1
|
Choi A, Kots ED, Singleton DT, Weinstein H, Whittaker GR. Analysis of the molecular determinants for furin cleavage of the spike protein S1/S2 site in defined strains of the prototype coronavirus murine hepatitis virus (MHV). Virus Res 2024; 340:199283. [PMID: 38043726 PMCID: PMC10755501 DOI: 10.1016/j.virusres.2023.199283] [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: 08/08/2023] [Revised: 11/07/2023] [Accepted: 11/21/2023] [Indexed: 12/05/2023]
Abstract
We analyzed the spike protein S1/S2 cleavage of selected strains of a prototype coronavirus, mouse hepatitis virus (MHV) by the cellular protease furin, in order to understand the structural requirements underlying the sequence selectivity of the scissile segment. The probability of cleavage of selected MHV strains was first evaluated from furin cleavage scores predicted by the ProP computer software, and then cleavage was measured experimentally with a fluorogenic peptide cleavage assay consisting of S1/S2 peptide mimics and purified furin. We found that in vitro cleavability varied across MHV strains in line with predicted results-but with the notable exception of MHV-A59, which was not cleaved despite a high score predicted for its sequence. Using the known X-Ray structure of furin in complex with a substrate-like inhibitor as an initial structural reference, we carried out molecular dynamics (MD) simulations to learn the modes of binding of the peptides in the furin active site, and the suitability of the complex for initiation of the enzymatic cleavage. We identified the 3D structural requirements of the furin active site configuration that enable bound peptides to undergo cleavage, and the way in which the various strains tested experimentally are fulfilling these requirements. We find that despite some flexibility in the organization of the peptide bound to the active site of the enzyme, the presence of a histidine at P2 of MHV-A59 fails to properly orient the sidechain of His194 of the furin catalytic triad and therefore produces a distortion that renders the peptide/complex structural configuration in the active site incompatible with requirements for cleavage initiation. The Ser/Thr in P1 of MHV-2 and MHV-S has a similar effect of distorting the conformation of the furin active site residues produced by the elimination of the canonical salt-bridge formed by arginine in P1 position. This work informs a study of coronavirus infection and pathogenesis with respect to the function of the viral spike protein, and suggests an important process of viral adaptation and evolution within the spike S1/S2 structural loop.
Collapse
Affiliation(s)
- Annette Choi
- Departments of Microbiology & Immunology, Cornell University, Ithaca, NY, USA
| | - Ekaterina D Kots
- Department of Physiology & Biophysics, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Harel Weinstein
- Department of Physiology & Biophysics, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
| | - Gary R Whittaker
- Departments of Microbiology & Immunology, Cornell University, Ithaca, NY, USA; Public & Ecosystem Health, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
2
|
Choi A, Kots ED, Singleton DT, Weinstein HA, Whittaker GR. Analysis of the molecular determinants for furin cleavage of the spike protein S1/S2 site in defined strains of the prototype coronavirus murine hepatitis virus (MHV). bioRxiv 2023:2023.01.11.523687. [PMID: 36711446 PMCID: PMC9882190 DOI: 10.1101/2023.01.11.523687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We have analyzed the spike protein S1/S2 cleavage site of selected strains of MHV by the cellular protease furin, in order to understand the structural requirements underlying the sequence selectivity of the scissile segment. The probability of cleavage of the various MHV strains was first evaluated from furin cleavage scores predicted by the ProP computer software, and then cleavage was measured experimentally with a fluorogenic peptide cleavage assay consisting of S1/S2 peptide mimics and purified furin. We found that in vitro cleavability varied across MHV strains in line with predicted results-but with the notable exception of MHV-A59, which was not cleaved despite a high score predicted for its sequence. Using the known X-Ray structure of furin in complex with a substrate-like inhibitor as an initial structural reference, we carried out molecular dynamics (MD) simulations to learn the modes of binding of the peptides in the furin active site, and the suitability of the complex for initiation of the enzymatic cleavage. We thus identified the 3D structural requirements of the furin active site configuration that enable bound peptides to undergo cleavage, and the way in which the various strains tested experimentally are fulfilling these requirements. We find that despite some flexibility in the organization of the peptide bound to the active site of the enzyme, the presence of a histidine at P2 of MHV-A59 fails to properly orient the sidechain of His194 of the furin catalytic triad and therefore produces a distortion that renders the peptide/complex structural configuration in the active site incompatible with requirements for cleavage initiation. The Ser/Thr in P1 of MHV-2 and MHV-S has a similar effect of distorting the conformation of the furin active site residues produced by the elimination of the canonical salt-bridge formed by arginine in P1 position. This work informs a study of coronavirus infection and pathogenesis with respect to the function of the viral spike protein, and suggests an important process of viral adaptation and evolution within the spike S1/S2 structural loop.
