1
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Jussupow A, Bartley D, Lapidus LJ, Feig M. COCOMO2: A coarse-grained model for interacting folded and disordered proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.29.620916. [PMID: 39554101 PMCID: PMC11565878 DOI: 10.1101/2024.10.29.620916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parameterized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multi-scale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.
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Affiliation(s)
- Alexander Jussupow
- Department of Biochemistry and Molecular Biology, East Lansing, MI 48824, USA
| | - Divya Bartley
- Department of Biochemistry and Molecular Biology, East Lansing, MI 48824, USA
| | - Lisa J. Lapidus
- Department of Physics and Astronomy Michigan State University, East Lansing, MI 48824, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, East Lansing, MI 48824, USA
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2
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Chee CH, Benharush R, Knight LR, Laaser JE. Segregative phase separation of strong polyelectrolyte complexes at high salt and high polymer concentrations. SOFT MATTER 2024; 20:8505-8514. [PMID: 39415735 DOI: 10.1039/d4sm00994k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
The phase behavior of polyelectrolyte complexes and coacervates (PECs) at low salt concentrations has been well characterized, but their behavior at concentrations well above the binodal is not well understood. Here, we investigate the phase behavior of stoichiometric poly(styrene sulfonate)/poly(diallyldimethylammonium) mixtures at high salt and high polymer concentrations. Samples were prepared by direct mixing of PSS/PDADMA PECs, water, and salt (KBr). Phase separation was observed at salt concentrations approximately 1 M above the binodal. Characterization by thermogravimetric analysis, FTIR, and NMR revealed that both phases contained significant amounts of polymer, and that the polymer-rich phase was enriched in PSS, while the polymer-poor phase was enriched in PDADMA. These results suggest that high salt concentrations drive salting out of the more hydrophobic polyelectrolyte (PSS), consistent with behavior observed in weak polyelectrolyte systems. Interestingly, at the highest salt and polymer concentrations studied, the polymer-rich phase contained both PSS and PDADMA, suggesting that high salt concentrations can drive salting out of partially-neutralized complexes as well. Characterization of the behavior of PECs in the high concentration limit appears to be a fruitful avenue for deepening fundamental understanding of the molecular-scale factors driving phase separation in these systems.
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Affiliation(s)
- Conner H Chee
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, PA, USA.
| | - Rotem Benharush
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, PA, USA.
| | - Lexi R Knight
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, PA, USA.
| | - Jennifer E Laaser
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, PA, USA.
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3
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Kim S, Lee NK, Jung Y, Johner A. Kinetics of Polyampholyte Dimerization: Influence of Charge Sequences. Polymers (Basel) 2024; 16:2928. [PMID: 39458755 PMCID: PMC11510756 DOI: 10.3390/polym16202928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2024] [Revised: 10/09/2024] [Accepted: 10/10/2024] [Indexed: 10/28/2024] Open
Abstract
Polyampholytes (PAs) exhibit complex behaviors in various environments influenced by their charge distribution. This study focuses on the kinetics of dimerization of PAs, aiming to elucidate the underlying mechanisms and clarify relevant characteristics of the charge sequence. We focus on PAs with non-zero net charges, employing molecular dynamics simulations and theoretical analyses to examine how charge sequences influence the rates of dimer formation and dissociation. Our findings reveal that the charge sequence of tails and the blockiness of the minority charge group markedly influence the kinetics of dimerization: large blockiness and tails with a high number of majority-type charges slow down the dissociation of dimers. Additionally, the presence of an extended (central) block of the majority charge promotes structural diversity. Within dimer states, blocks alternate between intra- and inter-chain contacts. The duration times in the dimer states are significantly longer than the typical dwell times of block inter-contacts, with a notable extension when multiple blocks are engaged. Intrinsically disordered proteins (IDPs) play crucial roles in cellular functions, primarily due to their ability to undergo rapid conformational changes and form transient complexes. These properties largely depend on the sequence of charged residues. We provide insights into the fundamental principles governing the structural and dynamical properties of polyampholytic IDP, emphasizing the importance of sequence-specific effects on both aggregation and dissociation.
