Major subdomain rearrangement in HIV-1 reverse transcriptase simulated by molecular dynamics

Proteins: Structure, Function and Genetics

Volumn 35, Issue 3, 1999, Pages 332-337

  Madrid, M ^a   Jacobo Molina, A ^b   Ding, J ^c   Arnold, E ^c  

^a PITTSBURGH SUPERCOMPUTING CENTER   (United States)

^b SCHOOL OF ENGINEERING AND SCIENCES   (Mexico)

^c RUTGERS UNIVERSITY   (United States)

Author keywords

Hinge movement; Molecular modeling; Subdomain displacement

Indexed keywords

RNA DIRECTED DNA POLYMERASE; VIRUS ENZYME;

ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME STRUCTURE; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; SIMULATION; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; HIV-1 REVERSE TRANSCRIPTASE; MODELS, MOLECULAR; PROTEIN CONFORMATION;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0033562423     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990515)35:3<332::AID-PROT7>3.0.CO;2-R     Document Type: Article

References (50)

1. Goff P. Retroviral reverse transcriptase: synthesis, structure and function. J Acquired Immune Deficiency Syndr 1990;3:817-831.
2. Voet D, Voet J. Biochemistry. New York: Wiley, 1995.
3. Jacobo-Molina A, Arnold E. HIV reverse transcriptase structure-function relationships. Biochemistry 1991;30:6351-6361.
4. Whitcomb JM, Hughes SH. Retroviral reverse transcription and integration: progress and problems. Annu Rev Cell Biol 1992;8:275-306.
5. Le Grice SFJ. Human immunodeficiency virus reverse transcriptase. In: Skalka AM, Goff SP, editors. Reverse transcriptase. Plainview, NY: Cold Spring Harbor Laboratory Press, 1993:163-191.
6. Arnold E, Das K, Ding J, Yadav PNS, Hsiou Y, Boyer PL, Hughes SH. Targeting HIV reverse transcriptase for anti-AIDS drug design: structural and biological considerations for chemotherapeutic strategies. Drug Design Discov 1996;13:29-47.
7. Larder BA. Inhibitors of HIV reverse transcriptase as antiviral agents and drug resistance. In: Skalka, AM, Goff SP, editors. Reverse transcriptase. Plainview, New York: Cold Spring Harbor Laboratory Press, 1993. p 205-222.
8. Tantillo C, Ding J, Jacobo-Molina A, Nanni RG, Boyer PL, Hughes SH, Pauwels R, Andries K, Janssen PAJ, Arnold E. Locations of anti-AIDS drug binding sites and resistance mutations in the three-dimensional structure of HIV-1 reverse transcriptase: implications for mechanisms of drug inhibition and resistance. J Mol Biol 1994;243:369-387.
9. De Clercq E. Antiviral therapy for human immunodeficiency virus infections. Clin Microbiol Rev 1995;8:200-239.
10. Ding J, Das K, Yadev PNS, Hsiou Y, Zhang W, Hughes SH, Arnold E. Structural studies of HIV-1 reverse transcriptase and implications for drug design. In: Structure based drug design. Veerapandian P, editor. New York: Marcel Dekker, 1997. p 41-82.
11. Kohlstaedt LA, Wang J, Friedman JM, Rice PA, Steitz TA. Crystal structure at 3.5 Å resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 1992;256:1783-1790.
12. Smerdon SJ, Jager J, Wang J, Kohlstaedt LA, Chirino AJ, Friedman JM, Rice PA, Steitz TA. Structure of the binding site for nonnucleoside inhibitors of reverse transcriptase of human immunodeficiency virus type 1. Proc Natl Acad Sci USA 1994;91:3911-3915.
13. Ding J, Das K, Tantillo C, Zhang W, Clark AD Jr, Jessen S, Lu X, Hsiou Y, Jacobo-Molina A, Andries K, Pauwels R, Moereels H, Koymans L, Janssen PAJ, Smith R, Koepke MK, Michejda C, Hughes SH, Arnold E. Structure of HIV-1 reverse transcriptase in a complex with the nonnucleoside inhibitor α-APA R 95845 at 2.8 Å resolution. Structure 1995;3:365-379.
