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Sabei A, Prentiss M, Prévost C. Modeling the Homologous Recombination Process: Methods, Successes and Challenges. Int J Mol Sci 2023; 24:14896. [PMID: 37834348 PMCID: PMC10573387 DOI: 10.3390/ijms241914896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Homologous recombination (HR) is a fundamental process common to all species. HR aims to faithfully repair DNA double strand breaks. HR involves the formation of nucleoprotein filaments on DNA single strands (ssDNA) resected from the break. The nucleoprotein filaments search for homologous regions in the genome and promote strand exchange with the ssDNA homologous region in an unbroken copy of the genome. HR has been the object of intensive studies for decades. Because multi-scale dynamics is a fundamental aspect of this process, studying HR is highly challenging, both experimentally and using computational approaches. Nevertheless, knowledge has built up over the years and has recently progressed at an accelerated pace, borne by increasingly focused investigations using new techniques such as single molecule approaches. Linking this knowledge to the atomic structure of the nucleoprotein filament systems and the succession of unstable, transient intermediate steps that takes place during the HR process remains a challenge; modeling retains a very strong role in bridging the gap between structures that are stable enough to be observed and in exploring transition paths between these structures. However, working on ever-changing long filament systems submitted to kinetic processes is full of pitfalls. This review presents the modeling tools that are used in such studies, their possibilities and limitations, and reviews the advances in the knowledge of the HR process that have been obtained through modeling. Notably, we will emphasize how cooperative behavior in the HR nucleoprotein filament enables modeling to produce reliable information.
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Affiliation(s)
- Afra Sabei
- CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Université de Paris, 13 Rue Pierre et Marie Curie, F-75005 Paris, France;
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, F-75005 Paris, France
| | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA02138, USA;
| | - Chantal Prévost
- CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Université de Paris, 13 Rue Pierre et Marie Curie, F-75005 Paris, France;
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, F-75005 Paris, France
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2
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Loiko N, Tereshkina K, Kovalenko V, Moiseenko A, Tereshkin E, Sokolova OS, Krupyanskii Y. DNA-Binding Protein Dps Protects Escherichia coli Cells against Multiple Stresses during Desiccation. BIOLOGY 2023; 12:853. [PMID: 37372138 DOI: 10.3390/biology12060853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/06/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Gradual dehydration is one of the frequent lethal yet poorly understood stresses that bacterial cells constantly face in the environment when their micro ecotopes dry out, as well as in industrial processes. Bacteria successfully survive extreme desiccation through complex rearrangements at the structural, physiological, and molecular levels, in which proteins are involved. The DNA-binding protein Dps has previously been shown to protect bacterial cells from many adverse effects. In our work, using engineered genetic models of E. coli to produce bacterial cells with overproduction of Dps protein, the protective function of Dps protein under multiple desiccation stresses was demonstrated for the first time. It was shown that the titer of viable cells after rehydration in the experimental variants with Dps protein overexpression was 1.5-8.5 times higher. Scanning electron microscopy was used to show a change in cell morphology upon rehydration. It was also proved that immobilization in the extracellular matrix, which is greater when the Dps protein is overexpressed, helps the cells survive. Transmission electron microscopy revealed disruption of the crystal structure of DNA-Dps crystals in E. coli cells that underwent desiccation stress and subsequent watering. Coarse-grained molecular dynamics simulations showed the protective function of Dps in DNA-Dps co-crystals during desiccation. The data obtained are important for improving biotechnological processes in which bacterial cells undergo desiccation.
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Affiliation(s)
- Nataliya Loiko
- Winogradsky Institute of Microbiology, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 117312 Moscow, Russia
| | - Ksenia Tereshkina
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladislav Kovalenko
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Andrey Moiseenko
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Eduard Tereshkin
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga S Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Yurii Krupyanskii
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
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3
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Backer AS, King GA, Biebricher AS, Shepherd JW, Noy A, Leake MC, Heller I, Wuite GJL, Peterman EJG. Elucidating the Role of Topological Constraint on the Structure of Overstretched DNA Using Fluorescence Polarization Microscopy. J Phys Chem B 2021; 125:8351-8361. [PMID: 34309392 PMCID: PMC8350907 DOI: 10.1021/acs.jpcb.1c02708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/01/2021] [Indexed: 11/29/2022]
Abstract
The combination of DNA force spectroscopy and polarization microscopy of fluorescent DNA intercalator dyes can provide valuable insights into the structure of DNA under tension. These techniques have previously been used to characterize S-DNA-an elongated DNA conformation that forms when DNA overstretches at forces ≥ 65 pN. In this way, it was deduced that the base pairs of S-DNA are highly inclined, relative to those in relaxed (B-form) DNA. However, it is unclear whether and how topological constraints on the DNA may influence the base-pair inclinations under tension. Here, we apply polarization microscopy to investigate the impact of DNA pulling geometry, torsional constraint, and negative supercoiling on the orientations of intercalated dyes during overstretching. In contrast to earlier predictions, the pulling geometry (namely, whether the DNA molecule is stretched via opposite strands or the same strand) is found to have little influence. However, torsional constraint leads to a substantial reduction in intercalator tilting in overstretched DNA, particularly in AT-rich sequences. Surprisingly, the extent of intercalator tilting is similarly reduced when the DNA molecule is negatively supercoiled up to a critical supercoiling density (corresponding to ∼70% reduction in the linking number). We attribute these observations to the presence of P-DNA (an overwound DNA conformation). Our results suggest that intercalated DNA preferentially flanks regions of P-DNA rather than those of S-DNA and also substantiate previous suggestions that P-DNA forms predominantly in AT-rich sequences.
