Chemical shift mapping is becoming a popular method for studying protein-protein interactions in solution. The technique is used to identify putative sites of interaction on a protein surface by detecting chemical shift perturbations in simple (1H, 15N)-HSQC NMR spectra of a uniformly labeled protein as a function of added (unlabeled) target protein. The high concentrations required for these experiments raise questions concerning the possibility for non-specific interactions being detected, thereby compromising the information obtained. We demonstrate here that the simple chemical shift mapping approach faithfully reproduces the known functional specificities among pairs of closely related proteins from the phosphoenolpyruvate:sugar phosphotransferase systems of Escherichia coli and Bacillus subtilis.
SHIFTCOR: Protein Chemical Shift Re-referencing
SHIFTCOR website
SHIFTCOR is an automated shift correction program that uses statistical methods to compare and correct SHIFTX-predicted shifts relative to an input set of observed chemical shifts. SHIFTCOR uses several simple statistical approaches and pre-determined cutoff values to identify and correct potential referencing, assignment and typographical errors. SHIFTCOR identifies potential chemical shift referencing problems by comparing the difference between the average value of each set (1Hα, 13Cα, 13Cβ, 13CO, 15N and 1HN) of observed and predicted chemical shifts. The difference...
gwnmr
NMR software
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01-10-2012 06:46 PM
RefDB: Re-referenced Protein Chemical Shift Database
RefDB website
In case of the BMRB, it is known that a significant portion of depositions use different or non-IUPAC chemical shift reference standards. This lack of uniformity makes it difficult to extract sequence/structure relationships from chemical shifts. Nearly 40% of protein entries deposited in the BioMagResBank appear to have at least one assignment error. In addition, it evident that protein NMR spectroscopists are increasingly adhering to recommended IUPAC (13)C and (15)N chemical shift referencing conventions, however, approximately 20% of newly deposited protein entries in the...
gwnmr
NMR software
0
01-10-2012 06:28 PM
SHIFTX2: significantly improved protein chemical shift prediction
SHIFTX2: significantly improved protein chemical shift prediction
Abstract A new computer program, called SHIFTX2, is described which is capable of rapidly and accurately calculating diamagnetic 1H, 13C and 15N chemical shifts from protein coordinate data. Compared to its predecessor (SHIFTX) and to other existing protein chemical shift prediction programs, SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3Ã? smaller) than the next best performing program. It also provides significantly more coverage (up to 10% more),...
nmrlearner
Journal club
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04-01-2011 09:31 PM
[NMR paper] Four-dimensional NMR spectroscopy of a 723-residue protein: chemical shift assignment
Four-dimensional NMR spectroscopy of a 723-residue protein: chemical shift assignments and secondary structure of malate synthase g.
Related Articles Four-dimensional NMR spectroscopy of a 723-residue protein: chemical shift assignments and secondary structure of malate synthase g.
J Am Chem Soc. 2002 Aug 28;124(34):10025-35
Authors: Tugarinov V, Muhandiram R, Ayed A, Kay LE
A four-dimensional (4-D) NMR study of Escherichia coli malate synthase G (MSG), a 723-residue monomeric enzyme (81.4 kDa), is described. Virtually complete backbone (1)HN,...
nmrlearner
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11-24-2010 08:58 PM
[NMR paper] NMR chemical shift mapping of the binding site of a protein proteinase inhibitor: cha
NMR chemical shift mapping of the binding site of a protein proteinase inhibitor: changes in the (1)H, (13)C and (15)N NMR chemical shifts of turkey ovomucoid third domain upon binding to bovine chymotrypsin A(alpha).
Related Articles NMR chemical shift mapping of the binding site of a protein proteinase inhibitor: changes in the (1)H, (13)C and (15)N NMR chemical shifts of turkey ovomucoid third domain upon binding to bovine chymotrypsin A(alpha).
J Mol Recognit. 2001 May-Jun;14(3):166-71
Authors: Song J, Markley JL
The substrate-like...
nmrlearner
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11-19-2010 08:32 PM
Protein secondary structure prediction using NMR chemical shift data.
Protein secondary structure prediction using NMR chemical shift data.
Related Articles Protein secondary structure prediction using NMR chemical shift data.
J Bioinform Comput Biol. 2010 Oct;8(5):867-84
Authors: Zhao Y, Alipanahi B, Li SC, Li M
Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b)...
nmrlearner
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10-29-2010 07:05 PM
Interpreting Protein Chemical Shift Data
Interpreting Protein Chemical Shift Data
Publication year: 2010
Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 5 August 2010</br>
David S., Wishart</br>
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nmrlearner
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08-16-2010 03:50 AM
A probabilistic approach for validating protein NMR chemical shift assignments
Abstract It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program...
Demonstration of protein-protein interaction specificity by NMR chemical shift mappin
Linear Mode
