1
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Carignano M, Kröger M, Almassalha LM, Agrawal V, Li WS, Pujadas-Liwag EM, Nap RJ, Backman V, Szleifer I. Local Volume Concentration, Packing Domains and Scaling Properties of Chromatin. ARXIV 2024:arXiv:2310.02257v2. [PMID: 38495560 PMCID: PMC10942481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions that can capture the observed behavior across imaging and sequencing based measures of chromatin organization. From nucleosome to chromosome scales, the model captures the overall chromatin organization as a corrugated system, with dense and dilute regions alternating in a manner that resembles the mixing of two disordered bi-continuous phases. This particular organizational topology is a consequence of the multiplicity of interactions and processes ocurring in the nuclei, and mimicked by the proposed return rules. Single configuration properties and ensemble averages show a robust agreement between theoretical and experimental results including chromatin volume concentration, contact probability, packing domain identification and size characterization, and packing scaling behavior. Model and experimental results suggest that there is an inherent chromatin organization regardless of the cell character and resistent to external forcings such as Rad21 degradation.
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Affiliation(s)
- Marcelo Carignano
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Martin Kröger
- Magnetism and Interface Physics & Computational Polymer Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Luay Matthew Almassalha
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago IL 60611, USA
| | - Vasundhara Agrawal
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Wing Shun Li
- Applied Physics Program, Northwestern University, Evanston, IL 60208, USA
| | | | - Rikkert J. Nap
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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2
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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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3
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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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4
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Lin X, Zhang B. Explicit ion modeling predicts physicochemical interactions for chromatin organization. eLife 2024; 12:RP90073. [PMID: 38289342 PMCID: PMC10945522 DOI: 10.7554/elife.90073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Molecular mechanisms that dictate chromatin organization in vivo are under active investigation, and the extent to which intrinsic interactions contribute to this process remains debatable. A central quantity for evaluating their contribution is the strength of nucleosome-nucleosome binding, which previous experiments have estimated to range from 2 to 14 kBT. We introduce an explicit ion model to dramatically enhance the accuracy of residue-level coarse-grained modeling approaches across a wide range of ionic concentrations. This model allows for de novo predictions of chromatin organization and remains computationally efficient, enabling large-scale conformational sampling for free energy calculations. It reproduces the energetics of protein-DNA binding and unwinding of single nucleosomal DNA, and resolves the differential impact of mono- and divalent ions on chromatin conformations. Moreover, we showed that the model can reconcile various experiments on quantifying nucleosomal interactions, providing an explanation for the large discrepancy between existing estimations. We predict the interaction strength at physiological conditions to be 9 kBT, a value that is nonetheless sensitive to DNA linker length and the presence of linker histones. Our study strongly supports the contribution of physicochemical interactions to the phase behavior of chromatin aggregates and chromatin organization inside the nucleus.
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Affiliation(s)
- Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
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5
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Li X, Chou T. Stochastic nucleosome disassembly mediated by remodelers and histone fragmentation. J Chem Phys 2023; 159:204107. [PMID: 38010331 PMCID: PMC10684310 DOI: 10.1063/5.0165136] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/14/2023] [Indexed: 11/29/2023] Open
Abstract
We construct and analyze monomeric and multimeric models of the stochastic disassembly of a single nucleosome. Our monomeric model predicts the time needed for a number of histone-DNA contacts to spontaneously break, leading to dissociation of a non-fragmented histone from DNA. The dissociation process can be facilitated by DNA binding proteins or processing molecular motors that compete with histones for histone-DNA contact sites. Eigenvalue analysis of the corresponding master equation allows us to evaluate histone detachment times under both spontaneous detachment and protein-facilitated processes. We find that competitive DNA binding of remodeling proteins can significantly reduce the typical detachment time but only if these remodelers have DNA-binding affinities comparable to those of histone-DNA contact sites. In the presence of processive motors, the histone detachment rate is shown to be proportional to the product of the histone single-bond dissociation constant and the speed of motor protein procession. Our simple intact-histone model is then extended to allow for multimeric nucleosome kinetics that reveal additional pathways of disassembly. In addition to a dependence of complete disassembly times on subunit-DNA contact energies, we show how histone subunit concentrations in bulk solutions can mediate the disassembly process by rescuing partially disassembled nucleosomes. Moreover, our kinetic model predicts that remodeler binding can also bias certain pathways of nucleosome disassembly, with higher remodeler binding rates favoring intact-histone detachment.
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Affiliation(s)
- Xiangting Li
- Department of Computational Medicine, University of California, Los Angeles, California 90095-1766, USA
| | - Tom Chou
- Author to whom correspondence should be addressed:
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6
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Carignano M, Kröger M, Almassalha L, Agrawal V, Li WS, Pujadas EM, Nap RJ, Backman V, Szleifer I. Local Volume Concentration, Packing Domains and Scaling Properties of Chromatin. RESEARCH SQUARE 2023:rs.3.rs-3399177. [PMID: 37886531 PMCID: PMC10602155 DOI: 10.21203/rs.3.rs-3399177/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions that is able to capture the observed behavior across imaging and sequencing based measures of chromatin organization. The SR-EV model takes the return rules of the Self Returning Random Walk, incorporates excluded volume interactions, chain connectivity and expands the length scales range from 10 nm to over 1 micron. The model is computationally fast and we created thousands of configurations that we grouped in twelve different ensembles according to the two main parameters of the model. The analysis of the configurations was done in a way completely analogous to the experimental treatments used to determine chromatin volume concentration, contact probability, packing domain identification and size characterization, and packing scaling behavior. We find a robust agreement between the theoretical and experimental results. The overall organization of the model chromatin is corrugated, with dense packing domains alternating with a very dilute regions in a manner that resembles the mixing of two disordered bi-continuous phases. The return rules combined with excluded volume interactions lead to the formation of packing domains. We observed a transition from a short scale regime to a long scale regime occurring at genomic separations of ~ 4 × 104 base pairs or ~ 100 nm in distance. The contact probability reflects this transition with a change in the scaling exponent from larger than -1 to approximately -1. The analysis of the pair correlation function reveals that chromatin organizes following a power law scaling with exponent D ∈ { 2 , 3 } in the transition region between the short and long distance regimes.
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Affiliation(s)
- Marcelo Carignano
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- These authors contributed equally: Marcelo Carignano. Martin Kröger and Luay Almassalha
| | - Martin Kröger
- Magnetism and Interface Physics & Computational Polymer Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
- These authors contributed equally: Marcelo Carignano. Martin Kröger and Luay Almassalha
| | - Luay Almassalha
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago IL 60611, USA
- These authors contributed equally: Marcelo Carignano. Martin Kröger and Luay Almassalha
| | - Vasundhara Agrawal
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Wing Shun Li
- Applied Physics Program, Northwestern University, Evanston, IL 60208, USA
| | - Emily M. Pujadas
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Rikkert J. Nap
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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7
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Li X, Chou T. Stochastic nucleosome disassembly mediated by remodelers and histone fragmentation. ARXIV 2023:arXiv:2309.02736v1. [PMID: 37731652 PMCID: PMC10508821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
We construct and analyze monomeric and multimeric models of the stochastic disassembly of a single nucleosome. Our monomeric model predicts the time needed for a number of histone-DNA contacts to spontaneously break, leading to dissociation of a non-fragmented histone from DNA. The dissociation process can be facilitated by DNA binding proteins or processing molecular motors that compete with histones for histone-DNA contact sites. Eigenvalue analysis of the corresponding master equation allows us to evaluate histone detachment times under both spontaneous detachment and protein-facilitated processes. We find that competitive DNA binding of remodeling proteins can significantly reduce the typical detachment time but only if these remodelers have DNA-binding affinities comparable to those of histone-DNA contact sites. In the presence of processive motors, the histone detachment rate is shown to be proportional to the product of the histone single-bond dissociation constant and the speed of motor protein procession. Our simple intact-histone model is then extended to allow for multimeric nucleosome kinetics that reveal additional pathways of disassembly. In addition to a dependence of complete disassembly times on subunit-DNA contact energies, we show how histone subunit concentrations in bulk solution can mediate the disassembly process by rescuing partially disassembled nucleosomes. Moreover, our kinetic model predicts that remodeler binding can also bias certain pathways of nucleosome disassembly, with higher remodeler binding rates favoring intact-histone detachment.
