Studies on the binding modes of Lassa nucleoprotein complexed with m7GpppG and dTTP by molecular dynamic simulations and free energy calculations

Journal of Biomolecular Structure and Dynamics

Volumn 31, Issue 3, 2013, Pages 299-315

  Li, Liang ^a   Li, Dan ^a   Chen, Hang ^a   Han, Ju Guang ^a  

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

Author keywords

Binding modes; Docking; dTTP and m7GpppG complexes; Lassa virus nucleoprotein; Molecular dynamics simulation

Indexed keywords

7 METHYLGUANOSINE TRIPHOSPHATE 5' NUCLEOTIDE; ARGININE; GUANOSINE TRIPHOSPHATE DERIVATIVE; HYDROGEN; PHOSPHATE; THREONINE; THYMIDINE TRIPHOSPHATE; UNCLASSIFIED DRUG; URIDINE TRIPHOSPHATE; VIRUS NUCLEOPROTEIN; VIRUS RNA;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; COMPUTER PROGRAM; CRYSTAL STRUCTURE; DECOMPOSITION; HYDROGEN BOND; LASSA VIRUS; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN STRUCTURE; RNA SYNTHESIS; RNA TRANSCRIPTION; X RAY CRYSTALLOGRAPHY;

AMINO ACIDS; DINUCLEOSIDE PHOSPHATES; HUMANS; HYDROGEN BONDING; LASSA VIRUS; MOLECULAR DYNAMICS SIMULATION; NUCLEOPROTEINS; PROTEIN BINDING; THERMODYNAMICS; THYMINE; THYMINE NUCLEOTIDES;

EID: 84875166754     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2012.703061     Document Type: Article

References (39)

