1
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Belato HB, Knight AL, D'Ordine AM, Pindi C, Fan Z, Luo J, Palermo G, Jogl G, Lisi GP. Structural and dynamic impacts of single-atom disruptions to guide RNA interactions within the recognition lobe of Geobacillus stearothermophilus Cas9. eLife 2025; 13:RP99275. [PMID: 40387084 PMCID: PMC12088677 DOI: 10.7554/elife.99275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2025] Open
Abstract
The intuitive manipulation of specific amino acids to alter the activity or specificity of CRISPR-Cas9 has been a topic of great interest. As a large multi-domain RNA-guided endonuclease, the intricate molecular crosstalk within the Cas9 protein hinges on its conformational dynamics, but a comprehensive understanding of the extent and timescale of the motions that drive its allosteric function and association with nucleic acids remains elusive. Here, we investigated the structure and multi-timescale molecular motions of the recognition (Rec) lobe of GeoCas9, a thermophilic Cas9 from Geobacillus stearothermophilus. Our results provide new atomic details about the GeoRec subdomains (GeoRec1, GeoRec2) and the full-length domain in solution. Two rationally designed mutants, K267E and R332A, enhanced and redistributed micro-millisecond flexibility throughout GeoRec, and NMR studies of the interaction between GeoRec and its guide RNA showed that mutations reduced this affinity and the stability of the ribonucleoprotein complex. Despite measured biophysical differences due to the mutations, DNA cleavage assays reveal no functional differences in on-target activity, and similar specificity. These data suggest that guide RNA interactions can be tuned at the biophysical level in the absence of major functional losses but also raise questions about the underlying mechanism of GeoCas9, since analogous single-point mutations have significantly impacted on- and off-target DNA editing in mesophilic Streptococcus pyogenes Cas9. A K267E/R332A double mutant did also did not enhance GeoCas9 specificity, highlighting the robust tolerance of mutations to the Rec lobe of GeoCas9 and species-dependent complexity of Rec across Cas9 paralogs. Ultimately, this work provides an avenue by which to modulate the structure, motion, and guide RNA interactions at the level of the Rec lobe of GeoCas9, setting the stage for future studies of GeoCas9 variants and their effect on its allosteric mechanism.
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Affiliation(s)
- Helen B Belato
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidenceUnited States
| | - Alexa L Knight
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidenceUnited States
| | - Alexandra M D'Ordine
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidenceUnited States
| | - Chinmai Pindi
- Departments of Bioengineering and Chemistry, University of California, RiversideRiversideUnited States
| | - Zhiqiang Fan
- Brown University Transgenic Mouse and Gene Targeting FacilityProvidenceUnited States
| | - Jinping Luo
- Brown University Transgenic Mouse and Gene Targeting FacilityProvidenceUnited States
| | - Giulia Palermo
- Departments of Bioengineering and Chemistry, University of California, RiversideRiversideUnited States
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidenceUnited States
- Brown University RNA CenterProvidenceUnited States
| | - George P Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidenceUnited States
- Brown University RNA CenterProvidenceUnited States
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2
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Woodward CH, Solieva SO, Hwang D, De Paula VS, Fabilane CS, Young MC, Trent T, Teeley EC, Majumdar A, Spangler JB, Bowman GR, Sgourakis NG. Regulating IL-2 Immune Signaling Function Via A Core Allosteric Structural Network. J Mol Biol 2025; 437:168892. [PMID: 39662679 PMCID: PMC12077578 DOI: 10.1016/j.jmb.2024.168892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 11/16/2024] [Accepted: 12/02/2024] [Indexed: 12/13/2024]
Abstract
Human interleukin-2 (IL-2) is a crucial cytokine for T cell regulation, with therapeutic potential in cancer and autoimmune diseases. However, IL-2's pleiotropic effects across different immune cell types often lead to toxicity and limited efficacy. Previous efforts to enhance IL-2's therapeutic profile have focused on modifying its receptor binding sites. Yet, the underlying dynamics and intramolecular networks contributing to IL-2 receptor recognition remain unexplored. This study presents a detailed characterization of IL-2 dynamics compared to two engineered IL-2 mutants, "superkines" S15 and S1, which exhibit biased signaling towards effector T cells. Using NMR spectroscopy and molecular dynamics simulations, we demonstrate significant variations in core dynamic pathways and conformational exchange rates across these three IL-2 variants. We identify distinct allosteric networks and minor state conformations in the superkines, despite their structural similarity to wild-type IL-2. Furthermore, we rationally design a mutation (L56A) in the S1 superkine's core network, which partially reverts its dynamics, receptor binding affinity, and T cell signaling behavior towards that of wild-type IL-2. Our results reveal that IL-2 superkine core dynamics play a critical role in their enhanced receptor binding and function, suggesting that modulating IL-2 dynamics and core allostery represents an untapped approach for designing immunotherapies with improved immune cell selectivity profiles.
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Affiliation(s)
- Claire H Woodward
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA; Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shahlo O Solieva
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel Hwang
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA; Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Viviane S De Paula
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA; Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Charina S Fabilane
- Translational Tissue Engineering Center, Johns Hopkins School of Medicine, Baltimore, MD, USA; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Michael C Young
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA; Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Tony Trent
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Ella C Teeley
- Department of Chemical & Biomolecular Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University, Baltimore, MD, USA
| | - Jamie B Spangler
- Translational Tissue Engineering Center, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Chemical & Biomolecular Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Gregory R Bowman
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Nikolaos G Sgourakis
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA; Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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3
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Woodward CH, Solieva SO, Hwang D, De Paula VS, Fabilane CS, Young MC, Trent T, Teeley EC, Majumdar A, Spangler JB, Bowman GR, Sgourakis NG. Regulating IL-2 immune signaling function via a core allosteric structural network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.07.617024. [PMID: 39416199 PMCID: PMC11482754 DOI: 10.1101/2024.10.07.617024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Human interleukin-2 (IL-2) is a crucial cytokine for T cell regulation, with therapeutic potential in cancer and autoimmune diseases. However, IL-2's pleiotropic effects across different immune cell types often lead to toxicity and limited efficacy. Previous efforts to enhance IL-2's therapeutic profile have focused on modifying its receptor binding sites. Yet, the underlying dynamics and intramolecular networks contributing to IL-2 receptor recognition remain unexplored. This study presents a detailed characterization of IL-2 dynamics compared to two engineered IL-2 mutants, "superkines" S15 and S1, which exhibit biased signaling towards effector T cells. Using NMR spectroscopy and molecular dynamics simulations, we demonstrate significant variations in core dynamic pathways and conformational exchange rates across these three IL-2 variants. We identify distinct allosteric networks and excited state conformations in the superkines, despite their structural similarity to wild-type IL-2. Furthermore, we rationally design a mutation (L56A) in the S1 superkine's core network, which partially reverts its dynamics, receptor binding affinity, and T cell signaling behavior towards that of wild-type IL-2. Our results reveal that IL-2 superkine core dynamics play a critical role in their enhanced receptor binding and function, suggesting that modulating IL-2 dynamics and core allostery represents an untapped approach for designing immunotherapies with improved immune cell selectivity profiles. Highlights NMR and molecular dynamics simulations revealed distinct conformational dynamics and allosteric networks in computationally re-designed IL-2 superkines compared to wild-type IL-2, despite their similar crystal structures.The superkines S1 and S15 exhibit altered sampling of excited state conformations at an intermediate timescale, with slower conformational exchange rates compared to wild-type IL-2.A rationally designed mutation (L56A) in the S1 superkine's core allosteric network partially reverted its dynamics, receptor binding affinity, and T cell signaling behavior towards that of wild-type IL-2.Our study demonstrates that IL-2 core dynamics play a critical role in receptor binding and signaling function, providing a foundation for engineering more selective IL-2-based immunotherapies.
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4
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Aute R, Waghela N, Deshmukh MV. Key arginine residues in R2D2 dsRBD1 and dsRBD2 lead the siRNA recognition in Drosophila melanogaster RNAi pathway. Biophys Chem 2024; 310:107247. [PMID: 38663122 DOI: 10.1016/j.bpc.2024.107247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/04/2024] [Accepted: 04/16/2024] [Indexed: 05/23/2024]
Abstract
In Drosophila melanogaster, Dcr-2:R2D2 heterodimer binds to the 21 nucleotide siRNA duplex to form the R2D2/Dcr-2 Initiator (RDI) complex, which is critical for the initiation of siRNA-induced silencing complex (RISC) assembly. During RDI complex formation, R2D2, a protein that contains three dsRNA binding domains (dsRBD), senses two aspects of the siRNA: thermodynamically more stable end (asymmetry sensing) and the 5'-phosphate (5'-P) recognition. Despite several detailed studies to date, the molecular determinants arising from R2D2 for performing these two tasks remain elusive. In this study, we have performed structural, biophysical, and biochemical characterization of R2D2 dsRBDs. We found that the solution NMR-derived structure of R2D2 dsRBD1 yielded a canonical α1-β1-β2-β3-α2 fold, wherein two arginine salt bridges provide additional stability to the R2D2 dsRBD1. Furthermore, we show that R2D2 dsRBD1 interacts with thermodynamically asymmetric siRNA duplex independent of its 5'-phosphorylation state, whereas R2D2 dsRBD2 prefers to interact with 5'-P siRNA duplex. The mutation of key arginine residues, R53 and R101, in concatenated dsRBDs of R2D2 results in a significant loss of siRNA duplex recognition. Our study deciphers the active roles of R2D2 dsRBDs by showing that dsRBD1 initiates siRNA recognition, whereas dsRBD2 senses 5'-phosphate as an authentic mark on functional siRNA.
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Affiliation(s)
- Ramdas Aute
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nilam Waghela
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mandar V Deshmukh
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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5
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Sayeesh PM, Iguchi M, Inomata K, Ikeya T, Ito Y. Structure and Dynamics of Drk-SH2 Domain and Its Site-Specific Interaction with Sev Receptor Tyrosine Kinase. Int J Mol Sci 2024; 25:6386. [PMID: 38928093 PMCID: PMC11203457 DOI: 10.3390/ijms25126386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
The Drosophila downstream receptor kinase (Drk), a homologue of human GRB2, participates in the signal transduction from the extracellular to the intracellular environment. Drk receives signals through the interaction of its Src homology 2 (SH2) domain with the phosphorylated tyrosine residue in the receptor tyrosine kinases (RTKs). Here, we present the solution NMR structure of the SH2 domain of Drk (Drk-SH2), which was determined in the presence of a phosphotyrosine (pY)-containing peptide derived from a receptor tyrosine kinase, Sevenless (Sev). The solution structure of Drk-SH2 possess a common SH2 domain architecture, consisting of three β strands imposed between two α helices. Additionally, we interpret the site-specific interactions of the Drk-SH2 domain with the pY-containing peptide through NMR titration experiments. The dynamics of Drk-SH2 were also analysed through NMR-relaxation experiments as well as the molecular dynamic simulation. The docking simulations of the pY-containing peptide onto the protein surface of Drk-SH2 provided the orientation of the peptide, which showed a good agreement with the analysis of the SH2 domain of GRB2.
