Publication date: Available online 16 May 2013 Source:Structure
Author(s): Vilas Menon , Brinda*K. Vallat , Joseph*M. Dybas , Andras Fiser
A remaining challenge in protein modeling is to predict structures for sequences with no sequence similarity to any experimentally solved structure. Based on earlier observations, the library of protein backbone supersecondary structure motifs (Smotifs) saturated about a decade ago. Therefore, it should be possible to build any structure from a combination of existing Smotifs with the help of limited experimental data that are sufficient to relate the backbone conformations of Smotifs between target proteins and known structures. Here, we present a hybrid modeling algorithm that relies on an exhaustive Smotif library and on nuclear magnetic resonance chemical shift patterns without any input of primary sequence information. In a test of 102 proteins, the algorithm delivered 90 homology-model-quality models, among them 24 high-quality ones, and a topologically correct solution for almost all cases. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available. Graphical abstract
[NMR paper] Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
J Biomol NMR. 2013 Apr 28;
Authors: Fritzsching KJ, Yang Y, Schmidt-Rohr K, Hong M
Abstract
We introduce a Python-based program that utilizes the large database of (13)C and (15)N chemical shifts in the Biological Magnetic...
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04-30-2013 10:21 PM
Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps
Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps
Available online 18 March 2013
Publication year: 2013
Source:Journal of Molecular Structure</br>
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NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from...
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03-19-2013 12:58 AM
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
VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy
VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy
Abstract Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR...
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12-22-2011 06:50 AM
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
[NMR paper] 1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary struct
1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary structure of glutamine-binding protein of Escherichia coli.
Related Articles 1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary structure of glutamine-binding protein of Escherichia coli.
J Biomol NMR. 1997 Feb;9(2):167-80
Authors: Yu J, Simplaceanu V, Tjandra NL, Cottam PF, Lukin JA, Ho C
1H, 13C, and 15N NMR assignments of the backbone atoms and beta-carbons have been made for liganded glutamine-binding protein (GlnBP) of Escherichia...
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08-22-2010 03:31 PM
[NMR paper] Chemical shift assignments and secondary structure of the Grb2 SH2 domain by heteronu
Chemical shift assignments and secondary structure of the Grb2 SH2 domain by heteronuclear NMR spectroscopy.
Related Articles Chemical shift assignments and secondary structure of the Grb2 SH2 domain by heteronuclear NMR spectroscopy.
J Biomol NMR. 1996 Mar;7(2):89-98
Authors: Wang YS, Frederick AF, Senior MM, Lyons BA, Black S, Kirschmeier P, Perkins LM, Wilson O
The growth factor receptor-bound protein-2 (Grb-2) is an adaptor protein that mediates signal transduction pathways. Chemical shift assignments were obtained for the SH2 domain of...
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08-22-2010 02:27 PM
[NMR paper] 1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and magnes
1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and magnesium-binding characteristics of the Bacillus subtilis response regulator, Spo0F, determined by heteronuclear high-resolution NMR.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles 1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and...
Modeling Proteins Using a Super-Secondary Structure Library and NMR Chemical Shift Information
Linear Mode
