1
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Tosti Guerra F, Poppleton E, Šulc P, Rovigatti L. ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems. J Chem Phys 2024; 160:205102. [PMID: 38814009 DOI: 10.1063/5.0202829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/04/2024] [Indexed: 05/31/2024] Open
Abstract
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales and system sizes involved. In this article, we present a new coarse-grained model for investigating the folding dynamics of nucleic acids. Our model represents three nucleotides with a patchy particle and is parameterized using well-established nearest-neighbor models. Thanks to the reduction of degrees of freedom and to a bond-swapping mechanism, our model allows for simulations at timescales and length scales that are currently inaccessible to more detailed models. To validate the performance of our model, we conducted extensive simulations of various systems: We examined the thermodynamics of DNA hairpins, capturing their stability and structural transitions, the folding of an MMTV pseudoknot, which is a complex RNA structure involved in viral replication, and also explored the folding of an RNA tile containing a k-type pseudoknot. Finally, we evaluated the performance of the new model in reproducing the melting temperatures of oligomers and the dependence on the toehold length of the displacement rate in toehold-mediated displacement processes, a key reaction used in molecular computing. All in all, the successful reproduction of experimental data and favorable comparisons with existing coarse-grained models validate the effectiveness of the new model.
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Affiliation(s)
- F Tosti Guerra
- Department of Physics, Sapienza University of Rome, Roma, Italy
| | - E Poppleton
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, USA
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - P Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, USA
- Department of Bioscience, School of Natural Sciences, Technical University Munich, Munich, Germany
| | - L Rovigatti
- Department of Physics, Sapienza University of Rome, Roma, Italy
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2
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Rao YF, Sun LZ, Luo MB. Na +-Mg 2+ ion effects on conformation and translocation dynamics of single-stranded RNA: Cooperation and competition. Int J Biol Macromol 2024; 267:131273. [PMID: 38569994 DOI: 10.1016/j.ijbiomac.2024.131273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024]
Abstract
The nanopore-based translocation of a single-stranded RNA (ssRNA) in mixed salt solution has garnered increasing interest for its biological and technological significance. However, it is challenging to comprehensively understand the effects of the mixed ion species on the translocation dynamics due to their cooperation and competition, which can be directly reflected by the ion screening and neutralizing effects, respectively. In this study, Langevin dynamics simulation is employed to investigate the properties of ssRNA conformation and translocation in mixed Na+-Mg2+ ion environments. Simulation results reveal that the ion screening effect dominates the change in the ssRNA conformational size, the ion neutralizing effect controls the capture rate of the ssRNA by the nanopore, and both of them take charge of the different changes in translocation time of the ssRNA under various mixed ion environments. Under high Na+ ion concentration, as Mg2+ concentration increases, the ion neutralizing effect strengthens, weakening the driving force inside the nanopore, leading to longer translocation time. Conversely, at low Na+ concentration, an increase in Mg2+ concentration enhances the ion screening effect, aiding in faster translocation. Furthermore, these simulation results will be explained by quantitative analysis, advancing a deeper understanding of the complicated effects of the mixed Na+-Mg2+ ions.
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Affiliation(s)
- Yi-Fan Rao
- School of Physics, Zhejiang University, Hangzhou 310027, China; Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Meng-Bo Luo
- School of Physics, Zhejiang University, Hangzhou 310027, China.
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3
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Laeremans W, Segers M, Voorspoels A, Carlon E, Hooyberghs J. Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs cgDNA. J Chem Phys 2024; 160:144105. [PMID: 38591677 DOI: 10.1063/5.0197053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/19/2024] [Indexed: 04/10/2024] Open
Abstract
Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the underlying atomistic description. We explore here a method for testing coarse-grained vs all-atom models using stiffness matrices in Fourier space (q-stiffnesses), which are particularly suited to probe DNA elasticity at different length scales. We focus on a class of coarse-grained rigid base DNA models known as cgDNA and its most recent version, cgDNA+. Our analysis shows that while cgDNA+ closely follows the q-stiffnesses of the all-atom model, the original cgDNA shows some deviations for twist and bending variables, which are rather strong in the q → 0 (long length scale) limit. The consequence is that while both cgDNA and cgDNA+ give a suitable description of local elastic behavior, the former misses some effects that manifest themselves at longer length scales. In particular, cgDNA performs poorly on twist stiffness, with a value much lower than expected for long DNA molecules. Conversely, the all-atom and cgDNA+ twist are strongly length scale dependent: DNA is torsionally soft at a few base pair distances but becomes more rigid at distances of a few dozen base pairs. Our analysis shows that the bending persistence length in all-atom and cgDNA+ is somewhat overestimated.
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Affiliation(s)
- Wout Laeremans
- Soft Matter and Biological Physics, Department of Applied Physics, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, Netherlands
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
- UHasselt, Faculty of Sciences, Data Science Institute, Theory Lab, Agoralaan, 3590 Diepenbeek, Belgium
| | - Midas Segers
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Aderik Voorspoels
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Enrico Carlon
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Jef Hooyberghs
- UHasselt, Faculty of Sciences, Data Science Institute, Theory Lab, Agoralaan, 3590 Diepenbeek, Belgium
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4
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Mondal B, Chakraborty D, Hori N, Nguyen HT, Thirumalai D. Competition between Stacking and Divalent Cation-Mediated Electrostatic Interactions Determines the Conformations of Short DNA Sequences. J Chem Theory Comput 2024; 20:2934-2946. [PMID: 38498914 DOI: 10.1021/acs.jctc.3c01193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Interplay between divalent cations (Mg2+ and Ca2+) and single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), as well as stacking interactions, is important in nucleosome stability and phase separation in nucleic acids. Quantitative techniques accounting for ion-DNA interactions are needed to obtain insights into these and related problems. Toward this end, we created a sequence-dependent computational TIS-ION model that explicitly accounts for monovalent and divalent ions. Simulations of the rigid 24 base-pair (bp) dsDNA and flexible ssDNA sequences, dT30 and dA30, with varying amounts of the divalent cations show that the calculated excess number of ions around the dsDNA and ssDNA agree quantitatively with ion-counting experiments. Using an ensemble of all-atom structures generated from coarse-grained simulations, we calculated the small-angle X-ray scattering profiles, which are in excellent agreement with experiments. Although ion-counting experiments mask the differences between Mg2+ and Ca2+, we find that Mg2+ binds to the minor grooves and phosphate groups, whereas Ca2+ binds specifically to the minor groove. Both Mg2+ and Ca2+ exhibit a tendency to bind to the minor groove of DNA as opposed to the major groove. The dA30 conformations are dominated by stacking interactions, resulting in structures with considerable helical order. The near cancellation of the favorable stacking and unfavorable electrostatic interactions leads to dT30 populating an ensemble of heterogeneous conformations. The successful applications of the TIS-ION model are poised to confront many problems in DNA biophysics.
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Affiliation(s)
- Balaka Mondal
- Department of Chemistry, The University of Texas, Austin, Texas 78712, United States
| | - Debayan Chakraborty
- Department of Chemistry, The University of Texas, Austin, Texas 78712, United States
| | - Naoto Hori
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Hung T Nguyen
- Department of Chemistry, The University of Texas, Austin, Texas 78712, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas, Austin, Texas 78712, United States
- Department of Physics, The University of Texas, Austin, Texas 78712, United States
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5
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Kapoor U, Kim YC, Mittal J. Coarse-Grained Models to Study Protein-DNA Interactions and Liquid-Liquid Phase Separation. J Chem Theory Comput 2024; 20:1717-1731. [PMID: 37988476 PMCID: PMC10911113 DOI: 10.1021/acs.jctc.3c00525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 10/20/2023] [Accepted: 10/27/2023] [Indexed: 11/23/2023]
Abstract
Recent advances in coarse-grained (CG) computational models for DNA have enabled molecular-level insights into the behavior of DNA in complex multiscale systems. However, most existing CG DNA models are not compatible with CG protein models, limiting their applications for emerging topics such as protein-nucleic acid assemblies. Here, we present a new computationally efficient CG DNA model. We first use experimental data to establish the model's ability to predict various aspects of DNA behavior, including melting thermodynamics and relevant local structural properties such as the major and minor grooves. We then employ an all-atom hydropathy scale to define nonbonded interactions between protein and DNA sites, to make our DNA model compatible with an existing CG protein model (HPS-Urry), which is extensively used to study protein phase separation, and show that our new model reasonably reproduces the experimental binding affinity for a prototypical protein-DNA system. To further demonstrate the capabilities of this new model, we simulate a full nucleosome with and without histone tails, on a microsecond time scale, generating conformational ensembles and provide molecular insights into the role of histone tails in influencing the liquid-liquid phase separation (LLPS) of HP1α proteins. We find that histone tails interact favorably with DNA, influencing the conformational ensemble of the DNA and antagonizing the contacts between HP1α and DNA, thus affecting the ability of DNA to promote LLPS of HP1α. These findings shed light on the complex molecular framework that fine-tunes the phase transition properties of heterochromatin proteins and contributes to heterochromatin regulation and function. Overall, the CG DNA model presented here is suitable to facilitate micrometer-scale studies with sub-nm resolution in many biological and engineering applications and can be used to investigate protein-DNA complexes, such as nucleosomes, or LLPS of proteins with DNA, enabling a mechanistic understanding of how molecular information may be propagated at the genome level.