14. Ren J, Esnouf R, Garman E, Somers D, Ross C, Kirby I, Keeling J, Darby G, Jones Y, Stuart D, Stammers D. High resolution structures of HIV-1 RT from four RT-inhibitor complexes. Nature Struct Biol 1995;2:293-302.
15. Ding J, Das K, Moereels H, Koymans L, Andries K, Janssen PA, Hughes SH, Arnold E. Structure of HIV-1 RT/TIBO R 86183 reveals similarity in the binding of diverse nonnucleoside inhibitors. Nature Struct Biol 1995;2:407-415.
16. Jacobo-Molina A, Ding J, Nanni RG, Clark AD Jr, Lu X, Tantillo C, Williams RL, Kamer G, Ferris AL, Clark P, Hizi A, Hughes SH, Arnold E. Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 Å resolution shows bent DNA. Proc Natl Acad Sci USA 1993;90:6320-6324.
17. Ding J, Hughes SH, Arnold E. Protein-nucleic acid interactions and DNA conformation in a complex of human immunodeficiency virus type 1 reverse transcriptase with a double-stranded DNA template-primer. Biopolymers 1997;44:125-138.
18. Hsiou Y, Ding J, Das K, Clark AD Jr, Hughes SH, Arnold E. Structure of unliganded HIV-1 reverse transcriptase at 2.7 Å resolution: implications of conformational changes for polymerization and inhibition mechanisms. Structure 1996;4:853-860.
19. Jager J, Smerdon SJ, Wang J, Boisvert DC, Steitz TA. Comparison of three different crystal forms shows HIV-1 reverse transcriptase displays an internal swivel motion. Structure 1994;2:869-876.
20. Esnouf R, Ren J, Ross C, Jones Y, Stammers D, Stuart D. Mechanism of inhibition of HIV-1 reverse transcriptase by nonnucleoside inhibitors. Nature Struct Biol 1995;2:303-308.
21. Raag R, Clark AD Jr, Ding J, Jacobo-Molina A, Lu X, Nanni RG, Tantillo C, Hughes SH, Arnold E. 3.0 Å crystal structure of HIV-1 reverse transcriptase without dsDNA reveals large-scale motion of p66 thumb subdomain. Am Crystallogr Assoc Mtg Abstr Ser 1994;2:22-44.
22. Rodgers DW, Gamblin SJ, Harris BA, Ray S, Culp JS, Hellmig B, Woolf DJ, Debouck C, Harrison SC. The structure of unliganded reverse transcriptase from the human immunodeficiency virus type 1. Proc Natl Acad Sci USA 1995;92:1222-1226.
23. Ren J, Esnouf R, Garman E, Sommers D, Ross C, Kirby I, Keeling J, Darby G, Jones Y, Stuart D, Stammers D. The structure of HIV-1 reverse transcriptase complexed with 9-cloro-TIBO: lessons for inhibitor design. Structure 1995;3:915-926..
24. Das K, Ding J, Hsiou J, Clark AD Jr, Moereels H, Koyman L, Andries K, Pauwels R, Janssen PA, Boyer PL, Clark P, Smith RH Jr, Kroeger Smith MB, Michejda CJ, Hughes SH, Arnold E. Crystal structure of 8-Cl and 9-Cl TIBO complexed with wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr 181 Cys HIV-1 RT drug-resistant mutant. J Mol Biol 1996;264:1085-1100.
25. Ding J, Das K, Hsiou Y, Sarafianos SG, Clark ADJr, Jacobo-Molina A, Tantillo C, Hughes SH, Arnold E. Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 Å resolution. J Mol Biol 1998;284: 1095-1111.
26. Huang H, Chopra R, Verdine GL, Harrison SC. Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science 1998;282:1669-1675.
27. Patel PH, Jacobo-Molina A, Ding J, Tantillo C, Clark AD Jr, Raag R, Nanni RG, Hughes SH, Arnold E. Insights into DNA polymerization mechanisms from structure and function analysis of HIV-1 reverse transcriptase. Biochemistry 1995;34:5351-5363.
28. Gerstein M, Lesk AM, Chothia C. Structural mechanisms for domain movements in proteins. Biochemistry 1994;33:6739-6749.
29. van Aalten DMF, Amadei A, Linssen AB, Eijsink VG, Vriend G, Berendsen HJ. The essential dynamics of thermolysin: confirmation of the hinge-bending motion and comparison of simulations in vacuum and water. Proteins 1995;22:45-54.
30. Arnold GE, Ornstein RL. Protein hinge bending as seen in molecular dynamics simulations of native and M61 mutant T4 lysozymes. Biopolymers 1997;41:533-544.
