Dynamics and Mechanism of DNA-Bending Proteins in Binding Site Recognition

Nonfiction, Science & Nature, Science, Physics, Spectrum Analysis, Biological Sciences, Biophysics
Cover of the book Dynamics and Mechanism of DNA-Bending Proteins in Binding Site Recognition by Yogambigai Velmurugu, Springer International Publishing
View on Amazon View on AbeBooks View on Kobo View on B.Depository View on eBay View on Walmart
Author: Yogambigai Velmurugu ISBN: 9783319451299
Publisher: Springer International Publishing Publication: November 29, 2016
Imprint: Springer Language: English
Author: Yogambigai Velmurugu
ISBN: 9783319451299
Publisher: Springer International Publishing
Publication: November 29, 2016
Imprint: Springer
Language: English

Using a novel approach that combines high temporal resolution of the laser T-jump technique with unique sets of fluorescent probes, this study unveils previously unresolved DNA dynamics during search and recognition by an architectural DNA bending protein and two DNA damage recognition proteins.

Many cellular processes involve special proteins that bind to specific DNA sites with high affinity.  How these proteins recognize their sites while rapidly searching amidst ~3 billion nonspecific sites in genomic DNA remains an outstanding puzzle. Structural studies show that proteins severely deform DNA at specific sites and indicate that DNA deformability is a key factor in site-specific recognition. However, the dynamics of DNA deformations have been difficult to capture, thus obscuring our understanding of recognition mechanisms. 

The experiments presented in this thesis uncover, for the first time, rapid (~100-500 microseconds) DNA unwinding/bending attributed to nonspecific interrogation, prior to slower (~5-50 milliseconds) DNA kinking/bending/nucleotide-flipping during recognition. These results help illuminate how a searching protein interrogates DNA deformability and eventually “stumbles” upon its target site. Submillisecond interrogation may promote preferential stalling of the rapidly scanning protein at cognate sites, thus enabling site-recognition.  Such multi-step search-interrogation-recognition processes through dynamic conformational changes may well be common to the recognition mechanisms for diverse DNA-binding proteins. 

View on Amazon View on AbeBooks View on Kobo View on B.Depository View on eBay View on Walmart

Using a novel approach that combines high temporal resolution of the laser T-jump technique with unique sets of fluorescent probes, this study unveils previously unresolved DNA dynamics during search and recognition by an architectural DNA bending protein and two DNA damage recognition proteins.

Many cellular processes involve special proteins that bind to specific DNA sites with high affinity.  How these proteins recognize their sites while rapidly searching amidst ~3 billion nonspecific sites in genomic DNA remains an outstanding puzzle. Structural studies show that proteins severely deform DNA at specific sites and indicate that DNA deformability is a key factor in site-specific recognition. However, the dynamics of DNA deformations have been difficult to capture, thus obscuring our understanding of recognition mechanisms. 

The experiments presented in this thesis uncover, for the first time, rapid (~100-500 microseconds) DNA unwinding/bending attributed to nonspecific interrogation, prior to slower (~5-50 milliseconds) DNA kinking/bending/nucleotide-flipping during recognition. These results help illuminate how a searching protein interrogates DNA deformability and eventually “stumbles” upon its target site. Submillisecond interrogation may promote preferential stalling of the rapidly scanning protein at cognate sites, thus enabling site-recognition.  Such multi-step search-interrogation-recognition processes through dynamic conformational changes may well be common to the recognition mechanisms for diverse DNA-binding proteins. 

More books from Springer International Publishing

Cover of the book Rainbows in Channeling of Charged Particles in Crystals and Nanotubes by Yogambigai Velmurugu
Cover of the book On the Move to Meaningful Internet Systems. OTM 2018 Conferences by Yogambigai Velmurugu
Cover of the book Mobile Marketing Channel by Yogambigai Velmurugu
Cover of the book Functional Imaging and Modeling of the Heart by Yogambigai Velmurugu
Cover of the book Computational Intelligence in Music, Sound, Art and Design by Yogambigai Velmurugu
Cover of the book Neuroanatomy and Pathology of Sporadic Alzheimer's Disease by Yogambigai Velmurugu
Cover of the book History of Number by Yogambigai Velmurugu
Cover of the book Dynamic Behavior of Materials, Volume 1 by Yogambigai Velmurugu
Cover of the book Survivors of Childhood and Adolescent Cancer by Yogambigai Velmurugu
Cover of the book Prokaryotic Systems Biology by Yogambigai Velmurugu
Cover of the book Global Mental Health by Yogambigai Velmurugu
Cover of the book Nationalism and the Haram al-Sharif/Temple Mount by Yogambigai Velmurugu
Cover of the book Challenges and Opportunities in the Digital Era by Yogambigai Velmurugu
Cover of the book Conductors, Semiconductors, Superconductors by Yogambigai Velmurugu
Cover of the book Building Trust in Information by Yogambigai Velmurugu
We use our own "cookies" and third party cookies to improve services and to see statistical information. By using this website, you agree to our Privacy Policy