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Affiliation(s)
- Adam S. Backer
- Apple Inc, 1 Apple Park Way, Cupertino, California 95014, United States
| | - Graeme A. King
- Institute
of Structural and Molecular Biology, University
College London, Gower Street, London WC1E
6BT, U.K.
| | - Andreas S. Biebricher
- Department
of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Jack W. Shepherd
- Department
of Physics, University of York, York YO10 5DD, U.K.
- Department
of Biology, University of York, York YO10 5DD, U.K.
| | - Agnes Noy
- Department
of Physics, University of York, York YO10 5DD, U.K.
| | - Mark C. Leake
- Department
of Physics, University of York, York YO10 5DD, U.K.
- Department
of Biology, University of York, York YO10 5DD, U.K.
| | - Iddo Heller
- Department
of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Gijs J. L. Wuite
- Department
of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Erwin J. G. Peterman
- Department
of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
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4
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Boyer B, Danilowicz C, Prentiss M, Prévost C. Weaving DNA strands: structural insight on ATP hydrolysis in RecA-induced homologous recombination. Nucleic Acids Res 2019; 47:7798-7808. [PMID: 31372639 PMCID: PMC6735932 DOI: 10.1093/nar/gkz667] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 07/12/2019] [Accepted: 07/19/2019] [Indexed: 01/01/2023] Open
Abstract
Homologous recombination is a fundamental process in all living organisms that allows the faithful repair of DNA double strand breaks, through the exchange of DNA strands between homologous regions of the genome. Results of three decades of investigation and recent fruitful observations have unveiled key elements of the reaction mechanism, which proceeds along nucleofilaments of recombinase proteins of the RecA family. Yet, one essential aspect of homologous recombination has largely been overlooked when deciphering the mechanism: while ATP is hydrolyzed in large quantity during the process, how exactly hydrolysis influences the DNA strand exchange reaction at the structural level remains to be elucidated. In this study, we build on a previous geometrical approach that studied the RecA filament variability without bound DNA to examine the putative implication of ATP hydrolysis on the structure, position, and interactions of up to three DNA strands within the RecA nucleofilament. Simulation results on modeled intermediates in the ATP cycle bring important clues about how local distortions in the DNA strand geometries resulting from ATP hydrolysis can aid sequence recognition by promoting local melting of already formed DNA heteroduplex and transient reverse strand exchange in a weaving type of mechanism.
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Affiliation(s)
- Benjamin Boyer
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005 Paris, France.,Presently in Laboratoire Génomique Bioinformatique et Applications, EA4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003 Paris, France
| | | | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Chantal Prévost
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005 Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
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5
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Drozdetski AV, Mukhopadhyay A, Onufriev AV. Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment. FRONTIERS IN PHYSICS 2019; 7:195. [PMID: 32601596 PMCID: PMC7323118 DOI: 10.3389/fphy.2019.00195] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As the bending deformation increases beyond a certain (polymer-specific) point, the change in the convexity properties of the effective bending energy of the polymer makes the harmonic deformation energetically unfavorable: in this strong bending regime the energy of the polymer varies linearly with the average bending angle as the system follows the convex hull of the deformation energy function. For double-stranded DNA, the effective bending deformation energy becomes non-convex for bends greater than ~ 2° per base-pair, equivalent to the curvature of a closed circular loop of ~ 160 base pairs. A simple equation is derived for the polymer loop energy that covers both the weak and strong bending regimes. The theory shows quantitative agreement with recent DNA cyclization experiments on short DNA fragments, while maintaining the expected agreement with experiment in the weak bending regime. Counter-intuitively, cyclization probability (j-factor) of very short DNA loops is predicted to increase with decreasing loop length; the j-factor reaches its minimum for loops of ≃ 45 base pairs. Atomistic simulations reveal that the attractive component of the short-range Lennard-Jones interaction between the backbone atoms can explain the underlying non-convexity of the DNA effective bending energy, leading to the linear bending regime. Applicability of the theory to protein-DNA complexes, including the nucleosome, is discussed.
