Related ArticlesProbability-based protein secondary structure identification using combined NMR chemical-shift data.
Protein Sci. 2002 Apr;11(4):852-61
Authors: Wang Y, Jardetzky O
For a long time, NMR chemical shifts have been used to identify protein secondary structures. Currently, this is accomplished through comparing the observed (1)H(alpha), (13)C(alpha), (13)C(beta), or (13)C' chemical shifts with the random coil values. Here, we present a new protocol, which is based on the joint probability of each of the three secondary structural types (beta-strand, alpha-helix, and random coil) derived from chemical-shift data, to identify the secondary structure. In combination with empirical smooth filters/functions, this protocol shows significant improvements in the accuracy and the confidence of identification. Updated chemical-shift statistics are reported, on the basis of which the reliability of using chemical shift to identify protein secondary structure is evaluated for each nucleus. The reliability varies greatly among the 20 amino acids, but, on average, is in the order of: (13)C(alpha)>(13)C'>(1)H(alpha)>(13)C(beta)>(15)N>(1)H(N) to distinguish an alpha-helix from a random coil; and (1)H(alpha)>(13)C(beta) >(1)H(N) approximately (13)C(alpha) approximately (13)C' approximately (15)N for a beta-strand from a random coil. Amide (15)N and (1)H(N) chemical shifts, which are generally excluded from the application, in fact, were found to be helpful in distinguishing a beta-strand from a random coil. In addition, the chemical-shift statistical data are compared with those reported previously, and the results are discussed. A JAVA User Interface program has been developed to make the entire procedure fully automated and is available via http://ccsr3150-p3.stanford.edu.
Rapid identification of protein-protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements.
Rapid identification of protein-protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements.
Rapid identification of protein-protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements.
J Struct Biol. 2011 Apr 9;
Authors: Kodama Y, Reese ML, Shimba N, Ono K, Kanamori E, Dötsch V, Noguchi S, Fukunishi Y, Suzuki EI, Shimada I, Takahashi H
Protein-protein interactions are necessary for various cellular...
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Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction.
Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction.
Related Articles Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction.
Structure. 2010 Dec 8;18(12):1678-1687
Authors: Masica DL, Ash JT, Ndao M, Drobny GP, Gray JJ
Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the...
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[NMR paper] Strategies for the NMR-based identification and optimization of allosteric protein kinase inhibitors.
Strategies for the NMR-based identification and optimization of allosteric protein kinase inhibitors.
Related Articles Strategies for the NMR-based identification and optimization of allosteric protein kinase inhibitors.
Chembiochem. 2005 Sep;6(9):1607-10
Authors: Jahnke W, Blommers MJ, Fernández C, Zwingelstein C, Amstutz R
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[NMR paper] A new combined computational and NMR-spectroscopical strategy for the identification
A new combined computational and NMR-spectroscopical strategy for the identification of additional conformational constraints of the bound ligand in an aprotic solvent.
Related Articles A new combined computational and NMR-spectroscopical strategy for the identification of additional conformational constraints of the bound ligand in an aprotic solvent.
Chembiochem. 2000 Oct 2;1(3):181-95
Authors: Siebert HC, André S, Asensio JL, Cańada FJ, Dong X, Espinosa JF, Frank M, Gilleron M, Kaltner H, Kozár T, Bovin NV, von Der Lieth CW, Vliegenthart JF,...
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NMR assignments and the identification of the secondary structure of the anti-retrovi
NMR assignments and the identification of the secondary structure of the anti-retroviral cytidine deaminase.
Related Articles NMR assignments and the identification of the secondary structure of the anti-retroviral cytidine deaminase.
Nucleic Acids Symp Ser (Oxf). 2008;(52):183-4
Authors: Furukawa A, Nagata T, Habu Y, Sugiyama R, Hayashi F, Yokoyama S, Takaku H, Katahira M
APOBEC3G (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G) is known to have a role in intrinsic cellular immunity against human immunodeficiency virus type1...
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Protein-ice interaction of an antifreeze protein observed with solid-state NMR [Chemi
Protein-ice interaction of an antifreeze protein observed with solid-state NMR
Siemer, A. B., Huang, K.-Y., McDermott, A. E....
Date: 2010-10-12
NMR on frozen solutions is an ideal method to study fundamental questions of macromolecular hydration, because the hydration shell of many biomolecules does not freeze together with bulk solvent. In the present study, we present previously undescribed NMR methods to study the interactions of proteins with their hydration shell and the ice lattice in frozen solution. We applied these methods to compare solvent interaction of an ice-binding...
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[NMR paper] Sequential assignments and identification of secondary structure elements of the coli
Sequential assignments and identification of secondary structure elements of the colicin E9 immunity protein in solution by homonuclear and heteronuclear NMR.
Related Articles Sequential assignments and identification of secondary structure elements of the colicin E9 immunity protein in solution by homonuclear and heteronuclear NMR.
Biochemistry. 1994 Oct 18;33(41):12347-55
Authors: Osborne MJ, Lian LY, Wallis R, Reilly A, James R, Kleanthous C, Moore GR
1H-1H, 1H-15N, and 1H-1H-15N multidimensional NMR spectroscopic studies of the 86 amino...
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[NMR paper] 1H NMR-based determination of the secondary structure of porcine pancreatic spasmolyt
1H NMR-based determination of the secondary structure of porcine pancreatic spasmolytic polypeptide: one of a new family of "trefoil" motif containing cell growth factors.
Related Articles 1H NMR-based determination of the secondary structure of porcine pancreatic spasmolytic polypeptide: one of a new family of "trefoil" motif containing cell growth factors.
Biochemistry. 1992 Feb 25;31(7):1998-2004
Authors: Carr MD
Two-dimensional 1H NMR spectroscopy has been used to obtain comprehensive sequence-specific resonance assignments for the...
Probability-based protein secondary structure identification using combined NMR chemi
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