Mechanism of flexibility control for ATP access of hepatitis C virus NS3 helicase

Journal of Biomolecular Structure and Dynamics

Volumn 31, Issue 2, 2013, Pages 129-141

  Palla, Mirkó ^a   Chen, Chien Pin ^a   Zhang, Yuan ^a   Li, Jingyuan ^b   Ju, Jingyue ^a   Liao, Jung Chi ^a  

^a 220 Mudd Building ^*  (United States)

^b INSTITUTE OF HIGH ENERGY PHYSICS   (China)

Author keywords

ATP binding cleft; Hinge motion; Molecular dynamics simulation; Pairwise distance analysis; RMSF analysis

Indexed keywords

ADENOSINE TRIPHOSPHATE; AMINO ACID; HELICASE; MUTANT PROTEIN; NONSTRUCTURAL PROTEIN 3; POLYNUCLEOTIDE; WATER;

ARTICLE; BINDING SITE; CONTROLLED STUDY; ENERGY; HEPATITIS C; HEPATITIS C VIRUS; HISTOGRAM; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE; ROOT MEAN SQUARE FLUCTUATION ANALYSIS;

ADENOSINE TRIPHOSPHATE; AMINO ACID MOTIFS; AMINO ACID SUBSTITUTION; CATALYTIC DOMAIN; HEPACIVIRUS; HYDROGEN BONDING; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; SOLVENTS; VIRAL NONSTRUCTURAL PROTEINS; WATER;

EID: 84875199633     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2012.698236     Document Type: Article

References (39)

