1
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Kovalevsky A, Aniana A, Coates L, Ghirlando R, Nashed NT, Louis JM. Visualizing the active site oxyanion loop transition upon ensitrelvir binding and transient dimerization of SARS-CoV-2 main protease. J Mol Biol 2024:168616. [PMID: 38762033 DOI: 10.1016/j.jmb.2024.168616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
N-terminal autoprocessing from its polyprotein precursor enables creating the mature-like stable dimer interface of SARS-CoV-2 main protease (MPro), concomitant with the active site oxyanion loop equilibrium transitioning to the active conformation (E*) and onset of catalytic activity. Through mutagenesis of critical interface residues and evaluating noncovalent inhibitor (ensitrelvir, ESV) facilitated dimerization through its weak binding to MPro, we demonstrate that residues extending from Ser1 through Glu14 are critical for dimerization. Combined mutations G11A, E290A and R298A (MProTM) restrict dimerization even upon binding of ESV to monomeric MProTM with an inhibitor dissociation constant of 7.4 ± 1.6 µM. Contrasting the covalent inhibitor NMV or GC373 binding to monomeric MPro, ESV binding enabled capturing the transition of the oxyanion loop conformations in the absence of a reactive warhead and independent of dimerization. Characterization of complexes by room-temperature X-ray crystallography reveals ESV bound to the E* state of monomeric MPro as well as an intermediate approaching the inactive state (E). It appears that the E* to E equilibrium shift occurs initially from G138-F140 residues, leading to the unwinding of the loop and formation of the 310-helix. Finally, we describe a transient dimer structure of the MPro precursor held together through interactions of residues A5-G11 with distinct states of the active sites, E and E*, likely representing an intermediate in the autoprocessing pathway.
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Affiliation(s)
- Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA.
| | - Annie Aniana
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA
| | - Leighton Coates
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA
| | - Nashaat T Nashed
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA.
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2
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Li M, Yang R, Chen X, Wang H, Ghirlando R, Dimitriadis EK, Craigie R. HIV-1 Integrase Assembles Multiple Species of Stable Synaptic Complex Intasomes That Are Active for Concerted DNA Integration In vitro. J Mol Biol 2024; 436:168557. [PMID: 38582148 DOI: 10.1016/j.jmb.2024.168557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/08/2024]
Abstract
Retroviral DNA integration is mediated by nucleoprotein complexes (intasomes) in which a pair of viral DNA ends are bridged by a multimer of integrase (IN). Most of the high-resolution structures of HIV-1 intasomes are based on an HIV-1 IN with an Sso7d protein domain fused to the N-terminus. Sso7d-IN aggregates much less than wild-type IN and has been critical for structural studies of HIV-1 intasomes. Unexpectedly, these structures revealed that the common core architecture that mediates catalysis could be assembled in various ways, giving rise to both tetrameric and dodecameric intasomes, together with other less well-characterized species. This differs from related retroviruses that assemble unique multimeric intasomes, although the number of protomers in the intasome varies between viruses. The question of whether the additional Sso7d domain contributes to the heterogeneity of HIV-1 intasomes is therefore raised. We have addressed this by biochemical and structural studies of intasomes assembled with wild-type HIV-1 IN. Negative stain and cryo-EM reveal a similar range of multimeric intasome species as with Sso7d-IN with the same common core architecture. Stacks of intasomes resulting from domain swapping are also seen with both wild-type and Sso7d-IN intasomes. The propensity to assemble multimeric intasome species is, therefore, an intrinsic property of HIV-1 IN and is not conferred by the presence of the Sso7d domain. The recently solved intasome structures of different retroviral species, which have been reported to be tetrameric, octameric, dodecameric, and hexadecameric, highlight how a common intasome core architecture can be assembled in different ways for catalysis.
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Affiliation(s)
- Min Li
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Renbin Yang
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xuemin Chen
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaibin Wang
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emilios K Dimitriadis
- Laboratory of Bioengineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert Craigie
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
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3
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Aniana A, Nashed NT, Ghirlando R, Coates L, Kneller DW, Kovalevsky A, Louis JM. Insights into the mechanism of SARS-CoV-2 main protease autocatalytic maturation from model precursors. Commun Biol 2023; 6:1159. [PMID: 37957287 PMCID: PMC10643566 DOI: 10.1038/s42003-023-05469-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023] Open
Abstract
A critical step for SARS-CoV-2 assembly and maturation involves the autoactivation of the main protease (MProWT) from precursor polyproteins. Upon expression, a model precursor of MProWT mediates its own release at its termini rapidly to yield a mature dimer. A construct with an E290A mutation within MPro exhibits time dependent autoprocessing of the accumulated precursor at the N-terminal nsp4/nsp5 site followed by the C-terminal nsp5/nsp6 cleavage. In contrast, a precursor containing E290A and R298A mutations (MProM) displays cleavage only at the nsp4/nsp5 site to yield an intermediate monomeric product, which is cleaved at the nsp5/nsp6 site only by MProWT. MProM and the catalytic domain (MPro1-199) fused to the truncated nsp4 region also show time-dependent conversion in vitro to produce MProM and MPro1-199, respectively. The reactions follow first-order kinetics indicating that the nsp4/nsp5 cleavage occurs via an intramolecular mechanism. These results support a mechanism involving an N-terminal intramolecular cleavage leading to an increase in the dimer population and followed by an intermolecular cleavage at the C-terminus. Thus, targeting the predominantly monomeric MPro precursor for inhibition may lead to the identification of potent drugs for treatment.
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Affiliation(s)
- Annie Aniana
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892-0520, USA
| | - Nashaat T Nashed
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892-0520, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892-0520, USA
| | - Leighton Coates
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Daniel W Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
- New England Biolabs, 240 County Road, Ipswich, MA, 01938-2723, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA.
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892-0520, USA.
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4
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Yu C, Nelson SL, Meisl G, Ghirlando R, Deshmukh L. Phase Separation and Fibrillization of Human Annexin A7 Are Mediated by Its Proline-Rich Domain. Biochemistry 2023; 62:3036-3040. [PMID: 37788367 PMCID: PMC10634317 DOI: 10.1021/acs.biochem.3c00349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/26/2023] [Indexed: 10/05/2023]
Abstract
Human annexin A7, a calcium- and phospholipid-binding protein, governs calcium homeostasis, plasma membrane repair, apoptosis, and tumor progression. A7 contains an N-terminal proline-rich domain (PRD; 180 residues, ∼24% prolines) that determines its functional specificity. Using microscopy and dye-binding assays, we show that recombinant A7 and its isolated PRD spontaneously phase separate into spherical condensates, which subsequently transform into β-sheet-rich fibrils. We demonstrate that fibrillization of A7-PRD proceeds via primary nucleation and fibril-catalyzed secondary nucleation processes, as determined by chemical kinetics, providing a mechanistic basis for its amyloid assembly. This study confirms and highlights a subclass of eukaryotic PRDs prone to forming aggregates with important physiological and pathological implications.
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Affiliation(s)
- Chenrong Yu
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
| | - Spencer L. Nelson
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
| | - Georg Meisl
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Rodolfo Ghirlando
- Laboratory
of Molecular Biology, National Institute
of Diabetes and Digestive and Kidney Diseases, National
Institutes of Health, Bethesda, Maryland 20892, United States
| | - Lalit Deshmukh
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
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5
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Shihora A, Elias RD, Hammond JA, Ghirlando R, Deshmukh L. ALS Variants of Annexin A11's Proline-Rich Domain Impair Its S100A6-Mediated Fibril Dissolution. ACS Chem Neurosci 2023; 14:2583-2589. [PMID: 37433222 PMCID: PMC10401653 DOI: 10.1021/acschemneuro.3c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/05/2023] [Indexed: 07/13/2023] Open
Abstract
Mutations in the proline-rich domain (PRD) of annexin A11 are linked to amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease, and generate abundant neuronal A11 inclusions by an unknown mechanism. Here, we demonstrate that recombinant A11-PRD and its ALS-associated variants form liquidlike condensates that transform into β-sheet-rich amyloid fibrils. Surprisingly, these fibrils dissolved in the presence of S100A6, an A11 binding partner overexpressed in ALS. The ALS variants of A11-PRD showed longer fibrillization half-times and slower dissolution, even though their binding affinities for S100A6 were not significantly affected. These findings indicate a slower fibril-to-monomer exchange for these ALS variants, resulting in a decreased level of S100A6-mediated fibril dissolution. These ALS-A11 variants are thus more likely to remain aggregated despite their slower fibrillization.
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Affiliation(s)
- Aman Shihora
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
| | - Ruben D. Elias
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
| | - John A. Hammond
- Scripps
Research Biophysics and Biochemistry Core, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Rodolfo Ghirlando
- Laboratory
of Molecular Biology, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Lalit Deshmukh
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
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6
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Il Ahn J, Zhang L, Ravishankar H, Fan L, Kirsch K, Zeng Y, Meng L, Park JE, Yun HY, Ghirlando R, Ma B, Ball D, Ku B, Nussinov R, Schmit JD, Heinz WF, Kim SJ, Karpova T, Wang YX, Lee KS. Author Correction: Architectural basis for cylindrical self-assembly governing Plk4-mediated centriole duplication in human cells. Commun Biol 2023; 6:784. [PMID: 37500946 PMCID: PMC10374603 DOI: 10.1038/s42003-023-05162-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Affiliation(s)
- Jong Il Ahn
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Liang Zhang
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Harsha Ravishankar
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, Small-Angle X-ray Scattering Core Facility, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Klara Kirsch
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yan Zeng
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lingjun Meng
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jung-Eun Park
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hye-Yeoung Yun
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
- School of Pharmacy, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - David Ball
- Laboratory of Receptor Biology and Gene Expression, Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, KS, 66506, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Seung Jun Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Tatiana Karpova
- Laboratory of Receptor Biology and Gene Expression, Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Kyung S Lee
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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7
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Elias RD, Zhu Y, Su Q, Ghirlando R, Zhang J, Deshmukh L. Reversible phase separation of ESCRT protein ALIX through tyrosine phosphorylation. Sci Adv 2023; 9:eadg3913. [PMID: 37450591 PMCID: PMC10348681 DOI: 10.1126/sciadv.adg3913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
Cytokinetic abscission, the last step of cell division, is regulated by the ESCRT machinery. In response to mitotic errors, ESCRT proteins, namely, ALIX, CHMP4B, and CHMP4C, accumulate in the cytosolic compartments termed "abscission checkpoint bodies" (ACBs) to delay abscission and prevent tumorigenesis. ALIX contributes to the biogenesis and stability of ACBs via an unknown mechanism. We show that ALIX phase separates into nondynamic condensates in vitro and in vivo, mediated by the amyloidogenic portion of its proline-rich domain. ALIX condensates confined CHMP4 paralogs in vitro. These condensates dissolved and reformed upon reversible tyrosine phosphorylation of ALIX, mediated by Src kinase and PTP1B, and sequestration of CHMP4C altered their Src-mediated dissolution. NMR analysis revealed how ALIX triggers the activation of CHMP4 proteins, which is required for successful abscission. These results implicate ALIX's phase separation in the modulation of ACBs. This study also highlights how posttranslational modifications can control protein phase separation.
