Thermodynamics of specific and non-specific DNA binding by the c-Myb DNA-binding domain

Journal of Molecular Biology
M OdaH Nakamura

Abstract

The thermodynamics of the c-Myb DNA-binding domain (R2R3) interaction with its target DNA have been analyzed using isothermal titration calorimetry and amino acid mutagenesis. The enthalpy of association between the standard R2R3, the Cys130 mutant substituted with Ile, and the cognate DNA is -12.5 (+/- 0.1) kcal mol-1 at pH 7.5 and at 20 degrees C, and this interaction is enthalpically driven throughout the physiological temperature range. In order to understand the DNA recognition mechanism, several pairs of interactions were investigated using single and multiple-base alterations with single and multiple-amino acid substituted mutants. The interactions between the standard R2R3 and many non-cognate DNAs were accompanied by binding enthalpy changes and heat capacity changes, although their affinities were reduced. The roles of the electrostatic interactions in binding to the cognate and the non-cognate DNAs were also analyzed from the dependency of the thermodynamic parameters on the salt concentration. The heat capacity change was found to be significantly dependent upon the salt concentration. Several mutant proteins bound to the multiple-base altered DNA with very small enthalpy changes, although they bound to the cognate ...Continue Reading

Citations

Jul 11, 2000·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·M Oda, H Nakamura
Sep 27, 2012·Proceedings of the National Academy of Sciences of the United States of America·Marcel GeertzSebastian J Maerkl
Jul 21, 2012·The Journal of Biological Chemistry·Katarina VisackaLubomir Tomaska
Dec 21, 2005·Genome Research·Robert A RollinsTimothy H Bestor
Sep 2, 2009·Microbiology and Molecular Biology Reviews : MMBR·Sacha A F T van HijumOscar P Kuipers
Oct 30, 2004·BMC Evolutionary Biology·Johannes BergMichael Lässig
Jan 12, 2007·BMC Structural Biology·Francesca SpyrakisAndrea Mozzarelli
Dec 24, 2014·Proceedings of the National Academy of Sciences of the United States of America·Michael Lynch, Kyle Hagner
Sep 29, 2004·Journal of Molecular Biology·William B PetersJohn W Shriver
Apr 16, 2008·The Plant Journal : for Cell and Molecular Biology·Jayson A PunwaniGary N Drews
Apr 28, 2011·The EMBO Journal·Tom J PettyThanos D Halazonetis
Jul 27, 1999·The Journal of Biological Chemistry·K B AnderssonO S Gabrielsen
Jun 27, 2020·Angewandte Chemie·Katharina AchaziGerd Multhaup
Jan 14, 2020·Free Radical Biology & Medicine·Miłosz Wieczór, Jacek Czub
Sep 7, 2014·The Plant Cell·Guillaume BartholeSébastien Baud
Oct 20, 2009·The Journal of Physical Chemistry. B·Michael R Duff, Challa V Kumar
Oct 28, 2009·Langmuir : the ACS Journal of Surfaces and Colloids·Michael R Duff, Challa V Kumar
May 13, 2021·Biophysics and Physicobiology·Maki Kawasaki, Masayuki Oda
Aug 7, 2010·The Journal of Physical Chemistry. B·Hemant SuryawanshiSouvik Maiti
May 22, 2008·Biochemistry·Lynn DeleeuwAndrew N Lane
Jun 12, 2003·Journal of Molecular Biology·Lawrence E Schaufler, Rachel E Klevit
Aug 21, 2021·Biophysical Chemistry·Yuhi HosoeMasayuki Oda
Apr 7, 2019·The Journal of Physical Chemistry. B·Qinghua LiaoShina Caroline Lynn Kamerlin
Jul 28, 2009·Journal of Molecular Biology·Sanjay NilapwarJohn E Ladbury

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.