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Affiliation(s)
- Utkarsh Kapoor
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 78743, United States
| | - Young C. Kim
- Center
for Materials Physics and Technology, Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Jeetain Mittal
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 78743, United States
- Department
of Chemistry, Texas A&M University, College Station, Texas 78743, United States
- Interdisciplinary
Graduate Program in Genetics in Genomics, Texas A&M University, College
Station, Texas 78743, United States
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6
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Chakraborty D, Mondal B, Thirumalai D. Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA-Protein Complexes. J Chem Theory Comput 2024; 20:1398-1413. [PMID: 38241144 DOI: 10.1021/acs.jctc.3c00833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
DNA-protein interactions are pervasive in a number of biophysical processes ranging from transcription and gene expression to chromosome folding. To describe the structural and dynamic properties underlying these processes accurately, it is important to create transferable computational models. Toward this end, we introduce Coarse-grained Force Field for Energy Estimation, COFFEE, a robust framework for simulating DNA-protein complexes. To brew COFFEE, we integrated the energy function in the self-organized polymer model with side-chains for proteins and the three interaction site model for DNA in a modular fashion, without recalibrating any of the parameters in the original force-fields. A unique feature of COFFEE is that it describes sequence-specific DNA-protein interactions using a statistical potential (SP) derived from a data set of high-resolution crystal structures. The only parameter in COFFEE is the strength (λDNAPRO) of the DNA-protein contact potential. For an optimal choice of λDNAPRO, the crystallographic B-factors for DNA-protein complexes with varying sizes and topologies are quantitatively reproduced. Without any further readjustments to the force-field parameters, COFFEE predicts scattering profiles that are in quantitative agreement with small-angle X-ray scattering experiments, as well as chemical shifts that are consistent with NMR. We also show that COFFEE accurately describes the salt-induced unraveling of nucleosomes. Strikingly, our nucleosome simulations explain the destabilization effect of ARG to LYS mutations, which do not alter the balance of electrostatic interactions but affect chemical interactions in subtle ways. The range of applications attests to the transferability of COFFEE, and we anticipate that it would be a promising framework for simulating DNA-protein complexes at the molecular length-scale.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
| | - Balaka Mondal
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
- Department of Physics, The University of Texas at Austin, 2515 Speedway, Austin 78712, Texas, United States
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7
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Sun LZ, Ying YJ. Moving dynamics of a nanorobot with three DNA legs on nanopore-based tracks. NANOSCALE 2023; 15:15794-15809. [PMID: 37740362 DOI: 10.1039/d3nr03747a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
DNA nanorobots have garnered increasing attention in recent years due to their unique advantages of modularity and algorithm simplicity. To accomplish specific tasks in complex environments, various walking strategies are required for the DNA legs of the nanorobot. In this paper, we employ computational simulations to investigate a well-designed DNA-legged nanorobot moving along a nanopore-based track on a planar membrane. The nanorobot consists of a large nanoparticle as the robot core and three single-stranded DNAs (ssDNAs) as the robot legs. The nanopores linearly embedded in the membrane serve as the toeholds for the robot legs. A charge gradient along the pore distribution mainly powers the activation of the nanorobot. The nanorobot can move in two modes: a walking mode, where the robot legs sequentially enter the nanopores, and a jumping mode, where the robot legs may skip a nanopore to reach the next one. Moreover, we observe that the moving dynamics of the nanorobot on the nanopore-based tracks depends on pore-pore distance, pore charge gradient, external voltage, and leg length.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Yao-Jun Ying
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
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8
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Chakraborty D, Mondal B, Thirumalai D. Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544064. [PMID: 37333386 PMCID: PMC10274755 DOI: 10.1101/2023.06.07.544064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
DNA-protein interactions are pervasive in a number of biophysical processes ranging from transcription, gene expression, to chromosome folding. To describe the structural and dynamic properties underlying these processes accurately, it is important to create transferable computational models. Toward this end, we introduce Coarse grained force field for energy estimation, COFFEE, a robust framework for simulating DNA-protein complexes. To brew COFFEE, we integrated the energy function in the Self-Organized Polymer model with Side Chains for proteins and the Three Interaction Site model for DNA in a modular fashion, without re-calibrating any of the parameters in the original force-fields. A unique feature of COFFEE is that it describes sequence-specific DNA-protein interactions using a statistical potential (SP) derived from a dataset of high-resolution crystal structures. The only parameter in COFFEE is the strength (λ D N A P R O ) of the DNA-protein contact potential. For an optimal choice of λ D N A P R O , the crystallographic B-factors for DNA-protein complexes, with varying sizes and topologies, are quantitatively reproduced. Without any further readjustments to the force-field parameters, COFFEE predicts the scattering profiles that are in quantitative agreement with SAXS experiments as well as chemical shifts that are consistent with NMR. We also show that COFFEE accurately describes the salt-induced unraveling of nucleosomes. Strikingly, our nucleosome simulations explain the destabilization effect of ARG to LYS mutations, which does not alter the balance of electrostatic interactions, but affects chemical interactions in subtle ways. The range of applications attests to the transferability of COFFEE, and we anticipate that it would be a promising framework for simulating DNA-protein complexes at the molecular length-scale.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
| | - Balaka Mondal
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
- Department of Physics, The University of Texas at Austin, 2515 Speedway,Austin TX 78712, USA
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9
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Wu Z, Wu JW, Michaudel Q, Jayaraman A. Investigating the Hydrogen Bond-Induced Self-Assembly of Polysulfamides Using Molecular Simulations and Experiments. Macromolecules 2023; 56:5033-5049. [PMID: 38362140 PMCID: PMC10865372 DOI: 10.1021/acs.macromol.3c01093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/08/2023] [Indexed: 02/17/2024]
Abstract
In this paper, we present a synergistic, experimental, and computational study of the self-assembly of N,N'-disubstituted polysulfamides driven by hydrogen bonds (H-bonds) between the H-bonding donor and acceptor groups present in repeating sulfamides as a function of the structural design of the polysulfamide backbone. We developed a coarse-grained (CG) polysulfamide model that captures the directionality of H-bonds between the sulfamide groups and used this model in molecular dynamics (MD) simulations to study the self-assembly of these polymers in implicit solvent. The CGMD approach was validated by reproducing experimentally observed trends in the extent of crystallinity for three polysulfamides synthesized with aliphatic and/or aromatic repeating units. After validation of our CGMD approach, we computationally predicted the effect of repeat unit bulkiness, length, and uniformity of segment lengths in the polymers on the extent of orientational and positional order among the self-assembled polysulfamide chains, providing key design principles for tuning the extent of crystallinity in polysulfamides in experiments. Those computational predictions were then experimentally tested through the synthesis and characterization of polysulfamide architectures.
