Literature DB >> 16277482

A general acid-base mechanism for the stabilization of a tetrahedral adduct in a serine-carboxyl peptidase: a computational study.

Haobo Guo1, Alexander Wlodawer, Hong Guo.   

Abstract

The QM/MM MD and free energy simulations show that serine-carboxyl peptidases (sedolisins) may stabilize the tetrahedral intermediates and tetrahedral adducts primarily through a general acid-base mechanism involving Asp (Asp164 for kumamolisin-As) rather than the oxyanion-hole interactions as in the cases of serine proteases.

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Year:  2005        PMID： 16277482     DOI： 10.1021/ja0520565

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN： 0002-7863            Impact factor:   15.419


  6 in total

1.  The importance of dynamics in substrate-assisted catalysis and specificity.

Authors:  Qin Xu; Haobo Guo; Alexander Wlodawer; Hong Guo
Journal:  J Am Chem Soc       Date:  2006-05-10       Impact factor: 15.419

Review 2.  Diversity, Structures, and Collagen-Degrading Mechanisms of Bacterial Collagenolytic Proteases.

Authors:  Yu-Zhong Zhang; Li-Yuan Ran; Chun-Yang Li; Xiu-Lan Chen
Journal:  Appl Environ Microbiol       Date:  2015-07-06       Impact factor: 4.792

3.  Understanding the autocatalytic process of pro-kumamolisin activation from molecular dynamics and quantum mechanical/molecular mechanical (QM/MM) free-energy simulations.

Authors:  Jianzhuang Yao; Alexander Wlodawer; Hong Guo
Journal:  Chemistry       Date:  2013-07-02       Impact factor: 5.236

4.  The QM/MM molecular dynamics and free energy simulations of the acylation reaction catalyzed by the serine-carboxyl peptidase kumamolisin-As.

Authors:  Qin Xu; Hao-Bo Guo; Alexander Wlodawer; Toru Nakayama; Hong Guo
Journal:  Biochemistry       Date:  2007-02-28       Impact factor: 3.162

5.  Clarification of the mechanism of acylation reaction and origin of substrate specificity of the serine-carboxyl peptidase sedolisin through QM/MM free energy simulations.

Authors:  Qin Xu; Jianzhuang Yao; Alexander Wlodawer; Hong Guo
Journal:  J Phys Chem B       Date:  2011-02-18       Impact factor: 2.991

6.  Density-functional tight-binding: basic concepts and applications to molecules and clusters.

Authors:  Fernand Spiegelman; Nathalie Tarrat; Jérôme Cuny; Leo Dontot; Evgeny Posenitskiy; Carles Martí; Aude Simon; Mathias Rapacioli
Journal:  Adv Phys X       Date:  2020-02-18
  6 in total

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