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Timr Š, Pleskot R, Kadlec J, Kohagen M, Magarkar A, Jungwirth P. Membrane Binding of Recoverin: From Mechanistic Understanding to Biological Functionality. ACS CENTRAL SCIENCE 2017; 3:868-874. [PMID: 28852701 PMCID: PMC5571466 DOI: 10.1021/acscentsci.7b00210] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Indexed: 06/07/2023]
Abstract
Recoverin is a neuronal calcium sensor involved in vision adaptation that reversibly associates with cellular membranes via its calcium-activated myristoyl switch. While experimental evidence shows that the myristoyl group significantly enhances membrane affinity of this protein, molecular details of the binding process are still under debate. Here, we present results of extensive molecular dynamics simulations of recoverin in the proximity of a phospholipid bilayer. We capture multiple events of spontaneous membrane insertion of the myristoyl moiety and confirm its critical role in the membrane binding. Moreover, we observe that the binding strongly depends on the conformation of the N-terminal domain. We propose that a suitable conformation of the N-terminal domain can be stabilized by the disordered C-terminal segment or by binding of the target enzyme, i.e., rhodopsin kinase. Finally, we find that the presence of negatively charged lipids in the bilayer stabilizes a physiologically functional orientation of the membrane-bound recoverin.
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Affiliation(s)
- Štěpán Timr
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Roman Pleskot
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Institute
of Experimental Botany, Czech Academy of
Sciences, Rozvojová
263, 16502 Prague
6, Czech Republic
| | - Jan Kadlec
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Miriam Kohagen
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Institute
for Computational Physics, University of
Stuttgart, Allmandring
3, Stuttgart, 70569, Germany
| | - Aniket Magarkar
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Faculty
of Pharmacy, University of Helsinki, Viikinkaari 5E, Helsinki, 00014 Finland
| | - Pavel Jungwirth
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
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Gong Y, Zhu Y, Zou Y, Ma B, Nussinov R, Zhang Q. Human Neuronal Calcium Sensor-1 Protein Avoids Histidine Residues To Decrease pH Sensitivity. J Phys Chem B 2017; 121:508-517. [PMID: 28030949 PMCID: PMC6413881 DOI: 10.1021/acs.jpcb.6b11094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
pH is highly regulated in mammalian central nervous systems. Neuronal calcium sensor-1 (NCS-1) can interact with numerous target proteins. Compared to that in the NCS-1 protein of Caenorhabditis elegans, evolution has avoided the placement of histidine residues at positions 102 and 83 in the NCS-1 protein of humans and Xenopus laevis, possibly to decrease the conformational sensitivity to pH gradients in synaptic processes. We used all-atom molecular dynamics simulations to investigate the effects of amino acid substitutions between species on human NCS-1 by substituting Arg102 and Ser83 for histidine at neutral (R102H and S83H) and acidic pHs (R102Hp and S83Hp). Our cumulative 5 μs simulations revealed that the R102H mutation slightly increases the structural flexibility of loop L2 and the R102Hp mutation decreases protein stability. Community network analysis illustrates that the R102H and S83H mutations weaken the interdomain and strengthen the intradomain communications. Secondary structure contents in the S83H and S83Hp mutants are similar to those in the wild type, whereas the global structural stabilities and salt-bridge probabilities decrease. This study highlights the conformational dynamics effects of the R102H and S83H mutations on the local structural flexibility and global stability of NCS-1, whereas protonated histidine decreases the stability of NCS-1. Thus, histidines at positions 102 and 83 may not be compatible with the function of NCS-1 whether in the neutral or protonated state.