31. Kasper P, Sterk M, Christen P, Gehring H. Molecular-dynamics simulation of domain movements in aspartate aminotransferase. Eur J Biochem 1996;240:751-755.
32. Kroeger-Smith MB, Rouzer CA, Taneyhill LA, Smith NA, Hughes SH, Boyer PL, Janssen PA, Moereels H, Koymans L, Arnold E, Ding J, Das K, Zhang W, Michejda CJ, Smith RH Jr. Molecular modeling studies of HIV-1 reverse transcriptase nonnucleoside inhibitors: total energy of complexation as a predictor of drug placement and activity. Protein Sci 1995;4:2203-2222.
33. Gussio R, Pattabiraman N, Zaharevitz DW, Kellogg GE, Topol IA, Rice WG, Schaeffer CA, Erickson JW, Burt SK. All-atom models for the non-nucleoside binding site of HIV-1 reverse transcriptase complexed with inhibitors: a 3D QSAR approach. J Med Chem 1996;39:1645-1650.
34. Mager PP. A check on rational drug design: molecular simulation of the allosteric inhibition of HIV-1 reverse transcriptase. Med Res Rev 1997;17:235-276.
35. Setlik RF, Shibata M, Ornstein RL, Rein R. A model of HIV-1 reverse transcriptase: possible mechanisms for AZT resistance. Mol Eng 1995;5:81-88.
36. Smith RH Jr, Michejda CJ, Hughes SH, Arnold E, Janssen PAJ, Smith MBK. Structure and mechanism of action of nonnucleoside inhibitors of HIV-1 reverse transcriptase: strategies to combat drug resistance. Theochem 1998;423:67-77.
37. Yadav PNS, Das K, Ding J, Arnold E, Yadav JS, Modak MJ. Structure-based design of inhibitors of HIV-1 reverse transcriptase: a potential class of bidentate nonnucleoside inhibitors. Theochem 1998;423:101-111.
38. Smith RH Jr, Jorgensen WL, Tirado-Rives J, Lamb ML, Janssen PAJ, Michejda CJ, Smith MB Kroeger. Prediction of binding affinities of TIBO inhibitors of HIV-1 reverse transcriptase using Monte Carlo simulations in a linear response method. J Med Chem 1998;41:5272-5286.
39. Bebenek K, Beard WA, Darden TA, Li L, Prasad R, Luxon BA, Gorenstein DG, Wilson SH, Kunkel TA. A minor groove binding track in reverse transcriptase. Nature Struct Biol 1997;4:194-197.
40. Pearlman D, Case DA, Caldwell JW, Ross WS, Cheatham TE III, Ferguson DM, Seibel GL, Singh UC, Weiner PK, Kollman PA. AMBER 4.1. San Francisco: University of California, 1995.
41. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
42. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta S Jr, Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 1984;106: 765-784.
43. Weiner SJ, Kollman PA, Nguyen DT, Case DA. An all atom force field for simulations of proteins and nucleic acids. J Comp Chem 1986;7:230-252.
44. van Gunsteren WF, Berendsen HJC. Algorithms for macromolecular dynamics and constraint dynamics. Mol Phys 1997;34:1311-1327.
45. Fox T, Kollman PA. The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: how well is the X-ray structure "maintained"? Proteins 1996;25:315-334.
46. Brooks III CL. Methodological advances in molecular dynamics simulations of biological systems. Curr Opin Struct Biol 1995;5:211-215.
47. Harte WE Jr, Swaminathan S, Beveridge DL. Molecular dynamics of HIV-1 protease. Proteins 1992;13:175-194.
48. Hermann T, Heumann H. Strained template under the thumbs: how reverse trancriptase of human immunodeficiency virus type 1 moves along its template. Eur J Biochem 1996;242:98-1003.
49. Sarafianos SG, Das K, Ding J, Hsiou Y, Hughes SH, Arnold E. Current perspectives on mechanisms of HIV-1 reverse transcriptase inhibition by nonnucleoside inhibitors. In: Bentley PH, O'Hanlon PJ, editors. Anti-infectives: recent advances in chemistry and structure-activity relationships. London: Royal Society of Chemistry Information Services, 1997:328-334.
50. Carson M. Ribbon models of macromolecules. J Mol Graph 1987;5:103-106.