1
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Biton YY. Effects of Protein-Induced Local Bending and Sequence Dependence on the Configurations of Supercoiled DNA Minicircles. J Chem Theory Comput 2018; 14:2063-2075. [PMID: 29558800 DOI: 10.1021/acs.jctc.7b01090] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yoav Y. Biton
- Department of Mechanical Engineering, SCE, Shamoon College of Engineering, Beer Sheva 84100, Israel
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2
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Chatzieleftheriou S, Adendorff MR, Lagaros ND. Generalized Potential Energy Finite Elements for Modeling Molecular Nanostructures. J Chem Inf Model 2016; 56:1963-1978. [DOI: 10.1021/acs.jcim.6b00356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Stavros Chatzieleftheriou
- Institute of Structural Analysis & Antiseismic Research, Department of Structural Engineering, School of Civil Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Zografou Campus, GR-15780 Athens, Greece
| | - Matthew R. Adendorff
- Laboratory of Computational Biology & Biophysics, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, United States
| | - Nikos D. Lagaros
- Institute of Structural Analysis & Antiseismic Research, Department of Structural Engineering, School of Civil Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Zografou Campus, GR-15780 Athens, Greece
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3
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Kim YJ, Kim DN. Structural Basis for Elastic Mechanical Properties of the DNA Double Helix. PLoS One 2016; 11:e0153228. [PMID: 27055239 PMCID: PMC4824394 DOI: 10.1371/journal.pone.0153228] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/25/2016] [Indexed: 01/20/2023] Open
Abstract
In this article, we investigate the principal structural features of the DNA double helix and their effects on its elastic mechanical properties. We develop, in the pursuit of this purpose, a helical continuum model consisting of a soft helical core and two stiff ribbons wrapping around it. The proposed model can reproduce the negative twist-stretch coupling of the helix successfully as well as its global stretching, bending, and torsional rigidities measured experimentally. Our parametric study of the model using the finite element method further reveals that the stiffness of phosphate backbones is a crucial factor for the counterintuitive overwinding behavior of the duplex and its extraordinarily high torsional rigidity, the major-minor grooves augment the twist-stretch coupling, and the change of the helicity might be responsible for the transition from a negative to a positive twist-stretching coupling when a tensile force is applied to the duplex.
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Affiliation(s)
- Young-Joo Kim
- Department of Mechanical and Aerospace Engineering, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Do-Nyun Kim
- Department of Mechanical and Aerospace Engineering, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea.,Institute of Advanced Machines and Design, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
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4
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Maciejczyk M, Spasic A, Liwo A, Scheraga HA. DNA Duplex Formation with a Coarse-Grained Model. J Chem Theory Comput 2014; 10:5020-5035. [PMID: 25400520 PMCID: PMC4230386 DOI: 10.1021/ct4006689] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Indexed: 01/23/2023]
Abstract
A middle-resolution coarse-grained model of DNA is proposed. The DNA chain is built of spherical and planar rigid bodies connected by elastic virtual bonds. The bonded part of the potential energy function is fit to potentials of mean force of model systems. The rigid bodies are sets of neutral, charged, and dipolar beads. Electrostatic and van der Waals interactions are parametrized by our recently developed procedure [Maciejczyk, M.; Spasic, A.; Liwo, A.; Scheraga, H.A. J. Comp. Chem.2010, 31, 1644]. Interactions with the solvent and an ionic cloud are approximated by a multipole-multipole Debye-Hückel model. A very efficient R-RATTLE algorithm, for integrating the movement of rigid bodies, is implemented. It is the first coarse-grained model, in which both bonded and nonbonded interactions were parametrized ab initio and which folds stable double helices from separated complementary strands, with the final conformation close to the geometry of experimentally determined structures.