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Affiliation(s)
| | | | - Alexey V. Onufriev
- Department of Physics, Virginia Tech, Blacksburg, VA, United States
- Department of Computer Science, Virginia Tech, Blacksburg, VA, United States
- Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, United States
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6
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Simonov KA. Strong deformations of DNA: Effect on the persistence length. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:114. [PMID: 30259229 DOI: 10.1140/epje/i2018-11722-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/30/2018] [Indexed: 06/08/2023]
Abstract
Extreme deformations of the DNA double helix attracted a lot of attention during the past decades. Particularly, the determination of the persistence length of DNA with extreme local disruptions, or kinks, has become a crucial problem in the studies of many important biological processes. In this paper we review an approach to calculate the persistence length of the double helix by taking into account the formation of kinks of arbitrary configuration. The reviewed approach improves the Kratky-Porod model to determine the type and nature of kinks that occur in the double helix, by measuring a reduction of the persistence length of the kinkable DNA.
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Affiliation(s)
- Kyryło A Simonov
- Fakultät für Mathematik, Universität Wien, Oskar-Morgenstern-Platz 1, 1090, Vienna, Austria.
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7
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Tavakoli S, Panaretos VM. Detecting and Localizing Differences in Functional Time Series Dynamics: A Case Study in Molecular Biophysics. J Am Stat Assoc 2016. [DOI: 10.1080/01621459.2016.1147355] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Shahin Tavakoli
- Statistical Laboratory, University of Cambridge, Cambridge, UK
| | - Victor M. Panaretos
- Institut de Mathématiques, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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8
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Mondal A, Bhattacherjee A. Searching target sites on DNA by proteins: Role of DNA dynamics under confinement. Nucleic Acids Res 2015; 43:9176-86. [PMID: 26400158 PMCID: PMC4627088 DOI: 10.1093/nar/gkv931] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/15/2015] [Accepted: 09/07/2015] [Indexed: 02/07/2023] Open
Abstract
DNA-binding proteins (DBPs) rapidly search and specifically bind to their target sites on genomic DNA in order to trigger many cellular regulatory processes. It has been suggested that the facilitation of search dynamics is achieved by combining 3D diffusion with one-dimensional sliding and hopping dynamics of interacting proteins. Although, recent studies have advanced the knowledge of molecular determinants that affect one-dimensional search efficiency, the role of DNA molecule is poorly understood. In this study, by using coarse-grained simulations, we propose that dynamics of DNA molecule and its degree of confinement due to cellular crowding concertedly regulate its groove geometry and modulate the inter-communication with DBPs. Under weak confinement, DNA dynamics promotes many short, rotation-decoupled sliding events interspersed by hopping dynamics. While this results in faster 1D diffusion, associated probability of missing targets by jumping over them increases. In contrast, strong confinement favours rotation-coupled sliding to locate targets but lacks structural flexibility to achieve desired specificity. By testing under physiological crowding, our study provides a plausible mechanism on how DNA molecule may help in maintaining an optimal balance between fast hopping and rotation-coupled sliding dynamics, to locate target sites rapidly and form specific complexes precisely.
