ArticleBiophysical chemistry
Molecular dynamics study of human carbonic anhydrase II in complex with Zn(2+) and acetazolamide on the basis of all-atom force field simulations.
Article in Biophysical chemistry. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 22 citations in OpenAlex.
- MM/GBSA prediction of relative binding affinities of carbonic anhydrase inhibitors: effect of atomic charges and comparison with Autodock4Journal of computer-aided molecular design · 2023Article
- Structural Characterization of Carbonic Anhydrase-Arylsulfonamide Complexes Using Ultraviolet Photodissociation Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2021Article
- Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.Journal of chemical information and modeling · 2020Article
- Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.ChemRxiv : the preprint server for chemistry · 2020Article
- Gibbs Free-Energy Gradient along the Path of Glucose Transport through Human Glucose Transporter 3.ACS chemical neuroscience · 2018Article
- Force Field Parametrization of Metal Ions from Statistical Learning Techniques.Journal of chemical theory and computation · 2018Article
- Affinity and path of binding xylopyranose unto E. coli xylose permease.Biochemical and biophysical research communications · 2017Article
- Network of Conformational Transitions Revealed by Molecular Dynamics Simulations of the Carbonic Anhydrase II Apo-Enzyme.ACS omega · 2017Article
- Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics.Biochemical and biophysical research communications · 2017Article
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4 authors at 1 institution in 1 country.
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Abstract
Human carbonic anhydrase II (hCAII) represents an ultimate example of the perfectly efficient metalloenzymes, which is capable of catalyzing the hydration of carbon dioxide with a rate approaching the diffusion controlled limit. Extensive experimental studies of this physiologically important metalloprotein have been done to elucidate the fundamentals of its enzymatic actions: what residues anchor the Zn(2+) (or another divalent cation) at the bottom of the binding pocket; how the relevant residues work concertedly with the divalent cation in the reversible conversions between CO2 and HCO3(-); what are the protonation states of the relevant residues and acetazolamide, an inhibitor complexed with hCAII, etc. In this article, we present a detailed computational study on the basis of the all-atom CHARMM force field where Zn(2+) is represented with a simple model of divalent cation using the transferrable parameters available from the current literature. We compute the hydration free energy of Zn(2+), the characteristics of hCAII-Zn(2+) complexation, and the absolute free energy of binding acetazolamide to the hCAII-Zn(2+) complex. In each of these three problems, our computed results agree with the experimental data within the known margin of error without making any case-by-case adjustments to the parameters. The quantitatively accurate insights we gain in this all-atom molecular dynamics study should be helpful in the search and design of more specific inhibitors of this and other carbonic anhydrases.
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