SAGA: rapid automatic mainchain NMR assignment for large proteins
Abstract Here we describe a new algorithm for automatically determining the mainchain sequential assignment of NMR spectra for proteins. Using only the customary triple resonance experiments, assignments can be quickly found for not only small proteins having rather complete data, but also for large proteins, even when only half the residues can be assigned. The result of the calculation is not the single best assignment according to some criterion, but rather a large number of satisfactory assignments that are summarized in such a way as to help the user identify portions of the sequence that are assigned with confidence, vs. other portions where the assignment has some correlated alternatives. Thus very imperfect initial data can be used to suggest future experiments.
Content Type Journal Article
DOI 10.1007/s10858-010-9403-2
Authors
Gordon M. Crippen, University of Michigan College of Pharmacy Ann Arbor MI 48109 USA
Aikaterini Rousaki, University of Michigan LSA Biophysics Ann Arbor MI 48109 USA
Matthew Revington, University of Michigan LSA Biophysics Ann Arbor MI 48109 USA
Yongbo Zhang, University of Michigan LSA Biophysics Ann Arbor MI 48109 USA
Erik R. P. Zuiderweg, University of Michigan Medical School Department of Biological Chemistry Ann Arbor MI 48109 USA
Recent advances in segmental isotope labeling of proteins: NMR applications to large proteins and glycoproteins
Recent advances in segmental isotope labeling of proteins: NMR applications to large proteins and glycoproteins
Abstract In the last 15 years substantial advances have been made to place isotope labels in native and glycosylated proteins for NMR studies and structure determination. Key developments include segmental isotope labeling using Native Chemical Ligation, Expressed Protein Ligation and Protein Trans-Splicing. These advances are pushing the size limit of NMR spectroscopy further making larger proteins accessible for this technique. It is just emerging that segmental isotope...
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Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies.
Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies.
Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies.
J Am Chem Soc. 2010 Dec 16;
Authors: Gossert AD, Hiller S, Ferna?ndez C
The detection and structural characterization of protein-ligand interactions by solution NMR is central to functional biology research as well as to drug discovery. Here we present a robust and highly automated procedure for obtaining the resonance assignments necessary for studies of such...
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Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies
Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies
Alvar D. Gossert, Sebastian Hiller and Ce?sar Ferna?ndez
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja108383x/aop/images/medium/ja-2010-08383x_0004.gif
Journal of the American Chemical Society
DOI: 10.1021/ja108383x
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/E3PMYeBSCeE
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[NMR paper] Rapid analysis of large protein-protein complexes using NMR-derived orientational con
Rapid analysis of large protein-protein complexes using NMR-derived orientational constraints: the 95 kDa complex of LpxA with acyl carrier protein.
Related Articles Rapid analysis of large protein-protein complexes using NMR-derived orientational constraints: the 95 kDa complex of LpxA with acyl carrier protein.
J Mol Biol. 2004 Nov 5;343(5):1379-89
Authors: Jain NU, Wyckoff TJ, Raetz CR, Prestegard JH
Characterization of protein-protein interactions that are critical to the specific function of many biological systems has become a primary...
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11-24-2010 10:03 PM
Corrigendum to “BEST-HNN and 2D (HN)NH experiments for rapid backbone assignment in p
Corrigendum to “BEST-HNN and 2D (HN)NH experiments for rapid backbone assignment in proteins”
Publication year: 2010
Source: Journal of Magnetic Resonance, In Press, Corrected Proof, Available online 15 September 2010</br>
Dinesh, Kumar , Subhradip, Paul , Ramakrishna V., Hosur</br>
Source: Journal of Magnetic Resonance
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[NMR paper] Rapid and simple approach for the NMR resonance assignment of the carbohydrate chains
Rapid and simple approach for the NMR resonance assignment of the carbohydrate chains of an intact glycoprotein. Application of gradient-enhanced natural abundance 1H-13C HSQC and HSQC-TOCSY to the alpha-subunit of human chorionic gonadotropin.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Rapid and simple approach for the NMR resonance assignment of the carbohydrate chains of an intact glycoprotein. Application of gradient-enhanced natural abundance 1H-13C HSQC and HSQC-TOCSY to the alpha-subunit of...
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08-22-2010 03:29 AM
[NMR paper] Prospects for NMR of large proteins.
Prospects for NMR of large proteins.
Related Articles Prospects for NMR of large proteins.
J Biomol NMR. 1993 Jul;3(4):375-85
Authors: Wagner G
During the last decade, solution structures of many small proteins have been solved by NMR. The size of proteins that are being analyzed by NMR seems to increase steadily. Protein structures up to 18 kD have been solved so far, and spectra of proteins up to 30 kD have been assigned. Thus, NMR emerges as an attractive technique, in particular for structural studies of proteins that cannot by...
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08-21-2010 11:53 PM
Mars - automatic backbone assignment of proteins
Link to the program
Mars - robust automatic backbone assignment of proteins.
Jung YS, Zweckstetter M. J Biomol NMR. 2004 Sep;30(1):11-23.
Abstract:
MARS is a program for robust automatic backbone assignment of 13C/15N labeled proteins. It can be applied independent of the assignment complexity, it does not require tight thresholds for establishing sequential connectivity or detailed adjustment of these thresholds, it can work with a wide variety of NMR experiments and it is robust against missing chemical shift information. In case of a known 3D structure, residual dipolar...
SAGA: rapid automatic mainchain NMR assignment for large proteins
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