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Affiliation(s)
- Anupam Mondal
- Center for Computational Biology, Indraprastha Institute of Information Technology (IIIT) Delhi, New Delhi-110020, India
| | - Arnab Bhattacherjee
- Center for Computational Biology, Indraprastha Institute of Information Technology (IIIT) Delhi, New Delhi-110020, India
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9
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Gu C, Zhang J, Yang YI, Chen X, Ge H, Sun Y, Su X, Yang L, Xie S, Gao YQ. DNA Structural Correlation in Short and Long Ranges. J Phys Chem B 2015; 119:13980-90. [PMID: 26439165 DOI: 10.1021/acs.jpcb.5b06217] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Recent single-molecule measurements have revealed the DNA allostery in protein/DNA binding. MD simulations showed that this allosteric effect is associated with the deformation properties of DNA. In this study, we used MD simulations to further investigate the mechanism of DNA structural correlation, its dependence on DNA sequence, and the chemical modification of the bases. Besides a random sequence, poly d(AT) and poly d(GC) are also used as simpler model systems, which show the different bending and twisting flexibilities. The base-stacking interactions and the methyl group on the 5-carbon site of thymine causes local structures and flexibility to be very different for the two model systems, which further lead to obviously different tendencies of the conformational deformations, including the long-range allosteric effects.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Sunney Xie
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
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10
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Prentiss M, Prévost C, Danilowicz C. Structure/function relationships in RecA protein-mediated homology recognition and strand exchange. Crit Rev Biochem Mol Biol 2015; 50:453-76. [DOI: 10.3109/10409238.2015.1092943] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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11
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Yang D, Boyer B, Prévost C, Danilowicz C, Prentiss M. Integrating multi-scale data on homologous recombination into a new recognition mechanism based on simulations of the RecA-ssDNA/dsDNA structure. Nucleic Acids Res 2015; 43:10251-63. [PMID: 26384422 PMCID: PMC4666392 DOI: 10.1093/nar/gkv883] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/23/2015] [Indexed: 12/11/2022] Open
Abstract
RecA protein is the prototypical recombinase. Members of the recombinase family can accurately repair double strand breaks in DNA. They also provide crucial links between pairs of sister chromatids in eukaryotic meiosis. A very broad outline of how these proteins align homologous sequences and promote DNA strand exchange has long been known, as are the crystal structures of the RecA-DNA pre- and postsynaptic complexes; however, little is known about the homology searching conformations and the details of how DNA in bacterial genomes is rapidly searched until homologous alignment is achieved. By integrating a physical model of recognition to new modeling work based on docking exploration and molecular dynamics simulation, we present a detailed structure/function model of homology recognition that reconciles extremely quick searching with the efficient and stringent formation of stable strand exchange products and which is consistent with a vast body of previously unexplained experimental results.
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Affiliation(s)
- Darren Yang
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Benjamin Boyer
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, IBPC, Paris, France
| | - Chantal Prévost
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, IBPC, Paris, France
| | | | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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12
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Danilowicz C, Yang D, Kelley C, Prévost C, Prentiss M. The poor homology stringency in the heteroduplex allows strand exchange to incorporate desirable mismatches without sacrificing recognition in vivo. Nucleic Acids Res 2015; 43:6473-85. [PMID: 26089391 PMCID: PMC4513875 DOI: 10.1093/nar/gkv610] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/31/2015] [Indexed: 11/15/2022] Open
Abstract
RecA family proteins are responsible for homology search and strand exchange. In bacteria, homology search begins after RecA binds an initiating single-stranded DNA (ssDNA) in the primary DNA-binding site, forming the presynaptic filament. Once the filament is formed, it interrogates double-stranded DNA (dsDNA). During the interrogation, bases in the dsDNA attempt to form Watson–Crick bonds with the corresponding bases in the initiating strand. Mismatch dependent instability in the base pairing in the heteroduplex strand exchange product could provide stringent recognition; however, we present experimental and theoretical results suggesting that the heteroduplex stability is insensitive to mismatches. We also present data suggesting that an initial homology test of 8 contiguous bases rejects most interactions containing more than 1/8 mismatches without forming a detectable 20 bp product. We propose that, in vivo, the sparsity of accidental sequence matches allows an initial 8 bp test to rapidly reject almost all non-homologous sequences. We speculate that once the initial test is passed, the mismatch insensitive binding in the heteroduplex allows short mismatched regions to be incorporated in otherwise homologous strand exchange products even though sequences with less homology are eventually rejected.
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Affiliation(s)
| | - Darren Yang
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Craig Kelley
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Chantal Prévost
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Univ. Paris Diderot, Sorbonne Paris Cité, IBPC, Paris, France
| | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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13
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Bhattacherjee A, Levy Y. Search by proteins for their DNA target site: 1. The effect of DNA conformation on protein sliding. Nucleic Acids Res 2014; 42:12404-14. [PMID: 25324308 PMCID: PMC4227778 DOI: 10.1093/nar/gku932] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The recognition of DNA-binding proteins (DBPs) to their specific site often precedes by a search technique in which proteins slide, hop along the DNA contour or perform inter-segment transfer and 3D diffusion to dissociate and re-associate to distant DNA sites. In this study, we demonstrated that the strength and nature of the non-specific electrostatic interactions, which govern the search dynamics of DBPs, are strongly correlated with the conformation of the DNA. We tuned two structural parameters, namely curvature and the extent of helical twisting in circular DNA. These two factors are mutually independent of each other and can modulate the electrostatic potential through changing the geometry of the circular DNA conformation. The search dynamics for DBPs on circular DNA is therefore markedly different compared with linear B-DNA. Our results suggest that, for a given DBP, the rotation-coupled sliding dynamics is precluded in highly curved DNA (as well as for over-twisted DNA) because of the large electrostatic energy barrier between the inside and outside of the DNA molecule. Under such circumstances, proteins prefer to hop in order to explore interior DNA sites. The change in the balance between sliding and hopping propensities as a function of DNA curvature or twisting may result in different search efficiency and speed.
