Molecular dynamics of complex biological and chemical systems is possible using personal computers due to increased computer performance and improved software design. Here we describe molecular dynamics methods using Not Another Molecular Dynamics (NAMD) and Visual Molecular Dynamics (VMD) programs that aid in understanding the structural effects a mutation has on a protein. We describe in silico methods for site-specific mutation to standard and phosphorylated amino acids. Molecular dynamics equilibrations are used to provide a means for measuring structural fluctuations. These fluctuations assist in defining a distance coordinate, or reaction coordinate, that is relevant to the function of the protein. Adaptive biasing force molecular dynamics are then demonstrated to evaluate the energy landscape, or potential of mean force, along the chosen reaction coordinate. The potential of mean force identifies variations of the predominant structures among mutants that may affect function.
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