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Affiliation(s)
- Xiangting Li
- Department of Computational Medicine, University of California, Los Angeles, CA 90095-1766 USA
| | - Tom Chou
- Department of Computational Medicine, University of California, Los Angeles, CA 90095-1766 USA
- Department of Mathematics, University of California, Los Angeles, CA 90095-1555 USA
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8
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Liu S, Wang C, Latham AP, Ding X, Zhang B. OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates. PLoS Comput Biol 2023; 19:e1011442. [PMID: 37695778 PMCID: PMC10513381 DOI: 10.1371/journal.pcbi.1011442] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/21/2023] [Accepted: 08/19/2023] [Indexed: 09/13/2023] Open
Abstract
Biomolecular condensates are important structures in various cellular processes but are challenging to study using traditional experimental techniques. In silico simulations with residue-level coarse-grained models strike a balance between computational efficiency and chemical accuracy. They could offer valuable insights by connecting the emergent properties of these complex systems with molecular sequences. However, existing coarse-grained models often lack easy-to-follow tutorials and are implemented in software that is not optimal for condensate simulations. To address these issues, we introduce OpenABC, a software package that greatly simplifies the setup and execution of coarse-grained condensate simulations with multiple force fields using Python scripting. OpenABC seamlessly integrates with the OpenMM molecular dynamics engine, enabling efficient simulations with performance on a single GPU that rivals the speed achieved by hundreds of CPUs. We also provide tools that convert coarse-grained configurations to all-atom structures for atomistic simulations. We anticipate that OpenABC will significantly facilitate the adoption of in silico simulations by a broader community to investigate the structural and dynamical properties of condensates.
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Affiliation(s)
- Shuming Liu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Cong Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Andrew P. Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Xinqiang Ding
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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9
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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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10
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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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11
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Liu S, Wang C, Latham A, Ding X, Zhang B. OpenABC Enables Flexible, Simplified, and Efficient GPU Accelerated Simulations of Biomolecular Condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537533. [PMID: 37131742 PMCID: PMC10153273 DOI: 10.1101/2023.04.19.537533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Biomolecular condensates are important structures in various cellular processes but are challenging to study using traditional experimental techniques. In silico simulations with residue-level coarse-grained models strike a balance between computational efficiency and chemical accuracy. They could offer valuable insights by connecting the emergent properties of these complex systems with molecular sequences. However, existing coarse-grained models often lack easy-to-follow tutorials and are implemented in software that is not optimal for condensate simulations. To address these issues, we introduce OpenABC, a software package that greatly simplifies the setup and execution of coarse-grained condensate simulations with multiple force fields using Python scripting. OpenABC seamlessly integrates with the OpenMM molecular dynamics engine, enabling efficient simulations with performances on a single GPU that rival the speed achieved by hundreds of CPUs. We also provide tools that convert coarse-grained configurations to all-atom structures for atomistic simulations. We anticipate that Open-ABC will significantly facilitate the adoption of in silico simulations by a broader community to investigate the structural and dynamical properties of condensates. Open-ABC is available at https://github.com/ZhangGroup-MITChemistry/OpenABC.
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Affiliation(s)
- Shuming Liu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cong Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Xinqiang Ding
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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12
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Shi D, Huang Y, Bai C. Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases. Polymers (Basel) 2023; 15:polym15071763. [PMID: 37050377 PMCID: PMC10096840 DOI: 10.3390/polym15071763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
The nucleosome, which organizes the long coil of genomic DNA in a highly condensed, polymeric way, is thought to be the basic unit of chromosomal structure. As the most important protein–DNA complex, its structural and dynamic features have been successively revealed in recent years. However, its regulatory mechanism, which is modulated by multiple factors, still requires systemic discussion. This study summarizes the regulatory factors of the nucleosome’s dynamic features from the perspective of histone modification, DNA methylation, and the nucleosome-interacting factors (transcription factors and nucleosome-remodeling proteins and cations) and focuses on the research exploring the molecular mechanism through both computational and experimental approaches. The regulatory factors that affect the dynamic features of nucleosomes are also discussed in detail, such as unwrapping, wrapping, sliding, and stacking. Due to the complexity of the high-order topological structures of nucleosomes and the comprehensive effects of regulatory factors, the research on the functional modulation mechanism of nucleosomes has encountered great challenges. The integration of computational and experimental approaches, the construction of physical modes for nucleosomes, and the application of deep learning techniques will provide promising opportunities for further exploration.
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Affiliation(s)
- Danfeng Shi
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Yuxin Huang
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
- Chenzhu (MoMeD) Biotechnology Co., Ltd., Hangzhou 310005, China
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13
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Lu W, Onuchic JN, Di Pierro M. An associative memory Hamiltonian model for DNA and nucleosomes. PLoS Comput Biol 2023; 19:e1011013. [PMID: 36972316 PMCID: PMC10079229 DOI: 10.1371/journal.pcbi.1011013] [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: 10/15/2022] [Revised: 04/06/2023] [Accepted: 03/08/2023] [Indexed: 03/29/2023] Open
Abstract
A model for DNA and nucleosomes is introduced with the goal of studying chromosomes from a single base level all the way to higher-order chromatin structures. This model, dubbed the Widely Editable Chromatin Model (WEChroM), reproduces the complex mechanics of the double helix including its bending persistence length and twisting persistence length, and their respective temperature dependence. The WEChroM Hamiltonian is composed of chain connectivity, steric interactions, and associative memory terms representing all remaining interactions leading to the structure, dynamics, and mechanical characteristics of the B-DNA. Several applications of this model are discussed to demonstrate its applicability. WEChroM is used to investigate the behavior of circular DNA in the presence of positive and negative supercoiling. We show that it recapitulates the formation of plectonemes and of structural defects that relax mechanical stress. The model spontaneously manifests an asymmetric behavior with respect to positive or negative supercoiling, similar to what was previously observed in experiments. Additionally, we show that the associative memory Hamiltonian is also capable of reproducing the free energy of partial DNA unwrapping from nucleosomes. WEChroM is designed to emulate the continuously variable mechanical properties of the 10nm fiber and, by virtue of its simplicity, is ready to be scaled up to molecular systems large enough to investigate the structural ensembles of genes. WEChroM is implemented in the OpenMM simulation toolkits and is freely available for public use.
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Affiliation(s)
- Weiqi Lu
- Center for Theoretical Biological Physics, & Department of Physics and Astronomy, Rice University, Houston, Texas, United States of America
| | - José N. Onuchic
- Center for Theoretical Biological Physics, & Department of Physics and Astronomy, Rice University, Houston, Texas, United States of America
- Department of Chemistry, & Department of Biosciences, Rice University, Houston, Texas, United States of America
- * E-mail: (JNO); (MDP)
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
- Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts, United States of America
- * E-mail: (JNO); (MDP)
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14
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Interdomain dynamics in human Replication Protein A regulates kinetics and thermodynamics of its binding to ssDNA. PLoS One 2023; 18:e0278396. [PMID: 36656834 PMCID: PMC9851514 DOI: 10.1371/journal.pone.0278396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 11/15/2022] [Indexed: 01/20/2023] Open
Abstract
Human Replication Protein A (hRPA) is a multidomain protein that interacts with ssDNA intermediates to provide the latter much-needed stability during DNA metabolism and maintain genomic integrity. Although the ssDNA organization with hRPA was studied recently through experimental means, characterizing the underlying mechanism at the atomic level remains challenging because of the dynamic domain architecture of hRPA and poorly understood heterogeneity of ssDNA-protein interactions. Here, we used a computational framework, precisely tailored to capture protein-ssDNA interactions, and investigated the binding of hRPA with a 60 nt ssDNA. Two distinct binding mechanisms are realized based on the hRPA domain flexibility. For a rigid domain architecture of hRPA, ssDNA binds sequentially with hRPA domains, resulting in slow association kinetics. The binding pathway involves the formation of stable and distinct intermediate states. On contrary, for a flexible domain architecture of hRPA, ssDNA binds synergistically to the A and B domains followed by the rest of hRPA. The domain dynamics in hRPA alleviates the free energy cost of domain orientation necessary for specific binding with ssDNA, leading to fast association kinetics along a downhill binding free energy landscape. An ensemble of free energetically degenerate intermediate states is encountered that makes it arduous to characterize them structurally. An excellent match between our results with the available experimental observations provides new insights into the rich dynamics of hRPA binding to ssDNA and in general paves the way to investigate intricate details of ssDNA-protein interactions, crucial for cellular functioning.
