Literature DB >> 23821374

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

Jianzhuang Yao1, Alexander Wlodawer, Hong Guo.   

Abstract

Entities:  

Keywords:  acid/base catalysis; autocatalysis; enzymes; molecular dynamics; zymogens

Mesh：

Substances：

Year:  2013        PMID： 23821374      PMCID： PMC6287267          DOI： 10.1002/chem.201301310

Source DB:  PubMed          Journal:  Chemistry        ISSN： 0947-6539            Impact factor:   5.236


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  15 in total

1.  Understanding the mechanism of deacylation reaction catalyzed by the serine carboxyl peptidase kumamolisin-As: insights from QM/MM free energy simulations.

Authors:  Qin Xu; Liyan Li; Hong Guo
Journal:  J Phys Chem B       Date:  2010-08-19       Impact factor: 2.991

2.  Scalable molecular dynamics with NAMD.

Authors:  James C Phillips; Rosemary Braun; Wei Wang; James Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D Skeel; Laxmikant Kalé; Klaus Schulten
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

3.  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

4.  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

5.  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

6.  Association of mutations in a lysosomal protein with classical late-infantile neuronal ceroid lipofuscinosis.

Authors:  D E Sleat; R J Donnelly; H Lackland; C G Liu; I Sohar; R K Pullarkat; P Lobel
Journal:  Science       Date:  1997-09-19       Impact factor: 47.728

7.  Purification and properties of a pepstatin-insensitive carboxyl proteinase from a gram-negative bacterium.

Authors:  K Oda; M Sugitani; K Fukuhara; S Murao
Journal:  Biochim Biophys Acta       Date:  1987-03-19

8.  Catalytic role of proton transfers in the formation of a tetrahedral adduct in a serine carboxyl peptidase.

Authors:  Haobo Guo; Alexander Wlodawer; Toru Nakayama; Qin Xu; Hong Guo
Journal:  Biochemistry       Date:  2006-08-01       Impact factor: 3.162

9.  The 1.4 a crystal structure of kumamolysin: a thermostable serine-carboxyl-type proteinase.

Authors:  Mireia Comellas-Bigler; Pablo Fuentes-Prior; Klaus Maskos; Robert Huber; Hiroshi Oyama; Kenichi Uchida; Ben M Dunn; Kohei Oda; Wolfram Bode
Journal:  Structure       Date:  2002-06       Impact factor: 5.006

10.  All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Authors:  A D MacKerell; D Bashford; M Bellott; R L Dunbrack; J D Evanseck; M J Field; S Fischer; J Gao; H Guo; S Ha; D Joseph-McCarthy; L Kuchnir; K Kuczera; F T Lau; C Mattos; S Michnick; T Ngo; D T Nguyen; B Prodhom; W E Reiher; B Roux; M Schlenkrich; J C Smith; R Stote; J Straub; M Watanabe; J Wiórkiewicz-Kuczera; D Yin; M Karplus
Journal:  J Phys Chem B       Date:  1998-04-30       Impact factor: 2.991
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  2 in total

Review 1.  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

2.  QM/MM free energy Simulations of an efficient Gluten Hydrolase (Kuma030) Implicate for a Reactant-State Based Protein-Design Strategy for General Acid/Base Catalysis.

Authors:  Xia Wang; Ruirui Li; Wenchao Cui; Qiang Li; Jianzhuang Yao
Journal:  Sci Rep       Date:  2018-05-04       Impact factor: 4.379
  2 in total

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