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Affiliation(s)
- Ruben D. Elias
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yingqi Zhu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Qi Su
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lalit Deshmukh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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8
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Il Ahn J, Zhang L, Ravishankar H, Fan L, Kirsch K, Zeng Y, Meng L, Park JE, Yun HY, Ghirlando R, Ma B, Ball D, Ku B, Nussinov R, Schmit JD, Heinz WF, Kim SJ, Karpova T, Wang YX, Lee KS. Architectural basis for cylindrical self-assembly governing Plk4-mediated centriole duplication in human cells. Commun Biol 2023; 6:712. [PMID: 37433832 PMCID: PMC10336005 DOI: 10.1038/s42003-023-05067-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 06/23/2023] [Indexed: 07/13/2023] Open
Abstract
Proper organization of intracellular assemblies is fundamental for efficient promotion of biochemical processes and optimal assembly functionality. Although advances in imaging technologies have shed light on how the centrosome is organized, how its constituent proteins are coherently architected to elicit downstream events remains poorly understood. Using multidisciplinary approaches, we showed that two long coiled-coil proteins, Cep63 and Cep152, form a heterotetrameric building block that undergoes a stepwise formation into higher molecular weight complexes, ultimately generating a cylindrical architecture around a centriole. Mutants defective in Cep63•Cep152 heterotetramer formation displayed crippled pericentriolar Cep152 organization, polo-like kinase 4 (Plk4) relocalization to the procentriole assembly site, and Plk4-mediated centriole duplication. Given that the organization of pericentriolar materials (PCM) is evolutionarily conserved, this work could serve as a model for investigating the structure and function of PCM in other species, while offering a new direction in probing the organizational defects of PCM-related human diseases.
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Affiliation(s)
- Jong Il Ahn
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Liang Zhang
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Harsha Ravishankar
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, Small-Angle X-ray Scattering Core Facility, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Klara Kirsch
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yan Zeng
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lingjun Meng
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jung-Eun Park
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hye-Yeoung Yun
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
- School of Pharmacy, Shanghai Jiao Tong University, 200240, Shanghai, P R China
| | - David Ball
- Laboratory of Receptor Biology and Gene Expression, Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, KS, 66506, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Seung Jun Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Tatiana Karpova
- Laboratory of Receptor Biology and Gene Expression, Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Kyung S Lee
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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9
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Luo W, Hickman AB, Genzor P, Ghirlando R, Furman C, Menshikh A, Haase A, Dyda F, Wilson M. Transposase N-terminal phosphorylation and asymmetric transposon ends inhibit piggyBac transposition in mammalian cells. Nucleic Acids Res 2022; 50:13128-13142. [PMID: 36537219 PMCID: PMC9825180 DOI: 10.1093/nar/gkac1191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/09/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
DNA transposon systems are widely used in mammalian cells for genetic modification experiments, but their regulation remains poorly understood. We used biochemical and cell-based assays together with AlphaFold modeling and rational protein redesign to evaluate aspects of piggyBac transposition including the previously unexplained role of the transposase N-terminus and the need for asymmetric transposon ends for cellular activity. We found that phosphorylation at predicted casein kinase II sites in the transposase N-terminus inhibits transposition, most likely by preventing transposase-DNA interactions. Deletion of the region containing these sites releases inhibition thereby enhancing activity. We also found that the N-terminal domain promotes transposase dimerization in the absence of transposon DNA. When the N-terminus is deleted, the transposase gains the ability to carry out transposition using symmetric transposon left ends. This novel activity is also conferred by appending a second C-terminal domain. When combined, these modifications together result in a transposase that is highly active when symmetric transposon ends are used. Our results demonstrate that transposase N-terminal phosphorylation and the requirement for asymmetric transposon ends both negatively regulate piggyBac transposition in mammalian cells. These novel insights into the mechanism and structure of the piggyBac transposase expand its potential use for genomic applications.
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Affiliation(s)
- Wentian Luo
- Department of Medicine, Division and Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Alison B Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pavol Genzor
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher M Furman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna Menshikh
- Department of Medicine, Division and Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Astrid Haase
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew H Wilson
- Department of Medicine, Division and Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Veterans Affairs, Nashville, TN 37212, USA
- Departments of Pharmacology and Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
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10
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Nashed NT, Kneller DW, Coates L, Ghirlando R, Aniana A, Kovalevsky A, Louis JM. Autoprocessing and oxyanion loop reorganization upon GC373 and nirmatrelvir binding of monomeric SARS-CoV-2 main protease catalytic domain. Commun Biol 2022; 5:976. [PMID: 36114420 PMCID: PMC9481597 DOI: 10.1038/s42003-022-03910-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/29/2022] [Indexed: 11/09/2022] Open
Abstract
The monomeric catalytic domain (residues 1–199) of SARS-CoV-2 main protease (MPro1-199) fused to 25 amino acids of its flanking nsp4 region mediates its autoprocessing at the nsp4-MPro1-199 junction. We report the catalytic activity and the dissociation constants of MPro1-199 and its analogs with the covalent inhibitors GC373 and nirmatrelvir (NMV), and the estimated monomer-dimer equilibrium constants of these complexes. Mass spectrometry indicates the presence of the accumulated adduct of NMV bound to MProWT and MPro1-199 and not of GC373. A room temperature crystal structure reveals a native-like fold of the catalytic domain with an unwound oxyanion loop (E state). In contrast, the structure of a covalent complex of the catalytic domain-GC373 or NMV shows an oxyanion loop conformation (E* state) resembling the full-length mature dimer. These results suggest that the E-E* equilibrium modulates autoprocessing of the main protease when converting from a monomeric polyprotein precursor to the mature dimer. Structural characterization and catalytic activity of SARS-CoV-2 main protease reveal minimal interface regions enabling dimer formation driven by inhibitor-induced conformational changes of the oxyanion loop.
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11
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Kothapalli R, Ghirlando R, Khan ZA, Chatterjee S, Kedei N, Chattoraj D. The dimerization interface of initiator RctB governs chaperone and enhancer dependence of Vibrio cholerae chromosome 2 replication. Nucleic Acids Res 2022; 50:4529-4544. [PMID: 35390166 PMCID: PMC9071482 DOI: 10.1093/nar/gkac210] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/01/2022] [Accepted: 03/20/2022] [Indexed: 11/13/2022] Open
Abstract
Protein function often requires remodeling of protein structure. In the well-studied iteron-containing plasmids, the initiator of replication has a dimerization interface that undergoes chaperone-mediated remodeling. This remodeling reduces dimerization and promotes DNA replication, since only monomers bind origin DNA. A structurally homologs interface exists in RctB, the replication initiator of Vibrio cholerae chromosome 2 (Chr2). Chaperones also promote Chr2 replication, although both monomers and dimers of RctB bind to origin, and chaperones increase the binding of both. Here we report how five changes in the dimerization interface of RctB affect the protein. The mutants are variously defective in dimerization, more active as initiator, and except in one case, unresponsive to chaperone (DnaJ). The results indicate that chaperones also reduce RctB dimerization and support the proposal that the paradoxical chaperone-promoted dimer binding likely represents sequential binding of monomers on DNA. RctB is also activated for replication initiation upon binding to a DNA site, crtS, and three of the mutants are also unresponsive to crtS. This suggests that crtS, like chaperones, reduces dimerization, but additional evidence suggests that the remodelling activities function independently. Involvement of two remodelers in reducing dimerization signifies the importance of dimerization in limiting Chr2 replication.
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Affiliation(s)
- Roopa Kothapalli
- Basic Research Laboratory, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA
| | - Zaki Ali Khan
- Basic Research Laboratory, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Soniya Chatterjee
- Basic Research Laboratory, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Noemi Kedei
- Collaborative Protein Technology Resource, OSTP, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Dhruba K Chattoraj
- Basic Research Laboratory, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
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12
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Nashed NT, Aniana A, Ghirlando R, Chiliveri SC, Louis JM. Modulation of the monomer-dimer equilibrium and catalytic activity of SARS-CoV-2 main protease by a transition-state analog inhibitor. Commun Biol 2022; 5:160. [PMID: 35233052 PMCID: PMC8888643 DOI: 10.1038/s42003-022-03084-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/28/2022] [Indexed: 12/17/2022] Open
Abstract
The role of dimer formation for the onset of catalytic activity of SARS-CoV-2 main protease (MProWT) was assessed using a predominantly monomeric mutant (MProM). Rates of MProWT and MProM catalyzed hydrolyses display substrate saturation kinetics and second-order dependency on the protein concentration. The addition of the prodrug GC376, an inhibitor of MProWT, to MProM leads to an increase in the dimer population and catalytic activity with increasing inhibitor concentration. The activity reaches a maximum corresponding to a dimer population in which one active site is occupied by the inhibitor and the other is available for catalytic activity. This phase is followed by a decrease in catalytic activity due to the inhibitor competing with the substrate. Detailed kinetics and equilibrium analyses are presented and a modified Michaelis-Menten equation accounts for the results. These observations provide conclusive evidence that dimer formation is coupled to catalytic activity represented by two equivalent active sites.
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Affiliation(s)
- Nashaat T Nashed
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Annie Aniana
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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13
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Chiliveri SC, Louis JM, Ghirlando R, Bax A. Transient lipid-bound states of spike protein heptad repeats provide insights into SARS-CoV-2 membrane fusion. Sci Adv 2021; 7:eabk2226. [PMID: 34623907 PMCID: PMC8500521 DOI: 10.1126/sciadv.abk2226] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Entry of SARS-CoV-2 into a host cell is mediated by spike, a class I viral fusion protein responsible for merging the viral and host cell membranes. Recent studies have revealed atomic-resolution models for both the postfusion 6-helix bundle (6HB) and the prefusion state of spike. However, a mechanistic understanding of the molecular basis for the intervening structural transition, important for the design of fusion inhibitors, has remained elusive. Using nuclear magnetic resonance spectroscopy and other biophysical methods, we demonstrate the presence of α-helical, membrane-bound, intermediate states of spike’s heptad repeat (HR1 and HR2) domains that are embedded at the lipid-water interface while in a slow dynamic equilibrium with the postfusion 6HB state. These results support a model where the HR domains lower the large energy barrier associated with membrane fusion by destabilizing the host and viral membranes, while 6HB formation actively drives their fusion by forcing physical proximity.
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Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Corresponding author. (S.C.C.); (A.B.)
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Corresponding author. (S.C.C.); (A.B.)
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14
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Bou-Nader C, Muecksch F, Brown JB, Gordon JM, York A, Peng C, Ghirlando R, Summers MF, Bieniasz PD, Zhang J. HIV-1 matrix-tRNA complex structure reveals basis for host control of Gag localization. Cell Host Microbe 2021; 29:1421-1436.e7. [PMID: 34384537 PMCID: PMC8650744 DOI: 10.1016/j.chom.2021.07.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/24/2021] [Accepted: 07/19/2021] [Indexed: 10/20/2022]
Abstract
The HIV-1 virion structural polyprotein, Gag, is directed to particle assembly sites at the plasma membrane by its N-terminal matrix (MA) domain. MA also binds to host tRNAs. To understand the molecular basis of MA-tRNA interaction and its potential function, we present a co-crystal structure of HIV-1 MA-tRNALys3 complex. The structure reveals a specialized group of MA basic and aromatic residues preconfigured to recognize the distinctive structure of the tRNA elbow. Mutational, cross-linking, fluorescence, and NMR analyses show that the crystallographically defined interface drives MA-tRNA binding in solution and living cells. The structure indicates that MA is unlikely to bind tRNA and membrane simultaneously. Accordingly, single-amino-acid substitutions that abolish MA-tRNA binding caused striking redistribution of Gag to the plasma membrane and reduced HIV-1 replication. Thus, HIV-1 exploits host tRNAs to occlude a membrane localization signal and control the subcellular distribution of its major structural protein.
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Affiliation(s)
- Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Janae B Brown
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Jackson M Gordon
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Ashley York
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Chen Peng
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Michael F Summers
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA; Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.
