Characterization of Nonspecific Protein−DNA Interactions by1H Paramagnetic Relaxation Enhancement

2004 ◽  
Vol 126 (40) ◽  
pp. 12800-12808 ◽  
Author(s):  
Junji Iwahara ◽  
Charles D. Schwieters ◽  
G. Marius Clore
Keyword(s):  
Paramagnetic Relaxation ◽  
Paramagnetic Relaxation Enhancement ◽  
Dna Interactions ◽  
Protein Dna Interactions

scholarly journals Paramagnetic relaxation enhancement‐assisted structural characterization of a partially disordered conformation of ubiquitin

2019 ◽  
Vol 28 (11) ◽  
pp. 1993-2003
Author(s):  
Takuro Wakamoto ◽  
Teppei Ikeya ◽  
Soichiro Kitazawa ◽  
Nicola J. Baxter ◽  
Mike P. Williamson ◽  
...  
Keyword(s):  
Structural Characterization ◽  
Paramagnetic Relaxation ◽  
Paramagnetic Relaxation Enhancement

SURFACE PLASMON RESONANCE SPECTROSCOPY AND QUARTZ CRYSTAL MICROBALANCE STUDY OF PROTEIN-DNA INTERACTIONS IN HORMONE RECEPTOR BIOLOGY

COSMOS ◽  
2009 ◽  
Vol 05 (01) ◽  
pp. 79-95
Author(s):  
XIAODI SU
Keyword(s):  
Surface Plasmon Resonance ◽  
Surface Plasmon ◽  
Quartz Crystal Microbalance ◽  
Conformational Changes ◽  
Plasmon Resonance ◽  
Quartz Crystal ◽  
Resonance Spectroscopy ◽  
Dna Interactions ◽  
Protein Dna Interactions

Surface plasmon resonance (SPR) spectroscopy and quartz crystal microbalance (QCM) are surface sensitive analytical techniques capable of real-time monitoring of biomolecular interactions. In this article we review our past work on the use of these two techniques for studying protein–DNA interactions, exemplified with estrogen receptors (ER) and their response elements (ERE). Various assay schemes have been developed for a comprehensive characterization of ER–ERE interactions in terms of sequence specificity, binding affinity, stoichiometry, ligand effects on binding dynamics and conformational changes in the proteins and DNA. These are all important characteristics underlining the mechanism of ER-mediated gene transcription. With these studies we have made the following demonstrations to describe the advantages of these two techniques, namely (i) SPR technique is superior and more versatile than conventional (electrophoretic mobility shift assay) EMSA for studying protein-DNA interactions; (ii) QCM is an alternative tool for studying conformational changes in protein–DNA complexes and (iii) combinational SPR and QCM analysis provides additional characterization of biomolecular films, e.g. film thickness, water content, and conformation rigidity etc.

Paramagnetic relaxation enhancement for the characterization of the conformational heterogeneity in two-domain proteins

2012 ◽  
Vol 14 (25) ◽  
pp. 9149 ◽  
Author(s):  
Ivano Bertini ◽  
Claudio Luchinat ◽  
Malini Nagulapalli ◽  
Giacomo Parigi ◽  
Enrico Ravera
Keyword(s):  
Paramagnetic Relaxation ◽  
Paramagnetic Relaxation Enhancement ◽  
Conformational Heterogeneity

scholarly journals Characterization of Protein-DNA Interactions Using Protein Microarrays

2011 ◽  
Vol 2011 (5) ◽  
pp. pdb.prot5614-pdb.prot5614 ◽  
Author(s):  
S. Hu ◽  
Z. Xie ◽  
S. Blackshaw ◽  
J. Qian ◽  
H. Zhu
Keyword(s):  
Protein Microarrays ◽  
Dna Interactions ◽  
Protein Dna Interactions

scholarly journals Characterization of Physical and Functional Anchor Site Interactions in Human Telomerase

2007 ◽  
Vol 27 (8) ◽  
pp. 3226-3240 ◽  
Author(s):  
Haley D. M. Wyatt ◽  
Deirdre A. Lobb ◽  
Tara L. Beattie
Keyword(s):  
Critical Role ◽  
Telomerase Rna ◽  
Dna Interactions ◽  
Telomeric Dna ◽  
Protein Subunit ◽  
Protein Dna Interactions ◽  
N Terminus ◽  
Human Telomerase ◽  
Linear Chromosomes

ABSTRACT Telomerase is a ribonucleoprotein reverse transcriptase (RT) that processively synthesizes telomeric repeats onto the ends of linear chromosomes to maintain genomic stability. It has been proposed that the N terminus of the telomerase protein subunit, telomerase RT (TERT), contains an anchor site that forms stable interactions with DNA to prevent enzyme-DNA dissociation during translocation and to promote realignment events that accompany each round of telomere synthesis. However, it is not known whether human TERT (hTERT) can directly interact with DNA in the absence of the telomerase RNA subunit. Here we use a novel primer binding assay to establish that hTERT forms stable and specific contacts with telomeric DNA in the absence of the human telomerase RNA component (hTR). We show that hTERT-mediated primer binding can be functionally uncoupled from telomerase-mediated primer extension. Our results demonstrate that the first 350 amino acids of hTERT have a critical role in regulating the strength and specificity of protein-DNA interactions, providing additional evidence that the TERT N terminus contains an anchor site. Furthermore, we establish that the RT domain of hTERT mediates important protein-DNA interactions. Collectively, these data suggest that hTERT contains distinct anchor regions that cooperate to help regulate telomerase-mediated DNA recognition and elongation.

A protein-based electrochemical method for label-free characterization of sequence-specific protein–DNA interactions

2011 ◽  
Vol 56 (16) ◽  
pp. 5759-5765 ◽  
Author(s):  
Jinhai Xu ◽  
Xiaodie He ◽  
Liling Jin ◽  
Lan Jiang ◽  
Yifeng Zhou ◽  
...  
Keyword(s):  
Electrochemical Method ◽  
Specific Protein ◽  
Label Free ◽  
Dna Interactions ◽  
Protein Dna Interactions
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