Over the past several years we have developed a novel approach to including pH in molecular dynamics simulations called CpHMD (Constant pH Molecular Dynamics). We have developed a hierarchy of models that include both implicit and explicit solvent frameworks to carry out molecular dynamics under conditions of constant pH and salt concentrations. In this talk I will provide an overview of these methods and discuss applications ranging from the creation of aggregation prone states in Alzheimer's A� to pH regulation of peptide structure formation in membrane environments to pH-catalyzed viral capsid maturation. These applications will illustrate the evolution of a powerful suite of simulation and modeling methodologies that enable one to begin to model pH and its consequences in cellular processes.

Understanding the role of acid in cellular processes with molecular simulations

247th National Meeting (2014)

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