76 Protein–DNA binding and breathing dynamics of DNA
نویسندگان
چکیده
منابع مشابه
Coupled dynamics of DNA-breathing and single-stranded DNA binding proteins
We study the size fluctuations of a local denaturation zone in a DNA molecule in the presence of proteins that selectively bind to single-stranded DNA, based on a (2 + 1)-dimensional master equation. By tuning the physical parameters we can drive the system from undisturbed bubble fluctuations to full, binding protein-induced denaturation. We determine the effective free energy landscape of the...
متن کاملComparative Investigation of R213G Mutation in DNA-Binding Domain of P53 Protein via Molecular Dynamics Simulation
Introduction: P53 is a tumor suppressor protein with numerous missense mutations identified in its gene. These mutations are observed in a vast number of cancers. R213G is one of them which has a role in metastatic lung cancers. In this research, R213G was studied in comparison with the wild type via molecular dynamics simulation. Method: For the three-dimensional structure of the wild-type P53...
متن کاملBreathing dynamics in heteropolymer DNA.
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule spectroscopy. The dynamical opening of DNA bubbles (DNA breathing) is supposedly crucial for biological functioning during, for instance, transcription initia...
متن کاملComparative Investigation of R213G Mutation in DNA-Binding Domain of P53 Protein via Molecular Dynamics Simulation
Introduction: P53 is a tumor suppressor protein with numerous missense mutations identified in its gene. These mutations are observed in a vast number of cancers. R213G is one of them which has a role in metastatic lung cancers. In this research, R213G was studied in comparison with the wild type via molecular dynamics simulation. Method: For the three-dimensional structure of the wild-type P53...
متن کاملBinding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics
Physicochemical properties of DNA, such as shape, affect protein-DNA recognition. However, the properties of DNA that are most relevant for predicting the binding sites of particular transcription factors (TFs) or classes of TFs have yet to be fully understood. Here, using a model that accurately captures the melting behavior and breathing dynamics (spontaneous local openings of the double heli...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Biomolecular Structure and Dynamics
سال: 2013
ISSN: 0739-1102,1538-0254
DOI: 10.1080/07391102.2013.786510