Quantum mechanical design of enzyme active sites.

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Quantum mechanical design of enzyme active sites. Abstract Text:

Xiyun Zhang,Jason Dechancie,Hakan Gunaydin,Arnab B Chowdry,Fernando R Clemente,Adam J T Smith,T M Handel,K N Houk,Xiyun Zhang,Jason DeChancie,Hakan Gunaydin,Arnab B Chowdry,Fernando R Clemente,Adam J T Smith,T M Handel,K N Houk,

The design of active sites has been carried out using quantum mechanical calculations to predict the rate-determining transition state of a desired reaction in presence of the optimal arrangement of catalytic functional groups (theozyme). Eleven versatile reaction targets were chosen, including hydrolysis, dehydration, isomerization, aldol, and Diels-Alder reactions. For each of the targets, the predicted mechanism and the rate-determining transition state (TS) of the uncatalyzed reaction in water is presented. For the rate-determining TS, a catalytic site was designed using naturalistic catalytic units followed by an estimation of the rate acceleration provided by a reoptimization of the catalytic site. Finally, the geometries of the sites were compared to the X-ray structures of related natural enzymes. Recent advances in computational algorithms and power, coupled with successes in computational protein design, have provided a powerful context for undertaking such an endeavor. We propose that theozymes are excellent candidates to serve as the active site models for design processes.

Quantum mechanical design of enzyme active sites. Publishing Authors By Initials

X Zhang,J Dechancie,H Gunaydin,AB Chowdry,FR Clemente,AJ Smith,TM Handel,KN Houk,X Zhang,J DeChancie,H Gunaydin,AB Chowdry,FR Clemente,AJ Smith,TM Handel,KN Houk,

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Quantum mechanical design of enzyme active sites. Journal Published:

PUBLICATION TYPE: Journal Article

Journal: The Journal of organic chemistry

VOLUME: 73

Page Numbers: 889-99

Journal Abbreviation: J. Org. Chem.

ISSN: 0022-3263

DAY: 8

MONTH: 01

YEAR: 2008

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LANGUAGE: eng

NlmUniqueID: 2985193

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Grant and Affiliation Information for Quantum mechanical design of enzyme active sites.

AFFILIATION: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093 and the Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095.

Country: United States

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MEDLINETA: J Org Chem

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