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15
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Ramaraju B, Nelson SL, Zheng W, Ghirlando R, Deshmukh L. Quantitative NMR Study of Insulin-Degrading Enzyme Using Amyloid-β and HIV-1 p6 Elucidates Its Chaperone Activity. Biochemistry 2021; 60:2519-2523. [PMID: 34342986 PMCID: PMC8895387 DOI: 10.1021/acs.biochem.1c00342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Insulin-degrading enzyme (IDE) hydrolyzes monomeric polypeptides, including amyloid-β (Aβ) and HIV-1 p6. It also acts as a nonproteolytic chaperone to prevent Aβ polymerization. Here we compare interactions of Aβ and non-amyloidogenic p6 with IDE. Although both exhibited similar proteolysis rates, the binding kinetics to an inactive IDE characterized using relaxation-based NMR were remarkably different. IDE and Aβ formed a sparsely populated complex with a lifetime of milliseconds in which a short hydrophobic cleavage segment of Aβ was anchored to IDE. Strikingly, a second and more stable complex was significantly populated with a subsecond lifetime owing to multiple intermolecular contacts between Aβ and IDE. By selectively sequestering Aβ in this nonproductive complex, IDE likely increases the critical concentration required for fibrillization. In contrast, IDE and p6 formed a transient, submillisecond complex involving a single anchoring p6 motif. Modulation of intermolecular interactions, thus, allows IDE to differentiate between non-amyloidogenic and amyloidogenic substrates.
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Affiliation(s)
- Bhargavi Ramaraju
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Spencer L Nelson
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, Arizona 85212, United States
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Lalit Deshmukh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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16
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Zhou BR, Feng H, Kale S, Fox T, Khant H, de Val N, Ghirlando R, Panchenko AR, Bai Y. Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms. Mol Cell 2021; 81:166-182.e6. [PMID: 33238161 PMCID: PMC7796963 DOI: 10.1016/j.molcel.2020.10.038] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/21/2020] [Accepted: 10/27/2020] [Indexed: 12/21/2022]
Abstract
The repeating structural unit of metazoan chromatin is the chromatosome, a nucleosome bound to a linker histone, H1. There are 11 human H1 isoforms with diverse cellular functions, but how they interact with the nucleosome remains elusive. Here, we determined the cryoelectron microscopy (cryo-EM) structures of chromatosomes containing 197 bp DNA and three different human H1 isoforms, respectively. The globular domains of all three H1 isoforms bound to the nucleosome dyad. However, the flanking/linker DNAs displayed substantial distinct dynamic conformations. Nuclear magnetic resonance (NMR) and H1 tail-swapping cryo-EM experiments revealed that the C-terminal tails of the H1 isoforms mainly controlled the flanking DNA orientations. We also observed partial ordering of the core histone H2A C-terminal and H3 N-terminal tails in the chromatosomes. Our results provide insights into the structures and dynamics of the chromatosomes and have implications for the structure and function of chromatin.
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Affiliation(s)
- Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hanqiao Feng
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seyit Kale
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balcova, Izmir 35330, Turkey
| | - Tara Fox
- Center of Macromolecular Microscopy, National Cancer Institute, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Htet Khant
- Center of Macromolecular Microscopy, National Cancer Institute, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Natalia de Val
- Center of Macromolecular Microscopy, National Cancer Institute, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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17
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Kosek D, Hickman AB, Ghirlando R, He S, Dyda F. Structures of ISCth4 transpososomes reveal the role of asymmetry in copy-out/paste-in DNA transposition. EMBO J 2021; 40:e105666. [PMID: 33006208 PMCID: PMC7780238 DOI: 10.15252/embj.2020105666] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/07/2020] [Accepted: 09/10/2020] [Indexed: 01/23/2023] Open
Abstract
Copy-out/paste-in transposition is a major bacterial DNA mobility pathway. It contributes significantly to the emergence of antibiotic resistance, often by upregulating expression of downstream genes upon integration. Unlike other transposition pathways, it requires both asymmetric and symmetric strand transfer steps. Here, we report the first structural study of a copy-out/paste-in transposase and demonstrate its ability to catalyze all pathway steps in vitro. X-ray structures of ISCth4 transposase, a member of the IS256 family of insertion sequences, bound to DNA substrates corresponding to three sequential steps in the reaction reveal an unusual asymmetric dimeric transpososome. During transposition, an array of N-terminal domains binds a single transposon end while the catalytic domain moves to accommodate the varying substrates. These conformational changes control the path of DNA flanking the transposon end and the generation of DNA-binding sites. Our results explain the asymmetric outcome of the initial strand transfer and show how DNA binding is modulated by the asymmetric transposase to allow the capture of a second transposon end and to integrate a circular intermediate.
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Affiliation(s)
- Dalibor Kosek
- Laboratory of Molecular BiologyNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Alison B Hickman
- Laboratory of Molecular BiologyNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Rodolfo Ghirlando
- Laboratory of Molecular BiologyNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Susu He
- Laboratory of Molecular BiologyNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMDUSA
- Present address:
State Key Laboratory of Pharmaceutical BiotechnologyMedical School of Nanjing UniversityNanjingJiangsuChina
| | - Fred Dyda
- Laboratory of Molecular BiologyNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMDUSA
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18
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Elias RD, Ma W, Ghirlando R, Schwieters CD, Reddy VS, Deshmukh L. Proline-rich domain of human ALIX contains multiple TSG101-UEV interaction sites and forms phosphorylation-mediated reversible amyloids. Proc Natl Acad Sci U S A 2020; 117:24274-24284. [PMID: 32917811 PMCID: PMC7533887 DOI: 10.1073/pnas.2010635117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Proline-rich domains (PRDs) are among the most prevalent signaling modules of eukaryotes but often unexplored by biophysical techniques as their heterologous recombinant expression poses significant difficulties. Using a "divide-and-conquer" approach, we present a detailed investigation of a PRD (166 residues; ∼30% prolines) belonging to a human protein ALIX, a versatile adaptor protein involved in essential cellular processes including ESCRT-mediated membrane remodeling, cell adhesion, and apoptosis. In solution, the N-terminal fragment of ALIX-PRD is dynamically disordered. It contains three tandem sequentially similar proline-rich motifs that compete for a single binding site on its signaling partner, TSG101-UEV, as evidenced by heteronuclear NMR spectroscopy. Global fitting of relaxation dispersion data, measured as a function of TSG101-UEV concentration, allowed precise quantitation of these interactions. In contrast to the soluble N-terminal portion, the C-terminal tyrosine-rich fragment of ALIX-PRD forms amyloid fibrils and viscous gels validated using dye-binding assays with amyloid-specific probes, congo red and thioflavin T (ThT), and visualized by transmission electron microscopy. Remarkably, fibrils dissolve at low temperatures (2 to 6 °C) or upon hyperphosphorylation with Src kinase. Aggregation kinetics monitored by ThT fluorescence shows that charge repulsion dictates phosphorylation-mediated fibril dissolution and that the hydrophobic effect drives fibril formation. These data illuminate the mechanistic interplay between interactions of ALIX-PRD with TSG101-UEV and polymerization of ALIX-PRD and its central role in regulating ALIX function. This study also demonstrates the broad functional repertoires of PRDs and uncovers the impact of posttranslational modifications in the modulation of reversible amyloids.
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Affiliation(s)
- Ruben D Elias
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Wen Ma
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Charles D Schwieters
- Division of Computational Biosciences, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892
| | - Vijay S Reddy
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Lalit Deshmukh
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093;
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19
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Dotas RR, Nguyen TT, Stewart CE, Ghirlando R, Potoyan DA, Venditti V. Hybrid Thermophilic/Mesophilic Enzymes Reveal a Role for Conformational Disorder in Regulation of Bacterial Enzyme I. J Mol Biol 2020; 432:4481-4498. [PMID: 32504625 DOI: 10.1016/j.jmb.2020.05.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/23/2020] [Accepted: 05/29/2020] [Indexed: 02/08/2023]
Abstract
Conformational disorder is emerging as an important feature of biopolymers, regulating a vast array of cellular functions, including signaling, phase separation, and enzyme catalysis. Here we combine NMR, crystallography, computer simulations, protein engineering, and functional assays to investigate the role played by conformational heterogeneity in determining the activity of the C-terminal domain of bacterial Enzyme I (EIC). In particular, we design chimeric proteins by hybridizing EIC from thermophilic and mesophilic organisms, and we characterize the resulting constructs for structure, dynamics, and biological function. We show that EIC exists as a mixture of active and inactive conformations and that functional regulation is achieved by tuning the thermodynamic balance between active and inactive states. Interestingly, we also present a hybrid thermophilic/mesophilic enzyme that is thermostable and more active than the wild-type thermophilic enzyme, suggesting that hybridizing thermophilic and mesophilic proteins is a valid strategy to engineer thermostable enzymes with significant low-temperature activity.
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Affiliation(s)
- Rochelle R Dotas
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | - Trang T Nguyen
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | - Charles E Stewart
- Macromolecular X-ray Crystallography Facility, Office of Biotechnology, Iowa State University, Ames, IA 50011, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Davit A Potoyan
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA; Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - Vincenzo Venditti
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA; Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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20
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Sherekar M, Han SW, Ghirlando R, Messing S, Drew M, Rabara D, Waybright T, Juneja P, O'Neill H, Stanley CB, Bhowmik D, Ramanathan A, Subramaniam S, Nissley DV, Gillette W, McCormick F, Esposito D. Biochemical and structural analyses reveal that the tumor suppressor neurofibromin (NF1) forms a high-affinity dimer. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49919-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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21
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Sherekar M, Han SW, Ghirlando R, Messing S, Drew M, Rabara D, Waybright T, Juneja P, O'Neill H, Stanley CB, Bhowmik D, Ramanathan A, Subramaniam S, Nissley DV, Gillette W, McCormick F, Esposito D. Biochemical and structural analyses reveal that the tumor suppressor neurofibromin (NF1) forms a high-affinity dimer. J Biol Chem 2019; 295:1105-1119. [PMID: 31836666 PMCID: PMC6983858 DOI: 10.1074/jbc.ra119.010934] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/10/2019] [Indexed: 12/28/2022] Open
Abstract
Neurofibromin is a tumor suppressor encoded by the NF1 gene, which is mutated in Rasopathy disease neurofibromatosis type I. Defects in NF1 lead to aberrant signaling through the RAS–mitogen-activated protein kinase pathway due to disruption of the neurofibromin GTPase-activating function on RAS family small GTPases. Very little is known about the function of most of the neurofibromin protein; to date, biochemical and structural data exist only for its GAP domain and a region containing a Sec-PH motif. To better understand the role of this large protein, here we carried out a series of biochemical and biophysical experiments, including size-exclusion chromatography–multiangle light scattering (SEC-MALS), small-angle X-ray and neutron scattering, and analytical ultracentrifugation, indicating that full-length neurofibromin forms a high-affinity dimer. We observed that neurofibromin dimerization also occurs in human cells and likely has biological and clinical implications. Analysis of purified full-length and truncated neurofibromin variants by negative-stain EM revealed the overall architecture of the dimer and predicted the potential interactions that contribute to the dimer interface. We could reconstitute structures resembling high-affinity full-length dimers by mixing N- and C-terminal protein domains in vitro. The reconstituted neurofibromin was capable of GTPase activation in vitro, and co-expression of the two domains in human cells effectively recapitulated the activity of full-length neurofibromin. Taken together, these results suggest how neurofibromin dimers might form and be stabilized within the cell.