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Affiliation(s)
- Maciej Maciejczyk
- Baker
Laboratory of Chemistry, Cornell University, Ithaca, New York 14850, United States
- Department
of Physics and Biophysics, Faculty of Food Sciences, University of Warmia and Mazury, 11-041 Olsztyn, Poland
| | - Aleksandar Spasic
- Baker
Laboratory of Chemistry, Cornell University, Ithaca, New York 14850, United States
- Department
of Biochemistry and Biophysics, University
of Rochester Medical Center, Rochester, New York 14642, United States
| | - Adam Liwo
- Baker
Laboratory of Chemistry, Cornell University, Ithaca, New York 14850, United States
- Faculty
of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland
| | - Harold A. Scheraga
- Baker
Laboratory of Chemistry, Cornell University, Ithaca, New York 14850, United States
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5
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Adhikari S, Saavedra Flores EI, Scarpa F, Chowdhury R, Friswell MI. A Hybrid Atomistic Approach for the Mechanics of Deoxyribonucleic Acid Molecules. J Nanotechnol Eng Med 2014. [DOI: 10.1115/1.4027690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The paper proposes a new modeling approach for the prediction and analysis of the mechanical properties in deoxyribonucleic acid (DNA) molecules based on a hybrid atomistic-finite element continuum representation. The model takes into account of the complex geometry of the DNA strands, a structural mechanics representation of the atomic bonds existing in the molecules and the mass distribution of the atoms by using a lumped parameter model. A 13-base-pair DNA model is used to illustrate the proposed approach. The properties of the equivalent bond elements used to represent the DNA model have been derived. The natural frequencies, vibration mode shapes, and equivalent continuum mechanical properties of the DNA strand are obtained. The results from our model compare well with a high-fidelity molecular mechanics simulation and existing MD and experimental data from open literature.
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Affiliation(s)
- S. Adhikari
- College of Engineering, Swansea University, Singleton Park, Swansea SA2 8PP, UK
| | - E. I. Saavedra Flores
- Departamento de Ingeniería en Obras Civiles, Universidad de Santiago de Chile, Avenue Ecuador 3659, Santiago, Chile
| | - F. Scarpa
- Bristol Centre for Nanoscience and Quantum Information (NSQI), Tyndall Avenue, Bristol BS8 1FD, UK
| | - R. Chowdhury
- Department of Civil Engineering, Indian Institute of Technology Roorkee, Roorkee 247 667, India
| | - M. I. Friswell
- College of Engineering, Swansea University, Singleton Park, Swansea SA2 8PP, UK
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6
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Edens LE, Brozik JA, Keller DJ. Coarse-grained model DNA: structure, sequences, stems, circles, hairpins. J Phys Chem B 2012; 116:14735-43. [PMID: 23157455 DOI: 10.1021/jp3009095] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A coarse-grained model for DNA that is intended to function realistically at the level of individual bases is reported. The model is composed of residues with up to eight coarse-grained beads each, which is sufficient for DNA-like base stacking and base-base recognition by hydrogen bonding. The beads interact by means of short-ranged pair potentials and a simple implicit solvent model. Movement is simulated by Brownian dynamics without hydrodynamic coupling. The main stabilizing forces are base stacking and hydrogen bonding, as modified by the effects of solvation. Complementary double-stranded chains of such residues form stable double helices over long runs (~10 μs) at or near room temperature, with structural parameters close to those of B-form DNA. Most mismatched chains or mismatched regions within a complementary molecule melt and become disordered. Long-range fluctuations and elastic properties, as measured by bending and twisting persistence lengths, are close to experimental values. Single-stranded chains are flexible, with transient stretches of free bases in equilibrium with globules stabilized by intrastrand stacking and hydrogen bonding. Model DNAs in covalently closed loops form right- or left-handed supercoils, depending on the sign of overtwist or undertwist. Short stem-loop structures melt at elevated temperatures and reanneal when the temperature is carefully lowered. Overall, most qualitative properties of real DNA arise naturally in the model from local interactions at the base-pair level.