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Affiliation(s)
- Arnab Bhattacherjee
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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14
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Maffeo C, Yoo J, Comer J, Wells DB, Luan B, Aksimentiev A. Close encounters with DNA. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:413101. [PMID: 25238560 PMCID: PMC4207370 DOI: 10.1088/0953-8984/26/41/413101] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.
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Affiliation(s)
- C Maffeo
- Department of Physics, University of Illinois, Urbana, IL, USA
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15
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16
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Strzelecki J, Peplowski L, Lenartowski R, Nowak W, Balter A. Mechanical transition in a highly stretched and torsionally constrained DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:020701. [PMID: 25353406 DOI: 10.1103/physreve.89.020701] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Indexed: 06/04/2023]
Abstract
We show results of our high force (up to 1.8 nN) atomic force microscopy force spectroscopy measurements of a double stranded DNA. We have found that the force spectra of torsionally constrained molecules display a small plateau occurring at a force of approximately 1 nN. This transition is absent in molecules with rotational freedom. Based on all-atom molecular dynamics simulations, we suggest that this plateau is a result of reducing the diameter of a double helix through extreme stretching. The simulation suggests that the molecule is forced into a form resembling an underwound P-DNA, with bases protruding outside of the backbones. These results broaden our understanding of the fundamental aspects of DNA nanomechanics.
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Affiliation(s)
- Janusz Strzelecki
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziądzka 5, 87-100 Toruń, Poland
| | - Lukasz Peplowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziądzka 5, 87-100 Toruń, Poland
| | - Robert Lenartowski
- Faculty of Biology and Environment Protection, Laboratory of Isotope and Instrumental Analysis, Lwowska 1, 87-100 Toruń, Poland
| | - Wieslaw Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziądzka 5, 87-100 Toruń, Poland
| | - Aleksander Balter
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziądzka 5, 87-100 Toruń, Poland
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17
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Naserian-Nik AM, Tahani M, Karttunen M. Molecular dynamics study of DNA oligomers under angled pulling. RSC Adv 2014. [DOI: 10.1039/c3ra45604h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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18
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Orosz Á, Mező G, Herényi L, Habdas J, Majer Z, Myśliwa-Kurdziel B, Tóth K, Csík G. Binding of new cationic porphyrin–tetrapeptide conjugates to nucleoprotein complexes. Biophys Chem 2013; 177-178:14-23. [DOI: 10.1016/j.bpc.2013.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 03/11/2013] [Accepted: 03/16/2013] [Indexed: 11/28/2022]
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19
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Severin PMD, Zou X, Schulten K, Gaub HE. Effects of cytosine hydroxymethylation on DNA strand separation. Biophys J 2013; 104:208-15. [PMID: 23332073 DOI: 10.1016/j.bpj.2012.11.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/10/2012] [Accepted: 11/13/2012] [Indexed: 12/22/2022] Open
Abstract
Cytosine hydroxymethylation is an epigenetic control factor in higher organisms. New discoveries of the biological roles of hydroxymethylation serve to raise questions about how this epigenetic modification exerts its functions and how organisms discriminate cytosine hydroxymethylation from methylation. Here, we report investigations that reveal an effect of cytosine hydroxymethylation on mechanical properties of DNA under load. The findings are based on molecular force assay measurements and steered molecular dynamics simulations. Molecular force assay experiments identified significant effects of hydroxymethylation on stretching-induced strand separation; the underlying physical mechanism has been revealed by steered molecular dynamics simulations. We find that hydroxymethylation can either upregulate or downregulate DNA's strand separation propensity, suggesting that hydroxymethylation can control gene expression by facilitating or obstructing the action of transcription machinery or the access to chromosomal DNA.
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Affiliation(s)
- Philip M D Severin
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, Munich, Germany
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20
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Naserian-Nik AM, Tahani M, Karttunen M. Pulling of double-stranded DNA by atomic force microscopy: a simulation in atomistic details. RSC Adv 2013. [DOI: 10.1039/c3ra23213a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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21
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Bansal A, Prasad M, Roy K, Kukreti S. A short GC-rich palindrome of human mannose receptor gene coding region displays a conformational switch. Biopolymers 2012; 97:950-62. [PMID: 22987586 DOI: 10.1002/bip.22111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Conformational switching in DNA is fundamental to biological processes. The structural status of a palindromic GC-rich dodecamer DNA sequence, integral part of human MRC2 coding region, and a related sequence of opposite polarity from human FDX1 gene were characterized and compared. UV-melting, circular dichroism, and gel electrophoresis experiments demonstrated the formation of intermolecular structures. Although stability and molecularity of both the oligomeric structures were found to be almost identical, their secondary structures differed remarkably as A1 MRC2 sequence showed A-like and B-like DNA conformation, whereas the A2 FDX1 sequence exhibited only the A-like signatures. The study is relevant for understanding structural polymorphism at genomic locations depending on DNA sequence and solution environment.