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Affiliation(s)
- Mukul Sherekar
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Sae-Won Han
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158.,Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Matthew Drew
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Dana Rabara
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Timothy Waybright
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Puneet Juneja
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University, Atlanta, Georgia 30322
| | - Hugh O'Neill
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830
| | | | | | | | - Sriram Subramaniam
- Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702.,Department of Biochemistry, Life Sciences Center, University of British Columbia, Vancouver, British Columbia V6T1Z3, Canada
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - William Gillette
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702.,Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
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McCall RM, Sievers ME, Fattah R, Ghirlando R, Pomerantsev AP, Leppla SH. Bacillus anthracis Virulence Regulator AtxA Binds Specifically to the pagA Promoter Region. J Bacteriol 2019; 201:e00569-19. [PMID: 31570528 PMCID: PMC6832065 DOI: 10.1128/jb.00569-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 01/12/2023] Open
Abstract
Anthrax toxin activator (AtxA) is the master virulence gene regulator of Bacillus anthracis It regulates genes on the chromosome as well as the pXO1 and pXO2 plasmids. It is not clear how AtxA regulates these genes, and direct binding of AtxA to its targets has not been shown. It has been previously suggested that AtxA and other proteins in the Mga/AtxA global transcriptional regulators family bind to the curvature of their DNA targets, although this has never been experimentally proven. Using electrophoretic mobility shift assays, we demonstrate that AtxA binds directly to the promoter region of pagA upstream of the RNA polymerase binding site. We also demonstrate that in vitro, CO2 appears to have no role in AtxA binding. However, phosphomimetic and phosphoablative substitutions in the phosphotransferase system (PTS) regulation domains (PRDs) do appear to influence AtxA binding and pagA regulation. In silico, in vitro, and in vivo analyses demonstrate that one of two hypothesized stem-loops located upstream of the RNA polymerase binding site in the pagA promoter region is important for AtxA binding in vitro and pagA regulation in vivo Our study clarifies the mechanism by which AtxA interacts with one of its targets.IMPORTANCE Anthrax toxin activator (AtxA) regulates the major virulence genes in Bacillus anthracis The bacterium produces the anthrax toxins, and understanding the mechanism of toxin production may facilitate the development of therapeutics for B. anthracis infection. Since the discovery of AtxA 25 years ago, the mechanism by which it regulates its targets has largely remained a mystery. Here, we provide evidence that AtxA binds to the promoter region of the pagA gene encoding the main central protective antigen (PA) component of the anthrax toxin. These data suggest that AtxA binding plays a direct role in gene regulation. Our work also assists in clarifying the role of CO2 in AtxA's gene regulation and provides more evidence for the role of AtxA phosphorylation in virulence gene regulation.
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Affiliation(s)
- Rita M McCall
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Mary E Sievers
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Rasem Fattah
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrei P Pomerantsev
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephen H Leppla
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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23
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Botos I, Lountos GT, Wu W, Cherry S, Ghirlando R, Kudzhaev AM, Rotanova TV, de Val N, Tropea JE, Gustchina A, Wlodawer A. Cryo-EM structure of substrate-free E. coli Lon protease provides insights into the dynamics of Lon machinery. Curr Res Struct Biol 2019; 1:13-20. [PMID: 34235464 PMCID: PMC8244335 DOI: 10.1016/j.crstbi.2019.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 11/24/2022] Open
Abstract
Energy-dependent Lon proteases play a key role in cellular regulation by degrading short-lived regulatory proteins and misfolded proteins in the cell. The structure of the catalytically inactive S679A mutant of Escherichia coli LonA protease (EcLon) has been determined by cryo-EM at the resolution of 3.5 Å. EcLonA without a bound substrate adopts a hexameric open-spiral quaternary structure that might represent the resting state of the enzyme. Upon interaction with substrate the open-spiral hexamer undergoes a major conformational change resulting in a compact, closed-circle hexamer as in the recent structure of a complex of Yersinia pestis LonA with a protein substrate. This major change is accomplished by the rigid-body rearrangement of the individual domains within the protomers of the complex around the hinge points in the interdomain linkers. Comparison of substrate-free and substrate-bound Lon structures allows to mark the location of putative pivotal points involved in such conformational changes.
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Affiliation(s)
- Istvan Botos
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - George T. Lountos
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Weimin Wu
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Scott Cherry
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Arsen M. Kudzhaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Tatyana V. Rotanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
- Electron Microscopy Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Joseph E. Tropea
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Alla Gustchina
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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24
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Fischer ES, Campbell WA, Liu S, Ghirlando R, Fattah RJ, Bugge TH, Leppla SH. Bismaleimide cross-linked anthrax toxin forms functional octamers with high specificity in tumor targeting. Protein Sci 2019; 28:1059-1070. [PMID: 30942916 DOI: 10.1002/pro.3613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/01/2019] [Indexed: 12/12/2022]
Abstract
In recent years, anthrax toxin has been reengineered to act as a highly specific antiangiogenic cancer therapeutic, shown to kill tumors in animal models. This has been achieved by modifying protective antigen (PA) so that its activation and toxicity require the presence of two proteases, matrix metalloproteinase (MMP) and urokinase plasminogen activator (uPA), which are upregulated in tumor microenvironments. These therapeutics consist of intercomplementing PA variants, which are individually nontoxic, but form functional toxins upon complementary oligomerization. Here, we have created a dual-protease requiring PA targeting system which utilizes bismaleimide cross-linked PA (CLPA) rather than the intercomplementing PA variants. Three different CLPA agents were tested and, as expected, found to exclusively form octamers. Two of the CLPA agents have in vitro toxicities equal to those of previous intercomplementing agents, while the third CLPA agent had compromised in vitro cleavage and was significantly less cytotoxic. We hypothesize this difference was due to steric hindrance caused by cross-linking two PA monomers in close proximity to the PA cleavage site. Overall, this work advances the development and use of the PA and LF tumor-targeting system as a practical cancer therapeutic, as it provides a way to reduce the drug components of the anthrax toxin drug delivery system from three to two, which may lower the cost and simplify testing in clinical trials. HIGHLIGHT: Previously, anthrax toxin has been reengineered to act as a highly specific antiangiogenic cancer therapeutic. Here, we present a version, which utilizes bismaleimide cross-linked protective antigen (PA) rather than intercomplementing PA variants. This advances the development of anthrax toxin as a practical cancer therapeutic as it reduces the components of the drug delivery system to two, which may lower the cost and simplify testing in clinical trials.
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Affiliation(s)
- Elyse S Fischer
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Warren A Campbell
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Shihui Liu
- Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, Bethesda, Maryland
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892
| | - Rasem J Fattah
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Thomas H Bugge
- Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, Bethesda, Maryland
| | - Stephen H Leppla
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
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25
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Agamasu C, Ghirlando R, Taylor T, Messing S, Tran TH, Bindu L, Tonelli M, Nissley DV, McCormick F, Stephen AG. KRAS Prenylation Is Required for Bivalent Binding with Calmodulin in a Nucleotide-Independent Manner. Biophys J 2019; 116:1049-1063. [PMID: 30846362 PMCID: PMC6428923 DOI: 10.1016/j.bpj.2019.02.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/30/2019] [Accepted: 02/04/2019] [Indexed: 12/11/2022] Open
Abstract
Deregulation of KRAS4b signaling pathway has been implicated in 30% of all cancers. Membrane localization of KRAS4b is an essential step for the initiation of the downstream signaling cascades that guide various cellular mechanisms. KRAS4b plasma membrane (PM) binding is mediated by the insertion of a prenylated moiety that is attached to the terminal carboxy-methylated cysteine, in addition to electrostatic interactions of its positively charged hypervariable region with anionic lipids. Calmodulin (CaM) has been suggested to selectively bind KRAS4b to act as a negative regulator of the RAS/mitogen-activated protein kinase (MAPK) signaling pathway by displacing KRAS4b from the membrane. However, the mechanism by which CaM can recognize and displace KRAS4b from the membrane is not well understood. In this study, we employed biophysical and structural techniques to characterize this mechanism in detail. We show that KRAS4b prenylation is required for binding to CaM and that the hydrophobic pockets of CaM can accommodate the prenylated region of KRAS4b, which might represent a novel CaM-binding motif. Remarkably, prenylated KRAS4b forms a 2:1 stoichiometric complex with CaM in a nucleotide-independent manner. The interaction between prenylated KRAS4b and CaM is enthalpically driven, and electrostatic interactions also contribute to the formation of the complex. The prenylated KRAS4b terminal KSKTKC-farnesylation and carboxy-methylation is sufficient for binding and defines the minimal CaM-binding motif. This is the same region implicated in membrane and phosphodiesterase6-δ binding. Finally, we provide a structure-based docking model by which CaM binds to prenylated KRAS4b. Our data provide new insights into the KRAS4b-CaM interaction and suggest a possible mechanism whereby CaM can regulate KRAS4b membrane localization.
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Affiliation(s)
- Constance Agamasu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Troy Taylor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Lakshman Bindu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Marco Tonelli
- National Magnetic Resource Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Frank McCormick
- Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland.
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26
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Agamasu C, Ghirlando R, Stephen A. Biophysical Insights into the KRAS4b-FMe-Calmodulin Interaction. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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27
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Zhou BR, Jiang J, Ghirlando R, Norouzi D, Sathish Yadav KN, Feng H, Wang R, Zhang P, Zhurkin V, Bai Y. Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures. J Mol Biol 2018; 430:3093-3110. [PMID: 29959925 DOI: 10.1016/j.jmb.2018.06.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/05/2018] [Accepted: 06/05/2018] [Indexed: 01/23/2023]
Abstract
It has long been suggested that chromatin may form a fiber with a diameter of ~30 nm that suppresses transcription. Despite nearly four decades of study, the structural nature of the 30-nm chromatin fiber and conclusive evidence of its existence in vivo remain elusive. The key support for the existence of specific 30-nm chromatin fiber structures is based on the determination of the structures of reconstituted nucleosome arrays using X-ray crystallography and single-particle cryo-electron microscopy coupled with glutaraldehyde chemical cross-linking. Here we report the characterization of these nucleosome arrays in solution using analytical ultracentrifugation, NMR, and small-angle X-ray scattering. We found that the physical properties of these nucleosome arrays in solution are not consistent with formation of just a few discrete structures of nucleosome arrays. In addition, we obtained a crystal of the nucleosome in complex with the globular domain of linker histone H5 that shows a new form of nucleosome packing and suggests a plausible alternative compact conformation for nucleosome arrays. Taken together, our results challenge the key evidence for the existence of a limited number of structures of reconstituted nucleosome arrays in solution by revealing that the reconstituted nucleosome arrays are actually best described as an ensemble of various conformations with a zigzagged arrangement of nucleosomes. Our finding has implications for understanding the structure and function of chromatin in vivo.
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Affiliation(s)
- Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiansheng Jiang
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Davood Norouzi
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - K N Sathish Yadav
- Laboratory of Structural Biophysics, National Cancer Institute, Frederick, MD 21701, USA
| | - Hanqiao Feng
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rui Wang
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ping Zhang
- Laboratory of Structural Biophysics, National Cancer Institute, Frederick, MD 21701, USA
| | - Victor Zhurkin
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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28
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Nguyen TT, Ghirlando R, Venditti V. The oligomerization state of bacterial enzyme I (EI) determines EI's allosteric stimulation or competitive inhibition by α-ketoglutarate. J Biol Chem 2018; 293:2631-2639. [PMID: 29317499 DOI: 10.1074/jbc.ra117.001466] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/04/2018] [Indexed: 11/06/2022] Open
Abstract
The bacterial phosphotransferase system (PTS) is a signal transduction pathway that couples phosphoryl transfer to active sugar transport across the cell membrane. The PTS is initiated by phosphorylation of enzyme I (EI) by phosphoenolpyruvate (PEP). The EI phosphorylation state determines the phosphorylation states of all other PTS components and is thought to play a central role in the regulation of several metabolic pathways and to control the biology of bacterial cells at multiple levels, for example, affecting virulence and biofilm formation. Given the pivotal role of EI in bacterial metabolism, an improved understanding of the mechanisms controlling its activity could inform future strategies for bioengineering and antimicrobial design. Here, we report an enzymatic assay, based on Selective Optimized Flip Angle Short Transient (SOFAST) NMR experiments, to investigate the effect of the small-molecule metabolite α-ketoglutarate (αKG) on the kinetics of the EI-catalyzed phosphoryl transfer reaction. We show that at experimental conditions favoring the monomeric form of EI, αKG promotes dimerization and acts as an allosteric stimulator of the enzyme. However, when the oligomerization state of EI is shifted toward the dimeric species, αKG functions as a competitive inhibitor of EI. We developed a kinetic model that fully accounted for the experimental data and indicated that bacterial cells might use the observed interplay between allosteric stimulation and competitive inhibition of EI by αKG to respond to physiological fluctuations in the intracellular environment. We expect that the mechanism for regulating EI activity revealed here is common to several other oligomeric enzymes.
