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Ginell GM, Emenecker RJ, Lotthammer JM, Usher ET, Holehouse AS. Direct prediction of intermolecular interactions driven by disordered regions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597104. [PMID: 38895487 PMCID: PMC11185574 DOI: 10.1101/2024.06.03.597104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Intrinsically disordered regions (IDRs) are critical for a wide variety of cellular functions, many of which involve interactions with partner proteins. Molecular recognition is typically considered through the lens of sequence-specific binding events. However, a growing body of work has shown that IDRs often interact with partners in a manner that does not depend on the precise order of the amino acid order, instead driven by complementary chemical interactions leading to disordered bound-state complexes. Despite this emerging paradigm, we lack tools to describe, quantify, predict, and interpret these types of structurally heterogeneous interactions from the underlying amino acid sequences. Here, we repurpose the chemical physics developed originally for molecular simulations to develop an approach for predicting intermolecular interactions between IDRs and partner proteins. Our approach enables the direct prediction of phase diagrams, the identification of chemically-specific interaction hotspots on IDRs, and a route to develop and test mechanistic hypotheses regarding IDR function in the context of molecular recognition. We use our approach to examine a range of systems and questions to highlight its versatility and applicability.
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Affiliation(s)
- Garrett M. Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Ryan. J Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Jeffrey M. Lotthammer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Emery T. Usher
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
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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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Zhou J, Wan Y, Cohen Stuart MA, Wang M, Wang J. Effects of Control Factors on Protein-Polyelectrolyte Complex Coacervation. Biomacromolecules 2023; 24:5759-5768. [PMID: 37955264 DOI: 10.1021/acs.biomac.3c00717] [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: 11/14/2023]
Abstract
Protein-polyelectrolyte complex coacervation is of particular interest for mimicking intracellular phase separation and organization. Yet, the challenge arises from regulating the coacervation due to the globular structure and anisotropic distributed charges of protein. Herein, we fully investigate the different control factors and reveal their effects on protein-polyelectrolyte coacervation. We prepared mixtures of BSA (bovine serum albumin) with different cationic polymers, which include linear and branched polyelectrolytes covering different spacer and charge groups, chain lengths, and polymer structures. With BSA-PDMAEMA [poly(N,N-dimethylaminomethyl methacrylate)] as the main investigated pair, we find that the moderate pH and ionic strength are essential for the adequate electrostatic interaction and formation of coacervate droplets. For most BSA-polymer mixtures, excess polyelectrolytes are required to achieve the full complexation, as evidenced by the deviated optimal charge mixing ratios from the charge stoichiometry. Polymers with longer chains or primary amine groups and a branched structure endow a strong electrostatic interaction with BSA and cause a bigger charge ratio deviation associated with the formation of solid-like coacervate complexes. Nevertheless, both the liquid- and solid-like coacervates hardly interrupt the BSA structure and activity, indicating the safe encapsulation of proteins by the coacervation with polyelectrolytes. Our study validates the crucial control of the diverse factors in regulating protein-polyelectrolyte coacervation, and the revealed principles shall be instructive for establishing other protein-based coacervations and boosting their potential applications.
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Affiliation(s)
- Jin Zhou
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China
| | - Yuting Wan
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China
| | - Martien A Cohen Stuart
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China
| | - Mingwei Wang
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China
| | - Junyou Wang
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China
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4
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Saar KL, Qian D, Good LL, Morgunov AS, Collepardo-Guevara R, Best RB, Knowles TPJ. Theoretical and Data-Driven Approaches for Biomolecular Condensates. Chem Rev 2023; 123:8988-9009. [PMID: 37171907 PMCID: PMC10375482 DOI: 10.1021/acs.chemrev.2c00586] [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: 08/23/2022] [Indexed: 05/14/2023]
Abstract
Biomolecular condensation processes are increasingly recognized as a fundamental mechanism that living cells use to organize biomolecules in time and space. These processes can lead to the formation of membraneless organelles that enable cells to perform distinct biochemical processes in controlled local environments, thereby supplying them with an additional degree of spatial control relative to that achieved by membrane-bound organelles. This fundamental importance of biomolecular condensation has motivated a quest to discover and understand the molecular mechanisms and determinants that drive and control this process. Within this molecular viewpoint, computational methods can provide a unique angle to studying biomolecular condensation processes by contributing the resolution and scale that are challenging to reach with experimental techniques alone. In this Review, we focus on three types of dry-lab approaches: theoretical methods, physics-driven simulations and data-driven machine learning methods. We review recent progress in using these tools for probing biomolecular condensation across all three fields and outline the key advantages and limitations of each of the approaches. We further discuss some of the key outstanding challenges that we foresee the community addressing next in order to develop a more complete picture of the molecular driving forces behind biomolecular condensation processes and their biological roles in health and disease.
