ArticlePLoS computational biology2014
Protein-protein docking with dynamic residue protonation states.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Chemically encoded pH-tunable covalent adhesion by a bacterial thioester domain.Science advances · 2026Article
- Selection of Novel DNA Aptamers against HPV16 Biomarker, E6: AnACS omega · 2026Article
- Thymoquinone and 3HQ synergy inhibits CTX-M-15 ESBL.Biomolecules & biomedicine · 2025Article
- Review
- Fine-tuning pH sensor H98 by remote essential residues in the hydrogen-bond network of mTASK-3.International journal of biological macromolecules · 2024Article
- Article
- Cysteine Cathepsins Inhibition Affects Their Expression and Human Renal Cancer Cell Phenotype.Cancers · 2020Article
- Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data.ACS central science · 2019Article
- Human Albumin Impairs Amyloid β-peptide Fibrillation Through its C-terminus: From docking Modeling to Protection Against Neurotoxicity in Alzheimer's disease.Computational and structural biotechnology journal · 2019Article
- Structural and kinetic basis for the selectivity of aducanumab for aggregated forms of amyloid-β.Scientific reports · 2018Article
- Structure-based cross-docking analysis of antibody-antigen interactions.Scientific reports · 2017Article
- The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.Journal of chemical theory and computation · 2017Article
- Protocols for Molecular Modeling with Rosetta3 and RosettaScripts.Biochemistry · 2016Review
- Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling.Biophysical journal · 2016Article
- An Integrated Framework Advancing Membrane Protein Modeling and Design.PLoS computational biology · 2015Article
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3 authors.
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Abstract
Protein-protein interactions depend on a host of environmental factors. Local pH conditions influence the interactions through the protonation states of the ionizable residues that can change upon binding. In this work, we present a pH-sensitive docking approach, pHDock, that can sample side-chain protonation states of five ionizable residues (Asp, Glu, His, Tyr, Lys) on-the-fly during the docking simulation. pHDock produces successful local docking funnels in approximately half (79/161) the protein complexes, including 19 cases where standard RosettaDock fails. pHDock also performs better than the two control cases comprising docking at pH 7.0 or using fixed, predetermined protonation states. On average, the top-ranked pHDock structures have lower interface RMSDs and recover more native interface residue-residue contacts and hydrogen bonds compared to RosettaDock. Addition of backbone flexibility using a computationally-generated conformational ensemble further improves native contact and hydrogen bond recovery in the top-ranked structures. Although pHDock is designed to improve docking, it also successfully predicts a large pH-dependent binding affinity change in the Fc-FcRn complex, suggesting that it can be exploited to improve affinity predictions. The approaches in the study contribute to the goal of structural simulations of whole-cell protein-protein interactions including all the environmental factors, and they can be further expanded for pH-sensitive protein design.
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