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15
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Mondal A, Mishra SK, Bhattacherjee A. Nucleosome breathing facilitates cooperative binding of pluripotency factors Sox2 and Oct4 to DNA. Biophys J 2022; 121:4526-4542. [PMID: 36321206 PMCID: PMC9748375 DOI: 10.1016/j.bpj.2022.10.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 09/08/2022] [Accepted: 10/26/2022] [Indexed: 12/15/2022] Open
Abstract
Critical lineage commitment events are staged by multiple transcription factors (TFs) binding to their cognate motifs, often positioned at nucleosome-enriched regions of chromatin. The underlying mechanism remains elusive due to difficulty in disentangling the heterogeneity in chromatin states. Using a novel coarse-grained model and molecular dynamics simulations, here we probe the association of Sox2 and Oct4 proteins that show clustered binding at the entry-exit region of a nucleosome. The model captures the conformational heterogeneity of nucleosome breathing dynamics that features repeated wrap-unwrap transitions of a DNA segment from one end of the nucleosome. During the dynamics, DNA forms bulges that diffuse stochastically and may regulate the target search dynamics of a protein by nonspecifically interacting with it. The overall search kinetics of the TF pair follows a "dissociation-compensated-association" mechanism, where Oct4 binding is facilitated by the association of Sox2. The cooperativity stems from a change in entropy caused by an alteration in the nucleosome dynamics upon TF binding. The binding pattern is consistent with a live-cell single-particle tracking experiment, suggesting the mechanism observed for clustered binding of a TF pair, which is a hallmark of cis-regulatory elements, has broader implications in understanding gene regulation in a complex chromatin environment.
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Affiliation(s)
- Anupam Mondal
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sujeet Kumar Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
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16
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Mondal A, Bhattacherjee A. Understanding protein diffusion on force-induced stretched DNA conformation. Front Mol Biosci 2022; 9:953689. [PMID: 36545509 PMCID: PMC9760818 DOI: 10.3389/fmolb.2022.953689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 11/22/2022] [Indexed: 12/11/2022] Open
Abstract
DNA morphology is subjected to environmental conditions and is closely coupled with its function. For example, DNA experiences stretching forces during several biological processes, including transcription and genome transactions, that significantly alter its conformation from that of B-DNA. Indeed, a well-defined 1.5 times extended conformation of dsDNA, known as Σ-DNA, has been reported in DNA complexes with proteins such as Rad51 and RecA. A striking feature in Σ-DNA is that the nucleobases are partitioned into triplets of three locally stacked bases separated by an empty rise gap of ∼ 5 Å. The functional role of such a DNA base triplet was hypothesized to be coupled with the ease of recognition of DNA bases by DNA-binding proteins (DBPs) and the physical origin of three letters (codon/anti-codon) in the genetic code. However, the underlying mechanism of base-triplet formation and the ease of DNA base-pair recognition by DBPs remain elusive. To investigate, here, we study the diffusion of a protein on a force-induced stretched DNA using coarse-grained molecular dynamics simulations. Upon pulling at the 3' end of DNA by constant forces, DNA exhibits a conformational transition from B-DNA to a ladder-like S-DNA conformation via Σ-DNA intermediate. The resulting stretched DNA conformations exhibit non-uniform base-pair clusters such as doublets, triplets, and quadruplets, of which triplets are energetically more stable than others. We find that protein favors the triplet formation compared to its unbound form while interacting non-specifically along DNA, and the relative population of it governs the ruggedness of the protein-DNA binding energy landscape and enhances the efficiency of DNA base recognition. Furthermore, we analyze the translocation mechanism of a DBP under different force regimes and underscore the significance of triplet formation in regulating the facilitated diffusion of protein on DNA. Our study, thus, provides a plausible framework for understanding the structure-function relationship between triplet formation and base recognition by a DBP and helps to understand gene regulation in complex regulatory processes.
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17
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Abstract
In anaphase, any unresolved DNA entanglements between the segregating sister chromatids can give rise to chromatin bridges. To prevent genome instability, chromatin bridges must be resolved prior to cytokinesis. The SNF2 protein PICH has been proposed to play a direct role in this process through the remodeling of nucleosomes. However, direct evidence of nucleosome remodeling by PICH has remained elusive. Here, we present an in vitro single-molecule assay that mimics chromatin under tension, as is found in anaphase chromatin bridges. Applying a combination of dual-trap optical tweezers and fluorescence imaging of PICH and histones bound to a nucleosome-array construct, we show that PICH is a tension- and ATP-dependent nucleosome remodeler that facilitates nucleosome unwrapping and then subsequently slides remaining histones along the DNA. This work elucidates the role of PICH in chromatin-bridge dissolution, and might provide molecular insights into the mechanisms of related SNF2 proteins.
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18
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Liu S, Lin X, Zhang B. Chromatin fiber breaks into clutches under tension and crowding. Nucleic Acids Res 2022; 50:9738-9747. [PMID: 36029149 PMCID: PMC9508854 DOI: 10.1093/nar/gkac725] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 07/08/2022] [Accepted: 08/12/2022] [Indexed: 11/18/2022] Open
Abstract
The arrangement of nucleosomes inside chromatin is of extensive interest. While in vitro experiments have revealed the formation of 30 nm fibers, most in vivo studies have failed to confirm their presence in cell nuclei. To reconcile the diverging experimental findings, we characterized chromatin organization using a residue-level coarse-grained model. The computed force–extension curve matches well with measurements from single-molecule experiments. Notably, we found that a dodeca-nucleosome in the two-helix zigzag conformation breaks into structures with nucleosome clutches and a mix of trimers and tetramers under tension. Such unfolded configurations can also be stabilized through trans interactions with other chromatin chains. Our study suggests that unfolding from chromatin fibers could contribute to the irregularity of in vivo chromatin configurations. We further revealed that chromatin segments with fibril or clutch structures engaged in distinct binding modes and discussed the implications of these inter-chain interactions for a potential sol–gel phase transition.
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Affiliation(s)
- Shuming Liu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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19
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Huertas J, Woods EJ, Collepardo-Guevara R. Multiscale modelling of chromatin organisation: Resolving nucleosomes at near-atomistic resolution inside genes. Curr Opin Cell Biol 2022; 75:102067. [DOI: 10.1016/j.ceb.2022.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/24/2022] [Accepted: 02/04/2022] [Indexed: 12/15/2022]
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20
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Jones M, Ashwood B, Tokmakoff A, Ferguson AL. Determining Sequence-Dependent DNA Oligonucleotide Hybridization and Dehybridization Mechanisms Using Coarse-Grained Molecular Simulation, Markov State Models, and Infrared Spectroscopy. J Am Chem Soc 2021; 143:17395-17411. [PMID: 34644072 PMCID: PMC8554761 DOI: 10.1021/jacs.1c05219] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 11/29/2022]
Abstract
A robust understanding of the sequence-dependent thermodynamics of DNA hybridization has enabled rapid advances in DNA nanotechnology. A fundamental understanding of the sequence-dependent kinetics and mechanisms of hybridization and dehybridization remains comparatively underdeveloped. In this work, we establish new understanding of the sequence-dependent hybridization/dehybridization kinetics and mechanism within a family of self-complementary pairs of 10-mer DNA oligomers by integrating coarse-grained molecular simulation, machine learning of the slow dynamical modes, data-driven inference of long-time kinetic models, and experimental temperature-jump infrared spectroscopy. For a repetitive ATATATATAT sequence, we resolve a rugged dynamical landscape comprising multiple metastable states, numerous competing hybridization/dehybridization pathways, and a spectrum of dynamical relaxations. Introduction of a G:C pair at the terminus (GATATATATC) or center (ATATGCATAT) of the sequence reduces the ruggedness of the dynamics landscape by eliminating a number of metastable states and reducing the number of competing dynamical pathways. Only by introducing a G:C pair midway between the terminus and the center to maximally disrupt the repetitive nature of the sequence (ATGATATCAT) do we recover a canonical "all-or-nothing" two-state model of hybridization/dehybridization with no intermediate metastable states. Our results establish new understanding of the dynamical richness of sequence-dependent kinetics and mechanisms of DNA hybridization/dehybridization by furnishing quantitative and predictive kinetic models of the dynamical transition network between metastable states, present a molecular basis with which to understand experimental temperature jump data, and furnish foundational design rules by which to rationally engineer the kinetics and pathways of DNA association and dissociation for DNA nanotechnology applications.
