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Constant pH molecular dynamics simulations: Current status and recent applications

CURRENT OPINION IN STRUCTURAL BIOLOGY (2022)

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Summary: A comprehensive computational study is presented on the mechanism of fluoride permeation through fluoride channels. The permeation mechanism of the F- anion is established, and the microscopic determinants of F- selectivity are revealed. The essential nature of electronic polarization during F- permeation is also demonstrated through computational modeling.

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Article Chemistry, Medicinal

Exploring the pH- and Ligand-Dependent Flap Dynamics of Malarial Plasmepsin II

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Summary: Malaria remains a global health threat with over 400,000 deaths in 2019. Understanding the conformational dynamics of plasmepsins at different pH and ligand conditions is crucial for antimalarial therapeutics. The study revealed the impact of substrate binding on the catalytic dyads D34 and D214, laying the groundwork for designing more potent and selective inhibitors for the entire family of plasmepsins.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2022)

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Article Chemistry, Physical

Approach to Study pH-Dependent Protein Association Using Constant-pH Molecular Dynamics: Application to the Dimerization of β-Lactoglobulin

Lucie da Rocha et al.

Summary: This research presents a detailed description of pH-dependent protein-protein association using constant-pH molecular dynamics (MD) simulations, with a focus on the dimerization of beta-lactoglobulin (BLG). Various analyses were performed to explore the effects of pH on the free energy and structure of the protein association. The findings highlight the importance of pH in protein associations.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2022)

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Article Biochemistry & Molecular Biology

pH and the Breast Cancer Recurrent Mutation D538G Affect the Process of Activation of Estrogen Receptor α

Vinicius M. de Oliveira et al.

Summary: In this study, computational and experimental techniques were used to investigate the dynamics of the activation process of ERα under different pH conditions and in the presence of a specific mutation. The results showed that the D538G mutation, associated with an increase in pH, promoted a strong stabilization of the active state of ERα. Additionally, the main protein regions that significantly influenced the activation process under different pH conditions were identified, potentially providing targets for the treatment of hormone-resistant breast cancer tumors.

BIOCHEMISTRY (2022)

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Article Biophysics

Proton coupling and the multiscale kinetic mechanism of a peptide transporter

Chenghan Li et al.

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BIOPHYSICAL JOURNAL (2022)

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Article Chemistry, Medicinal

Novel US-CpHMD Protocol to Study the Protonation-Dependent Mechanism of the ATP/ADP Carrier

Nuno F. B. Oliveira et al.

Summary: In this study, we designed a protocol combining constant-pH molecular dynamics (CpHMD) simulations with an umbrella sampling (US) scheme (US-CpHMD) to investigate the mechanism of ADP/ATP transport by the mitochondrial membrane carrier protein AAC. Our results showed that AAC exhibited selectivity in the import of ADP compared to ATP, but no selectivity in the export process. We also observed transient protonation of both substrates during the import process, which could counteract the unfavorable mitochondrial membrane potential. These findings provide important insights into the structural features and electrostatic interactions involved in the protein function and demonstrate the potential of the US-CpHMD protocol in studying other membrane protein transport processes.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2022)

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Article Chemistry, Physical

Constant pH Coarse-Grained Molecular Dynamics with Stochastic Charge Neutralization

Alexander van Teijlingen et al.

Summary: This study develops a simulation method for biochemical systems that considers pH dependence and demonstrates its effectiveness through experimental validation.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2022)

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Article Multidisciplinary Sciences

Molecular determinants of pH sensing in the proton-activated chloride channel

James Osei-Owusu et al.

Summary: In response to acidic pH, the proton-activated chloride (PAC) channel opens to transport anions across cellular membranes, playing important roles in cellular physiology and acidosis-related diseases. Through mutagenesis and electrophysiological studies, this research identifies critical residues, including histidine and aspartic acid, as potential pH sensors for human PAC. The study also reveals that the beta 12 strand and the joint region between upper and lower extracellular domains allosterically regulate proton-dependent PAC activation.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

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Article Chemistry, Physical

Galvani Offset Potential and Constant-pH Simulations of Membrane Proteins

Olivier Bignucolo et al.

Summary: A central problem in computational biophysics is the treatment of titratable residues in molecular dynamics simulations. Conventional methods assume a fixed ionization state for these residues, which is limited. Constant-pH simulation methods provide a more realistic approach by allowing the ionization state to vary statistically. These methods sample all accessible configurations and ionization states properly weighted according to their Boltzmann factor.

JOURNAL OF PHYSICAL CHEMISTRY B (2022)

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Article Chemistry, Physical

The pH-dependent gating of the human voltage-gated proton channel from computational simulations

Christophe Jardin et al.

Summary: The gating of the voltage-gated proton channel H(V)1 is strongly regulated by pH. Experimental investigations and simulations have identified the involvement of titratable amino acids in pH sensing and gating of the channel. Changes in pH cause conformational changes and movement of specific amino acids that ultimately control channel activation.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2022)

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Article Chemistry, Physical

BLaDE: A Basic Lambda Dynamics Engine for GPU-Accelerated Molecular Dynamics Free Energy Calculations

Ryan L. Hayes et al.

Summary: This paper introduces a basic Lambda dynamics engine called BLaDE, which allows for alchemical free energy simulations on GPUs and is faster than current GPU implementations. Research shows that BLaDE's performance in standard molecular dynamics is competitive with the highly optimized OpenMM GPU code.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Article Multidisciplinary Sciences

How μ-opioid receptor recognizes fentanyl

Quynh N. Vo et al.

