Before reaching their targets, sequence-specific DNA-binding proteins nonspecifically bind to DNA through electrostatic interactions and stochastically change their locations on DNA. Investigations into the dynamics of DNA-scanning by proteins are nontrivial due to the simultaneous presence of multiple translocation mechanisms and many sites for the protein to nonspecifically bind to DNA. Nuclear magnetic resonance (NMR) spectroscopy can provide information about the target DNA search processes...
[NMR paper] Facilitated Protein Association via Engineered Target Search Pathways Visualized by Paramagnetic NMR Spectroscopy.
Facilitated Protein Association via Engineered Target Search Pathways Visualized by Paramagnetic NMR Spectroscopy.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/https:--linkinghub.elsevier.com-ihub-images-cellhub.gif Related Articles Facilitated Protein Association via Engineered Target Search Pathways Visualized by Paramagnetic NMR Spectroscopy.
Structure. 2018 May 01;:
Authors: An SY, Kim EH, Suh JY
Abstract
Proteins assemble to form functional complexes via the progressive evolution of nonspecific complexes...
nmrlearner
Journal club
0
05-22-2018 08:59 PM
Facilitated Protein Association via Engineered Target Search Pathways Visualized by Paramagnetic NMR Spectroscopy
Facilitated Protein Association via Engineered Target Search Pathways Visualized by Paramagnetic NMR Spectroscopy
Publication date: Available online 17 May 2018
Source:Structure</br>
Author(s): So Young An, Eun-Hee Kim, Jeong-Yong Suh</br>
Proteins assemble to form functional complexes via the progressive evolution of nonspecific complexes formed by transient encounters. This target search process generally involves multiple routes that lead the initial encounters to the final complex. In this study, we have employed NMR paramagnetic relaxation enhancement to...
nmrlearner
Journal club
0
05-17-2018 04:09 PM
[NMR paper] NMR-based investigations into target DNA search processes of proteins.
NMR-based investigations into target DNA search processes of proteins.
Related Articles NMR-based investigations into target DNA search processes of proteins.
Methods. 2018 May 09;:
Authors: Iwahara J, Zandarashvili L, Kemme CA, Esadze A
Abstract
To perform their function, transcription factors and DNA-repair/modifying enzymes must first locate their targets in the vast presence of nonspecific, but structurally similar sites on genomic DNA. Before reaching their targets, these proteins stochastically scan DNA and dynamically move...
nmrlearner
Journal club
0
05-13-2018 02:32 PM
NMR-based investigations into target DNA search processes of proteins
NMR-based investigations into target DNA search processes of proteins
Publication date: Available online 10 May 2018
Source:Methods</br>
Author(s): Junji Iwahara, Levani Zandarashvili, Catherine A. Kemme, Alexandre Esadze</br>
To perform their function, transcription factors and DNA-repair/modifying enzymes must first locate their targets in the vast presence of nonspecific, but structurally similar sites on genomic DNA. Before reaching their targets, these proteins stochastically scan DNA and dynamically move from one site to another on DNA. Solution NMR...
nmrlearner
Journal club
0
05-10-2018 01:31 PM
[NMR paper] A Discrete-State Kinetics Model for NMR-Based Analysis of Protein Translocation on DNA at Equilibrium.
A Discrete-State Kinetics Model for NMR-Based Analysis of Protein Translocation on DNA at Equilibrium.
Related Articles A Discrete-State Kinetics Model for NMR-Based Analysis of Protein Translocation on DNA at Equilibrium.
J Phys Chem B. 2017 Sep 19;:
Authors: Sahu D, Iwahara J
Abstract
In the target DNA search process, sequence-specific DNA-binding proteins first nonspecifically bind to DNA and stochastically move from one site to another before reaching their targets. To rigorously assess how the translocation process...
nmrlearner
Journal club
0
09-21-2017 02:38 AM
Intra- and intermolecular translocation of the bi-domain transcription factor Oct1 characterized by liquid crystal and paramagnetic NMR.
Intra- and intermolecular translocation of the bi-domain transcription factor Oct1 characterized by liquid crystal and paramagnetic NMR.
Intra- and intermolecular translocation of the bi-domain transcription factor Oct1 characterized by liquid crystal and paramagnetic NMR.
Proc Natl Acad Sci U S A. 2011 May 31;108(22):E169-76
Authors: Takayama Y, Clore GM
Abstract
The intra- and intermolecular translocation processes whereby the bi-domain transcription factor Oct1 searches for its specific DNA target site have been investigated by...
nmrlearner
Journal club
1
08-25-2011 07:02 AM
NMR Studies of Translocation of the Zif268 Protein between Its Target DNA Sites
NMR Studies of Translocation of the Zif268 Protein between Its Target DNA Sites
http://pubs.acs.org//appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi100962h/aop/images/medium/bi-2010-00962h_0005.gifBiochemistry, Volume 0, Issue 0, Articles ASAP (As Soon As Publishable).
More...
nmrlearner
Journal club
0
08-31-2010 10:50 PM
NMR studies of translocation of the Zif268 protein between its target DNA sites.
NMR studies of translocation of the Zif268 protein between its target DNA sites.
Related Articles NMR studies of translocation of the Zif268 protein between its target DNA sites.
Biochemistry. 2010 Aug 19;
Authors: Takayama Y, Sahu D, Iwahara J
Zif268 is a zinc-finger protein containing three Cys2-His2-type zinc-finger domains that bind the target DNA sequence GCGTGGGCG in a cooperative manner. In this work, we characterized translocation of the Zif268 protein between its target DNA sites using NMR spectroscopy. The residual dipolar coupling...
Analyzing paramagnetic NMR data on target DNA search by proteins using a discrete-state kinetic model for translocation
Linear Mode
