Nature of the Molecular Interaction in DNA-Protein Complexes

Abstract

DNA base methylation at the O6 point of guanine is a major cause of cancer. This methylation transits from G:C to A:T mutation pairs during the DNA replication and translation process. The O6-alkylguanine-DNA alkylguanine (AGT) serves as a non methylating agent, which repairs methylation damage at the O6 point of guanine and O4 point of cytosine by direct damage reversal mechanism. Despite the identification of its role in the methylation damage repair process in the human body, a detailed study is necessary to unlock the underlying mechanism during this methyl transfer process. The present work is focused on the microscopic investigation of DNA-AGT interaction to explore the more insight on DNA damage repair mechanism. Molecular dynamics (MD) simulation has been carried out to investigate structural basis of the DNA methylation damage repair mechanism, modeling three basic structures: pre-methyl transfer condition (complex-I), transient intermediate state (complex-II), and post-methyl transfer condition (complex-III). Complex-I represents the formation of the DNA-AGT complex and complex-III represents the deformation of the complex AGT from DNA. Complex-II is a close representation of the transient intermediate state of complex-I and complex-II. The structural and thermodynamic stability of each complex was examined with several physical aspects. Formation of hydrogen bonds as well as energy contributions due to electrostatic as well as van der Waals interactions were taken into consideration to investigate favorable binding of the molecules in all three complexes, which agree with the findings of Daniels et al., 2004. Steered Molecular Dynamics (SMD) results showed that the force in pre-methyl transfer process was greater than that of the post-methyl transfer condition referring to a more favorable binding between DNA and AGT in complex-I. Our findings on force of binding between DNA and AGT agree with AFM experiment of Tessmer and Fried, 2014; and DFT results of Jena et al., 2009. The study was further extended to investigate the changes in the free energy during the interaction of pre- and post-methyl transfer: the former with methylated GUA7 in DNA and the later with methylated CYS145 in AGT. The umbrella sampling method was utilized to calculate the free energy and the results suggested that the change in free energy during the pre-methyl transfer process is greater than that of the post-methyl transfer by 1.3 kcal/mol thereby demonstrating the stronger binding affinity of methylated GUA with AGT than that of the complex in which methylation lies at AGT. Our free energy result agrees with the outcomes of Hu et al., 2007.