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Affiliation(s)
- Lance E Edens
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, United States
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7
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Hirsh AD, Lillian TD, Lionberger TA, Perkins NC. DNA modeling reveals an extended lac repressor conformation in classic in vitro binding assays. Biophys J 2011; 101:718-26. [PMID: 21806940 DOI: 10.1016/j.bpj.2011.06.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 06/03/2011] [Accepted: 06/21/2011] [Indexed: 10/17/2022] Open
Abstract
Protein-mediated DNA looping, such as that induced by the lactose repressor (LacI) of Escherichia coli, is a well-known gene regulation mechanism. Although researchers have given considerable attention to DNA looping by LacI, many unanswered questions about this mechanism, including the role of protein flexibility, remain. Recent single-molecule observations suggest that the two DNA-binding domains of LacI are capable of splaying open about the tetramerization domain into an extended conformation. We hypothesized that if recent experiments were able to reveal the extended conformation, it is possible that such structures occurred in previous studies as well. In this study, we tested our hypothesis by reevaluating two classic in vitro binding assays using a computational rod model of DNA. The experiments and computations evaluate the looping of both linear DNA and supercoiled DNA minicircles over a broad range of DNA interoperator lengths. The computed energetic minima align well with the experimentally observed interoperator length for optimal loop stability. Of equal importance, the model reveals that the most stable loops for linear DNA occur when LacI adopts the extended conformation. In contrast, for DNA minicircles, optimal stability may arise from either the closed or the extended protein conformation depending on the degree of supercoiling and the interoperator length.
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Affiliation(s)
- Andrew D Hirsh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA
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8
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Daniels BC, Sethna JP. Nucleation at the DNA supercoiling transition. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:041924. [PMID: 21599217 DOI: 10.1103/physreve.83.041924] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Indexed: 05/30/2023]
Abstract
Twisting DNA under a constant applied force reveals a thermally activated transition into a state with a supercoiled structure known as a plectoneme. Using transition-state theory, we predict the rate of this plectoneme nucleation to be of order 10(4) Hz. We reconcile this with experiments that have measured hopping rates of order 10 Hz by noting that the viscous drag on the bead used to manipulate the DNA limits the measured rate. We find that the intrinsic bending caused by disorder in the base-pair sequence is important for understanding the free-energy barrier that governs the transition. Both analytic and numerical methods are used in the calculations. We provide extensive details on the numerical methods for simulating the elastic rod model with and without disorder.
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Affiliation(s)
- Bryan C Daniels
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA
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9
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Looping charged elastic rods: applications to protein-induced DNA loop formation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 40:69-80. [PMID: 20963409 DOI: 10.1007/s00249-010-0628-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 09/07/2010] [Accepted: 09/09/2010] [Indexed: 10/18/2022]
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10
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Ma L, Yethiraj A, Chen X, Cui Q. A computational framework for mechanical response of macromolecules: application to the salt concentration dependence of DNA bendability. Biophys J 2009; 96:3543-54. [PMID: 19413960 DOI: 10.1016/j.bpj.2009.01.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Revised: 01/19/2009] [Accepted: 01/23/2009] [Indexed: 11/17/2022] Open
Abstract
A computational framework is presented for studying the mechanical response of macromolecules. The method combines a continuum mechanics (CM) model for the mechanical properties of the macromolecule with a continuum electrostatic (CE) treatment of solvation. The molecules are represented by their shape and key physicochemical characteristics such as the distribution of materials properties and charge. As a test case, we apply the model to the effect of added salt on the bending of DNA. With a simple representation of DNA, the CM/CE framework using a Debye-Hückel model leads to results that are in good agreement with both analytical theories and recent experiments, including a modified Odijk-Skolnick-Fixman theory that takes the finite length of DNA into consideration. Calculations using a more sophisticated CE model (Poisson-Boltzmann), however, suffer from convergence problems, highlighting the importance of balancing numerical accuracy in the CM and CE models when dealing with very large systems, particularly those with a high degree of symmetry.
