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Improvements to the CLOUDS protocol:...

Bermejo, Guillermo A.

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Improvements to the CLOUDS protocol: Determination of protein folds from sparse NMR data via unconnected proton configurations.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Improvements to the CLOUDS protocol: Determination of protein folds from sparse NMR data via unconnected proton configurations./
Author:	Bermejo, Guillermo A.
Description:	99 p.
Notes:	Adviser: Miguel Llinas.
Contained By:	Dissertation Abstracts International68-06B.
Subject:	Biophysics, General. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3269540
ISBN:	9780549089483

Improvements to the CLOUDS protocol: Determination of protein folds from sparse NMR data via unconnected proton configurations.
Bermejo, Guillermo A.

Improvements to the CLOUDS protocol: Determination of protein folds from sparse NMR data via unconnected proton configurations. - 99 p.

Adviser: Miguel Llinas.

Thesis (Ph.D.)--Carnegie Mellon University, 2007.

In this Thesis, we study the determination of protein global folds from partially deuterated samples, given NMR nuclear Overhauser effect (NOE) data only, without any assignment information. A novel computational method, Sparse-Constraint CLOUDS (SC-CLOUDS), was developed for this purpose, inspired by the CLOUDS protocol, originally implemented with fully protonated proteins (Grishaev and Llinas, 2002a; Grishaev and Llinas, 2002b). All stages of the method were tested with the publicly available experimental dataset on the 58-residue Z domain of Staphylococcal protein A (Zheng et al., 2003). Furthermore, simulated data from five additional structures were used to test the method with other protein folds.

ISBN: 9780549089483Subjects--Topical Terms:

1019105
Biophysics, General.

Improvements to the CLOUDS protocol: Determination of protein folds from sparse NMR data via unconnected proton configurations.
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020 $a 9780549089483
035 $a (UMI)AAI3269540
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040 $a UMI $c UMI
100 1 $a Bermejo, Guillermo A. $3 1263720
245 1 0 $a Improvements to the CLOUDS protocol: Determination of protein folds from sparse NMR data via unconnected proton configurations.
300 $a 99 p.
500 $a Adviser: Miguel Llinas.
500 $a Source: Dissertation Abstracts International, Volume: 68-06, Section: B, page: 3620.
502 $a Thesis (Ph.D.)--Carnegie Mellon University, 2007.
520 $a In this Thesis, we study the determination of protein global folds from partially deuterated samples, given NMR nuclear Overhauser effect (NOE) data only, without any assignment information. A novel computational method, Sparse-Constraint CLOUDS (SC-CLOUDS), was developed for this purpose, inspired by the CLOUDS protocol, originally implemented with fully protonated proteins (Grishaev and Llinas, 2002a; Grishaev and Llinas, 2002b). All stages of the method were tested with the publicly available experimental dataset on the 58-residue Z domain of Staphylococcal protein A (Zheng et al., 2003). Furthermore, simulated data from five additional structures were used to test the method with other protein folds.
520 $a SC-CLOUDS, relies on the calculation of a 1H-only structure or cloud, directly from unassigned NOE restraints derived from 13C- and 15N-edited NOESY spectra. Initially, each proton in the cloud is only labeled with its 1H-13C/ 15N chemical shifts, and has to be identified relative to the chemical structure of the protein. Such cloud interpretation is performed by searching on graphs condensing the structural information in the cloud. First, an H N chain is traced by systematically searching for all possible chains, keeping the one with the minimum sum of sequential distances. Next, complete proton identification is attempted by grouping side-chain protons and H Ns in the chain, into amino acid residues. This is achieved by a bipartite graph matching protocol that scores a set of [HN, side-chain] proton pairs according to their proximity in the cloud. The thus identified protons automatically yield the assignments of their chemical shift labels and the NOES, which can now be used for structure calculation with RosettaNMR (Bowers et al., 2000), a protocol that incorporates structural bias derived from protein databases. The protocol produced Z domain structural models of similar accuracy to those conventionally generated (Zheng et al., 2003), when compared to an NMR model derived from a fully protonated sample (Tashiro et al., 1997). Tests with simulated data on other folds yielded structures with accuracies consistent with those generally obtained via conventional approaches.
520 $a Since the quality of proton clouds depends on the accuracy of the estimation of cross-relaxation rates from NOESY experiments, we perform a computational study on the effect missing NOE information has on the relaxation matrix algorithm MIDGE (Madrid et al., 1991). In addition, we test a new strategy to counteract the lack of NOE information at a given mixing time by incorporating data obtained from relaxation matrix optimizations performed with other NOE matrices in a mixing time series.
590 $a School code: 0041.
650 4 $a Biophysics, General. $3 1019105
650 4 $a Chemistry, Biochemistry. $3 1017722
650 4 $a Chemistry, Physical. $3 560527
690 $a 0487
690 $a 0494
690 $a 0786
710 2 $a Carnegie Mellon University. $3 1018096
773 0 $t Dissertation Abstracts International $g 68-06B.
790 $a 0041
790 1 0 $a Llinas, Miguel, $e advisor
791 $a Ph.D.
792 $a 2007
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3269540