Literature DB >> 23422068

Chemical shifts in biomolecules.

David A Case1.   

Abstract

NMR chemical shifts are sensitive probes of structure and dynamics in proteins. Empirical models, based on a large database of measured shifts, take an input structure and provide increasingly accurate estimates of the corresponding shifts. Quantum chemical calculations can provide the same information, with greater generality but (currently) with less accuracy. These methods are now providing new ways to approach NMR structure determination, and new insights into the conformational dynamics of proteins.
Copyright © 2013. Published by Elsevier Ltd.

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Year:  2013        PMID: 23422068      PMCID: PMC3877577          DOI: 10.1016/j.sbi.2013.01.007

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  43 in total

1.  Ab Initio Methods for the Calculation of NMR Shielding and Indirect Spinminus signSpin Coupling Constants.

Authors:  Trygve Helgaker; Michał Jaszuński; Kenneth Ruud
Journal:  Chem Rev       Date:  1999-01-13       Impact factor: 60.622

2.  The Xplor-NIH NMR molecular structure determination package.

Authors:  Charles D Schwieters; John J Kuszewski; Nico Tjandra; G Marius Clore
Journal:  J Magn Reson       Date:  2003-01       Impact factor: 2.229

3.  Protein structure validation using side-chain chemical shifts.

Authors:  Aleksandr B Sahakyan; Andrea Cavalli; Wim F Vranken; Michele Vendruscolo
Journal:  J Phys Chem B       Date:  2012-04-15       Impact factor: 2.991

4.  Toward the Quantum Chemical Calculation of NMR Chemical Shifts of Proteins. 2. Level of Theory, Basis Set, and Solvents Model Dependence.

Authors:  Andrea Frank; Heiko M Möller; Thomas E Exner
Journal:  J Chem Theory Comput       Date:  2012-03-30       Impact factor: 6.006

5.  Protein structure determination from NMR chemical shifts.

Authors:  Andrea Cavalli; Xavier Salvatella; Christopher M Dobson; Michele Vendruscolo
Journal:  Proc Natl Acad Sci U S A       Date:  2007-05-29       Impact factor: 11.205

6.  Ab initio calculations of NMR chemical shifts.

Authors:  Leah B Casabianca; Angel C de Dios
Journal:  J Chem Phys       Date:  2008-02-07       Impact factor: 3.488

7.  4D prediction of protein (1)H chemical shifts.

Authors:  Juuso Lehtivarjo; Tommi Hassinen; Samuli-Petrus Korhonen; Mikael Peräkylä; Reino Laatikainen
Journal:  J Biomol NMR       Date:  2009-10-30       Impact factor: 2.835

Review 8.  The use of chemical shifts and their anisotropies in biomolecular structure determination.

Authors:  D A Case
Journal:  Curr Opin Struct Biol       Date:  1998-10       Impact factor: 6.809

9.  Probing chemical shifts of invisible states of proteins with relaxation dispersion NMR spectroscopy: how well can we do?

Authors:  D Flemming Hansen; Pramodh Vallurupalli; Patrik Lundström; Philipp Neudecker; Lewis E Kay
Journal:  J Am Chem Soc       Date:  2008-02-01       Impact factor: 15.419

10.  In support of the BMRB.

Authors:  John L Markley; Hideo Akutsu; Tetsuo Asakura; Marc Baldus; Rolf Boelens; Alexandre Bonvin; Robert Kaptein; Ad Bax; Irina Bezsonova; Michael R Gryk; Jeffrey C Hoch; Dmitry M Korzhnev; Mark W Maciejewski; Dave Case; Walter J Chazin; Timothy A Cross; Sonja Dames; Horst Kessler; Oliver Lange; Tobias Madl; Bernd Reif; Michael Sattler; David Eliezer; Alan Fersht; Julie Forman-Kay; Lewis E Kay; James Fraser; John Gross; Tanja Kortemme; Andrej Sali; Toshimichi Fujiwara; Kevin Gardner; Xuelian Luo; Jose Rizo-Rey; Michael Rosen; Roberto R Gil; Chien Ho; Gordon Rule; Angela M Gronenborn; Rieko Ishima; Judith Klein-Seetharaman; Pei Tang; Patrick van der Wel; Yan Xu; Stephan Grzesiek; Sebastian Hiller; Joachim Seelig; Ernest D Laue; Helen Mott; Daniel Nietlispach; Igor Barsukov; Lu-Yun Lian; David Middleton; Tharin Blumenschein; Geoffrey Moore; Iain Campbell; Jason Schnell; Ioannis John Vakonakis; Anthony Watts; Maria R Conte; James Mason; Mark Pfuhl; Mark R Sanderson; Jeremy Craven; Michael Williamson; Cyril Dominguez; Gordon Roberts; Ulrich Günther; Michael Overduin; Joern Werner; Philip Williamson; Claudia Blindauer; Matthew Crump; Paul Driscoll; Tom Frenkiel; Alexander Golovanov; Steve Matthews; John Parkinson; Dusan Uhrin; Mark Williams; David Neuhaus; Hartmut Oschkinat; Andres Ramos; David E Shaw; Christoph Steinbeck; Michele Vendruscolo; Geerten W Vuister; Kylie J Walters; Harel Weinstein; Kurt Wüthrich; Shigeyuki Yokoyama
Journal:  Nat Struct Mol Biol       Date:  2012-09       Impact factor: 15.369

