Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex

Biophysical Journal

Volumn 80, Issue 6, 2001, Pages 2833-2842

  Reyes, Carolina M ^a   Nifosi, Riccardo ^b   Frankel, Alan D ^c   Kollman, Peter A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c INFM   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ION; TRANSACTIVATOR PROTEIN; VIRUS RNA; WATER;

ARTICLE; BINDING AFFINITY; BOVINE IMMUNODEFICIENCY LIKE VIRUS; CALCULATION; MOLECULAR DYNAMICS; NONHUMAN; PROTEIN RNA BINDING; RIGIDITY; RNA ANALYSIS; RNA STRUCTURE; SIMULATION; STRUCTURE ANALYSIS;

BOVINAE; BOVINE IMMUNODEFICIENCY VIRUS; BOVINE IMMUNODEFICIENCY-LIKE VIRUS;

EID: 0034999080     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(01)76250-9     Document Type: Article

References (45)

1. Aboul-ela, F., J. Kara, and G. Varani. 1995. The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein. J. Mol. Biol. 253:313-332.
2. Aboul-ela, F., and G. Varani. 1998. Recognition of HIV-1 TAR RNA by Tat protein and Tat-derived peptides. Theochem. J. Mol. Struct. 423: 29-39.
3. Bayer, P., M. Kraft, A. Ejchart, M. Westendorp, R. Frank, and P. Rosch. 1995. Structural studies of HIV-1 Tat protein. J. Mol. Biol. 247: 529-535.
4. Berendsen, H. C., J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. 1981. Interaction models for water in relation to protein hydration. In Intermolecular Forces. B. Pullman, editor. Reidel, Dordrecht, The Netherlands. 331-342.
5. Burley, S. K., and G. A. Petsko. 1985. Aromatic-aromatic interaction: a mechanism of protein structure stabilization. Science. 229:23-28.
6. Calnan, B. J., B. Tidor, S. Biancalana, D. Hudson, and A. D. Frankel. 1991. Arginine-mediated RNA recognition - the arginine fork. Science. 252: 1167-1171.
7. Cheatham, T. E., and P. A. Kollman. 1996. Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. J. Mol. Biol. 259:434-444.
8. Cheatham, T. E., J. Srinivasan, D. A. Case, and P. A. Kollman. 1998. Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. J. Biomol. Struct. Dyn. 16:265-280.
9. Chen, L., and A. D. Frankel. 1995. A peptide interaction in the major groove of RNA resembles protein interactions in the minor groove of DNA. Proc. Natl. Acad. Sci. U.S.A. 92:5077-5081.
10. Chong, L. T., Y. Duan, L. Wang, I. Massova, and P. A. Kollman. 1999. Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. Proc. Natl. Acad. Sci. U.S.A. 96: 14330-14335.
11. Cornell, W. D., P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179, 1995.
12. Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald: an N • log(N) method for Ewald sums in large systems. J. Chem. Phys. 98: 10089-10092.
13. Ferrin, T. E., C. C. Huang, L. E. Jarvis, and R. Langridge. 1988. The MIDAS display system. J. Mol. Graphics. 6:13-27.
14. Frankel, A. D. 2000. Fitting peptides into the RNA world. Curr. Opin. Struct. Biol. 10:332-340.
15. Greenbaum, N. L. 1996. How Tat targets TAR: structure of the BIV peptide RNA complex. Structure. 4:5-9.
16. Hermann, T., and E. Westhof. 1999. Simulations of the dynamics at an RNA-protein interface. Nat. Struct. Biol. 6:540-544.
17. Jones, K. A., and B. M. Peterlin. 1994. Control of RNA initiation and elongation at the HIV-I promoter. Annu. Rev. Biochem. 63:717-743.
18. Jorgensen, W. L., J. Chandreskhar, J. D. Madura, R. W. Imprey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
19. Massova, I., and P. A. Kollman. 1999. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J. Am. Chem. Soc. 121:8133-8143.
20. Massova, I., and P. A. Kollman. 2000. Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding. Perspectives in Drug Discovery and Design. 18:1-23.
21. Mujeeb, A., T. G. Parslow, Y. C. Yuan, and T. L. James. 1996. Aqueous solution structure of a hybrid lentiviral Tat peptide and a model of its interaction with HIV-1 TAR RNA. J. Biomol. Struct. Dyn. 13:649-660.
