Substrate shape determines specificity of recognition for HIV-1 protease: Analysis of crystal structures of six substrate complexes

Structure

Volumn 10, Issue 3, 2002, Pages 369-381

  Prabu Jeyabalan, Moses ^a   Nalivaika, Ellen ^a   Schiffer, Celia A ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

Crystal structure; HIV 1 protease; Specificity; Substrate recognition; Toroidal shape; Water structure

Indexed keywords

AMINO ACID; PEPTIDE; PROTEINASE; WATER;

AMINO ACID SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; ENZYME BINDING; ENZYME DEGRADATION; ENZYME SPECIFICITY; HUMAN IMMUNODEFICIENCY VIRUS 1; HYDROGEN BOND; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; STRUCTURE ANALYSIS; WATER STRUCTURE;

BINDING SITES; CRYSTALLOGRAPHY, X-RAY; GENE PRODUCTS, GAG; HIV PROTEASE; HUMANS; HYDROGEN BONDING; LIGANDS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SUBSTRATE SPECIFICITY; WATER;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; RNA VIRUSES;

EID: 0036121219     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(02)00720-7     Document Type: Article

References (64)

1. International response to the HIV/AIDS epidemic: Planning for success
2. Antiretroviral therapy for HIV infection in 1988: Updated recommendations of the International AIDS Society - USA Panel
3. Report of the NIH panel to define principles of therapy of HIV infection
4. Guidelines for the use of antiretroviral agents in HIV-1 infected adults and adolescents
5. Prevention and treatment of pediatric HIV infection
6. Decline in deaths from AIDS due to new antiretrovirals
7. Improved survival among HIV-infected individuals following initiation of antiretroviral therapy
8. New drug combinations against highly drug-resistant HIV isolates in vitro
9. HIV drug resistance and the other causes of treatment failure
10. Viral resistance patterns selected by antiretroviral drugs and their potential to guide treatment choice
11. Viral resistance and the selection of antiretroviral combinations
12. Drug resistance and its implications in the management of HIV infection
13. Changing treatment strategies and goals
14. HIV pathogenesis and treatment strategies
15. Human immunodeficiency virus type 1 protease inhibitors
16. HIV-protease inhibitors
17. Structure-based inhibitors of HIV-1 protease
18. Fidelity of HIV-1 reverse transcriptase copying RNA in vitro
19. The accuracy of reverse transcriptase from HIV-1
20. Fidelity of two retroviral reverse transcriptases during DNA-dependent DNA synthesis in vitro
21. HIV population dynamics in vivo: Implications for genetic variation, pathogenesis and therapy
22. HIV viral dynamics
23. Genetic variation in HTLV-III/LAV over time in patients with AIDS or at risk for AIDS
24. Dynamics of HIV-1 replication in vivo
25. Active human immunodeficiency virus protease is required for viral infectivity
26. The HIV-1 protease as a therapeutic target for AIDS
27. Crystal structures of the inactive D30N mutant of feline immunodeficiency virus protease complexed with a substrate and an inhibitor
28. How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease
29. Structural implications of drug-resistant mutants of HIV-1 protease: High-resolution crystal structures of the mutant protease/substrate analogue complexes
30. Conserved folding in retroviral proteases: Crystal structure of a synthetic HIV-1 protease
31. Defining the level of human immunodeficiency virus type 1 (HIV-1) protease activity required for HIV-1 particle maturation and infectivity
32. Trans-dominant inhibitory human immunodeficiency virus type 1 protease monomers prevent protease activation and virion maturation
33. Structural and kinetic analysis of drug resistant mutants of HIV-1 protease
34. Use of steady state kinetic methods to elucidate the kinetic and chemical mechanisms of retroviral proteases
35. Substrate-dependent mechanisms in the catalysis of human immunodeficiency virus protease
36. Kinetics analysis of consecutive HIV proteolytic cleavages of the Gag-Pol polyprotein
37. Drug-resistant HIV-1 proteases identify enzyme residues important for substrate selection and catalytic rate
38. Inhibition and catalytic mechanism of HIV-1 aspartic protease
39. Comparison of the substrate specificity of the human T-cell leukemia virus and human immunodeficiency virus proteinases
40. Crystallographic analysis of human immunodeficiency virus 1 protease with an analog of the conserved CA-p2 substrate - Interactions with frequently occurring glutamic acid residue at P2′ position of substrates
41. Energy calculations and analysis of HIV-1 protease-inhibitor crystal structures
42. The interpretation of protein structures: Estimation of static accessibility
43. Shape complementarity at protein/protein interfaces
44. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
45. Structure of HIV-1 protease with KNI-272, a tight-binding transition-state analog containing allophyenylnorstatine
46. Human immunodeficiency virus reverse transcriptase and protease sequence database
47. Distribution of water around amino acid residues in proteins
48. Analysis of protein main-chain solvation as a function of secondary structure
49. Buried waters and internal cavities in monomeric proteins
50. Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme
51. Locating and characterizing binding sites on proteins
52. Role of water in plasticity, stability, and action of proteins: The crystal structures of lysozyme at very low levels of hydration
53. Hydrogen bonding, hydrophobic interactions, and failure of the rigid receptor hypothesis
54. Autoprocessing: An essential step for the activation of HIV-1 protease
55. Large scale purification and refolding of HIV-1 protease from Escherichia coli inclusion bodies
56. Crystal structure of a complex of HIV-1 protease with a dihydroxyethylene-containing inhibitor: Comparisons with molecular modeling
57. Oscillation data reduction program
58. Crystallography and NMR system: A new software suite for macromolecular structure determination
59. Molecular recognition of macrocyclic peptidomimetic inhibitors by HIV-1 protease
60. CHAIN - A crystallographic modeling program
61. Procheck: A program to check the stereochemical quality of protein structures
62. The MIDAS display system