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Affiliation(s)
- Yehong Gong
- College of Physical Education and Training, Shanghai University of Sport, 399 Chang Hai Road, Shanghai, 200438, China
| | - Yuzhen Zhu
- Shanghai Normal University Physical Education College, 100 Gui Lin Road, Shanghai, 200234, China
| | - Yu Zou
- College of Physical Education and Training, Shanghai University of Sport, 399 Chang Hai Road, Shanghai, 200438, China
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Department of Human Genetics and Molecular Medicine, Sackler Inst. of Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport, 399 Chang Hai Road, Shanghai, 200438, China
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3
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Gc JB, Johnson KA, Husby ML, Frick CT, Gerstman BS, Stahelin RV, Chapagain PP. Interdomain salt-bridges in the Ebola virus protein VP40 and their role in domain association and plasma membrane localization. Protein Sci 2016; 25:1648-58. [PMID: 27328459 DOI: 10.1002/pro.2969] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 06/09/2016] [Accepted: 06/15/2016] [Indexed: 02/03/2023]
Abstract
The Ebola virus protein VP40 is a transformer protein that possesses an extraordinary ability to accomplish multiple functions by transforming into various oligomeric conformations. The disengagement of the C-terminal domain (CTD) from the N-terminal domain (NTD) is a crucial step in the conformational transformations of VP40 from the dimeric form to the hexameric form or octameric ring structure. Here, we use various molecular dynamics (MD) simulations to investigate the dynamics of the VP40 protein and the roles of interdomain interactions that are important for the domain-domain association and dissociation, and report on experimental results of the behavior of mutant variants of VP40. The MD studies find that various salt-bridge interactions modulate the VP40 domain dynamics by providing conformational specificity through interdomain interactions. The MD simulations reveal a novel salt-bridge between D45-K326 when the CTD participates in a latch-like interaction with the NTD. The D45-K326 salt-bridge interaction is proposed to help domain-domain association, whereas the E76-K291 interaction is important for stabilizing the closed-form structure. The effects of the removal of important VP40 salt-bridges on plasma membrane (PM) localization, VP40 oligomerization, and virus like particle (VLP) budding assays were investigated experimentally by live cell imaging using an EGFP-tagged VP40 system. It is found that the mutations K291E and D45K show enhanced PM localization but D45K significantly reduced VLP formation.
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Affiliation(s)
- Jeevan B Gc
- Department of Physics, Florida International University, Miami, Florida, 33199
| | - Kristen A Johnson
- Department of Chemistry and Biochemistry, the Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, 46556.,Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana, 46556
| | - Monica L Husby
- Department of Chemistry and Biochemistry, the Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, 46556.,Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana, 46556
| | - Cary T Frick
- Department of Chemistry and Biochemistry, the Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, 46556.,Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana, 46556
| | - Bernard S Gerstman
- Department of Physics, Florida International University, Miami, Florida, 33199.,Biomolecular Science Institute, Florida International University, Miami, Florida, 33199
| | - Robert V Stahelin
- Department of Chemistry and Biochemistry, the Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, 46556.,Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana, 46556.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, Indiana, 46617
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, Florida, 33199.,Biomolecular Science Institute, Florida International University, Miami, Florida, 33199
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Zhu Y, Ma B, Nussinov R, Zhang Q. Temperature-Dependent Conformational Properties of Human Neuronal Calcium Sensor-1 Protein Revealed by All-Atom Simulations. J Phys Chem B 2016; 120:3551-9. [PMID: 27007011 PMCID: PMC6415918 DOI: 10.1021/acs.jpcb.5b12299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Neuronal calcium sensor-1 (NCS-1) protein has orthologues from Saccharomyces cerevisiae to human with highly conserved amino acid sequences. NCS-1 is an important factor controlling the animal's response to temperature change. This leads us to investigate the temperature effects on the conformational dynamics of human NCS-1 at 310 and 316 K by all-atom molecular dynamics (MD) simulations and dynamic community network analysis. Four independent 500 ns MD simulations show that secondary structure content at 316 K is similar to that at 310 K, whereas the global protein structure is expanded. Loop 3 (L3) adopts an extended state occuping the hydrophobic crevice, and the number of suboptimal communication paths between residue D176 and V190 is reduced at 316 K. The dynamic community network analysis suggests that the interdomain correlation is weakened, and the intradomain coupling is strengthened at 316 K. The elevated temperature reduces the number of the salt bridges, especially in C-domain. This study suggests that the elevated temperature affects the conformational dynamics of human NCS-1 protein. Comparison of the structural dynamics of R102Q mutant and Δ176-190 truncated NCS-1 suggests that the structural and dynamical response of NCS-1 protein to elevated temperature may be one of its intrinsic functional properties.
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Affiliation(s)
- Yuzhen Zhu
- College of Physical Education and Training, Shanghai University of Sport, 399 Chang Hai Road, Shanghai, 200438, China
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport, 399 Chang Hai Road, Shanghai, 200438, China
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