Publication date: Available online 7 March 2015 Source:Journal of Magnetic Resonance
Author(s): Da-Wei Li , Dan Meng , Rafael Brüschweiler
A robust NMR resonance assignment method is introduced for proteins whose 3D structure has previously been determined by X-ray crystallography. The goal of the method is to obtain a subset of correct assignments from a parsimonious set of 3D NMR experiments of 15N, 13C labeled proteins. Chemical shifts of sequential residue pairs are predicted from static protein structures using PPM_One, which are then compared with the corresponding experimental shifts. Globally optimized weighted matching identifies the assignments that are robust with respect to small changes in NMR cross-peak positions. The method, termed PASSPORT, is demonstrated for 4 proteins with 100 - 250 amino acids using 3D NHCA and a 3D CBCA(CO)NH experiments as input producing correct assignments with high reliability for 22% of the residues. The method, which works best for Gly, Ala, Ser, and Thr residues, provides assignments that serve as anchor points for additional assignments by both manual and semi-automated methods or they can be directly used for further studies, e.g. on ligand binding, protein dynamics, or post-translational modification, such as phosphorylation. Graphical abstract
[NMR paper] An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction.
An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction.
Related Articles An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction.
J Biomol NMR. 2014 Jun 19;
Authors: Wiedemann C, Bellstedt P, Herbst C, Görlach M, Ramachandran R
Abstract
A procedure for the simultaneous acquisition of {HNCOCANH & HCCCONH} chemical shift correlation spectra employing sequential data acquisition for moderately sized...
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06-20-2014 08:14 PM
An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction
An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction
Abstract
A procedure for the simultaneous acquisition of {HNCOCANH & HCCCONH} chemical shift correlation spectra employing sequential \(^{1}\hbox {H}\) data acquisition for moderately sized proteins is presented. The suitability of the approach for obtaining sequential resonance assignments, including complete ...
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06-19-2014 10:21 PM
[NMR paper] EZ-ASSIGN, a program for exhaustive NMR chemical shift assignments of large proteins from complete or incomplete triple-resonance data.
EZ-ASSIGN, a program for exhaustive NMR chemical shift assignments of large proteins from complete or incomplete triple-resonance data.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles EZ-ASSIGN, a program for exhaustive NMR chemical shift assignments of large proteins from complete or incomplete triple-resonance data.
J Biomol NMR. 2013 Sep 11;
Authors: Zuiderweg ER, Bagai I, Rossi P, Bertelsen EB
Abstract
For several of the proteins...
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09-12-2013 11:02 PM
Influence of 1H chemical shift assignments of the interface residues on structure determinations of homodimeric proteins
Influence of 1H chemical shift assignments of the interface residues on structure determinations of homodimeric proteins
Publication year: 2012
Source:Journal of Magnetic Resonance</br>
Yi-Jan Lin, Donata K. Kirchner, Peter Güntert</br>
Homodimeric proteins pose a difficulty for NMR structure determination because the degeneracy of the chemical shifts in the two identical monomers implies an ambiguity in all assignments of distance restraints. For homodimeric proteins, residues involved in the interface between two monomers provide essential intermolecular NOEs. The...
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07-14-2012 01:53 PM
Structure-based prediction of methyl chemical shifts in proteins
Structure-based prediction of methyl chemical shifts in proteins
Abstract Protein methyl groups have recently been the subject of much attention in NMR spectroscopy because of the opportunities that they provide to obtain information about the structure and dynamics of proteins and protein complexes. With the advent of selective labeling schemes, methyl groups are particularly interesting in the context of chemical shift based protein structure determination, an approach that to date has exploited primarily the mapping between protein structures and backbone chemical shifts. In order to...
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07-15-2011 09:10 PM
[NMR paper] CAMRA: chemical shift based computer aided protein NMR assignments.
CAMRA: chemical shift based computer aided protein NMR assignments.
Related Articles CAMRA: chemical shift based computer aided protein NMR assignments.
J Biomol NMR. 1998 Oct;12(3):395-405
Authors: Gronwald W, Willard L, Jellard T, Boyko RF, Rajarathnam K, Wishart DS, Sönnichsen FD, Sykes BD
A suite of programs called CAMRA (Computer Aided Magnetic Resonance Assignment) has been developed for computer assisted residue-specific assignments of proteins. CAMRA consists of three units: ORB, CAPTURE and PROCESS. ORB predicts NMR chemical shifts...
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11-17-2010 11:15 PM
Protein secondary structure prediction using NMR chemical shift data.
Protein secondary structure prediction using NMR chemical shift data.
Related Articles Protein secondary structure prediction using NMR chemical shift data.
J Bioinform Comput Biol. 2010 Oct;8(5):867-84
Authors: Zhao Y, Alipanahi B, Li SC, Li M
Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b)...
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10-29-2010 07:05 PM
SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of
Abstract NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and 13Cβ chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures,...