Simulating Protein Structures, Complexes, And Dynamics

点击翻译按钮获取中文摘要

Our investigation of the structure and function of carboxypeptidase E was published, and our study of the dynamics of loop formation in disordered peptides is in press. The design of a stable four-helix bundle protein using several experimental and modeling techniques is also in press. We are preparing a manuscript characterizing antibiotic binding to dihydrofolate reductase. We continue to refine our model of the human calcium receptor. Two papers on the catalytic mechanism of chorismate mutase studied using the combined potentials of quantum mechanics and molecular mechanics are in press. A manuscript on the mechanism of N-actyltransferase is in progress. A paper that describes the simulation of molecular dynamics to investigate the hydrogen bonding interactions between aldose reductase and its inhibitor tolrestat has been accepted for publication. Quantum chemical calculations are being carried out to invesigate the binding mode of the anti-cancer agent geldanamycin to hsp90. Quantum chemical calculations are also being carried out to quantify the interaction energy between propanediol and water molecules. Molecular modeling studies on the A-beta amyloid probes are also being carried out to establish a structure-activity relationship. A hybrid algorithm combining the maximum entropy method and nonlinear least-squares fitting was developed to analyze kinetics data. Fluorescence studies of protein folding were analyzed. The computer program, called MemExp, is available online. A paper describing this work was published, and a follow-up extension to the software is in press.