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Lin M, Cui W, Tian H, Zhang Y, Chen C, Yang X, Chi H, Mu Z, Chen C, Wang Z, Ji X, Yang H, Lin Z. Structural Basis of Zika Virus Helicase in RNA Unwinding and ATP Hydrolysis. ACS Infect Dis 2022; 8:150-158. [PMID: 34904824 DOI: 10.1021/acsinfecdis.1c00455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The flavivirus nonstructural protein 3 helicase (NS3hel) is a multifunctional domain protein that is associated with DNA/RNA helicase, nucleoside triphosphatase (NTPase), and RNA 5'-triphosphatase (RTPase) activities. As an NTPase-dependent superfamily 2 (SF2) member, NS3hel employs an NTP-driven motor force to unwind double-stranded RNA while translocating along single-stranded RNA and is extensively involved in the viral replication process. Although the structures of SF2 helicases are widely investigated as promising drug targets, the mechanism of energy transduction between NTP hydrolysis and the RNA binding sites in ZIKV NS3hel remains elusive. Here, we report the crystal structure of ZIKV NS3hel in complex with its natural substrates ATP-Mn2+ and ssRNA. Distinct from other members of the Flavivirus genus, ssRNA binding to ZIKV NS3hel induces relocation of the active water molecules and ATP-associated metal ions in the NTP hydrolysis active site, which promotes the hydrolysis of ATP and the production of AMP. Our findings highlight the importance of the allosteric role of ssRNA on the modulation of ATP hydrolysis and energy utilization.
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Affiliation(s)
- Mengmeng Lin
- School of Life Sciences, Tianjin University, Tianjin 300072, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Wen Cui
- School of Life Sciences, Tianjin University, Tianjin 300072, China
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Hongliang Tian
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Yan Zhang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Chen Chen
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Xiaoyun Yang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Heng Chi
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Zhongyu Mu
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Cheng Chen
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Zefang Wang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Xiaoyun Ji
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Haitao Yang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Zhi Lin
- School of Life Sciences, Tianjin University, Tianjin 300072, China
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An in silico approach to analyze HCV genotype-specific binding-site variation and its effect on drug-protein interaction. Sci Rep 2020; 10:20885. [PMID: 33257748 PMCID: PMC7705671 DOI: 10.1038/s41598-020-77720-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 09/18/2020] [Indexed: 01/06/2023] Open
Abstract
Genotype variation in viruses can affect the response of antiviral treatment. Several studies have established approaches to determine genotype-specific variations; however, analyses to determine the effect of these variations on drug–protein interactions remain unraveled. We present an in-silico approach to explore genotype-specific variations and their effect on drug–protein interaction. We have used HCV NS3 helicase and fluoroquinolones as a model for drug–protein interaction and have investigated the effect of amino acid variations in HCV NS3 of genotype 1a, 1b, 2b and 3a on NS3-fluoroquinolone interaction. We retrieved 687, 667, 101 and 248 nucleotide sequences of HCV NS3 genotypes 1a, 1b, 2b, and 3a, respectively, and translated these into amino acid sequences and used for genotype variation analysis, and also to construct 3D protein models for 2b and 3a genotypes. For 1a and 1b, crystal structures were used. Drug–protein interactions were determined using molecular docking analyses. Our results revealed that individual genotype-specific HCV NS3 showed substantial sequence heterogeneity that resulted in variations in docking interactions. We believe that our approach can be extrapolated to include other viruses to study the clinical significance of genotype-specific variations in drug–protein interactions.
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Thirumalai D, Hyeon C, Zhuravlev PI, Lorimer GH. Symmetry, Rigidity, and Allosteric Signaling: From Monomeric Proteins to Molecular Machines. Chem Rev 2019; 119:6788-6821. [DOI: 10.1021/acs.chemrev.8b00760] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D. Thirumalai
- Department of Chemistry, The University of Texas, Austin, Texas 78712, United States
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Pavel I. Zhuravlev
- Biophysics Program, Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - George H. Lorimer
- Biophysics Program, Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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Togashi Y, Flechsig H. Coarse-Grained Protein Dynamics Studies Using Elastic Network Models. Int J Mol Sci 2018; 19:ijms19123899. [PMID: 30563146 PMCID: PMC6320916 DOI: 10.3390/ijms19123899] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 11/28/2018] [Accepted: 12/03/2018] [Indexed: 01/03/2023] Open
Abstract
Elastic networks have been used as simple models of proteins to study their slow structural dynamics. They consist of point-like particles connected by linear Hookean springs and hence are convenient for linear normal mode analysis around a given reference structure. Furthermore, dynamic simulations using these models can provide new insights. As the computational cost associated with these models is considerably lower compared to that of all-atom models, they are also convenient for comparative studies between multiple protein structures. In this review, we introduce examples of coarse-grained molecular dynamics studies using elastic network models and their derivatives, focusing on the nonlinear phenomena, and discuss their applicability to large-scale macromolecular assemblies.
