ArticleProteins2011
In silico modeling of pH-optimum of protein-protein binding.
Article in Proteins, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Functional and Structural Characterization of Pathogenicity of Human Arginine-Histidine Variants.Journal of computational biophysics and chemistry · 2025Article
- Computing the pH-Dependent Thermodynamics of the Allostery between Dimerization and Palmitate Binding in β-Lactoglobulin.The journal of physical chemistry. B · 2025Article
- Online Mixed-Bed Ion Exchange Chromatography for Native Top-Down Proteomics of Complex Mixtures.Journal of proteome research · 2024Article
- How to Personalize General Anesthesia-A Prospective Theoretical Approach to Conformational Changes of Halogenated Anesthetics in Fire Smoke Poisoning.International journal of molecular sciences · 2024Article
- 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
- Electrostatics in Computational Biophysics and Its Implications for Disease Effects.International journal of molecular sciences · 2022Review
- Approach to Study pH-Dependent Protein Association Using Constant-pH Molecular Dynamics: Application to the Dimerization of β-Lactoglobulin.Journal of chemical theory and computation · 2022Article
- Measuring how two proteins affect each other's net charge in a crowded environment.Protein science : a publication of the Protein Society · 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
- A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation.Mathematical biosciences and engineering : MBE · 2020Article
- DelPhi Suite: New Developments and Review of Functionalities.Journal of computational chemistry · 2019Article
- Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling.Journal of chemical theory and computation · 2018Article
- Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes.Proteins · 2017Article
- Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols.Journal of computational chemistry · 2016Article
- DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs.Bioinformatics (Oxford, England) · 2016Article
- Computation of pH-dependent binding free energies.Biopolymers · 2016Review
- Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria.PLoS computational biology · 2015Article
- Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies.The journal of physical chemistry. B · 2015Article
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3 authors.
Funding
Abstract
Protein-protein association is a pH-dependent process and thus the binding affinity depends on the local pH. In vivo the association occurs in a particular cellular compartment, where the individual monomers are supposed to meet and form a complex. Since the monomers and the complex exist in the same micro environment, it is plausible that they coevolved toward its properties, in particular, toward the characteristic subcellular pH. Here we show that the pH at which the monomers are most stable (pH-optimum) or the pH at which stability is almost pH-independent (pH-flat) of monomers are correlated with the pH-optimum of maximal affinity (pH-optimum of binding) or pH interval at which affinity is almost pH-independent (pH-flat of binding) of the complexes made of the corresponding monomers. The analysis of interfacial properties of protein complexes demonstrates that pH-dependent properties can be roughly estimated using the interface charge alone. In addition, we introduce a parameter beta, proportional to the square root of the absolute product of the net charges of monomers, and show that protein complexes characterized with small or very large beta tend to have neutral pH-optimum. Further more, protein complexes made of monomers carrying the same polarity net charge at neutral pH have either very low or very high pH-optimum of binding. These findings are used to propose empirical rule for predicting pH-optimum of binding provided that the amino acid compositions of the corresponding monomers are available.
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