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Affiliation(s)
- Michael
S. Jones
- Pritzker
School of Molecular Engineering, The University
of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United
States
| | - Brennan Ashwood
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Andrew L. Ferguson
- Pritzker
School of Molecular Engineering, The University
of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United
States
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21
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Yoshua SB, Watson GD, Howard JAL, Velasco-Berrelleza V, Leake MC, Noy A. Integration host factor bends and bridges DNA in a multiplicity of binding modes with varying specificity. Nucleic Acids Res 2021; 49:8684-8698. [PMID: 34352078 PMCID: PMC8421141 DOI: 10.1093/nar/gkab641] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 07/02/2021] [Accepted: 07/16/2021] [Indexed: 11/29/2022] Open
Abstract
Nucleoid-associated proteins (NAPs) are crucial in organizing prokaryotic DNA and regulating genes. Vital to these activities are complex nucleoprotein structures, however, how these form remains unclear. Integration host factor (IHF) is an Escherichia coli NAP that creates very sharp bends in DNA at sequences relevant to several functions including transcription and recombination, and is also responsible for general DNA compaction when bound non-specifically. We show that IHF–DNA structural multimodality is more elaborate than previously thought, and provide insights into how this drives mechanical switching towards strongly bent DNA. Using single-molecule atomic force microscopy and atomic molecular dynamics simulations we find three binding modes in roughly equal proportions: ‘associated’ (73° of DNA bend), ‘half-wrapped’ (107°) and ‘fully-wrapped’ (147°), only the latter occurring with sequence specificity. We show IHF bridges two DNA double helices through non-specific recognition that gives IHF a stoichiometry greater than one and enables DNA mesh assembly. We observe that IHF-DNA structural multiplicity is driven through non-specific electrostatic interactions that we anticipate to be a general NAP feature for physical organization of chromosomes.
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Affiliation(s)
- Samuel B Yoshua
- Department of Physics, University of York, York YO10 5DD, UK
| | - George D Watson
- Department of Physics, University of York, York YO10 5DD, UK
| | | | | | - Mark C Leake
- Department of Physics, University of York, York YO10 5DD, UK.,Department of Biology, University of York, York YO10 5DD, UK
| | - Agnes Noy
- Department of Physics, University of York, York YO10 5DD, UK
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22
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Brandani GB, Tan C, Takada S. The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study. PLoS Comput Biol 2021; 17:e1009253. [PMID: 34314440 PMCID: PMC8345847 DOI: 10.1371/journal.pcbi.1009253] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 08/06/2021] [Accepted: 07/06/2021] [Indexed: 11/23/2022] Open
Abstract
The organization of nucleosomes along the Eukaryotic genome is maintained over time despite disruptive events such as replication. During this complex process, histones and DNA can form a variety of non-canonical nucleosome conformations, but their precise molecular details and roles during nucleosome assembly remain unclear. In this study, employing coarse-grained molecular dynamics simulations and Markov state modeling, we characterized the complete kinetics of nucleosome assembly. On the nucleosome-positioning 601 DNA sequence, we observe a rich transition network among various canonical and non-canonical tetrasome, hexasome, and nucleosome conformations. A low salt environment makes nucleosomes stable, but the kinetic landscape becomes more rugged, so that the system is more likely to be trapped in off-pathway partially assembled intermediates. Finally, we find that the co-operativity between DNA bending and histone association enables positioning sequence motifs to direct the assembly process, with potential implications for the dynamic organization of nucleosomes on real genomic sequences. Nucleosomes are biomolecular complexes formed by DNA wrapped around histone proteins. They represent the basic units of Eukaryotic chromosomes, compacting the genome so that it fits into the small nucleus, and regulating important biological processes such as gene expression. Nucleosomes are disassembled during disruptive events such as DNA replication, and re-assembled afterwards to preserve the correct organization of chromatin. However, the molecular details of nucleosome assembly are still not well understood. In particular, experiments found that histones and DNA may associate into a variety of non-canonical complexes, but their precise conformation and role during assembly remain unclear. In this study, we addressed these problems by performing extensive molecular dynamics simulations of nucleosomes undergoing assembly and disassembly. The simulations reveal many insights into the kinetics of assembly, the structure of non-canonical nucleosome intermediates, and the influence of salt concentration and DNA sequence on the assembly process.
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Affiliation(s)
- Giovanni B. Brandani
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
- * E-mail: (GBB); (ST)
| | - Cheng Tan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
- * E-mail: (GBB); (ST)
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23
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Lin X, Leicher R, Liu S, Zhang B. Cooperative DNA looping by PRC2 complexes. Nucleic Acids Res 2021; 49:6238-6248. [PMID: 34057467 PMCID: PMC8216278 DOI: 10.1093/nar/gkab441] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 04/25/2021] [Accepted: 05/07/2021] [Indexed: 01/14/2023] Open
Abstract
Polycomb repressive complex 2 (PRC2) is an essential protein complex that silences gene expression via post-translational modifications of chromatin. This paper combined homology modeling, atomistic and coarse-grained molecular dynamics simulations, and single-molecule force spectroscopy experiments to characterize both its full-length structure and PRC2-DNA interactions. Using free energy calculations with a newly parameterized protein-DNA force field, we studied a total of three potential PRC2 conformations and their impact on DNA binding and bending. Consistent with cryo-EM studies, we found that EZH2, a core subunit of PRC2, provides the primary interface for DNA binding, and its curved surface can induce DNA bending. Our simulations also predicted the C2 domain of the SUZ12 subunit to contact DNA. Multiple PRC2 complexes bind with DNA cooperatively via allosteric communication through the DNA, leading to a hairpin-like looped configuration. Single-molecule experiments support PRC2-mediated DNA looping and the role of AEBP2 in regulating such loop formation. The impact of AEBP2 can be partly understood from its association with the C2 domain, blocking C2 from DNA binding. Our study suggests that accessory proteins may regulate the genomic location of PRC2 by interfering with its DNA interactions.
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Affiliation(s)
- Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rachel Leicher
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY 10065, USA.,Tri-Institutional PhD Program in Chemical Biology, New York, NY 10065, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY 10065, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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24
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Lin X, Qi Y, Latham AP, Zhang B. Multiscale modeling of genome organization with maximum entropy optimization. J Chem Phys 2021; 155:010901. [PMID: 34241389 PMCID: PMC8253599 DOI: 10.1063/5.0044150] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022] Open
Abstract
Three-dimensional (3D) organization of the human genome plays an essential role in all DNA-templated processes, including gene transcription, gene regulation, and DNA replication. Computational modeling can be an effective way of building high-resolution genome structures and improving our understanding of these molecular processes. However, it faces significant challenges as the human genome consists of over 6 × 109 base pairs, a system size that exceeds the capacity of traditional modeling approaches. In this perspective, we review the progress that has been made in modeling the human genome. Coarse-grained models parameterized to reproduce experimental data via the maximum entropy optimization algorithm serve as effective means to study genome organization at various length scales. They have provided insight into the principles of whole-genome organization and enabled de novo predictions of chromosome structures from epigenetic modifications. Applications of these models at a near-atomistic resolution further revealed physicochemical interactions that drive the phase separation of disordered proteins and dictate chromatin stability in situ. We conclude with an outlook on the opportunities and challenges in studying chromosome dynamics.
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Affiliation(s)
- Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Yifeng Qi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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25
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Reddy G, Thirumalai D. Asymmetry in histone rotation in forced unwrapping and force quench rewrapping in a nucleosome. Nucleic Acids Res 2021; 49:4907-4918. [PMID: 33877361 PMCID: PMC8136794 DOI: 10.1093/nar/gkab263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/25/2021] [Accepted: 03/30/2021] [Indexed: 01/07/2023] Open
Abstract
Single molecule pulling experiments have shown that DNA in the nucleosomes unwraps in two stages from the histone protein core (HPC). The first stage, attributed to the rupture of the outer DNA turn, occurs between 3 and 5 pNs, and is reversible. The inner DNA turn ruptures irreversibly at forces between 9 and 15 pNs (or higher) in the second stage. Molecular simulations using the Self-Organized Polymer model capture the experimental findings. The unwrapping of the outer DNA turn is independent of the pulling direction. The rupture of the DNA inner turn depends on the pulling direction and involves overcoming substantial energetic (most likely electrostatic in origin) and kinetic barriers. They arise because the mechanical force has to generate sufficient torque to rotate the HPC by 180°. On the other hand, during the rewrapping process, HPC rotation is stochastic, with force playing no role. The assembly of the outer DNA wrap upon force quench nearly coincides with the unwrapping process, confirming the reversibility of the outer turn rupture. The asymmetry in HPC rotation during unwrapping and rewrapping explains the observed hysteresis in the stretch-release cycles in experiments. We propose experiments to test the prediction that HPC rotation produces kinetic barriers in the unwrapping process.
