The conformational properties of an 18 residues peptide spanning the entire sequence, L1KTPA5QFDAD10ELRAA15MKG, of the first helix (A-helix) of domain 2 of annexin I, were thoroughly investigated. This fragment exhibits several singular features, and in particular, two successive potential capping boxes, T3xxQ6 and D8xxE11. The former corresponds to the native hydrogen bond network stabilizing the alpha helix N-terminus in the protein; the latter is a non-native capping box able to break the helix at residue D8, and is observed in the domain 2 partially folded state. Using 2D-NMR techniques, we showed that two main populations of conformers coexist in aqueous solution. The first corresponds to a single helix extending from T3 to K17. The second corresponds to a broken helix at residue Ds. Four mutants, T3A, F7A, D8A, and E11A, were designed to further analyze the role of key amino acids in the equilibrium between the two ensembles of conformers. The sensitivity of NMR parameters to account for the variations in the populations of conformers was evaluated for each peptide. Our data show the delta13Calpha chemical shift to be the most relevant parameter. We used it to estimate the population ratio in the various peptides between the two main ensembles of conformers, the full helix and the broken helix. For the WT, E11A, and F7A peptides, these ratios are respectively 35/65, 60/40, 60/40. Our results were compared to the data obtained from helix/coil transition algorithms.
Identification of helix capping and beta-turn motifs from NMR chemical shifts
Identification of helix capping and beta-turn motifs from NMR chemical shifts
Abstract We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and 13Cβ chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of beta-turns: I, II, I', II' and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and β-turn motifs are used as input data for...
nmrlearner
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02-11-2012 10:31 AM
[Question from NMRWiki Q&A forum] Dimer and tetramer equilibrium identification of protein with NMR experiments
Dimer and tetramer equilibrium identification of protein with NMR experiments
Dear nmr wikiers
could you please let me know is their any nmr experment to identification of Dimer and tetramer equilibrium of protein with NMR experiments ?
thanks in advance .
Regards
nmrlearner
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06-22-2011 03:51 PM
Target immobilization as a strategy for NMR-based fragment screening: comparison of TINS, STD, and SPR for fragment hit identification.
Target immobilization as a strategy for NMR-based fragment screening: comparison of TINS, STD, and SPR for fragment hit identification.
Target immobilization as a strategy for NMR-based fragment screening: comparison of TINS, STD, and SPR for fragment hit identification.
J Biomol Screen. 2010 Sep;15(8):978-89
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Fragment-based drug discovery (FBDD) has become a widely accepted tool that is complementary to high-throughput screening (HTS) in developing...
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01-13-2011 12:00 PM
[NMR paper] Determination of conformational equilibrium of peptides in solution by NMR spectrosco
Determination of conformational equilibrium of peptides in solution by NMR spectroscopy and theoretical conformational analysis: application to the calibration of mean-field solvation models.
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Authors: Groth M, Malicka J, Rodziewicz- Motowid?o S, Czaplewski C, Klaudel L, Wiczk W, Liwo A
Peptides occur in...
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11-19-2010 08:32 PM
[NMR paper] Structural changes caused by site-directed mutagenesis of tyrosine-98 in Desulfovibri
Structural changes caused by site-directed mutagenesis of tyrosine-98 in Desulfovibrio vulgaris flavodoxin delineated by 1H and 15N NMR spectroscopy: implications for redox potential modulation.
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Biochemistry. 1994 Dec 27;33(51):15298-308
Authors: Stockman BJ, Richardson TE, Swenson RP
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nmrlearner
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08-22-2010 03:29 AM
[NMR paper] NMR and protein folding: equilibrium and stopped-flow studies.
NMR and protein folding: equilibrium and stopped-flow 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 NMR and protein folding: equilibrium and stopped-flow studies.
Protein Sci. 1993 Dec;2(12):2007-14
Authors: Frieden C, Hoeltzli SD, Ropson IJ
NMR studies are now unraveling the structure of intermediates...
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08-22-2010 03:01 AM
[NMR paper] Conformational studies on a peptide fragment representing the RNA-binding N-terminus
Conformational studies on a peptide fragment representing the RNA-binding N-terminus of a viral coat protein using circular dichroism and NMR spectroscopy.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Conformational studies on a peptide fragment representing the RNA-binding N-terminus of a viral coat protein using circular dichroism and NMR spectroscopy.
Eur J Biochem. 1991 Oct 15;201(2):489-94
Authors: van der Graaf M, Hemminga MA
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08-21-2010 11:12 PM
[NMR paper] Conformational studies on a peptide fragment representing the RNA-binding N-terminus
Conformational studies on a peptide fragment representing the RNA-binding N-terminus of a viral coat protein using circular dichroism and NMR spectroscopy.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Conformational studies on a peptide fragment representing the RNA-binding N-terminus of a viral coat protein using circular dichroism and NMR spectroscopy.
Eur J Biochem. 1991 Oct 15;201(2):489-94
Authors: van der Graaf M, Hemminga MA
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A conformational equilibrium in a protein fragment caused by two consecutive capping
Linear Mode
