Literature DB >> 16773613

Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases.

Guillermina Estiu1, Dimas Suárez, Kenneth M Merz.   

Abstract

Herein we briefly review theoretical contributions that have increased our understanding of the structure and function of metallo-beta-lactamases and ureases. Both are bimetallic metalloenzymes, with the former containing two zinc ions and the latter containing two nickel ions. We describe the use of several different methodologies, including quantum chemical calculations, molecular dynamic simulations, as well as mixed QM/MM approaches and how they have impacted our understanding of the structure and function of metallo-beta-lactamases and ureases.

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Year:  2006        PMID: 16773613     DOI: 10.1002/jcc.20411

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  8 in total

1.  Role of zinc content on the catalytic efficiency of B1 metallo beta-lactamases.

Authors:  Matteo Dal Peraro; Alejandro J Vila; Paolo Carloni; Michael L Klein
Journal:  J Am Chem Soc       Date:  2007-02-17       Impact factor: 15.419

Review 2.  Overcoming differences: The catalytic mechanism of metallo-β-lactamases.

Authors:  María-Rocío Meini; Leticia I Llarrull; Alejandro J Vila
Journal:  FEBS Lett       Date:  2015-08-20       Impact factor: 4.124

3.  Identification of novel urease inhibitors by high-throughput virtual and in vitro screening.

Authors:  Obaid-Ur-Rahman Abid; Tariq Mahmood Babar; Farukh Iftakhar Ali; Shahzad Ahmed; Abdul Wadood; Nasim Hasan Rama; Reaz Uddin; Ajmal Khan; M Iqbal Choudhary
Journal:  ACS Med Chem Lett       Date:  2010-05-10       Impact factor: 4.345

4.  Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field.

Authors:  Johnny C Wu; Jean-Philip Piquemal; Robin Chaudret; Peter Reinhardt; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2010-07-13       Impact factor: 6.006

5.  Structural Survey of Zinc Containing Proteins and the Development of the Zinc AMBER Force Field (ZAFF).

Authors:  Martin B Peters; Yue Yang; Bing Wang; László Füsti-Molnár; Michael N Weaver; Kenneth M Merz
Journal:  J Chem Theory Comput       Date:  2010-09-14       Impact factor: 6.006

6.  Biapenem inactivation by B2 metallo β-lactamases: energy landscape of the hydrolysis reaction.

Authors:  Sharon H Ackerman; Domenico L Gatti
Journal:  PLoS One       Date:  2013-01-24       Impact factor: 3.240

7.  Molecular Dynamics Study of Helicobacter pylori Urease.

Authors:  Mona S Minkara; Melek N Ucisik; Michael N Weaver; Kenneth M Merz
Journal:  J Chem Theory Comput       Date:  2014-03-25       Impact factor: 6.006

8.  Selective recognition of parallel and anti-parallel thrombin-binding aptamer G-quadruplexes by different fluorescent dyes.

Authors:  Dan Zhao; Xiongwei Dong; Nan Jiang; Dan Zhang; Changlin Liu
Journal:  Nucleic Acids Res       Date:  2014-09-22       Impact factor: 16.971

  8 in total

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