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Affiliation(s)
- Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - D Thirumalai
- Department of Chemistry, The University of Texas, Austin, TX 78712, USA
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26
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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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27
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Surprising Twists in Nucleosomal DNA with Implication for Higher-order Folding. J Mol Biol 2021; 433:167121. [PMID: 34192585 DOI: 10.1016/j.jmb.2021.167121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 11/21/2022]
Abstract
While nucleosomes are dynamic entities that must undergo structural deformations to perform their functions, the general view from available high-resolution structures is a largely static one. Even though numerous examples of twist defects have been documented, the DNA wrapped around the histone core is generally thought to be overtwisted. Analysis of available high-resolution structures from the Protein Data Bank reveals a heterogeneous distribution of twist along the nucleosomal DNA, with clear patterns that are consistent with the literature, and a significant fraction of structures that are undertwisted. The subtle differences in nucleosomal DNA folding, which extend beyond twist, have implications for nucleosome disassembly and modeled higher-order structures. Simulations of oligonucleosome arrays built with undertwisted models behave very differently from those constructed from overtwisted models, in terms of compaction and inter-nucleosome contacts, introducing configurational changes equivalent to those associated with 2-3 base-pair changes in nucleosome spacing. Differences in the nucleosomal DNA pathway, which underlie the way that DNA enters and exits the nucleosome, give rise to different nucleosome-decorated minicircles and affect the topological mix of configurational states.
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28
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Alvarado W, Moller J, Ferguson AL, de Pablo JJ. Tetranucleosome Interactions Drive Chromatin Folding. ACS CENTRAL SCIENCE 2021; 7:1019-1027. [PMID: 34235262 PMCID: PMC8227587 DOI: 10.1021/acscentsci.1c00085] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Indexed: 06/10/2023]
Abstract
The multiscale organizational structure of chromatin in eukaryotic cells is instrumental to DNA transcription, replication, and repair. At mesoscopic length scales, nucleosomes pack in a manner that serves to regulate gene expression through condensation and expansion of the genome. The particular structures that arise and their respective thermodynamic stabilities, however, have yet to be fully resolved. In this study, we combine molecular modeling using the 1CPN mesoscale model of chromatin with nonlinear manifold learning to identify and characterize the structure and free energy of metastable states of short chromatin segments comprising between 4- and 16-nucleosomes. Our results reveal the formation of two previously characterized tetranucleosomal conformations, the "α-tetrahedron" and the "β-rhombus", which have been suggested to play an important role in the accessibility of DNA and, respectively, induce local chromatin compaction or elongation. The spontaneous formation of these motifs is potentially responsible for the slow nucleosome dynamics observed in experimental studies. Increases of the nucleosome repeat length are accompanied by more pronounced structural irregularity and flexibility and, ultimately, a dynamic liquid-like behavior that allows for frequent structural reorganization. Our findings indicate that tetranucleosome motifs are intrinsically stable structural states, driven by local internucleosomal interactions, and support a mechanistic picture of chromatin packing, dynamics, and accessibility that is strongly influenced by emergent local mesoscale structure.
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Affiliation(s)
- Walter Alvarado
- Biophysical
Sciences, University of Chicago, Chicago, Illinois 60637 United States
| | - Joshua Moller
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637 United States
| | - Andrew L. Ferguson
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637 United States
| | - Juan J. de Pablo
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637 United States
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29
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Farr SE, Woods EJ, Joseph JA, Garaizar A, Collepardo-Guevara R. Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions. Nat Commun 2021; 12:2883. [PMID: 34001913 PMCID: PMC8129070 DOI: 10.1038/s41467-021-23090-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/23/2021] [Indexed: 12/19/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) is an important mechanism that helps explain the membraneless compartmentalization of the nucleus. Because chromatin compaction and LLPS are collective phenomena, linking their modulation to the physicochemical features of nucleosomes is challenging. Here, we develop an advanced multiscale chromatin model-integrating atomistic representations, a chemically-specific coarse-grained model, and a minimal model-to resolve individual nucleosomes within sub-Mb chromatin domains and phase-separated systems. To overcome the difficulty of sampling chromatin at high resolution, we devise a transferable enhanced-sampling Debye-length replica-exchange molecular dynamics approach. We find that nucleosome thermal fluctuations become significant at physiological salt concentrations and destabilize the 30-nm fiber. Our simulations show that nucleosome breathing favors stochastic folding of chromatin and promotes LLPS by simultaneously boosting the transient nature and heterogeneity of nucleosome-nucleosome contacts, and the effective nucleosome valency. Our work puts forward the intrinsic plasticity of nucleosomes as a key element in the liquid-like behavior of nucleosomes within chromatin, and the regulation of chromatin LLPS.
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Affiliation(s)
- Stephen E Farr
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Esmae J Woods
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Jerelle A Joseph
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Adiran Garaizar
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
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30
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Sun T, Minhas V, Korolev N, Mirzoev A, Lyubartsev AP, Nordenskiöld L. Bottom-Up Coarse-Grained Modeling of DNA. Front Mol Biosci 2021; 8:645527. [PMID: 33816559 PMCID: PMC8010198 DOI: 10.3389/fmolb.2021.645527] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/22/2021] [Indexed: 12/22/2022] Open
Abstract
Recent advances in methodology enable effective coarse-grained modeling of deoxyribonucleic acid (DNA) based on underlying atomistic force field simulations. The so-called bottom-up coarse-graining practice separates fast and slow dynamic processes in molecular systems by averaging out fast degrees of freedom represented by the underlying fine-grained model. The resulting effective potential of interaction includes the contribution from fast degrees of freedom effectively in the form of potential of mean force. The pair-wise additive potential is usually adopted to construct the coarse-grained Hamiltonian for its efficiency in a computer simulation. In this review, we present a few well-developed bottom-up coarse-graining methods, discussing their application in modeling DNA properties such as DNA flexibility (persistence length), conformation, "melting," and DNA condensation.
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Affiliation(s)
- Tiedong Sun
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Vishal Minhas
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Alexander Mirzoev
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Alexander P. Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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31
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Ding X, Lin X, Zhang B. Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface. Nat Commun 2021; 12:1091. [PMID: 33597548 PMCID: PMC7889939 DOI: 10.1038/s41467-021-21377-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 01/22/2021] [Indexed: 01/01/2023] Open
Abstract
The three-dimensional organization of chromatin is expected to play critical roles in regulating genome functions. High-resolution characterization of its structure and dynamics could improve our understanding of gene regulation mechanisms but has remained challenging. Using a near-atomistic model that preserves the chemical specificity of protein-DNA interactions at residue and base-pair resolution, we studied the stability and folding pathways of a tetra-nucleosome. Dynamical simulations performed with an advanced sampling technique uncovered multiple pathways that connect open chromatin configurations with the zigzag crystal structure. Intermediate states along the simulated folding pathways resemble chromatin configurations reported from in situ experiments. We further determined a six-dimensional free energy surface as a function of the inter-nucleosome distances via a deep learning approach. The zigzag structure can indeed be seen as the global minimum of the surface. However, it is not favored by a significant amount relative to the partially unfolded, in situ configurations. Chemical perturbations such as histone H4 tail acetylation and thermal fluctuations can further tilt the energetic balance to stabilize intermediate states. Our study provides insight into the connection between various reported chromatin configurations and has implications on the in situ relevance of the 30 nm fiber. The three-dimensional organization of chromatin plays critical roles in regulating genome function. Here the authors apply a near atomistic model to study the structure and dynamics of the chromatin folding unit - the tetra-nucleosome - to provide insight into how chromatin folds.
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Affiliation(s)
- Xinqiang Ding
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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32
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Kenzaki H, Takada S. Linker DNA Length is a Key to Tri-nucleosome Folding. J Mol Biol 2020; 433:166792. [PMID: 33383034 DOI: 10.1016/j.jmb.2020.166792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/07/2020] [Accepted: 12/22/2020] [Indexed: 01/18/2023]
Abstract
The folding of a nucleosome array has long been one of the fundamental and unsolved problems in chromatin biology. In this study, we address how nucleosome array folding depends on the length of linker DNA. We performed molecular dynamics simulations of a tri-nucleosome, a minimal model of chromatin folding, with various linker lengths (LLs) ranging from 20 to 40 base pairs (bps). We found that the tri-nucleosome folding strongly depends on LLs, and classified the structure ensemble into five classes, named from trinuc-1 to trinuc-5. As a function of LL, the different classes appear, on average, every 2 bps with a period of 10 bps, and are characterized by distinct inter-nucleosome interactions. The trinuc-1 conformation corresponds to LL ~ 10n, where n is an integer, and is stabilized by the tight packing between the first and the third nucleosomes, consistent with a zigzag fiber form. Structures of the other four classes are more diverse and distributed continuously in the space of possible configurations. Histone-DNA electrostatic interactions in the tri-nucleosome are further analyzed.