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Affiliation(s)
- Liang Ma
- Graduate Program in Biophysics, University of Wisconsin-Madison, Madison, Wisconsin, USA
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11
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Towles KB, Beausang JF, Garcia HG, Phillips R, Nelson PC. First-principles calculation of DNA looping in tethered particle experiments. Phys Biol 2009; 6:025001. [PMID: 19571369 PMCID: PMC3298194 DOI: 10.1088/1478-3975/6/2/025001] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We calculate the probability of DNA loop formation mediated by regulatory proteins such as Lac repressor (LacI), using a mathematical model of DNA elasticity. Our model is adapted to calculating quantities directly observable in tethered particle motion (TPM) experiments, and it accounts for all the entropic forces present in such experiments. Our model has no free parameters; it characterizes DNA elasticity using information obtained in other kinds of experiments. It assumes a harmonic elastic energy function (or wormlike chain type elasticity), but our Monte Carlo calculation scheme is flexible enough to accommodate arbitrary elastic energy functions. We show how to compute both the 'looping J factor' (or equivalently, the looping free energy) for various DNA construct geometries and LacI concentrations, as well as the detailed probability density function of bead excursions. We also show how to extract the same quantities from recent experimental data on TPM, and then compare to our model's predictions. In particular, we present a new method to correct observed data for finite camera shutter time and other experimental effects. Although the currently available experimental data give large uncertainties, our first-principles predictions for the looping free energy change are confirmed to within about 1 k(B)T, for loops of length around 300 basepairs. More significantly, our model successfully reproduces the detailed distributions of bead excursion, including their surprising three-peak structure, without any fit parameters and without invoking any alternative conformation of the LacI tetramer. Indeed, the model qualitatively reproduces the observed dependence of these distributions on tether length (e.g., phasing) and on LacI concentration (titration). However, for short DNA loops (around 95 basepairs) the experiments show more looping than is predicted by the harmonic-elasticity model, echoing other recent experimental results. Because the experiments we study are done in vitro, this anomalously high looping cannot be rationalized as resulting from the presence of DNA-bending proteins or other cellular machinery. We also show that it is unlikely to be the result of a hypothetical 'open' conformation of the LacI tetramer.
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Affiliation(s)
- Kevin B Towles
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John F Beausang
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hernan G Garcia
- Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rob Phillips
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Philip C Nelson
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA
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12
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Swigon D. The Mathematics of DNA Structure, Mechanics, and Dynamics. MATHEMATICS OF DNA STRUCTURE, FUNCTION AND INTERACTIONS 2009. [DOI: 10.1007/978-1-4419-0670-0_14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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13
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Habibi M, Ribe NM, Bonn D. Coiling of elastic ropes. PHYSICAL REVIEW LETTERS 2007; 99:154302. [PMID: 17995172 DOI: 10.1103/physrevlett.99.154302] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Indexed: 05/25/2023]
Abstract
A rope falling onto a solid surface typically forms a series of regular coils. Here, we study this phenomenon using laboratory experiments (with cotton threads and softened spaghetti) and an asymptotic "slender-rope" numerical model. The excellent agreement between the two with no adjustable parameters allows us to determine a complete phase diagram for elastic coiling comprising three basic regimes involving different force balances (elastic, gravitational, and inertial) together with resonant "whirling string" and "whirling shaft" eigenmodes in the inertial regime.
