors regulates receptor activation and pathway selection. Nat Commun 2019; 10:667. [PMID: 30737406 PMCID: PMC6368630 DOI: 10.1038/s41467-019-08630-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/22/2019] [Indexed: 12/21/2022] Open
Abstract
Class F receptors are considered valuable therapeutic targets due to their role in human disease, but structural changes accompanying receptor activation remain unexplored. Employing population and cancer genomics data, structural analyses, molecular dynamics simulations, resonance energy transfer-based approaches and mutagenesis, we identify a conserved basic amino acid in TM6 in Class F receptors that acts as a molecular switch to mediate receptor activation. Across all tested Class F receptors (FZD4,5,6,7, SMO), mutation of the molecular switch confers an increased potency of agonists by stabilizing an active conformation as assessed by engineered mini G proteins as conformational sensors. Disruption of the switch abrogates the functional interaction between FZDs and the phosphoprotein Dishevelled, supporting conformational selection as a prerequisite for functional selectivity. Our studies reveal the molecular basis of a common activation mechanism conserved in all Class F receptors, which facilitates assay development and future discovery of Class F receptor-targeting drugs. Class F receptors are therapeutic targets in human disease and understanding their structural changes during receptor activation may provide important pharmacological insight. Here, the authors combine computational and experimental methods to identify a molecular switch in TM6/7 of Class F receptors that mediates receptor activation.
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Affiliation(s)
- Shane C Wright
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Paweł Kozielewicz
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Maria Kowalski-Jahn
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Julian Petersen
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Carl-Fredrik Bowin
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Greg Slodkowicz
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - Maria Marti-Solano
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - David Rodríguez
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, P.O. Box 596, SE-751 24, Uppsala, Sweden
| | - Belma Hot
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Najeah Okashah
- Department of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, Georgia, 30912, USA
| | - Katerina Strakova
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Jana Valnohova
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, Georgia, 30912, USA
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, P.O. Box 596, SE-751 24, Uppsala, Sweden
| | - Gunnar Schulte
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden.
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45
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Abstract
The widespread application of sequencing technologies, used for example to obtain data from healthy individuals or patient cohorts, has led to the identification of numerous mutations, the effect of which remains largely unclear. Therefore, developing approaches allowing accurate in‐silico prediction of mutation effects is becoming increasingly important. In their recent study, Beltrao and colleagues (Wagih et al , 2018 ) describe an integrative approach for determining the effects of mutations from the perspective of protein structure, conservation and transcription factor binding. This allows for predicting the mechanisms underlying the most impactful variants rather than just identifying these variants.
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46
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Torrent M, Chalancon G, de Groot NS, Wuster A, Madan Babu M. Cells alter their tRNA abundance to selectively regulate protein synthesis during stress conditions. Sci Signal 2018; 11:11/546/eaat6409. [PMID: 30181241 PMCID: PMC6130803 DOI: 10.1126/scisignal.aat6409] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Decoding the information in mRNA during protein synthesis relies on tRNA adaptors, the abundance of which can affect the decoding rate and translation efficiency. To determine whether cells alter tRNA abundance to selectively regulate protein expression, we quantified changes in the abundance of individual tRNAs at different time points in response to diverse stress conditions in Saccharomyces cerevisiae. We found that the tRNA pool was dynamic and rearranged in a manner that facilitated selective translation of stress-related transcripts. Through genomic analysis of multiple data sets, stochastic simulations, and experiments with designed sequences of proteins with identical amino acids but altered codon usage, we showed that changes in tRNA abundance affected protein expression independently of factors such as mRNA abundance. We suggest that cells alter their tRNA abundance to selectively affect the translation rates of specific transcripts to increase the amounts of required proteins under diverse stress conditions.
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Affiliation(s)
- Marc Torrent
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK. .,Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Guilhem Chalancon
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Natalia S de Groot
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Arthur Wuster
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - M Madan Babu
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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Li Y, Sahni N, Pancsa R, McGrail DJ, Xu J, Hua X, Coulombe-Huntington J, Ryan M, Tychhon B, Sudhakar D, Hu L, Tyers M, Jiang X, Lin SY, Babu MM, Yi S. Revealing the Determinants of Widespread Alternative Splicing Perturbation in Cancer. Cell Rep 2018; 21:798-812. [PMID: 29045845 DOI: 10.1016/j.celrep.2017.09.071] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 08/10/2017] [Accepted: 09/21/2017] [Indexed: 12/25/2022] Open
Abstract
It is increasingly appreciated that alternative splicing plays a key role in generating functional specificity and diversity in cancer. However, the mechanisms by which cancer mutations perturb splicing remain unknown. Here, we developed a network-based strategy, DrAS-Net, to investigate more than 2.5 million variants across cancer types and link somatic mutations with cancer-specific splicing events. We identified more than 40,000 driver variant candidates and their 80,000 putative splicing targets deregulated in 33 cancer types and inferred their functional impact. Strikingly, tumors with splicing perturbations show reduced expression of immune system-related genes and increased expression of cell proliferation markers. Tumors harboring different mutations in the same gene often exhibit distinct splicing perturbations. Further stratification of 10,000 patients based on their mutation-splicing relationships identifies subtypes with distinct clinical features, including survival rates. Our work reveals how single-nucleotide changes can alter the repertoires of splicing isoforms, providing insights into oncogenic mechanisms for precision medicine.
