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About this Research Topic

Manuscript Submission Deadline 03 March 2023

Solution pH is a crucial environmental variable that has a profound impact on the structure, dynamics, and function of biomolecules. Biomolecules can acquire or lose protons in response to changes in solution pH, modulating various biological processes such as cellular respiration, cell homeostasis, substrate/ion transport across membranes, enzyme catalysis, protein folding, protein–ligand recognition, drug delivery, and viral infection. Incorporating pH effects into biomolecular modeling will advance our understanding of the molecular mechanisms of biological processes and better supplement wet lab researches. In this Research Topic, we will cover recent developments and applications of pH-dependent or proton-coupled biomolecular modeling techniques.

Despite tremendous advancements in computing power, biomolecular modeling at constant pH remains challenging due to the complexity of the pH-dependent biological processes. A thorough understanding of these processes requires full-spectrum knowledge of proton binding and transport mechanisms, as well as the coupled biological consequences such as drug–target recognition and protein conformational changes. Because of the problem’s multiscale nature, proper tools should be employed to handle distinct scenarios of varying complexity and atomic resolution, i.e., multiscale modeling. E.g., use quantum mechanics-based reactive simulation methods to explicitly model microscopic proton binding, use constant-pH molecular dynamics (CpHMD) to simulate larger-scale proton-coupled conformational changes, and use kinetic theory to inspect the macroscopic outcomes of proton binding that can be virtually detected by experiments. The main interest of this Research Topic is multiscale modeling of pH-dependent biomolecular processes.

This Research Topic is interested in Original Research, Review, Mini Review, and Method articles that cover, but is not limited to, the following themes:
 Developments of pH-dependent or proton-coupled modeling techniques
 Developments of methods to calculate pK a values of biomolecular ionizable groups (empirical, continuum model, CpHMD, QM-based, AI/ML-based, etc.)
 Simulation of pH-dependent biomolecular structure–function relationship (e.g., enzyme activity, protein stability & folding, etc.)
 Simulation of pH-dependent biomolecular aggregation, assembly, and organization
 Simulation of pH-dependent drug–target recognition
 Simulation of pH effects in lipid bilayers, lipid interactions with proteins, peptides, drugs, etc.
 Simulation of proton-coupled membrane carriers/channels using conventional, CpHMD, reactive
MD, free energy calculation, or enhanced sampling simulations
 Simulation of coupled pH and redox processes
 Simulation of pH effects in coarse-grained models

Keywords: ph, proton transfer, electrostatics, computer simulation, multiscale modeling


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

Solution pH is a crucial environmental variable that has a profound impact on the structure, dynamics, and function of biomolecules. Biomolecules can acquire or lose protons in response to changes in solution pH, modulating various biological processes such as cellular respiration, cell homeostasis, substrate/ion transport across membranes, enzyme catalysis, protein folding, protein–ligand recognition, drug delivery, and viral infection. Incorporating pH effects into biomolecular modeling will advance our understanding of the molecular mechanisms of biological processes and better supplement wet lab researches. In this Research Topic, we will cover recent developments and applications of pH-dependent or proton-coupled biomolecular modeling techniques.

Despite tremendous advancements in computing power, biomolecular modeling at constant pH remains challenging due to the complexity of the pH-dependent biological processes. A thorough understanding of these processes requires full-spectrum knowledge of proton binding and transport mechanisms, as well as the coupled biological consequences such as drug–target recognition and protein conformational changes. Because of the problem’s multiscale nature, proper tools should be employed to handle distinct scenarios of varying complexity and atomic resolution, i.e., multiscale modeling. E.g., use quantum mechanics-based reactive simulation methods to explicitly model microscopic proton binding, use constant-pH molecular dynamics (CpHMD) to simulate larger-scale proton-coupled conformational changes, and use kinetic theory to inspect the macroscopic outcomes of proton binding that can be virtually detected by experiments. The main interest of this Research Topic is multiscale modeling of pH-dependent biomolecular processes.

This Research Topic is interested in Original Research, Review, Mini Review, and Method articles that cover, but is not limited to, the following themes:
 Developments of pH-dependent or proton-coupled modeling techniques
 Developments of methods to calculate pK a values of biomolecular ionizable groups (empirical, continuum model, CpHMD, QM-based, AI/ML-based, etc.)
 Simulation of pH-dependent biomolecular structure–function relationship (e.g., enzyme activity, protein stability & folding, etc.)
 Simulation of pH-dependent biomolecular aggregation, assembly, and organization
 Simulation of pH-dependent drug–target recognition
 Simulation of pH effects in lipid bilayers, lipid interactions with proteins, peptides, drugs, etc.
 Simulation of proton-coupled membrane carriers/channels using conventional, CpHMD, reactive
MD, free energy calculation, or enhanced sampling simulations
 Simulation of coupled pH and redox processes
 Simulation of pH effects in coarse-grained models

Keywords: ph, proton transfer, electrostatics, computer simulation, multiscale modeling


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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