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Affiliation(s)
| | | | | | - Teppei Ikeya
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan; (P.M.S.); (M.I.); (K.I.)
| | - Yutaka Ito
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan; (P.M.S.); (M.I.); (K.I.)
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6
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Kirschner H, John M, Zhou T, Bachmann N, Schultz A, Hofmann E, Bandow JE, Scherkenbeck J, Metzler-Nolte N, Stoll R. Structural Insights into Antibacterial Payload Release from Gold Nanoparticles Bound to E. coli Peptide Deformylase. ChemMedChem 2024; 19:e202300538. [PMID: 38057137 DOI: 10.1002/cmdc.202300538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/10/2023] [Indexed: 12/08/2023]
Abstract
The lack of new antibiotics and the rapidly rising number of pathogens resistant to antibiotics pose a serious problem to mankind. In bacteria, the cell membrane provides the first line of defence to antibiotics by preventing them from reaching their molecular target. To overcome this entrance barrier, it has been suggested[1] that small Gold-Nanoparticles (AuNP) could possibly function as drug delivery systems for antibiotic ligands. Using actinonin-based ligands, we provide here proof-of-principle of AuNP functionalisation, the capability to bind and inhibit the target protein of the ligand, and the possibility to selectively release the antimicrobial payload. To this end, we successfully synthesised AuNP coated with thio-functionalised actinonin and a derivative. Interactions between 15N-enriched His-peptide deformylase 1-147 from E. coli (His-ecPDF 1-147) and compound-coated AuNP were investigated via 2D 1H-15N-HSQC NMR spectra proving the direct binding to His-ecPDF 1-147. More importantly by adding dithiothreitol (DTT), we show that the derivative is successfully released from AuNPs while still bound to His-ecPDF 1-147. Our findings indicate that AuNP-conjugated ligands can address and bind intracellular target proteins. The system introduced here presents a new delivery platform for antibiotics and allows for the easy optimisation of ligand coated AuNPs.
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Affiliation(s)
- Hendrik Kirschner
- Biochemistry II, Biomolecular NMR Spectroscopy, RUBiospec|NMR and PhenomeCentre@RUBUAR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Milena John
- Inorganic Chemistry I - Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Tianyi Zhou
- Bioorganic Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstraße 20, 42119, Wuppertal, Germany
| | - Nathalie Bachmann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - André Schultz
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Julia Elisabeth Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Jürgen Scherkenbeck
- Bioorganic Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstraße 20, 42119, Wuppertal, Germany
| | - Nils Metzler-Nolte
- Inorganic Chemistry I - Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Raphael Stoll
- Biochemistry II, Biomolecular NMR Spectroscopy, RUBiospec|NMR and PhenomeCentre@RUBUAR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
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7
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Skeens E, Sinha S, Ahsan M, D’Ordine AM, Jogl G, Palermo G, Lisi GP. High-fidelity, hyper-accurate, and evolved mutants rewire atomic-level communication in CRISPR-Cas9. SCIENCE ADVANCES 2024; 10:eadl1045. [PMID: 38446895 PMCID: PMC10917355 DOI: 10.1126/sciadv.adl1045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
The high-fidelity (HF1), hyper-accurate (Hypa), and evolved (Evo) variants of the CRISPR-associated protein 9 (Cas9) endonuclease are critical tools to mitigate off-target effects in the application of CRISPR-Cas9 technology. The mechanisms by which mutations in recognition subdomain 3 (Rec3) mediate specificity in these variants are poorly understood. Here, solution nuclear magnetic resonance and molecular dynamics simulations establish the structural and dynamic effects of high-specificity mutations in Rec3, and how they propagate the allosteric signal of Cas9. We reveal conserved structural changes and dynamic differences at regions of Rec3 that interface with the RNA:DNA hybrid, transducing chemical signals from Rec3 to the catalytic His-Asn-His (HNH) domain. The variants remodel the communication sourcing from the Rec3 α helix 37, previously shown to sense target DNA complementarity, either directly or allosterically. This mechanism increases communication between the DNA mismatch recognition helix and the HNH active site, shedding light on the structure and dynamics underlying Cas9 specificity and providing insight for future engineering principles.
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Affiliation(s)
- Erin Skeens
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Souvik Sinha
- Department of Bioengineering, University of California, Riverside, Riverside, CA, USA
| | - Mohd Ahsan
- Department of Bioengineering, University of California, Riverside, Riverside, CA, USA
| | - Alexandra M. D’Ordine
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Giulia Palermo
- Department of Bioengineering, University of California, Riverside, Riverside, CA, USA
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
| | - George P. Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
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8
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Skeens E, Sinha S, Ahsan M, D'Ordine AM, Jogl G, Palermo G, Lisi GP. High-Fidelity, Hyper-Accurate, and Evolved Mutants Rewire Atomic Level Communication in CRISPR-Cas9. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554853. [PMID: 37662375 PMCID: PMC10473742 DOI: 10.1101/2023.08.25.554853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The Cas9-HF1, HypaCas9, and evoCas9 variants of the Cas9 endonuclease are critical tools to mitigate off-target effects in the application of CRISPR-Cas9 technology. The mechanisms by which mutations in the Rec3 domain mediate specificity in these variants are poorly understood. Here, solution NMR and molecular dynamics simulations establish the structural and dynamic effects of high-specificity mutations in Rec3, and how they propagate the allosteric signal of Cas9. We reveal conserved structural changes and peculiar dynamic differences at regions of Rec3 that interface with the RNA:DNA hybrid, transducing chemical signals from Rec3 to the catalytic HNH domain. The variants remodel the communication sourcing from the Rec3 α-helix 37, previously shown to sense target DNA complementarity, either directly or allosterically. This mechanism increases communication between the DNA mismatch recognition helix and the HNH active site, shedding light on the structure and dynamics underlying Cas9 specificity and providing insight for future engineering principles.
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9
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Belato HB, Norbrun C, Luo J, Pindi C, Sinha S, D’Ordine AM, Jogl G, Palermo G, Lisi GP. Disruption of electrostatic contacts in the HNH nuclease from a thermophilic Cas9 rewires allosteric motions and enhances high-temperature DNA cleavage. J Chem Phys 2022; 157:225103. [PMID: 36546784 PMCID: PMC9759293 DOI: 10.1063/5.0128815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
Allosteric signaling within multidomain proteins is a driver of communication between spatially distant functional sites. Understanding the mechanism of allosteric coupling in large multidomain proteins is the most promising route to achieving spatial and temporal control of the system. The recent explosion of CRISPR-Cas9 applications in molecular biology and medicine has created a need to understand how the atomic level protein dynamics of Cas9, which are the driving force of its allosteric crosstalk, influence its biophysical characteristics. In this study, we used a synergistic approach of nuclear magnetic resonance (NMR) and computation to pinpoint an allosteric hotspot in the HNH domain of the thermostable GeoCas9. We show that mutation of K597 to alanine disrupts a salt-bridge network, which in turn alters the structure, the timescale of allosteric motions, and the thermostability of the GeoHNH domain. This homologous lysine-to-alanine mutation in the extensively studied mesophilic S. pyogenes Cas9 similarly alters the dynamics of the SpHNH domain. We have previously demonstrated that the alteration of allostery via mutations is a source for the specificity enhancement of SpCas9 (eSpCas9). Hence, this may also be true in GeoCas9.
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Affiliation(s)
- Helen B. Belato
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Carmelissa Norbrun
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Jinping Luo
- Brown University Transgenic Mouse and Gene Targeting Facility, Providence, Rhode Island 02903, USA
| | - Chinmai Pindi
- Departments of Bioengineering and Chemistry, University of California Riverside, Riverside, California 92521, USA
| | - Souvik Sinha
- Departments of Bioengineering and Chemistry, University of California Riverside, Riverside, California 92521, USA
| | - Alexandra M. D’Ordine
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Giulia Palermo
- Departments of Bioengineering and Chemistry, University of California Riverside, Riverside, California 92521, USA
| | - George P. Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
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10
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Sethi A, Horne CR, Fitzgibbon C, Wilde K, Davies KA, Garnish SE, Jacobsen AV, Samson AL, Hildebrand JM, Wardak A, Czabotar PE, Petrie EJ, Gooley PR, Murphy JM. Membrane permeabilization is mediated by distinct epitopes in mouse and human orthologs of the necroptosis effector, MLKL. Cell Death Differ 2022; 29:1804-1815. [PMID: 35264780 PMCID: PMC9433430 DOI: 10.1038/s41418-022-00965-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 12/18/2022] Open
Abstract
Necroptosis is a lytic programmed cell death pathway with origins in innate immunity that is frequently dysregulated in inflammatory diseases. The terminal effector of the pathway, MLKL, is licensed to kill following phosphorylation of its pseudokinase domain by the upstream regulator, RIPK3 kinase. Phosphorylation provokes the unleashing of MLKL's N-terminal four-helix bundle (4HB or HeLo) domain, which binds and permeabilizes the plasma membrane to cause cell death. The precise mechanism by which the 4HB domain permeabilizes membranes, and how the mechanism differs between species, remains unclear. Here, we identify the membrane binding epitope of mouse MLKL using NMR spectroscopy. Using liposome permeabilization and cell death assays, we validate K69 in the α3 helix, W108 in the α4 helix, and R137/Q138 in the first brace helix as crucial residues for necroptotic signaling. This epitope differs from the phospholipid binding site reported for human MLKL, which comprises basic residues primarily located in the α1 and α2 helices. In further contrast to human and plant MLKL orthologs, in which the α3-α4 loop forms a helix, this loop is unstructured in mouse MLKL in solution. Together, these findings illustrate the versatility of the 4HB domain fold, whose lytic function can be mediated by distinct epitopes in different orthologs.