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Affiliation(s)
- Zijie Wu
- Department
of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, Delaware 19716, United States
| | - Jiun Wei Wu
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Quentin Michaudel
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Materials Science & Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Arthi Jayaraman
- Department
of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, Delaware 19716, United States
- Department
of Materials Science and Engineering, University
of Delaware, 201 DuPont Hall, Newark, Delaware 19716, United States
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10
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Mu ZC, Tan YL, Liu J, Zhang BG, Shi YZ. Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding. Molecules 2023; 28:4833. [PMID: 37375388 DOI: 10.3390/molecules28124833] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
DNA carries the genetic information required for the synthesis of RNA and proteins and plays an important role in many processes of biological development. Understanding the three-dimensional (3D) structures and dynamics of DNA is crucial for understanding their biological functions and guiding the development of novel materials. In this review, we discuss the recent advancements in computer methods for studying DNA 3D structures. This includes molecular dynamics simulations to analyze DNA dynamics, flexibility, and ion binding. We also explore various coarse-grained models used for DNA structure prediction or folding, along with fragment assembly methods for constructing DNA 3D structures. Furthermore, we also discuss the advantages and disadvantages of these methods and highlight their differences.
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Affiliation(s)
- Zi-Chun Mu
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
- School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan 430073, China
| | - Ya-Lan Tan
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
| | - Jie Liu
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
| | - Ben-Gong Zhang
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
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11
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Kapoor U, Kim YC, Mittal J. A coarse-grained DNA model to study protein-DNA interactions and liquid-liquid phase separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541513. [PMID: 37292850 PMCID: PMC10245785 DOI: 10.1101/2023.05.19.541513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recent advances in coarse-grained (CG) computational models for DNA have enabled molecular-level insights into the behavior of DNA in complex multiscale systems. However, most existing CG DNA models are not compatible with CG protein models, limiting their applications for emerging topics such as protein-nucleic acid assemblies. Here, we present a new computationally efficient CG DNA model. We first use experimental data to establish the model's ability to predict various aspects of DNA behavior, including melting thermodynamics and relevant local structural properties such as the major and minor grooves. We then employ an all-atom hydropathy scale to define non-bonded interactions between protein and DNA sites, to make our DNA model compatible with an existing CG protein model (HPS-Urry), that is extensively used to study protein phase separation, and show that our new model reasonably reproduces the experimental binding affinity for a prototypical protein-DNA system. To further demonstrate the capabilities of this new model, we simulate a full nucleosome with and without histone tails, on a microsecond timescale, generating conformational ensembles and provide molecular insights into the role of histone tails in influencing the liquid-liquid phase separation (LLPS) of HP1α proteins. We find that histone tails interact favorably with DNA, influencing the conformational ensemble of the DNA and antagonizing the contacts between HP1α and DNA, thus affecting the ability of DNA to promote LLPS of HP1α. These findings shed light on the complex molecular framework that fine-tunes the phase transition properties of heterochromatin proteins and contributes to heterochromatin regulation and function. Overall, the CG DNA model presented here is suitable to facilitate micron-scale studies with sub-nm resolution in many biological and engineering applications and can be used to investigate protein-DNA complexes, such as nucleosomes, or LLPS of proteins with DNA, enabling a mechanistic understanding of how molecular information may be propagated at the genome level.
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Affiliation(s)
- Utkarsh Kapoor
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 78743, United States
| | - Young C. Kim
- Center for Materials Physics and Technology, Naval Research Laboratory, Washington, District of Columbia
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 78743, United States
- Department of Chemistry, Texas A&M University, College Station, Texas 78743, United States
- Interdisciplinary Graduate Program in Genetics in Genomics, Texas A&M University, College Station, Texas 78743, United States
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12
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Bakhshandeh F, Saha S, Sen P, Sakib S, MacLachlan R, Kanji F, Osman E, Soleymani L. A universal bacterial sensor created by integrating a light modulating aptamer complex with photoelectrochemical signal readout. Biosens Bioelectron 2023; 235:115359. [PMID: 37187062 DOI: 10.1016/j.bios.2023.115359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/05/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023]
Abstract
Photoelectrochemical (PEC) signal transduction is of great interest for ultrasensitive biosensing; however, signal-on PEC assays that do not require target labeling remain elusive. In this work, we developed a signal-on biosensor that uses nucleic acids to modulate PEC currents upon target capture. Target presence removes a biorecognition probe from a DNA duplex carrying a gold nanoparticle, bringing the gold nanoparticle in direct contact to the photoelectrode and increasing the PEC current. This assay was used to develop a universal bacterial detector by targeting peptidoglycan using an aptamer, demonstrating a limit-of-detection of 82 pg/mL (13 pM) in buffer and 239 pg/mL (37 pM) in urine for peptidoglycan and 1913 CFU/mL forEscherichia coliin urine. When challenged with a panel of unknown targets, the sensor identified samples with bacterial contamination versus fungi. The versatility of the assay was further demonstrated by analyzing DNA targets, which yielded a limit-of-detection of 372 fM.
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Affiliation(s)
- Fatemeh Bakhshandeh
- Department of Engineering Physics, 1280 Main Street West, L8S 4L8, Hamilton, Ontario, Canada
| | - Sudip Saha
- School of Biomedical Engineering, 1280 Main Street West, L8S 4L8, Hamilton, Ontario, Canada
| | - Payel Sen
- Department of Engineering Physics, 1280 Main Street West, L8S 4L8, Hamilton, Ontario, Canada
| | - Sadman Sakib
- Department of Engineering Physics, 1280 Main Street West, L8S 4L8, Hamilton, Ontario, Canada
| | - Roderick MacLachlan
- Department of Engineering Physics, 1280 Main Street West, L8S 4L8, Hamilton, Ontario, Canada
| | - Farhaan Kanji
- Department of Engineering Physics, 1280 Main Street West, L8S 4L8, Hamilton, Ontario, Canada
| | - Enas Osman
- School of Biomedical Engineering, 1280 Main Street West, L8S 4L8, Hamilton, Ontario, Canada
| | - Leyla Soleymani
- Department of Engineering Physics, 1280 Main Street West, L8S 4L8, Hamilton, Ontario, Canada; School of Biomedical Engineering, 1280 Main Street West, L8S 4L8, Hamilton, Ontario, Canada; Michael G. DeGroote Institute for Infectious Disease Research, 1280 Main Street West, L8S 4L8, Hamilton, Ontario, Canada.
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13
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Saliba D, Luo X, Rizzuto FJ, Sleiman HF. Programming rigidity into size-defined wireframe DNA nanotubes. NANOSCALE 2023; 15:5403-5413. [PMID: 36826342 DOI: 10.1039/d2nr06185f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Nanotubes built from DNA hold promise for several biological and materials applications, due to their high aspect ratio and encapsulation potential. A particularly appealing goal is to control the size, shape, and dynamic behaviour of DNA nanotubes with minimal design alteration, as nanostructures of varying morphologies and lengths have been shown to exhibit distinct cellular uptake, encapsulation behaviour, and in vivo biodistribution. Herein, we report a systematic investigation, combining experimental and computational design, to modulate the length, flexibility, and longitudinal patterns of wireframe DNA nanotubes. Subtle design changes govern the structure and properties of our nanotubes, which are built from a custom-made, long, and size-defined template strand to which DNA rungs and linkers are attached. Unlike DNA origami, these custom-made strands possess regions with repeating sequences at strategic locations, thereby reducing the number of strands necessary for assembly. Through strand displacement, the nanotubes can be reversibly altered between extended and collapsed morphologies. These design concepts enable fine-tuning of the nanotube stiffness and may pave the way for the development of designer nanotubes for a variety of applications, including the study of cellular internalization, biodistribution, and uptake mechanisms for structures of varied shapes and sizes.
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Affiliation(s)
- Daniel Saliba
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.
| | - Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.
| | - Felix J Rizzuto
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.
