Literature DB >> 12547439

Molecular dynamics simulations of metalloproteins.

Lucia Banci1.   

Abstract

Molecular dynamics simulations are now commonly applied to metalloproteins, despite the challenges introduced by the presence of metal ions. Force field parameters are nowadays available also for these 'exotic' atoms and several biological systems have been successfully studied. Some of the most relevant results and methodological advancements are reviewed.

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Year:  2003        PMID： 12547439     DOI： 10.1016/s1367-5931(02)00014-5

Source DB:  PubMed          Journal:  Curr Opin Chem Biol        ISSN： 1367-5931            Impact factor:   8.822


  17 in total

Review 1.  Metal Ion Modeling Using Classical Mechanics.

Authors:  Pengfei Li; Kenneth M Merz
Journal:  Chem Rev       Date:  2017-01-03       Impact factor: 60.622

2.  Nuclear magnetic resonance signal chemical shifts and molecular simulations: a multidisciplinary approach to modeling copper protein structures.

Authors:  Jacopo Sgrignani; Roberta Pierattelli
Journal:  J Biol Inorg Chem       Date:  2011-08-13       Impact factor: 3.358

3.  Selective cysteine modification of metal-free human metallothionein 1a and its isolated domain fragments: Solution structural properties revealed via ESI-MS.

Authors:  Gordon W Irvine; Melissa Santolini; Martin J Stillman
Journal:  Protein Sci       Date:  2017-03-01       Impact factor: 6.725

4.  Importance of electrostatic polarizability in calculating cysteine acidity constants and copper(I) binding energy of Bacillus subtilis CopZ.

Authors:  Timothy H Click; Sergei Y Ponomarev; George A Kaminski
Journal:  J Comput Chem       Date:  2012-02-27       Impact factor: 3.376

5.  Developing multisite empirical force field models for Pt(II) and cisplatin.

Authors:  John P Cvitkovic; George A Kaminski
Journal:  J Comput Chem       Date:  2016-11-11       Impact factor: 3.376

6.  Electrostatic polarization is crucial in reproducing Cu(I) interaction energies and hydration.

Authors:  Sergei Y Ponomarev; Timothy H Click; George A Kaminski
Journal:  J Phys Chem B       Date:  2011-07-28       Impact factor: 2.991

7.  A Transferable Non-bonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins.

Authors:  Ruibo Wu; Zhenyu Lu; Zexing Cao; Yingkai Zhang
Journal:  J Chem Theory Comput       Date:  2011-02-08       Impact factor: 6.006

8.  Structures and free energy landscapes of aqueous zinc(II)-bound amyloid-β(1-40) and zinc(II)-bound amyloid-β(1-42) with dynamics.

Authors:  Olivia Wise-Scira; Liang Xu; George Perry; Orkid Coskuner
Journal:  J Biol Inorg Chem       Date:  2012-06-07       Impact factor: 3.358

9.  Modeling and dynamical analysis of the full-length structure of factor XII with zinc.

Authors:  Evren Kılınç; Ahmet Can Timucin; Suleyman Selim Cinaroglu; Emel Timucin
Journal:  J Mol Model       Date:  2022-04-25       Impact factor: 1.810

10.  Exploring the recognition of quadruplex DNA by an engineered Cys2-His2 zinc finger protein.

Authors:  Sylvain Ladame; James A Schouten; Jose Roldan; James E Redman; Stephen Neidle; Shankar Balasubramanian
Journal:  Biochemistry       Date:  2006-02-07       Impact factor: 3.162
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