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On the use of NMR spin relaxation sp...

O'Connell, Nichole E.

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On the use of NMR spin relaxation spectroscopy to characterize conformational dynamics in proteins.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	On the use of NMR spin relaxation spectroscopy to characterize conformational dynamics in proteins./
Author:	O'Connell, Nichole E.
Description:	232 p.
Notes:	Source: Dissertation Abstracts International, Volume: 71-11, Section: B, page: 6629.
Contained By:	Dissertation Abstracts International71-11B.
Subject:	Chemistry, Biochemistry. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3428696
ISBN:	9781124283883

On the use of NMR spin relaxation spectroscopy to characterize conformational dynamics in proteins.
O'Connell, Nichole E.

On the use of NMR spin relaxation spectroscopy to characterize conformational dynamics in proteins. - 232 p.

Source: Dissertation Abstracts International, Volume: 71-11, Section: B, page: 6629.

Thesis (Ph.D.)--Columbia University, 2010.

An accurate description of protein function is incomplete without detailed understanding of the motions that contribute to function. Nuclear magnetic resonance (NMR) spin relaxation spectroscopy is among the most powerful techniques available to measure protein dynamics at atomic detail on multiple time scales. Two investigations of protein dynamics were undertaken to characterize: ( i) the equilibrium unfolding of the villin headpiece protein (HP67) and (ii) changes in dynamics associated with specific DNA binding by the Drosophila Hox transcription factor, Sex combs reduced (Scr). Additionally, triple-resonance NMR spectroscopy was used to identify asparagine deamidation in Scr and a time series of 15N- 1H heteronuclear correlation spectra was employed to quantify the rate of deamidation.

ISBN: 9781124283883Subjects--Topical Terms:

1017722
Chemistry, Biochemistry.

On the use of NMR spin relaxation spectroscopy to characterize conformational dynamics in proteins.
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020 $a 9781124283883
035 $a (UMI)AAI3428696
035 $a AAI3428696
040 $a UMI $c UMI
100 1 $a O'Connell, Nichole E. $3 1683931
245 1 0 $a On the use of NMR spin relaxation spectroscopy to characterize conformational dynamics in proteins.
300 $a 232 p.
500 $a Source: Dissertation Abstracts International, Volume: 71-11, Section: B, page: 6629.
500 $a Adviser: Arthur G. Palmer, III.
502 $a Thesis (Ph.D.)--Columbia University, 2010.
520 $a An accurate description of protein function is incomplete without detailed understanding of the motions that contribute to function. Nuclear magnetic resonance (NMR) spin relaxation spectroscopy is among the most powerful techniques available to measure protein dynamics at atomic detail on multiple time scales. Two investigations of protein dynamics were undertaken to characterize: ( i) the equilibrium unfolding of the villin headpiece protein (HP67) and (ii) changes in dynamics associated with specific DNA binding by the Drosophila Hox transcription factor, Sex combs reduced (Scr). Additionally, triple-resonance NMR spectroscopy was used to identify asparagine deamidation in Scr and a time series of 15N- 1H heteronuclear correlation spectra was employed to quantify the rate of deamidation.
520 $a Identification and characterization of ensembles of intermediate states remain important objectives in describing protein folding in atomic detail. HP67 consists of an N-terminal subdomain that transiently unfolds at equilibrium while the stable C-terminal subdomain remains natively folded. Transition between folded and unfolded states of the N-terminal domain has been characterized previously by 15N NMR relaxation dispersion measurements [Grey et al., J. Mol. Biol. (2006) 355, 1078]. Herein, analysis of 13C spin relaxation further characterizes backbone and hydrophobic core contributions to the unfolding process. Relaxation dispersion of 13Calpha and methyl 13C spins was measured and fit to a model detailing kinetic, thermodynamic and structural details of dynamic processes within the protein. Results for 13C and 15N spins yield a consistent model in which the partially unfolded intermediate maintains residual structure for residues near the unprotonated His 41 imidazole ring and at the interface between the N- and C-terminal subdomains. Additionally, a faster process was detected that appears to represent local dynamics within the folded state of the molecule and is largely confined to the N-terminal domain hydrophobic core and the interfacial hydrophobic core between the two subdomains.
520 $a Hox transcription factors of D. melanogaster have a substantial degree of sequence and structural similarity. As such, determining the mechanisms by which DNA binding specificity is achieved remains an important goal in developmental and structural biology alike. This work aims to characterize changes in protein dynamics associated with specific binding in an effort identify energetic and structural contributions to DNA binding specificity. Conformational dynamics of apo-state Scr are reported, however studies of the DNA-bound state were intractable due to insolubility of the protein-DNA complex.
520 $a Spontaneous deamidation of asparagine to aspartate or iso-aspartate is a common non-enzymatic modification in proteins. Herein, the conventional HNCACB experiment is used to identify the presence of iso-aspartate in an aged Scr sample. The rate of deamidation is quantified by monitoring the intensity decay of asparagine NH2 side-chain resonances in a 15N- 1H fHSQC time series. Deamidation of Asparagine -3 in the Scr linker domain was observed and shown to deamidate readily, having a half-life of 26 +/- 1 days.
590 $a School code: 0054.
650 4 $a Chemistry, Biochemistry. $3 1017722
650 4 $a Biophysics, General. $3 1019105
690 $a 0487
690 $a 0786
710 2 $a Columbia University. $3 571054
773 0 $t Dissertation Abstracts International $g 71-11B.
790 1 0 $a Palmer, Arthur G., III, $e advisor
790 $a 0054
791 $a Ph.D.
792 $a 2010
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3428696