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14
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Maksudov F, Kliuchnikov E, Pierson D, Ujwal M, Marx KA, Chanda A, Barsegov V. Therapeutic phosphorodiamidate morpholino oligonucleotides: Physical properties, solution structures, and folding thermodynamics. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:631-647. [PMID: 36910708 PMCID: PMC9996446 DOI: 10.1016/j.omtn.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Elucidating the structure-function relationships for therapeutic RNA mimicking phosphorodiamidate morpholino oligonucleotides (PMOs) is challenging due to the lack of information about their structures. While PMOs have been approved by the US Food and Drug Administration for treatment of Duchenne muscular dystrophy, no structural information on these unique, charge-neutral, and stable molecules is available. We performed circular dichroism and solution viscosity measurements combined with molecular dynamics simulations and machine learning to resolve solution structures of 22-mer, 25-mer, and 30-mer length PMOs. The PMO conformational dynamics are defined by the competition between non-polar nucleobases and uncharged phosphorodiamidate groups for shielding from solvent exposure. PMO molecules form non-canonical, partially helical, stable folded structures with a small 1.4- to 1.7-nm radius of gyration, low count of three to six base pairs and six to nine base stacks, characterized by -34 to -51 kcal/mol free energy, -57 to -103 kcal/mol enthalpy, and -23 to -53 kcal/mol entropy for folding. The 4.5- to 6.2-cm3/g intrinsic viscosity and Huggins constant of 4.5-9.9 are indicative of extended and aggregating systems. The results obtained highlight the importance of the conformational ensemble view of PMO solution structures, thermodynamic stability of their non-canonical structures, and concentration-dependent viscosity properties. These principles form a paradigm to understand the structure-properties-function relationship for therapeutic PMOs to advance the design of new RNA-mimic-based drugs.
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Affiliation(s)
- Farkhad Maksudov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
| | | | - Daniel Pierson
- Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA
| | | | - Kenneth A. Marx
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
- Inciton, Inc., Andover, MA 01854, USA
| | - Arani Chanda
- Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA
- Corresponding author: Arani Chanda, Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA.
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
- Inciton, Inc., Andover, MA 01854, USA
- Corresponding author: Valeri Barsegov, Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA.
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15
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Brandani GB, Gopi S, Yamauchi M, Takada S. Molecular dynamics simulations for the study of chromatin biology. Curr Opin Struct Biol 2022; 77:102485. [PMID: 36274422 DOI: 10.1016/j.sbi.2022.102485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/05/2022] [Accepted: 09/18/2022] [Indexed: 12/14/2022]
Abstract
The organization of Eukaryotic DNA into chromatin has profound implications for the processing of genetic information. In the past years, molecular dynamics (MD) simulations proved to be a powerful tool to investigate the mechanistic basis of chromatin biology. We review recent all-atom and coarse-grained MD studies revealing how the structure and dynamics of chromatin underlie its biological functions. We describe the latest method developments; the structural fluctuations of nucleosomes and the various factors affecting them; the organization of chromatin fibers, with particular emphasis on its liquid-like character; the interactions and dynamics of transcription factors on chromatin; and how chromatin organization is modulated by molecular motors acting on DNA.
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Affiliation(s)
- Giovanni B Brandani
- Department of Biophysics, Graduate School of Science, Kyoto University, Japan.
| | - Soundhararajan Gopi
- Department of Biophysics, Graduate School of Science, Kyoto University, Japan
| | - Masataka Yamauchi
- Department of Biophysics, Graduate School of Science, Kyoto University, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Japan
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16
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Natmai S, Kuntip N, Japrung D, Pongprayoon P. The aggregation of multiple miR-29a cancer biomarkers induced by graphene quantum dots: Molecular dynamics simulations. J Mol Graph Model 2022; 116:108267. [PMID: 35849900 DOI: 10.1016/j.jmgm.2022.108267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/26/2022] [Accepted: 06/30/2022] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play a role in regulating gene expression. MiRNAs are focused on as potential cancer biomarkers due to their involvement in the cancer development. New effective techniques for extracting miRNA from a biological matrix is important. Recently, graphene quantum dots (GQDs) have been used to detect DNA/RNA in many sensor platforms, but the application in miRNA extraction remains limited. To extract miRNAs, the miRNA adsorption and desorption on GQD are the key. Thus, in this work, the adsorption mechanism of excess miRNA on GQD in solution is revealed using Molecular dynamics simulations. The miRNA assemblies on one and two GQDs were studied to explore the possibility of using GQD for miRNA extraction. The folded miR-29a molecule, one of key cancer biomarkers, is used as an miRNA model. Three systems with one (6miR) and two GQDs (with parallel (6miR_2GP) and sandwich (6miR_2GS) organisations) in six-miR-29a solution were set. The data show excess miR-29a can reduce the miR-29a-GQD binding efficiency. The opening of intrabase pairing of GQD-absorbed miR-29a facilitates the interbase coupling resulting in the self-aggregation of miR-29a. The GQD organisation also affects the miR-29a adsorption ability. The additional GQDs result in the tighter miR-29a adsorption which can retard the miR-29a desorption. The proper GQD concentration is thus important to successfully collect all miR-29a and accommodate the easy miR-29a dissociation. Our results can be useful for a design of DNA probe and choosing decent nanosized GRA concentration for experimental setups.
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Affiliation(s)
- Saowalak Natmai
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Nattapon Kuntip
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Deanpen Japrung
- National Nanotechnology Center, National Science and Technology Development Agency, Thailand Science Park, Pathumthani, 12120, Thailand
| | - Prapasiri Pongprayoon
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand; Center for Advanced Studied in Nanotechnology for Chemical, Food, and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, 10900, Thailand.
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17
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Prakash DL, Gosavi S. The diversity of protein-protein interaction interfaces within T=3 icosahedral viral capsids. Front Mol Biosci 2022; 9:967877. [PMID: 36339706 PMCID: PMC9631432 DOI: 10.3389/fmolb.2022.967877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
Some non-enveloped virus capsids assemble from multiple copies of a single type of coat-protein (CP). The comparative energetics of the diverse CP-CP interfaces present in such capsids likely govern virus assembly-disassembly mechanisms. The T = 3 icosahedral capsids comprise 180 CP copies arranged about two-, three-, five- and six-fold axes of (quasi-)rotation symmetry. Structurally diverse CPs can assemble into T = 3 capsids. Specifically, the Leviviridae CPs are structurally distinct from the Bromoviridae, Tombusviridae and Tymoviridae CPs which fold into the classic “jelly-roll” fold. However, capsids from across the four families are known to disassemble into dimers. To understand whether the overall symmetry of the capsid or the structural details of the CP determine virus assembly-disassembly mechanisms, we analyze the different CP-CP interfaces that occur in the four virus families. Previous work studied protein homodimer interfaces using interface size (relative to the monomer) and hydrophobicity. Here, we analyze all CP-CP interfaces using these two parameters and find that the dimerization interface (present between two CPs congruent through a two-fold axis of rotation) has a larger relative size in the Leviviridae than in the other viruses. The relative sizes of the other Leviviridae interfaces and all the jelly-roll interfaces are similar. However, the dimerization interfaces across families have slightly higher hydrophobicity, potentially making them stronger than other interfaces. Finally, although the CP-monomers of the jelly-roll viruses are structurally similar, differences in their dimerization interfaces leads to varied dimer flexibility. Overall, differences in CP-structures may induce different modes of swelling and assembly-disassembly in the T = 3 viruses.
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18
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Mu ZC, Tan YL, Zhang BG, Liu J, Shi YZ. Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions. PLoS Comput Biol 2022; 18:e1010501. [PMID: 36260618 PMCID: PMC9621594 DOI: 10.1371/journal.pcbi.1010501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/31/2022] [Accepted: 09/27/2022] [Indexed: 11/07/2022] Open
Abstract
The three-dimensional (3D) structure and stability of DNA are essential to understand/control their biological functions and aid the development of novel materials. In this work, we present a coarse-grained (CG) model for DNA based on the RNA CG model proposed by us, to predict 3D structures and stability for both dsDNA and ssDNA from the sequence. Combined with a Monte Carlo simulated annealing algorithm and CG force fields involving the sequence-dependent base-pairing/stacking interactions and an implicit electrostatic potential, the present model successfully folds 20 dsDNAs (≤52nt) and 20 ssDNAs (≤74nt) into the corresponding native-like structures just from their sequences, with an overall mean RMSD of 3.4Å from the experimental structures. For DNAs with various lengths and sequences, the present model can make reliable predictions on stability, e.g., for 27 dsDNAs with/without bulge/internal loops and 24 ssDNAs including pseudoknot, the mean deviation of predicted melting temperatures from the corresponding experimental data is only ~2.0°C. Furthermore, the model also quantificationally predicts the effects of monovalent or divalent ions on the structure stability of ssDNAs/dsDNAs. To determine 3D structures and quantify stability of single- (ss) and double-stranded (ds) DNAs is essential to unveil the mechanisms of their functions and to further guide the production and development of novel materials. Although many DNA models have been proposed to reproduce the basic structural, mechanical, or thermodynamic properties of dsDNAs based on the secondary structure information or preset constraints, there are very few models can be used to investigate the ssDNA folding or dsDNA assembly from the sequence. Furthermore, due to the polyanionic nature of DNAs, metal ions (e.g., Na+ and Mg2+) in solutions can play an essential role in DNA folding and dynamics. Nevertheless, ab initio predictions for DNA folding in ion solutions are still an unresolved problem. In this work, we developed a novel coarse-grained model to predict 3D structures and thermodynamic stabilities for both ssDNAs and dsDNAs in monovalent/divalent ion solutions from their sequences. As compared with the extensive experimental data and available existing models, we showed that the present model can successfully fold simple DNAs into their native-like structures, and can also accurately reproduce the effects of sequence and monovalent/divalent ions on structure stability for ssDNAs including pseudoknot and dsDNAs with/without bulge/internal loops.
