The objective of the research is to be able to properly define a simplified energy potential and find the conformations that have the minimum energy according to the potential. We have developed a thermodynamic model of protein folding that incorporates both hydrophobicity and polar interactions. The model uses a united atom representation, but with polar hydrogens explicitly represented. The energy potential of the model consists of two parts: (1) Hydrophobic interaction, measured by the surface area of non-polar groups (exposed to both the solvent and polar groups); (2) Polar group interaction, measured by the number of stand-alone HDs and HAs and the number of HDs and HAs in conflicts in protein interior. We have searched representative portions of the conformational space and find that our energy potential recognizes the native conformations. The software tools provided by the Computer Graphics Laboratory, e.g., MIDAS, are essential in my research. (2) Strategies in designing protein sequences The objective of the research is to design a sequence that will has a given structure as its """"""""native"""""""" structure, i.e., the structure with the global minimum energy by some definition of energy potentials. The large number of conformationally distinct lowest energy states and near-lowest energy states of a sequence is suspected to be a main factor in the failure of a designed protein to fold. In our search, we use a simplified model of proteins to discuss how to reduce conformational degeneracy. The software tools provided by the Computer Graphics Laboratory, e.g., MIDAS, are essential in my research.
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