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Affiliation(s)
- Aparna Bansal
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi (North Campus), Delhi 110007, India
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22
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Manghi M, Destainville N, Palmeri J. Mesoscopic models for DNA stretching under force: New results and comparison with experiments. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2012; 35:110. [PMID: 23099534 DOI: 10.1140/epje/i2012-12110-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 09/21/2012] [Accepted: 09/26/2012] [Indexed: 06/01/2023]
Abstract
Single-molecule experiments on double-stranded B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity. The nature and the critical forces of these transitions depend on DNA base sequence, loading rate, salt conditions and temperature. It has been proposed that the first transition, at forces of 60-80 pN, is a transition from B to S-DNA, viewed as a stretched duplex DNA, while the second one, at stronger forces, is a strand peeling resulting in single-stranded DNAs (ssDNA), similar to thermal denaturation. But due to experimental conditions these two transitions can overlap, for instance for poly(dA-dT). In an attempt to propose a coherent picture compatible with this variety of experimental observations, we derive an analytical formula using a coupled discrete worm-like chain-Ising model. Our model takes into account bending rigidity, discreteness of the chain, linear and non-linear (for ssDNA) bond stretching. In the limit of zero force, this model simplifies into a coupled model already developed by us for studying thermal DNA melting, establishing a connection with previous fitting parameter values for denaturation profiles. Our results are summarized as follows: i) ssDNA is fitted, using an analytical formula, over a nano-Newton range with only three free parameters, the contour length, the bending modulus and the monomer size; ii) a surprisingly good fit on this force range is possible only by choosing a monomer size of 0.2 nm, almost 4 times smaller than the ssDNA nucleobase length; iii) mesoscopic models are not able to fit B to ssDNA (or S to ss) transitions; iv) an analytical formula for fitting B to S transitions is derived in the strong force approximation and for long DNAs, which is in excellent agreement with exact transfer matrix calculations; v) this formula fits perfectly well poly(dG-dC) and λ-DNA force-extension curves with consistent parameter values; vi) a coherent picture, where S to ssDNA transitions are much more sensitive to base-pair sequence than the B to S one, emerges. This relatively simple model might allow one to further study quantitatively the influence of salt concentration and base-pairing interactions on DNA force-induced transitions.
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Affiliation(s)
- Manoel Manghi
- Laboratoire de Physique Théorique (IRSAMC), Université de Toulouse, UPS, F-31062, Toulouse, France.
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23
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Abstract
Mixed-sequence DNA molecules undergo mechanical overstretching by approximately 70% at 60-70 pN. Since its initial discovery 15 y ago, a debate has arisen as to whether the molecule adopts a new form [Cluzel P, et al. (1996) Science 271:792-794; Smith SB, Cui Y, Bustamante C (1996) Science 271:795-799], or simply denatures under tension [van Mameren J, et al. (2009) Proc Natl Acad Sci USA 106:18231-18236]. Here, we resolve this controversy by using optical tweezers to extend small 60-64 bp single DNA duplex molecules whose base content can be designed at will. We show that when AT content is high (70%), a force-induced denaturation of the DNA helix ensues at 62 pN that is accompanied by an extension of the molecule of approximately 70%. By contrast, GC-rich sequences (60% GC) are found to undergo a reversible overstretching transition into a distinct form that is characterized by a 51% extension and that remains base-paired. For the first time, results proving the existence of a stretched basepaired form of DNA can be presented. The extension observed in the reversible transition coincides with that produced on DNA by binding of bacterial RecA and human Rad51, pointing to its possible relevance in homologous recombination.