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Affiliation(s)
- Zi-Chun Mu
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
- School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, China
| | - Ya-Lan Tan
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
| | - Ben-Gong Zhang
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
| | - Jie Liu
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
- * E-mail:
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19
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Sun LZ, Qian JL, Cai P, Xu X. Mutual effects between single-stranded DNA conformation and Na +-Mg 2+ ion competition in mixed salt solutions. Phys Chem Chem Phys 2022; 24:20867-20881. [PMID: 36043348 DOI: 10.1039/d2cp02737b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ion-dependence of single-stranded DNA (ssDNA) conformational changes has attracted growing attention because of its biological and technological importance. Although single-species ion effects have been extensively explored, it is challenging to study the ssDNA conformational properties under mixed monovalent/divalent ion conditions due to the complications of ssDNA flexibility and ion-ion competition. In this study, we apply Langevin dynamics simulations to investigate mixed Na+/Mg2+ ion-dependent ssDNA conformations. The ssDNA structure is described using a coarse-grained model, in which the phosphate, base, and sugar of each nucleotide are represented by three different beads. A novel improvement in our simulation model is that mixed-salt-related electrostatic interactions are computed via combining Manning counterion condensation (MCC) theory with the Monte Carlo tightly bound ion (MCTBI) model. Based on this MCC-MCTBI combination, we report new empirical functions to describe the ion-concentration-dependent and ssDNA conformation/structure-dependent electrostatic effects. The calculation results relating to the ion binding properties and the simulation results relating to the ssDNA conformational properties are validated against experimental results. In addition, our simulation results suggest a quantitative relationship between the ssDNA conformation and Na+-Mg2+ competition; this in turn reveals their mutual impact in the ion atmosphere.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Jun-Lin Qian
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Pinggen Cai
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, 213001, China
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20
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Segers M, Voorspoels A, Sakaue T, Carlon E. Mechanical properties of nucleic acids and the non-local twistable wormlike chain model. J Chem Phys 2022; 156:234105. [PMID: 35732531 DOI: 10.1063/5.0089166] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mechanical properties of nucleic acids play an important role in many biological processes that often involve physical deformations of these molecules. At sufficiently long length scales (say, above ∼20-30 base pairs), the mechanics of DNA and RNA double helices is described by a homogeneous Twistable Wormlike Chain (TWLC), a semiflexible polymer model characterized by twist and bending stiffnesses. At shorter scales, this model breaks down for two reasons: the elastic properties become sequence-dependent and the mechanical deformations at distal sites get coupled. We discuss in this paper the origin of the latter effect using the framework of a non-local Twistable Wormlike Chain (nlTWLC). We show, by comparing all-atom simulations data for DNA and RNA double helices, that the non-local couplings are of very similar nature in these two molecules: couplings between distal sites are strong for tilt and twist degrees of freedom and weak for roll. We introduce and analyze a simple double-stranded polymer model that clarifies the origin of this universal distal couplings behavior. In this model, referred to as the ladder model, a nlTWLC description emerges from the coarsening of local (atomic) degrees of freedom into angular variables that describe the twist and bending of the molecule. Different from its local counterpart, the nlTWLC is characterized by a length-scale-dependent elasticity. Our analysis predicts that nucleic acids are mechanically softer at the scale of a few base pairs and are asymptotically stiffer at longer length scales, a behavior that matches experimental data.
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Affiliation(s)
- Midas Segers
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Aderik Voorspoels
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Kanagawa, Japan
| | - Enrico Carlon
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
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21
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Qian JL, Sun LZ. Dataset of normalized probability distributions of virtual bond lengths, bond angles, and dihedral angles for the coarse-grained single-stranded DNA structures. Data Brief 2022; 42:108284. [PMID: 35637888 PMCID: PMC9142626 DOI: 10.1016/j.dib.2022.108284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 11/06/2022] Open
Abstract
The utility of the coarse-grained (CG) single-stranded DNA (ssDNA) model can drastically reduce the compute time for simulating the ssDNA dynamics. The model-matched CG potentials and the inherent potential constants can be derived by coarse-graining the experimentally measured ssDNA structures. A useful and widespread treatment of the CG model is to use three different pseudo-atoms P, S, and B to represent the atomic groups of phosphate, sugar, and base, respectively, in each nucleotide of the ssDNA structures. The three pseudo-atoms generate nine types of the structural parameters to characterize the unstructured ssDNA conformations, including three (virtual) bond lengths (P-S, S-B, and S-P) between two neighbouring beads, four bond angles (P-S-P, S-P-S, P-S-B, and B-S-P) between three adjacent bonds, and two dihedral angles (P-S-P-S and S-P-S-P) between three successive bonds. This paper mainly presents the data of normalized probability distributions of the bond lengths, bond angles, and dihedral angles for the CG ssDNAs.
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22
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Assenza S, Pérez R. Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA. J Chem Theory Comput 2022; 18:3239-3256. [PMID: 35394775 PMCID: PMC9097290 DOI: 10.1021/acs.jctc.2c00138] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
We introduce MADna,
a sequence-dependent coarse-grained model of
double-stranded DNA (dsDNA), where each nucleotide is described by
three beads localized at the sugar, at the base moiety, and at the
phosphate group, respectively. The sequence dependence is included
by considering a step-dependent parametrization of the bonded interactions,
which are tuned in order to reproduce the values of key observables
obtained from exhaustive atomistic simulations from the literature.
The predictions of the model are benchmarked against an independent
set of all-atom simulations, showing that it captures with high fidelity
the sequence dependence of conformational and elastic features beyond
the single step considered in its formulation. A remarkably good agreement
with experiments is found for both sequence-averaged and sequence-dependent
conformational and elastic features, including the stretching and
torsion moduli, the twist–stretch and twist–bend couplings,
the persistence length, and the helical pitch. Overall, for the inspected
quantities, the model has a precision comparable to atomistic simulations,
hence providing a reliable coarse-grained description for the rationalization
of single-molecule experiments and the study of cellular processes
involving dsDNA. Owing to the simplicity of its formulation, MADna
can be straightforwardly included in common simulation engines. Particularly,
an implementation of the model in LAMMPS is made available on an online
repository to ease its usage within the DNA research community.
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23
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Sun LZ, Qian JL, Cai P, Hu HX, Xu X, Luo MB. Mg2+ effects on the single-stranded DNA conformations and nanopore translocation dynamics. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.124895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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24
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Wei X, Chen C, Zhao Y, Harazinska E, Bathe M, Hernandez R. Molecular Structure of Single-Stranded DNA on the ZnS Surface of Quantum Dots. ACS NANO 2022; 16:6666-6675. [PMID: 35405067 PMCID: PMC9048700 DOI: 10.1021/acsnano.2c01178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
DNA-based nanoparticle assemblies have emerged as leading candidates in the development of bioimaging materials, photonic devices, and computing materials. Here, we combine atomistic simulations and experiments to characterize the wrapping mechanism of chimeric single-stranded DNA (ssDNA) on CdSe-ZnS (core-shell) quantum dots (QDs) at different ratios of the phosphorothioate (PS) modification of the bases. We use an implicit solvent, all-atom ssDNA model to match the experimentally calculated ssDNA conformation at low salt concentrations. Through simulation, we find that 3-mercaptopropionic acid (MPA) induces electrostatic repulsion and O-(2-mercaptoethyl)-Ó-methyl-hexa (ethylene glycol) (mPEG) induces steric exclusion, and both reduce the binding affinity of ssDNA. In both simulation and experiment, we find that ssDNA is closer to the QD surface when the QD size is larger. The effect of the PS-base ratio on the conformation of ssDNA is also elaborated in this work. We found through MD simulations, and confirmed by transmission electron microscopy, that the maximum valence numbers are 1, 2, and 3 on QDs of 6, 9, and 14 nm in diameter, respectively. We conclude that the maximum ssDNA valence number is linearly related to the QD size, n ∝ R, and justify this finding through an electrostatic repulsion mechanism.