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Protein pKa Prediction with Machine Learning

Zhitao Cai et al.

Summary: This study introduces a deep learning-based protein pK(a) predictor DeepKa, trained and validated using pK(a) values derived from continuous constant-pH molecular dynamics simulations, showing high prediction accuracy comparable to benchmarking simulations and potential for machine learning development. The grid charge representation proposed in this work is shown to be general and applicable to other topics like protein-ligand binding affinity prediction.

ACS OMEGA (2021)

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Article Chemistry, Physical

pH Effects and Cooperativity among Key Titratable Residues for Escherichia coli Glycinamide Ribonucleotide Transformylase

Pancham Lal Gupta et al.

Summary: Researchers investigated E. coli GAR Tfase, aiming to predict the pH-activity curve using computational methods. By identifying catalytic residues in specific protonation states and considering the coupling between protonation states and conformational states, they accurately identified acid and base catalysts and explained the pH-activity curve at an atomistic level.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

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pH and Charged Mutations Modulate Cold Shock Protein Folding and Stability: A Constant pH Monte Carlo Study

Vinicius M. de Oliveira et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

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Exploring Coupled Redox and pH Processes with a Force-Field-Based Approach: Applications to Five Different Systems

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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

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M2 amphipathic helices facilitate pH-dependent conformational transition in influenza A virus

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Catalytic Site pKa Values of Aspartic, Cysteine, and Serine Proteases: Constant pH MD Simulations

Florian Hofer et al.

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Exploring pH Dependent Host/Guest Binding Affinities

Thomas J. Paul et al.

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Improved GROMOS 54A7 Charge Sets for Phosphorylated Tyr, Ser, and Thr to Deal with pH-Dependent Binding Phenomena

Nuno F. B. Oliveira et al.

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Alternative proton-binding site and long-distance coupling in Escherichia coli sodium-proton antiporter NhaA

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Proton-Coupled Conformational Activation of SARS Coronavirus Main Proteases and Opportunity for Designing Small-Molecule Broad-Spectrum Targeted Covalent Inhibitors

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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

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Effect of pH on the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment

Diana Lousa et al.

SCIENTIFIC REPORTS (2020)

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Constant-pH Brownian Dynamics Simulations of a Protein near a Charged Surface

Jan M. Antosiewicz et al.

ACS OMEGA (2020)

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Article Mathematical & Computational Biology

PKAD: a database of experimentally measured pKa values of ionizable groups in proteins

Swagata Pahari et al.

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OPEP6: A New Constant-pH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field

Fernando Luis Barroso da Silva et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)

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Assessing Lysine and Cysteine Reactivities for Designing Targeted Covalent Kinase Inhibitors

Ruibin Liu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

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CpHMD-Then-QM/MM Identification of the Amino Acids Responsible for the Anabaena Sensory Rhodopsin pH-Dependent Electronic Absorption Spectrum

Elisa Pieri et al.

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How Electrostatic Coupling Enables Conformational Plasticity in a Tyrosine Kinase

Cheng-Chieh Tsai et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

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Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules

Zhi Yue et al.

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GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: pKa Predictions with Single-pH Simulations

Robert C. Harris et al.

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Membrane-Induced pKa Shifts in wt-pHLIP and Its L16H Variant

Diogo Vila-Vicosa et al.

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Predicting Catalytic Proton Donors and Nucleophiles in Enzymes: How Adding Dynamics Helps Elucidate the Structure Function Relationships

Yandong Huang et al.

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Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

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Computational scheme for pH-dependent binding free energy calculation with explicit solvent

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Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer

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All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water

Yandong Huang et al.

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Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA

Yandong Huang et al.

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Constant-pH Hybrid Nonequilibrium Molecular Dynamics Monte Carlo Simulation Method

Yunjie Chen et al.

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Membrane Environment Modulates the pKa Values of Transmembrane Helices

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Protocols Utilizing Constant pH Molecular Dynamics to Compute pH-Dependent Binding Free Energies

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Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange

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Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

Jason M. Swails et al.

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Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism

Garrett B. Goh et al.

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Unraveling a Trap-and-Trigger Mechanism in the pH-Sensitive Self-Assembly of Spider Silk Proteins

Jason A. Wallace et al.

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Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics

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Multisite λ Dynamics for Simulated Structure-Activity Relationship Studies

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Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange

Jason A. Wallace et al.

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Progress in the prediction of pKa values in proteins

Emil Alexov et al.

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Constant pH Replica Exchange Molecular Dynamics in Biomolecules Using a Discrete Protonation Model

Yilin Meng et al.

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Molecular Dynamics at Constant pH and Reduction Potential: Application to Cytochrome c3

Miguel Machuqueiro et al.

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Constant-pH molecular dynamics with ionic strength effects: Protonation-conformation coupling in decalysine

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Constant pH molecular dynamics with proton tautomerism

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Constant-pH molecular dynamics using continuous titration coordinates

MS Lee et al.

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Constant-pH molecular dynamics simulations: a test case of succinic acid

M Dlugosz et al.

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Constant pH molecular dynamics in generalized born implicit solvent

J Mongan et al.

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Simulating proteins at constant pH:: An approach combining molecular dynamics and Monte Carlo simulation

R Bürgi et al.

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