Literature DB >> 17268593

Accurate metal-site structures in proteins obtained by combining experimental data and quantum chemistry.

Ulf Ryde1.   

Abstract

The use of molecular mechanics calculations to supplement experimental data in standard X-ray crystallography and NMR refinements is discussed and it is shown that structures can be locally improved by the use of quantum chemical calculations. Such calculations can also be used to interpret the structures, e.g. to decide the protonation state of metal-bound ligands. They have shown that metal sites in crystal structures are frequently photoreduced or disordered, which makes the interpretation of the structures hard. Similar methods can be used for EXAFS refinements to obtain a full atomic structure, rather than a set of metal-ligand distances.

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Year:  2006        PMID: 17268593     DOI: 10.1039/b614448a

Source DB:  PubMed          Journal:  Dalton Trans        ISSN: 1477-9226            Impact factor:   4.390


  8 in total

1.  PDB ligand conformational energies calculated quantum-mechanically.

Authors:  Markus Sitzmann; Iwona E Weidlich; Igor V Filippov; Chenzhong Liao; Megan L Peach; Wolf-Dietrich Ihlenfeldt; Rajeshri G Karki; Yulia V Borodina; Raul E Cachau; Marc C Nicklaus
Journal:  J Chem Inf Model       Date:  2012-02-21       Impact factor: 4.956

2.  Analyses of cobalt-ligand and potassium-ligand bond lengths in metalloproteins: trends and patterns.

Authors:  Natércia F Brás; António J M Ribeiro; Marina Oliveira; Nathália M Paixão; Juan A Tamames; Pedro A Fernandes; Maria J Ramos
Journal:  J Mol Model       Date:  2014-05-22       Impact factor: 1.810

3.  Quantum Refinement Does Not Support Dinuclear Copper Sites in Crystal Structures of Particulate Methane Monooxygenase.

Authors:  Lili Cao; Octav Caldararu; Amy C Rosenzweig; Ulf Ryde
Journal:  Angew Chem Int Ed Engl       Date:  2017-12-08       Impact factor: 15.336

4.  QM/MM X-ray refinement of zinc metalloenzymes.

Authors:  Xue Li; Seth A Hayik; Kenneth M Merz
Journal:  J Inorg Biochem       Date:  2010-01-07       Impact factor: 4.155

5.  Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.

Authors:  Jennifer R Calhoun; Weixia Liu; Katrin Spiegel; Matteo Dal Peraro; Michael L Klein; Kathleen G Valentine; A Joshua Wand; William F DeGrado
Journal:  Structure       Date:  2008-02       Impact factor: 5.006

6.  Conformational variability of benzamidinium-based inhibitors.

Authors:  Xue Li; Xiao He; Bing Wang; Kenneth Merz
Journal:  J Am Chem Soc       Date:  2009-06-10       Impact factor: 15.419

Review 7.  Quantum crystallography.

Authors:  Simon Grabowsky; Alessandro Genoni; Hans-Beat Bürgi
Journal:  Chem Sci       Date:  2017-03-27       Impact factor: 9.825

8.  Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data.

Authors:  Octav Caldararu; Francesco Manzoni; Esko Oksanen; Derek T Logan; Ulf Ryde
Journal:  Acta Crystallogr D Struct Biol       Date:  2019-03-28       Impact factor: 7.652

  8 in total

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