ArticleChemistry (Weinheim an der Bergstrasse, Germany)2018
Using the Relative Energy Gradient Method with Interacting Quantum Atoms to Determine the Reaction Mechanism and Catalytic Effects in the Peptide Hydrolysis in HIV-1 Protease.
Article in Chemistry (Weinheim an der Bergstrasse, Germany), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 42 citations in OpenAlex.
- Interacting Quantum Atoms Analysis of Covalent and Collective Interactions in Single Elongated Carbon-Carbon Bonds.Molecules (Basel, Switzerland) · 2025Article
- Metal-Ligand Cooperation in N-H Activation: Bridging Electron-Pushing Formalism and Energy Descriptors.Inorganic chemistry · 2025Article
- Application of the FFLUX Force Field to Molecular Crystals: A Study of Formamide.Journal of chemical theory and computation · 2023Article
- How to Compute Atomistic Insight in DFT Clusters: The REG-IQA Approach.Journal of chemical information and modeling · 2023Article
- Linking the Interatomic Exchange-Correlation Energy to ExperimentalThe journal of physical chemistry. A · 2023Article
- Non-covalent interactions from a Quantum Chemical Topology perspective.Journal of molecular modeling · 2022Article
- An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Analysis of the Anomeric Effect.Molecules (Basel, Switzerland) · 2022Article
- Interacting Quantum Atoms-A Review.Molecules (Basel, Switzerland) · 2020Review
- An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Study of the Halogen Bond with Explicit Analysis of Electron Correlation.Molecules (Basel, Switzerland) · 2020Article
- Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design.ACS omega · 2020Article
- Aqueous pKCommunications chemistry · 2020Article
- Does the Intra-Atomic Deformation Energy of Interacting Quantum Atoms Represent Steric Energy?ChemistryOpen · 2019Article
- A relative energy gradient (REG) study of the planar and perpendicular torsional energy barriers in biphenyl.Theoretical chemistry accounts · 2019Article
- Using the Relative Energy Gradient Method with Interacting Quantum Atoms to Determine the Reaction Mechanism and Catalytic Effects in the Peptide Hydrolysis in HIV-1 Protease.Chemistry (Weinheim an der Bergstrasse, Germany) · 2018Article
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3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
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 17 689 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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