Microscopic understanding of the conformational features of a protein–DNA complex

Literature Information

Publication Date 2017-11-21
DOI 10.1039/C7CP05161A
Impact Factor 3.676
Authors

Sandip Mondal, Kaushik Chakraborty


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Abstract

Protein–DNA interactions play crucial roles in different biological processes. Binding of a protein to its target DNA is the key step at different stages of genetic activities. In this article, we have carried out atomistic molecular dynamics simulations to understand the microscopic conformational and dynamical features of the N-terminal domain of the λ-repressor protein and its operator DNA in their complexed state. The calculations revealed that the overall flexibility of the protein and the DNA components reduces due to complex formation. In particular, increased ordering of the DNA sugar rings bound to the protein is found to be associated with modified ring puckering. Attempts have been made to study the effect of complexation on the internal motions of the protein and the DNA components. It is demonstrated that the non-uniform ordering of the side chains of lysine residues in the consensus sequence leads to differential behavior of the two monomers of the homodimeric protein.

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Source Journal

Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
CiteScore: 5.5
Self-citation Rate: 10.3%
Articles per Year: 3036

Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.

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