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Affiliation(s)
| | - Rodolfo Ghirlando
- the Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Vincenzo Venditti
- From the Department of Chemistry and .,the Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011 and
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29
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Chiliveri SC, Louis JM, Ghirlando R, Baber JL, Bax A. Tilted, Uninterrupted, Monomeric HIV-1 gp41 Transmembrane Helix from Residual Dipolar Couplings. J Am Chem Soc 2017; 140:34-37. [PMID: 29277995 DOI: 10.1021/jacs.7b10245] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cryo-electron microscopy and X-ray crystallography have shown that the pre- and postfusion states of the HIV-1 gp41 viral coat protein, although very different from one another, each adopt C3 symmetric structures. A stable homotrimeric structure for the transmembrane domain (TM) also was modeled and supported by experimental data. For a C3 symmetric structure, alignment in an anisotropic medium must be axially symmetric, with the unique axis of the alignment tensor coinciding with the C3 axis. However, NMR residual dipolar couplings (RDCs) measured under three different alignment conditions were found to be incompatible with C3 symmetry. Subsequent measurements by paramagnetic relaxation enhancement, analytical ultracentrifugation, and DEER EPR, indicate that the transmembrane domain is monomeric. 15N NMR relaxation data and RDCs show that TM is highly ordered and uninterrupted for a total length of 32 residues, extending well into the membrane proximal external region.
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Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - John M Louis
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Rodolfo Ghirlando
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - James L Baber
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Ad Bax
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
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30
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Chittori S, Hong J, Saunders H, Feng H, Ghirlando R, Kelly AE, Bai Y, Subramaniam S. Structural mechanisms of centromeric nucleosome recognition by the kinetochore protein CENP-N. Science 2017; 359:339-343. [PMID: 29269420 DOI: 10.1126/science.aar2781] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/12/2017] [Indexed: 11/02/2022]
Abstract
Accurate chromosome segregation requires the proper assembly of kinetochore proteins. A key step in this process is the recognition of the histone H3 variant CENP-A in the centromeric nucleosome by the kinetochore protein CENP-N. We report cryo-electron microscopy (cryo-EM), biophysical, biochemical, and cell biological studies of the interaction between the CENP-A nucleosome and CENP-N. We show that human CENP-N confers binding specificity through interactions with the L1 loop of CENP-A, stabilized by electrostatic interactions with the nucleosomal DNA. Mutational analyses demonstrate analogous interactions in Xenopus, which are further supported by residue-swapping experiments involving the L1 loop of CENP-A. Our results are consistent with the coevolution of CENP-N and CENP-A and establish the structural basis for recognition of the CENP-A nucleosome to enable kinetochore assembly and centromeric chromatin organization.
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Affiliation(s)
- Sagar Chittori
- Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Jingjun Hong
- Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Hayden Saunders
- Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Hanqiao Feng
- Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD 20892, USA
| | - Alexander E Kelly
- Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA.
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA.
| | - Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA.
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31
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Xiao H, Wang F, Wisniewski J, Shaytan AK, Ghirlando R, FitzGerald PC, Huang Y, Wei D, Li S, Landsman D, Panchenko AR, Wu C. Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres. Genes Dev 2017; 31:1958-1972. [PMID: 29074736 PMCID: PMC5710141 DOI: 10.1101/gad.304782.117] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/05/2017] [Indexed: 12/16/2022]
Abstract
Histone CENP-A-containing nucleosomes play an important role in nucleating kinetochores at centromeres for chromosome segregation. However, the molecular mechanisms by which CENP-A nucleosomes engage with kinetochore proteins are not well understood. Here, we report the finding of a new function for the budding yeast Cse4/CENP-A histone-fold domain interacting with inner kinetochore protein Mif2/CENP-C. Strikingly, we also discovered that AT-rich centromere DNA has an important role for Mif2 recruitment. Mif2 contacts one side of the nucleosome dyad, engaging with both Cse4 residues and AT-rich nucleosomal DNA. Both interactions are directed by a contiguous DNA- and histone-binding domain (DHBD) harboring the conserved CENP-C motif, an AT hook, and RK clusters (clusters enriched for arginine-lysine residues). Human CENP-C has two related DHBDs that bind preferentially to DNA sequences of higher AT content. Our findings suggest that a DNA composition-based mechanism together with residues characteristic for the CENP-A histone variant contribute to the specification of centromere identity.
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Affiliation(s)
- Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Feng Wang
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jan Wisniewski
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Alexey K Shaytan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Peter C FitzGerald
- Genome Analysis Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yingzi Huang
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Debbie Wei
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Shipeng Li
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Carl Wu
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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Passos DO, Li M, Yang R, Rebensburg SV, Ghirlando R, Jeon Y, Shkriabai N, Kvaratskhelia M, Craigie R, Lyumkis D. Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome. Science 2017; 355:89-92. [PMID: 28059769 DOI: 10.1126/science.aah5163] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/02/2016] [Indexed: 12/25/2022]
Abstract
Like all retroviruses, HIV-1 irreversibly inserts a viral DNA (vDNA) copy of its RNA genome into host target DNA (tDNA). The intasome, a higher-order nucleoprotein complex composed of viral integrase (IN) and the ends of linear vDNA, mediates integration. Productive integration into host chromatin results in the formation of the strand transfer complex (STC) containing catalytically joined vDNA and tDNA. HIV-1 intasomes have been refractory to high-resolution structural studies. We used a soluble IN fusion protein to facilitate structural studies, through which we present a high-resolution cryo-electron microscopy (cryo-EM) structure of the core tetrameric HIV-1 STC and a higher-order form that adopts carboxyl-terminal domain rearrangements. The distinct STC structures highlight how HIV-1 can use the common retroviral intasome core architecture to accommodate different IN domain modules for assembly.
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Affiliation(s)
- Dario Oliveira Passos
- Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Min Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Renbin Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephanie V Rebensburg
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Youngmin Jeon
- Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Nikoloz Shkriabai
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Robert Craigie
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dmitry Lyumkis
- Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Verardi R, Kim JS, Ghirlando R, Banerjee A. Structural Basis for Substrate Recognition by the Ankyrin Repeat Domain of Human DHHC17 Palmitoyltransferase. Structure 2017; 25:1337-1347.e6. [PMID: 28757145 DOI: 10.1016/j.str.2017.06.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/25/2017] [Accepted: 06/28/2017] [Indexed: 12/01/2022]
Abstract
DHHC enzymes catalyze palmitoylation, a major post-translational modification that regulates a number of key cellular processes. There are up to 24 DHHCs in mammals and hundreds of substrate proteins that get palmitoylated. However, how DHHC enzymes engage with their substrates is still poorly understood. There is currently no structural information about the interaction between any DHHC enzyme and protein substrates. In this study we have investigated the structural and thermodynamic bases of interaction between the ankyrin repeat domain of human DHHC17 (ANK17) and Snap25b. We solved a high-resolution crystal structure of the complex between ANK17 and a peptide fragment of Snap25b. Through structure-guided mutagenesis, we discovered key residues in DHHC17 that are critically important for interaction with Snap25b. We further extended our finding by showing that the same residues are also crucial for the interaction of DHHC17 with Huntingtin, one of its most physiologically relevant substrates.
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Affiliation(s)
- Raffaello Verardi
- Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, National Institute of Child Health and Human Development, National Institutes of Health, 35A Convent Drive, Bethesda, MD 20892, USA
| | - Jin-Sik Kim
- Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, National Institute of Child Health and Human Development, National Institutes of Health, 35A Convent Drive, Bethesda, MD 20892, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anirban Banerjee
- Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, National Institute of Child Health and Human Development, National Institutes of Health, 35A Convent Drive, Bethesda, MD 20892, USA.
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Abstract
Lectins are carbohydrate-binding proteins unrelated to antibodies or enzymes. While carbohydrates are present on all cells and pathogens, lectins are also ubiquitous in nature and their interactions with glycans mediate countless biological and physical interactions. Due to the multivalency found in both lectins and their glycan-binding partners, complete characterization of these interactions can be complex and typically requires the use of multiple complimentary techniques. In this chapter, we provide a general strategy and protocols for chemical and biophysical approaches that can be used to characterize carbohydrate-mediated interactions in the context of individual oligosaccharides, as part of a glycoprotein, and ending with visualization of interactions with whole virions.
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Affiliation(s)
- Sabrina Lusvarghi
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jack R Davison
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Carole A Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States.
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Kang H, Oka S, Lee DY, Park J, Aponte AM, Jung YS, Bitterman J, Zhai P, He Y, Kooshapur H, Ghirlando R, Tjandra N, Lee SB, Kim MK, Sadoshima J, Chung JH. Sirt1 carboxyl-domain is an ATP-repressible domain that is transferrable to other proteins. Nat Commun 2017; 8:15560. [PMID: 28504272 PMCID: PMC5440690 DOI: 10.1038/ncomms15560] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 04/08/2017] [Indexed: 12/26/2022] Open
Abstract
Sirt1 is an NAD+-dependent protein deacetylase that regulates many physiological functions, including stress resistance, adipogenesis, cell senescence and energy production. Sirt1 can be activated by energy deprivation, but the mechanism is poorly understood. Here, we report that Sirt1 is negatively regulated by ATP, which binds to the C-terminal domain (CTD) of Sirt1. ATP suppresses Sirt1 activity by impairing the CTD's ability to bind to the deacetylase domain as well as its ability to function as the substrate recruitment site. ATP, but not NAD+, causes a conformational shift to a less compact structure. Mutations that prevent ATP binding increase Sirt1's ability to promote stress resistance and inhibit adipogenesis under high-ATP conditions. Interestingly, the CTD can be attached to other proteins, thereby converting them into energy-regulated proteins. These discoveries provide insight into how extreme energy deprivation can impact Sirt1 activity and underscore the complex nature of Sirt1 structure and regulation.
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Affiliation(s)
- Hyeog Kang
- Laboratory of Obesity and Aging Research, Genetics and Development Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Shinichi Oka
- Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers University, New Jersey Medical School, Newark, New Jersey 07101, USA
| | - Duck-Yeon Lee
- Biochemistry Core Facility, Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Junhong Park
- Tulane University School of Medicine, Department of Pathology, New Orleans, Louisiana 70112, USA
| | - Angel M. Aponte
- Proteomics Core Facility, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Young-Sang Jung
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul 120-140, Republic of Korea
| | - Jacob Bitterman
- Laboratory of Obesity and Aging Research, Genetics and Development Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Peiyong Zhai
- Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers University, New Jersey Medical School, Newark, New Jersey 07101, USA
| | - Yi He
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Hamed Kooshapur
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Nico Tjandra
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sean B. Lee
- Tulane University School of Medicine, Department of Pathology, New Orleans, Louisiana 70112, USA
| | - Myung K. Kim
- Laboratory of Obesity and Aging Research, Genetics and Development Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Junichi Sadoshima
- Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers University, New Jersey Medical School, Newark, New Jersey 07101, USA
| | - Jay H. Chung
- Laboratory of Obesity and Aging Research, Genetics and Development Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Libich DS, Tugarinov V, Ghirlando R, Clore GM. Confinement and Stabilization of Fyn SH3 Folding Intermediate Mimetics within the Cavity of the Chaperonin GroEL Demonstrated by Relaxation-Based NMR. Biochemistry 2017; 56:903-906. [PMID: 28156097 DOI: 10.1021/acs.biochem.6b01237] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction of two folding intermediate mimetics of the model protein substrate Fyn SH3 with the chaperonin GroEL, a supramolecular foldase/unfoldase machine, has been investigated by 15N relaxation-based nuclear magnetic resonance spectroscopy (lifetime line broadening, dark state exchange saturation transfer, and relaxation dispersion). The two mimetics comprise C-terminal truncations of wild-type and triple-mutant (A39V/N53P/V55L) Fyn SH3 in which the C-terminal strand of the SH3 domain is unfolded, while preserving the remaining domain structure. Quantitative analysis of the data reveals that a mobile state of the SH3 domain confined and tethered within the cavity of GroEL, possibly through interactions with the disordered, methionine-rich C-terminal tail(s), can be detected, and that the native state of the folding intermediate mimetics is stabilized by both confinement within and binding to apo GroEL. These data provide a basis for understanding the passive activity of GroEL as a foldase/unfoldase: the unfolded state, in the absence of hydrophobic GroEL-binding consensus sequences, is destabilized within the cavity because of its larger radius of gyration compared to that of the folding intermediate, while the folding intermediate is stabilized relative to the native state because of exposure of a hydrophobic patch that favors GroEL binding.