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Affiliation(s)
- Ashish Sethi
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Cheree Fitzgibbon
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Karyn Wilde
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, Lucas Heights, NSW, 2234, Australia
| | - Katherine A Davies
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Sarah E Garnish
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Annette V Jacobsen
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - André L Samson
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Joanne M Hildebrand
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Ahmad Wardak
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Emma J Petrie
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Paul R Gooley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
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11
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Fernández-Quintero ML, DeRose EF, Gabel SA, Mueller GA, Liedl KR. Nanobody Paratope Ensembles in Solution Characterized by MD Simulations and NMR. Int J Mol Sci 2022; 23:5419. [PMID: 35628231 PMCID: PMC9141556 DOI: 10.3390/ijms23105419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/02/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
Variable domains of camelid antibodies (so-called nanobodies or VHH) are the smallest antibody fragments that retain complete functionality and therapeutic potential. Understanding of the nanobody-binding interface has become a pre-requisite for rational antibody design and engineering. The nanobody-binding interface consists of up to three hypervariable loops, known as the CDR loops. Here, we structurally and dynamically characterize the conformational diversity of an anti-GFP-binding nanobody by using molecular dynamics simulations in combination with experimentally derived data from nuclear magnetic resonance (NMR) spectroscopy. The NMR data contain both structural and dynamic information resolved at various timescales, which allows an assessment of the quality of protein MD simulations. Thus, in this study, we compared the ensembles for the anti-GFP-binding nanobody obtained from MD simulations with results from NMR. We find excellent agreement of the NOE-derived distance maps obtained from NMR and MD simulations and observe similar conformational spaces for the simulations with and without NOE time-averaged restraints. We also compare the measured and calculated order parameters and find generally good agreement for the motions observed in the ps-ns timescale, in particular for the CDR3 loop. Understanding of the CDR3 loop dynamics is especially critical for nanobodies, as this loop is typically critical for antigen recognition.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria;
| | - Eugene F. DeRose
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Dr. MD-MR-01, Research Triangle Park, NC 27709, USA; (E.F.D.); (S.A.G.)
| | - Scott A. Gabel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Dr. MD-MR-01, Research Triangle Park, NC 27709, USA; (E.F.D.); (S.A.G.)
| | - Geoffrey A. Mueller
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Dr. MD-MR-01, Research Triangle Park, NC 27709, USA; (E.F.D.); (S.A.G.)
| | - Klaus R. Liedl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria;
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12
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Bukhteeva I, Hrunyk NI, Yusypovych YM, Shalovylo YI, Kovaleva V, Nesmelova IV. Structure, dynamics, and function of PsDef2 defensin from Pinus sylvestris. Structure 2022; 30:753-762.e5. [PMID: 35334207 DOI: 10.1016/j.str.2022.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/25/2022] [Accepted: 02/28/2022] [Indexed: 11/19/2022]
Abstract
Plant defensins demonstrate high structural stability at extreme temperatures and pH values and, in general, are non-toxic to mammalian cells. These properties make them attractive candidates for use in biotechnology and biomedicine. Knowing the structure-function relationship is desirable to guide the design of plant defensin-based applications. Thus far, the broad range of biological activities was described only for one defensin from gymnosperms, the defensin PsDef1 from Scots pine. Here, we report that closely related defensin from the same taxonomy group, PsDef2, differing from PsDef1 by six amino acids, also possesses antimicrobial, antibacterial, and insect α-amylase inhibitory activities. We also report the solution structure and dynamics properties of PsDef2 assessed using a combination of experimental nuclear magnetic resonance (NMR) techniques. Lastly, we perform a comparative analysis of PsDef2 and PsDef1 gaining a molecular-level insight into their structure-dynamics-function relationship.
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Affiliation(s)
- Irina Bukhteeva
- Department of Physics and Optical Science, University of North Carolina, Charlotte, NC 28223, USA
| | - Natalia I Hrunyk
- The Laboratory of Molecular Genetic Markers in Plants, Ukrainian National Forestry University, Lviv 79057, Ukraine
| | - Yuri M Yusypovych
- The Laboratory of Molecular Genetic Markers in Plants, Ukrainian National Forestry University, Lviv 79057, Ukraine
| | - Yulia I Shalovylo
- The Laboratory of Molecular Genetic Markers in Plants, Ukrainian National Forestry University, Lviv 79057, Ukraine
| | - Valentina Kovaleva
- The Laboratory of Molecular Genetic Markers in Plants, Ukrainian National Forestry University, Lviv 79057, Ukraine
| | - Irina V Nesmelova
- Department of Physics and Optical Science, University of North Carolina, Charlotte, NC 28223, USA.
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13
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Belato HB, D'Ordine AM, Nierzwicki L, Arantes PR, Jogl G, Palermo G, Lisi GP. Structural and dynamic insights into the HNH nuclease of divergent Cas9 species. J Struct Biol 2022; 214:107814. [PMID: 34871741 PMCID: PMC8917064 DOI: 10.1016/j.jsb.2021.107814] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/15/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022]
Abstract
CRISPR-Cas9 is a widely used biochemical tool with applications in molecular biology and precision medicine. The RNA-guided Cas9 protein uses its HNH endonuclease domain to cleave the DNA strand complementary to its endogenous guide RNA. In this study, novel constructs of HNH from two divergent organisms, G. stearothermophilus (GeoHNH) and S. pyogenes (SpHNH) were engineered from their respective full-length Cas9 proteins. Despite low sequence similarity, the X-ray crystal structures of these constructs reveal that the core of HNH surrounding the active site is conserved. Structure prediction of the full-length GeoCas9 protein using Phyre2 and AlphaFold2 also showed that the crystallographic construct of GeoHNH represents the structure of the domain within the full-length GeoCas9 protein. However, significant differences are observed in the solution dynamics of structurally conserved regions of GeoHNH and SpHNH, the latter of which was shown to use such molecular motions to propagate the DNA cleavage signal. Indeed, molecular simulations show that the intradomain signaling pathways, which drive SpHNH function, are non-specific and poorly formed in GeoHNH. Taken together, these outcomes suggest mechanistic differences between mesophilic and thermophilic Cas9 species.
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Affiliation(s)
- Helen B Belato
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, USA
| | - Alexandra M D'Ordine
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, USA
| | - Lukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, Riverside, CA, USA
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, Riverside, CA, USA
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, USA
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, Riverside, CA, USA; Department of Chemistry, University of California Riverside, Riverside, CA, USA.
| | - George P Lisi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, USA.
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14
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Kawale AA, Burmann BM. Characterization of backbone dynamics using solution NMR spectroscopy to discern the functional plasticity of structurally analogous proteins. STAR Protoc 2021; 2:100919. [PMID: 34761231 PMCID: PMC8567434 DOI: 10.1016/j.xpro.2021.100919] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Abstract
The comprehensive delineation of inherent dynamic motions embedded in proteins, which can be crucial for their functional repertoire, is often essential yet remains poorly understood in the majority of cases. In this protocol, we outline detailed descriptions of the necessary steps for employing solution NMR spectroscopy for the in-depth amino acid level understanding of backbone dynamics of proteins. We describe the application of the protocol on the structurally analogous Tudor domains with disparate functionalities as a model system. For complete details on the use and execution of this protocol, please refer to Kawale and Burmann (2021).
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Affiliation(s)
- Ashish A Kawale
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Björn M Burmann
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
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15
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Nierzwicki L, East KW, Morzan UN, Arantes PR, Batista VS, Lisi GP, Palermo G. Enhanced specificity mutations perturb allosteric signaling in CRISPR-Cas9. eLife 2021; 10:e73601. [PMID: 34908530 PMCID: PMC8741213 DOI: 10.7554/elife.73601] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/14/2021] [Indexed: 11/13/2022] Open
Abstract
CRISPR-Cas9 (clustered regularly interspaced short palindromic repeat and associated Cas9 protein) is a molecular tool with transformative genome editing capabilities. At the molecular level, an intricate allosteric signaling is critical for DNA cleavage, but its role in the specificity enhancement of the Cas9 endonuclease is poorly understood. Here, multi-microsecond molecular dynamics is combined with solution NMR and graph theory-derived models to probe the allosteric role of key specificity-enhancing mutations. We show that mutations responsible for increasing the specificity of Cas9 alter the allosteric structure of the catalytic HNH domain, impacting the signal transmission from the DNA recognition region to the catalytic sites for cleavage. Specifically, the K855A mutation strongly disrupts the allosteric connectivity of the HNH domain, exerting the highest perturbation on the signaling transfer, while K810A and K848A result in more moderate effects on the allosteric communication. This differential perturbation of the allosteric signal correlates to the order of specificity enhancement (K855A > K848A ~ K810A) observed in biochemical studies, with the mutation achieving the highest specificity most strongly perturbing the signaling transfer. These findings suggest that alterations of the allosteric communication from DNA recognition to cleavage are critical to increasing the specificity of Cas9 and that allosteric hotspots can be targeted through mutational studies for improving the system's function.
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Affiliation(s)
- Lukasz Nierzwicki
- Department of Bioengineering and Department of Chemistry, University of California, RiversideRiversideUnited States
| | - Kyle W East
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidenceUnited States
| | - Uriel N Morzan
- International Centre for Theoretical PhysicsTriesteItaly
| | - Pablo R Arantes
- Department of Bioengineering and Department of Chemistry, University of California, RiversideRiversideUnited States
| | | | - George P Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidenceUnited States
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California, RiversideRiversideUnited States
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16
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Structural Insights into the Unique Modes of Relaxin-Binding and Tethered-Agonist Mediated Activation of RXFP1 and RXFP2. J Mol Biol 2021; 433:167217. [PMID: 34454945 DOI: 10.1016/j.jmb.2021.167217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/09/2021] [Accepted: 08/19/2021] [Indexed: 01/01/2023]
Abstract
Our poor understanding of the mechanism by which the peptide-hormone H2 relaxin activates its G protein coupled receptor, RXFP1 and the related receptor RXFP2, has hindered progress in its therapeutic development. Both receptors possess large ectodomains, which bind H2 relaxin, and contain an N-terminal LDLa module that is essential for receptor signaling and postulated to be a tethered agonist. Here, we show that a conserved motif (GDxxGWxxxF), C-terminal to the LDLa module, is critical for receptor activity. Importantly, this motif adopts different structures in RXFP1 and RXFP2, suggesting distinct activation mechanisms. For RXFP1, the motif is flexible, weakly associates with the LDLa module, and requires H2 relaxin binding to stabilize an active conformation. Conversely, the GDxxGWxxxF motif in RXFP2 is more closely associated with the LDLa module, forming an essential binding interface for H2 relaxin. These differences in the activation mechanism will aid drug development targeting these receptors.
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17
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Kawale AA, Burmann BM. Inherent backbone dynamics fine-tune the functional plasticity of Tudor domains. Structure 2021; 29:1253-1265.e4. [PMID: 34197736 DOI: 10.1016/j.str.2021.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 04/19/2021] [Accepted: 06/04/2021] [Indexed: 10/21/2022]
Abstract
Tudor domains are crucial for mediating a diversity of protein-protein or protein-DNA interactions involved in nucleic acid metabolism. Using solution NMR spectroscopy, we assess the comprehensive understanding of the dynamical properties of the respective Tudor domains from four different bacterial (Escherichia coli) proteins UvrD, Mfd, RfaH, and NusG involved in different aspects of bacterial transcription regulation and associated processes. These proteins are benchmarked to the canonical Tudor domain fold from the human SMN protein. The detailed analysis of protein backbone dynamics and subsequent analysis by the Lipari-Szabo model-free approach revealed subtle differences in motions of the amide-bond vector on both pico- to nanosecond and micro- to millisecond timescales. On these timescales, our comparative approach reveals the usefulness of discrete amplitudes of dynamics to discern the different functionalities for Tudor domains exhibiting promiscuous binding, including the metamorphic Tudor domain included in the study.
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Affiliation(s)
- Ashish A Kawale
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 40530 Gothenburg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Björn M Burmann
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 40530 Gothenburg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden.
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18
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Li X, Mizsei R, Tan K, Mallis RJ, Duke-Cohan JS, Akitsu A, Tetteh PW, Dubey A, Hwang W, Wagner G, Lang MJ, Arthanari H, Wang JH, Reinherz EL. Pre-T cell receptors topologically sample self-ligands during thymocyte β-selection. Science 2021; 371:181-185. [PMID: 33335016 PMCID: PMC8011828 DOI: 10.1126/science.abe0918] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/03/2020] [Indexed: 11/02/2022]
Abstract
Self-discrimination, a critical but ill-defined molecular process programmed during thymocyte development, requires myriad pre-T cell receptors (preTCRs) and αβTCRs. Using x-ray crystallography, we show how a preTCR applies the concave β-sheet surface of its single variable domain (Vβ) to "horizontally" grab the protruding MHC α2-helix. By contrast, αβTCRs purpose all six complementarity-determining region (CDR) loops of their paired VαVβ module to recognize peptides bound to major histocompatibility complex molecules (pMHCs) in "vertical" head-to-head binding. The preTCR topological fit ensures that CDR3β reaches the peptide's featured C-terminal segment for pMHC sampling, establishing the subsequent αβTCR canonical docking mode. "Horizontal" docking precludes germline CDR1β- and CDR2β-MHC binding to broaden β-chain repertoire diversification before αβTCR-mediated selection refinement. Thus, one subunit successively attunes the recognition logic of related multicomponent receptors.