Collapse
Affiliation(s)
- Annette Choi
- Departments of Microbiology & Immunology, Cornell University, Ithaca, NY, USA
| | - Ekaterina D. Kots
- Department of Physiology & Biophysics, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Harel A. Weinstein
- Department of Physiology & Biophysics, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Gary R. Whittaker
- Departments of Microbiology & Immunology, Cornell University, Ithaca, NY, USA
- Department of Public & Ecosystem Health, Cornell University, Ithaca, NY, USA
| |
Collapse
|
3
|
Kots ED, Weinstein H. Intermediates, state transitions, and ligand coupling in the dynamic mechanism of the hEAAT3 glutamate transporter. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2579] [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: 11/02/2022] Open
|
4
|
Kots ED, Osei-Owusu J, Qiu Z, Weinstein H. Allosteric pathways of pH-sensitivity in a proton activated chloride channel. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.505] [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: 11/02/2022] Open
|
5
|
Kots ED, Shore DM, Weinstein H. Adaptive Sampling using a Geometric Brownian Motion Model to Predict MD Trajectory Mobility on a Free Energy Surface. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.690] [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: 11/26/2022] Open
|
6
|
Kots ED, Shore DM, Weinstein H. A New Constant pH Method to Simultaneously Predict pH-Induced Conformational Changes and Individual PKA Values in Large Biomolecules. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1098] [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: 11/25/2022] Open
|
7
|
Grigorenko BL, Kots ED, Nemukhin AV. Diversity of mechanisms in Ras-GAP catalysis of guanosine triphosphate hydrolysis revealed by molecular modeling. Org Biomol Chem 2020; 17:4879-4891. [PMID: 31041977 DOI: 10.1039/c9ob00463g] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The mechanism of the deceptively simple reaction of guanosine triphosphate (GTP) hydrolysis catalyzed by the cellular protein Ras in complex with the activating protein GAP is an important issue because of the significance of this reaction in cancer research. We show that molecular modeling of GTP hydrolysis in the Ras-GAP active site reveals a diversity of mechanisms of the intrinsic chemical reaction depending on molecular groups at position 61 in Ras occupied by glutamine in the wild-type enzyme. First, a comparison of reaction energy profiles computed at the quantum mechanics/molecular mechanics (QM/MM) level shows that an assignment of the Gln61 side chain in the wild-type Ras either to QM or to MM parts leads to different scenarios corresponding to the glutamine-assisted or the substrate-assisted mechanisms. Second, replacement of Gln61 by the nitro-analog of glutamine (NGln) or by Glu, applied in experimental studies, results in two more scenarios featuring the so-called two-water and the concerted-type mechanisms. The glutamine-assisted mechanism in the wild-type Ras-GAP, in which the conserved Gln61 plays a decisive role, switching between the amide and imide tautomer forms, is consistent with the known experimental results of structural, kinetic and spectroscopy studies. The results emphasize the role of the Ras residue Gln61 in Ras-GAP catalysis and explain the retained catalytic activity of the Ras-GAP complex towards GTP hydrolysis in the Gln61NGln and Gln61Glu mutants of Ras.
