Related ArticlesA random graph approach to NMR sequential assignment.
J Comput Biol. 2005 Jul-Aug;12(6):569-83
Authors: Bailey-Kellogg C, Chainraj S, Pandurangan G
Nuclear magnetic resonance (NMR) spectroscopy allows scientists to study protein structure, dynamics and interactions in solution. A necessary first step for such applications is determining the resonance assignment, mapping spectral data to atoms and residues in the primary sequence. Automated resonance assignment algorithms rely on information regarding connectivity (e.g., through-bond atomic interactions) and amino acid type, typically using the former to determine strings of connected residues and the latter to map those strings to positions in the primary sequence. Significant ambiguity exists in both connectivity and amino acid type information. This paper focuses on the information content available in connectivity alone and develops a novel random-graph theoretic framework and algorithm for connectivity-driven NMR sequential assignment. Our random graph model captures the structure of chemical shift degeneracy, a key source of connectivity ambiguity. We then give a simple and natural randomized algorithm for finding optimal assignments as sets of connected fragments in NMR graphs. The algorithm naturally and efficiently reuses substrings while exploring connectivity choices; it overcomes local ambiguity by enforcing global consistency of all choices. By analyzing our algorithm under our random graph model, we show that it can provably tolerate relatively large ambiguity while still giving expected optimal performance in polynomial time. We present results from practical applications of the algorithm to experimental datasets from a variety of proteins and experimental set-ups. We demonstrate that our approach is able to overcome significant noise and local ambiguity in identifying significant fragments of sequential assignments.
[NMR paper] Accepting its random coil nature allows a partial NMR assignment of the neuronal Tau
Accepting its random coil nature allows a partial NMR assignment of the neuronal Tau protein.
Related Articles Accepting its random coil nature allows a partial NMR assignment of the neuronal Tau protein.
Chembiochem. 2004 Dec 3;5(12):1639-46
Authors: Smet C, Leroy A, Sillen A, Wieruszeski JM, Landrieu I, Lippens G
A combined strategy to obtain a partial NMR assignment of the neuronal Tau protein is presented. Confronted with the extreme spectral degeneracy that the spectrum of this 441 amino acid long unstructured protein presents, we have...
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[NMR paper] Proline-directed random-coil chemical shift values as a tool for the NMR assignment o
Proline-directed random-coil chemical shift values as a tool for the NMR assignment of the tau phosphorylation sites.
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Chembiochem. 2004 Jan 3;5(1):73-8
Authors: Lippens G, Wieruszeski JM, Leroy A, Smet C, Sillen A, Buée L, Landrieu I
NMR spectroscopy of the full-length neuronal Tau protein has proved to be difficult due to the length of the protein and the unfavorable amino acid composition. We show that the...
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[NMR paper] Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignme
Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignments.
Related Articles Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignments.
J Biomol NMR. 2003 Dec;27(4):313-21
Authors: Slupsky CM, Boyko RF, Booth VK, Sykes BD
Complete and accurate NMR spectral assignment is a prerequisite for high-throughput automated structure determination of biological macromolecules. However, completely automated assignment procedures generally encounter difficulties for all but the most ideal data...
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[NMR paper] Use of graph theory for secondary structure recognition and sequential assignment in
Use of graph theory for secondary structure recognition and sequential assignment in heteronuclear (13C, 15N) NMR spectra: application to HU protein from Bacillus stearothermophilus.
Related Articles Use of graph theory for secondary structure recognition and sequential assignment in heteronuclear (13C, 15N) NMR spectra: application to HU protein from Bacillus stearothermophilus.
Biopolymers. 1996 Nov;39(5):691-707
Authors: van Geerestein-Ujah EC, Mariani M, Vis H, Boelens R, Kaptein R
A computer-assisted procedure, based upon a branch of...
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[NMR paper] Graph-theoretical assignment of secondary structure in multidimensional protein NMR s
Graph-theoretical assignment of secondary structure in multidimensional protein NMR spectra: application to the lac repressor headpiece.
Related Articles Graph-theoretical assignment of secondary structure in multidimensional protein NMR spectra: application to the lac repressor headpiece.
J Biomol NMR. 1995 Jul;6(1):67-78
Authors: van Geerestein-Ujah EC, Slijper M, Boelens R, Kaptein R
A novel procedure is presented for the automatic identification of secondary structures in proteins from their corresponding NOE data. The method uses a branch...
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[NMR paper] Sequential assignment of the backbone nuclei (1H, 15N and 13C) of c-H-ras p21 (1-166)
Sequential assignment of the backbone nuclei (1H, 15N and 13C) of c-H-ras p21 (1-166).GDP using a novel 4D NMR strategy.
Related Articles Sequential assignment of the backbone nuclei (1H, 15N and 13C) of c-H-ras p21 (1-166).GDP using a novel 4D NMR strategy.
J Biomol NMR. 1992 Nov;2(6):639-46
Authors: Campbell-Burk SL, Domaille PJ, Starovasnik MA, Boucher W, Laue ED
The c-H-ras p21 protein is the product of the human ras proto-oncogene, a member of a ubiquitous eukaryotic gene family which is highly conserved in evolution. These proteins play...
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[NMR paper] A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: h
A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin.
Related Articles A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin.
Biochemistry. 1990 May 15;29(19):4659-67
Authors: Ikura M, Kay LE, Bax A
A novel approach is described for obtaining sequential assignment of the backbone 1H, 13C, and 15N...
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Sequential Assignment of Spin systems
hi,
I am new to the protein NMR Field.I want to assign spin numbers to 120 amonoacid residues of a protein.I am cluless how to assing these number to each.Could anyone help me? Here is the primary sequence f a protein domain-
ISLLAQRQQF WIQLEFHSRI TRGERHGVID HVGLGVQSQQ RSNGFLTSLC ILRPHYASLS LALEKAQLHS LLCEETDGEG TLEYGFMGQV KSRFTDLSRP NLFCRHLGQL LPLLRVCRDV
I am expecing your help.Thank you.
A random graph approach to NMR sequential assignment.
Linear Mode
