Related ArticlesHigh-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases.
Protein Sci. 2005 Jun;14(6):1597-608
Authors: Liu G, Li Z, Chiang Y, Acton T, Montelione GT, Murray D, Szyperski T
The structural biology of proteins mediating iron-sulfur (Fe-S) cluster assembly is central for understanding several important biological processes. Here we present the NMR structure of the 16-kDa protein YgdK from Escherichia coli, which shares 35% sequence identity with the E. coli protein SufE. The SufE X-ray crystal structure was solved in parallel with the YdgK NMR structure in the Northeast Structural Genomics (NESG) consortium. Both proteins are (1) key components for Fe-S metabolism, (2) exhibit the same distinct fold, and (3) belong to a family of at least 70 prokaryotic and eukaryotic sequence homologs. Accurate homology models were calculated for the YgdK/SufE family based on YgdK NMR and SufE crystal structure. Both structural templates contributed equally, exemplifying synergy of NMR and X-ray crystallography. SufE acts as an enhancer of the cysteine desulfurase activity of SufS by SufE-SufS complex formation. A homology model of CsdA, a desulfurase encoded in the same operon as YgdK, was modeled using the X-ray structure of SufS as a template. Protein surface and electrostatic complementarities strongly suggest that YgdK and CsdA likewise form a functional two-component desulfurase complex. Moreover, structural features of YgdK and SufS, which can be linked to their interaction with desulfurases, are conserved in all homology models. It thus appears very likely that all members of the YgdK/SufE family act as enhancers of Suf-S-like desulfurases. The present study exemplifies that "refined" selection of two (or more) targets enables high-quality homology modeling of large protein families.
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Abstract While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1H chemical shifts in which molecular motions, the...
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[NMR paper] Improving the quality of protein structures derived by NMR spectroscopy.
Improving the quality of protein structures derived by NMR spectroscopy.
Related Articles Improving the quality of protein structures derived by NMR spectroscopy.
J Biomol NMR. 2002 Mar;22(3):281-9
Authors: Spronk CA, Linge JP, Hilbers CW, Vuister GW
Biomolecular structures provide the basis for many studies in several research areas such as homology modelling, structure-based drug design and functional genomics. It is an important prerequisite that the structure is reliable in terms of accurate description of the experimental data, and in...
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[NMR paper] The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general
The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases.
Related Articles The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases.
EMBO J. 1998 Nov 2;17(21):6377-84
Authors: Stoldt M, Wöhnert J, Görlach M, Brown LR
The structure of the Escherichia coli ribosomal protein L25 has been determined to an r.m.s. displacement of backbone heavy atoms of 0.62 +/- 0.14 A by multi-dimensional...
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[NMR paper] Improving the quality of NMR and crystallographic protein structures by means of a co
Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases.
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 Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases.
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[NMR paper] AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved
AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
Related Articles AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
J Biomol NMR. 1996 Dec;8(4):477-86
Authors: Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM
The AQUA and PROCHECK-NMR programs provide a means of validating the geometry and restraint violations of an ensemble of protein structures solved by solution NMR. The outputs include a detailed breakdown of the restraint violations, a...
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[NMR paper] An approach to protein homology modelling based on an ensemble of NMR structures: app
An approach to protein homology modelling based on an ensemble of NMR structures: application to the Sox-5 HMG-box protein.
Related Articles An approach to protein homology modelling based on an ensemble of NMR structures: application to the Sox-5 HMG-box protein.
Protein Eng. 1995 Jul;8(7):615-25
Authors: Adzhubei AA, Laughton CA, Neidle S
A new approach has been developed to reduce multiple protein structures obtained from NMR structure analysis to a smaller number of representative structures which still reflect the structural diversity of...
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[NMR paper] Application of 1H NMR chemical shifts to measure the quality of protein structures.
Application of 1H NMR chemical shifts to measure the quality of protein structures.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Application of 1H NMR chemical shifts to measure the quality of protein structures.
J Mol Biol. 1995 Apr 7;247(4):541-6
Authors: Williamson MP, Kikuchi J, Asakura T
We have developed a program that can calculate proton NMR chemical shifts for proteins, using a set of co-ordinates provided for example from an X-ray or NMR structure. When...
High-quality homology models derived from NMR and X-ray structures of E. coli protein
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