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Affiliation(s)
- Hiroo Kenzaki
- Information Systems Division, Head Office for Information Systems and Cybersecurity, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo, Kyoto 606-8502, Japan.
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33
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Leicher R, Ge EJ, Lin X, Reynolds MJ, Xie W, Walz T, Zhang B, Muir TW, Liu S. Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin. Proc Natl Acad Sci U S A 2020; 117:30465-30475. [PMID: 33208532 PMCID: PMC7720148 DOI: 10.1073/pnas.2003395117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) installs and spreads repressive histone methylation marks on eukaryotic chromosomes. Because of the key roles that PRC2 plays in development and disease, how this epigenetic machinery interacts with DNA and nucleosomes is of major interest. Nonetheless, the mechanism by which PRC2 engages with native-like chromatin remains incompletely understood. In this work, we employ single-molecule force spectroscopy and molecular dynamics simulations to dissect the behavior of PRC2 on polynucleosome arrays. Our results reveal an unexpectedly diverse repertoire of PRC2 binding configurations on chromatin. Besides reproducing known binding modes in which PRC2 interacts with bare DNA, mononucleosomes, and adjacent nucleosome pairs, our data also provide direct evidence that PRC2 can bridge pairs of distal nucleosomes. In particular, the "1-3" bridging mode, in which PRC2 engages two nucleosomes separated by one spacer nucleosome, is a preferred low-energy configuration. Moreover, we show that the distribution and stability of different PRC2-chromatin interaction modes are modulated by accessory subunits, oncogenic histone mutations, and the methylation state of chromatin. Overall, these findings have implications for the mechanism by which PRC2 spreads histone modifications and compacts chromatin. The experimental and computational platforms developed here provide a framework for understanding the molecular basis of epigenetic maintenance mediated by Polycomb-group proteins.
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Affiliation(s)
- Rachel Leicher
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY 10065
- Tri-Institutional PhD Program in Chemical Biology, New York, NY 10065
| | - Eva J Ge
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Matthew J Reynolds
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY 10065
| | - Wenjun Xie
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY 10065
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139;
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY 10065;
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34
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Mondal A, Bhattacherjee A. Mechanism of Dynamic Binding of Replication Protein A to ssDNA. J Chem Inf Model 2020; 60:5057-5069. [PMID: 32990435 DOI: 10.1021/acs.jcim.0c00564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Replication protein A (RPA) serves as a hub protein inside eukaryotic cells, where it coordinates crucial DNA metabolic processes and activates the DNA-damage response system. A characteristic feature of its action is to associate with single-stranded DNA (ssDNA) intermediates before handing them over to downstream proteins. The length of ssDNA intermediates differs for different pathways. This means that RPA must have mechanisms for selective processing of ssDNA intermediates based on their length, the knowledge of which is fundamental to elucidate when and how DNA repair and replication processes are symphonized. By employing extensive molecular dynamics simulations, we investigated the mechanism of binding of RPA to ssDNA of different lengths. We show that the binding involves dynamic equilibrium with a stable intermediate, the population of which increases with the length of ssDNA. The vital underlying factors are decoded through collective variable principal component analysis. It suggests a differently orchestrated set of interactions that define the action of RPA based on the length of ssDNA intermediates. We further estimated the association kinetics that matches excellently well with previous experimental studies and probed the diffusion mechanism of RPA to ssDNA. RPA diffuses on short ssDNA through progressive "bulge" formation. With long ssDNA, we observed a conformational change in ssDNA coupled with its binding to RPA in a cooperative fashion. This unanticipated binding mechanism successfully explains how the "short-lived", long ssDNA intermediates are processed quickly in vivo. This study thus reveals the molecular basis of several recent experimental observations related to RPA binding to ssDNA and provides novel insights into the RPA functioning in DNA repair and replication.
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Affiliation(s)
- Anupam Mondal
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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35
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Kono H, Ishida H. Nucleosome unwrapping and unstacking. Curr Opin Struct Biol 2020; 64:119-125. [DOI: 10.1016/j.sbi.2020.06.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 05/31/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023]
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36
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Moller J, de Pablo JJ. Bottom-Up Meets Top-Down: The Crossroads of Multiscale Chromatin Modeling. Biophys J 2020; 118:2057-2065. [PMID: 32320675 DOI: 10.1016/j.bpj.2020.03.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/04/2020] [Accepted: 03/20/2020] [Indexed: 01/19/2023] Open
Abstract
Chromatin can be viewed as a hierarchically structured fiber that regulates gene expression. It consists of a complex network of DNA and proteins whose characteristic dynamical modes facilitate compaction and rearrangement in the cell nucleus. These modes stem from chromatin's fundamental unit, the nucleosome, and their effects are propagated across length scales. Understanding the effects of nucleosome dynamics on the chromatin fiber, primarily through post-translational modifications that occur on the histones, is of central importance to epigenetics. Within the last decade, imaging and chromosome conformation capture techniques have revealed a number of structural and statistical features of the packaged chromatin fiber at a hitherto unavailable level of resolution. Such experiments have led to increased efforts to develop polymer models that aim to reproduce, explain, and predict the contact probability scaling and density heterogeneity. At nanometer scales, available models have focused on the role of the nucleosome and epigenetic marks on local chromatin structure. At micrometer scales, existing models have sought to explain scaling laws and density heterogeneity. Less work, however, has been done to reconcile these two approaches: bottom-up and top-down models of chromatin. In this perspective, we highlight the multiscale simulation models that are driving toward an understanding of chromatin structure and function, from the nanometer to the micron scale, and we highlight areas of opportunity and some of the prospects for new frameworks that bridge these two scales. Taken together, experimental and modeling advances over the last few years have established a robust platform for the study of chromatin fiber structure and dynamics, which will be of considerable use to the chromatin community in developing an understanding of the interplay between epigenomic regulation and molecular structure.
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Affiliation(s)
- Joshua Moller
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Juan J de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois; Material Science Division, Argonne National Laboratory, Lemont, Illinois.
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37
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Spakowitz AJ. Polymer physics across scales: Modeling the multiscale behavior of functional soft materials and biological systems. J Chem Phys 2019; 151:230902. [DOI: 10.1063/1.5126852] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Andrew J. Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
- Biophysics Program, Stanford University, Stanford, California 94305, USA
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38
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Ensembles of Breathing Nucleosomes: A Computational Study. Biophys J 2019; 118:2297-2308. [PMID: 31882248 DOI: 10.1016/j.bpj.2019.11.3395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/15/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
About three-fourths of the human DNA molecules are wrapped into nucleosomes, protein spools with DNA. Nucleosomes are highly dynamic, transiently exposing their DNA through spontaneous unspooling. Recent experiments allowed to observe the DNA of an ensemble of such breathing nucleosomes through x-ray diffraction with contrast matching between the solvent and the protein core. In this study, we calculate such an ensemble through a Monte Carlo simulation of a coarse-grained nucleosome model with sequence-dependent DNA mechanics. Our analysis gives detailed insights into the sequence dependence of nucleosome breathing observed in the experiment and allows us to determine the adsorption energy of the DNA bound to the protein core as a function of the ionic strength. Moreover, we predict the breathing behavior of other potentially interesting sequences and compare the findings to earlier related experiments.