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Affiliation(s)
- Yuichi Togashi
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
- RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.
- Cybermedia Center, Osaka University, 5-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Holger Flechsig
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.
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Zheng W, Wen H, Iacobucci GJ, Popescu GK. Probing the Structural Dynamics of the NMDA Receptor Activation by Coarse-Grained Modeling. Biophys J 2017. [PMID: 28636915 DOI: 10.1016/j.bpj.2017.04.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
N-Methyl-D-aspartate (NMDA) receptors are glutamate-gated excitatory channels that play essential roles in brain functions. High-resolution structures have been solved for an allosterically inhibited and agonist-bound form of a functional NMDA receptor; however, other key functional states (particularly the active open-channel state) were only resolved at moderate resolutions by cryo-electron microscopy (cryo-EM). To decrypt the mechanism of the NMDA receptor activation, structural modeling is essential to provide presently missing information about structural dynamics. We performed systematic coarse-grained modeling using an elastic network model and related modeling/analysis tools (e.g., normal mode analysis, flexibility and hotspot analysis, cryo-EM flexible fitting, and transition pathway modeling) based on an active-state cryo-EM map. We observed extensive conformational changes that allosterically couple the extracellular regulatory and agonist-binding domains to the pore-forming trans-membrane domain (TMD), and validated these, to our knowledge, new observations against known mutational and functional studies. Our results predict two key modes of collective motions featuring shearing/twisting of the extracellular domains relative to the TMD, reveal subunit-specific flexibility profiles, and identify functional hotspot residues at key domain-domain interfaces. Finally, by examining the conformational transition pathway between the allosterically inhibited form and the active form, we predict a discrete sequence of domain motions, which propagate from the extracellular domains to the TMD. In summary, our results offer rich structural and dynamic information, which is consistent with the literature on structure-function relationships in NMDA receptors, and will guide in-depth studies on the activation dynamics of this important neurotransmitter receptor.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, State University of New York at Buffalo, Buffalo, New York.
| | - Han Wen
- Department of Physics, State University of New York at Buffalo, Buffalo, New York
| | - Gary J Iacobucci
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, New York
| | - Gabriela K Popescu
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, New York
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Zheng W. Probing the structural dynamics of the CRISPR-Cas9 RNA-guided DNA-cleavage system by coarse-grained modeling. Proteins 2017; 85:342-353. [PMID: 27936513 DOI: 10.1002/prot.25229] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 10/31/2016] [Accepted: 11/28/2016] [Indexed: 12/15/2022]
Abstract
In the adaptive immune systems of many bacteria and archaea, the Cas9 endonuclease forms a complex with specific guide/scaffold RNA to identify and cleave complementary target sequences in foreign DNA. This DNA targeting machinery has been exploited in numerous applications of genome editing and transcription control. However, the molecular mechanism of the Cas9 system is still obscure. Recently, high-resolution structures have been solved for Cas9 in different structural forms (e.g., unbound forms, RNA-bound binary complexes, and RNA-DNA-bound tertiary complexes, corresponding to an inactive state, a pre-target-bound state, and a cleavage-competent or product state), which offered key structural insights to the Cas9 mechanism. To further probe the structural dynamics of Cas9 interacting with RNA and DNA at the amino-acid level of details, we have performed systematic coarse-grained modeling using an elastic network model and related analyses. Our normal mode analysis predicted a few key modes of collective motions that capture the observed conformational changes featuring large domain motions triggered by binding of RNA and DNA. Our flexibility analysis identified specific regions with high or low flexibility that coincide with key functional sites (such as DNA/RNA-binding sites, nuclease cleavage sites, and key hinges). We also identified a small set of hotspot residues that control the energetics of functional motions, which overlap with known functional sites and offer promising targets for future mutagenesis efforts to improve the specificity of Cas9. Finally, we modeled the conformational transitions of Cas9 from the unbound form to the binary complex and then the tertiary complex, and predicted a distinct sequence of domain motions. In sum, our findings have offered rich structural and dynamic details relevant to the Cas9 machinery, and will guide future investigation and engineering of the Cas9 systems. Proteins 2017; 85:342-353. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, State University of New York at Buffalo, Buffalo, New York, 14260