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Affiliation(s)
- M Habibi
- Institute for Advanced Studies in Basic Sciences, Zanjan 45195-1159, Iran
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14
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Goyal S, Lillian T, Blumberg S, Meiners JC, Meyhöfer E, Perkins NC. Intrinsic curvature of DNA influences LacR-mediated looping. Biophys J 2007; 93:4342-59. [PMID: 17766355 PMCID: PMC2098735 DOI: 10.1529/biophysj.107.112268] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein-mediated DNA looping is a common mechanism for regulating gene expression. Loops occur when a protein binds to two operators on the same DNA molecule. The probability of looping is controlled, in part, by the basepair sequence of inter-operator DNA, which influences its structural properties. One structural property is the intrinsic or stress-free curvature. In this article, we explore the influence of sequence-dependent intrinsic curvature by exercising a computational rod model for the inter-operator DNA as applied to looping of the LacR-DNA complex. Starting with known sequences for the inter-operator DNA, we first compute the intrinsic curvature of the helical axis as input to the rod model. The crystal structure of the LacR (with bound operators) then defines the requisite boundary conditions needed for the dynamic rod model that predicts the energetics and topology of the intervening DNA loop. A major contribution of this model is its ability to predict a broad range of published experimental data for highly bent (designed) sequences. The model successfully predicts the loop topologies known from fluorescence resonance energy transfer measurements, the linking number distribution known from cyclization assays with the LacR-DNA complex, the relative loop stability known from competition assays, and the relative loop size known from gel mobility assays. In addition, the computations reveal that highly curved sequences tend to lower the energetic cost of loop formation, widen the energy distribution among stable and meta-stable looped states, and substantially alter loop topology. The inclusion of sequence-dependent intrinsic curvature also leads to nonuniform twist and necessitates consideration of eight distinct binding topologies from the known crystal structure of the LacR-DNA complex.
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Affiliation(s)
- Sachin Goyal
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, USA
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15
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Gao M, Sotomayor M, Villa E, Lee EH, Schulten K. Molecular mechanisms of cellular mechanics. Phys Chem Chem Phys 2006; 8:3692-706. [PMID: 16896432 DOI: 10.1039/b606019f] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mechanical forces play an essential role in cellular processes as input, output, and signals. Various protein complexes in the cell are designed to handle, transform and use such forces. For instance, proteins of muscle and the extracellular matrix can withstand considerable stretching forces, hearing-related and mechanosensory proteins can transform weak mechanical stimuli into electrical signals, and regulatory proteins are suited to forcing DNA into loops to control gene expression. Here we review the structure-function relationship of four protein complexes with well defined and representative mechanical functions. The first example is titin, a protein that confers passive elasticity on muscle. The second system is the elastic extracellular matrix protein, fibronectin, and its cellular receptor integrin. The third protein system is the transduction apparatus in hearing and other mechanical senses, likely containing cadherin and ankyrin repeats. The last system is the lac repressor protein, which regulates gene expression by looping DNA. This review focuses on atomic level descriptions of the physical mechanisms underlying the various mechanical functions of the stated proteins.
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Affiliation(s)
- Mu Gao
- Beckman Institute, Department of Physics, Center for Biophysics and Computational Biology, College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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16
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Bon M, Marenduzzo D, Cook PR. Modeling a self-avoiding chromatin loop: relation to the packing problem, action-at-a-distance, and nuclear context. Structure 2006; 14:197-204. [PMID: 16472739 DOI: 10.1016/j.str.2005.10.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2005] [Revised: 09/19/2005] [Accepted: 10/04/2005] [Indexed: 11/18/2022]
Abstract
There is now convincing evidence that genomes are organized into loops, and that looping brings distant genes together so that they can bind to local concentrations of polymerases in "factories" or "hubs." As there remains no systematic analysis of how looping affects the probability that a gene can access binding sites in such factories/hubs, we used an algorithm that we devised and Monte Carlo methods to model a DNA or chromatin loop as a semiflexible (self-avoiding) tube attached to a sphere; we examine how loop thickness, rigidity, and contour length affect where particular segments of the loop lie relative to binding sites on the sphere. Results are compared with those obtained with the traditional model of an (infinitely thin) freely jointed chain. They provide insights into the packing problem (how long genomes are packed into small nuclei), and action-at-a-distance (how firing of one origin or gene can prevent firing of an adjacent one).
