Related ArticlesImprovement of hydrogen bond geometry in protein NMR structures by residual dipolar couplings--an assessment of the interrelation of NMR restraints.
J Biomol NMR. 2004 Jan;28(1):31-41
Authors: Jensen PR, Axelsen JB, Lerche MH, Poulsen FM
We have examined how the hydrogen bond geometry in three different proteins is affected when structural restraints based on measurements of residual dipolar couplings are included in the structure calculations. The study shows, that including restraints based solely on (1)H(N)-(15)N residual dipolar couplings has pronounced impact on the backbone rmsd and Ramachandran plot but does not improve the hydrogen bond geometry. In the case of chymotrypsin inhibitor 2 the addition of (13)CO-(13)C(alpha) and (15)N-(13)CO one bond dipolar couplings as restraints in the structure calculations improved the hydrogen bond geometry to a quality comparable to that obtained in the 1.8 A resolution X-ray structure of this protein. A systematic restraint study was performed, in which four types of restraints, residual dipolar couplings, hydrogen bonds, TALOS angles and NOEs, were allowed in two states. This study revealed the importance of using several types of residual dipolar couplings to get good hydrogen bond geometry. The study also showed that using a small set of NOEs derived only from the amide protons, together with a full set of residual dipolar couplings resulted in structures of very high quality. When reducing the NOE set, it is mainly the side-chain to side-chain NOEs that are removed. Despite of this the effect on the side-chain packing is very small when a reduced NOE set is used, which implies that the over all fold of a protein structure is mainly determined by correct folding of the backbone.
How uniform is the peptide plane geometry? A high-accuracy NMR study of dipolar Cαâ??Câ?²/HNâ??N cross-correlated relaxation
How uniform is the peptide plane geometry? A high-accuracy NMR study of dipolar Cαâ??Câ?²/HNâ??N cross-correlated relaxation
Abstract Highly precise and accurate measurements of very small NMR cross-correlated relaxation rates, namely those between protein HiNâ??Ni and Ciâ??1αâ??Ciâ??1â?² dipoles, are demonstrated with an error of 0.03 sâ??1 for GB3. Because the projection angles between the two dipole vectors are very close to the magic angle the rates range only from â??0.2 to +0.2 sâ??1. Small changes of the average vector orientations have a dramatic impact on the relative values....
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Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings.
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings.
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings.
J Am Chem Soc. 2011 Apr 5;
Authors: Sgourakis NG, Lange OF, Dimaio F, Andre? I, Fitzkee NC, Rossi P, Montelione GT, Bax A, Baker D
Symmetric protein dimers, trimers, and higher-order cyclic oligomers play key roles in many biological processes. However, structural studies of oligomeric systems by solution NMR...
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04-07-2011 09:54 PM
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings
Nikolaos G. Sgourakis, Oliver F. Lange, Frank DiMaio, Ingemar Andre?, Nicholas C. Fitzkee, Paolo Rossi, Gaetano T. Montelione, Ad Bax and David Baker
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja111318m/aop/images/medium/ja-2010-11318m_0008.gif
Journal of the American Chemical Society
DOI: 10.1021/ja111318m
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...
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[NMR paper] Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data.
Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data.
Related Articles Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data.
Proteins. 2005 Aug 15;60(3):367-81
Authors: van Dijk AD, Fushman D, Bonvin AM
When classical, Nuclear Overhauser Effect (NOE)-based approaches fail, it is possible, given high-resolution...
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12-01-2010 06:56 PM
[NMR paper] The importance of being ordered: improving NMR structures using residual dipolar coup
The importance of being ordered: improving NMR structures using residual dipolar couplings.
Related Articles The importance of being ordered: improving NMR structures using residual dipolar couplings.
C R Biol. 2002 Sep;325(9):957-66
Authors: Gronenborn AM
Residual dipolar couplings arise from small degrees of alignment of molecules in a magnetic field. Most biomolecules lack sufficient intrinsic magnetic susceptibility anisotropies for practical purposes; however, alignment can be achieved using dilute aqueous phospholipid mixtures, colloidal...
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11-24-2010 08:58 PM
[NMR paper] Detecting protein kinase recognition modes of calmodulin by residual dipolar coupling
Detecting protein kinase recognition modes of calmodulin by residual dipolar couplings in solution NMR.
Related Articles Detecting protein kinase recognition modes of calmodulin by residual dipolar couplings in solution NMR.
Biochemistry. 2002 Oct 29;41(43):12899-906
Authors: Mal TK, Skrynnikov NR, Yap KL, Kay LE, Ikura M
Calmodulin-regulated serine/threonine kinases (CaM kinases) play crucial roles in Ca2+-dependent signaling transduction pathways in eukaryotes. Despite having a similar overall molecular architecture of catalytic and...
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11-24-2010 08:58 PM
[NMR paper] Temperature-dependence of protein hydrogen bond properties as studied by high-resolut
Temperature-dependence of protein hydrogen bond properties as studied by high-resolution NMR.
Related Articles Temperature-dependence of protein hydrogen bond properties as studied by high-resolution NMR.
J Mol Biol. 2002 Apr 12;317(5):739-52
Authors: Cordier F, Grzesiek S
The temperature-dependence of a large number of NMR parameters describing hydrogen bond properties in the protein ubiquitin was followed over a range from 5 to 65 degrees C. The parameters comprise hydrogen bond (H-bond) scalar couplings, h3JNC', chemical shifts, amide...
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11-24-2010 08:49 PM
[NMR paper] Protein structural motif recognition via NMR residual dipolar couplings.
Protein structural motif recognition via NMR residual dipolar couplings.
Related Articles Protein structural motif recognition via NMR residual dipolar couplings.
J Am Chem Soc. 2001 Feb 14;123(6):1222-9
Authors: Andrec M, Du P, Levy RM
NMR residual dipolar couplings have great potential to provide rapid structural information for proteins in the solution state. This information even at low resolution may be used to advantage in proteomics projects that seek to annotate large numbers of gene products for entire genomes. In this paper, we...
Improvement of hydrogen bond geometry in protein NMR structures by residual dipolar c
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