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Affiliation(s)
- Xiaolong Li
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Réka Mizsei
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Kemin Tan
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, USA
| | - Robert J Mallis
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Dermatology, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jonathan S Duke-Cohan
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Aoi Akitsu
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Paul W Tetteh
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Abhinav Dubey
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
- Department of Materials Science & Engineering, Texas A&M University, College Station, TX, USA
- Department of Physics & Astronomy, Texas A&M University, College Station, TX, USA
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Republic of Korea
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jia-Huai Wang
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Ellis L Reinherz
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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19
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Ghasriani H, Frahm GE, Johnston MJW, Aubin Y. Effects of Excipients on the Structure and Dynamics of Filgrastim Monitored by Thermal Unfolding Studies by CD and NMR Spectroscopy. ACS OMEGA 2020; 5:31845-31857. [PMID: 33344838 PMCID: PMC7745408 DOI: 10.1021/acsomega.0c04692] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/24/2020] [Indexed: 06/02/2023]
Abstract
Product excipients are used to confer a number of desirable properties on the drug substance to maintain or improve stability and facilitate drug delivery. This is especially important for products where the active pharmaceutical ingredient (API) is a recombinant protein. In this study, we aimed to determine if excipients and formulation conditions affect the structure and/or modulate the dynamics of the protein API of filgrastim products. Samples of uniformly labeled 15N-Met-granulocyte-colony stimulating factor (GCSF) were prepared at 100 μM (near formulation concentration) with various concentrations of individual components (polysorbate-20 and -80, sorbitol) and three pH values. Nuclear magnetic resonance (NMR) spectroscopy techniques were applied to measure chemical shift perturbation (CSP) to detect structural changes, and relaxation parameters (T 1, T 2, and heteronuclear Overhauser effect) were measured to probe the effects on protein backbone motions. In parallel, the same solution conditions were subjected to protein thermal unfolding studies monitored by circular dichroism spectropolarimetry (CD). Detergents (polysorbate-20 and 80) do not induce any observable changes on the protein structure and do not modify its dynamics at formulation concentration. Lowering pH to 4.0, a condition known to stabilize the conformation of filgrastim, as well as the addition of sorbitol produced changes of the fast motion dynamics in the nanosecond and picosecond timescale. NMR-derived order parameters, which measure the local conformational entropy of the protein backbone, show that lowering pH leads to a compaction of the four-helix bundle while the addition of sorbitol relaxes helices B and C, thereby reducing the mobility of loop CD. CSPs and measurements of protein dynamics via NMR-derived order parameters provide a description in structural and motional terms at an atomic resolution on how formulation components contribute to the stabilization of filgrastim products.
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Affiliation(s)
| | | | | | - Yves Aubin
- . Phone: 613-791-1500. Fax: 613-941-8933. 251 Sir Frederick Banting Driveway, Tunney’s Pasture, A/L
2201E, Ottawa, Ontario, Canada K1A 0K9
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20
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Steiner A, Schlepckow K, Brunner B, Steiner H, Haass C, Hagn F. γ-Secretase cleavage of the Alzheimer risk factor TREM2 is determined by its intrinsic structural dynamics. EMBO J 2020; 39:e104247. [PMID: 32830336 PMCID: PMC7560206 DOI: 10.15252/embj.2019104247] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/14/2022] Open
Abstract
Sequence variants of the microglial expressed TREM2 (triggering receptor expressed on myeloid cells 2) are a major risk factor for late onset Alzheimer's disease. TREM2 requires a stable interaction with DAP12 in the membrane to initiate signaling, which is terminated by TREM2 ectodomain shedding and subsequent intramembrane cleavage by γ-secretase. To understand the structural basis for the specificity of the intramembrane cleavage event, we determined the solution structure of the TREM2 transmembrane helix (TMH). Caused by the presence of a charged amino acid in the membrane region, the TREM2-TMH adopts a kinked structure with increased flexibility. Charge removal leads to TMH stabilization and reduced dynamics, similar to its structure in complex with DAP12. Strikingly, these dynamical features match with the site of the initial γ-secretase cleavage event. These data suggest an unprecedented cleavage mechanism by γ-secretase where flexible TMH regions act as key determinants of substrate cleavage specificity.
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Affiliation(s)
- Andrea Steiner
- Bavarian NMR Center at the Department of Chemistry and Institute for Advanced StudyTechnical University of MunichGarchingGermany
- Institute of Structural BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | - Kai Schlepckow
- German Center for Neurodegenerative Diseases (DZNE) MunichMunichGermany
| | - Bettina Brunner
- German Center for Neurodegenerative Diseases (DZNE) MunichMunichGermany
| | - Harald Steiner
- German Center for Neurodegenerative Diseases (DZNE) MunichMunichGermany
- Biomedical Center (BMC)Chair of Metabolic BiochemistryFaculty of MedicineLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Christian Haass
- German Center for Neurodegenerative Diseases (DZNE) MunichMunichGermany
- Biomedical Center (BMC)Chair of Metabolic BiochemistryFaculty of MedicineLudwig‐Maximilians‐Universität MünchenMunichGermany
- Munich Cluster for Systems Neurology (SyNergy)MunichGermany
| | - Franz Hagn
- Bavarian NMR Center at the Department of Chemistry and Institute for Advanced StudyTechnical University of MunichGarchingGermany
- Institute of Structural BiologyHelmholtz Zentrum MünchenNeuherbergGermany
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21
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Fridmanis J, Otikovs M, Brangulis K, Tārs K, Jaudzems K. Solution NMR structure of Borrelia burgdorferi outer surface lipoprotein BBP28, a member of the mlp protein family. Proteins 2020; 89:588-594. [PMID: 32949018 DOI: 10.1002/prot.26011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 07/05/2020] [Accepted: 09/13/2020] [Indexed: 12/19/2022]
Abstract
Lyme disease is the most widespread vector-transmitted disease in North America and Europe, caused by infection with Borrelia burgdorferi sensu lato complex spirochetes. We report the solution NMR structure of the B. burgdorferi outer surface lipoprotein BBP28, a member of the multicopy lipoprotein (mlp) family. The structure comprises a tether peptide, five α-helices and an extended C-terminal loop. The fold is similar to that of Borrelia turicatae outer surface protein BTA121, which is known to bind lipids. These results contribute to the understanding of Lyme disease pathogenesis by revealing the molecular structure of a protein from the widely found mlp family.
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Affiliation(s)
| | | | - Kalvis Brangulis
- Latvian Biomedical Research and Study Centre, Riga, Latvia.,Department of Human Physiology and Biochemistry, Riga Stradins University, Riga, Latvia
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Centre, Riga, Latvia.,Department of Molecular Biology, University of Latvia, Riga, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Riga, Latvia.,Department of Organic Chemistry, University of Latvia, Riga, Latvia
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22
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Comparative structure, dynamics and evolution of acyl-carrier proteins from Borrelia burgdorferi, Brucella melitensis and Rickettsia prowazekii. Biochem J 2020; 477:491-508. [PMID: 31922183 DOI: 10.1042/bcj20190797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/08/2020] [Accepted: 01/10/2020] [Indexed: 12/11/2022]
Abstract
Acyl carrier proteins (ACPs) are small helical proteins found in all kingdoms of life, primarily involved in fatty acid and polyketide biosynthesis. In eukaryotes, ACPs are part of the fatty acid synthase (FAS) complex, where they act as flexible tethers for the growing lipid chain, enabling access to the distinct active sites in FAS. In the type II synthesis systems found in bacteria and plastids, these proteins exist as monomers and perform various processes, from being a donor for synthesis of various products such as endotoxins, to supplying acyl chains for lipid A and lipoic acid FAS (quorum sensing), but also as signaling molecules, in bioluminescence and activation of toxins. The essential and diverse nature of their functions makes ACP an attractive target for antimicrobial drug discovery. Here, we report the structure, dynamics and evolution of ACPs from three human pathogens: Borrelia burgdorferi, Brucella melitensis and Rickettsia prowazekii, which could facilitate the discovery of new inhibitors of ACP function in pathogenic bacteria.
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23
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Abstract
Structural biology often focuses primarily on three-dimensional structures of biological macromolecules, deposited in the Protein Data Bank (PDB). This resource is a remarkable entity for the world-wide scientific and medical communities, as well as the general public, as it is a growing translation into three-dimensional space of the vast information in genomic databases, e.g. GENBANK. There is, however, significantly more to understanding biological function than the three-dimensional coordinate space for ground-state structures of biomolecules. The vast array of biomolecules experiences natural dynamics, interconversion between multiple conformational states, and molecular recognition and allosteric events that play out on timescales ranging from picoseconds to seconds. This wide range of timescales demands ingenious and sophisticated experimental tools to sample and interpret these motions, thus enabling clearer insight into functional annotation of the PDB. NMR spectroscopy is unique in its ability to sample this range of timescales at atomic resolution and in physiologically relevant conditions using spin relaxation methods. The field is constantly expanding to provide new creative experiments, to yield more detailed coverage of timescales, and to broaden the power of interpretation and analysis methods. This review highlights the current state of the methodology and examines the extension of analysis tools for more complex experiments and dynamic models. The future for understanding protein dynamics is bright, and these extended tools bring greater compatibility with developments in computational molecular dynamics, all of which will further our understanding of biological molecular functions. These facets place NMR as a key component in integrated structural biology.
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24
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Orriss GL, To V, Moya-Torres A, Seabrook G, O'Neil J, Stetefeld J. Solution structure of the cytoplasmic domain of NhaP2 a K +/H + antiporter from Vibrio cholera. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183225. [PMID: 32126231 DOI: 10.1016/j.bbamem.2020.183225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/08/2020] [Accepted: 02/10/2020] [Indexed: 11/24/2022]
Abstract
NhaP2 is a K+/H+ antiporter from Vibrio cholerae which consists of a transmembrane domain and a cytoplasmic domain of approximately 200 amino acids, both of which are required for cholera infectivity. Here we present the solution structure for a 165 amino acid minimal cytoplasmic domain (P2MIN) form of the protein. The structure reveals a compact N-terminal domain which resembles a Regulator of Conductance of K+ channels (RCK) domain connected to a more open C-terminal domain via a flexible 20 amino acid linker. NMR titration experiments showed that the protein binds ATP through its N-terminal domain, which was further supported by waterLOGSY and Saturation Transfer Difference NMR experiments. The two-domain organisation of the protein was confirmed by BIOSAXS, which also revealed that there are no detectable-ATP-induced conformational changes in the protein structure. Finally, in contrast to all known RCK domain structures solved to date, the current work shows that the protein is a monomer.
