Energy calculations and analysis of HIV-1 protease-inhibitor crystal structures
| Autor: | Irene T. Weber, Clare E. Sansom, Martine Prévost, Shoshana Wodak, Alexander Wlodawer, Alia Gustchina, Jean Richelle |
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| Rok vydání: | 1994 |
| Předmět: |
Models
Molecular Chemical Phenomena Stereochemistry medicine.medical_treatment Molecular Sequence Data Bioengineering Biochemistry HIV-1 protease HIV Protease medicine HIV Protease Inhibitor Molecule Amino Acid Sequence Molecular Biology Protease biology Chemistry Hydrogen bond Chemistry Physical Active site Hydrogen Bonding Interaction energy HIV Protease Inhibitors Enzyme inhibitor biology.protein HIV-1 Thermodynamics Crystallization Biotechnology |
| Zdroj: | Protein engineering. 7(3) |
| ISSN: | 0269-2139 |
| Popis: | The interactions between HIV-1 protease and its bound inhibitors have been investigated by molecular mechanics calculations and by analysis of crystal structures of the complexes in order to determine general rules for inhibitor and substrate binding to the protease. Fifteen crystal structures of HIV-1 protease with different peptidomimetic inhibitors showed conservation of hydrogen bond interactions between the main chain C = O and NH groups of the inhibitors and the C = O and NH groups of the protease extending from P3 C = O to P3' NH. The mean length of the hydrogen bonds between the inhibitor and the flexible flaps and the conserved water molecule (2.9 A) is slightly shorter than the mean length of hydrogen bonds between the inhibitor and the more rigid active site region (3.1 A) of the protease. The two hydrogen bonds between the conserved water and P2 and P1' carbonyl oxygen atoms of the inhibitor are the shortest and are predicted to be important for the tight binding of inhibitors. Molecular mechanics analysis of three crystal structures of HIV-1 protease with different inhibitors with independent calculations using the programs Discover and Brugel gave an estimate of 56-68% for the contribution of all the inhibitor main chain atoms to the total calculated protease-inhibitor interaction energy. The contribution of individual inhibitor residues to the interaction energy was calculated using Brugel. The main chain atoms of residue P2 had a consistently large favorable contribution to the total interaction energy, probably due to the presence of the two short hydrogen bonds to the flexible flap.(ABSTRACT TRUNCATED AT 250 WORDS) |
| Databáze: | OpenAIRE |
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