期刊
CHEMISTRY-A EUROPEAN JOURNAL
卷 24, 期 43, 页码 11200-11210出版社
WILEY-V C H VERLAG GMBH
DOI: 10.1002/chem.201802035
关键词
enzymes; peptides; quantum chemical topology; quantum atoms; reaction mechanisms
资金
- EPSRC [EP/K005472]
- EPSRC DTA studentship
- EPSRC [EP/K005472/1] Funding Source: UKRI
The reaction mechanism in an active site is of the utmost importance when trying to understand the role that an enzyme plays in biological processes. In a recently published paper [Theor. Chem. Acc. 2017, 136, 86], we formalised the Relative Energy Gradient (REG) method for automating an Interacting Quantum Atoms (IQA) analysis. Here, the REG method is utilised to determine the mechanism of peptide hydrolysis in the aspartic active site of the enzyme HIV-1 Protease. Using the REG method along with the IQA approach we determine the mechanism of peptide hydrolysis without employing any arbitrary parameters and with remarkable ease (albeit at large computational cost: the system contains 133 atoms, which means that there are 17689 individual IQA terms to be calculated). When REG and IQA work together it is possible to determine a reaction mechanism at atomistic resolution from data directly derived from quantum calculations, without arbitrary parameters. Moreover, the mechanism determined by this novel method gives concrete insight into how the active site residues catalyse peptide hydrolysis.
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