The 13C Chemical-Shift Index: A simple method for the identification of protein secondary structure using 13C chemical-shift data

Wishart, David S.; Sykes, Brian D.

doi:10.1007/bf00175245

Cited by 2,031 publications

(1,776 citation statements)

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“…16 We thus compared the H-D exchange of backbone NHs between WT and Y9P I27 domains. We first confirmed that NMR chemical shift indexes that reflect secondary structures 17 were similar for WT and Y9P I27 domains [ Fig. 3(A)], as suggested by their similar CD spectra [ Fig.…”

Section: Resultssupporting

confidence: 59%

Structural basis for unfolding pathway‐dependent stability of proteins: Vectorial unfolding versus global unfolding

et al. 2010

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Point mutations in proteins can have different effects on protein stability depending on the mechanism of unfolding. In the most interesting case of I27, the Ig-like module of the muscle protein titin, one point mutation (Y9P) yields opposite effects on protein stability during denaturantinduced ''global unfolding'' versus ''vectorial unfolding'' by mechanical pulling force or cellular unfolding systems. Here, we assessed the reason for the different effects of the Y9P mutation of I27 on the overall molecular stability and N-terminal unraveling by NMR. We found that the Y9P mutation causes a conformational change that is transmitted through b-sheet structures to reach the central hydrophobic core in the interior and alters its accessibility to bulk solvent, which leads to destabilization of the hydrophobic core. On the other hand, the Y9P mutation causes a bend in the backbone structure, which leads to the formation of a more stable N-terminal structure probably through enhanced hydrophobic interactions.

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Section: Resultssupporting

confidence: 59%

Structural basis for unfolding pathway‐dependent stability of proteins: Vectorial unfolding versus global unfolding

et al. 2010

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“…The NOE experiments were carried out with a relaxation delay of 4.4 s, which is 4^6 times the 15 N T 1 values. The secondary structure was assigned using the chemical shift index (CK and HK) [15,16] and the sequential NH(i)3NH(i+1) and CKH(i)3CKH(i+3, 4) NOEs.…”

Section: Methodsmentioning

confidence: 99%

NMR assignments and secondary structure of the UvrC binding domain of UvrB

Alexandrovich¹,

Sanderson²,

Moolenaar³

et al. 1999

FEBS Letters

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The 55 residue C-terminal domain of UvrB that interacts with UvrC during excision repair in Escherichia coli has been expressed and purified as a (His) 6 fusion construct. The fragment forms a stable folded domain in solution. Heteronuclear NMR experiments were used to obtain extensive 15 N, 13 C and 1 H NMR assignments. NOESY and chemical shift data showed that the protein comprises two helices from residues 630 to 648 and from 652 to 670. 15 N relaxation data also show that the first 11 and last three residues are unstructured. The effective rotational correlation time within the structured region is not consistent with a monomer. This oligomerisation may be relevant to the mode of dimerisation of UvrB with the homologous domain of UvrC.z 1999 Federation of European Biochemical Societies.

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“…The NOEs were used along with Ca chemical shifts and 3 J HNHA scalar coupling values from the isotropic soft HNCA-E-COSY experiment to identify secondary structure types. 28 To aid in structure determination, a set of short range and long range interresidue NOEs was identified and treated more quantitatively. Peak intensities were compared separately with average intensities of HAÀ ÀHN and HNÀ ÀHN peaks from regions known to be in well defined a-helices and classed based on intensities being the same or stronger than the HNÀ ÀHN standard (strong), the same as the HNÀ ÀHA standard (medium) or weaker than either (weak).…”

Section: Nmr Data Processing and Analysismentioning

confidence: 99%

Structure determination of a new protein from backbone‐centered NMR data and NMR‐assisted structure prediction

Mayer

Bansal

et al. 2006

Proteins

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Targeting of proteins for structure determination in structural genomic programs often includes the use of threading and fold recognition methods to exclude proteins belonging to well-populated fold families, but such methods can still fail to recognize preexisting folds. The authors illustrate here a method in which limited amounts of structural data are used to improve an initial homology search and the data are subsequently used to produce a structure by data-constrained refinement of an identified structural template. The data used are primarily NMR-based residual dipolar couplings, but they also include additional chemical shift and backbone-nuclear Overhauser effect data. Using this methodology, a backbone structure was efficiently produced for a 10 kDa protein (PF1455) from Pyrococcus furiosus. Its relationship to existing structures and its probable function are discussed. Proteins 2006;65:480-489.

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The 13C Chemical-Shift Index: A simple method for the identification of protein secondary structure using 13C chemical-shift data

Cited by 2,031 publications

References 35 publications

Structural basis for unfolding pathway‐dependent stability of proteins: Vectorial unfolding versus global unfolding

Structural basis for unfolding pathway‐dependent stability of proteins: Vectorial unfolding versus global unfolding

NMR assignments and secondary structure of the UvrC binding domain of UvrB

Structure determination of a new protein from backbone‐centered NMR data and NMR‐assisted structure prediction

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