MOLECULAR DYNAMICS SIMULATION OF ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE AND I

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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. UW PICO(tm) 4.0 File: mcb030036p.abs Keywords: molecular dynamics Abstract: Proteins play an important biological role in all living organisms. Understanding protein folding is a key element in addressing a structure-function correlation in biological molecules. Being able to predict how a given protein sequence folds into a three dimensional structure is expected to have a significant impact on protein structure prediction and protein design. While the backbone plays a key role in protein folding, not every peptide bond is required for a protein to fold. A systematic analysis is necessary to identify regions essential for a protein to fold. Analysis of the effects of cleavage at all positions along the sequence on the structure will reveal the distribution of the folding elements within the primary structure. We are carrying out molecular dynamics simulations of the native DHFR from Escherichia coli and several of its circular permuted variants at standar temperature in order to assign the folding elements and to study their relative stabilities.