Literature DB >> 18786394

Accurate NMR structures through minimization of an extended hybrid energy.

Michael Nilges1, Aymeric Bernard, Benjamin Bardiaux, Thérèse Malliavin, Michael Habeck, Wolfgang Rieping.   

Abstract

The use of generous distance bounds has been the hallmark of NMR structure determination. However, bounds necessitate the estimation of data quality before the calculation, reduce the information content, introduce human bias, and allow for major errors in the structures. Here, we propose a new rapid structure calculation scheme based on Bayesian analysis. The minimization of an extended energy function, including a new type of distance restraint and a term depending on the data quality, results in an estimation of the data quality in addition to coordinates. This allows for the determination of the optimal weight on the experimental information. The resulting structures are of better quality and closer to the X-ray crystal structure of the same molecule. With the new calculation approach, the analysis of discrepancies from the target distances becomes meaningful. The strategy may be useful in other applications-for example, in homology modeling.

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Year:  2008        PMID: 18786394     DOI: 10.1016/j.str.2008.07.008

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.006


  24 in total

1.  Get5 carboxyl-terminal domain is a novel dimerization motif that tethers an extended Get4/Get5 complex.

Authors:  Justin W Chartron; David G VanderVelde; Meera Rao; William M Clemons
Journal:  J Biol Chem       Date:  2012-01-17       Impact factor: 5.157

2.  Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools.

Authors:  Chris A E M Spronk; Szymon Żerko; Michał Górka; Wiktor Koźmiński; Benjamin Bardiaux; Barbara Zambelli; Francesco Musiani; Mario Piccioli; Priyanka Basak; Faith C Blum; Ryan C Johnson; Heidi Hu; D Scott Merrell; Michael Maroney; Stefano Ciurli
Journal:  J Biol Inorg Chem       Date:  2018-09-27       Impact factor: 3.358

3.  Automated structure modeling of large protein assemblies using crosslinks as distance restraints.

Authors:  Mathias Ferber; Jan Kosinski; Alessandro Ori; Umar J Rashid; María Moreno-Morcillo; Bernd Simon; Guillaume Bouvier; Paulo Ricardo Batista; Christoph W Müller; Martin Beck; Michael Nilges
Journal:  Nat Methods       Date:  2016-04-25       Impact factor: 28.547

4.  Blind testing of routine, fully automated determination of protein structures from NMR data.

Authors:  Antonio Rosato; James M Aramini; Cheryl Arrowsmith; Anurag Bagaria; David Baker; Andrea Cavalli; Jurgen F Doreleijers; Alexander Eletsky; Andrea Giachetti; Paul Guerry; Aleksandras Gutmanas; Peter Güntert; Yunfen He; Torsten Herrmann; Yuanpeng J Huang; Victor Jaravine; Hendrik R A Jonker; Michael A Kennedy; Oliver F Lange; Gaohua Liu; Thérèse E Malliavin; Rajeswari Mani; Binchen Mao; Gaetano T Montelione; Michael Nilges; Paolo Rossi; Gijs van der Schot; Harald Schwalbe; Thomas A Szyperski; Michele Vendruscolo; Robert Vernon; Wim F Vranken; Sjoerd de Vries; Geerten W Vuister; Bin Wu; Yunhuang Yang; Alexandre M J J Bonvin
Journal:  Structure       Date:  2012-02-08       Impact factor: 5.006

5.  Structure and Assembly of the Enterohemorrhagic Escherichia coli Type 4 Pilus.

Authors:  Benjamin Bardiaux; Gisele Cardoso de Amorim; Areli Luna Rico; Weili Zheng; Ingrid Guilvout; Camille Jollivet; Michael Nilges; Edward H Egelman; Nadia Izadi-Pruneyre; Olivera Francetic
Journal:  Structure       Date:  2019-05-02       Impact factor: 5.006

6.  Structure of the C-Terminal Helical Repeat Domain of Eukaryotic Elongation Factor 2 Kinase.

Authors:  Nathan Will; Andrea Piserchio; Isaac Snyder; Scarlet B Ferguson; David H Giles; Kevin N Dalby; Ranajeet Ghose
Journal:  Biochemistry       Date:  2016-09-14       Impact factor: 3.162

7.  Structure of the K-turn U4 RNA: a combined NMR and SANS study.

Authors:  Melanie Falb; Irene Amata; Frank Gabel; Bernd Simon; Teresa Carlomagno
Journal:  Nucleic Acids Res       Date:  2010-05-13       Impact factor: 16.971

Review 8.  Uncertainty in integrative structural modeling.

Authors:  Dina Schneidman-Duhovny; Riccardo Pellarin; Andrej Sali
Journal:  Curr Opin Struct Biol       Date:  2014-08-28       Impact factor: 6.809

9.  Functional and structural insights of a Staphylococcus aureus apoptotic-like membrane peptide from a toxin-antitoxin module.

Authors:  Nour Sayed; Sylvie Nonin-Lecomte; Stéphane Réty; Brice Felden
Journal:  J Biol Chem       Date:  2012-11-05       Impact factor: 5.157

10.  Interplay of Disorder and Sequence Specificity in the Formation of Stable Dynein-Dynactin Complexes.

Authors:  Nikolaus M Loening; Sanjana Saravanan; Nathan E Jespersen; Kayla Jara; Elisar Barbar
Journal:  Biophys J       Date:  2020-08-05       Impact factor: 4.033

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