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 (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., 13Câ??13C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (â??0.75) commensurate to the control (â??0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.
Content Type Journal Article
Category Article
Pages 1-16
DOI 10.1007/s10858-011-9576-3
Authors
Michael C. Brothers, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Anna E. Nesbitt, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Michael J. Hallock, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Sanjeewa G. Rupasinghe, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Ming Tang, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Jason Harris, Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
Jerome Baudry, Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
Mary A. Schuler, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Chad M. Rienstra, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids
Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids
Abstract Unravelling the complex correlation between chemical shifts of 13 C α, 13 C β, 13 C�, 1 H α, 15 N, 1 H N atoms in amino acids of proteins from NMR experiment and local structural environments of amino acids facilitates the assignment of secondary structures of proteins. This is an important impetus for both determining the three-dimensional structure and understanding the biological function of proteins. The previous...
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[NMR paper] Phosphorylated amino acids: model compounds for solid-state 31P NMR spectroscopic stu
Phosphorylated amino acids: model compounds for solid-state 31P NMR spectroscopic studies of proteins.
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Magn Reson Chem. 2004 Apr;42(4):369-72
Authors: Iuga A, Brunner E
Solid-state 31P NMR spectroscopy was applied to measure the isotropic chemical shifts, chemical shift anisotropies and asymmetry parameters of three phosphorylated amino acids, O-phospho-L-serine, O-phospho-L-threonine and O-phospho-L-tyrosine. The...
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Protein secondary structure prediction using NMR chemical shift data.
Protein secondary structure prediction using NMR chemical shift data.
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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] 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 03:03 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.
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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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[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...
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The predictive accuracy of secondary chemical shifts is more affected by protein seco
Abstract Biomolecular NMR spectroscopy frequently employs estimates of protein secondary structure using secondary chemical shift (Î?δ) values, measured as the difference between experimental and random coil chemical shifts (RCCS). Most published random coil data have been determined in aqueous conditions, reasonable for non-membrane proteins, but potentially less relevant for membrane proteins. Two new RCCS sets are presented here, determined in dimethyl sulfoxide (DMSO) and chloroform:methanol:water (4:4:1 by volume) at 298 K. A web-based program, CS-CHEMeleon, has been implemented to...
VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy
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