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Sinha S, Pindi C, Ahsan M, Arantes PR, Palermo G. Machines on Genes through the Computational Microscope. J Chem Theory Comput 2023; 19:1945-1964. [PMID: 36947696 PMCID: PMC10104023 DOI: 10.1021/acs.jctc.2c01313] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Macromolecular machines acting on genes are at the core of life's fundamental processes, including DNA replication and repair, gene transcription and regulation, chromatin packaging, RNA splicing, and genome editing. Here, we report the increasing role of computational biophysics in characterizing the mechanisms of "machines on genes", focusing on innovative applications of computational methods and their integration with structural and biophysical experiments. We showcase how state-of-the-art computational methods, including classical and ab initio molecular dynamics to enhanced sampling techniques, and coarse-grained approaches are used for understanding and exploring gene machines for real-world applications. As this review unfolds, advanced computational methods describe the biophysical function that is unseen through experimental techniques, accomplishing the power of the "computational microscope", an expression coined by Klaus Schulten to highlight the extraordinary capability of computer simulations. Pushing the frontiers of computational biophysics toward a pragmatic representation of large multimegadalton biomolecular complexes is instrumental in bridging the gap between experimentally obtained macroscopic observables and the molecular principles playing at the microscopic level. This understanding will help harness molecular machines for medical, pharmaceutical, and biotechnological purposes.
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Affiliation(s)
- Souvik Sinha
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - Chinmai Pindi
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - Mohd Ahsan
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - Pablo R. Arantes
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
- Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
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Abstract
The protein HIV Reverse Transcriptase (HIV RT) synthesizes a DNA strand according to a template. During the synthesis, the polymerase slides on the double stranded DNA to allow the entry of a new nucleotide to the active site. We use Molecular Dynamics simulations to estimate the free energy profile and the time scale of the DNA-protein's relative displacement in the complex's closed state. We illustrate that the presence of the catalytic magnesium slows down the process. Upon removing the catalytic magnesium ion, the process is rapid and significantly faster than reopening the active site in preparation for the new substrate. We speculate that magnesium regulates DNA translocation. The magnesium locks the DNA into a specific orientation during the chemical addition of the nucleotide. The release of Mg2+ eases DNA sliding and the acceptance of a new substrate.
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Affiliation(s)
- Hao Wang
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ron Elber
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, Texas 78712, United States.,Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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Bolhuis PG, Swenson DWH. Transition Path Sampling as Markov Chain Monte Carlo of Trajectories: Recent Algorithms, Software, Applications, and Future Outlook. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202000237] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Peter G. Bolhuis
- Amsterdam Center for Multiscale Modeling van 't Hoff Institute for Molecular Sciences University of Amsterdam PO Box 94157 1090 GD Amsterdam The Netherlands
| | - David W. H. Swenson
- Centre Blaise Pascal Ecole Normale Superieure 46, allée d'Italie 69364 Lyon Cedex 07 France
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Maffeo C, Chou HY, Aksimentiev A. Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations. ADVANCED THEORY AND SIMULATIONS 2019; 2:1800191. [PMID: 31728433 PMCID: PMC6855400 DOI: 10.1002/adts.201800191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 12/15/2022]
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. In this review, we describe 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. We highlight the use of diverse computational methods to address specific problems of the fields and discuss unexplored possibilities that lie ahead for the computational approaches in these areas.