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24
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Siriwong K, Voityuk AA. Electron transfer in DNA. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1102] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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25
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Garrec J, Patel C, Rothlisberger U, Dumont E. Insights into Intrastrand Cross-Link Lesions of DNA from QM/MM Molecular Dynamics Simulations. J Am Chem Soc 2012; 134:2111-9. [DOI: 10.1021/ja2084042] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Julian Garrec
- Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Chandan Patel
- Université de Lyon, Institut de Chimie de Lyon, CNRS, Ecole normale
supérieure de Lyon, 46 allée d’Italie, 69364
Lyon Cedex 07, France
| | - Ursula Rothlisberger
- Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Elise Dumont
- Université de Lyon, Institut de Chimie de Lyon, CNRS, Ecole normale
supérieure de Lyon, 46 allée d’Italie, 69364
Lyon Cedex 07, France
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26
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Beierlein FR, Kneale GG, Clark T. Predicting the effects of basepair mutations in DNA-protein complexes by thermodynamic integration. Biophys J 2011; 101:1130-8. [PMID: 21889450 DOI: 10.1016/j.bpj.2011.07.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 06/28/2011] [Accepted: 07/05/2011] [Indexed: 10/17/2022] Open
Abstract
Thermodynamically rigorous free energy methods in principle allow the exact computation of binding free energies in biological systems. Here, we use thermodynamic integration together with molecular dynamics simulations of a DNA-protein complex to compute relative binding free energies of a series of mutants of a protein-binding DNA operator sequence. A guanine-cytosine basepair that interacts strongly with the DNA-binding protein is mutated into adenine-thymine, cytosine-guanine, and thymine-adenine. It is shown that basepair mutations can be performed using a conservative protocol that gives error estimates of ∼10% of the change in free energy of binding. Despite the high CPU-time requirements, this work opens the exciting opportunity of being able to perform basepair scans to investigate protein-DNA binding specificity in great detail computationally.
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Affiliation(s)
- Frank R Beierlein
- Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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27
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Zou X, Ma W, Solov'yov IA, Chipot C, Schulten K. Recognition of methylated DNA through methyl-CpG binding domain proteins. Nucleic Acids Res 2011; 40:2747-58. [PMID: 22110028 PMCID: PMC3315304 DOI: 10.1093/nar/gkr1057] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
DNA methylation is a key regulatory control route in epigenetics, involving gene silencing and chromosome inactivation. It has been recognized that methyl-CpG binding domain (MBD) proteins play an important role in interpreting the genetic information encoded by methylated DNA (mDNA). Although the function of MBD proteins has attracted considerable attention and is well characterized, the mechanism underlying mDNA recognition by MBD proteins is still poorly understood. In this article, we demonstrate that the methyl-CpG dinucleotides are recognized at the MBD–mDNA interface by two MBD arginines through an interplay of hydrogen bonding and cation-π interaction. Through molecular dynamics and quantum-chemistry calculations we investigate the methyl-cytosine recognition process and demonstrate that methylation enhances MBD–mDNA binding by increasing the hydrophobic interfacial area and by strengthening the interaction between mDNA and MBD proteins. Free-energy perturbation calculations also show that methylation yields favorable contribution to the binding free energy for MBD–mDNA complex.
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Affiliation(s)
- Xueqing Zou
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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28
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Khazanov N, Levy Y. Sliding of p53 along DNA Can Be Modulated by Its Oligomeric State and by Cross-Talks between Its Constituent Domains. J Mol Biol 2011; 408:335-55. [DOI: 10.1016/j.jmb.2011.01.059] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 01/24/2011] [Accepted: 01/29/2011] [Indexed: 12/21/2022]
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29
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Saladin A, Amourda C, Poulain P, Férey N, Baaden M, Zacharias M, Delalande O, Prévost C. Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments. Nucleic Acids Res 2010; 38:6313-23. [PMID: 20507912 PMCID: PMC2965220 DOI: 10.1093/nar/gkq459] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Homologous recombination is a fundamental process enabling the repair of double-strand breaks with a high degree of fidelity. In prokaryotes, it is carried out by RecA nucleofilaments formed on single-stranded DNA (ssDNA). These filaments incorporate genomic sequences that are homologous to the ssDNA and exchange the homologous strands. Due to the highly dynamic character of this process and its rapid propagation along the filament, the sequence recognition and strand exchange mechanism remains unknown at the structural level. The recently published structure of the RecA/DNA filament active for recombination (Chen et al., Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structure, Nature 2008, 453, 489) provides a starting point for new exploration of the system. Here, we investigate the possible geometries of association of the early encounter complex between RecA/ssDNA filament and double-stranded DNA (dsDNA). Due to the huge size of the system and its dense packing, we use a reduced representation for protein and DNA together with state-of-the-art molecular modeling methods, including systematic docking and virtual reality simulations. The results indicate that it is possible for the double-stranded DNA to access the RecA-bound ssDNA while initially retaining its Watson–Crick pairing. They emphasize the importance of RecA L2 loop mobility for both recognition and strand exchange.