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Affiliation(s)
- George L Orriss
- University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Vu To
- University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Aniel Moya-Torres
- University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Genevieve Seabrook
- The OCI/UHN High Field NMR Facility, MaRS Toronto Medical Discovery Tower, 101 College Street, Toronto, Ontario M5C 1L7, Canada
| | - Joe O'Neil
- University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Jörg Stetefeld
- University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada.
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25
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Structural and dynamic insights revealing how lipase binding domain MD1 of Pseudomonas aeruginosa foldase affects lipase activation. Sci Rep 2020; 10:3578. [PMID: 32107397 PMCID: PMC7046727 DOI: 10.1038/s41598-020-60093-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/10/2020] [Indexed: 01/13/2023] Open
Abstract
Folding and cellular localization of many proteins of Gram-negative bacteria rely on a network of chaperones and secretion systems. Among them is the lipase-specific foldase Lif, a membrane-bound steric chaperone that tightly binds (KD = 29 nM) and mediates folding of the lipase LipA, a virulence factor of the pathogenic bacterium P. aeruginosa. Lif consists of five-domains, including a mini domain MD1 essential for LipA folding. However, the molecular mechanism of Lif-assisted LipA folding remains elusive. Here, we show in in vitro experiments using a soluble form of Lif (sLif) that isolated MD1 inhibits sLif-assisted LipA activation. Furthermore, the ability to activate LipA is lost in the variant sLifY99A, in which the evolutionary conserved amino acid Y99 from helix α1 of MD1 is mutated to alanine. This coincides with an approximately three-fold reduced affinity of the variant to LipA together with increased flexibility of sLifY99A in the complex as determined by polarization-resolved fluorescence spectroscopy. We have solved the NMR solution structures of P. aeruginosa MD1 and variant MD1Y99A revealing a similar fold indicating that a structural modification is likely not the reason for the impaired activity of variant sLifY99A. Molecular dynamics simulations of the sLif:LipA complex in connection with rigidity analyses suggest a long-range network of interactions spanning from Y99 of sLif to the active site of LipA, which might be essential for LipA activation. These findings provide important details about the putative mechanism for LipA activation and point to a general mechanism of protein folding by multi-domain steric chaperones.
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26
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Wang J, Murphy EJ, Nix JC, Jones DNM. Aedes aegypti Odorant Binding Protein 22 selectively binds fatty acids through a conformational change in its C-terminal tail. Sci Rep 2020; 10:3300. [PMID: 32094450 PMCID: PMC7039890 DOI: 10.1038/s41598-020-60242-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/10/2020] [Indexed: 12/20/2022] Open
Abstract
Aedes aegypti is the primary vector for transmission of Dengue, Zika and chikungunya viruses. Previously it was shown that Dengue virus infection of the mosquito led to an in increased expression of the odorant binding protein 22 (AeOBP22) within the mosquito salivary gland and that siRNA mediated knockdown of AeOBP22 led to reduced mosquito feeding behaviors. Insect OBPs are implicated in the perception, storage and transport of chemosensory signaling molecules including air-borne odorants and pheromones. AeOBP22 is unusual as it is additionally expressed in multiple tissues, including the antenna, the male reproductive glands and is transferred to females during reproduction, indicating multiple roles in the mosquito life cycle. However, it is unclear what role it plays in these tissues and what ligands it interacts with. Here we present solution and X-ray crystallographic studies that indicate a potential role of AeOBP22 binding to fatty acids, and that the specificity for longer chain fatty acids is regulated by a conformational change in the C-terminal tail that leads to creation of an enlarged binding cavity that enhances binding affinity. This study sheds light onto the native ligands for AeOBP22 and provides insight into its potential functions in different tissues.
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Affiliation(s)
- Jing Wang
- Dept. of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, 12801 East 17th Ave, Aurora, CO, 80045, USA
| | - Emma J Murphy
- Dept. of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, 12801 East 17th Ave, Aurora, CO, 80045, USA
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, USA
| | - Jay C Nix
- Molecular Biology Consortium, Beamline 4.2.2, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - David N M Jones
- Dept. of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, 12801 East 17th Ave, Aurora, CO, 80045, USA.
- Program in Structural Biology and Biochemistry, University of Colorado School of Medicine, Anschutz Medical Campus, 12801 East 17th Ave, Aurora, CO, 80045, USA.
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27
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Orton H, Huber T, Otting G. Paramagpy: software for fitting magnetic susceptibility tensors using paramagnetic effects measured in NMR spectra. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:1-12. [PMID: 37904891 PMCID: PMC10500712 DOI: 10.5194/mr-1-1-2020] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/20/2020] [Indexed: 11/01/2023]
Abstract
Paramagnetic metal ions with fast-relaxing electrons generate pseudocontact shifts (PCSs), residual dipolar couplings (RDCs), paramagnetic relaxation enhancements (PREs) and cross-correlated relaxation (CCR) in the nuclear magnetic resonance (NMR) spectra of the molecules they bind to. These effects offer long-range structural information in molecules equipped with binding sites for such metal ions. Here we present the new open-source software Paramagpy, which has been written in Python 3 with a graphic user interface. Paramagpy combines the functionalities of different currently available programs to support the fitting of magnetic susceptibility tensors using PCS, RDC, PRE and CCR data and molecular coordinates in Protein Data Bank (PDB) format, including a convenient graphical user interface. Paramagpy uses efficient fitting algorithms to avoid local minima and supports corrections to back-calculated PCS and PRE data arising from cross-correlation effects with chemical shift tensors. The source code is available from 10.5281/zenodo.3594568 .
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Affiliation(s)
- Henry William Orton
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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28
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East KW, Newton JC, Morzan UN, Narkhede Y, Acharya A, Skeens E, Jogl G, Batista VS, Palermo G, Lisi GP. Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics. J Am Chem Soc 2020; 142:1348-1358. [PMID: 31885264 PMCID: PMC7497131 DOI: 10.1021/jacs.9b10521] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
CRISPR-Cas9 is a widely employed genome-editing tool with functionality reliant on the ability of the Cas9 endonuclease to introduce site-specific breaks in double-stranded DNA. In this system, an intriguing allosteric communication has been suggested to control its DNA cleavage activity through flexibility of the catalytic HNH domain. Here, solution NMR experiments and a novel Gaussian-accelerated molecular dynamics (GaMD) simulation method are used to capture the structural and dynamic determinants of allosteric signaling within the HNH domain. We reveal the existence of a millisecond time scale dynamic pathway that spans HNH from the region interfacing the adjacent RuvC nuclease and propagates up to the DNA recognition lobe in full-length CRISPR-Cas9. These findings reveal a potential route of signal transduction within the CRISPR-Cas9 HNH nuclease, advancing our understanding of the allosteric pathway of activation. Further, considering the role of allosteric signaling in the specificity of CRISPR-Cas9, this work poses the mechanistic basis for novel engineering efforts aimed at improving its genome-editing capability.
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Affiliation(s)
- Kyle W. East
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
| | - Jocelyn C. Newton
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
| | - Uriel N. Morzan
- Department of Chemistry, Yale University, New Haven, CT 06520 , United States
| | - Yogesh Narkhede
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - Atanu Acharya
- Department of Chemistry, Yale University, New Haven, CT 06520 , United States
| | - Erin Skeens
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
| | - Victor S. Batista
- Department of Chemistry, Yale University, New Haven, CT 06520 , United States
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - George P. Lisi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
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29
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Bennet IA, Finger LD, Baxter NJ, Ambrose B, Hounslow AM, Thompson MJ, Exell JC, Shahari NNBM, Craggs TD, Waltho JP, Grasby JA. Regional conformational flexibility couples substrate specificity and scissile phosphate diester selectivity in human flap endonuclease 1. Nucleic Acids Res 2019; 46:5618-5633. [PMID: 29718417 PMCID: PMC6009646 DOI: 10.1093/nar/gky293] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 04/09/2018] [Indexed: 02/07/2023] Open
Abstract
Human flap endonuclease-1 (hFEN1) catalyzes the divalent metal ion-dependent removal of single-stranded DNA protrusions known as flaps during DNA replication and repair. Substrate selectivity involves passage of the 5'-terminus/flap through the arch and recognition of a single nucleotide 3'-flap by the α2-α3 loop. Using NMR spectroscopy, we show that the solution conformation of free and DNA-bound hFEN1 are consistent with crystal structures; however, parts of the arch region and α2-α3 loop are disordered without substrate. Disorder within the arch explains how 5'-flaps can pass under it. NMR and single-molecule FRET data show a shift in the conformational ensemble in the arch and loop region upon addition of DNA. Furthermore, the addition of divalent metal ions to the active site of the hFEN1-DNA substrate complex demonstrates that active site changes are propagated via DNA-mediated allostery to regions key to substrate differentiation. The hFEN1-DNA complex also shows evidence of millisecond timescale motions in the arch region that may be required for DNA to enter the active site. Thus, hFEN1 regional conformational flexibility spanning a range of dynamic timescales is crucial to reach the catalytically relevant ensemble.
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Affiliation(s)
- Ian A Bennet
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - L David Finger
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Nicola J Baxter
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S10 2TN, UK.,Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, UK
| | - Benjamin Ambrose
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S10 2TN, UK
| | - Mark J Thompson
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Jack C Exell
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Nur Nazihah B Md Shahari
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Timothy D Craggs
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Jonathan P Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S10 2TN, UK.,Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, UK
| | - Jane A Grasby
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
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30
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Kaltenbach M, Burke JR, Dindo M, Pabis A, Munsberg FS, Rabin A, Kamerlin SCL, Noel JP, Tawfik DS. Evolution of chalcone isomerase from a noncatalytic ancestor. Nat Chem Biol 2018; 14:548-555. [PMID: 29686356 DOI: 10.1038/s41589-018-0042-3] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 03/01/2018] [Indexed: 11/09/2022]
Abstract
The emergence of catalysis in a noncatalytic protein scaffold is a rare, unexplored event. Chalcone isomerase (CHI), a key enzyme in plant flavonoid biosynthesis, is presumed to have evolved from a nonenzymatic ancestor related to the widely distributed fatty-acid binding proteins (FAPs) and a plant protein family with no isomerase activity (CHILs). Ancestral inference supported the evolution of CHI from a protein lacking isomerase activity. Further, we identified four alternative founder mutations, i.e., mutations that individually instated activity, including a mutation that is not phylogenetically traceable. Despite strong epistasis in other cases of protein evolution, CHI's laboratory reconstructed mutational trajectory shows weak epistasis. Thus, enantioselective CHI activity could readily emerge despite a catalytically inactive starting point. Accordingly, X-ray crystallography, NMR, and molecular dynamics simulations reveal reshaping of the active site toward a productive substrate-binding mode and repositioning of the catalytic arginine that was inherited from the ancestral fatty-acid binding proteins.
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Affiliation(s)
- Miriam Kaltenbach
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Jason R Burke
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Mirco Dindo
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel.,Department of Neuroscience, Biomedicine and Movement Sciences, Biological Chemistry Section, University of Verona, Verona, Italy
| | - Anna Pabis
- Uppsala Biomedicinsk Centrum, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Fabian S Munsberg
- Uppsala Biomedicinsk Centrum, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Avigayel Rabin
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel.,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Shina C L Kamerlin
- Uppsala Biomedicinsk Centrum, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Joseph P Noel
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Dan S Tawfik
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel.
