Related ArticlesRefinement of the main chain directed assignment strategy for the analysis of 1H NMR spectra of proteins.
Biophys J. 1991 May;59(5):1101-12
Authors: Wand AJ, Nelson SJ
The underlying basis of the main chain directed (MCD) resonance assignment strategy for the analysis of 1H NMR spectra of proteins is reexamined. The criteria used in the construction of the patterns used in the MCD method have been extended to increase the robustness of the approach to the presence of variable protein secondary structure and significant spectral degeneracy. These criteria have led to the development of several dozen patterns exclusively involving the short distance relationships between main chain amide NH-C alpha-H-C beta H (NAB) J-coupled subspin systems of the amino acid residues. The MCD patterns have been examined for fidelity and frequency of occurrence in a database composed of the high resolution crystal structures of 39 proteins. The analysis has identified several extremely robust patterns, suitable for initiating a hierarchical construction of units of secondary structure based upon a systematic analysis of two-dimensional nuclear Overhauser effect spectra. A formal procedure, suitable for the computer assisted application of the MCD strategy, is developed. This procedure, termed MCDPAT, has been applied to the analysis of the crystal structures of human ubiquitin, T4 lysozyme, and ribonuclease A. It has been found that the MCDPAT procedure is conservative producing no significant errors and is globally successful in correctly identifying the appropriate units of secondary structure contained in these three proteins.
Extension of the HA-detection based approach: (HCA)CON(CA)H and (HCA)NCO(CA)H experiments for the main-chain assignment of intrinsically disordered proteins
Extension of the HA-detection based approach: (HCA)CON(CA)H and (HCA)NCO(CA)H experiments for the main-chain assignment of intrinsically disordered proteins
Abstract Extensive resonance overlap exacerbates assignment of intrinsically disordered proteins (IDPs). This issue can be circumvented by utilizing 15N, 13Cā?² and 1HN spins, where the chemical shift dispersion is mainly dictated by the characteristics of consecutive amino acid residues. Especially 15N and 13Cā?² spins offer superior chemical shift dispersion in comparison to 13CĪ± and 13CĪ² spins. However, HN-detected experiments...
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An intraresidual i(HCA)CO(CA)NH experiment for the assignment of main-chain resonances in 15N, 13C labeled proteins
An intraresidual i(HCA)CO(CA)NH experiment for the assignment of main-chain resonances in 15N, 13C labeled proteins
Abstract An improved pulse sequence, intraresidual i(HCA)CO(CA)NH, is described for establishing solely 13Cā?²(i), 15N(i), 1HN(i) connectivities in uniformly 15N/13C-labeled proteins. In comparison to the ā??out-and-backā?? style intra-HN(CA)CO experiment, the new pulse sequence offers at least two-fold higher experimental resolution in the 13Cā?² dimension and on average 1.6 times higher sensitivity especially for residues in Ī±-helices. Performance of the new experiment...
[NMR paper] Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studi
Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studies of R. capsulatus ferrocytochrome c2.
Related Articles Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studies of R. capsulatus ferrocytochrome c2.
Biochemistry. 2001 Jun 5;40(22):6559-69
Authors: Flynn PF, Bieber Urbauer RJ, Zhang H, Lee AL, Wand AJ
A detailed characterization of the main chain and side chain dynamics in R. capsulatus ferrocytochrome c(2) derived from (2)H NMR relaxation of methyl group resonances is...
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[NMR paper] The NOESY jigsaw: automated protein secondary structure and main-chain assignment fro
The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data.
Related Articles The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data.
J Comput Biol. 2000;7(3-4):537-58
Authors: Bailey-Kellogg C, Widge A, Kelley JJ, Berardi MJ, Bushweller JH, Donald BR
High-throughput, data-directed computational protocols for Structural Genomics (or Proteomics) are required in order to evaluate the protein products of genes for structure and...
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[NMR paper] Detection of very weak side chain-main chain hydrogen bonding interactions in medium-
Detection of very weak side chain-main chain hydrogen bonding interactions in medium-size 13C/15N-labeled proteins by sensitivity-enhanced NMR spectroscopy.
Related Articles Detection of very weak side chain-main chain hydrogen bonding interactions in medium-size 13C/15N-labeled proteins by sensitivity-enhanced NMR spectroscopy.
J Biomol NMR. 2000 May;17(1):79-82
Authors: Liu A, Hu W, Majumdar A, Rosen MK, Patel DJ
We describe the direct observation of very weak side chain-main chain hydrogen bonding interactions in medium-size 13C/15N-labeled...
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[NMR paper] NMR analysis of main-chain conformational preferences in an unfolded fibronectin-bind
NMR analysis of main-chain conformational preferences in an unfolded fibronectin-binding protein.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles NMR analysis of main-chain conformational preferences in an unfolded fibronectin-binding protein.
J Mol Biol. 1997 Nov 28;274(2):152-9
Authors: Penkett CJ, Redfield C, Dodd I, Hubbard J, McBay DL, Mossakowska DE, Smith RA, Dobson CM, Smith LJ
A 130-residue fragment of the Staphylococcus aureus fibronectin-binding protein has...
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[NMR paper] Analysis of main chain torsion angles in proteins: prediction of NMR coupling constan
Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations.
J Mol Biol. 1996 Jan 26;255(3):494-506
Authors: Smith LJ, Bolin KA, Schwalbe H, MacArthur MW, Thornton JM, Dobson CM
Using a data base of 85 high resolution protein...