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Affiliation(s)
- Xingfei Wei
- Department
of Chemistry, Chemical & Biomolecular Engineering and Materials Science
& Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Chi Chen
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yinong Zhao
- Department
of Chemistry, Chemical & Biomolecular Engineering and Materials Science
& Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ewa Harazinska
- Department
of Chemistry, Chemical & Biomolecular Engineering and Materials Science
& Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Mark Bathe
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rigoberto Hernandez
- Department
of Chemistry, Chemical & Biomolecular Engineering and Materials Science
& Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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25
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González-Olvera JC, Zamorano-Carrillo A, Arreola-Jardón G, Pless RC. Residue interactions affecting the deprotonation of internal guanine moieties in oligodeoxyribonucleotides, calculated by FMO methods. J Mol Model 2022; 28:43. [DOI: 10.1007/s00894-022-05033-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/18/2022] [Indexed: 11/24/2022]
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26
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Bae S, Kim JS. Potential of Mean Force for DNA Wrapping Around a Cationic Nanoparticle. J Chem Theory Comput 2021; 17:7952-7961. [PMID: 34792353 DOI: 10.1021/acs.jctc.1c00797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Sharp bending and wrapping of DNA around proteins and nanoparticles (NPs) has been of extensive research interest. Here, we present the potential of mean force (PMF) for wrapping a DNA double helix around a cationic NP using coarse-grained models of a double-stranded DNA and a cationic NP. Starting from a NP wrapped around by DNA, the PMF was calculated along the distance between the center of the NP and one end of the DNA molecule. A relationship between the distance and the extent of DNA wrapping is used to calculate the PMF as a function of DNA wrapping around a NP. In particular, the PMF was compared for two DNA sequences of (AT)25/(AT)25 and (AC)25/(GT)25, for which the persistence lengths are different by ∼10 nm. The simulation results provide solid evidence of the thermodynamic preference for complex formation of a cationic NP with more flexible DNA over the less flexible DNA. Furthermore, we estimated the elastic energy of DNA bending, which was in good order-of-magnitude agreement with the theoretical prediction of elastic rods. This work suggests that the variation of sequence-dependent DNA flexibility can be utilized in DNA nanotechnologies, in which the position and dynamics of NPs are regulated on large-scale DNA structures, or the structural transformation of DNA is triggered by the sequence-dependent binding of NPs.
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Affiliation(s)
- Sehui Bae
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jun Soo Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
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27
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Kuntip N, Japrung D, Pongprayoon P. Modeling the Adsorption of the miR-29a Cancer Biomarker on a Graphene Quantum Dot. ACS OMEGA 2021; 6:21764-21772. [PMID: 34471778 PMCID: PMC8388069 DOI: 10.1021/acsomega.1c03404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/30/2021] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules associated with the regulation of gene expression in organisms. MiRNAs are focused on as potential cancer biomarkers due to their involvement in cancer development. New potential techniques for miRNA detection are rapidly developed, while there is a lack of effective extraction approaches, especially for miRNAs. Recently, graphene quantum dots (GQDs) have been involved in many disease biosensor platforms including miRNA detection, but no application in miRNA extraction is studied. To extract miRNAs, miRNA adsorption and desorption on GQDs are the key. Thus, in this work, the adsorption mechanism of miRNA on GQDs in solution is revealed using molecular dynamics simulations. The aim is to explore the possibility of using GQDs for miRNA extraction. The folded miR-29a molecule, one of the key cancer biomarkers, is used as a miRNA model. Two systems with one (1miR) and four (4miR) chains of miR-29a were set. MiR-29a molecules in all systems are simultaneously adsorbed on the GQD surface. Our finding highlights the ability of the GQD in collecting miRNAs in solution. In 1miR, the whole miR-29a chain sits on the GQD face, whereas all miR-29a molecules in 4miR show the "clamping" conformation. No "lying flat" orientation of miR-29a is observed due to the existence of the preserved hairpin region. Interestingly, the 5' end shows tighter binding than the 3' terminus. A design of complementary DNA with the recognition segment involving the sequences close to the 3' end can promote effective miR-29a desorption.
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Affiliation(s)
- Nattapon Kuntip
- Department
of Chemistry, Faculty of Science, Kasetsart
University, Chatuchak, Bangkok 10900, Thailand
| | - Deanpen Japrung
- National
Nanotechnology Center, National Science
and Technology Development Agency, Thailand Science Park, Pathumthani 12120, Thailand
- . Phone:+66-2564-6665. Fax:+66-25647000
| | - Prapasiri Pongprayoon
- Department
of Chemistry, Faculty of Science, Kasetsart
University, Chatuchak, Bangkok 10900, Thailand
- Center
for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural
Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
- . Phone: +66-2562-5555. Fax:+66-2579-3955
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Bae S, Oh I, Yoo J, Kim JS. Effect of DNA Flexibility on Complex Formation of a Cationic Nanoparticle with Double-Stranded DNA. ACS OMEGA 2021; 6:18728-18736. [PMID: 34337212 PMCID: PMC8319935 DOI: 10.1021/acsomega.1c01709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
We present extensive molecular dynamics simulations of a cationic nanoparticle and a double-stranded DNA molecule to discuss the effect of DNA flexibility on the complex formation of a cationic nanoparticle with double-stranded DNA. Martini coarse-grained models were employed to describe double-stranded DNA molecules with two different flexibilities and cationic nanoparticles with three different electric charges. As the electric charge of a cationic nanoparticle increases, the degree of DNA bending increases, eventually leading to the wrapping of DNA around the nanoparticle at high electric charges. However, a small increase in the persistence length of DNA by 10 nm requires a cationic nanoparticle with a markedly increased electric charge to bend and wrap DNA around. Thus, a more flexible DNA molecule bends and wraps around a cationic nanoparticle with an intermediate electric charge, whereas a less flexible DNA molecule binds to a nanoparticle with the same electric charge without notable bending. This work provides solid evidence that a small difference in DNA flexibility (as small as 10 nm in persistence length) has a substantial influence on the complex formation of DNA with proteins from a biological perspective and suggests that the variation of sequence-dependent DNA flexibility can be utilized in DNA nanotechnology as a new tool to manipulate the structure of DNA molecules mediated by nanoparticle binding.
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Affiliation(s)
- Sehui Bae
- Department
of Chemistry and Nanoscience, Ewha Womans
University, Seoul 03760, Republic of Korea
| | - Inrok Oh
- LG
Chem Ltd., LG Science Park, Seoul 07796, Republic of Korea
| | - Jejoong Yoo
- Department
of Physics, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jun Soo Kim
- Department
of Chemistry and Nanoscience, Ewha Womans
University, Seoul 03760, Republic of Korea
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29
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Abstract
DNA dynamics can only be understood by taking into account its complex mechanical behavior at different length scales. At the micrometer level, the mechanical properties of single DNA molecules have been well-characterized by polymer models and are commonly quantified by a persistence length of 50 nm (~150 bp). However, at the base pair level (~3.4 Å), the dynamics of DNA involves complex molecular mechanisms that are still being deciphered. Here, we review recent single-molecule experiments and molecular dynamics simulations that are providing novel insights into DNA mechanics from such a molecular perspective. We first discuss recent findings on sequence-dependent DNA mechanical properties, including sequences that resist mechanical stress and sequences that can accommodate strong deformations. We then comment on the intricate effects of cytosine methylation and DNA mismatches on DNA mechanics. Finally, we review recently reported differences in the mechanical properties of DNA and double-stranded RNA, the other double-helical carrier of genetic information. A thorough examination of the recent single-molecule literature permits establishing a set of general 'rules' that reasonably explain the mechanics of nucleic acids at the base pair level. These simple rules offer an improved description of certain biological systems and might serve as valuable guidelines for future design of DNA and RNA nanostructures.
