Related ArticlesInfluence of chemical shift tolerances on NMR structure calculations using ARIA protocols for assigning NOE data.
J Biomol NMR. 2005 Jan;31(1):21-34
Authors: Fossi M, Linge J, Labudde D, Leitner D, Nilges M, Oschkinat H
Large-scale protein structure determination by NMR via automatic assignment of NOESY spectra requires the adjustment of several parameters for optimal performance. Among those are the chemical shift tolerance windows (delta), which allow for the compensation of badly matching chemical shifts in the assignment-list and peak-lists, and the maximum number of assignment possibilities allowed per peak (n(max)). Here, we test the influence of different values for Delta and n(max) on the performance of automated assignment of NOESY spectra by ARIA. Using Cesta.py (a Python script available from http://pasteur.fr/binfs/), we analyse the number of rejected peaks and the average number of assignments as a function of Delta and derive criteria for optimising delta and n(max) prior to structure calculation. The analysis also makes it possible to detect inconsistencies in the dataset, e.g., badly matching frequencies in the NOESY peak-lists and in the provided assignment-list. We show that ARIA can deal with a large number of assignment possibilities for each peak, provided the correct option is present, and that consequently narrow tolerances should be avoided.
1H NMR Chemical Shift Calculations as a Probe of Supramolecular Host–Guest Geometry
1H NMR Chemical Shift Calculations as a Probe of Supramolecular Host–Guest Geometry
Jeffrey S. Mugridge, Robert G. Bergman and Kenneth N. Raymond
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja202254x/aop/images/medium/ja-2011-02254x_0010.gif
Journal of the American Chemical Society
DOI: 10.1021/ja202254x
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http://feeds.feedburner.com/~r/acs/jacsat/~4/wR-1b5WtJhc
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[NMR paper] NMR structure determination of proteins supplemented by quantum chemical calculations
NMR structure determination of proteins supplemented by quantum chemical calculations: detailed structure of the Ca2+ sites in the EGF34 fragment of protein S.
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J Biomol NMR. 2005 Feb;31(2):97-114
Authors: Hsiao YW, Drakenberg T, Ryde U
We present and test two methods to use quantum chemical calculations to improve standard protein structure refinement by molecular...
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[NMR paper] Structure of an elastin-mimetic polypeptide by solid-state NMR chemical shift analysi
Structure of an elastin-mimetic polypeptide by solid-state NMR chemical shift analysis.
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Biopolymers. 2003 Oct;70(2):158-68
Authors: Hong M, Isailovic D, McMillan RA, Conticello VP
The conformation of an elastin-mimetic recombinant protein, 39, is investigated using solid-state NMR spectroscopy. The protein is extensively labeled with 13C and 15N, and two-dimensional 13C-13C and 15N-13C correlation experiments were carried out to resolve and...
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[NMR paper] Influence of the completeness of chemical shift assignments on NMR structures obtaine
Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment.
Related Articles Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment.
J Struct Funct Genomics. 2003;4(2-3):179-89
Authors: Jee J, Güntert P
Reliable automated NOE assignment and structure calculation on the basis of a largely complete, assigned input chemical shift list and a list of unassigned NOESY cross peaks has recently become feasible for routine NMR protein...
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Protein secondary structure prediction using NMR chemical shift data.
Protein secondary structure prediction using NMR chemical shift data.
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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)...
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[NMR paper] Chemical shift assignments and secondary structure of the Grb2 SH2 domain by heteronu
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J Biomol NMR. 1996 Mar;7(2):89-98
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The growth factor receptor-bound protein-2 (Grb-2) is an adaptor protein that mediates signal transduction pathways. Chemical shift assignments were obtained for the SH2 domain of...
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[NMR paper] 1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and magnes
1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and magnesium-binding characteristics of the Bacillus subtilis response regulator, Spo0F, determined by heteronuclear high-resolution NMR.
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 1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and...
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Effect of chemical shift tolerance on ARIA results
Influence of chemical shift tolerances on NMR structure calculations using ARIA protocols for assigning NOE data.
Fossi M, Linge J, Labudde D, Leitner D, Nilges M, Oschkinat H.
Forschungsinstitut fur Molekulare Pharmakologie, Robert-Rossle-Str. 10, 13125, Berlin, Germany, oschkinat@fmp-berlin.de.
J Biomol NMR. 2005 Jan;31(1):21-34.
Large-scale protein structure determination by NMR via automatic assignment of NOESY spectra requires the adjustment of several parameters for optimal performance. Among those are the chemical shift tolerance windows (Delta), which allow for the...