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31
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Sarr M, Kronqvist N, Chen G, Aleksis R, Purhonen P, Hebert H, Jaudzems K, Rising A, Johansson J. A spidroin-derived solubility tag enables controlled aggregation of a designed amyloid protein. FEBS J 2018; 285:1873-1885. [PMID: 29604175 DOI: 10.1111/febs.14451] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/08/2018] [Accepted: 03/26/2018] [Indexed: 12/31/2022]
Abstract
Amyloidogenesis is associated with more than 30 diseases, but the molecular mechanisms involved in cell toxicity and fibril formation remain largely unknown. The inherent tendency of amyloid-forming proteins to aggregate renders expression, purification, and experimental studies challenging. NT* is a solubility tag derived from a spider silk protein that was recently introduced for the production of several aggregation-prone peptides and proteins at high yields. Herein, we investigate whether fusion to NT* can prevent amyloid fibril formation and enable controlled aggregation for experimental studies. As an example of an amyloidogenic protein, we chose the de novo-designed polypeptide β17. The fusion protein NT*-β17 was recombinantly expressed in Escherichia coli to produce high amounts of soluble and mostly monomeric protein. Structural analysis showed that β17 is kept in a largely unstructured conformation in fusion with NT*. After proteolytic release, β17 adopts a β-sheet conformation in a pH- and salt-dependent manner and assembles into amyloid-like fibrils. The ability of NT* to prevent premature aggregation and to enable structural studies of prefibrillar states may facilitate investigation of proteins involved in amyloid diseases.
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Affiliation(s)
- Médoune Sarr
- Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Huddinge, Sweden
| | - Nina Kronqvist
- Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Huddinge, Sweden
| | - Gefei Chen
- Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Huddinge, Sweden
| | - Rihards Aleksis
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Pasi Purhonen
- Department of Biosciences and Nutrition, Karolinska Institutet, and School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Huddinge, Sweden
| | - Hans Hebert
- Department of Biosciences and Nutrition, Karolinska Institutet, and School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Huddinge, Sweden
| | - Kristaps Jaudzems
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Anna Rising
- Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Huddinge, Sweden.,Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Johansson
- Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Huddinge, Sweden
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32
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Lisi GP, Currier AA, Loria JP. Glutamine Hydrolysis by Imidazole Glycerol Phosphate Synthase Displays Temperature Dependent Allosteric Activation. Front Mol Biosci 2018; 5:4. [PMID: 29468164 PMCID: PMC5808140 DOI: 10.3389/fmolb.2018.00004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/09/2018] [Indexed: 11/13/2022] Open
Abstract
The enzyme imidazole glycerol phosphate synthase (IGPS) is a model for studies of long-range allosteric regulation in enzymes. Binding of the allosteric effector ligand N'-[5'-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide-ribonucleotide (PRFAR) stimulates millisecond (ms) timescale motions in IGPS that enhance its catalytic function. We studied the effect of temperature on these critical conformational motions and the catalytic mechanism of IGPS from the hyperthermophile Thermatoga maritima in an effort to understand temperature-dependent allostery. Enzyme kinetic and NMR dynamics measurements show that apo and PRFAR-activated IGPS respond differently to changes in temperature. Multiple-quantum Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments performed at 303, 323, and 343 K (30, 50, and 70°C) reveal that millisecond flexibility is enhanced to a higher degree in apo IGPS than in the PRFAR-bound enzyme as the sample temperature is raised. We find that the flexibility of the apo enzyme is nearly identical to that of its PRFAR activated state at 343 K, whereas conformational motions are considerably different between these two forms of the enzyme at room temperature. Arrhenius analyses of these flexible sites show a varied range of activation energies that loosely correlate to allosteric communities identified by computational methods and reflect local changes in dynamics that may facilitate conformational sampling of the active conformation. In addition, kinetic assays indicate that allosteric activation by PRFAR decreases to 65-fold at 343 K, compared to 4,200-fold at 303 K, which mirrors the decreased effect of PRFAR on ms motions relative to the unactivated enzyme. These studies indicate that at the growth temperature of T. maritima, PFRAR is a weaker allosteric activator than it is at room temperature and illustrate that the allosteric mechanism of IGPS is temperature dependent.
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Affiliation(s)
- George P Lisi
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Allen A Currier
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - J Patrick Loria
- Department of Chemistry, Yale University, New Haven, CT, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
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33
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Xu S, Ni S, Kennedy MA. NMR Analysis of Amide Hydrogen Exchange Rates in a Pentapeptide-Repeat Protein from A. thaliana. Biophys J 2017; 112:2075-2088. [PMID: 28538145 DOI: 10.1016/j.bpj.2017.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 03/15/2017] [Accepted: 04/10/2017] [Indexed: 11/26/2022] Open
Abstract
At2g44920 from Arabidopsis thaliana is a pentapeptide-repeat protein (PRP) composed of 25 repeats capped by N- and C-terminal α-helices. PRP structures are dominated by four-sided right-handed β-helices typically consisting of mixtures of type II and type IV β-turns. PRPs adopt repeated five-residue (Rfr) folds with an Rfr consensus sequence (STAV)(D/N)(L/F)(S/T/R)(X). Unlike other PRPs, At2g44920 consists exclusively of type II β-turns. At2g44920 is predicted to be located in the thylakoid lumen although its biochemical function remains unknown. Given its unusual structure, we investigated the biophysical properties of At2g44920 as a representative of the β-helix family to determine if it had exceptional global stability, backbone dynamics, or amide hydrogen exchange rates. Circular dichroism measurements yielded a melting point of 62.8°C, indicating unexceptional global thermal stability. Nuclear spin relaxation measurements indicated that the Rfr-fold core was rigid with order parameters ranging from 0.7 to 0.9. At2g44920 exhibited a striking range of amide hydrogen exchange rates spanning 10 orders of magnitude, with lifetimes ranging from minutes to several months. A weak correlation was found among hydrogen exchange rates, hydrogen bonding energies, and amino acid solvent-accessible areas. Analysis of contributions from fast (approximately picosecond to nanosecond) backbone dynamics to amide hydrogen exchange rates revealed that the average order parameter of amides undergoing fast exchange was significantly smaller compared to those undergoing slow exchange. Importantly, the activation energies for amide hydrogen exchange were found to be generally higher for the slowest exchanging amides in the central Rfr coil and decreased toward the terminal coils. This could be explained by assuming that the concerted motions of two preceding or following coils required for hydrogen bond disruption and amide hydrogen exchange have a higher activation energy compared to that required for displacement of a single coil to facilitate amide hydrogen exchange in either the terminal or penultimate coils.
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Affiliation(s)
- Shenyuan Xu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio
| | - Shuisong Ni
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio.
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34
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NMR structure, conformational dynamics, and biological activity of Ps Def1 defensin from Pinus sylvestris. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1085-1094. [DOI: 10.1016/j.bbapap.2017.05.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/14/2017] [Accepted: 05/16/2017] [Indexed: 12/31/2022]
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35
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Altering the allosteric pathway in IGPS suppresses millisecond motions and catalytic activity. Proc Natl Acad Sci U S A 2017; 114:E3414-E3423. [PMID: 28396388 DOI: 10.1073/pnas.1700448114] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Imidazole glycerol phosphate synthase (IGPS) is a V-type allosteric enzyme, meaning that its catalytic rate is critically dependent on activation by its allosteric ligand, N'-[(5'-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR). The allosteric mechanism of IGPS is reliant on millisecond conformational motions for efficient catalysis. We engineered four mutants of IGPS designed to disrupt millisecond motions and allosteric coupling to identify regions that are critical to IGPS function. Multiple-quantum Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments and NMR chemical shift titrations reveal diminished enzyme flexibility and a reshaping of the allosteric connectivity in each mutant construct, respectively. The functional relevance of the observed motional quenching is confirmed by significant reductions in glutaminase kinetic activity and allosteric ligand binding affinity. This work presents relevant conclusions toward the control of protein allostery and design of unique allosteric sites for potential enzyme inhibitors with regulatory or therapeutic benefit.
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36
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Aleksis R, Jaudzems K, Muceniece R, Liepinsh E. Lunasin is a redox sensitive intrinsically disordered peptide with two transiently populated α-helical regions. Peptides 2016; 85:56-62. [PMID: 27639324 DOI: 10.1016/j.peptides.2016.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/13/2016] [Accepted: 09/14/2016] [Indexed: 10/21/2022]
Abstract
Lunasin is a 43 amino acid peptide with anti-cancer, antioxidant, anti-inflammatory and cholesterol-lowering properties. Although the mechanism of action of lunasin has been characterized to some extent, its exact three-dimensional structure as well as the function of the N-terminal sequence remains unknown. We established a novel method for the production of recombinant lunasin that allows efficient isotope labeling for NMR studies. Initial studies showed that lunasin can exist in a reduced or oxidized state with an intramolecular disulfide bond depending on solution conditions. The structure of both forms of the peptide at pH 3.5 and 6.5 was characterized by CD spectroscopy and multidimensional NMR methods. The data indicate that lunasin belongs to the class of intrinsically disordered proteins. The analysis of secondary structure propensities indicates the presence of two helical regions and an extended (beta strand) conformation at the C-terminus. We hypothesize that the transient secondary structure elements could be stabilized upon interaction with the histones H3 and H4. The newly discovered redox properties of lunasin could explain its antioxidant and anti-inflammatory activity.
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Affiliation(s)
- Rihards Aleksis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Ruta Muceniece
- Faculty of Medicine, University of Latvia, 19 Raina Blvd, Riga, LV-1586, Latvia
| | - Edvards Liepinsh
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia.
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37
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Liu Z, Huang X, Hu L, Pham L, Poole KM, Tang Y, Mahon BP, Tang W, Li K, Goldfarb NE, Dunn BM, McKenna R, Fanucci GE. Effects of Hinge-region Natural Polymorphisms on Human Immunodeficiency Virus-Type 1 Protease Structure, Dynamics, and Drug Pressure Evolution. J Biol Chem 2016; 291:22741-22756. [PMID: 27576689 DOI: 10.1074/jbc.m116.747568] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/30/2016] [Indexed: 11/06/2022] Open
Abstract
Multidrug resistance to current Food and Drug Administration-approved HIV-1 protease (PR) inhibitors drives the need to understand the fundamental mechanisms of how drug pressure-selected mutations, which are oftentimes natural polymorphisms, elicit their effect on enzyme function and resistance. Here, the impacts of the hinge-region natural polymorphism at residue 35, glutamate to aspartate (E35D), alone and in conjunction with residue 57, arginine to lysine (R57K), are characterized with the goal of understanding how altered salt bridge interactions between the hinge and flap regions are associated with changes in structure, motional dynamics, conformational sampling, kinetic parameters, and inhibitor affinity. The combined results reveal that the single E35D substitution leads to diminished salt bridge interactions between residues 35 and 57 and gives rise to the stabilization of open-like conformational states with overall increased backbone dynamics. In HIV-1 PR constructs where sites 35 and 57 are both mutated (e.g. E35D and R57K), x-ray structures reveal an altered network of interactions that replace the salt bridge thus stabilizing the structural integrity between the flap and hinge regions. Despite the altered conformational sampling and dynamics when the salt bridge is disrupted, enzyme kinetic parameters and inhibition constants are similar to those obtained for subtype B PR. Results demonstrate that these hinge-region natural polymorphisms, which may arise as drug pressure secondary mutations, alter protein dynamics and the conformational landscape, which are important thermodynamic parameters to consider for development of inhibitors that target for non-subtype B PR.