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30
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Sengar A, Ouldridge TE, Henrich O, Rovigatti L, Šulc P. A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results. Front Mol Biosci 2021; 8:693710. [PMID: 34235181 PMCID: PMC8256390 DOI: 10.3389/fmolb.2021.693710] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model's fundamental properties. We outline how simulation results can be interpreted in terms of-and feed into our understanding of-less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile.
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Affiliation(s)
- A. Sengar
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - T. E. Ouldridge
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - O. Henrich
- Department of Physics, SUPA, University of Strathclyde, Glasgow, United Kingdom
| | - L. Rovigatti
- Department of Physics, Sapienza University of Rome, Rome, Italy
- CNR Institute of Complex Systems, Sapienza University of Rome, Rome, Italy
| | - P. Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
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31
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Skoruppa E, Voorspoels A, Vreede J, Carlon E. Length-scale-dependent elasticity in DNA from coarse-grained and all-atom models. Phys Rev E 2021; 103:042408. [PMID: 34005944 DOI: 10.1103/physreve.103.042408] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/25/2021] [Indexed: 12/24/2022]
Abstract
We investigate the influence of nonlocal couplings on the torsional and bending elasticities of DNA. Such couplings have been observed in the past by several simulation studies. Here, we use a description of DNA conformations based on the variables tilt, roll, and twist. Our analysis of both coarse-grained (oxDNA) and all-atom models indicates that these share strikingly similar features: there are strong off-site couplings for tilt-tilt and twist-twist, while they are much weaker in the roll-roll case. By developing an analytical framework to estimate bending and torsional persistence lengths in nonlocal DNA models, we show how off-site interactions generate a length-scale-dependent elasticity. Based on the simulation-generated elasticity data, the theory predicts a significant length-scale-dependent effect on torsional fluctuations but only a modest effect on bending fluctuations. These results are in agreement with experiments probing DNA mechanics from single base pair to kilobase pair scales.
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Affiliation(s)
- Enrico Skoruppa
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Aderik Voorspoels
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Jocelyne Vreede
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Enrico Carlon
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
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32
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Gravina NM, Gumbart JC, Kim HD. Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding. J Phys Chem B 2021; 125:4016-4024. [PMID: 33870695 DOI: 10.1021/acs.jpcb.1c00432] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Annealing between sticky ends of DNA is an intermediate step in ligation. It can also be utilized to program specific binding sites for DNA tile and origami assembly. This reaction is generally understood as a bimolecular reaction dictated by the local concentration of the sticky ends. Its dependence on the relative orientation between the sticky ends, however, is less understood. Here we report on the interactions between DNA sticky ends using the coarse-grained oxDNA model; specifically, we consider how the orientational alignment of the double-stranded DNA (dsDNA) segments affects the time required for the sticky ends to bind, τb. We specify the orientation of the dsDNA segments with three parameters: θ, which measures the angle between the helical axes, and ϕ1 and ϕ2, which measure rotations of each strand around the helical axis. We find that the binding time depends strongly on both θ and ϕ2: ∼20-fold change with θ and 10-fold change with ϕ2. The binding time is the fastest when the helical axes of duplexes are pointing toward each other and the sticky ends protrude from the farthest two points. Our result is relevant for predicting hybridization efficiency of sticky ends that are rotationally restricted.
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Affiliation(s)
- Nicholas M Gravina
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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33
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Procyk J, Poppleton E, Šulc P. Coarse-grained nucleic acid-protein model for hybrid nanotechnology. SOFT MATTER 2021; 17:3586-3593. [PMID: 33398312 DOI: 10.1039/d0sm01639j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The emerging field of hybrid DNA-protein nanotechnology brings with it the potential for many novel materials which combine the addressability of DNA nanotechnology with the versatility of protein interactions. However, the design and computational study of these hybrid structures is difficult due to the system sizes involved. To aid in the design and in silico analysis process, we introduce here a coarse-grained DNA/RNA-protein model that extends the oxDNA/oxRNA models of DNA/RNA with a coarse-grained model of proteins based on an anisotropic network model representation. Fully equipped with analysis scripts and visualization, our model aims to facilitate hybrid nanomaterial design towards eventual experimental realization, as well as enabling study of biological complexes. We further demonstrate its usage by simulating DNA-protein nanocage, DNA wrapped around histones, and a nascent RNA in polymerase.
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Affiliation(s)
- Jonah Procyk
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA.
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34
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Jayaraman A. 100th Anniversary of Macromolecular Science Viewpoint: Modeling and Simulation of Macromolecules with Hydrogen Bonds: Challenges, Successes, and Opportunities. ACS Macro Lett 2020; 9:656-665. [PMID: 35648569 DOI: 10.1021/acsmacrolett.0c00134] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Macromolecular materials with directional interactions such as hydrogen bonds exhibit numerous attractive features in terms of structure, thermodynamics, and dynamics. Besides enabling precise tuning of desirable geometries in the assembled state (e.g., programmable coordination numbers depending on the valency of the directional interaction), mixing in a blend/composite through stabilization via hydrogen bonds between the various components, hydrogen bonds can also impart responsiveness to external stimuli (e.g., temperature, pH). In biomacromolecules (e.g., proteins, DNA, polysaccharides), hydrogen bonds play a key role in stabilizing secondary and tertiary structures, which in turn define the function of these macromolecules. In this Viewpoint, I present the challenges, successes, and opportunities for molecular modeling and simulations to conduct fundamental and application-focused research on macromolecular materials with hydrogen bonding interactions. The past successes and limitations of atomistic simulations are discussed first, followed by highlights from recent developments in coarse-grained modeling and their use in studies of (synthetic and biologically relevant) macromolecular materials. Model development focused on polynucleotides (e.g., DNA, RNA, etc.), polypeptides, polysaccharides, and synthetic polymers at experimentally relevant conditions are highlighted. This viewpoint ends with potential future directions for macromolecular modeling and simulations with other types of directional interactions beyond hydrogen bonding.
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Affiliation(s)
- Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
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35
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Mishra G, Bigman LS, Levy Y. ssDNA diffuses along replication protein A via a reptation mechanism. Nucleic Acids Res 2020; 48:1701-1714. [PMID: 31919510 PMCID: PMC7038930 DOI: 10.1093/nar/gkz1202] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/23/2019] [Accepted: 01/08/2020] [Indexed: 01/30/2023] Open
Abstract
Replication protein A (RPA) plays a critical role in all eukaryotic DNA processing involving single-stranded DNA (ssDNA). Contrary to the notion that RPA provides solely inert protection to transiently formed ssDNA, the RPA-ssDNA complex acts as a dynamic DNA processing unit. Here, we studied the diffusion of RPA along 60 nt ssDNA using a coarse-grained model in which the ssDNA-RPA interface was modeled by both aromatic and electrostatic interactions. Our study provides direct evidence of bulge formation during the diffusion of ssDNA along RPA. Bulges can form at a few sites along the interface and store 1-7 nt of ssDNA whose release, upon bulge dissolution, leads to propagation of ssDNA diffusion. These findings thus support the reptation mechanism, which involves bulge formation linked to the aromatic interactions, whose short range nature reduces cooperativity in ssDNA diffusion. Greater cooperativity and a larger diffusion coefficient for ssDNA diffusion along RPA are observed for RPA variants with weaker aromatic interactions and for interfaces homogenously stabilized by electrostatic interactions. ssDNA propagation in the latter instance is characterized by lower probabilities of bulge formation; thus, it may fit the sliding-without-bulge model better than the reptation model. Thus, the reptation mechanism allows ssDNA mobility despite the extensive and high affinity interface of RPA with ssDNA. The short-range aromatic interactions support bulge formation while the long-range electrostatic interactions support the release of the stored excess ssDNA in the bulge and thus the overall diffusion.
