NMR Structural Inference of Symmetric Homo-Oligomers.
J Comput Biol. 2011 Jun 30;
Authors: Chandola H, Yan AK, Potluri S, Donald BR, Bailey-Kellogg C
Abstract Symmetric homo-oligomers represent a majority of proteins, and determining their structures helps elucidate important biological processes, including ion transport, signal transduction, and transcriptional regulation. In order to account for the noise and sparsity in the distance restraints used in Nuclear Magnetic Resonance (NMR) structure determination of cyclic (C(n)) symmetric homo-oligomers, and the resulting uncertainty in the determined structures, we develop a Bayesian structural inference approach. In contrast to traditional NMR structure determination methods, which identify a small set of low-energy conformations, the inferential approach characterizes the entire posterior distribution of conformations. Unfortunately, traditional stochastic techniques for inference may under-sample the rugged landscape of the posterior, missing important contributions from high-quality individual conformations and not accounting for the possible aggregate effects on inferred quantities from numerous unsampled conformations. However, by exploiting the geometry of symmetric homo-oligomers, we develop an algorithm that provides provable guarantees for the posterior distribution and the inferred mean atomic coordinates. Using experimental restraints for three proteins, we demonstrate that our approach is able to objectively characterize the structural diversity supported by the data. By simulating spurious and missing restraints, we further demonstrate that our approach is robust, degrading smoothly with noise and sparsity.
PMID: 21718128 [PubMed - as supplied by publisher]
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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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
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[NMR paper] High-throughput inference of protein-protein interfaces from unassigned NMR data.
High-throughput inference of protein-protein interfaces from unassigned NMR data.
Related Articles High-throughput inference of protein-protein interfaces from unassigned NMR data.
Bioinformatics. 2005 Jun;21 Suppl 1:i292-301
Authors: Mettu RR, Lilien RH, Donald BR
SUMMARY: We cast the problem of identifying protein-protein interfaces, using only unassigned NMR spectra, into a geometric clustering problem. Identifying protein-protein interfaces is critical to understanding inter- and intra-cellular communication, and NMR allows the study of...
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11-25-2010 08:21 PM
[NMR paper] NMR studies of the aggregation of glucagon-like peptide-1: formation of a symmetric h
NMR studies of the aggregation of glucagon-like peptide-1: formation of a symmetric helical dimer.
Related Articles NMR studies of the aggregation of glucagon-like peptide-1: formation of a symmetric helical dimer.
FEBS Lett. 2002 Mar 27;515(1-3):165-70
Authors: Chang X, Keller D, O'Donoghue SI, Led JJ
Nuclear magnetic resonance (NMR) spectroscopy reveals that higher-order aggregates of glucagon-like peptide-1-(7-36)-amide (GLP-1) in pure water at pH 2.5 are disrupted by 35% 2,2,2-trifluoroethanol (TFE), and form a stable and highly symmetric...
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11-24-2010 08:49 PM
Structural NMR of Protein Oligomers using Hybrid Methods.
Structural NMR of Protein Oligomers using Hybrid Methods.
Related Articles Structural NMR of Protein Oligomers using Hybrid Methods.
J Struct Biol. 2010 Nov 10;
Authors: Wang X, Lee HW, Liu Y, Prestegard JH
Solving structures of native oligomeric protein complexes using traditional high resolution NMR techniques remains challenging. However, increased utilization of computational platforms, and integration of information from less traditional NMR techniques with data from other complementary biophysical methods, promises to extend the boundary of...
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11-16-2010 04:13 PM
[NMR paper] High resolution NMR solution structure of the leucine zipper domain of the c-Jun homo
High resolution NMR solution structure of the leucine zipper domain of the c-Jun homodimer.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-standard-jbc_full_free.gif Related Articles High resolution NMR solution structure of the leucine zipper domain of the c-Jun homodimer.
J Biol Chem. 1996 Jun 7;271(23):13663-7
Authors: Junius FK, O'Donoghue SI, Nilges M, Weiss AS, King GF
The solution structure of the c-Jun leucine zipper domain has been determined to high resolution using a new...
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[NMR paper] A calculation strategy for the structure determination of symmetric dimers by 1H NMR.
A calculation strategy for the structure determination of symmetric dimers by 1H NMR.
Related Articles A calculation strategy for the structure determination of symmetric dimers by 1H NMR.
Proteins. 1993 Nov;17(3):297-309
Authors: Nilges M
The structure determination of symmetric dimers by NMR is impeded by the ambiguity of inter- and intramonomer NOE crosspeaks. In this paper, a calculation strategy is presented that allows the calculation of dimer structures without resolving the ambiguity by additional experiments (like asymmetric...
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[NMR paper] Disulfide bonds in homo- and heterodimers of EF-hand subdomains of calbindin D9k: sta
Disulfide bonds in homo- and heterodimers of EF-hand subdomains of calbindin D9k: stability, calcium binding, and NMR studies.
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 Disulfide bonds in homo- and heterodimers of EF-hand subdomains of calbindin D9k: stability, calcium binding, and NMR studies.
Protein Sci. 1993 Jun;2(6):985-1000
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