An all-atom molecular dynamics study of the anti-interferon signaling of Ebola virus: Interaction mechanisms of EBOV VP24 binding to Karyopherin alpha5

Molecular BioSystems

Volumn 13, Issue 5, 2017, Pages 1031-1045

  Ding, Jing Na ^a,b   Zhang, Yan Jun ^a   Zhong, Hui ^a   Ao, Cheng Cheng ^a   Li, Jing ^b   Han, Ju Guang ^a  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b Anqing Medical College   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BETA INTERFERON; KARYOPHERIN ALPHA; PROTEIN BINDING; VIRAL PROTEIN; VP24 PROTEIN, EBOLA VIRUS;

BINDING SITE; CHEMISTRY; EBOLAVIRUS; GENETICS; HYDROGEN BOND; METABOLISM; MOLECULAR DYNAMICS; MOLECULAR MODEL; MUTATION; SIGNAL TRANSDUCTION; X RAY CRYSTALLOGRAPHY;

ALPHA KARYOPHERINS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; EBOLAVIRUS; HYDROGEN BONDING; INTERFERON-BETA; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MUTATION; PROTEIN BINDING; SIGNAL TRANSDUCTION; VIRAL PROTEINS;

EID: 85021723561     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/c7mb00136c     Document Type: Article

References (42)

