ArticleThe journal of physical chemistry. B2022
Characterizing Protein Protonation Microstates Using Monte Carlo Sampling.
Article in The journal of physical chemistry. B, 2022. 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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Who cites it
9 citing papers in PubMed.
- Kinase inhibitors can change protonation or tautomeric state upon binding.bioRxiv : the preprint server for biology · 2026Article
- Roles of Hydration in Protein-Ligand Binding: Passive or Active Participant?The journal of physical chemistry. A · 2025Article
- Allostery without Conformational Change: A Native Mass Spectrometry Perspective.The journal of physical chemistry. B · 2025Article
- Photosystem II: Probing Protons and Breaking Barriers.Biochemistry · 2025Review
- Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications.Journal of chemical theory and computation · 2025Article
- Contribution of Protonation to the Dielectric Relaxation Arising from Bacteriopheophytin Reductions in the Photosynthetic Reaction Centers ofBiomolecules · 2024Article
- Biomolecular Electrostatic Phenomena: An Evergreen Field.The journal of physical chemistry. B · 2023Article
- Tools for analyzing protonation states and for tracing proton transfer pathways with examples from the Rb. sphaeroides photosynthetic reaction centers.Photosynthesis research · 2023Article
- Electrostatics in Computational Biophysics and Its Implications for Disease Effects.International journal of molecular sciences · 2022Review
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Proteins are polyelectrolytes with acidic and basic amino acids Asp, Glu, Arg, Lys, and His, making up ≈25% of the residues. The protonation state of residues, cofactors, and ligands defines a "protonation microstate". In an ensemble of proteins some residues will be ionized and others neutral, leading to a mixture of protonation microstates rather than in a single one as is often assumed. The microstate distribution changes with pH. The protein environment also modifies residue proton affinity so microstate distributions change in different reaction intermediates or as ligands are bound. Particular protonation microstates may be required for function, while others exist simply because there are many states with similar energy. Here, the protonation microstates generated in Monte Carlo sampling in MCCE are characterized in HEW lysozyme as a function of pH and bacterial photosynthetic reaction centers (RCs) in different reaction intermediates. The lowest energy and highest probability microstates are compared. The Δ
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