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Affiliation(s)
- Christopher Maffeo
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
| | - Han-Yi Chou
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
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5
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Wu WJ, Yang W, Tsai MD. How DNA polymerases catalyse replication and repair with contrasting fidelity. Nat Rev Chem 2017. [DOI: 10.1038/s41570-017-0068] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Wilson KA, Wetmore SD. Conformational Flexibility of the Benzyl-Guanine Adduct in a Bypass Polymerase Active Site Permits Replication: Insights from Molecular Dynamics Simulations. Chem Res Toxicol 2017; 30:2013-2022. [PMID: 28810119 DOI: 10.1021/acs.chemrestox.7b00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Katie A. Wilson
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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7
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Matute RA, Yoon H, Warshel A. Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase β. Proteins 2016; 84:1644-1657. [PMID: 27488241 DOI: 10.1002/prot.25106] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/22/2016] [Indexed: 12/18/2022]
Abstract
Elucidating the catalytic mechanism of DNA polymerase is crucial for a progress in the understanding of the control of replication fidelity. This work tries to advance the mechanistic understanding by analyzing the observed effect of mutations of the acidic groups in the active site of Polymerase β as well as the pH effect on the rate constant. The analysis involves both empirical valence bond (EVB) free energy calculations and considerations of the observed pH dependence of the reaction. The combined analysis indicates that the proton transfer (PT) from the nucleophilic O3' has two possible pathways, one to D256 and the second to the bulk. We concluded based on calculations and the experimental pH profile that the most likely path for the wild-type (WT) and the D256E and D256A mutants is a PT to the bulk, although the WT may also use a PT to Asp 256. Our analysis highlights the need for very extensive sampling in the calculations of the activation barrier and also clearly shows that ab initio QM/MM calculations that do not involve extensive sampling are unlikely to give a clear quantitative picture of the reaction mechanism. Proteins 2016; 84:1644-1657. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ricardo A Matute
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, California, 90089-1062
| | - Hanwool Yoon
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, California, 90089-1062
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, California, 90089-1062.
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Kim T, Freudenthal BD, Beard WA, Wilson SH, Schlick T. Insertion of oxidized nucleotide triggers rapid DNA polymerase opening. Nucleic Acids Res 2016; 44:4409-24. [PMID: 27034465 PMCID: PMC4872097 DOI: 10.1093/nar/gkw174] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/04/2016] [Indexed: 11/21/2022] Open
Abstract
A novel mechanism is unveiled to explain why a pro-mutagenic nucleotide lesion (oxidized guanine, 8-oxoG) causes the mammalian DNA repair polymerase-β (pol-β) to rapidly transition to an inactive open conformation. The mechanism involves unexpected features revealed recently in time-lapse crystallography. Specifically, a delicate water network associated with a lesion-stabilizing auxilliary product ion Mg(p) triggers a cascade of events that leads to poor active site geometry and the rupture of crucial molecular interactions between key residues in both the anti(8-oxoG:C) and syn(8-oxoG:A) systems. Once the base pairs in these lesioned systems are broken, dislocation of both Asp192 (a metal coordinating ligand) and the oxoG phosphate group (PO4) interfere with the hydrogen bonding between Asp192 and Arg258, whose rotation toward Asp192 is crucial to the closed-to-open enzyme transition. Energetically, the lesioned open states are similar in energy to those of the corresponding closed complexes after chemistry, in marked contrast to the unlesioned pol-β anti(G:C) system, whose open state is energetically higher than the closed state. The delicate surveillance system offers a fundamental protective mechanism in the cell that triggers DNA repair events which help deter insertion of oxidized lesions.
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Affiliation(s)
- Taejin Kim
- Department of Chemistry, New York University, 10th Floor Silver Center, 100 Washington Square East, New York, NY 10003, USA
| | - Bret D Freudenthal
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - William A Beard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 10th Floor Silver Center, 100 Washington Square East, New York, NY 10003, USA Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
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Freudenthal BD, Beard WA, Wilson SH. New structural snapshots provide molecular insights into the mechanism of high fidelity DNA synthesis. DNA Repair (Amst) 2015; 32:3-9. [PMID: 26002198 DOI: 10.1016/j.dnarep.2015.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Time-lapse X-ray crystallography allows visualization of intermediate structures during the DNA polymerase catalytic cycle. Employing time-lapse crystallography with human DNA polymerase β has recently allowed us to capture and solve novel intermediate structures that are not stable enough to be analyzed by traditional crystallography. The structures of these intermediates reveals exciting surprises about active site metal ions and enzyme conformational changes as the reaction proceeds from the ground state to product release. In this perspective, we provide an overview of recent advances in understanding the DNA polymerase nucleotidyl transferase reaction and highlight both the significance and mysteries of enzyme efficiency and specificity that remain to be solved.
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Affiliation(s)
- Bret D Freudenthal
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, United States
| | - William A Beard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, United States
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, United States.
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