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Affiliation(s)
- Zhanglong Liu
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Xi Huang
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Lingna Hu
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Linh Pham
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Katye M Poole
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Yan Tang
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Brian P Mahon
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Wenxing Tang
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Kunhua Li
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Nathan E Goldfarb
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Ben M Dunn
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Robert McKenna
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Gail E Fanucci
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
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38
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Lisi GP, Manley GA, Hendrickson H, Rivalta I, Batista VS, Loria JP. Dissecting Dynamic Allosteric Pathways Using Chemically Related Small-Molecule Activators. Structure 2016; 24:1155-66. [PMID: 27238967 PMCID: PMC4938718 DOI: 10.1016/j.str.2016.04.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/20/2016] [Accepted: 04/22/2016] [Indexed: 01/26/2023]
Abstract
The allosteric mechanism of the heterodimeric enzyme imidazole glycerol phosphate synthase was studied in detail with solution nuclear magnetic resonance spectroscopy and molecular dynamics simulations. We studied IGPS in complex with a series of allosteric activators corresponding to a large range of catalytic rate enhancements (26- to 4,900-fold), in which ligand binding is entropically driven. Conformational flexibility on the millisecond timescale plays a crucial role in intersubunit communication. Carr-Purcell-Meiboom-Gill relaxation dispersion experiments probing Ile, Leu, and Val methyl groups reveal that the apo- and glutamine-mimicked complexes are static on the millisecond timescale. Domain-wide motions are stimulated in the presence of the allosteric activators. These studies, in conjunction with ligand titrations, demonstrate that the allosteric network is widely dispersed and varies with the identity of the effector. Furthermore, we find that stronger allosteric ligands create more conformational flexibility on the millisecond timescale throughout HisF. This domain-wide loosening leads to maximum catalytic activity.
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Affiliation(s)
- George P Lisi
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Gregory A Manley
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | | | - Ivan Rivalta
- École Normale Supérieure de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, 46, Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT 06520, USA.
| | - J Patrick Loria
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
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39
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Conformational dynamics of a G-protein α subunit is tightly regulated by nucleotide binding. Proc Natl Acad Sci U S A 2016; 113:E3629-38. [PMID: 27298341 DOI: 10.1073/pnas.1604125113] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Heterotrimeric G proteins play a pivotal role in the signal-transduction pathways initiated by G-protein-coupled receptor (GPCR) activation. Agonist-receptor binding causes GDP-to-GTP exchange and dissociation of the Gα subunit from the heterotrimeric G protein, leading to downstream signaling. Here, we studied the internal mobility of a G-protein α subunit in its apo and nucleotide-bound forms and characterized their dynamical features at multiple time scales using solution NMR, small-angle X-ray scattering, and molecular dynamics simulations. We find that binding of GTP analogs leads to a rigid and closed arrangement of the Gα subdomain, whereas the apo and GDP-bound forms are considerably more open and dynamic. Furthermore, we were able to detect two conformational states of the Gα Ras domain in slow exchange whose populations are regulated by binding to nucleotides and a GPCR. One of these conformational states, the open state, binds to the GPCR; the second conformation, the closed state, shows no interaction with the receptor. Binding to the GPCR stabilizes the open state. This study provides an in-depth analysis of the conformational landscape and the switching function of a G-protein α subunit and the influence of a GPCR in that landscape.
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40
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Khan SN, Charlier C, Augustyniak R, Salvi N, Déjean V, Bodenhausen G, Lequin O, Pelupessy P, Ferrage F. Distribution of Pico- and Nanosecond Motions in Disordered Proteins from Nuclear Spin Relaxation. Biophys J 2016; 109:988-99. [PMID: 26331256 PMCID: PMC4564687 DOI: 10.1016/j.bpj.2015.06.069] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 05/15/2015] [Accepted: 06/23/2015] [Indexed: 11/30/2022] Open
Abstract
Intrinsically disordered proteins and intrinsically disordered regions (IDRs) are ubiquitous in the eukaryotic proteome. The description and understanding of their conformational properties require the development of new experimental, computational, and theoretical approaches. Here, we use nuclear spin relaxation to investigate the distribution of timescales of motions in an IDR from picoseconds to nanoseconds. Nitrogen-15 relaxation rates have been measured at five magnetic fields, ranging from 9.4 to 23.5 T (400-1000 MHz for protons). This exceptional wealth of data allowed us to map the spectral density function for the motions of backbone NH pairs in the partially disordered transcription factor Engrailed at 11 different frequencies. We introduce an approach called interpretation of motions by a projection onto an array of correlation times (IMPACT), which focuses on an array of six correlation times with intervals that are equidistant on a logarithmic scale between 21 ps and 21 ns. The distribution of motions in Engrailed varies smoothly along the protein sequence and is multimodal for most residues, with a prevalence of motions around 1 ns in the IDR. We show that IMPACT often provides better quantitative agreement with experimental data than conventional model-free or extended model-free analyses with two or three correlation times. We introduce a graphical representation that offers a convenient platform for a qualitative discussion of dynamics. Even when relaxation data are only acquired at three magnetic fields that are readily accessible, the IMPACT analysis gives a satisfactory characterization of spectral density functions, thus opening the way to a broad use of this approach.
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Affiliation(s)
- Shahid N Khan
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Cyril Charlier
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Rafal Augustyniak
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Nicola Salvi
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, BCH, Lausanne, Switzerland
| | - Victoire Déjean
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Geoffrey Bodenhausen
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France; Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, BCH, Lausanne, Switzerland
| | - Olivier Lequin
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Philippe Pelupessy
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Fabien Ferrage
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France.
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41
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Rubino JT, Martinelli M, Cantini F, Castagnetti A, Leuzzi R, Banci L, Scarselli M. Structural characterization of zinc-bound Zmp1, a zinc-dependent metalloprotease secreted by Clostridium difficile. J Biol Inorg Chem 2016; 21:185-96. [PMID: 26711661 DOI: 10.1007/s00775-015-1319-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/28/2015] [Indexed: 10/22/2022]
Abstract
Proteases are commonly secreted by microorganisms. In some pathogens, they can play a series of functional roles during infection, including maturation of cell surface or extracellular virulence factors, interference with host cell signaling, massive host tissue destruction, and dissolution of infection-limiting clots through degradation of the host proteins devoted to the coagulation cascade. We previously reported the identification and characterization of Zmp1, a zinc-dependent metalloprotease secreted by Clostridium difficile, demonstrated that Zmp1 is able to degrade fibrinogen in vitro, and identified two residues necessary to the catalytic activity. In the present work, we solved the solution structure of Zmp1 by Nuclear Magnetic Resonance (NMR) and compared it with the recently solved X-ray structures of substrate-bound and substrate-free Zmp1, highlighting similarities and differences. We also combined the structural characterization to biochemical assays and site-directed mutagenesis, to provide new insights into the catalytic site and on the residues responsible for substrate specificity. The Zmp1 structure showed similarity to the catalytic domain of Anthrax Lethal Factor of Bacillus anthracis. Analogies and differences in the catalytic and in the substrate-binding sites of the two proteins are discussed.
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Affiliation(s)
- Jeffrey T Rubino
- Magnetic Resonance Center, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | | | - Francesca Cantini
- Magnetic Resonance Center, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Andrea Castagnetti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Rosanna Leuzzi
- GSK Vaccines SrL, Via Fiorentina, 1, 53100, Siena, Italy
| | - Lucia Banci
- Magnetic Resonance Center, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
- Department of Chemistry, University of Florence, Sesto Fiorentino, Italy.
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42
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To V, Dzananovic E, McKenna SA, O’Neil J. The Dynamic Landscape of the Full-Length HIV-1 Transactivator of Transcription. Biochemistry 2016; 55:1314-25. [DOI: 10.1021/acs.biochem.5b01178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vu To
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Edis Dzananovic
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Sean A. McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Joe O’Neil
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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43
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Gu Y, Hansen AL, Peng Y, Brüschweiler R. Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yina Gu
- Department of Chemistry and Biochemistry The Ohio State University 100 West 18th Avenue Columbus OH 43210 USA
| | - Alexandar L. Hansen
- Campus Chemical Instrument Center The Ohio State University 460 W. 12th Avenue Columbus OH 43210 USA
| | - Yu Peng
- Department of Chemistry and Biochemistry The Ohio State University 100 West 18th Avenue Columbus OH 43210 USA
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry The Ohio State University 100 West 18th Avenue Columbus OH 43210 USA
- Campus Chemical Instrument Center The Ohio State University 460 W. 12th Avenue Columbus OH 43210 USA
- Department of Biological Chemistry and Pharmacology The Ohio State University 1645 Neil Avenue Columbus OH 43210 USA
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44
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Gu Y, Hansen AL, Peng Y, Brüschweiler R. Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data. Angew Chem Int Ed Engl 2016; 55:3117-9. [PMID: 26821600 DOI: 10.1002/anie.201511711] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Indexed: 01/03/2023]
Abstract
Functional motions of (15)N-labeled proteins can be monitored by solution NMR spin relaxation experiments over a broad range of timescales. These experiments however typically take of the order of several days to a week per protein. Recently, NMR chemical exchange saturation transfer (CEST) experiments have emerged to probe slow millisecond motions complementing R1ρ and CPMG-type experiments. CEST also simultaneously reports on site-specific R1 and R2 parameters. It is shown here how CEST-derived R1 and R2 relaxation parameters can be measured within a few hours at an accuracy comparable to traditional relaxation experiments. Using a "lean" version of the model-free approach S(2) order parameters can be determined that match those from the standard model-free approach applied to (15)N R1, R2 , and {(1)H}-(15)N NOE data. The new methodology, which is demonstrated for ubiquitin and arginine kinase (42 kDa), should serve as an effective screening tool of protein dynamics from picosecond-to-millisecond timescales.
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Affiliation(s)
- Yina Gu
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Alexandar L Hansen
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Yu Peng
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA. .,Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA. .,Department of Biological Chemistry and Pharmacology, The Ohio State University, 1645 Neil Avenue, Columbus, OH, 43210, USA.