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39
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Dey P, Bhattacherjee A. Mechanism of Facilitated Diffusion of DNA Repair Proteins in Crowded Environment: Case Study with Human Uracil DNA Glycosylase. J Phys Chem B 2019; 123:10354-10364. [DOI: 10.1021/acs.jpcb.9b07342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Pinki Dey
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India 110067
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India 110067
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40
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Lequieu J, Córdoba A, Moller J, de Pablo JJ. 1CPN: A coarse-grained multi-scale model of chromatin. J Chem Phys 2019; 150:215102. [PMID: 31176328 DOI: 10.1063/1.5092976] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A central question in epigenetics is how histone modifications influence the 3D structure of eukaryotic genomes and, ultimately, how this 3D structure is manifested in gene expression. The wide range of length scales that influence the 3D genome structure presents important challenges; epigenetic modifications to histones occur on scales of angstroms, yet the resulting effects of these modifications on genome structure can span micrometers. There is a scarcity of computational tools capable of providing a mechanistic picture of how molecular information from individual histones is propagated up to large regions of the genome. In this work, a new molecular model of chromatin is presented that provides such a picture. This new model, referred to as 1CPN, is structured around a rigorous multiscale approach, whereby free energies from an established and extensively validated model of the nucleosome are mapped onto a reduced coarse-grained topology. As such, 1CPN incorporates detailed physics from the nucleosome, such as histone modifications and DNA sequence, while maintaining the computational efficiency that is required to permit kilobase-scale simulations of genomic DNA. The 1CPN model reproduces the free energies and dynamics of both single nucleosomes and short chromatin fibers, and it is shown to be compatible with recently developed models of the linker histone. It is applied here to examine the effects of the linker DNA on the free energies of chromatin assembly and to demonstrate that these free energies are strongly dependent on the linker DNA length, pitch, and even DNA sequence. The 1CPN model is implemented in the LAMMPS simulation package and is distributed freely for public use.
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Affiliation(s)
- Joshua Lequieu
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Andrés Córdoba
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Joshua Moller
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Juan J de Pablo
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
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41
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Parsons T, Zhang B. Critical role of histone tail entropy in nucleosome unwinding. J Chem Phys 2019; 150:185103. [PMID: 31091895 DOI: 10.1063/1.5085663] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The nucleosome is the fundamental packaging unit for the genome. It must remain tightly wound to ensure genome stability while simultaneously being flexible enough to keep the DNA molecule accessible for genome function. The set of physicochemical interactions responsible for the delicate balance between these naturally opposed processes have not been determined due to challenges in resolving partially unwound nucleosome configurations at atomic resolution. Using a near atomistic protein-DNA model and advanced sampling techniques, we calculate the free energy cost of nucleosome DNA unwinding. Our simulations identify a large energetic barrier that decouples the outer and the inner DNA unwinding into two separate processes, occurring on different time scales. This dynamical decoupling allows the exposure of outer DNA at a modest cost to ensure accessibility while keeping the inner DNA and the histone core intact to maintain stability. We also reveal that this energetic barrier arises from a delayed loss of contacts between disordered histone tails and the DNA and is, surprisingly, largely offset by an entropic contribution from these tails. Implications of this enthalpy entropy compensation for the regulation of nucleosome stability and genome function are discussed.
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Affiliation(s)
- Thomas Parsons
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA
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42
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Moller J, Lequieu J, de Pablo JJ. The Free Energy Landscape of Internucleosome Interactions and Its Relation to Chromatin Fiber Structure. ACS CENTRAL SCIENCE 2019; 5:341-348. [PMID: 30834322 PMCID: PMC6396382 DOI: 10.1021/acscentsci.8b00836] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Indexed: 05/11/2023]
Abstract
The supramolecular chromatin fiber is governed by molecular scale energetics and interactions. Such energetics originate from the fiber's building block, the nucleosome core particle (NCP). In recent years, the chromatin fiber has been examined through perturbative methods in attempts to extract the energetics of nucleosome association in the fiber. This body of work has led to different results from experiments and simulations concerning the nucleosome-nucleosome energetics. Here, we expand on previous experiments and use coarse-grained simulations to evaluate the energetics inherent to nucleosomes across a variety of parameters in configurational and environmental space. Through this effort, we are able to uncover molecular processes that are critical to understanding the 30 nm chromatin fiber structure. In particular, we describe the NCP-NCP interactions by relying on an anisotropic energetic landscape, rather than a single potential energy value. The attractions in that landscape arise predominantly from the highly anisotropic interactions provided by the NCP histone N-terminal domain (NTD) tails. Our results are found to be in good agreement with recent nucleosome interaction experiments that suggest a maximum interaction energy of 2.69k B T. Furthermore, we examine the influence of crucial epigenetic modifications, such as acetylation of the H4 tail, and how they modify the underlying landscape. Our results for acetylated NCP interactions are also in agreement with experiment. We additionally find an induced chirality in NCP-NCP interactions upon acetylation that reduces interactions which would correspond to a left-handed superhelical chromatin fiber.
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Affiliation(s)
- Joshua Moller
- Institute
for Molecular Engineering, University of
Chicago, Chicago, Illinois 60637, United States
| | - Joshua Lequieu
- Institute
for Molecular Engineering, University of
Chicago, Chicago, Illinois 60637, United States
- Chemical
Engineering, University of California Santa
Barbara, Santa Barbara, California 93106, United States
| | - Juan J. de Pablo
- Institute
for Molecular Engineering, University of
Chicago, Chicago, Illinois 60637, United States
- Materials
Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
- E-mail for J.J.d.P.:
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43
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Winogradoff D, Aksimentiev A. Molecular Mechanism of Spontaneous Nucleosome Unraveling. J Mol Biol 2019; 431:323-335. [PMID: 30468737 PMCID: PMC6331254 DOI: 10.1016/j.jmb.2018.11.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/26/2018] [Accepted: 11/12/2018] [Indexed: 11/18/2022]
Abstract
Meters of DNA wrap around histone proteins to form nucleosomes and fit inside the micron-diameter nucleus. For the genetic information encoded in the DNA to become available for transcription, replication, and repair, the DNA-histone assembly must be disrupted. Experiment has indicated that the outer stretches of nucleosomal DNA "breathe" by spontaneously detaching from and reattaching to the histone core. Here, we report direct observation of spontaneous DNA breathing in atomistic molecular dynamics simulations, detailing a microscopic mechanism of the DNA breathing process. According to our simulations, the outer stretches of nucleosomal DNA detach in discrete steps involving 5 or 10 base pairs, with the detachment process being orchestrated by the motion of several conserved histone residues. The inner stretches of nucleosomal DNA are found to be more stably associated with the histone core by more abundant nonspecific DNA-protein contacts, providing a microscopic interpretation of nucleosome unraveling experiments. The CG content of nucleosomal DNA is found to anticorrelate with the extent of unwrapping, supporting the possibility that AT-rich segments may signal the start of transcription by forming less stable nucleosomes.
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Affiliation(s)
- David Winogradoff
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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44
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Dynamics of Chromatin Fibers: Comparison of Monte Carlo Simulations with Force Spectroscopy. Biophys J 2018; 115:1644-1655. [PMID: 30236784 PMCID: PMC6225046 DOI: 10.1016/j.bpj.2018.06.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 06/15/2018] [Accepted: 06/19/2018] [Indexed: 12/17/2022] Open
Abstract
To elucidate conformational dynamics of chromatin fibers, we compared available force-spectroscopy measurements with extensive Monte Carlo simulations of nucleosome arrays under external force. Our coarse-grained model of chromatin includes phenomenological energy terms for the DNA-histone adhesion and the internucleosome stacking interactions. We found that the Monte Carlo fiber ensembles simulated with increasing degrees of DNA unwrapping and the stacking energy 8 kT can account for the intricate force-extension response observed experimentally. Our analysis shows that at low external forces (F < 3.0 picoNewtons), the DNA ends in nucleosomes breathe by ∼10 bp. Importantly, under these conditions, the fiber is highly dynamic, exhibiting continuous unstacking-restacking transitions, allowing accessibility of transcription factors to DNA, while maintaining a relatively compact conformation. Of note, changing the stacking interaction by a few kT, an in silico way to mimic histone modifications, is sufficient to transform an open chromatin state into a compact fiber. The fibers are mostly two-start zigzag folds with rare occurrences of three- to five-start morphologies. The internucleosome stacking is lost during the linear response regime. At the higher forces exceeding 4 picoNewtons, the nucleosome unwrapping becomes stochastic and asymmetric, with one DNA arm opened by ∼55 bp and the other arm only by ∼10 bp. Importantly, this asymmetric unwrapping occurs for any kind of sequence, including the symmetric ones. Our analysis brings new, to our knowledge, insights in dynamics of chromatin modulated by histone epigenetic modifications and molecular motors such as RNA polymerase.
