ArticleProteins2014
Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.
Article in Proteins, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
- Benchmark Study for Calculations of pKa Values of Metal Ligands in Proteins.Journal of chemical theory and computation · 2026Article
- Molecular Origins of pH Gradients in Charge-Regulated Biomolecular Condensates.bioRxiv : the preprint server for biology · 2026Article
- Biomolecular Condensates Act as Distinct Solvation Environments That Reshape Amino Acid pJournal of the American Chemical Society · 2026Article
- GPU-Accelerated Implementation of Constant-pH Molecular Dynamics in NAMD.Journal of chemical information and modeling · 2025Article
- Adding the AMBER 14SB Force Field to the Stochastic Titration CpHMD Method.Journal of chemical theory and computation · 2025Article
- Characterizing RNA Oligomers Using Stochastic Titration Constant-pH Metadynamics Simulations.Journal of chemical information and modeling · 2025Article
- Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications.Journal of chemical theory and computation · 2025Article
- Constant pH Simulation with FMM Electrostatics in GROMACS. (B) GPU Accelerated Hamiltonian Interpolation.Journal of chemical theory and computation · 2025Article
- KaMLs for Predicting Protein pJournal of chemical theory and computation · 2025Article
- KaMLs for Predicting Protein pbioRxiv : the preprint server for biology · 2025Article
- Force Field Limitations of All-Atom Continuous Constant pH Molecular Dynamics.The journal of physical chemistry. B · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- How to Sample Dozens of Substitutions per Site with λ Dynamics.Journal of chemical theory and computation · 2024Article
- How is Membrane Permeation of Small Ionizable Molecules Affected by Protonation Kinetics?The journal of physical chemistry. B · 2024Article
- The Electronic Structure of Genome Editors from the First Principles.Electronic structure (Bristol, England) · 2023Article
- GPU-Accelerated All-Atom Particle-Mesh Ewald Continuous Constant pH Molecular Dynamics in Amber.Journal of chemical theory and computation · 2022Article
- Review
- Constant pH molecular dynamics simulations: Current status and recent applications.Current opinion in structural biology · 2022Review
- Increasing the Realism ofJournal of chemical theory and computation · 2022Article
- Extending the Stochastic Titration CpHMD to CHARMM36m.The journal of physical chemistry. B · 2022Article
6 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMD(MSλD)). In the CPHMD(MSλD) framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMD(MSλD) simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal protein L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMD(MSλD) framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules-proteins and nucleic acids is now possible.
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