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Affiliation(s)
- David S Libich
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - Vitali Tugarinov
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - Rodolfo Ghirlando
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - G Marius Clore
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
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Lusvarghi S, Lohith K, Morin-Leisk J, Ghirlando R, Hinshaw JE, Bewley CA. Binding Site Geometry and Subdomain Valency Control Effects of Neutralizing Lectins on HIV-1 Viral Particles. ACS Infect Dis 2016; 2:882-891. [PMID: 27669574 DOI: 10.1021/acsinfecdis.6b00139] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Carbohydrate binding proteins such as griffithsin, cyanovirin-N, and BanLec are potent HIV entry inhibitors and promising microbicides. Each binds to high-mannose glycans on the surface envelope glycoprotein gp120, yet the mechanisms by which they engage viral spikes and exhibit inhibition constants ranging from nanomolar to picomolar are not understood. To determine the structural and mechanistic basis for recognition and potency, we selected a panel of lectins possessing different valencies per subunit, oligomeric states, and relative orientations of carbohydrate binding sites to systematically probe their contributions to inhibiting viral entry. Cryo-electron micrographs and immuno gold staining of lectin-treated viral particles revealed two distinct effects-namely, viral aggregation or clustering of the HIV-1 envelope on the viral membrane-that were dictated by carbohydrate binding site geometry and valency. "Sandwich" surface plasmon resonance experiments revealed that a second binding event occurs only for those lectins that could aggregate viral particles. Furthermore, picomolar Kd values were observed for the second binding event, providing a mechanism by which picomolar IC50 values are achieved. We suggest that these binding and aggregation phenomena translate to neutralization potency.
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Affiliation(s)
- Sabrina Lusvarghi
- Laboratory of Bioorganic
Chemistry, ‡Laboratory of Cell and Molecular Biology and #Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Center Drive, Bethesda, Maryland 20892, United States
| | - Katheryn Lohith
- Laboratory of Bioorganic
Chemistry, ‡Laboratory of Cell and Molecular Biology and #Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Center Drive, Bethesda, Maryland 20892, United States
| | - Jeanne Morin-Leisk
- Laboratory of Bioorganic
Chemistry, ‡Laboratory of Cell and Molecular Biology and #Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Center Drive, Bethesda, Maryland 20892, United States
| | - Rodolfo Ghirlando
- Laboratory of Bioorganic
Chemistry, ‡Laboratory of Cell and Molecular Biology and #Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Center Drive, Bethesda, Maryland 20892, United States
| | - Jenny E. Hinshaw
- Laboratory of Bioorganic
Chemistry, ‡Laboratory of Cell and Molecular Biology and #Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Center Drive, Bethesda, Maryland 20892, United States
| | - Carole A. Bewley
- Laboratory of Bioorganic
Chemistry, ‡Laboratory of Cell and Molecular Biology and #Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Center Drive, Bethesda, Maryland 20892, United States
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Schmidt T, Ghirlando R, Baber J, Clore GM. Quantitative Resolution of Monomer-Dimer Populations by Inversion Modulated DEER EPR Spectroscopy. Chemphyschem 2016; 17:2987-2991. [PMID: 27442455 PMCID: PMC5590656 DOI: 10.1002/cphc.201600726] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Indexed: 12/13/2022]
Abstract
A simple method, based on inversion modulated double electron-electron resonance electron paramagnetic resonance (DEER EPR) spectroscopy, is presented for determining populations of monomer and dimer in proteins (as well as any other biological macromolecules). The method is based on analysis of modulation depth versus electron double resonance (ELDOR) pulse flip angle. High accuracy is achieved by complete deuteration, extensive sampling of a large number of ELDOR pulse flip angle values, and combined analysis of differently labeled spin samples. We demonstrate the method using two different proteins: an obligate monomer exemplified by the small immunoglobulin binding B domain of protein A, and the p66 subunit of HIV-1 reverse transcriptase which exists as an equilibrium mixture of monomer and dimer species whose relative populations are affected by glycerol content. This information is crucial for quantitative analysis of distance distributions involving proteins that may exist as mixtures of monomer, dimer and high order multimers under the conditions of the DEER EPR experiment.
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Affiliation(s)
- Thomas Schmidt
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Rodolfo Ghirlando
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - James Baber
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
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Almawi AW, Matthews LA, Larasati, Myrox P, Boulton S, Lai C, Moraes T, Melacini G, Ghirlando R, Duncker BP, Guarné A. 'AND' logic gates at work: Crystal structure of Rad53 bound to Dbf4 and Cdc7. Sci Rep 2016; 6:34237. [PMID: 27681475 PMCID: PMC5041073 DOI: 10.1038/srep34237] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 09/07/2016] [Indexed: 01/07/2023] Open
Abstract
Forkhead-associated (FHA) domains are phosphopeptide recognition modules found in many signaling proteins. The Saccharomyces cerevisiae protein kinase Rad53 is a key regulator of the DNA damage checkpoint and uses its two FHA domains to interact with multiple binding partners during the checkpoint response. One of these binding partners is the Dbf4-dependent kinase (DDK), a heterodimer composed of the Cdc7 kinase and its regulatory subunit Dbf4. Binding of Rad53 to DDK, through its N-terminal FHA (FHA1) domain, ultimately inhibits DDK kinase activity, thereby preventing firing of late origins. We have previously found that the FHA1 domain of Rad53 binds simultaneously to Dbf4 and a phosphoepitope, suggesting that this domain functions as an 'AND' logic gate. Here, we present the crystal structures of the FHA1 domain of Rad53 bound to Dbf4, in the presence and absence of a Cdc7 phosphorylated peptide. Our results reveal how the FHA1 uses a canonical binding interface to recognize the Cdc7 phosphopeptide and a non-canonical interface to bind Dbf4. Based on these data we propose a mechanism to explain how Rad53 enhances the specificity of FHA1-mediated transient interactions.
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Affiliation(s)
- Ahmad W. Almawi
- Department of Biochemistry and Biomedical Sciences, ON, Canada
| | | | - Larasati
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Polina Myrox
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Stephen Boulton
- Department of Chemistry and Chemical Biology, McMaster University, ON, Canada
| | - Christine Lai
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Trevor Moraes
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, McMaster University, ON, Canada
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Alba Guarné
- Department of Biochemistry and Biomedical Sciences, ON, Canada,
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Abstract
Ghirlando and Felsenfeld review recent major advances in understanding the multiple roles of CTCF in gene regulation and genome organization and especially in how such domains are generated and organized. The role of the zinc finger protein CTCF in organizing the genome within the nucleus is now well established. Widely separated sites on DNA, occupied by both CTCF and the cohesin complex, make physical contacts that create large loop domains. Additional contacts between loci within those domains, often also mediated by CTCF, tend to be favored over contacts between loci in different domains. A large number of studies during the past 2 years have addressed the questions: How are these loops generated? What are the effects of disrupting them? Are there rules governing large-scale genome organization? It now appears that the strongest and evolutionarily most conserved of these CTCF interactions have specific rules for the orientation of the paired CTCF sites, implying the existence of a nonequilibrium mechanism of generation. Recent experiments that invert, delete, or inactivate one of a mating CTCF pair result in major changes in patterns of organization and gene expression in the surrounding regions. What remain to be determined are the detailed molecular mechanisms for re-establishing loop domains and maintaining them after replication and mitosis. As recently published data show, some mechanisms may involve interactions with noncoding RNAs as well as protein cofactors. Many CTCF sites are also involved in other functions such as modulation of RNA splicing and specific regulation of gene expression, and the relationship between these activities and loop formation is another unanswered question that should keep investigators occupied for some time.
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Affiliation(s)
- Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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Louis JM, Baber JL, Ghirlando R, Aniana A, Bax A, Roche J. Insights into the Conformation of the Membrane Proximal Regions Critical to the Trimerization of the HIV-1 gp41 Ectodomain Bound to Dodecyl Phosphocholine Micelles. PLoS One 2016; 11:e0160597. [PMID: 27513582 PMCID: PMC4981318 DOI: 10.1371/journal.pone.0160597] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/21/2016] [Indexed: 01/06/2023] Open
Abstract
The transitioning of the ectodomain of gp41 from a pre-hairpin to a six-helix bundle conformation is a crucial aspect of virus-cell fusion. To gain insight into the intermediary steps of the fusion process we have studied the pH and dodecyl phosphocholine (DPC) micelle dependent trimer association of gp41 by systematic deletion analysis of an optimized construct termed 17-172 (residues 528 to 683 of Env) that spans the fusion peptide proximal region (FPPR) to the membrane proximal external region (MPER) of gp41, by sedimentation velocity and double electron-electron resonance (DEER) EPR spectroscopy. Trimerization at pH 7 requires the presence of both the FPPR and MPER regions. However, at pH 4, the protein completely dissociates to monomers. DEER measurements reveal a partial fraying of the C-terminal MPER residues in the 17-172 trimer while the other regions, including the FPPR, remain compact. In accordance, truncating nine C-terminal MPER residues (675-683) in the 17-172 construct does not shift the trimer-monomer equilibrium significantly. Thus, in the context of the gp41 ectodomain spanning residues 17-172, trimerization is clearly dependent on FPPR and MPER regions even when the terminal residues of MPER unravel. The antibody Z13e1, which spans both the 2F5 and 4E10 epitopes in MPER, binds to 17-172 with a Kd of 1 ± 0.12 μM. Accordingly, individual antibodies 2F5 and 4E10 also recognize the 17-172 trimer/DPC complex. We propose that binding of the C-terminal residues of MPER to the surface of the DPC micelles models a correct positioning of the trimeric transmembrane domain anchored in the viral membrane.
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Affiliation(s)
- John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (JL)); (JR)
| | - James L. Baber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Annie Aniana
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
- * E-mail: (JL)); (JR)
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Van Q, Gillette WK, Esposito D, Ghirlando R, Heinrich F, Stephen AG. Abstract 1879: Structural and biochemical characterization of farnesylated and methylated KRAS-membrane interactions. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-1879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
KRAS4b, which is frequently mutated in pancreatic, colon and lung cancers, is processed in several enzymatic steps that results in the addition of a farnesyl and a methyl group to the terminal cysteine residue. Plasma membrane localization of KRAS4b requires this processing along with a polybasic stretch of lysines within the hypervariable region. KRAS4b can bind to RAF-RBD in solution but membrane bound KRAS4b is required for RAF-kinase activation. In order to determine why membrane interaction of KRAS4b is required for MAPK signal transduction we under took a structural and biochemical analysis of KRAS4b-membrane interactions. We have developed methods using an engineered baculovirus for the insect cell production of farnesylated and methylated KRAS4b (KRAS4b-FME) and this material was used in these studies. We have demonstrated that the stable interaction of KRAS4b-FME to lipid Nanodiscs and tethered lipid bilayers is dependent on the presence of anionic phospholipids. Using analytical ultracentrifugation we have evaluated the binding stoichiometry of KRAS4b-FME with Nanodiscs. In addition we have used neutron reflectivity to determine the orientation of KRAS4b-FME on tethered lipid bilayers.