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45
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Tan C, Takada S. Dynamic and Structural Modeling of the Specificity in Protein–DNA Interactions Guided by Binding Assay and Structure Data. J Chem Theory Comput 2018; 14:3877-3889. [DOI: 10.1021/acs.jctc.8b00299] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Cheng Tan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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46
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Brandani GB, Niina T, Tan C, Takada S. DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations. Nucleic Acids Res 2018; 46:2788-2801. [PMID: 29506273 PMCID: PMC5887990 DOI: 10.1093/nar/gky158] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/05/2018] [Accepted: 02/20/2018] [Indexed: 11/13/2022] Open
Abstract
While nucleosomes are highly stable structures as fundamental units of chromatin, they also slide along the DNA, either spontaneously or by active remodelers. Here, we investigate the microscopic mechanisms of nucleosome sliding by multiscale molecular simulations, characterizing how the screw-like motion of DNA proceeds via the formation and propagation of twist defects. Firstly, coarse-grained molecular simulations reveal that the sliding dynamics is highly dependent on DNA sequence. Depending on the sequence and the nucleosome super-helical location, we find two distinct types of twist defects: a locally under-twisted DNA region, previously observed in crystal structures, and a locally over-twisted DNA, an unprecedented feature. The stability of the over-twist defect was confirmed via all-atom simulations. Analysis of our trajectories via Markov state modeling highlights how the sequence-dependence of the sliding dynamics is due to the different twist defect energy costs, and in particular how nucleosome regions where defects cannot easily form introduce the kinetic bottlenecks slowing down repositioning. Twist defects can also mediate sliding of nucleosomes made with strong positioning sequences, albeit at a much lower diffusion coefficient, due to a high-energy intermediate state. Finally, we discuss how chromatin remodelers may exploit these spontaneous fluctuations to induce unidirectional sliding of nucleosomes.
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Affiliation(s)
- Giovanni B Brandani
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Toru Niina
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Cheng Tan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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47
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Kono H, Sakuraba S, Ishida H. Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA. PLoS Comput Biol 2018; 14:e1006024. [PMID: 29505570 PMCID: PMC5854429 DOI: 10.1371/journal.pcbi.1006024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 03/15/2018] [Accepted: 02/01/2018] [Indexed: 11/19/2022] Open
Abstract
The eukaryotic genome is packaged into a nucleus in the form of chromatin. The fundamental structural unit of chromatin is a protein-DNA complex, the nucleosome, where 146 or 147 base pairs of DNA wrap 1.75 times around a histone core. To function in cellular processes, however, nucleosomal DNA must be unwrapped. Although this unwrapping has been experimentally investigated, details of the process at an atomic level are not yet well understood. Here, we used molecular dynamics simulation with an enhanced sampling method to calculate the free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA. A free energy change of about 11.5 kcal/mol for the unwrapping agrees well with values obtained in single molecule experiments. This simulation revealed a variety of conformational states, indicating there are many potential paths to outer superhelicdal turn unwrapping, but the dominant path is likely asymmetric. At one end of the DNA, the first five bps unwrap, after which a second five bps unwrap at the same end with no increase in free energy. The unwrapping then starts at the other end of the DNA, where 10 bps are unwrapped. During further unwrapping of 15 bps, the unwrapping advances at one of the ends, after which the other end of the DNA unwraps to complete the unwrapping of the outer superhelical turn. These results provide insight into the construction, disruption, and repositioning of nucleosomes, which are continuously ongoing during cellular processes.
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Affiliation(s)
- Hidetoshi Kono
- Molecular Modeling and Simulation Group, Department of Quantum Beam Life Science, National Institutes for Quantum and Radiological Science and Technology, Umemidai, Kizugawa, Kyoto, Japan
- * E-mail:
| | - Shun Sakuraba
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
| | - Hisashi Ishida
- Molecular Modeling and Simulation Group, Department of Quantum Beam Life Science, National Institutes for Quantum and Radiological Science and Technology, Umemidai, Kizugawa, Kyoto, Japan
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48
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Shimizu M, Takada S. Reconstruction of Atomistic Structures from Coarse-Grained Models for Protein-DNA Complexes. J Chem Theory Comput 2018; 14:1682-1694. [PMID: 29397721 DOI: 10.1021/acs.jctc.7b00954] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While coarse-grained (CG) simulations have widely been used to accelerate structure sampling of large biomolecular complexes, they are unavoidably less accurate and thus the reconstruction of all-atom (AA) structures and the subsequent refinement is desirable. In this study we developed an efficient method to reconstruct AA structures from sampled CG protein-DNA complex models, which attempts to model the protein-DNA interface accurately. First we developed a method to reconstruct atomic details of DNA structures from a three-site per nucleotide CG model, which uses a DNA fragment library. Next, for the protein-DNA interface, we referred to the side chain orientations in the known structure of the target interface when available. The other parts are modeled by existing tools. We confirmed the accuracy of the protocol in various aspects including the structure deviation in the self-reproduction, the base pair reproducibility, atomic contacts at the protein-DNA interface, and feasibility of the posterior AA simulations.
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Affiliation(s)
- Masahiro Shimizu
- Department of Biophysics, Graduate School of Science , Kyoto University , Sakyo, Kyoto 606-8502 Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science , Kyoto University , Sakyo, Kyoto 606-8502 Japan
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49
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Potoyan DA, Bueno C, Zheng W, Komives EA, Wolynes PG. Resolving the NFκB Heterodimer Binding Paradox: Strain and Frustration Guide the Binding of Dimeric Transcription Factors. J Am Chem Soc 2017; 139:18558-18566. [PMID: 29183131 DOI: 10.1021/jacs.7b08741] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many eukaryotic transcription factors function after forming oligomers. The choice of protein partners is a nonrandom event that has distinct functional consequences for gene regulation. In the present work we examine three dimers of transcription factors in the NFκB family: p50p50, p50p65, and p65p65. The NFκB dimers bind to a myriad of genomic sites and switch the targeted genes on or off with precision. The p65p50 heterodimer of NFκB is the strongest DNA binder, and its unbinding is controlled kinetically by molecular stripping from the DNA induced by IκB. In contrast, the homodimeric forms of NFκB, p50p50 and p65p65, bind DNA with significantly less affinity, which places the DNA residence of the homodimers under thermodynamic rather than kinetic control. It seems paradoxical that the heterodimer should bind more strongly than either of the symmetric homodimers since DNA is a nearly symmetric target. Using a variety of energy landscape analysis tools, here we uncover the features in the molecular architecture of NFκB dimers that are responsible for these drastically different binding free energies. We show that frustration in the heterodimer interface gives the heterodimer greater conformational plasticity, allowing the heterodimer to better accommodate the DNA. We also show how the elastic energy and mechanical strain in NFκB dimers can be found by extracting the principal components of the fluctuations in Cartesian coordinates as well as fluctuations in the space of physical contacts, which are sampled via simulations with a predictive energy landscape Hamiltonian. These energetic contributions determine the specific detailed mechanisms of binding and stripping for both homo- and heterodimers.
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Affiliation(s)
- Davit A Potoyan
- Department of Chemistry, Iowa State University , Ames, Iowa 50011, United States.,Department of Chemistry and Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States
| | - Carlos Bueno
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States
| | - Weihua Zheng
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California San Diego , La Jolla, California 92093, United States
| | - Peter G Wolynes
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States
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50
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Lequieu J, Schwartz DC, de Pablo JJ. In silico evidence for sequence-dependent nucleosome sliding. Proc Natl Acad Sci U S A 2017; 114:E9197-E9205. [PMID: 29078285 PMCID: PMC5676884 DOI: 10.1073/pnas.1705685114] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nucleosomes represent the basic building block of chromatin and provide an important mechanism by which cellular processes are controlled. The locations of nucleosomes across the genome are not random but instead depend on both the underlying DNA sequence and the dynamic action of other proteins within the nucleus. These processes are central to cellular function, and the molecular details of the interplay between DNA sequence and nucleosome dynamics remain poorly understood. In this work, we investigate this interplay in detail by relying on a molecular model, which permits development of a comprehensive picture of the underlying free energy surfaces and the corresponding dynamics of nucleosome repositioning. The mechanism of nucleosome repositioning is shown to be strongly linked to DNA sequence and directly related to the binding energy of a given DNA sequence to the histone core. It is also demonstrated that chromatin remodelers can override DNA-sequence preferences by exerting torque, and the histone H4 tail is then identified as a key component by which DNA-sequence, histone modifications, and chromatin remodelers could in fact be coupled.
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Affiliation(s)
- Joshua Lequieu
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637
| | - David C Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706
- UW-Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706
| | - Juan J de Pablo
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637;
- Materials Science Division, Argonne National Laboratory, Argonne, IL 60439
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