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Affiliation(s)
- Garima Mishra
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.,Department of Physics, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Lavi S Bigman
- 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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36
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Xu J, Miyamoto S, Tojo S, Kawai K. Sulfonated Pyrene as a Photoregulator for Single‐Stranded DNA Looping. Chemistry 2020; 26:5075-5084. [DOI: 10.1002/chem.202000184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/14/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Jie Xu
- The Institute of Scientific and Industrial Research (SANKEN)Osaka University Mihogaoka 8-1 Ibaraki, Osaka 567-0047 Japan
| | - Shunichi Miyamoto
- The Institute of Scientific and Industrial Research (SANKEN)Osaka University Mihogaoka 8-1 Ibaraki, Osaka 567-0047 Japan
| | - Sachiko Tojo
- The Institute of Scientific and Industrial Research (SANKEN)Osaka University Mihogaoka 8-1 Ibaraki, Osaka 567-0047 Japan
| | - Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN)Osaka University Mihogaoka 8-1 Ibaraki, Osaka 567-0047 Japan
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37
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Plumridge A, Andresen K, Pollack L. Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics. J Am Chem Soc 2019; 142:109-119. [PMID: 31804813 DOI: 10.1021/jacs.9b04461] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Disordered homopolymeric regions of single-stranded RNA, such as U or A tracts, are found within functional RNAs where they play distinct roles in defining molecular structure and facilitating recognition by partners. Despite this prominence, details of conformational and biophysical properties of these regions have not yet been resolved. We apply a number of experimental techniques to investigate the conformations of these biologically important motifs and provide quantitative measurements of their ion atmospheres. Single strands of RNA display pronounced sequence-dependent conformations that relate to the unique ion atmospheres each attracts. Chains of rU bases are relatively unstructured under all conditions, while chains of rA bases display distinct ordering through stacking or clustering motifs, depending on the composition of the surrounding solution. These dramatic structural differences are consistent with the measured disparity in ion composition and atmospheres around each homopolymer, revealing a complex interplay of base, ion, and single-strand ordering. The unique structural and ionic signatures of homopolymer ssRNAs explains their role(s) in folding structured RNAs and may explain their distinct recognition by protein partners.
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Affiliation(s)
- Alex Plumridge
- School of Applied and Engineering Physics , Cornell University , Ithaca , New York 14853 , United States
| | - Kurt Andresen
- Department of Physics , Gettysburg College , Gettysburg , Pennsylvania 17325 , United States
| | - Lois Pollack
- School of Applied and Engineering Physics , Cornell University , Ithaca , New York 14853 , United States
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38
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Snodin BEK, Schreck JS, Romano F, Louis AA, Doye JPK. Coarse-grained modelling of the structural properties of DNA origami. Nucleic Acids Res 2019; 47:1585-1597. [PMID: 30605514 PMCID: PMC6379721 DOI: 10.1093/nar/gky1304] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/17/2018] [Accepted: 12/20/2018] [Indexed: 01/12/2023] Open
Abstract
We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origami, focussing on archetypal 2D and 3D origami. The model reproduces well the characteristic pattern of helix bending in a 2D origami, showing that it stems from the intrinsic tendency of anti-parallel four-way junctions to splay apart, a tendency that is enhanced both by less screened electrostatic interactions and by increased thermal motion. We also compare to the structure of a 3D origami whose structure has been determined by cryo-electron microscopy. The oxDNA average structure has a root-mean-square deviation from the experimental structure of 8.4 Å, which is of the order of the experimental resolution. These results illustrate that the oxDNA model is capable of providing detailed and accurate insights into the structure of DNA origami, and has the potential to be used to routinely pre-screen putative origami designs and to investigate the molecular mechanisms that regulate the properties of DNA origami.
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Affiliation(s)
- Benedict E K Snodin
- Physical, and Theoretical Chemistry Laboratory, Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
| | - John S Schreck
- Department of Chemical Engineering, Columbia University, 500 W 120th Street, New York, NY 10027, USA
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Universit Ca' Foscari, Via Torino 155, 30172 Venezia Mestre, Italy
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, UK
| | - Jonathan P K Doye
- Physical, and Theoretical Chemistry Laboratory, Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
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39
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Caraglio M, Skoruppa E, Carlon E. Overtwisting induces polygonal shapes in bent DNA. J Chem Phys 2019; 150:135101. [PMID: 30954045 DOI: 10.1063/1.5084950] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
By combining analytical results and simulations of various coarse-grained models, we investigate the minimal energy shape of DNA minicircles which are torsionally constrained by an imposed over or undertwist. We show that twist-bend coupling, a cross interaction term discussed in the recent DNA literature, induces minimal energy shapes with a periodic alternation of parts with high and low curvature resembling rounded polygons. We briefly discuss the possible experimental relevance of these findings. We finally show that the twist and bending energies of minicircles are governed by renormalized stiffness constants, rather than the bare ones. This has important consequences for the analysis of experiments involving circular DNA meant to determine DNA elastic constants.
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Affiliation(s)
- Michele Caraglio
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Enrico Skoruppa
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Enrico Carlon
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
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40
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Pal A, Levy Y. Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins. PLoS Comput Biol 2019; 15:e1006768. [PMID: 30933978 PMCID: PMC6467422 DOI: 10.1371/journal.pcbi.1006768] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 04/16/2019] [Accepted: 01/01/2019] [Indexed: 02/06/2023] Open
Abstract
Recognition of single-stranded DNA (ssDNA) or single-stranded RNA (ssRNA) is important for many fundamental cellular functions. A variety of single-stranded DNA-binding proteins (ssDBPs) and single-stranded RNA-binding proteins (ssRBPs) have evolved that bind ssDNA and ssRNA, respectively, with varying degree of affinities and specificities to form complexes. Structural studies of these complexes provide key insights into their recognition mechanism. However, computational modeling of the specific recognition process and to predict the structure of the complex is challenging, primarily due to the heterogeneity of their binding energy landscape and the greater flexibility of ssDNA or ssRNA compared with double-stranded nucleic acids. Consequently, considerably fewer computational studies have explored interactions between proteins and single-stranded nucleic acids compared with protein interactions with double-stranded nucleic acids. Here, we report a newly developed energy-based coarse-grained model to predict the structure of ssDNA–ssDBP and ssRNA–ssRBP complexes and to assess their sequence-specific interactions and stabilities. We tuned two factors that can modulate specific recognition: base–aromatic stacking strength and the flexibility of the single-stranded nucleic acid. The model was successfully applied to predict the binding conformations of 12 distinct ssDBP and ssRBP structures with their cognate ssDNA and ssRNA partners having various sequences. Estimated binding energies agreed well with the corresponding experimental binding affinities. Bound conformations from the simulation showed a funnel-shaped binding energy distribution where the native-like conformations corresponded to the energy minima. The various ssDNA–protein and ssRNA–protein complexes differed in the balance of electrostatic and aromatic energies. The lower affinity of the ssRNA–ssRBP complexes compared with the ssDNA–ssDBP complexes stems from lower flexibility of ssRNA compared to ssDNA, which results in higher rate constants for the dissociation of the complex (koff) for complexes involving the former. Quantifying bimolecular self-assembly is pivotal to understanding cellular function. In recent years, a large progress has been made in understanding the structure and biophysics of protein-protein interactions. Particularly, various computational tools are available for predicting these structures and to estimate their stability and the driving forces of their formation. The understating of the interactions between proteins and nucleic acids, however, is still limited, presumably due to the involvement of non-specific interactions as well as the high conformational plasticity that may demand an induced-fit mechanism. In particular, the interactions between proteins and single-stranded nucleic acids (i.e., single-stranded DNA and RNA) is very challenging due to their high flexibility. Furthermore, the interface between proteins and single-stranded nucleic acids is often chemically more heterogeneous than the interface between proteins and double-stranded DNA. In this study, we developed a coarse-grained computational model to predict the structure of complexes between proteins and single-stranded nucleic acids. The model was applied to estimate binding affinities and the estimated binding energies agreed well with the corresponding experimental binding affinities. The kinetics of association as well as the specificity of the complexes between proteins and ssDNA are different than those with ssRNA, mostly due to differences in their conformational flexibility.
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Affiliation(s)
- Arumay Pal
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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41
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Connolly M, Arra A, Zvoda V, Steinbach PJ, Rice PA, Ansari A. Static Kinks or Flexible Hinges: Multiple Conformations of Bent DNA Bound to Integration Host Factor Revealed by Fluorescence Lifetime Measurements. J Phys Chem B 2018; 122:11519-11534. [DOI: 10.1021/acs.jpcb.8b07405] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mitchell Connolly
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Aline Arra
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Viktoriya Zvoda
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Peter J. Steinbach
- Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Phoebe A. Rice
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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