Literature DB >> 16669642

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

Qin Xu1, Haobo Guo, Alexander Wlodawer, Hong Guo.   

Abstract

The QM/MM MD and free energy simulations show that the dynamics involving a His residue at the P1 site of the substrate may play an important role in substrate-assisted catalysis and specificity for a serine-carboxyl peptidase.

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Year:  2006        PMID： 16669642      PMCID： PMC2530918          DOI： 10.1021/ja058831y

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


  22 in total

Review 1.  Substrate-assisted catalysis: molecular basis and biological significance.

Authors:  W Dall'Acqua; P Carter
Journal:  Protein Sci       Date:  2000-01       Impact factor: 6.725

2.  Collagenolytic serine-carboxyl proteinase from Alicyclobacillus sendaiensis strain NTAP-1: purification, characterization, gene cloning, and heterologous expression.

Authors:  Naoki Tsuruoka; Toru Nakayama; Masako Ashida; Hisashi Hemmi; Masahiro Nakao; Hiroyuki Minakata; Hiroshi Oyama; Kohei Oda; Tokuzo Nishino
Journal:  Appl Environ Microbiol       Date:  2003-01       Impact factor: 4.792

3.  Substrate-assisted catalysis of peptide bond formation by the ribosome.

Authors:  Joshua S Weinger; K Mark Parnell; Silke Dorner; Rachel Green; Scott A Strobel
Journal:  Nat Struct Mol Biol       Date:  2004-10-10       Impact factor: 15.369

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

Authors:  Haobo Guo; Alexander Wlodawer; Hong Guo
Journal:  J Am Chem Soc       Date:  2005-11-16       Impact factor: 15.419

5.  Carboxyl proteinase from Pseudomonas defines a novel family of subtilisin-like enzymes.

Authors:  A Wlodawer; M Li; Z Dauter; A Gustchina; K Uchida; H Oyama; B M Dunn; K Oda
Journal:  Nat Struct Biol       Date:  2001-05

Review 6.  Evolutionary divergence of substrate specificity within the chymotrypsin-like serine protease fold.

Authors:  J J Perona; C S Craik
Journal:  J Biol Chem       Date:  1997-11-28       Impact factor: 5.157

7.  Structural and enzymatic properties of the sedolisin family of serine-carboxyl peptidases.

Authors:  Alexander Wlodawer; Mi Li; Alla Gustchina; Hiroshi Oyama; Ben M Dunn; Kohei Oda
Journal:  Acta Biochim Pol       Date:  2003       Impact factor: 2.149

8.  Inhibitor complexes of the Pseudomonas serine-carboxyl proteinase.

Authors:  A Wlodawer; M Li; A Gustchina; Z Dauter; K Uchida; H Oyama; N E Goldfarb; B M Dunn; K Oda
Journal:  Biochemistry       Date:  2001-12-25       Impact factor: 3.162

9.  A catalytic diad involved in substrate-assisted catalysis: NMR study of hydrogen bonding and dynamics at the active site of phosphatidylinositol-specific phospholipase C.

Authors:  M Ryan; T Liu; F W Dahlquist; O H Griffith
Journal:  Biochemistry       Date:  2001-08-14       Impact factor: 3.162

10.  Crystal structure of carnitine acetyltransferase and implications for the catalytic mechanism and fatty acid transport.

Authors:  Gerwald Jogl; Liang Tong
Journal:  Cell       Date:  2003-01-10       Impact factor: 41.582
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  7 in total

1.  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

2.  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

3.  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

4.  Eta(z)/kappa: a transverse relaxation optimized spectroscopy NMR experiment measuring longitudinal relaxation interference.

Authors:  Daniel S Weaver; Erik R P Zuiderweg
Journal:  J Chem Phys       Date:  2008-04-21       Impact factor: 3.488

5.  Crystal structure of a type II dihydrofolate reductase catalytic ternary complex.

Authors:  Joseph M Krahn; Michael R Jackson; Eugene F DeRose; Elizabeth E Howell; Robert E London
Journal:  Biochemistry       Date:  2007-12-04       Impact factor: 3.162

Review 6.  Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies.

Authors:  Brigitta Elsässer; Peter Goettig
Journal:  Int J Mol Sci       Date:  2021-03-22       Impact factor: 5.923

7.  Tales of Dihydrofolate Binding to R67 Dihydrofolate Reductase.

Authors:  Michael R Duff; Shaileja Chopra; Michael Brad Strader; Pratul K Agarwal; Elizabeth E Howell
Journal:  Biochemistry       Date:  2015-12-21       Impact factor: 3.162
  7 in total

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