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Affiliation(s)
- Michaël Bon
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, United Kingdom
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17
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Shih CC, Georghiou S. Large-amplitude fast motions in double-stranded DNA driven by solvent thermal fluctuations. Biopolymers 2006; 81:450-63. [PMID: 16419073 DOI: 10.1002/bip.20444] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The nature of the internal dynamics of double-stranded DNA in aqueous environment remains to be established. We consider the motions to stem from thermal fluctuations/dissipations of the harmonic modes of beads (bases and sugars) in a cylindrical geometry that are tracked through the stochastic Langevin trajectories; these are characterized by parameters obtained from published data. The present approach has allowed a comparative study of the dynamics for DNA lengths in the range of 20-600 base pairs. For this range, we find that rotational motions about directions parallel to the helix axis (opening, twist) and perpendicular to it (propeller-twist, roll) contribute significantly to the dynamics. For a 20-mer at a solvent viscosity of 1 cP, the calculated fluorescence anisotropy profile exhibits a fast decay in the subnanosecond range due to large-amplitude fluctuations at the mesoscopic level. This feature reproduces the experimental behavior well, and suggests a possible way for the initiation of biological processes: they may be suddenly triggered on this scale through the occurrence of favorable thermal fluctuations. This analysis also reveals that, as is the case for a 20-mer, the dynamics of longer N-mers are dominated by internal motions, and are modulated by the viscosity of the solvent, in agreement with our previous experimental observations. Moreover, the model indicates that occurrence of partially concerted rotations of the bases due to thermal fluctuations can possibly be sustained over a DNA length of the order of 100 A at 1 ns, suggesting a possible mechanism for action-at-a-distance in transcription.
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Affiliation(s)
- Chia C Shih
- Department of Physics, University of Tennessee, Knoxville, TN 37996-1200, USA.
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18
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Abstract
The lack of a rigorous analytical theory for DNA looping has caused many DNA-loop-mediated phenomena to be interpreted using theories describing the related process of DNA cyclization. However, distinctions in the mechanics of DNA looping versus cyclization can have profound quantitative effects on the thermodynamics of loop closure. We have extended a statistical mechanical theory recently developed for DNA cyclization to model DNA looping, taking into account protein flexibility. Notwithstanding the underlying theoretical similarity, we find that the topological constraint of loop closure leads to the coexistence of multiple classes of loops mediated by the same protein structure. These loop topologies are characterized by dramatic differences in twist and writhe; because of the strong coupling of twist and writhe within a loop, DNA looping can exhibit a complex overall helical dependence in terms of amplitude, phase, and deviations from uniform helical periodicity. Moreover, the DNA-length dependence of optimal looping efficiency depends on protein elasticity, protein geometry, and the presence of intrinsic DNA bends. We derive a rigorous theory of loop formation that connects global mechanical and geometric properties of both DNA and protein and demonstrates the importance of protein flexibility in loop-mediated protein-DNA interactions.
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Affiliation(s)
- Yongli Zhang
- Department of Molecular Biophysics, Yale University, New Haven, Connecticut, USA
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19
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Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K. Scalable molecular dynamics with NAMD. J Comput Chem 2005; 26:1781-802. [PMID: 16222654 PMCID: PMC2486339 DOI: 10.1002/jcc.20289] [Citation(s) in RCA: 12248] [Impact Index Per Article: 644.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.