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Affiliation(s)
- Adrien Saladin
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris, MTI, France
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30
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Totsingan F, Jain V, Bracken WC, Faccini A, Tedeschi T, Marchelli R, Corradini R, Kallenbach NR, Green MM. Conformational Heterogeneity in PNA:PNA Duplexes. Macromolecules 2010. [DOI: 10.1021/ma902797f] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Filbert Totsingan
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003
- Herman F. Mark Polymer Research Institute, Polytechnic Institute of New York University, 6 MetroTech Center, Brooklyn, New York 11201
- Dipartimento di Chimica Organica ed Industriale, Università di Parma, Via G.P. Usberti 17/A, 43100 Parma, Italy
| | - Vipul Jain
- Herman F. Mark Polymer Research Institute, Polytechnic Institute of New York University, 6 MetroTech Center, Brooklyn, New York 11201
| | - W. Clay Bracken
- Department of Biochemistry, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10021
| | - Andrea Faccini
- Dipartimento di Chimica Organica ed Industriale, Università di Parma, Via G.P. Usberti 17/A, 43100 Parma, Italy
| | - Tullia Tedeschi
- Dipartimento di Chimica Organica ed Industriale, Università di Parma, Via G.P. Usberti 17/A, 43100 Parma, Italy
| | - Rosangela Marchelli
- Dipartimento di Chimica Organica ed Industriale, Università di Parma, Via G.P. Usberti 17/A, 43100 Parma, Italy
| | - Roberto Corradini
- Dipartimento di Chimica Organica ed Industriale, Università di Parma, Via G.P. Usberti 17/A, 43100 Parma, Italy
| | - Neville R. Kallenbach
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003
| | - Mark M. Green
- Herman F. Mark Polymer Research Institute, Polytechnic Institute of New York University, 6 MetroTech Center, Brooklyn, New York 11201
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31
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Voityuk AA. Can charge transfer in DNA significantly be modulated by varying the pi stack conformation? J Phys Chem B 2010; 113:14365-8. [PMID: 19795825 DOI: 10.1021/jp908603w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA is an ideal target for single-molecule manipulations. The conformation of stacked basepairs in DNA depends sensitively on various factors such as temperature, the kind of solvent and counterions, changes in the backbone, applied forces, etc. This raises the question of whether the rate of charge transfer (CT) through the stack can be considerably enhanced by tuning of "observed" DNA conformations. Using a stochastic approach to account for the effects of thermal fluctuations, we study how the efficiency of CT in poly(dA)-poly(dT) and poly(dG)-poly(dC) sequences will change by variation of the pi stack structure. The CT process is shown to be not very sensitive to the torsional angle (twist) while affected more strongly by altering translation modes (shift and slide). We conclude that the design of basepair stacks with significantly improved electrical conductivity, as compared to poly(dG)-poly(dC), appears to be quite elusive. Specific changes of the pi stack structure can increase the efficiency of CT by a factor of approximately 3 (e.g., in systems with negative shift); much stronger effects can hardly be expected. This result, formally derived for molecular ensembles, should also be applicable for single-molecule systems because of the strong effects of dynamical disordering.
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32
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Carrillo JMY, Dobrynin AV. Effect of the Electrostatic Interactions on Stretching of Semiflexible and Biological Polyelectrolytes. Macromolecules 2010. [DOI: 10.1021/ma902304x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Jan-Michael Y. Carrillo
- Polymer Program, Institute of Materials Science and Department of Physics, University of Connecticut, Storrs, Connecticut 06269-3136
| | - Andrey V. Dobrynin
- Polymer Program, Institute of Materials Science and Department of Physics, University of Connecticut, Storrs, Connecticut 06269-3136
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33
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Lee EH, Hsin J, Sotomayor M, Comellas G, Schulten K. Discovery through the computational microscope. Structure 2010; 17:1295-306. [PMID: 19836330 DOI: 10.1016/j.str.2009.09.001] [Citation(s) in RCA: 228] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Revised: 09/01/2009] [Accepted: 09/03/2009] [Indexed: 11/17/2022]
Abstract
All-atom molecular dynamics simulations have become increasingly popular as a tool to investigate protein function and dynamics. However, researchers are concerned about the short time scales covered by simulations, the apparent impossibility to model large and integral biomolecular systems, and the actual predictive power of the molecular dynamics methodology. Here we review simulations that were in the past both hotly disputed and considered key successes, namely of proteins with mainly mechanical functions (titin, fibrinogen, ankyrin, and cadherin). The simulation work covered shows how state-of-the-art modeling alleviates some of the prior concerns and how unrefuted discoveries are made through the "computational microscope."
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Affiliation(s)
- Eric H Lee
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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