期刊
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
卷 138, 期 50, 页码 16283-16298出版社
AMER CHEMICAL SOC
DOI: 10.1021/jacs.6b06856
关键词
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资金
- Polish Ministry of Science and Higher Education (Iuventus Plus program) [0478/IP3/2015/73]
- Spanish Ministerio de Economia y Competitividad [CTQ2015-66223-C2-1-P]
- Generalitat Valenciana [PrometeoII/2014/022]
- Universitat Jaume I [P1 1B2014-26]
- USA National Institute of Health [NIH R01 GM065368]
HIV-1 Protease (HIV-1 PR) is one of the three enzymes essential for the replication process of HIV-1 virus, which explains why it has been the main target for design of drugs against acquired immunodeficiency syndrome (AIDS). This work is focused on exploring the proteolysis reaction catalyzed by HIV-1 PR, with special attention to the dynamic and electrostatic effects governing its catalytic power. Free energy surfaces for all possible mechanisms have been computed in terms of potentials of mean force (PMFs) within hybrid QM/MM potentials, with the QM subset of atoms described at semiempirical (AM1) and DFT (M06-2X) level. The results suggest that the most favorable reaction mechanism involves formation of a gem-diol intermediate, whose decomposition into the product complex would correspond to the rate-limiting step. The agreement between the activation free energy of this step with experimental data, as well as kinetic isotope effects (KIEs), supports this prediction. The role of the protein dynamic was studied by protein isotope labeling in the framework of the Variational Transition State Theory. The predicted enzyme KIEs, also very close to the values measured experimentally, reveal a measurable but small dynamic effect. Our calculations show how the contribution of dynamic effects to the effective activation free energy appears to be below 1 kcal.mol(-1). On the contrary, the electric field created by the protein in the active site of the enzyme emerges as being critical for the electronic reorganization required during the reaction. These electrostatic properties of the active site could be used as a mold for future drug design.
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