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Affiliation(s)
- Kadi L. Saar
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
- Transition
Bio Ltd., Cambridge, United Kingdom
| | - Daoyuan Qian
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Lydia L. Good
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Alexey S. Morgunov
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Rosana Collepardo-Guevara
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
- Department
of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Robert B. Best
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Tuomas P. J. Knowles
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, Cambridge CB3 0HE, United Kingdom
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5
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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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6
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Valdes-Garcia G, Gamage K, Smith C, Martirosova K, Feig M, Lapidus LJ. The effect of polymer length in liquid-liquid phase separation. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101415. [PMID: 37325682 PMCID: PMC10270681 DOI: 10.1016/j.xcrp.2023.101415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Understanding the thermodynamics that drive liquid-liquid phase separation (LLPS) is quite important given the number of diverse biomolecular systems undergoing this phenomenon. Many studies have focused on condensates of long polymers, but very few systems of short-polymer condensates have been observed and studied. Here, we study a short-polymer system of various lengths of poly-adenine RNA and peptides formed by the RGRGG sequence repeats to understand the underlying thermodynamics of LLPS. Using the recently developed COCOMO coarse-grained (CG) model, we predicted condensates for lengths as short as 5-10 residues, which was then confirmed by experiment, making this one of the smallest LLPS systems yet observed. A free-energy model reveals that the length dependence of condensation is driven primarily by entropy of confinement. The simplicity of this system will provide the basis for understanding more biologically realistic systems.
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Affiliation(s)
- Gilberto Valdes-Garcia
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- These authors contributed equally
| | - Kasun Gamage
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
- These authors contributed equally
| | - Casey Smith
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
| | - Karina Martirosova
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Lisa J. Lapidus
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
- Lead contact
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Zeng X, Pappu RV. Developments in describing equilibrium phase transitions of multivalent associative macromolecules. Curr Opin Struct Biol 2023; 79:102540. [PMID: 36804705 PMCID: PMC10732938 DOI: 10.1016/j.sbi.2023.102540] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/24/2022] [Accepted: 01/16/2023] [Indexed: 02/18/2023]
Abstract
Biomolecular condensates are distinct cellular bodies that form and dissolve reversibly to organize cellular matter and biochemical reactions in space and time. Condensates are thought to form and dissolve under the influence of spontaneous and driven phase transitions of multivalent associative macromolecules. These include phase separation, which is defined by segregation of macromolecules from the solvent or from one another, and percolation or gelation, which is an inclusive networking transition driven by reversible associations among multivalent macromolecules. Considerable progress has been made to model sequence-specific phase transitions, especially for intrinsically disordered proteins. Here, we summarize the state-of-the-art of theories and computations aimed at understanding and modeling sequence-specific, thermodynamically controlled, coupled associative and segregative phase transitions of archetypal multivalent macromolecules.
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Affiliation(s)
- Xiangze Zeng
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA. https://twitter.com/@xiangzezeng
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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8
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Her C, Phan TM, Jovic N, Kapoor U, Ackermann BE, Rizuan A, Kim Y, Mittal J, Debelouchina G. Molecular interactions underlying the phase separation of HP1α: role of phosphorylation, ligand and nucleic acid binding. Nucleic Acids Res 2022; 50:12702-12722. [PMID: 36537242 PMCID: PMC9825191 DOI: 10.1093/nar/gkac1194] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 11/04/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Heterochromatin protein 1α (HP1α) is a crucial element of chromatin organization. It has been proposed that HP1α functions through liquid-liquid phase separation (LLPS), which allows it to compact chromatin into transcriptionally repressed heterochromatin regions. In vitro, HP1α can undergo phase separation upon phosphorylation of its N-terminus extension (NTE) and/or through interactions with DNA and chromatin. Here, we combine computational and experimental approaches to elucidate the molecular interactions that drive these processes. In phosphorylation-driven LLPS, HP1α can exchange intradimer hinge-NTE interactions with interdimer contacts, which also leads to a structural change from a compacted to an extended HP1α dimer conformation. This process can be enhanced by the presence of positively charged HP1α peptide ligands and disrupted by the addition of negatively charged or neutral peptides. In DNA-driven LLPS, both positively and negatively charged peptide ligands can perturb phase separation. Our findings demonstrate the importance of electrostatic interactions in HP1α LLPS where binding partners can modulate the overall charge of the droplets and screen or enhance hinge region interactions through specific and non-specific effects. Our study illuminates the complex molecular framework that can fine-tune the properties of HP1α and that can contribute to heterochromatin regulation and function.
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Affiliation(s)
| | | | - Nina Jovic
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Utkarsh Kapoor
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Bryce E Ackermann
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Young C Kim
- Center for Materials Physics and Technology, Naval Research Laboratory, WA, DC, USA
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