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Affiliation(s)
- Seowon Kim
- Department of Physics and Astronomy, Sejong University, Seoul 05006, Republic of Korea
| | - Nam-Kyung Lee
- Department of Physics and Astronomy, Sejong University, Seoul 05006, Republic of Korea
| | - Youngkyun Jung
- Supercomputing Center, Korea Institute of Science and Technology Information, Daejeon 34141, Republic of Korea;
| | - Albert Johner
- Institut Charles Sadron CNRS-Unistra, 6 rue Boussingault, 67083 Strasbourg, CEDEX, France
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4
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Ou X, Tang Z, Ye Y, Chen X, Huang Y. Macromolecular Crowding Effect on Chitosan-Hyaluronic Acid Complexation and the Activity of Encapsulated Catalase. Biomacromolecules 2024; 25:3840-3849. [PMID: 38801711 DOI: 10.1021/acs.biomac.4c00445] [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: 05/29/2024]
Abstract
The associative phase separation of charged biomacromolecules plays a key role in many biophysical events that take place in crowded intracellular environments. Such natural polyelectrolyte complexation and phase separation often occur at nonstoichiometric charge ratios with the incorporation of bioactive proteins, which is not studied as extensively as those complexations at stoichiometric ratios. In this work, we investigated how the addition of a crowding agent (polyethylene glycol, PEG) affected the complexation between chitosan (CS) and hyaluronic acid (HA), especially at nonstoichiometric ratios, and the encapsulation of enzyme (catalase, CAT) by the colloidal complexes. The crowded environment promoted colloidal phase separation at low charge ratios, forming complexes with increased colloidal and dissolution stability, which resulted in a smaller size and polydispersity (PDI). The binding isotherms revealed that the addition of PEG greatly enhanced the ion-pairing strength (with increased ion-pairing equilibrium constant Ka from 4.92 × 104 without PEG to 1.08 × 106 with 200 g/L PEG) and switched the coacervation from endothermic to exothermic, which explained the promoted complexation and phase separation. At the stoichiometric charge ratio, the enhanced CS-HA interaction in crowded media generated a more solid-like coacervate phase with a denser network, slower chain relaxation, and higher modulus. Moreover, both crowding and complex encapsulation enhanced the activity and catalytic efficiency of CAT, represented by a 2-fold increase in catalytic efficiency (Kcat/Km) under 100 g/L PEG crowding and CS-HA complex encapsulation. This is likely due to the lower polarity in the microenvironment surrounding the enzyme molecules. By a systematic investigation of both nonstoichiometric and stoichiometric charge ratios under macromolecular crowding, this work provided new insights into the complexation between natural polyelectrolytes in a scenario closer to an intracellular environment.
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Affiliation(s)
- Xiatong Ou
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Minhou County, Fuzhou 350108, Fujian, China
| | - Ziyao Tang
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Minhou County, Fuzhou 350108, Fujian, China
| | - Yanqi Ye
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Minhou County, Fuzhou 350108, Fujian, China
| | - Xiaochao Chen
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Minhou County, Fuzhou 350108, Fujian, China
- Chuanhua Kechuang Building, Ningwei Street, Xiaoshan District, Zhejiang Novofacies Biotech Co., Ltd., Hangzhou 311215, Zhejiang, China
| | - Yan Huang
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Minhou County, Fuzhou 350108, Fujian, China
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5
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Alfano C, Fichou Y, Huber K, Weiss M, Spruijt E, Ebbinghaus S, De Luca G, Morando MA, Vetri V, Temussi PA, Pastore A. Molecular Crowding: The History and Development of a Scientific Paradigm. Chem Rev 2024; 124:3186-3219. [PMID: 38466779 PMCID: PMC10979406 DOI: 10.1021/acs.chemrev.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.
