Publication date: Available online 15 July 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
Author(s): Mark V. Berjanskii, David S. Wishart
Chemical shifts are among the most informative parameters in protein NMR. They provide wealth of information about protein secondary and tertiary structure, protein flexibility, and protein-ligand binding. In this report, we review the progress in interpreting and utilizing protein chemical shifts that has occurred over the past 25years, with a particular focus on the large body of work arising from our group and other Canadian NMR laboratories. More specifically, this review focuses on describing, assessing, and providing some historical context for various chemical shift-based methods to: (1) determine protein secondary and super-secondary structure; (2) derive protein torsion angles; (3) assess protein flexibility; (4) predict residue accessible surface area; (5) refine 3D protein structures; (6) determine 3D protein structures and (7) characterize intrinsically disordered proteins. This review also briefly covers some of the methods that we previously developed to predict chemical shifts from 3D protein structures and/or protein sequence data. It is hoped that this review will help to increase awareness of the considerable utility of NMR chemical shifts in structural biology and facilitate more widespread adoption of chemical-shift based methods by the NMR spectroscopists, structural biologists, protein biophysicists, and biochemists worldwide. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
[NMR paper] A robust algorithm for optimizing protein structures with NMR chemical shifts.
A robust algorithm for optimizing protein structures with NMR chemical shifts.
Related Articles A robust algorithm for optimizing protein structures with NMR chemical shifts.
J Biomol NMR. 2015 Sep 7;
Authors: Berjanskii M, Arndt D, Liang Y, Wishart DS
Abstract
Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts....
Interpreting Protein Structural Dynamics from NMR Chemical Shifts
Interpreting Protein Structural Dynamics from NMR Chemical Shifts
Paul Robustelli, Kate A. Stafford and Arthur G. Palmer
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja300265w/aop/images/medium/ja-2012-00265w_0003.gif
Journal of the American Chemical Society
DOI: 10.1021/ja300265w
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03-28-2012 09:28 PM
Unraveling the 13C NMR Chemical Shiftsin Single-Walled Carbon Nanotubes: Dependence on Diameter and ElectronicStructure
Unraveling the 13C NMR Chemical Shiftsin Single-Walled Carbon Nanotubes: Dependence on Diameter and ElectronicStructure
Chaiwat Engtrakul, Veronica M. Irurzun, Erica L. Gjersing, Josh M. Holt, Brian A. Larsen, Daniel E. Resasco and Jeffrey L. Blackburn
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja211181q/aop/images/medium/ja-2011-11181q_0004.gif
Journal of the American Chemical Society
DOI: 10.1021/ja211181q
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02-29-2012 10:20 AM
4D prediction of protein 1H chemical shifts
4D prediction of protein 1H chemical shifts
Abstract A 4D approach for protein 1H chemical shift prediction was explored. The 4th dimension is the molecular flexibility, mapped using molecular dynamics simulations. The chemical shifts were predicted with a principal component model based on atom coordinates from a database of 40 protein structures. When compared to the corresponding non-dynamic (3D) model, the 4th dimension improved prediction by 6â??7%. The prediction method achieved RMS errors of 0.29 and 0.50 ppm for Hα and HN shifts, respectively. However, for individual proteins...
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01-09-2011 12:46 PM
[NMR paper] Secondary structural effects on protein NMR chemical shifts.
Secondary structural effects on protein NMR chemical shifts.
Related Articles Secondary structural effects on protein NMR chemical shifts.
J Biomol NMR. 2004 Nov;30(3):233-44
Authors: Wang Y
For an amino acid in protein, its chemical shift, delta(phi, psi)(s), is expressed as a function of its backbone torsion angles (phi and psi) and secondary state (s): delta(phi, psi)(s=deltaphi, psi)_coil+Deltadelta(phi, psi)_s), where delta(phi, psi)(coil) represents its chemical shift at coil state (s=coil); Delta delta(phi, psi)(s) (s=sheet or helix) is...
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11-24-2010 10:03 PM
Mapping of protein structural ensembles by chemical shifts
Abstract Applying the chemical shift prediction programs SHIFTX and SHIFTS to a data base of protein structures with known chemical shifts we show that the averaged chemical shifts predicted from the structural ensembles explain better the experimental data than the lowest energy structures. This is in agreement with the fact that proteins in solution occur in multiple conformational states in fast exchange on the chemical shift time scale. However, in contrast to the real conditions in solution at ambient temperatures, the standard NMR structural calculation methods as well chemical shift...
Unraveling the meaning of chemical shifts in protein NMR
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