NDLI: Evaluation and ranking of enzyme designs.

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Evaluation and ranking of enzyme designs.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Röthlisberger, Daniela Kiss, Gert Baker, David Houk, K. N.
Description	Country affiliation: United States Author Affiliation: Kiss G ( Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA.)
Abstract	In 2008, a successful computational design procedure was reported that yielded active enzyme catalysts for the Kemp elimination. Here, we studied these proteins together with a set of previously unpublished inactive designs to determine the sources of activity or lack thereof, and to predict which of the designed structures are most likely to be catalytic.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 molecular dynamics, and a general MD protocol was established. 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 considerations, it has now become feasible to rank and refine candidates computationally prior to and in conjunction with experimentation, thus markedly increasing the efficiency of the enzyme design process.
ISSN	09618368
e-ISSN	1469896X
DOI	10.1002/pro.462
Journal	Protein Science
Issue Number	9
Volume Number	19
Language	English
Publisher	Wiley-Blackwell (on behalf of The Protein Society)
Publisher Date	2010-09-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Enzymes Chemistry Molecular Dynamics Simulation Catalysis Catalytic Domain Hydrogen Bonding Protein Conformation Quantum Theory Research Support, Non-u.s. Gov't Discipline Biochemistry
Content Type	Text
Resource Type	Article
Subject	Medicine Molecular Biology Biochemistry

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