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Affiliation(s)
- Caterina Alfano
- Structural
Biology and Biophysics Unit, Fondazione
Ri.MED, 90100 Palermo, Italy
| | - Yann Fichou
- CNRS,
Bordeaux INP, CBMN UMR 5248, IECB, University
of Bordeaux, F-33600 Pessac, France
| | - Klaus Huber
- Department
of Chemistry, University of Paderborn, 33098 Paderborn, Germany
| | - Matthias Weiss
- Experimental
Physics I, Physics of Living Matter, University
of Bayreuth, 95440 Bayreuth, Germany
| | - Evan Spruijt
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Simon Ebbinghaus
- Lehrstuhl
für Biophysikalische Chemie and Research Center Chemical Sciences
and Sustainability, Research Alliance Ruhr, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Giuseppe De Luca
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Valeria Vetri
- Dipartimento
di Fisica e Chimica − Emilio Segrè, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Annalisa Pastore
- King’s
College London, Denmark
Hill Campus, SE5 9RT London, United Kingdom
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6
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Shi G, Schweizer KS. Theory of the center-of-mass diffusion and viscosity of microstructured and variable sequence copolymer liquids. SOFT MATTER 2023; 19:8893-8910. [PMID: 37955602 DOI: 10.1039/d3sm01193c] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Biomolecular condensates formed through the phase separation of proteins and nucleic acids are widely observed, offering a fundamental means of organizing intracellular materials in a membrane-less fashion. Traditionally, these condensates have been regarded as homogeneous isotropic liquids. However, in analogy with some synthetic copolymer systems, our recent theoretical research has demonstrated that model biomolecular condensates can exhibit a microemulsion-like internal structure, contingent upon the specific sequence, inter-chain site-site interactions, and concentrated phase polymer density. Motivated by these considerations, here we present a microscopic dynamical theory for the self-diffusion constant and viscosity of a simpler class of model systems - concentrated unentangled A/B regular multiblock copolymer solutions. Our approach integrates static equilibrium local and microdomain scale structural information obtained from PRISM integral equation theory and the time evolution of the autocorrelation function of monomer scale forces at the center-of-mass level to determine the polymer diffusion constant and viscosity in a weak caging regime far from a glass or gel transition. We focus on regular multi-block systems both for simplicity and for its relevance to synthetic macromolecular science. The impact of sequence and inter-chain attraction strength on the slowing down of copolymer mass transport and flow due to local clustering enhanced collisional friction and emergent microdomain scale ordering are established. Analytic analysis and metrics employed in the study of biomolecular condensates are employed to identify key order parameters that quantity how attractive forces, packing structure, multiblock sequence, and copolymer density determine dynamical slowing down above and below the crossover to a fluctuating polymeric microemulsion state.
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Affiliation(s)
- Guang Shi
- Department of Materials Science, University of Illinois, Urbana, Illinois 61801, USA.
| | - Kenneth S Schweizer
- Department of Materials Science, University of Illinois, Urbana, Illinois 61801, USA.
- Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, Illinois 61801, USA
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, USA
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7
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Sárkány Z, Rocha F, Bratek‐Skicki A, Tompa P, Macedo‐Ribeiro S, Martins PM. Quantification of Surface Tension Effects and Nucleation-and-Growth Rates during Self-Assembly of Biological Condensates. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301501. [PMID: 37279376 PMCID: PMC10427409 DOI: 10.1002/advs.202301501] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/12/2023] [Indexed: 06/08/2023]
Abstract
Liquid-solid and liquid-liquid phase separation (PS) drives the formation of functional and disease-associated biological assemblies. Principles of phase equilibrium are here employed to derive a general kinetic solution that predicts the evolution of the mass and size of biological assemblies. Thermodynamically, protein PS is determined by two measurable concentration limits: the saturation concentration and the critical solubility. Due to surface tension effects, the critical solubility can be higher than the saturation concentration for small, curved nuclei. Kinetically, PS is characterized by the primary nucleation rate constant and a combined rate constant accounting for growth and secondary nucleation. It is demonstrated that the formation of a limited number of large condensates is possible without active mechanisms of size control and in the absence of coalescence phenomena. The exact analytical solution can be used to interrogate how the elementary steps of PS are affected by candidate drugs.