1. E. Simon-Loriere O. Faye O. Faye L. Koivogui N. Magassouba S. Keita J.-M. Thiberge L. Diancourt C. Bouchier M. Vandenbogaert V. Caro G. Fall J. P. Buchmann C. B. Matranga P. C. Sabeti J.-C. Manuguerra E. C. Holmes A. A. Sall Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic Nature 2015 524 102 U210
2. J. H. Kuhn S. Becker H. Ebihara T. W. Geisbert K. M. Johnson Y. Kawaoka W. I. Lipkin A. I. Negredo S. V. Netesov S. T. Nichol G. Palacios C. J. Peters A. Tenorio V. E. Volchkov P. B. Jahrling Proposal for a revised taxonomy of the family Filoviridae: classification, names of taxa and viruses, and virus abbreviations Arch. Virol. 2010 155 2083 2103
3. T. Hoenen A. Groseth D. Falzarano H. Feldmann Ebola virus: unravelling pathogenesis to combat a deadly disease Trends Mol. Med. 2006 12 206 215
4. W. Xu M. R. Edwards D. M. Borek A. R. Feagins A. Mittal J. B. Alinger K. N. Berry B. Yen J. Hamilton T. J. Brett R. V. Pappu D. W. Leung C. F. Basler G. K. Amarasinghe Ebola Virus VP24 Targets a Unique NLS Binding Site on Karyopherin Alpha 5 to Selectively Compete with Nuclear Import of Phosphorylated STAT1 Cell Host Microbe 2014 16 187 200
5. T. Kortemme D. Baker A simple physical model for binding energy hot spots in protein-protein complexes Proc. Natl. Acad. Sci. U. S. A. 2002 99 14116 14121
6. P. Ramanan R. S. Shabman C. S. Brown G. K. Amarasinghe C. F. Basler D. W. Leung Filoviral Immune Evasion Mechanisms Viruses-Basel 2011 3 1634 1649
7. S. P. Reid L. W. Leung A. L. Hartman O. Martinez M. L. Shaw C. Carbonnelle V. E. Volchkov S. T. Nichol C. F. Basler Ebola virus VP24 binds karyopherin alpha 1 and blocks STAT1 nuclear accumulation J. Virol. 2006 80 5156 5167
8. R. J. Wool-Lewis P. Bates Characterization of Ebola virus entry by using pseudotyped viruses: Identification of receptor-deficient cell lines J. Virol. 1998 72 3155 3160
9. M. Mateo S. P. Reid L. W. Leung C. F. Basler V. E. Volchkov Ebolavirus VP24 Binding to Karyopherins Is Required for Inhibition of Interferon Signaling J. Virol. 2010 84 1169 1175
10. K. Melen R. Fagerlund J. Franke M. Kohler L. Kinnunen I. Julkunen Importin alpha nuclear localization signal binding sites for STAT1, STAT2, and influenza a virus nucleoprotein J. Biol. Chem. 2003 278 28193 28200
11. K. M. McBride N. C. Reich The ins and outs of STAT1 nuclear transport Sci STKE 2003 2003 RE13 RE13
12. F. Qin W. Ye Y. Chen X. Chen Y. Li J. Zhang H.-F. Chen Specific recognition between intrinsically disordered LEF and DNA Phys. Chem. Chem. Phys. 2012 14 538 545
13. Q. Xue Q.-C. Zheng J.-L. Zhang Y.-L. Cui H.-X. Zhang Exploring the Mechanism How Marburg Virus VP35 Recognizes and Binds dsRNA by Molecular Dynamics Simulations and Free Energy Calculations Biopolymers 2014 101 849 860
14. I. O. Omotuyi Ebola virus envelope glycoprotein derived peptide in human Furin-bound state: computational studies J. Biomol. Struct. Dyn. 2015 33 461 470
15. Q. Xue J.-L. Zhang Q.-C. Zheng Y.-L. Cui L. Chen W.-T. Chu H.-X. Zhang Exploring the Molecular Basis of dsRNA Recognition by Mss116p Using Molecular Dynamics Simulations and Free-Energy Calculations Langmuir 2013 29 11135 11144
16. AccelrysSoftwareInc. Discovery Studio Modeling Environment. 4.5, Accelrys Software Inc., San Diego, 2007
17. Schrodinger, LLC, the PyMOL Molecular Graphics System, Version 1.3r1, 2010
18. Schrodinger, LLC, the AxPyMOL Molecular Graphics Plugin for Microsoft PowerPoint, Version 1.0, 2010
19. W. L. Jorgensen J. Chandrasekhar J. D. Madura R. W. Impey M. L. Klein Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983 79 926 935
20. R. Anandakrishnan B. Aguilar A. V. Onufriev H++ 3.0: automating p K prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations Nucleic Acids Res. 2012 40 W537 W541
21. W. Zhang, T. Hou, C. Schafmeister, W. S. Ross and D. A. Case, Amber Tools 1.2: LEaP and Gleap, University of Texas Health Center at Houston, University of California, University of Pittsburgh, Houston, San Diego, PA, 2009
22. D. A. Case T. E. Cheatham T. Darden H. Gohlke R. Luo K. M. Merz A. Onufriev C. Simmerling B. Wang R. J. Woods The Amber biomolecular simulation programs J. Comput. Chem. 2005 26 1668 1688
23. V. Hornak R. Abel A. Okur B. Strockbine A. Roitberg C. Simmerling Comparison of multiple amber force fields and development of improved protein backbone parameters Proteins: Struct., Funct., Bioinf. 2006 65 712 725
24. Y.-J. Zhang J.-N. Ding H. Zhong C.-P. Sun J.-G. Han Molecular dynamics exploration of the binding mechanism and properties of single-walled carbon nanotube to WT and mutant VP35 FBP region of Ebola virus J. Biol. Phys. 2017 43 149 165
25. T. Darden D. York L. Pedersen Particle mesh ewald-an N.LOG (N) method for ewald sums in large systems J. Chem. Phys. 1993 98 10089 10092
26. J. P. Ryckaert G. Ciccotti H. J. C. Berendsen Numerical-Integration of Cartesian Equations of Motion OF A System With Constraints-Molecular-Dynamics of N-Alkanes J. Comput. Phys. 1977 23 327 341
27. D. R. Roe T. E. CheathamIII PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data J. Chem. Theory Comput. 2013 9 3084 3095
28. E. F. Pettersen T. D. Goddard C. C. Huang G. S. Couch D. M. Greenblatt E. C. Meng T. E. Ferrin UCSF chimera-A visualization system for exploratory research and analysis J. Comput. Chem. 2004 25 1605 1612
29. P. A. Kollman I. Massova C. Reyes B. Kuhn S. H. Huo L. Chong M. Lee T. Lee Y. Duan W. Wang O. Donini P. Cieplak J. Srinivasan D. A. Case T. E. Cheatham Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models Acc. Chem. Res. 2000 33 889 897
30. Y. J. Zhang J. N. Ding T. T. Feng J. G. Han Exploring interaction mechanisms of the inhibitor binding to the VP35 IID region of Ebola virus by all atom molecular dynamics simulation method Proteins: Struct., Funct., Bioinf. 2015 83 2263 2278
31. R.-N. Zhao S. Fan J.-G. Han G. Liu Molecular dynamics study of segment peptides of Bax, Bim, and Mcl-1 BH3 domain of the apoptosis-regulating proteins bound to the anti-apoptotic Mcl-1 protein J. Biomol. Struct. Dyn. 2015 33 1067 1081
32. B. R. Miller III T. D. McGee Jr.J. M. Swails N. Homeyer H. Gohlke A. E. Roitberg MMPBSA. py: an efficient program for end-state free energy calculations J. Chem. Theory Comput. 2012 8 3314 3321
33. Y. Zhang H. Chen J. G. Han Insight into the binding modes of Lassa nucleoprotein complexed with ssRNA by molecular dynamic simulations and free energy calculations J. Biomol. Struct. Dyn. 2015 33 946 960
34. S. Huo I. Massova P. A. Kollman Computational alanine scanning of the 1: 1 human growth hormone-receptor complex J. Comput. Chem. 2002 23 15 27
35. D. Li J.-G. Han H. Chen L. Li R.-N. Zhao G. Liu Y. Duan Insights into the structural function of the complex of HIV-1 protease with TMC-126: molecular dynamics simulations and free-energy calculations J. Mol. Model. 2012 18 1841 1854
36. I. Massova P. A. Kollman Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies J. Am. Chem. Soc. 1999 121 8133 8143
37. T. Kortemme D. E. Kim D. Baker Computational alanine scanning of protein-protein interfaces Sci STKE 2004 2004 pl2
38. S. A. Deshmukh Z. Li G. Kamath K. J. Suthar S. K. R. S. Sankaranarayanan D. C. Mancini Atomistic insights into solvation dynamics and conformational transformation in thermo-sensitive and non-thermo-sensitive oligomers Polymer 2013 54 210 222
39. E. Fuglebakk J. Echave N. Reuter Measuring and comparing structural fluctuation patterns in large protein datasets Bioinformatics 2012 28 2431 2440
40. Y. Mao Dynamical Basis for Drug Resistance of HIV-1 Protease BMC Struct. Biol. 2011 11 31
41. M. Balmith M. E. S. Soliman Non-active site mutations disturb the loop dynamics, dimerization, viral budding and egress of VP40 of the Ebola virus Mol. BioSyst. 2017 13 585 597
42. H. Gohlke C. Kiel D. A. Case Insights into Protein-Protein Binding by Binding Free Energy Calculation and Free Energy Decomposition for the Ras-Raf and Ras-RalGDS Complexes J. Mol. Biol. 2003 330 891 913