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  11 in total

1.  Determination of accurate backbone chemical shift tensors in microcrystalline proteins by integrating MAS NMR and QM/MM.

Authors:  Matthew Fritz; Caitlin M Quinn; Mingzhang Wang; Guangjin Hou; Xingyu Lu; Leonardus M I Koharudin; Jochem Struppe; David A Case; Tatyana Polenova; Angela M Gronenborn
Journal:  Phys Chem Chem Phys       Date:  2018-04-04       Impact factor: 3.676

2.  Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations.

Authors:  Honglue Shi; Mary C Clay; Atul Rangadurai; Bharathwaj Sathyamoorthy; David A Case; Hashim M Al-Hashimi
Journal:  J Biomol NMR       Date:  2018-04-19       Impact factor: 2.835

3.  Characterizing Watson-Crick versus Hoogsteen Base Pairing in a DNA-Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically 13C- and 15N-Labeled DNA.

Authors:  Huiqing Zhou; Bharathwaj Sathyamoorthy; Allison Stelling; Yu Xu; Yi Xue; Ying Zhang Pigli; David A Case; Phoebe A Rice; Hashim M Al-Hashimi
Journal:  Biochemistry       Date:  2019-04-05       Impact factor: 3.162

4.  Dynamic Water-Mediated Hydrogen Bonding in a Collagen Model Peptide.

Authors:  Iwen Fu; David A Case; Jean Baum
Journal:  Biochemistry       Date:  2015-10-06       Impact factor: 3.162

5.  AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.

Authors:  Jason Swails; Tong Zhu; Xiao He; David A Case
Journal:  J Biomol NMR       Date:  2015-08-02       Impact factor: 2.835

6.  Finding Our Way in the Dark Proteome.

Authors:  Asmit Bhowmick; David H Brookes; Shane R Yost; H Jane Dyson; Julie D Forman-Kay; Daniel Gunter; Martin Head-Gordon; Gregory L Hura; Vijay S Pande; David E Wemmer; Peter E Wright; Teresa Head-Gordon
Journal:  J Am Chem Soc       Date:  2016-07-19       Impact factor: 15.419

Review 7.  Information flow and protein dynamics: the interplay between nuclear magnetic resonance spectroscopy and molecular dynamics simulations.

Authors:  Nina Pastor; Carlos Amero
Journal:  Front Plant Sci       Date:  2015-05-05       Impact factor: 5.753

8.  Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics.

Authors:  Anders S Christensen; Troels E Linnet; Mikael Borg; Wouter Boomsma; Kresten Lindorff-Larsen; Thomas Hamelryck; Jan H Jensen
Journal:  PLoS One       Date:  2013-12-31       Impact factor: 3.240

9.  The Mutational Landscape of the Oncogenic MZF1 SCAN Domain in Cancer.

Authors:  Mads Nygaard; Thilde Terkelsen; André Vidas Olsen; Valentina Sora; Juan Salamanca Viloria; Fabio Rizza; Sanne Bergstrand-Poulsen; Miriam Di Marco; Mette Vistesen; Matteo Tiberti; Matteo Lambrughi; Marja Jäättelä; Tuula Kallunki; Elena Papaleo
Journal:  Front Mol Biosci       Date:  2016-12-15

10.  Protein structure refinement using a quantum mechanics-based chemical shielding predictor.

Authors:  Lars A Bratholm; Jan H Jensen
Journal:  Chem Sci       Date:  2016-12-01       Impact factor: 9.825

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