This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The goal of this proposal is to further develop a basic work flow to refine a phylogenetic inference of ancestral protein sequences. In general, the phylogenetic inference is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Moreover, these studies are not capable to specify structural and functional changes along molecular evolution processes. In this project, molecular modeling and computational simulation will be employed to further refine predicted ancestral protein sequences and their possible structures. The approach combines quantum mechanical and molecular dynamics studies to address the challenge. In this project, we are focusing on structures and functions of glucosidsases which are enzymes involved in breaking down complex carbohydrates. Computational refinement of predicted ancestral protein sequences and structures of glucosidsase family proteins requires an intense computation. This study possibly will shed some light on how evolutionary changes affect on structure and functions of enzymes.
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