Related ArticlesSorting signals from protein NMR spectra: SPI, a Bayesian protocol for uncovering spin systems.
J Biomol NMR. 2002 Nov;24(3):203-13
Authors: Grishaev A, Llinás M
Grouping of spectral peaks into J-connected spin systems is essential in the analysis of macromolecular NMR data as it provides the basis for disentangling chemical shift degeneracies. It is a mandatory step before resonance and NOESY cross-peak identities can be established. We have developed SPI, a computational protocol that scrutinizes peak lists from homo- and hetero-nuclear multidimensional NMR spectra and progressively assembles sets of resonances into consensus J- and/or NOE-connected spin systems. SPI estimates the likelihood of nuclear spin resonances appearing at defined frequencies given sets of cross-peaks measured from multi-dimensional experiments. It quantifies spin system matching probabilities via Bayesian inference. The protocol takes advantage of redundancies in the number of connectivities revealed by suites of diverse NMR experiments, systematically tracking the adequacy of each grouping hypothesis. SPI was tested on 2D homonuclear and 2D/3D(15)N-edited data recorded from two protein modules, the col 2 domain of matrix metalloproteinase-2 (MMP-2) and the kringle 2 domain of plasminogen, of 60 and 83 amino acid residues, respectively. For these protein domains SPI identifies approximately 95% unambiguous resonance frequencies, a relatively good performance vis-ŕ-vis the reported 'manual' (interactive) analyses. Abbreviations and Acronyms: SPI, SPin Identification; BMRB, BioMagResBank (Madison, WI).
[U. of Ottawa NMR Facility Blog] Sorting Out NOE's for Exchanging Rotomers
Sorting Out NOE's for Exchanging Rotomers
2D NOESY spectra contain cross peaks from both NOE interactions and peaks due to rotomers in slow exchange with one another on the NMR tine scale. For small molecules, the cross peaks resulting from slowly exchanging rotomers are of the same sign as the diagonal peaks. The NOE cross peaks, on the other hand, are of opposite sign compared to the diagonal peaks. When both types of correlations are present there may be more NOE correlations than expected. What follows is an example of this. The figure below shows a color coded chemical structure of a...
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01-19-2012 09:19 PM
[KPWU blog] NMR protocol (recipe)?make stretch gel for protein RDC measurement
NMR protocol (recipe)?make stretch gel for protein RDC measurement
I bought the starter kit (NE-373-B-6/4.2) at NewEraNMR for RDC experiment on Varian NMR (with 700 MHz grade) and I decided to stretch the gel a lot, so 6mm-wide gel chamber and “6mm-4.2mm gel funnel” are included. The NMR tube seems to be more fragile than Wilmad products I often used, so I also ordered http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=587&subd=kpwu&ref=&feed=1
Go to KPWU blog to read complete post.
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10-20-2011 09:45 AM
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...
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures.
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures.
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures.
Proteins. 2011 Jan 6;
Authors: Bernard A, Vranken WF, Bardiaux B, Nilges M, Malliavin TE
The classical procedure for nuclear magnetic resonance structure calculation allocates empirical distance ranges and uses historical values for weighting factors. However, Bayesian analysis suggests that there are more optimal...
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03-03-2011 12:34 PM
[NMR paper] Cell-free protein production and labeling protocol for NMR-based structural proteomic
Cell-free protein production and labeling protocol for NMR-based structural proteomics.
Related Articles Cell-free protein production and labeling protocol for NMR-based structural proteomics.
Nat Methods. 2004 Nov;1(2):149-53
Authors: Vinarov DA, Lytle BL, Peterson FC, Tyler EM, Volkman BF, Markley JL
Structural proteomics requires robust, scalable methods. Here we describe a wheat germ cell-free platform for protein production that supports efficient NMR structural studies of eukaryotic proteins and offers advantages over cell-based methods....
Sorting signals from protein NMR spectra: SPI, a Bayesian protocol for uncovering spi
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