1. Abrams, C.F., & Vanden-Eijnden, E. (2010). Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics. Proceedings of the National Academy of Sciences USA, 107, 4961-4966. doi: 10.1073/pnas.0914540107
2. Berendsen, H. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91, 43-56. doi: 10.1016/0010-4655(95)00042-E
3. Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren, W.F., & Hermans, J. (1981). Interaction models for water in relation to protein hydration. Intermolecular Forces, 11, 331-338. doi: 10.1111/j.1574-695X.1996.tb00128.x
4. Boehr, D.D., Nussinov, R., & Wright, P.E. (2009). The role of dynamic conformational ensembles in biomolecular recognition. Nature Chemical Biology, 5, 789-796. doi: 10.1038/nchembio.232
5. Carlson, H.A., & McCammon, J.A. (2000). Accommodating protein flexibility in computational drug design. Molecular Pharmacology, 57. 213-218Retrieved from http://molpharm.aspetjournals.org/content/57/2/213.full
6. Caruthers, J.M., & McKay, D.B. (2002). Helicase structure and mechanism. Current Opinion in Structural Biology, 12, 123-133. doi: 10.1016/S0959-440X(02)00298-1
7. Choo, Q.L., Kuo, G., Weiner, A.J., Overby, L.R., Bradley, D.W., & Houghton, M. (1989). Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science, 244, 359-362. doi: 10.1126/science. 2523562
8. De Francesco, R., & Migliaccio, G. (2005). Challenges and successes in developing new therapies for hepatitis C. Nature, 436, 953-960. doi: 10.1038/nature04080
9. Dodson, G., & Verma, C.S. (2006). Protein flexibility: Its role in structure and mechanism revealed by molecular simulations. Cellular and Molecular Life Sciences, 63, 207-219. doi: 10.1007/s00018-005-5236-7
10. Druker, B.J., Talpaz, M., Resta, D.J., Peng, B., Buchdunger, E., Ford, J.M.,⋯ Sawyers, C.L. (2001). Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia. The New England Journal of Medicine, 344, 1031-1037. doi: 10.1056/NEJM200104053441401
11. Dumont, S., Cheng, W., Serebrov, V., Beran, R.K., Tinoco, I. Jr., Pyle, A.M., & Bustamante, C. (2006). RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP. Nature, 439, 105-108. doi:10.1038/nature04331
12. Durrant, J.D., & McCammon, J.A. (2010). Computer-aided drug-discovery techniques that account for receptor flexibility. Current Opinion in Pharmacology, 10, 770-774. doi:10.1016/j.coph.2010.09.001
13. Frick, D.N. (2003). Helicases as antiviral drug targets. Drug News Perspect, 16, 355-362.
14. Gorbalenya, A.E., & Koonin, E.V. (1993). Helicases: Amino acid sequence comparisons and structure-function relationships.Current Opinion in Structural Biology, 3, 419-429. doi: 10.1016/S0959-440X(05)80116-2
15. Grant, B.J., Gorfe, A.A., & McCammon, J.A. (2010). Large conformational changes in proteins: Signaling and other functions. Current Opinion in Structural Biology, 20, 142-147. doi: 10.1016/j.sbi.2009.12.004
16. Gu, M., & Rice, C.M. (2010). Three conformational snapshotsof the hepatitis C virus NS3 helicase reveal a ratchet translocationmechanism. Proceedings of the National Academyof Sciences USA, 107, 521-528. doi: 10.1073/pnas.0913380107
17. Guex, N., & Peitsch, M.C. (1997). SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis, 18, 2714-2723. doi: 10.1002/elps.1150181505
18. Hockney, R.W. (1970). The potential calculation and some applications. Methods in Computational Physics, 9, 136-211.
19. Ivetac, A., & McCammon, J.A. (2011). Molecular recognition in the case of flexible targets. Current Pharmaceutical Design, 17, 1663-1671.
20. Ivetac, A., & McCammon, J.A. (2012). A molecular dynamics ensemble-based approach for the mapping of druggable binding sites. Methods in Molecular Biology, 819, 3-12. doi: 10.1007/978-1-61779-465-0-1
21. Karplus, M., & Kuriyan, J. (2005). Molecular dynamics and protein function. Proceedings of the National Academy of Sciences USA, 102, 6679-6685. doi: 10.1073/pnas.0408930102
22. Kim, D.W., Kim, J., Gwack, Y., Han, J.H., & Choe, J. (1997). Mutational analysis of the hepatitis C virus RNA helicase. Journal of Virology, 71, 9400-9409.
23. Kim, J.L., Morgenstern, K.A., Griffith, J.P., Dwyer, M.D., Thomson, J.A., Murcko, M.A., ⋯ Caron, P.R. (1998). Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: The crystal structure provides insights into the mode of unwinding. Structure, 6, 89-100. doi: 10.1016/S0969-2126(98) 00010-0
24. Korolev, S., Yao, N., Lohman, T.M., Weber, P.C., & Waksman, G. (1998). Comparisons between the structures of HCV and Rep helicases reveal structural similarities between SF1 and SF2 super-families of helicases. Protein Science, 7, 605-610. doi: 10.1002/pro.5560070309
25. Kwong, A.D., Kim, J.L., & Lin, C. (2000). Structure and function of hepatitis C virus NS3 helicase. Current Topics in Microbiology and Immunology, 242, 171-196.
26. Li, G., & Cui, Q. (2004). Mechanochemical coupling in myosin: A Theoretical analysis with molecular dynamics and combined QM/MM reaction path calculations. The Journal of Physical Chemistry B, 108, 3342-3357. doi: 10.1021/jp0371783
27. Liao, J.C. (2011). Mechanical transduction mechanisms of RecA-like molecular motors. Journal of Biomolecular Structure & Dynamics, 29, 497-507.
28. Liao, J.C., Sun, S., Chandler, D., & Oster, G. (2004). The conformational states of Mg.ATP in water. European Biophysics Journal, 33, 29-37. doi: 10.1007/s00249-003-0339-2
29. Min, K.H., Sung, Y.C., Choi, S.Y., & Ahn, B.Y. (1999). Functional interactions between conserved motifs of the hepatitis C virus RNA helicase protein NS3. Virus Genes, 19, 33-43. doi: 10.1023/A:1008184522153
30. Preugschat, F., Averett, D.R., Clarke, B.E., & Porter, D.J. (1996). A steady-state and pre-steady-state kinetic analysis of the NTPase activity associated with the hepatitis C virus NS3 helicase domain. Journal of Biological Chemistry, 271, 24449-24457. doi: 10.1074/jbc.271.40.24449
31. Roy, S., & Thakur, A.R. (2010). 20ns molecular dynamics simulation of the antennapedia homeodomain-DNA complex: Water interaction and DNA structure analysis. Journal of Biomolecular Structure & Dynamics, 27, 443-456.
32. Sotomayor, M., & Schulten, K. (2007). Single-molecule experiments in vitro and in silico. Science, 316, 1144-1148. doi: 10.1126/science.1137591
33. Soultanas, P., Dillingham, M.S., Velankar, S.S., & Wigley, D.B. (1999). DNA binding mediates conformational changes and metal ion coordination in the active site of PcrA helicase. Journal of Molecular Biology, 290, 137-148. doi: 10.1006/jmbi.1999.2873
34. Suzich, J.A., Tamura, J.K., Palmer-Hill, F., Warrener, P., Grakoui, A., Rice, C.M., Feinstone, S.M., & Collett, M.S. (1993). Hepatitis C virus NS3 protein polynucleotide-stimulated nucleoside triphosphatase and comparison with the related pestivirus and flavivirus enzymes. Journal of Virology, 67, 6152-6158.
35. Tai, C.L., Pan, W.C., Liaw, S.H., Yang, U.C., Hwang, L.H., & Chen, D.S. (2001). Structure-based mutational analysis of the hepatitis C virus NS3 helicase. Journal of Virology, 75, 8289-8297.
36. Wang, J., Cieplak, P., & Kollman, P.A. (2000). How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? Journal of Computational Chemistry, 21, 1049-1074. doi: 10.1002/1096-987X(200009)21: 12<1049:: AID-JCC3>3.3.CO;2-6
37. Wright, P.E., & Dyson, H.J. (2009). Linking folding and binding. Current Opinion in Structural Biology, 19, 31-38. doi:10.1016/j.sbi.2008.12.003
38. Yu, J., Ha, T., & Schulten, K. (2006). Structure-based model of the stepping motor of PcrA helicase. Biophysical Journal, 91, 2097-2114. doi: 10.1529/biophysj.106.088203
39. Zheng, W., Liao, J.C., Brooks, B.R., & Doniach, S. (2007). Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model. Proteins, 67, 886-896. doi: 10.1002/prot.21326