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Affiliation(s)
- Zsuzsa Sárkány
- IBMC − Instituto de Biologia Molecular e CelularUniversidade do PortoPorto4150–180Portugal
- i3S − Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPorto4150–180Portugal
| | - Fernando Rocha
- LEPABE − Laboratory for Process Engineering Environment Biotechnology and EnergyFaculdade de Engenharia da Universidade do PortoPorto4200‐465Portugal
| | - Anna Bratek‐Skicki
- Jerzy Haber Institute of Catalysis and Surface ChemistryPolish Academy of SciencesNiezapominajek 8KrakowPL30239Poland
- VIB‐VUB Center for Structural BiologyVlaams Instituut voor BiotechnologyBrussels1050 IxellesBelgium
- Structural Biology Brussels (SBB)Bioengineering Sciences DepartmentVrije Universiteit Brussel (VUB)BrusselsB‐1050Belgium
| | - Peter Tompa
- VIB‐VUB Center for Structural BiologyVlaams Instituut voor BiotechnologyBrussels1050 IxellesBelgium
- Structural Biology Brussels (SBB)Bioengineering Sciences DepartmentVrije Universiteit Brussel (VUB)BrusselsB‐1050Belgium
- Institute of EnzymologyResearch Centre for Natural SciencesBudapest1117Hungary
| | - Sandra Macedo‐Ribeiro
- IBMC − Instituto de Biologia Molecular e CelularUniversidade do PortoPorto4150–180Portugal
- i3S − Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPorto4150–180Portugal
| | - Pedro M. Martins
- IBMC − Instituto de Biologia Molecular e CelularUniversidade do PortoPorto4150–180Portugal
- i3S − Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPorto4150–180Portugal
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8
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Perillo MA, Burgos I, Clop EM, Sanchez JM, Nolan V. The role of water in reactions catalysed by hydrolases under conditions of molecular crowding. Biophys Rev 2023; 15:639-660. [PMID: 37681097 PMCID: PMC10480385 DOI: 10.1007/s12551-023-01104-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/23/2023] [Indexed: 09/09/2023] Open
Abstract
Under macromolecular crowding (MC) conditions such as cellular, extracellular, food and other environments of biotechnological interest, the thermodynamic activity of the different macromolecules present in the system is several orders of magnitude higher than in dilute solutions. In this state, the diffusion rates are affected by the volume exclusion induced by the crowders. Immiscible liquid phases, which may arise in MC by liquid-liquid phase separation, may induce a dynamic confinement of reactants, products and/or enzymes, tuning reaction rates. In cellular environments and other crowding conditions, membranes and macromolecules provide, on the whole, large surfaces that can perturb the solvent, causing its immobilisation by adsorption in the short range and also affecting the solvent viscosity in the long range. The latter phenomenon can affect the conformation of a protein and/or the degree of association of its protomers and, consequently, its activity. Changes in the water structure can also alter the enzyme-substrate interaction, and, in the case of hydrolytic enzymes, where water is one of the substrates, it also affects the reaction mechanism. Here, we review the evidence for how macromolecular crowding affects the catalysis induced by hydrolytic enzymes, focusing on the structure and dynamics of water.
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Affiliation(s)
- Maria A. Perillo
- Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina
- CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
| | - Inés Burgos
- CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
- Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química Industrial y Aplicada, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina
| | - Eduardo M. Clop
- Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina
- CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
| | - Julieta M. Sanchez
- Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina
- CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
- Institut de Biotecnologia I de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Departament de Genètica I de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- CIBER de Bioingeniería Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, 08193 Barcelona, Spain
| | - Verónica Nolan
- Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina
- CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
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9
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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: 2] [Impact Index Per Article: 2.0] [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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10
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Bai Q, Liu Z, Chen J, Liang D. Crowded Environment Regulates the Coacervation of Biopolymers via Nonspecific Interactions. Biomacromolecules 2023; 24:283-293. [PMID: 36511362 DOI: 10.1021/acs.biomac.2c01129] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The membrane-less organelles (MLOs) with subcompartments are formed via liquid-liquid phase separation (LLPS) in the crowded cell interior whose background molecules are up to 400 mg/mL. It is still a puzzle how the background molecules regulate the formation, dynamics, and functions of MLOs. Using biphasic coacervate droplets formed by poly(l-lysine) (PLL), quaternized dextran (Q-dextran), and single-stranded oligonucleotides (ss-oligo) as a model of MLO, we online monitored the LLPS process in Bovine Serine Albumin (BSA) solution up to 200.0 mg/mL. Negatively charged BSA is able to form complex or coacervate with positively charged PLL and Q-dextran and thus participates in the LLPS via nonspecific interactions. Results show that BSA effectively regulates the LLPS by controlling the phase distribution, morphologies, and kinetics. With increasing BSA concentration, the spherical biphasic droplets evolve in sequence into phase-inverted flower-like structure, worm-like chains, network structures, and confined coacervates. Each kind of morphology is formed via its own specific growth and fusion pathway. Our work suggests that MLOs could be controlled solely by the crowded environment and provides a further step toward understanding the life process in cell.