Citation Format: Que Van, William K. Gillette, Dominic Esposito, Rodolfo Ghirlando, Frank Heinrich, Andrew G. Stephen. Structural and biochemical characterization of farnesylated and methylated KRAS-membrane interactions. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1879.
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Affiliation(s)
- Que Van
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | | | - Dominic Esposito
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Rodolfo Ghirlando
- 2National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD
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Ma J, Metrick M, Ghirlando R, Zhao H, Schuck P. Variable-Field Analytical Ultracentrifugation: I. Time-Optimized Sedimentation Equilibrium. Biophys J 2016; 109:827-37. [PMID: 26287634 DOI: 10.1016/j.bpj.2015.07.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 06/26/2015] [Accepted: 07/07/2015] [Indexed: 10/23/2022] Open
Abstract
Sedimentation equilibrium (SE) analytical ultracentrifugation (AUC) is a gold standard for the rigorous determination of macromolecular buoyant molar masses and the thermodynamic study of reversible interactions in solution. A significant experimental drawback is the long time required to attain SE, which is usually on the order of days. We have developed a method for time-optimized SE (toSE) with defined time-varying centrifugal fields that allow SE to be attained in a significantly (up to 10-fold) shorter time than is usually required. To achieve this, numerical Lamm equation solutions for sedimentation in time-varying fields are computed based on initial estimates of macromolecular transport properties. A parameterized rotor-speed schedule is optimized with the goal of achieving a minimal time to equilibrium while limiting transient sample preconcentration at the base of the solution column. The resulting rotor-speed schedule may include multiple over- and underspeeding phases, balancing the formation of gradients from strong sedimentation fluxes with periods of high diffusional transport. The computation is carried out in a new software program called TOSE, which also facilitates convenient experimental implementation. Further, we extend AUC data analysis to sedimentation processes in such time-varying centrifugal fields. Due to the initially high centrifugal fields in toSE and the resulting strong migration, it is possible to extract sedimentation coefficient distributions from the early data. This can provide better estimates of the size of macromolecular complexes and report on sample homogeneity early on, which may be used to further refine the prediction of the rotor-speed schedule. In this manner, the toSE experiment can be adapted in real time to the system under study, maximizing both the information content and the time efficiency of SE experiments.
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Affiliation(s)
- Jia Ma
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland
| | - Michael Metrick
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland.
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Abstract
Studies of the physical properties of nucleic acids began almost immediately following the discovery of the DNA structure. Early investigations focused on the stability and specificity of multi-strand polynucleotide complexes, then gradually on their interaction with other molecules, particularly proteins. As molecular and structural biology expanded to provide detailed information about biochemical mechanisms, physical studies eventually acquired the additional constraint that they should be relevant to functioning biological systems. We describe work in our laboratory that began with investigations of relatively simple questions about the role of electrostatic interactions in the stabilization of multi-strand nucleic acid structures, and evolved to studies of chromatin structure in vitro and within the nucleus.
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Affiliation(s)
- Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892
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45
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Abstract
The structure of the 30-nm chromatin fiber has provided, over the years, an important reference in chromatin studies. Originally derived from electron microscopic studies of soluble chromatin fibers released by restriction digestion, the gross structural features of such fragments have been supported by biophysical methods such as low angle X-ray and neutron scattering, sedimentation, light scattering, and electric dichroism. Electron microscopy and sedimentation velocity measurements demonstrated that reconstituted chromatin fibers, prepared from repeating arrays of high affinity nucleosome positioning sequences, retain the same overall features as observed for native chromatin fibers. It had been suggested that the 30 nm fiber might be the form assumed in vivo by transcriptionally silent chromatin, but individual gene or genome-wide studies of chromatin released from nuclei do not reveal any such simple correlation. Furthermore, even though the 30 nm fiber has been thought to represent an intermediate in the hierarchical folding of DNA into chromosomes, most analyses of chromatin folding within the nucleus do not detect any regular extended compact structures. However, there are important exceptions in chicken erythroid cell nuclei as well as in transcribed regions that form extended loops. Localized domains within the nucleus, either at the surface of chromosome domains or constrained as a specialized kind of constitutive heterochromatin by specific DNA binding proteins, may adopt 30 nm fiber-like structures.
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Affiliation(s)
- Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0540
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Abstract
Ferritin is a ubiquitous iron storage protein utilized as a nanomaterial for labeling biomolecules and nanoparticle construction. Commercially available preparations of horse spleen ferritin, widely used as a starting material, contain a distribution of ferritins with different iron loads. We describe a detailed approach to the enrichment of differentially loaded ferritin molecules by common biophysical techniques such as size exclusion chromatography and preparative ultracentrifugation, and characterize these preparations by dynamic light scattering, and analytical ultracentrifugation. We demonstrate a combination of methods to standardize an approach for determining the chemical load of nearly any particle, including nanoparticles and metal colloids. Purification and characterization of iron content in monodisperse ferritin species is particularly critical for several applications in nanomaterial science.
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Affiliation(s)
- Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda MD 20892
| | - Radina Mutskova
- Honors College, Integrated Life Sciences, University of Maryland, College Park MD 20742
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47
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Vrentas C, Ghirlando R, Keefer A, Hu Z, Tomczak A, Gittis AG, Murthi A, Garboczi DN, Gottesman S, Leppla SH. Hfqs in Bacillus anthracis: Role of protein sequence variation in the structure and function of proteins in the Hfq family. Protein Sci 2015; 24:1808-19. [PMID: 26271475 DOI: 10.1002/pro.2773] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/13/2015] [Indexed: 11/10/2022]
Abstract
Hfq proteins in Gram-negative bacteria play important roles in bacterial physiology and virulence, mediated by binding of the Hfq hexamer to small RNAs and/or mRNAs to post-transcriptionally regulate gene expression. However, the physiological role of Hfqs in Gram-positive bacteria is less clear. Bacillus anthracis, the causative agent of anthrax, uniquely expresses three distinct Hfq proteins, two from the chromosome (Hfq1, Hfq2) and one from its pXO1 virulence plasmid (Hfq3). The protein sequences of Hfq1 and 3 are evolutionarily distinct from those of Hfq2 and of Hfqs found in other Bacilli. Here, the quaternary structure of each B. anthracis Hfq protein, as produced heterologously in Escherichia coli, was characterized. While Hfq2 adopts the expected hexamer structure, Hfq1 does not form similarly stable hexamers in vitro. The impact on the monomer-hexamer equilibrium of varying Hfq C-terminal tail length and other sequence differences among the Hfqs was examined, and a sequence region of the Hfq proteins that was involved in hexamer formation was identified. It was found that, in addition to the distinct higher-order structures of the Hfq homologs, they give rise to different phenotypes. Hfq1 has a disruptive effect on the function of E. coli Hfq in vivo, while Hfq3 expression at high levels is toxic to E. coli but also partially complements Hfq function in E. coli. These results set the stage for future studies of the roles of these proteins in B. anthracis physiology and for the identification of sequence determinants of phenotypic complementation.
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Affiliation(s)
- Catherine Vrentas
- NIAID, National Institutes of Health (NIH), 33 North Drive, Bethesda, Maryland
| | | | - Andrea Keefer
- NIAID, National Institutes of Health (NIH), 33 North Drive, Bethesda, Maryland
| | - Zonglin Hu
- NIAID, National Institutes of Health (NIH), 33 North Drive, Bethesda, Maryland
| | | | - Apostolos G Gittis
- Structural Biology Section, Research Technologies Branch, NIAID, NIH, Twinbrook II, 12441 Parklawn Drive, Rockville, Maryland
| | - Athulaprabha Murthi
- NIAID, National Institutes of Health (NIH), 33 North Drive, Bethesda, Maryland
| | - David N Garboczi
- Structural Biology Section, Research Technologies Branch, NIAID, NIH, Twinbrook II, 12441 Parklawn Drive, Rockville, Maryland
| | | | - Stephen H Leppla
- NIAID, National Institutes of Health (NIH), 33 North Drive, Bethesda, Maryland
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Inagaki S, Ghirlando R, Vishnivetskiy SA, Homan KT, White JF, Tesmer JJG, Gurevich VV, Grisshammer R. G Protein-Coupled Receptor Kinase 2 (GRK2) and 5 (GRK5) Exhibit Selective Phosphorylation of the Neurotensin Receptor in Vitro. Biochemistry 2015; 54:4320-9. [PMID: 26120872 PMCID: PMC4512254 DOI: 10.1021/acs.biochem.5b00285] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
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G protein-coupled
receptor kinases (GRKs) play an important role
in the desensitization of G protein-mediated signaling of G protein-coupled
receptors (GPCRs). The level of interest in mapping their phosphorylation
sites has increased because recent studies suggest that the differential
pattern of receptor phosphorylation has distinct biological consequences. In vitro phosphorylation experiments using well-controlled
systems are useful for deciphering the complexity of these physiological
reactions and understanding the targeted event. Here, we report on
the phosphorylation of the class A GPCR neurotensin receptor 1 (NTSR1)
by GRKs under defined experimental conditions afforded by nanodisc
technology. Phosphorylation of NTSR1 by GRK2 was agonist-dependent,
whereas phosphorylation by GRK5 occurred in an activation-independent
manner. In addition, the negatively charged lipids in the immediate
vicinity of NTSR1 directly affect phosphorylation by GRKs. Identification
of phosphorylation sites in agonist-activated NTSR1 revealed that
GRK2 and GRK5 target different residues located on the intracellular
receptor elements. GRK2 phosphorylates only the C-terminal Ser residues,
whereas GRK5 phosphorylates Ser and Thr residues located in intracellular
loop 3 and the C-terminus. Interestingly, phosphorylation assays using
a series of NTSR1 mutants show that GRK2 does not require acidic residues
upstream of the phospho-acceptors for site-specific phosphorylation,
in contrast to the β2-adrenergic and μ-opioid
receptors. Differential phosphorylation of GPCRs by GRKs is thought
to encode a particular signaling outcome, and our in vitro study revealed NTSR1 differential phosphorylation by GRK2 and GRK5.
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Affiliation(s)
- Sayaka Inagaki
- †Membrane Protein Structure Function Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland 20852, United States
| | - Rodolfo Ghirlando
- ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, United States
| | - Sergey A Vishnivetskiy
- §Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Kristoff T Homan
- ∥Departments of Pharmacology and Biological Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jim F White
- †Membrane Protein Structure Function Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland 20852, United States
| | - John J G Tesmer
- ∥Departments of Pharmacology and Biological Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vsevolod V Gurevich
- §Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Reinhard Grisshammer
- †Membrane Protein Structure Function Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland 20852, United States
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49
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Potapov A, Yau WM, Ghirlando R, Thurber KR, Tycko R. Successive Stages of Amyloid-β Self-Assembly Characterized by Solid-State Nuclear Magnetic Resonance with Dynamic Nuclear Polarization. J Am Chem Soc 2015; 137:8294-307. [PMID: 26068174 PMCID: PMC5559291 DOI: 10.1021/jacs.5b04843] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Self-assembly of amyloid-β (Aβ) peptides in human brain tissue leads to neurodegeneration in Alzheimer's disease (AD). Amyloid fibrils, whose structures have been extensively characterized by solid state nuclear magnetic resonance (ssNMR) and other methods, are the thermodynamic end point of Aβ self-assembly. Oligomeric and protofibrillar assemblies, whose structures are less well-understood, are also observed as intermediates in the assembly process in vitro and have been implicated as important neurotoxic species in AD. We report experiments in which the structural evolution of 40-residue Aβ (Aβ40) is monitored by ssNMR measurements on frozen solutions prepared at four successive stages of the self-assembly process. Measurements on transient intermediates are enabled by ssNMR signal enhancements from dynamic nuclear polarization (DNP) at temperatures below 30 K. DNP-enhanced ssNMR data reveal a monotonic increase in conformational order from an initial state comprised primarily of monomers and small oligomers in solution at high pH, to larger oligomers near neutral pH, to metastable protofibrils, and finally to fibrils. Surprisingly, the predominant molecular conformation, indicated by (13)C NMR chemical shifts and by side chain contacts between F19 and L34 residues, is qualitatively similar at all stages. However, the in-register parallel β-sheet supramolecular structure, indicated by intermolecular (13)C spin polarization transfers, does not develop before the fibril stage. This work represents the first application of DNP-enhanced ssNMR to the characterization of peptide or protein self-assembly intermediates.
