Related ArticlesNMR solution structure, backbone mobility, and homology modeling of c-type cytochromes from gram-positive bacteria.
Chembiochem. 2002 Apr 2;3(4):299-310
Authors: Banci L, Bertini I, Ciurli S, Dikiy A, Dittmer J, Rosato A, Sciara G, Thompsett AR
The solution structure of oxidized cytochrome c(553) (71 amino acid residues) from the Gram-positive bacterium Bacillus pasteurii is here reported and compared with the available crystal structure. The solution structure is obtained from 1609 meaningful NOE data (22.7 per residue), 76 dihedral angles, and 59 pseudocontact shifts. The root mean square deviations from the average structure are 0.25+/-0.07 and 0.59+/-0.13 A for the backbone and all heavy atoms, respectively, and the quality assessment of the structure is satisfactory. The solution structure closely reproduces the fold observed in the crystal structure. The backbone mobility was then investigated through amide (15)N relaxation rate and (15)N-(1)H NOE measurements. The protein is rigid in both the sub-nanosecond and millisecond time scales, probably due to the relatively large heme:number of amino acids ratio. Modeling of eight c-type cytochromes from other Gram-positive bacteria with a high sequence identity (>30 %) to the present cytochrome c(553) was performed. Analysis of consensus features accounts for the relatively low reduction potential as being due to extensive heme hydration and indicates residues 34-35, 44-46, 69-72, and 75 as a conserved hydrophobic patch for the interaction with a protein partner. At variance with mitochondrial c-type cytochrome, this protein does not experience pH-dependent coordination equilibria. The reasons for this difference are analyzed.
Development of Non-Peptide Ligands of Growth Factor Receptor-Bound Protein 2-Src Homology 2 Domain Using Molecular Modeling and NMR Spectroscopy (†).
Development of Non-Peptide Ligands of Growth Factor Receptor-Bound Protein 2-Src Homology 2 Domain Using Molecular Modeling and NMR Spectroscopy (†).
Development of Non-Peptide Ligands of Growth Factor Receptor-Bound Protein 2-Src Homology 2 Domain Using Molecular Modeling and NMR Spectroscopy (†).
J Med Chem. 2011 Jan 27;
Authors: Orcajo-Rinco?n AL, Ortega-Gutie?rrez S, Serrano P, Torrecillas IR, Wu?thrich K, Campillo M, Pardo L, Viso A, Benhamu? B, Lo?pez-Rodri?guez ML
We report a novel series of non-peptide ligands that inhibit the growth...
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01-29-2011 12:35 PM
Optimization of amino acid type-specific (13)C and (15)N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm.
Optimization of amino acid type-specific (13)C and (15)N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm.
Optimization of amino acid type-specific (13)C and (15)N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm.
J Biomol NMR. 2010 Dec 18;
Authors: Hefke F, Bagaria A, Reckel S, Ullrich SJ, Dötsch V, Glaubitz C, Güntert P
We present a computational method for finding optimal labeling patterns for the backbone...
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12-21-2010 01:00 PM
Optimization of amino acid type-specific 13C and 15N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm
Optimization of amino acid type-specific 13C and 15N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm
Abstract We present a computational method for finding optimal labeling patterns for the backbone assignment of membrane proteins and other large proteins that cannot be assigned by conventional strategies. Following the approach of Kainosho and Tsuji (Biochemistry 21:6273â??6279 (1982)), types of amino acids are labeled with 13C or/and 15N such that cross peaks between 13CO(i â?? 1) and 15NH(i) result only for pairs...
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12-21-2010 02:14 AM
[NMR paper] Structural insight into human Zn(2+)-bound S100A2 from NMR and homology modeling.
Structural insight into human Zn(2+)-bound S100A2 from NMR and homology modeling.
Related Articles Structural insight into human Zn(2+)-bound S100A2 from NMR and homology modeling.
Biochem Biophys Res Commun. 2001 Oct 26;288(2):462-7
Authors: Randazzo A, Acklin C, Schäfer BW, Heizmann CW, Chazin WJ
The S100 subfamily of EF-hand proteins is distinguished by the binding of Zn(2+) in addition to Ca(2+). In an effort to understand the role of Zn(2+) in modulating the activity of S100 proteins, we have carried out heteronuclear NMR studies of...
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11-19-2010 08:44 PM
[NMR paper] A model for human cytochrome P450 2D6 based on homology modeling and NMR studies of s
A model for human cytochrome P450 2D6 based on homology modeling and NMR studies of substrate binding.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles A model for human cytochrome P450 2D6 based on homology modeling and NMR studies of substrate binding.
Biochemistry. 1996 Apr 9;35(14):4540-50
Authors: Modi S, Paine MJ, Sutcliffe MJ, Lian LY, Primrose WU, Wolf CR, Roberts GC
The cytochrome P450 responsible for the debrisoquine/sparteine polymorphism (P450 2D6) has been produced in large...
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08-22-2010 02:27 PM
[NMR paper] NMR characterization of side chain flexibility and backbone structure in the type I a
NMR characterization of side chain flexibility and backbone structure in the type I antifreeze protein at near freezing temperatures.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles NMR characterization of side chain flexibility and backbone structure in the type I antifreeze protein at near freezing temperatures.
Biochemistry. 1996 Dec 24;35(51):16698-704
Authors: Gronwald W, Chao H, Reddy DV, Davies PL, Sykes BD, Sönnichsen FD
The flexibility of the polar side chains in the...
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08-22-2010 02:20 PM
[NMR paper] NMR characterization and solution structure determination of the oxidized cytochrome
NMR characterization and solution structure determination of the oxidized cytochrome c7 from Desulfuromonas acetoxidans.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-custom-pnas_full_free.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles NMR characterization and solution structure determination of the oxidized cytochrome c7 from Desulfuromonas acetoxidans.
Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14396-400
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Protein Structure Prediction: Threading & Homology Modeling - Thomas Steinke
Protein Structure Prediction: Threading & Homology Modeling - Thomas Steinke, Zuse Institute Berlin, Berlin Center for Genom Based Bioinformatics
http://lectures.molgen.mpg.de/Algorithmische_Bioinformatik_WS0405/material/Steinke_lecture_19_1.pdf
NMR solution structure, backbone mobility, and homology modeling of c-type cytochrome
Linear Mode