Collapse
Affiliation(s)
- Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | | | | |
Collapse
|
8
|
Grigorenko BL, Kots ED, Krylov AI, Nemukhin AV. Modeling of the glycine tripeptide cyclization in the Ser65Gly/Tyr66Gly mutant of green fluorescent protein. Mendeleev Communications 2019. [DOI: 10.1016/j.mencom.2019.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
9
|
Kots ED, Khrenova MG, Nemukhin AV, Varfolomeev SD. Aspartoacylase: a central nervous system enzyme. Structure, catalytic activity and regulation mechanisms. Russ Chem Rev 2019. [DOI: 10.1070/rcr4842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
10
|
Kots ED, Khrenova MG, Nemukhin AV. Allosteric Control of N-Acetyl-Aspartate Hydrolysis by the Y231C and F295S Mutants of Human Aspartoacylase. J Chem Inf Model 2018; 59:2299-2308. [DOI: 10.1021/acs.jcim.8b00666] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ekaterina D. Kots
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow, 119334, Russian Federation
| | - Maria G. Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation
- Federal Research Center of Biotechnology, Bach Institute of Biochemistry, Russian Academy of Sciences, Leninskiy Prospect 33, 119071 Moscow, Russian Federation
| | - Alexander V. Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow, 119334, Russian Federation
| |
Collapse
|
11
|
Khrenova MG, Kots ED, Varfolomeev SD, Lushchekina SV, Nemukhin AV. Three Faces of N-Acetylaspartate: Activator, Substrate, and Inhibitor of Human Aspartoacylase. J Phys Chem B 2017; 121:9389-9397. [DOI: 10.1021/acs.jpcb.7b08759] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria G. Khrenova
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Ekaterina D. Kots
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Sergey D. Varfolomeev
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Sofya V. Lushchekina
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexander V. Nemukhin
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
| |
Collapse
|
12
|
Kots ED, Lushchekina SV, Varfolomeev SD, Nemukhin AV. Role of Protein Dimeric Interface in Allosteric Inhibition of N-Acetyl-Aspartate Hydrolysis by Human Aspartoacylase. J Chem Inf Model 2017; 57:1999-2008. [PMID: 28737906 DOI: 10.1021/acs.jcim.7b00133] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The results of molecular modeling suggest a mechanism of allosteric inhibition upon hydrolysis of N-acetyl-aspartate (NAA), one of the most abundant amino acid derivatives in brain, by human aspartoacylase (hAsp). Details of this reaction are important to suggest the practical ways to control the enzyme activity. Search for allosteric sites using the Allosite web server and SiteMap analysis allowed us to identify substrate binding pockets located at the interface between the subunits of the hAsp dimer molecule. Molecular docking of NAA to the pointed areas at the dimer interface predicted a specific site, in which the substrate molecule interacts with the Gly237, Arg233, Glu290, and Lys292 residues. Analysis of multiple long-scaled molecular dynamics trajectories (the total simulation time exceeded 1.5 μs) showed that binding of NAA to the identified allosteric site induced significant rigidity to the protein loops with the amino acid side chains forming gates to the enzyme active site. Application of the protein dynamical network algorithms showed that substantial reorganization of the signal propagation pathways of intersubunit communication in the dimer occurred upon allosteric NAA binding to the remote site. The modeling approaches provide an explanation to the observed decrease of the reaction rate of NAA hydrolysis by hAsp at high substrate concentrations.
Collapse
Affiliation(s)
- Ekaterina D Kots
- Department of Chemistry, Lomonosov Moscow State University , Moscow 119991, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow 119334, Russia
| | - Sofya V Lushchekina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow 119334, Russia
| | - Sergey D Varfolomeev
- Department of Chemistry, Lomonosov Moscow State University , Moscow 119991, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow 119334, Russia
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University , Moscow 119991, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow 119334, Russia
| |
Collapse
|
13
|
Lushchekina SV, Kots ED, Novichkova DA, Petrov KA, Masson P. Role of Acetylcholinesterase in β-Amyloid Aggregation Studied by Accelerated Molecular Dynamics. BioNanoSci 2016. [DOI: 10.1007/s12668-016-0375-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
14
|
Kots ED, Khrenova MG, Lushchekina SV, Varfolomeev SD, Grigorenko BL, Nemukhin AV. Modeling the Complete Catalytic Cycle of Aspartoacylase. J Phys Chem B 2016; 120:4221-31. [DOI: 10.1021/acs.jpcb.6b02542] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ekaterina D. Kots
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie
Gory 1/3, Moscow 119991, Russian Federation
- N.M.
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow 119334, Russian Federation
| | - Maria G. Khrenova
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie
Gory 1/3, Moscow 119991, Russian Federation
| | - Sofya V. Lushchekina
- N.M.
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow 119334, Russian Federation
| | - Sergei D. Varfolomeev
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie
Gory 1/3, Moscow 119991, Russian Federation
- N.M.