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Affiliation(s)
- Alexey Potapov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Kent R. Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
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50
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Zhao H, Ghirlando R, Alfonso C, Arisaka F, Attali I, Bain DL, Bakhtina MM, Becker DF, Bedwell GJ, Bekdemir A, Besong TMD, Birck C, Brautigam CA, Brennerman W, Byron O, Bzowska A, Chaires JB, Chaton CT, Cölfen H, Connaghan KD, Crowley KA, Curth U, Daviter T, Dean WL, Díez AI, Ebel C, Eckert DM, Eisele LE, Eisenstein E, England P, Escalante C, Fagan JA, Fairman R, Finn RM, Fischle W, de la Torre JG, Gor J, Gustafsson H, Hall D, Harding SE, Cifre JGH, Herr AB, Howell EE, Isaac RS, Jao SC, Jose D, Kim SJ, Kokona B, Kornblatt JA, Kosek D, Krayukhina E, Krzizike D, Kusznir EA, Kwon H, Larson A, Laue TM, Le Roy A, Leech AP, Lilie H, Luger K, Luque-Ortega JR, Ma J, May CA, Maynard EL, Modrak-Wojcik A, Mok YF, Mücke N, Nagel-Steger L, Narlikar GJ, Noda M, Nourse A, Obsil T, Park CK, Park JK, Pawelek PD, Perdue EE, Perkins SJ, Perugini MA, Peterson CL, Peverelli MG, Piszczek G, Prag G, Prevelige PE, Raynal BDE, Rezabkova L, Richter K, Ringel AE, Rosenberg R, Rowe AJ, Rufer AC, Scott DJ, Seravalli JG, Solovyova AS, Song R, Staunton D, Stoddard C, Stott K, Strauss HM, Streicher WW, Sumida JP, Swygert SG, Szczepanowski RH, Tessmer I, Toth RT, Tripathy A, Uchiyama S, Uebel SFW, Unzai S, Gruber AV, von Hippel PH, Wandrey C, Wang SH, Weitzel SE, Wielgus-Kutrowska B, Wolberger C, Wolff M, Wright E, Wu YS, Wubben JM, Schuck P. A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation. PLoS One 2015; 10:e0126420. [PMID: 25997164 PMCID: PMC4440767 DOI: 10.1371/journal.pone.0126420] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 04/02/2015] [Indexed: 12/21/2022] Open
Abstract
Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304 ± 0.188) S (4.4%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of ± 0.030 S (0.7%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Carlos Alfonso
- Analytical Ultracentrifugacion and Light Scattering Facility, Centro de Investigaciones Biológicas, CSIC, Madrid, 28040, Spain
| | - Fumio Arisaka
- Life Science Research Center, Nihon University, College of Bioresource Science, Fujisawa, 252–0880, Japan
| | - Ilan Attali
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - David L. Bain
- Department of Pharmaceutical Sciences, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, 80045, United States of America
| | - Marina M. Bakhtina
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, Ohio, 43210, United States of America
| | - Donald F. Becker
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States of America
| | - Gregory J. Bedwell
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, 35294, United States of America
| | - Ahmet Bekdemir
- Supramolecular Nanomaterials and Interfaces Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
| | - Tabot M. D. Besong
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | | | - Chad A. Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390, United States of America
| | - William Brennerman
- Beckman Coulter, Inc., Life Science Division, Indianapolis, Indiana, 46268, United States of America
| | - Olwyn Byron
- School of Life Sciences, University of Glasgow, Glasgow, G37TT, United Kingdom
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, 02–089, Poland
| | - Jonathan B. Chaires
- JG Brown Cancer Center, University of Louisville, Louisville, Kentucky, 40202, United States of America
| | - Catherine T. Chaton
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, United States of America
| | - Helmut Cölfen
- Physical Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Keith D. Connaghan
- Department of Pharmaceutical Sciences, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, 80045, United States of America
| | - Kimberly A. Crowley
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, 01605, United States of America
| | - Ute Curth
- Institute for Biophysical Chemistry, Hannover Medical School, 30625, Hannover, Germany
| | - Tina Daviter
- Institute of Structural and Molecular Biology Biophysics Centre, Birkbeck, University of London and University College London, London, WC1E 7HX, United Kingdom
| | - William L. Dean
- JG Brown Cancer Center, University of Louisville, Louisville, Kentucky, 40202, United States of America
| | - Ana I. Díez
- Department of Physical Chemistry, University of Murcia, Murcia, 30071, Spain
| | - Christine Ebel
- Univ. Grenoble Alpes, IBS, F-38044, Grenoble, France
- CNRS, IBS, F-38044, Grenoble, France
- CEA, IBS, F-38044, Grenoble, France
| | - Debra M. Eckert
- Protein Interactions Core, Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, 84112, United States of America
| | - Leslie E. Eisele
- Wadsworth Center, New York State Department of Health, Albany, New York, 12208, United States of America
| | - Edward Eisenstein
- Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland, 20850, United States of America
| | - Patrick England
- Institut Pasteur, Centre of Biophysics of Macromolecules and Their Interactions, Paris, 75724, France
| | - Carlos Escalante
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, 23220, United States of America
| | - Jeffrey A. Fagan
- Materials Science and Engineering Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899, United States of America
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041, United States of America
| | - Ron M. Finn
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | | | - Jayesh Gor
- Department of Structural and Molecular Biology, Darwin Building, University College London, London, WC1E 6BT, United Kingdom
| | | | - Damien Hall
- Research School of Chemistry, Section on Biological Chemistry, The Australian National University, Acton, ACT 0200, Australia
| | - Stephen E. Harding
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | | | - Andrew B. Herr
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, United States of America
| | - Elizabeth E. Howell
- Biochemistry, Cell and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee, 37996–0840, United States of America
| | - Richard S. Isaac
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
- Tetrad Graduate Program, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Shu-Chuan Jao
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Biophysics Core Facility, Scientific Instrument Center, Academia Sinica, Taipei, 115, Taiwan
| | - Davis Jose
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - Soon-Jong Kim
- Department of Chemistry, Mokpo National University, Muan, 534–729, Korea
| | - Bashkim Kokona
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041, United States of America
| | - Jack A. Kornblatt
- Enzyme Research Group, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Dalibor Kosek
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Prague, 12843, Czech Republic
| | - Elena Krayukhina
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Daniel Krzizike
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Eric A. Kusznir
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-LaRoche Ltd., Basel, 4070, Switzerland
| | - Hyewon Kwon
- Analytical Biopharmacy Core, University of Washington, Seattle, Washington, 98195, United States of America
| | - Adam Larson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
- Tetrad Graduate Program, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Thomas M. Laue
- Department of Biochemistry, University of New Hampshire, Durham, New Hampshire, 03824, United States of America
| | - Aline Le Roy
- Univ. Grenoble Alpes, IBS, F-38044, Grenoble, France
- CNRS, IBS, F-38044, Grenoble, France
- CEA, IBS, F-38044, Grenoble, France
| | - Andrew P. Leech
- Technology Facility, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, 06120, Halle, Germany
| | - Karolin Luger
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Juan R. Luque-Ortega
- Analytical Ultracentrifugacion and Light Scattering Facility, Centro de Investigaciones Biológicas, CSIC, Madrid, 28040, Spain
| | - Jia Ma
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Carrie A. May
- Department of Biochemistry, University of New Hampshire, Durham, New Hampshire, 03824, United States of America
| | - Ernest L. Maynard
- Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20814, United States of America
| | - Anna Modrak-Wojcik
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, 02–089, Poland
| | - Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, Bio21 Instute of Molecular Science and Biotechnology, University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Norbert Mücke
- Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, 69120, Germany
| | | | - Geeta J. Narlikar
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Masanori Noda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Amanda Nourse
- Molecular Interaction Analysis Shared Resource, St. Jude Children’s Research Hospital, Memphis, Tennessee, 38105, United States of America
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Prague, 12843, Czech Republic
| | - Chad K. Park
- Analytical Biophysics & Materials Characterization, Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721, United States of America
| | - Jin-Ku Park
- Central Instrument Center, Mokpo National University, Muan, 534–729, Korea
| | - Peter D. Pawelek
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Erby E. Perdue
- Beckman Coulter, Inc., Life Science Division, Indianapolis, Indiana, 46268, United States of America
| | - Stephen J. Perkins
- Department of Structural and Molecular Biology, Darwin Building, University College London, London, WC1E 6BT, United Kingdom
| | - Matthew A. Perugini
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Craig L. Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, 01605, United States of America
| | - Martin G. Peverelli
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Grzegorz Piszczek
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Gali Prag
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Peter E. Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, 35294, United States of America
| | - Bertrand D. E. Raynal
- Institut Pasteur, Centre of Biophysics of Macromolecules and Their Interactions, Paris, 75724, France
| | - Lenka Rezabkova
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Klaus Richter
- Department of Chemistry and Center for Integrated Protein Science, Technische Universität München, 85748, Garching, Germany
| | - Alison E. Ringel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States of America
| | - Rose Rosenberg
- Physical Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Arthur J. Rowe
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | - Arne C. Rufer
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-LaRoche Ltd., Basel, 4070, Switzerland
| | - David J. Scott
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, OX11 0FA, United Kingdom
| | - Javier G. Seravalli
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States of America
| | - Alexandra S. Solovyova
- Proteome and Protein Analysis, University of Newcastle, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Renjie Song
- Wadsworth Center, New York State Department of Health, Albany, New York, 12208, United States of America
| | - David Staunton
- Molecular Biophysics Suite, Department of Biochemistry, Oxford, Oxon, OX1 3QU, United Kingdom
| | - Caitlin Stoddard
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
- Tetrad Graduate Program, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Katherine Stott
- Biochemistry Department, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | | | - Werner W. Streicher
- Protein Function and Interactions, Novo Nordisk Foundation Center for Protein Research, Copenhagen, 2200, Denmark
| | - John P. Sumida
- Analytical Biopharmacy Core, University of Washington, Seattle, Washington, 98195, United States of America
| | - Sarah G. Swygert
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, 01605, United States of America
| | - Roman H. Szczepanowski
- Core Facility, International Institute of Molecular and Cell Biology, Warsaw, 02–109, Poland
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080, Würzburg, Germany
| | - Ronald T. Toth
- Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas, 66047, United States of America
| | - Ashutosh Tripathy
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States of America
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Stephan F. W. Uebel
- Biochemistry Core Facility, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Satoru Unzai
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230–0045, Japan
| | - Anna Vitlin Gruber
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Peter H. von Hippel
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - Christine Wandrey
- Laboratoire de Médecine Régénérative et de Pharmacobiologie, Ecole Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
| | - Szu-Huan Wang
- Biophysics Core Facility, Scientific Instrument Center, Academia Sinica, Taipei, 115, Taiwan
| | - Steven E. Weitzel
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, 02–089, Poland
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States of America
| | - Martin Wolff
- ICS-6, Structural Biochemistry, Research Center Juelich, 52428, Juelich, Germany
| | - Edward Wright
- Biochemistry, Cell and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee, 37996–0840, United States of America
| | - Yu-Sung Wu
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware, 19716, United States of America
| | - Jacinta M. Wubben
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
- * E-mail:
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