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Affiliation(s)
- Yongsheng Li
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Nidhi Sahni
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Rita Pancsa
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Juan Xu
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Xu Hua
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jasmin Coulombe-Huntington
- Institute for Research in Immunology and Cancer, Department of Medicine, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Michael Ryan
- In Silico Solutions, Falls Church, VA 22043, USA
| | - Boranai Tychhon
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dhanistha Sudhakar
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Limei Hu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael Tyers
- Institute for Research in Immunology and Cancer, Department of Medicine, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Xiaoqian Jiang
- Division of Biomedical Informatics, University of California at San Diego, La Jolla, CA 92093, USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - M Madan Babu
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Song Yi
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Sente A, Peer R, Srivastava A, Baidya M, Lesk AM, Balaji S, Shukla AK, Babu MM, Flock T. Molecular mechanism of modulating arrestin conformation by GPCR phosphorylation. Nat Struct Mol Biol 2018; 25:538-545. [PMID: 29872229 DOI: 10.1038/s41594-018-0071-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 04/25/2018] [Indexed: 01/14/2023]
Abstract
Arrestins regulate the signaling of ligand-activated, phosphorylated G-protein-coupled receptors (GPCRs). Different patterns of receptor phosphorylation (phosphorylation barcode) can modulate arrestin conformations, resulting in distinct functional outcomes (for example, desensitization, internalization, and downstream signaling). However, the mechanism of arrestin activation and how distinct receptor phosphorylation patterns could induce different conformational changes on arrestin are not fully understood. We analyzed how each arrestin amino acid contributes to its different conformational states. We identified a conserved structural motif that restricts the mobility of the arrestin finger loop in the inactive state and appears to be regulated by receptor phosphorylation. Distal and proximal receptor phosphorylation sites appear to selectively engage with distinct arrestin structural motifs (that is, micro-locks) to induce different arrestin conformations. These observations suggest a model in which different phosphorylation patterns of the GPCR C terminus can combinatorially modulate the conformation of the finger loop and other phosphorylation-sensitive structural elements to drive distinct arrestin conformation and functional outcomes.
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Affiliation(s)
| | - Raphael Peer
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Ashish Srivastava
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
| | - Mithu Baidya
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
| | - Arthur M Lesk
- MRC Laboratory of Molecular Biology, Cambridge, UK.,Department of Biochemistry and Molecular Biology and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, USA
| | | | - Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Tilman Flock
- MRC Laboratory of Molecular Biology, Cambridge, UK. .,Fitzwilliam College, University of Cambridge, Cambridge, UK. .,Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland.
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49
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Ravarani CN, Erkina TY, De Baets G, Dudman DC, Erkine AM, Babu MM. High-throughput discovery of functional disordered regions: investigation of transactivation domains. Mol Syst Biol 2018; 14:e8190. [PMID: 29759983 PMCID: PMC5949888 DOI: 10.15252/msb.20188190] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Over 40% of proteins in any eukaryotic genome encode intrinsically disordered regions (IDRs) that do not adopt defined tertiary structures. Certain IDRs perform critical functions, but discovering them is non‐trivial as the biological context determines their function. We present IDR‐Screen, a framework to discover functional IDRs in a high‐throughput manner by simultaneously assaying large numbers of DNA sequences that code for short disordered sequences. Functionality‐conferring patterns in their protein sequence are inferred through statistical learning. Using yeast HSF1 transcription factor‐based assay, we discovered IDRs that function as transactivation domains (TADs) by screening a random sequence library and a designed library consisting of variants of 13 diverse TADs. Using machine learning, we find that segments devoid of positively charged residues but with redundant short sequence patterns of negatively charged and aromatic residues are a generic feature for TAD functionality. We anticipate that investigating defined sequence libraries using IDR‐Screen for specific functions can facilitate discovering novel and functional regions of the disordered proteome as well as understand the impact of natural and disease variants in disordered segments.
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Affiliation(s)
| | | | | | | | | | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, UK
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50
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Abstract
Achieving functional specificity while minimizing cost to fitness is a key constraint during evolution. Formation of biological condensates by liquid-liquid phase separation (LLPS) appears to serve as an important regulatory mechanism to generate moderate specificity in molecular recognition while maintaining a reasonable cost for fitness in terms of design complexity. Formation of biological condensates serves as a unique mechanism of molecular recognition achieving some level of specificity without a huge cost to fitness. Rapid formation of biological condensates in vivo induced by specific cellular or environmental triggers has been shown to be an important mechanism for increasing cellular fitness. Here we discuss the functions and regulation of biological condensates, especially those formed by LLPS, involving interactions between proteins and nucleic acids. These condensates are spatially isolated within the cytosol or nucleus and can facilitate specific biochemical functions under conditions such as stress. The misregulation of biological condensates resulting in nondynamic aggregates has been implicated in a number of diseases. Understanding the functional importance of biological condensates and their regulation opens doors for development of therapies targeting dysfunctional biological condensates, as well as spatiotemporal engineering of functions in cells.
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Affiliation(s)
- Xiao-Han Li
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , U.K
| | - Pavithra L Chavali
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , U.K
| | - Rita Pancsa
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , U.K
| | - Sreenivas Chavali
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , U.K
| | - M Madan Babu
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , U.K
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