This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. In 2008, a successful computational design procedure was reported that yielded active enzyme catalysts for the Kemp elimination and the retro-aldol reaction. We studied these proteins together with a set of previously unpublished inactive designs in order to determine the sources of activity or lack thereof, and to predict which of the designed structures are most likely to be catalytic. Methods that range from quantum mechanics (QM) on truncated model systems to the treatment of the full protein with ONIOM QM/MM and AMBER molecular dynamics (MD) were explored. The most effective procedure involved explicit-solvent, periodic-boundary molecular dynamics, and a general MD protocol was established (see supporting information """"""""Evaluation and Ranking of Enzyme Designs with Molecular Dynamics""""""""). Substantial deviations from the ideal catalytic geometries were observed for a number of designs. Penetration of water into the catalytic site and insufficient residue-packing around the active site are the main factors that can cause enzyme designs to be inactive. Where in the past, computational evaluations of designed enzymes were too time-extensive for practical consideration, it has now become feasible to rank candidates computationally prior to and in conjunction with experimentation, thus markedly increasing the efficiency of the enzyme design process. Employing computational resources from the DESRES Anton machine will be instrumental to further develop and refine our MD-assisted enzyme design protocol and to facilitate the production of next-generation catalysts for a plethora of useful applications that range from alternative fuels to regenerating human tissue elasticity to novel passive immunizations and gene therapy.
Showing the most recent 10 out of 292 publications
