NDLI: Binding Selectivity of RecA to a single stranded DNA, a computational approach

Content Provider	Springer Nature Link
Author	Carra, Claudio Cucitta, Francis A.
Copyright Year	2010
Abstract	Homologous recombination (HR) is the major DNA double strand break repair pathway which maintains the genomic integrity. It is fundamental for the survivability and functionality of all organisms. One of the initial steps in HR is the formation of the nucleoprotein filament composed by a single stranded DNA chain surrounded by the recombinases protein. The filament orchestrates the search for an undamaged homologue, as a template for the repair process. Our theoretical study was aimed at elucidating the selectivity of the interaction between a monomer of the recombinases enzyme in the Escherichia coli, EcRecA, the bacterial homologue of human Rad51, with a series of oligonucleotides of nine bases length. The complex, equilibrated for 20 ns with Langevian dynamics, was inserted in a periodic box with a 8 Å buffer of water molecules explicitly described by the TIP3P model. The absolute binding free energies are calculated in an implicit solvent using the Poisson-Boltzmann (PB) and the generalized Born (GB) solvent accessible surface area, using the MM-PB(GB)SA model. The solute entropic contribution is also calculated by normal mode analysis. The results underline how a significant contribution of the binding free energy is due to the interaction with the Arg196, a critical amino acid for the activity of the enzyme. The study revealed how the binding affinity of EcRecA is significantly higher toward dT9 rather than dA9, as expected from the experimental results.
Starting Page	133
Ending Page	150
Page Count	18
File Format	PDF
ISSN	16102940
Journal	Journal of Molecular Modeling
Volume Number	17
Issue Number	1
e-ISSN	09485023
Language	English
Publisher	Springer-Verlag
Publisher Date	2010-04-13
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Binding EcRecA Homologous recombination MM-PBSA Molecular dynamics Computer Application in Life Sciences Life Sciences Health Informatics Molecular Medicine Biomedicine general Computer Applications in Chemistry
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Physical and Theoretical Chemistry Computational Theory and Mathematics Catalysis Inorganic Chemistry Computer Science Applications

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