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45
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A High Affinity hRpn2-Derived Peptide That Displaces Human Rpn13 from Proteasome in 293T Cells. PLoS One 2015; 10:e0140518. [PMID: 26466095 PMCID: PMC4605517 DOI: 10.1371/journal.pone.0140518] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 09/28/2015] [Indexed: 01/08/2023] Open
Abstract
Rpn13 is a proteasome ubiquitin receptor that has emerged as a therapeutic target for human cancers. Its ubiquitin-binding activity is confined to an N-terminal Pru (pleckstrin-like receptor for ubiquitin) domain that also docks it into the proteasome, while its C-terminal DEUBAD (DEUBiquitinase ADaptor) domain recruits deubiquitinating enzyme Uch37 to the proteasome. Bis-benzylidine piperidone derivatives that were found to bind covalently to Rpn13 C88 caused the accumulation of polyubiquitinated proteins as well as ER stress-related apoptosis in various cancer cell lines, including bortezomib-resistant multiple myeloma lines. We find that a 38-amino acid peptide derived from the C-terminus of proteasome PC repeat protein hRpn2/PSMD1 binds to hRpn13 Pru domain with 12 nM affinity. By using NMR, we identify the hRpn13-interacting amino acids in this hRpn2 fragment, some of which are conserved among eukaryotes. Importantly, we find the hRpn2-derived peptide to immunoprecipitate endogenous Rpn13 from 293T cells, and to displace it from the proteasome. These findings indicate that this region of hRpn2 is the primary binding site for hRpn13 in the proteasome. Moreover, the hRpn2-derived peptide was no longer able to interact with endogenous hRpn13 when a strictly conserved phenylalanine (F948 in humans) was replaced with arginine or a stop codon, or when Y950 and I951 were substituted with aspartic acid. Finally, over-expression of the hRpn2-derived peptide leads to an increased presence of ubiquitinated proteins in 293T cells. We propose that this hRpn2-derived peptide could be used to develop peptide-based strategies that specifically target hRpn13 function in the proteasome.
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46
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Herring CA, Singer CM, Ermakova EA, Khairutdinov BI, Zuev YF, Jacobs DJ, Nesmelova IV. Dynamics and thermodynamic properties of CXCL7 chemokine. Proteins 2015; 83:1987-2007. [PMID: 26297927 DOI: 10.1002/prot.24913] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 08/05/2015] [Accepted: 08/18/2015] [Indexed: 11/09/2022]
Abstract
Chemokines form a family of signaling proteins mainly responsible for directing the traffic of leukocytes, where their biological activity can be modulated by their oligomerization state. We characterize the dynamics and thermodynamic stability of monomer and homodimer structures of CXCL7, one of the most abundant platelet chemokines, using experimental methods that include circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy, and computational methods that include the anisotropic network model (ANM), molecular dynamics (MD) simulations and the distance constraint model (DCM). A consistent picture emerges for the effects of dimerization and Cys5-Cys31 and Cys7-Cys47 disulfide bonds formation. The presence of disulfide bonds is not critical for maintaining structural stability in the monomer or dimer, but the monomer is destabilized more than the dimer upon removal of disulfide bonds. Disulfide bonds play a key role in shaping the characteristics of native state dynamics. The combined analysis shows that upon dimerization flexibly correlated motions are induced between the 30s and 50s loop within each monomer and across the dimer interface. Interestingly, the greatest gain in flexibility upon dimerization occurs when both disulfide bonds are present, and the homodimer is least stable relative to its two monomers. These results suggest that the highly conserved disulfide bonds in chemokines facilitate a structural mechanism that is tuned to optimally distinguish functional characteristics between monomer and dimer.
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Affiliation(s)
- Charles A Herring
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, 28223
| | - Christopher M Singer
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, 28223
| | - Elena A Ermakova
- Kazan Institute of Biochemistry and Biophysics, Kazan, 40111, Russia
| | | | - Yuriy F Zuev
- Kazan Institute of Biochemistry and Biophysics, Kazan, 40111, Russia
| | - Donald J Jacobs
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, 28223.,Center for Biomedical Engineering, University of North Carolina, Charlotte, North Carolina, 28223
| | - Irina V Nesmelova
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, 28223.,Center for Biomedical Engineering, University of North Carolina, Charlotte, North Carolina, 28223
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47
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Zook J, Mo G, Sisco NJ, Craciunescu FM, Hansen DT, Baravati B, Cherry BR, Sykes K, Wachter R, Van Horn WD, Fromme P. NMR Structure of Francisella tularensis Virulence Determinant Reveals Structural Homology to Bet v1 Allergen Proteins. Structure 2015; 23:1116-22. [PMID: 26004443 DOI: 10.1016/j.str.2015.03.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 03/09/2015] [Accepted: 03/13/2015] [Indexed: 01/22/2023]
Abstract
Tularemia is a potentially fatal bacterial infection caused by Francisella tularensis, and is endemic to North America and many parts of northern Europe and Asia. The outer membrane lipoprotein, Flpp3, has been identified as a virulence determinant as well as a potential subunit template for vaccine development. Here we present the first structure for the soluble domain of Flpp3 from the highly infectious Type A SCHU S4 strain, derived through high-resolution solution nuclear magnetic resonance (NMR) spectroscopy; the first structure of a lipoprotein from the genus Francisella. The Flpp3 structure demonstrates a globular protein with an electrostatically polarized surface containing an internal cavity-a putative binding site based on the structurally homologous Bet v1 protein family of allergens. NMR-based relaxation studies suggest loop regions that potentially modulate access to the internal cavity. The Flpp3 structure may add to the understanding of F. tularensis virulence and contribute to the development of effective vaccines.
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Affiliation(s)
- James Zook
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA; Center for Membrane Proteins in Infectious Diseases, Arizona State University, Tempe, AZ 85287, USA
| | - Gina Mo
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Nicholas J Sisco
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA; Magnetic Resonance Research Center, Arizona State University, Tempe, AZ 85287, USA; The Virginia G. Piper Center for Personalized Diagnostics, Arizona State University, Tempe, AZ 85281, USA
| | - Felicia M Craciunescu
- Center for Membrane Proteins in Infectious Diseases, Arizona State University, Tempe, AZ 85287, USA; Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Debra T Hansen
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA; Center for Membrane Proteins in Infectious Diseases, Arizona State University, Tempe, AZ 85287, USA; Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Bobby Baravati
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA; Center for Membrane Proteins in Infectious Diseases, Arizona State University, Tempe, AZ 85287, USA
| | - Brian R Cherry
- Magnetic Resonance Research Center, Arizona State University, Tempe, AZ 85287, USA
| | - Kathryn Sykes
- Center for Membrane Proteins in Infectious Diseases, Arizona State University, Tempe, AZ 85287, USA; Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Rebekka Wachter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA; Center for Membrane Proteins in Infectious Diseases, Arizona State University, Tempe, AZ 85287, USA
| | - Wade D Van Horn
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA; Magnetic Resonance Research Center, Arizona State University, Tempe, AZ 85287, USA; The Virginia G. Piper Center for Personalized Diagnostics, Arizona State University, Tempe, AZ 85281, USA.
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA; Center for Membrane Proteins in Infectious Diseases, Arizona State University, Tempe, AZ 85287, USA.
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Berry RE, Muthu D, Yang F, Walker FA. NMR studies of the dynamics of high-spin nitrophorins: comparative studies of NP4 and NP2 at close to physiological pH. Biochemistry 2015; 54:221-39. [PMID: 25486224 PMCID: PMC4303294 DOI: 10.1021/bi501305a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
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The
β-barrel nitrophorin (NP) heme proteins are found in
the saliva of the blood-sucking insect Rhodnius prolixus, which synthesizes and stores nitric oxide (NO) in the salivary
glands. NO is bound to iron of the NPs and is released by dilution
and an increase in pH when the insect spits its saliva into the tissues
of a victim, to aid in obtaining a blood meal. In the adult insect,
there are four nitrophorins, NP1–NP4, which have sequence similarities
in two pairs, NP1 and NP4 (90% identical) and NP2 and NP3 (80% identical).
The available crystal structures of NP4 have been used to propose
that pH-dependent changes in the conformation of two loops between
adjacent β-strands at the front opening of the protein, the
A–B and G–H loops, determine the rate of NO release.
At pH 7.3, NP4 releases NO 17 times faster than NP2 does. In this
work, the aqua complexes of NP4 and NP2 have been investigated by
nuclear magnetic resonance (NMR) relaxation measurements to probe
the pico- to nanosecond and micro- to millisecond time scale motions
at two pH values, 6.5 and 7.3. It is found that NP4-OH2 is fairly rigid and only residues in the loop regions show dynamics
at pH 6.5; at pH 7.3, much more dynamics of the loops and most of
the β-strands are observed while the α-helices remain
fairly rigid. In comparison, NP2-OH2 shows much less dynamics,
albeit somewhat more than that of the previously reported NP2-NO complex
[Muthu, D., Berry, R. E., Zhang, H., and Walker, F. A. (2013) Biochemistry 52, 7910–7925]. The reasons for this
major difference between NP4 and NP2 are discussed.
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Affiliation(s)
- Robert E Berry
- Department of Chemistry and Biochemistry, The University of Arizona , 1306 East University Boulevard, Tucson, Arizona 85721-0041, United States
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Liu Q, Shi C, Yu L, Zhang L, Xiong Y, Tian C. General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations. Biochem Biophys Res Commun 2015; 457:467-72. [PMID: 25600810 DOI: 10.1016/j.bbrc.2015.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 01/07/2015] [Indexed: 11/30/2022]
Abstract
Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of (15)N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S(2)) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S(2)) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S(2) values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S(2) parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S(2) calculated from the experimental NMR relaxation measurements, in a site-specific manner.
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Affiliation(s)
- Qing Liu
- Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Chaowei Shi
- Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Lu Yu
- Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, PR China; High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031, PR China
| | - Longhua Zhang
- Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Ying Xiong
- Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, PR China.
| | - Changlin Tian
- Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, PR China; High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031, PR China.
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50
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Joseph S, Kwan AH, Stokes PH, Mackay JP, Cubeddu L, Matthews JM. The structure of an LIM-only protein 4 (LMO4) and Deformed epidermal autoregulatory factor-1 (DEAF1) complex reveals a common mode of binding to LMO4. PLoS One 2014; 9:e109108. [PMID: 25310299 PMCID: PMC4195752 DOI: 10.1371/journal.pone.0109108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/27/2014] [Indexed: 12/23/2022] Open
Abstract
LIM-domain only protein 4 (LMO4) is a widely expressed protein with important roles in embryonic development and breast cancer. It has been reported to bind many partners, including the transcription factor Deformed epidermal autoregulatory factor-1 (DEAF1), with which LMO4 shares many biological parallels. We used yeast two-hybrid assays to show that DEAF1 binds both LIM domains of LMO4 and that DEAF1 binds the same face on LMO4 as two other LMO4-binding partners, namely LIM domain binding protein 1 (LDB1) and C-terminal binding protein interacting protein (CtIP/RBBP8). Mutagenic screening analysed by the same method, indicates that the key residues in the interaction lie in LMO4LIM2 and the N-terminal half of the LMO4-binding domain in DEAF1. We generated a stable LMO4LIM2-DEAF1 complex and determined the solution structure of that complex. Although the LMO4-binding domain from DEAF1 is intrinsically disordered, it becomes structured on binding. The structure confirms that LDB1, CtIP and DEAF1 all bind to the same face on LMO4. LMO4 appears to form a hub in protein-protein interaction networks, linking numerous pathways within cells. Competitive binding for LMO4 therefore most likely provides a level of regulation between those different pathways.
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Affiliation(s)
- Soumya Joseph
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Ann H. Kwan
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Philippa H. Stokes
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Joel P. Mackay
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Liza Cubeddu
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
- School of Science and Health, University of Western Sydney, Campbelltown, NSW Australia
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