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Affiliation(s)
- James C Phillips
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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20
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Villa E, Balaeff A, Schulten K. Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. Proc Natl Acad Sci U S A 2005; 102:6783-8. [PMID: 15863616 PMCID: PMC1100768 DOI: 10.1073/pnas.0409387102] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Indexed: 11/18/2022] Open
Abstract
A multiscale simulation of a complex between the lac repressor protein (LacI) and a 107-bp-long DNA segment is reported. The complex between the repressor and two operator DNA segments is described by all-atom molecular dynamics; the size of the simulated system comprises either 226,000 or 314,000 atoms. The DNA loop connecting the operators is modeled as a continuous elastic ribbon, described mathematically by the nonlinear Kirchhoff differential equations with boundary conditions obtained from the coordinates of the terminal base pairs of each operator. The forces stemming from the looped DNA are included in the molecular dynamics simulations; the loop structure and the forces are continuously recomputed because the protein motions during the simulations shift the operators and the presumed termini of the loop. The simulations reveal the structural dynamics of the LacI-DNA complex in unprecedented detail. The multiple domains of LacI exhibit remarkable structural stability during the simulation, moving much like rigid bodies. LacI is shown to absorb the strain from the looped DNA mainly through its mobile DNA-binding head groups. Even with large fluctuating forces applied, the head groups tilt strongly and keep their grip on the operator DNA, while the remainder of the protein retains its V-shaped structure. A simulated opening of the cleft of LacI by 500-pN forces revealed the interactions responsible for locking LacI in the V-conformation.
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Affiliation(s)
- Elizabeth Villa
- Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois, 405 North Mathews Avenue, Urbana, IL 61801, USA
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Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K. Scalable molecular dynamics with NAMD. J Comput Chem 2005. [DOI: 10.1002/jcc.20289 http://www.ks.uiuc.edu/research/namd] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Aksimentiev A, Heng JB, Timp G, Schulten K. Microscopic Kinetics of DNA Translocation through synthetic nanopores. Biophys J 2004; 87:2086-97. [PMID: 15345583 PMCID: PMC1304610 DOI: 10.1529/biophysj.104.042960] [Citation(s) in RCA: 284] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2004] [Accepted: 07/01/2004] [Indexed: 11/18/2022] Open
Abstract
We have previously demonstrated that a nanometer-diameter pore in a nanometer-thick metal-oxide-semiconductor-compatible membrane can be used as a molecular sensor for detecting DNA. The prospects for using this type of device for sequencing DNA are avidly being pursued. The key attribute of the sensor is the electric field-induced (voltage-driven) translocation of the DNA molecule in an electrolytic solution across the membrane through the nanopore. To complement ongoing experimental studies developing such pores and measuring signals in response to the presence of DNA, we conducted molecular dynamics simulations of DNA translocation through the nanopore. A typical simulated system included a patch of a silicon nitride membrane dividing water solution of potassium chloride into two compartments connected by the nanopore. External electrical fields induced capturing of the DNA molecules by the pore from the solution and subsequent translocation. Molecular dynamics simulations suggest that 20-basepair segments of double-stranded DNA can transit a nanopore of 2.2 x 2.6 nm(2) cross section in a few microseconds at typical electrical fields. Hydrophobic interactions between DNA bases and the pore surface can slow down translocation of single-stranded DNA and might favor unzipping of double-stranded DNA inside the pore. DNA occluding the pore mouth blocks the electrolytic current through the pore; these current blockades were found to have the same magnitude as the blockade observed when DNA transits the pore. The feasibility of using molecular dynamics simulations to relate the level of the blocked ionic current to the sequence of DNA was investigated.
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Affiliation(s)
- Aleksij Aksimentiev
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Travers AA, Thompson JMT. An introduction to the mechanics of DNA. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2004; 362:1265-1279. [PMID: 15306450 DOI: 10.1098/rsta.2004.1392] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This article gives an overview of recent research on the mechanical properties and spatial deformations of the DNA molecule. Globally the molecule behaves like a uniform elastic rod, and its twisting and writhing govern its compaction and packaging within a cell. Meanwhile high mechanical stresses can induce structural transitions of DNA giving, for example, a phase diagram in the space of the applied tension and torque. Locally, the mechanical properties vary according to the local sequence organization. These variations play a vital role in the biological functioning of the molecule.
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Affiliation(s)
- A A Travers
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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