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Affiliation(s)
- Qingwen Bai
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Zhijun Liu
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Jiaxin Chen
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
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11
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Valdes-Garcia G, Heo L, Lapidus LJ, Feig M. Modeling Concentration-dependent Phase Separation Processes Involving Peptides and RNA via Residue-Based Coarse-Graining. J Chem Theory Comput 2023; 19:10.1021/acs.jctc.2c00856. [PMID: 36607820 PMCID: PMC10323037 DOI: 10.1021/acs.jctc.2c00856] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Biomolecular condensation, especially liquid-liquid phase separation, is an important physical process with relevance for a number of different aspects of biological functions. Key questions of what drives such condensation, especially in terms of molecular composition, can be addressed via computer simulations, but the development of computationally efficient yet physically realistic models has been challenging. Here, the coarse-grained model COCOMO is introduced that balances the polymer behavior of peptides and RNA chains with their propensity to phase separate as a function of composition and concentration. COCOMO is a residue-based model that combines bonded terms with short- and long-range terms, including a Debye-Hückel solvation term. The model is highly predictive of experimental data on phase-separating model systems. It is also computationally efficient and can reach the spatial and temporal scales on which biomolecular condensation is observed with moderate computational resources.
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Affiliation(s)
- Gilberto Valdes-Garcia
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Lim Heo
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Lisa J. Lapidus
- 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
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12
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Ma L, Fang X, Wang C. Peptide-based coacervates in therapeutic applications. Front Bioeng Biotechnol 2023; 10:1100365. [PMID: 36686257 PMCID: PMC9845597 DOI: 10.3389/fbioe.2022.1100365] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
Coacervates are droplets formed by liquid‒liquid phase separation. An increasing number of studies have reported that coacervates play an important role in living cells, such as in the generation of membraneless organelles, and peptides contribute to condensate droplet formation. Peptides with versatile functional groups and special secondary structures, including α-helices, β-sheets and intrinsically disordered regions, provide novel insights into coacervation, such as biomimetic protocells, neurodegenerative diseases, modulations of signal transmission, and drug delivery systems. In this review, we introduce different types of peptide-based coacervates and the principles of their interactions. Additionally, we summarize the thermodynamic and kinetic mechanisms of peptide-based coacervates and the associated factors, including salt, pH, and temperature, affecting the phase separation process. We illustrate recent studies on modulating the functions of peptide-based coacervates applied in biological diseases. Finally, we propose their promising broad applications and describe the challenges of peptide-based coacervates in the future.
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Affiliation(s)
- Lilusi Ma
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaocui Fang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China,University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Xiaocui Fang, ; Chen Wang,
| | - Chen Wang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China,University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Xiaocui Fang, ; Chen Wang,
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Skvortsova P, Shurpik D, Stoikov I, Khairutdinov B. Pillar[5]arene-induced DNA condensation: Liquid–liquid phase separation in pillar[5]arene-oligonucleotide system. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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14
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Bai Q, Chen X, Chen J, Liu Z, Lin YN, Yang S, Liang D. Morphology and Dynamics of Coexisting Phases in Coacervate Solely Controlled by Crowded Environment. ACS Macro Lett 2022; 11:1107-1111. [PMID: 36006377 DOI: 10.1021/acsmacrolett.2c00409] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The membraneless organelles (MLOs) play a key role in the cell, yet it is unclear what controls the morphology and dynamics of MLOs in crowded cell medium. Using a biphasic coacervate droplet as a model of MLO, we online monitored the liquid-liquid phase separation process in crowded medium provided by poly(ethylene oxide) (PEO) or dextran. In PEO solution, which has an affinity with the inner phase, the spherical droplets evolve into clusters, networks, and completely phase inverted spheres in sequence with increasing PEO concentration, while in dextran solution, which has an affinity with the outer phase, the coacervates maintain the morphology but vary in phase ratio. Flower-like and even Janus structures are formed in the mixed PEO/dextran medium. Our work demonstrates that MLOs could be controlled solely by the crowded cell medium.