1. Bayly, C.I., Cieplak, P., Cornell, W., & Kollman, P.A. (1993). A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model. The Journal of Physical Chemistry, 97, 10269-10280.
2. Brunotte, L., Kerber, R., Shang, W., Hauer, F., Hass, M., Gabriel, M., Svergun, D.I. (2011). Structure of the Lassa virus nucleoprotein revealed by X-ray crystallography, small-angle X-ray scattering, and electron microscopy. Journal of Biological Chemistry, 286, 38748-38756.
3. Buchmeier, M.J., de la Torre, J.C., & Peters, C.J. (2007). Are-naviridae: The viruses and their replication. In D.L. Knipe & P.M. Howley (Eds.), Fields virology (2, pp. 1791-1828). Philadelphia, PA: Lippincott Williams & Wilkins.
4. Case, D.A., Cheatham, T.E.III. Darden, T., Gohlke, H., Luo, R., Merz, K.M. Jr. Woods, R.J. (2005). The Amber bio-molecular simulation programs. Journal of Computational Chemistry, 26, 1668-1688.
5. Chemical Computing Group. (2009). The molecular operating environment (MOE). Montreal, QC: Chemical Computing Group Inc.
6. Csermely, P., Palotai, R., & Nussinov, R. (2010). Induced fit, conformational selection and independent dynamic segments: An extended view of binding events. Trends in Biochemical Sciences, 35, 539-546.
7. Duan, Y., Wu, C., Chowdhury, S., Lee, M.C., Xiong, G., Zhang, W., Lee, T. (2003). A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry, 24, 1999-2012.
8. Essmann, U., Perera, L., Berkowitz, M.L., Darden, T., Lee, H., & Pedersen, L.G. (1995). A smooth particle mesh Ewald method. Journal of Chemical Physics, 103, 8577-8593.
9. Feig, M., & Brooks, C.L.III (2002). Evaluating CASP4 predictions with physical energy functions. Proteins: Structure. Function, and Bioinformatics, 49, 232-245.
10. Gourmala, C, Luo, Y., Barbault, F., Zhang, Y., Ghalem, S., Maurel, F., & Fan, B.T. (2007). Elucidation of the LewisX-LewisX carbohydrate interaction with molecular dynamics simulations: A glycosynapse model. Journal of Molecular Structure: THEOCHEM, 821, 22-29.
11. Haas, W.H., Breuer, T., Pfaff, G., Schmitz, H., Köhler, P., Asper, M.,.. Fleischer, K. (2003). Imported Lassa fever in Germany: Surveillance and management of contact persons. Clinical Infectious Diseases, 36, 1254-1258. (Pubitemid 36629934)
12. Hass, M., Gölnitz, U., Müller, S., Becker-Ziaja, B., & Günther, S. (2004). Replicon system for Lassa virus. Journal of Virology, 78, 13793-13803. (Pubitemid 39612776)
13. Hastie, K.M., Liu, T., Li, S., King, L.B., Ngo, N., Zandonatti, M.A.,.. Saphire, E.O. (2011). Crystal structure of the Lassa virus nucleoprotein-RNA complex reveals a gating mechanism for RNA binding. Proceedings of the National Academy of Sciences, 108, 19365-19370.
14. Holmes, G.P, McCormick, J.B., Trock, S.C., Chase, R.A., Lewis, S.M., Mason, C.A.,.. McDonnell, M.K. (1990). Lassa fever in the United States. New England Journal of Medicine, 323, 1120-1123.
15. Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics, 65, 712-725. (Pubitemid 44583220)
16. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., & Klein, M.L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79, 926-935.
17. Kottalam, J., & Case, D. (1990). Langevin modes of macro-molecules: Applications to crambin and DNA hexamers. Biopolymers, 29, 1409-1421. (Pubitemid 20180262)
18. Lee, M.C., & Duan, Y (2004). Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model. Proteins: Structure, Function, and Bioinformatics, 55, 620-634. (Pubitemid 38620087)
19. Liu, W., Zhao, R., McFarland, C, Kieft, J., Niedzwiecka, A., Jankowska-Anyszka, M.,.. Davis, R.E. (2009). Structural insights into parasite eIF4E binding specificity for m7G and m2, 2, 7G mRNA caps. Journal of Biological Chemistry, 284, 31336-31349.
20. Lopez, N., Jacamo, R., & Franze-Fernandez, M.T. (2001). Transcription and RNA replication of Tacaribe virus genome and antigenome analogs require N and L proteins: Z protein is an inhibitor of these processes. Journal of Virology, 75, 12241-12251. (Pubitemid 33115897)
21. McCormick, J. (1990). Arenaviruses. In D.L. Knipe & P.M. Howley (Eds.), Fields virology (2, pp. 1245-1267). Lippin-cott Williams & Wilkins.
22. McCormick, J.B., King, I.J., Webb, P.A., Scribner, C.L., Craven, R.B., Johnson, K.M.,.. Belmont-Williams, R. (1986). Lassa fever. New England Journal of Medicine, 314, 20-26.
23. Oelschlaeger, P., Schmid, R.D., & Pleiss, J. (2003a). Insight into the mechanism of the IMP-1 metallo-(3-lactamase by molecular dynamics simulations. Protein Engineering, 16, 341-350. (Pubitemid 36806925)
24. Oelschlaeger, P., Schmid, R.D., & Pleiss, J. (2003b). Modeling domino effects in enzymes: Molecular basis of the substrate specificity of the bacterial metallo-(3-lactamases IMP-1 and IMP-6f. Biochemistry, 42, 8945-8956. (Pubitemid 36935402)
25. Ogbu, O., Ajuluchukwu, E., & Uneke, C. (2007). Lassa fever in West African sub-region: An overview. Journal of Vector Borne Diseases, 44, 1-11. (Pubitemid 46383872)
26. Pang, Y.P. (1999). Novel zinc protein molecular dynamics simulations: Steps toward antiangiogenesis for cancer treatment. Journal of Molecular Modeling, 5, 196-202.
27. Pang, Y.P. (2001). Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotri-esterase using the cationic dummy atom method. Proteins: Structure, Function, and Bioinformatics, 45, 183-189.
28. Pang, Y.P., Davis, J., Wang, S., Park, J.G., Nambiar, M.P., Schmidt, J.J., & Millard, C.B. (2010). Small molecules showing significant protection of mice against botulinum neurotoxin serotype A. PLoS ONE, 5, e10129.
29. Pang, Y.P., Vummenthala, A., Mishra, R.K., Park, J.G., Wang, S., Davis, J., Schmidt, J.J. (2009). Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design. PLoS ONE, 4, e7730.
30. Pang, Y.P., Xu, K., Yazal, J.E., & Prendergast, F.G. (2000). Successful molecular dynamics simulation of the zinc-bound farnesyltransferase using the cationic dummy atom approach. Protein Science, 9, 1857-1865.
31. Park, J.G., Sill, P.C., Makiyi, E.F., Garcia-Sosa, A.T., Millard, C.B., Schmidt, J.J., & Pang, Y.P. (2006). Serotype-selec-tive, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A. Bioorganic & Medicinal Chemistry, 14, 395-408. (Pubitemid 41767599)
32. Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Chea-tham, T.E., DeBolt, S., Kollman, P. (1995). AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Computer Physics Communications, 91, 1-41.
33. Pinschewer, D.D., Perez, M., & de la Torre, J.C. (2003). Role of the virus nucleoprotein in the regulation of lymphocytic choriomeningitis virus transcription and RNA replication. Journal of Virology, 77, 3882-3887. (Pubitemid 36297310)
34. Qi, X., Lan, S., Wang, W., Schelde, L.M.L., Dong, H., Wallat, G.D., Dong, C. (2010). Cap binding and immune evasion revealed by Lassa nucleoprotein structure. Nature, 468, 779-783.
35. Rey, F.A. (2010). Virology: One protein, many functions. Nature, 468, 773-775.
36. Ryckaert, J.P., Ciccotti, G., & Berendsen, H.J.C. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23, 327-341.
37. Schuttelkopf, A.W., & Van Aalten, D.M.F. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica Section D: Biological Crystallography, 60, 1355-1363. (Pubitemid 41079731)
38. Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., & Case, D.A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25, 1157-1174.
39. Xu, M., & Lill, M.A. (2011). Significant enhancement of docking sensitivity using implicit ligand sampling. Journal of Chemical Information and Modeling, 51, 693-706.