Rapid sampling of the conformational and sequence spaces is crucial for computational protein engineering. We have developed multiple protein models to sample dynamics of various time and length scales with discrete molecular dynamics (DMD). We also developed the atomic Medusa molecular modeling tool, which allows rapid sampling of the sequence space and evaluation of the associated free energy changes. Using DMD and/or Medusa, we are able to efficiently sample the sequence and conformations space of proteins. For example, using Medusa we are able to accurately predict the stability change of proteins upon mutations (http://eris.dokhlab.org). In collaboration with experimentalists, we have strategically designed destabilizing mutations of Galpha protein in yeast to study different degradations pathways via poly-ubiquitination and mono-ubiquitination. In another application, EGFP was broken into halves without fluorescence. Using DMD to sample the folding dynamics of each of halves and also the complex, we showed that a fluorogenic chromophore can self-catalytically form within an isolated N-terminal fragment of the EGFP. In vitro studies indicates that restoration of the split protein fluorescence can be driven by nucleic acid complementary interactions. In our assay, fluorescence development is fast (within a few minutes) when complementary oligonucleotide-linked fragments of the split EGFP are combined (Dimidov et al., PNAS 103: 2052-2056,2006).

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