Publication year: 2011 Source: Progress in Nuclear Magnetic Resonance Spectroscopy, Available online 12 October 2011
Magnus*Kjaergaard, Flemming M.*Poulsen
Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids
Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids
Abstract Unravelling the complex correlation between chemical shifts of 13 C α, 13 C β, 13 C�, 1 H α, 15 N, 1 H N atoms in amino acids of proteins from NMR experiment and local structural environments of amino acids facilitates the assignment of secondary structures of proteins. This is an important impetus for both determining the three-dimensional structure and understanding the biological function of proteins. The previous...
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11-14-2011 08:45 AM
[KPWU blog] Web Severs for prediction of disordered regions (DRs) in proteins
Web Severs for prediction of disordered regions (DRs) in proteins
This list of web severs is obtained from the published paper “Evaluation of disorder predictions in CASP9” by*Andriy Kryshtafovych. List of web servers and the methods descriptions (copy from table III of Kryshtafovych’s paper). Please read the paper for details of methods and performance. PrDOS2*(http://prdos.hgc.jp/cgi-bin/top.cgi) SVM algorithm based on sequence profiles combined with a template-based http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=513&subd=kpwu&ref=&feed=1
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09-05-2011 07:55 PM
Structure-based prediction of methyl chemical shifts in proteins
Structure-based prediction of methyl chemical shifts in proteins
Abstract Protein methyl groups have recently been the subject of much attention in NMR spectroscopy because of the opportunities that they provide to obtain information about the structure and dynamics of proteins and protein complexes. With the advent of selective labeling schemes, methyl groups are particularly interesting in the context of chemical shift based protein structure determination, an approach that to date has exploited primarily the mapping between protein structures and backbone chemical shifts. In order to...
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07-15-2011 09:10 PM
Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH
Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH
Abstract Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins. The quality of the secondary chemical shifts is dependent on an appropriate choice of random coil chemical shifts. We report random coil chemical shifts and sequence correction factors determined for a GGXGG peptide series following the approach of Schwarzinger et al. (J Am Chem Soc 123(13):2970â??2978, 2001). The chemical shifts are...
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01-17-2011 02:40 AM
Strategy for complete NMR assignment of disordered proteins with highly repetitive se
Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments
Abstract A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly repetitive sequence is presented. The protocol is based on three resolution-enhanced NMR experiments: 5D HN(CA)CONH provides sequential connectivity, 5D HabCabCONH is utilized to identify amino acid types, and 5D HC(CC-TOCSY)CONH is used to assign the side-chain resonances. The improved resolution was achieved by a combination of high...
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10-06-2010 02:16 AM
Strategy for complete NMR assignment of disordered proteins with highly repetitive se
Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments.
Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments.
J Biomol NMR. 2010 Oct 2;
Authors: MotáÄ?ková V, NováÄ?ek J, Zawadzka-Kazimierczuk A, Kazimierczuk K, ZÃ*dek L, Sanderová H, Krásný L, KoźmiÅ?ski W, SklenáÅ? V
A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly...
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10-05-2010 12:11 PM
[NMR paper] NMR chemical shifts and structure refinement in proteins.
NMR chemical shifts and structure refinement in proteins.
Related Articles NMR chemical shifts and structure refinement in proteins.
J Biomol NMR. 1993 Sep;3(5):607-12
Authors: Laws DD, de Dios AC, Oldfield E
Computation of the 13C alpha chemical shifts (or shieldings) of glycine, alanine and valine residues in bovine and Drosophila calmodulins and Staphylococcal nuclease, and comparison with experimental values, is reported using a gauge-including atomic orbital quantum-chemical approach. The full approximately 24 ppm shielding range is...
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08-22-2010 03:01 AM
Analysis of and chemical shifts of cysteine and cystine residues in proteins: a quant
Abstract Cysteines possess a unique property among the 20 naturally occurring amino acids: it can be present in proteins in either the reduced or oxidized form, and can regulate the activity of some proteins. Consequently, to augment our previous treatment of the other types of residues, the
13\textC\upalpha and
13\textC\upbeta chemical shifts of 837 cysteines in disulfide-bonded cystine from a set of seven non-redundant proteins, determined by X-ray crystallography and NMR spectroscopy, were computed at the DFT level of theory. Our results indicate that the errors between observed...
Disordered proteins studied by chemical shifts
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