ArticleJournal of biomolecular structure & dynamics2018
Coupled molecular dynamics and continuum electrostatic method to compute the ionization pKa's of proteins as a function of pH. Test on a large set of proteins.
Article in Journal of biomolecular structure & dynamics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed, 14 citations in OpenAlex.
- Testing a Heterogeneous Polarizable Continuum Model against Exact Poisson Boundary Conditions.Journal of chemical theory and computation · 2025Article
- Electrostatic Environment of Proteorhodopsin Affects the pKa of Its Buried Primary Proton Acceptor.Biophysical journal · 2020Article
- Outline of an experimental design aimed to detect a protein A mirror image in solution.PeerJ physical chemistry · 2019Article
- A comprehensive analysis of the computed tautomer fractions of the imidazole ring of histidines in Loligo vulgaris.Journal of biomolecular structure & dynamics · 2018Article
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Authors and funding
3 authors at 3 institutions in 3 countries.
Funding
Abstract
A computational method, to predict the pKa values of the ionizable residues Asp, Glu, His, Tyr, and Lys of proteins, is presented here. Calculation of the electrostatic free-energy of the proteins is based on an efficient version of a continuum dielectric electrostatic model. The conformational flexibility of the protein is taken into account by carrying out molecular dynamics simulations of 10 ns in implicit water. The accuracy of the proposed method of calculation of pKa values is estimated from a test set of experimental pKa data for 297 ionizable residues from 34 proteins. The pKa-prediction test shows that, on average, 57, 86, and 95% of all predictions have an error lower than 0.5, 1.0, and 1.5 pKa units, respectively. This work contributes to our general understanding of the importance of protein flexibility for an accurate computation of pKa, providing critical insight about the significance of the multiple neutral states of acid and histidine residues for pKa-prediction, and may spur significant progress in our effort to develop a fast and accurate electrostatic-based method for pKa-predictions of proteins as a function of pH.
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