Quantum-Chemical Study of the Catalytic Mechanism of Aspartic Proteinases

Antonov, V.K.; Alexandrov, Svobodan

doi:10.1007/978-1-4684-6012-4_17

Advances in Experimental Medicine and Biology

1991

DOI: 10.1007/978-1-4684-6012-4_17

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Quantum-Chemical Study of the Catalytic Mechanism of Aspartic Proteinases

V.K. Antonov¹,

Svobodan Alexandrov²

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2018

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Cited by 2 publications

References 7 publications

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Analysis of the structure of HIV-1 protease complexed with a hexapeptide inhibitor. Part II: Molecular dynamic studies of the active site region

et al. 1997

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Six models of the catalytic site of HIV-1 protease complexed with a reduced peptide inhibitor, MVT-101, were investigated. These studies focused on the details of protonation of the active site, its total net charge and hydrogen bonding pattern, which was consistent with both the observed coplanar configuration of the acidic groups of the catalytic aspartates (Asp-25 and Asp-125) and the observed binding mode of the inhibitor. Molecular dynamic simulations using AMBER 4.0 indicated that the active site should be neutral. The planarity of the aspartate dyad may be due to the formation of two hydrogen bonds: one between the inner O delta 1 oxygen atoms of the two catalytic aspartates and another between the O delta 2 atom of Asp-125 and the nitrogen atom of the reduced peptide bond of the bound inhibitor. This would require two additional protonations, either of both aspartates, or of one Asp and the amido nitrogen atom of Nle-204. Our results favor the Asp-inhibitor protonation but the other one is not excluded. Implications of these findings for the mechanism of enzymatic catalysis are discussed. Dynamic properties of the hydrogen bond network in the active site and an analysis of the interaction energy between the inhibitor and the protease are presented.

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Analysis of the structure of HIV-1 protease complexed with a hexapeptide inhibitor. Part II: Molecular dynamic studies of the active site region

et al. 1997

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Kinetics of enzymatic reactions in the production of fish protein hydrolysates

Novikov

Derkach

Kuchina

et al. 2018

Journal of Dispersion Science and Technology

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Quantum-Chemical Study of the Catalytic Mechanism of Aspartic Proteinases

Cited by 2 publications

References 7 publications

Analysis of the structure of HIV-1 protease complexed with a hexapeptide inhibitor. Part II: Molecular dynamic studies of the active site region

Analysis of the structure of HIV-1 protease complexed with a hexapeptide inhibitor. Part II: Molecular dynamic studies of the active site region

Kinetics of enzymatic reactions in the production of fish protein hydrolysates

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