ArticleProteins2017
Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes.
Article in Proteins, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- CAP: Commutative algebra prediction of protein-nucleic acid binding affinities.Machine learning: science and technology · 2025Article
- A role for pH dynamics regulating transcription factor DNA-binding selectivity.Nucleic acids research · 2025Article
- PKAD-2: New entries and expansion of functionalities of the database of experimentally measured pKa's of proteins.Journal of computational biophysics and chemistry · 2023Article
- Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome.Frontiers in molecular biosciences · 2023Article
- Electrostatics in Computational Biophysics and Its Implications for Disease Effects.International journal of molecular sciences · 2022Review
- The pH Effects on SARS-CoV and SARS-CoV-2 Spike Proteins in the Process of Binding to hACE2.Pathogens (Basel, Switzerland) · 2022Article
- The pH Effects on SARS-CoV and SARS-CoV-2 Spike Proteins in the Process of Binding to hACE2.Research square · 2021Article
- Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease.International journal of molecular sciences · 2021Article
- Electrostatic features for nucleocapsid proteins of SARS-CoV and SARS-CoV-2.Mathematical biosciences and engineering : MBE · 2021Article
- Article
- Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi.Journal of chemical information and modeling · 2020Article
- Computational Approaches to Prioritize Cancer Driver Missense Mutations.International journal of molecular sciences · 2018Review
- Prediction of pKa Values for Neutral and Basic Drugs based on Hybrid Artificial Intelligence Methods.Scientific reports · 2018Article
- Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver.Bioinformatics (Oxford, England) · 2018Article
- Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents.Frontiers in molecular biosciences · 2018Article
- VEGF and VEGFR2 bind to similar pH-sensitive sites on fibronectin, exposed by heparin-mediated conformational changes.The Journal of biological chemistryArticle
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2 authors.
Funding
Abstract
Protein-nucleic acid interactions play a crucial role in many biological processes. This work investigates the changes of pKa values and protonation states of ionizable groups (including nucleic acid bases) that may occur at protein-nucleic acid binding. Taking advantage of the recently developed pKa calculation tool DelphiPka, we utilize the large protein-nucleic acid interaction database (NPIDB database) to model pKa shifts caused by binding. It has been found that the protein's interfacial basic residues experience favorable electrostatic interactions while the protein acidic residues undergo proton uptake to reduce the energy cost upon the binding. This is in contrast with observations made for protein-protein complexes. In terms of DNA/RNA, both base groups and phosphate groups of nucleotides are found to participate in binding. Some DNA/RNA bases undergo pKa shifts at complex formation, with the binding process tending to suppress charged states of nucleic acid bases. In addition, a weak correlation is found between the pH-optimum of protein-DNA/RNA binding free energy and the pH-optimum of protein folding free energy. Overall, the pH-dependence of protein-nucleic acid binding is not predicted to be as significant as that of protein-protein association. Proteins 2017; 85:282-295. © 2016 Wiley Periodicals, Inc.
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