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Zheng W, Qin F. A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation. ACTA ACUST UNITED AC 2016; 145:443-56. [PMID: 25918362 PMCID: PMC4411258 DOI: 10.1085/jgp.201411335] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Coarse-grained modeling and all-atom molecular dynamics simulation provide insight into the mechanism for heat activation of TRPV1 gating. The transient receptor potential (TRP) channels act as key sensors of various chemical and physical stimuli in eukaryotic cells. Despite years of study, the molecular mechanisms of TRP channel activation remain unclear. To elucidate the structural, dynamic, and energetic basis of gating in TRPV1 (a founding member of the TRPV subfamily), we performed coarse-grained modeling and all-atom molecular dynamics (MD) simulation based on the recently solved high resolution structures of the open and closed form of TRPV1. Our coarse-grained normal mode analysis captures two key modes of collective motions involved in the TRPV1 gating transition, featuring a quaternary twist motion of the transmembrane domains (TMDs) relative to the intracellular domains (ICDs). Our transition pathway modeling predicts a sequence of structural movements that propagate from the ICDs to the TMDs via key interface domains (including the membrane proximal domain and the C-terminal domain), leading to sequential opening of the selectivity filter followed by the lower gate in the channel pore (confirmed by modeling conformational changes induced by the activation of ICDs). The above findings of coarse-grained modeling are robust to perturbation by lipids. Finally, our MD simulation of the ICD identifies key residues that contribute differently to the nonpolar energy of the open and closed state, and these residues are predicted to control the temperature sensitivity of TRPV1 gating. These computational predictions offer new insights to the mechanism for heat activation of TRPV1 gating, and will guide our future electrophysiology and mutagenesis studies.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics and Department of Physiology and Biophysical Sciences, State University of New York at Buffalo, Buffalo, NY 14260
| | - Feng Qin
- Department of Physics and Department of Physiology and Biophysical Sciences, State University of New York at Buffalo, Buffalo, NY 14260
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Pérez-Villa A, Darvas M, Bussi G. ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations. Nucleic Acids Res 2015; 43:8725-34. [PMID: 26358809 PMCID: PMC4605317 DOI: 10.1093/nar/gkv872] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/18/2015] [Indexed: 01/05/2023] Open
Abstract
Non-structural protein 3 (NS3) helicase from hepatitis C virus is an enzyme that unwinds and translocates along nucleic acids with an ATP-dependent mechanism and has a key role in the replication of the viral RNA. An inchworm-like mechanism for translocation has been proposed based on crystal structures and single molecule experiments. We here perform atomistic molecular dynamics in explicit solvent on the microsecond time scale of the available experimental structures. We also construct and simulate putative intermediates for the translocation process, and we perform non-equilibrium targeted simulations to estimate their relative stability. For each of the simulated structures we carefully characterize the available conformational space, the ligand binding pocket, and the RNA binding cleft. The analysis of the hydrogen bond network and of the non-equilibrium trajectories indicates an ATP-dependent stabilization of one of the protein conformers. Additionally, enthalpy calculations suggest that entropic effects might be crucial for the stabilization of the experimentally observed structures.
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Affiliation(s)
- Andrea Pérez-Villa
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 265, Via Bonomea, I-34136 Trieste, Italy
| | - Maria Darvas
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 265, Via Bonomea, I-34136 Trieste, Italy
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 265, Via Bonomea, I-34136 Trieste, Italy
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Flechsig H. Computational biology approach to uncover hepatitis C virus helicase operation. World J Gastroenterol 2014; 20:3401-3409. [PMID: 24707123 PMCID: PMC3974507 DOI: 10.3748/wjg.v20.i13.3401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 01/06/2014] [Accepted: 03/06/2014] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) helicase is a molecular motor that splits nucleic acid duplex structures during viral replication, therefore representing a promising target for antiviral treatment. Hence, a detailed understanding of the mechanism by which it operates would facilitate the development of efficient drug-assisted therapies aiming to inhibit helicase activity. Despite extensive investigations performed in the past, a thorough understanding of the activity of this important protein was lacking since the underlying internal conformational motions could not be resolved. Here we review investigations that have been previously performed by us for HCV helicase. Using methods of structure-based computational modelling it became possible to follow entire operation cycles of this motor protein in structurally resolved simulations and uncover the mechanism by which it moves along the nucleic acid and accomplishes strand separation. We also discuss observations from that study in the light of recent experimental studies that confirm our findings.
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Zheng W. All-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex. Proteins 2014; 82:1376-86. [DOI: 10.1002/prot.24505] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 12/11/2013] [Accepted: 01/06/2014] [Indexed: 01/03/2023]
Affiliation(s)
- Wenjun Zheng
- Department of Physics; University at Buffalo, State University of New York; New York
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