Simulating Protein Structures, Complexes, And Dynamics

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We refined our homology model of the human calcium receptor, and a paper analyzing loop-deletion mutants was published. Two additional papers are in press; one includes a homology model of the Saccharomyces cerevisiae homolog of arylalkylamine N-acetyltransferase, and the other involves modeling of the J3-crystallin of the jellyfish lens. Another study that investigates the structure and function of carboxypeptidase E has been submitted for publication. We have also simulated the dynamics of short peptides in solution using Langevin dynamics and a simplified nonbond potential. A manuscript describing this work is in preparation. Also, our study of antibiotic binding to dihydrofolate reductase is ongoing. We modeled the binding mode of substrate 3,4-dihydroxyphenylglycolaldehyde and its derivatives at the active site of aldose reductase (submitted for publication). We have also studied the oxidation mechansim of aldose reductase with trans-naphthalene-1,2 dihydrodiol (in press). Utilizing combined potentials of quantum mechanics and molecular mechanics, we have investigated the catalytic mechansim of chorismate mutase (submitted for pubilcation) and Serotonin N-acetyltransferase (manuscript in preparation).