Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations

Abstract

Reproduction, the hallmark of biological activity, requires making an accurate copy of the genetic material to allow the progeny to inherit parental traits. In all living cells, the process of DNA replication is carried out by a concerted action of multiple protein species forming a loose protein-nucleic acid complex, the replisome. Proofreading and error correction generally accompany replication but also occur independently, safeguarding genetic information through all phases of the cell cycle. Advances in biochemical characterization of intracellular processes, proteomics, and the advent of single-molecule biophysics have brought about a treasure trove of information awaiting to be assembled into an accurate mechanistic model of the DNA replication process. This review describes recent efforts to model elements of DNA replication and repair processes using computer simulations, an approach that has gained immense popularity in many areas of molecular biophysics but has yet to become mainstream in the DNA metabolism community. It highlights the use of diverse computational methods to address specific problems of the fields and discusses unexplored possibilities that lie ahead for the computational approaches in these areas.

Single-molecule biophysics experiments in silico: Towards a physical model of a replisome

“…Rather than examining the absolute rates, such simulations could be used to compare the exchange rates, for example, probing how the exchange rate depends on the length of the ssDNA or perhaps on modifications of the SSB structure. Our simulation approach could be generalized to model competitive binding of SSB and other DNA-binding proteins, such as RecA, to the same DNA fragment, providing insights into the microscopic mechanisms of DNA repair [31].…”

“…Among the most popular computational approaches, explicit solvent all-atom MD simulations have been applied widely to study the molecular mechanisms underlying biological and biotechnological systems [18,27,21,14,31]. However, the explicit representation of each atom limits routine application of the method to small systems and/or relatively short timescales.…”

Single-molecule biophysics experiments in silico: Toward a physical model of a replisome

“…Among the most popular computational approaches, explicit solvent all-atom MD simulations have been applied widely to study the molecular mechanisms underlying biological and biotechnological systems ( Karplus and McCammon, 2002 ; Lindahl and Sansom, 2008 ; Klepeis et al., 2009 ; Hollingsworth and Dror, 2018 ; Maffeo et al., 2019 ). However, the explicit representation of each atom limits routine application of the method to small systems and/or relatively short timescales.…”

Protein-Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations

“…In addition to the structural biology techniques, many other experimental techniques including Förster resonance energy transfer (FRET) 13-14 , nuclear magnetic resonance (NMR) 15-16 , mass spectrometry 17-18 , small angle X-ray scattering (SAXS) 19 , electrophoretic mobility shift assay (EMSA) 20-22 , footprinting 20-21 , crosslinking 21, 23 and chromatin immunoprecipitation (ChIP) 20-21, 24-25 focus on proteins-nucleic acids interactions and their dynamics during the biological processes. In addition to these studies, computational approaches based on molecular dynamics (MD) simulations have provided important insights on the dynamics of protein-nucleic acid interactions at the atomistic details 26-32 . MD simulations are used to obtain mechanistic understanding of the roles that protein-nucleic acid interactions play in biological processes 27-28, 32-33 .…”

“…In addition to these studies, computational approaches based on molecular dynamics (MD) simulations have provided important insights on the dynamics of protein-nucleic acid interactions at the atomistic details 26-32 . MD simulations are used to obtain mechanistic understanding of the roles that protein-nucleic acid interactions play in biological processes 27-28, 32-33 . Studies have also shown the importance of force field choice in simulations to reproduce experimental values with high accuracy as they demonstrated that imperfections in the results can occur 29, 34-35 .…”