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Affiliation(s)
- Qingwen Bai
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xu Chen
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiaxin Chen
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhijun Liu
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ya-Nan Lin
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shuang Yang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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15
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Liu Z, Chen J, Bai Q, Lin YN, Liang D. Coacervate Formed by an ATP-Binding Aptamer and Its Dynamic Behavior under Nonequilibrium Conditions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6425-6434. [PMID: 35543367 DOI: 10.1021/acs.langmuir.2c00580] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Although numerous protocell models have been developed to explore the possible pathway of the origin of life on the early earth, few truly fulfill the roles of the DNA/RNA sequence and ATP molecules, which are keys to cell replication and evolution. The ATP-binding aptamer offers an opportunity to combine sequence and energy molecules. In this work, we choose the coacervate droplet as the protocell model and investigate the interaction of the DNA aptamer, poly(l-lysine)(PLL), and ATP under varying conditions. PLL and aptamers form solid precipitates, which spontaneously transform to coacervate droplets as ATP is introduced. The selective uptake and sequestration of exogenous molecules is achieved by the ATP-containing coacervates. As an electric field is applied to expel ATP, the portion of the droplet deficient in ATP becomes solid. The solid/liquid phase ratio is tunable by varying the electric field strength and excitation time. Together with the vacuolization process, a solid head with a soft mouth periodically opening and closing is created. Moreover, the composite coacervate droplet gradually grows as it is treated with an electric field and cannot recover to the original liquid phase after the power is turned off and replenished with ATP. Our work highlights that the proper integration of the DNA sequence, ATP, and energy input could be a powerful strategy for creating a protocell with certain living features.
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Affiliation(s)
- Zhijun Liu
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiaxin Chen
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qingwen Bai
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ya-Nan Lin
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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Keating CD, Pappu RV. Liquid-Liquid Phase Separation: A Widespread and Versatile Way to Organize Aqueous Solutions. J Phys Chem B 2021; 125:12399-12400. [PMID: 34788996 DOI: 10.1021/acs.jpcb.1c08831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christine D Keating
- Department of Chemistry, Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biolgical Systems Engineering Campus, Washington University in Saint Louis, Box 1097, One Brookings Drive, St. Louis, Missouri 63130, United States
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Keating CD, Pappu RV. Liquid-Liquid Phase Separation: A Widespread and Versatile Way to Organize Aqueous Solutions. J Phys Chem Lett 2021; 12:10994-10995. [PMID: 34788997 DOI: 10.1021/acs.jpclett.1c03352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Christine D Keating
- Department of Chemistry, Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biolgical Systems Engineering Campus, Washington University in Saint Louis, Box 1097, One Brookings Drive, St. Louis, Missouri 63130, United States
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Vweza AO, Song CG, Chong KT. Liquid-Liquid Phase Separation in the Presence of Macromolecular Crowding and State-dependent Kinetics. Int J Mol Sci 2021; 22:6675. [PMID: 34206440 PMCID: PMC8268629 DOI: 10.3390/ijms22136675] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/13/2021] [Accepted: 06/14/2021] [Indexed: 12/27/2022] Open
Abstract
Biomolecular condensates formed via liquid-liquid phase separation (LLPS) are increasingly being shown to play major roles in cellular self-organization dynamics in health and disease. It is well established that macromolecular crowding has a profound impact on protein interactions, particularly those that lead to LLPS. Although synthetic crowding agents are used during in vitro LLPS experiments, they are considerably different from the highly crowded nucleo-/cytoplasm and the effects of in vivo crowding remain poorly understood. In this work, we applied computational modeling to investigate the effects of macromolecular crowding on LLPS. To include biologically relevant LLPS dynamics, we extended the conventional Cahn-Hilliard model for phase separation by coupling it to experimentally derived macromolecular crowding dynamics and state-dependent reaction kinetics. Through extensive field-theoretic computer simulations, we show that the inclusion of macromolecular crowding results in late-stage coarsening and the stabilization of relatively smaller condensates. At a high crowding concentration, there is an accelerated growth and late-stage arrest of droplet formation, effectively resulting in anomalous labyrinthine morphologies akin to protein gelation observed in experiments. These results not only elucidate the crowder effects observed in experiments, but also highlight the importance of including state-dependent kinetics in LLPS models, and may help in designing further experiments to probe the intricate roles played by LLPS in self-organization dynamics of cells.
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Affiliation(s)
- Alick-O. Vweza
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; (A.-O.V.); (C.-G.S.)
| | - Chul-Gyu Song
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; (A.-O.V.); (C.-G.S.)
- Advanced Biomedical Imaging Center, Jeonbuk National University, Jeonju 54896, Korea
| | - Kil-To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; (A.-O.V.); (C.-G.S.)
- Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, Korea
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