22. Nicholls, A., K. A. Sharp, and B. Honig. 1990. DelPhi. Department of Biochemistry and Molecular Biophysics, Columbia University, New York.
23. Nifosi, R., C. Reyes, and P. A. Kollman. 2000. Molecular dynamics studies of the HIV-1. TAR and its complex with argininamide. Nucleic Acids Res. 28:4944-4955.
24. Puglisi, J. D., L. Chen, S. Blanchard, and A. D. Frankel. 1995. Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex. Science. 270:1200-1203.
25. Puglisi, J. D., L. Chen, A. D. Frankel, and J. R. Williamson. 1993. Role of RNA structure in arginine recognition of TAR RNA. Proc. Natl. Acad. Sci. U.S.A. 90:3680-3684.
26. Puglisi, J. D., R. Y. Tan, B. J. Calnan, A. D. Frankel, and J. R. Williamson. 1992b. Conformation of the TAR RNA-Arginine Complex By NMR Spectroscopy. Science. 257:76-80.
27. Rana, T. M., and K. T. Jeang. 1999. Biochemical and functional interactions between HIV-1 Tat protein and TAR RNA. Arch. Biochem. Biophys. 365:175-185.
28. Reyes, C. M., and P. A. Kollman. 1999. Molecular dynamics studies of U1A-RNA complexes. RNA-a Publication of the RNA Society. 5:235-244.
29. Reyes, C., and P. A. Kollman. 2000a. Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change. J. Mol. Biol. 297:1145-1158.
30. Reyes, C. M., and P. A. Kollman. 2000b. Investigating the binding specificity of U1A-RNA by computational mutagenesis. J. Mol. Biol. 295: 1-6.
31. Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equation of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23: 327-341.
32. Sanner, M. F., A. J. Olson, and J. C. Spehner. 1996. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers. 38:305-320.
33. Sharp, K. A., and B. Honig. 1990. Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Biophys. Chem. 19:301-332.
34. Sitkoff, D., K. A. Sharp, and B. Honig. 1994. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98:1978-1988.
35. Smith, C. A., S. Crotty, Y. Harada, and A. D. Frankel. 1998. Altering the context of an RNA bulge switches the binding specificities of two viral Tat proteins. Biochemistry. 37:10808-10814.
36. Smith, K. C., and B. Honig. 1994. Evaluation of the conformational free energies of loops in proteins. Proteins: Struct., Funct., Genet. 18: 119-132.
37. Srinivasan, J., T. E. Cheatham, P. Cieplak, P. A. Kollman, and D. A. Case. 1998a. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J. Am. Chem. Soc. 120:9401-9409.
38. Srinivasan, J., J. Miller, P. A. Kollman, and D. A. Case. 1998b. Continuum solvent studies of the stability of RNA hairpin loops and helices. J. Biomol. Struct. Dyn. 16:671-675, 677-682.
39. Sticht, H., D. Willbold, P. Bayer, A. Ejchart, F. Hermann, R. Rosinarbesfeld, A. Gazit, A. Yaniv, R. Frank, and P. Rosch. 1993. Equine infectious anemia virus Tat is a predominantly helical protein. Eur. J. Biochem. 218:973-976.
40. Sussman, J. L., D. W. Lin, J. S. Jiang, N. O. Manning, J. Prilusky, O. Ritter, and E. E. Abola. 1998. Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules. Acta Crystallogr. D. 54:1078-1084.
41. Tan, R. Y., and A. D. Frankel. 1995. Structural variety of arginine-rich RNA-binding peptides. Proc. Natl. Acad. Sci. U.S.A. 92:5282-5286.
42. Tang, Y., and L. Nilsson. 1999. Molecular dynamics simulations of the complex between human U1A protein and hairpin II of U1 small nuclear RNA and of free RNA in solution. Biophys. J. 77:1284-1305.
43. Tao, J., and A. D. Frankel. 1992. Specific binding of arginine to TAR RNA. Proc. Natl. Acad. Sci. U.S.A. 89:2723-2726.
44. Willbold, D., A. U. Metzger, H. Sticht, K. C. Gallert, R. Voit, N. Dank, P. Bayer, G. Krauss, R. S. Goody, and P. Rosch. 1998. Equine infectious anemia virus transactivator is a homeodomain-type protein. J. Mol. Biol. 277:749-755.
45. Ye, X. M., R. A. Kumar, and D. J. Patel. 1995. Molecular recognition in the bovine immunodeficiency virus Tat peptide TAR RNA complex. Chemistry and Biology. 2:827-840.