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow 119334, Russian Federation
| | - Bella L. Grigorenko
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie
Gory 1/3, Moscow 119991, Russian Federation
- N.M.
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow 119334, Russian Federation
| | - Alexander V. Nemukhin
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie
Gory 1/3, Moscow 119991, Russian Federation
- N.M.
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow 119334, Russian Federation
| |
Collapse
|
15
|
Khrenova MG, Kots ED, Nemukhin AV. Reaction Mechanism of Guanosine Triphosphate Hydrolysis by the Vision-Related Protein Complex Arl3-RP2. J Phys Chem B 2016; 120:3873-9. [PMID: 27043216 DOI: 10.1021/acs.jpcb.6b03363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Complexes of small GTPases with GTPase-activating proteins have been intensively studied with the main focus on the complex of H-Ras with p120GAP (Ras-GAP). The detailed mechanism of GTP hydrolysis is still unresolved. To clarify it, we calculated the energy profile of GTP hydrolysis in the active site of a recently characterized vision-related member of this family, the Arl3-RP2 complex. The mechanism suggested in this study retains the main features of GTP hydrolysis by the Ras-GAP complex, but the relative energies of the corresponding intermediates are different and an additional intermediate exists in the Arl3-RP2 complex compared with the Ras-GAP. These differences arise from small deviations in the catalytic arginine conformation of the active site. In the Arl3-RP2 complex, the first two intermediates, corresponding to the Pγ-Oβγ bond cleavage and the glutamine-assisted proton transfer, are almost isoenergetic with the ES complex. Numerical simulations of the kinetic curves demonstrate that the concentrations of these intermediates are comparable with that of ES during the reaction. The calculated IR spectra reveal specific vibrational bands, corresponding to these intermediates. These specific features of the Arl3-RP2 complex open the opportunity to identify spectroscopically two more reaction intermediates in GTP hydrolysis in addition to the ES and EP complexes.
Collapse
Affiliation(s)
- Maria G Khrenova
- Chemistry Department, Lomonosov Moscow State University , Leninskie Gory 1/3, Moscow, 119991, Russian Federation
| | - Ekaterina D Kots
- Chemistry Department, Lomonosov Moscow State University , Leninskie Gory 1/3, Moscow, 119991, Russian Federation.,N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Kosygina 4, Moscow, 119334, Russian Federation
| | - Alexander V Nemukhin
- Chemistry Department, Lomonosov Moscow State University , Leninskie Gory 1/3, Moscow, 119991, Russian Federation.,N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Kosygina 4, Moscow, 119334, Russian Federation
| |
Collapse
|
16
|
Semenov VE, Giniyatullin RK, Lushchekina SV, Kots ED, Petrov KA, Nikitashina AD, Minnekhanova OA, Zobov VV, Nikolsky EE, Masson P, Reznik VS. Macrocyclic derivatives of 6-methyluracil as ligands of the peripheral anionic site of acetylcholinesterase. Med Chem Commun 2014. [DOI: 10.1039/c4md00225c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pyrimidinophanes 2a,b bind AChE in the PAS or in the active centre depending on the nature of the spacer between ammonium moieties. Pyrimidinophane 2b and its acyclic counterpart abolished symptoms of muscle weakness.
Collapse
Affiliation(s)
| | | | | | | | - Konstantin A. Petrov
- A. E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan 420088, Russia
- Kazan Institute of Biochemistry and Biophysics
- Kazan 420111, Russia
- Kazan Federal University
| | - Alexandra D. Nikitashina
- A. E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan 420088, Russia
- Kazan Institute of Biochemistry and Biophysics
- Kazan 420111, Russia
- Kazan Federal University
| | | | - Vladimir V. Zobov
- A. E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan 420088, Russia
- Kazan Federal University
- Kazan 420000, Russia
| | - Evgeny E. Nikolsky
- A. E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan 420088, Russia
- Kazan Institute of Biochemistry and Biophysics
- Kazan 420111, Russia
- Kazan Federal University
| | - Patrick Masson
- Kazan Federal University
- Kazan 420000, Russia
- DYNAMOP
- Institut de Biologie Structurale
- Grenoble 38000, France
| | - Vladimir S. Reznik
- A. E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan 420088, Russia
| |
Collapse
|