1
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King MR, Ruff KM, Pappu RV. Emergent microenvironments of nucleoli. Nucleus 2024; 15:2319957. [PMID: 38443761 PMCID: PMC10936679 DOI: 10.1080/19491034.2024.2319957] [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] [Received: 09/04/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
In higher eukaryotes, the nucleolus harbors at least three sub-phases that facilitate multiple functionalities including ribosome biogenesis. The three prominent coexisting sub-phases are the fibrillar center (FC), the dense fibrillar component (DFC), and the granular component (GC). Here, we review recent efforts in profiling sub-phase compositions that shed light on the types of physicochemical properties that emerge from compositional biases and territorial organization of specific types of macromolecules. We highlight roles played by molecular grammars which refers to protein sequence features including the substrate binding domains, the sequence features of intrinsically disordered regions, and the multivalence of these distinct types of domains / regions. We introduce the concept of a barcode of emergent physicochemical properties of nucleoli. Although our knowledge of the full barcode remains incomplete, we hope that the concept prompts investigations into undiscovered emergent properties and engenders an appreciation for how and why unique microenvironments control biochemical reactions.
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Affiliation(s)
- Matthew R. King
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| | - Kiersten M. Ruff
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
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2
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Ouyang S, Wang F, Liu Y, Hu Z, Li M, Wu Y, Li Z, Qian J, Wang L, Ma S. Current status of research on polysaccharide-based functional gradient gel materials: A review. Carbohydr Polym 2024; 344:122520. [PMID: 39218545 DOI: 10.1016/j.carbpol.2024.122520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/09/2024] [Accepted: 07/17/2024] [Indexed: 09/04/2024]
Abstract
Functional gradient materials with material property anisotropy are one of the hotspots of current new material research. The gradient change of material properties comes from the change of the content of one or more components in the material, which is closely related to the preparation process of the material. Meanwhile, polysaccharide materials, as an environmentally friendly and green material, have attracted extensive attention from researchers. This paper focuses on the preparation process of functional gradient gel materials based on polysaccharides, analyzes the laws affecting the distribution of substances during the molding process from the basic principles of material molding, and clarifies the advantages and disadvantages of various methods, so as to promote the innovation of the theory of the preparation method of functional gradient gel materials. At the same time, the specific applications that can be realized by the gradient materials are introduced and compared with the traditional homogeneous materials to elucidate the enhancement of the usage properties brought by their unique gradient structure or properties, which will play a certain role as a reference for the direction of the application of the subsequent materials.
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Affiliation(s)
- Shiqiang Ouyang
- Jiangsu Provincial Key Laboratory of Food Advanced Manufacturing Equipment Technology, School of Mechanical Engineering, Jiangnan University, Wuxi 214122, China
| | - Feijie Wang
- Jiangsu Provincial Key Laboratory of Food Advanced Manufacturing Equipment Technology, School of Mechanical Engineering, Jiangnan University, Wuxi 214122, China
| | - Yichi Liu
- Jiangsu Provincial Key Laboratory of Food Advanced Manufacturing Equipment Technology, School of Mechanical Engineering, Jiangnan University, Wuxi 214122, China
| | - Zihan Hu
- Jiangsu Provincial Key Laboratory of Food Advanced Manufacturing Equipment Technology, School of Mechanical Engineering, Jiangnan University, Wuxi 214122, China
| | - Mengdi Li
- Jiangsu Provincial Key Laboratory of Food Advanced Manufacturing Equipment Technology, School of Mechanical Engineering, Jiangnan University, Wuxi 214122, China
| | - Yiting Wu
- Jiangsu Provincial Key Laboratory of Food Advanced Manufacturing Equipment Technology, School of Mechanical Engineering, Jiangnan University, Wuxi 214122, China
| | - Zhihua Li
- Jiangsu Provincial Key Laboratory of Food Advanced Manufacturing Equipment Technology, School of Mechanical Engineering, Jiangnan University, Wuxi 214122, China
| | - Jing Qian
- Jiangsu Provincial Key Laboratory of Food Advanced Manufacturing Equipment Technology, School of Mechanical Engineering, Jiangnan University, Wuxi 214122, China
| | - Liqiang Wang
- Jiangsu Provincial Key Laboratory of Food Advanced Manufacturing Equipment Technology, School of Mechanical Engineering, Jiangnan University, Wuxi 214122, China.
| | - Shufeng Ma
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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3
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Baksi A, Zerze H, Agrawal A, Karim A, Zerze GH. The molecular picture of the local environment in a stable model coacervate. Commun Chem 2024; 7:222. [PMID: 39349768 PMCID: PMC11442467 DOI: 10.1038/s42004-024-01304-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 09/11/2024] [Indexed: 10/04/2024] Open
Abstract
Complex coacervates play essential roles in various biological processes and applications. Although substantial progress has been made in understanding the molecular interactions driving complex coacervation, the mechanisms stabilizing coacervates against coalescence remain experimentally challenging and not fully elucidated. We recently showed that polydiallyldimethylammonium chloride (PDDA) and adenosine triphosphate (ATP) coacervates stabilize upon their transfer to deionized (DI) water. Here, we perform molecular dynamics simulations of PDDA-ATP coacervates in supernatant and DI water, to understand the ion dynamics and structure within stable coacervates. We found that transferring the coacervates to DI water results in an immediate ejection of a significant fraction of small ions (Na+ and Cl-) from the surface of the coacervates to DI water. We also observed a notable reduction in the mobility of these counterions in coacervates when in DI water, both in the cluster-forming and slab simulations, together with a lowered displacement of PDDA and ATP. These results suggest that the initial ejection of the ions from the coacervates in DI water may induce an interfacial skin layer formation, inhibiting further mobility of ions in the skin layer.
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Affiliation(s)
- Atanu Baksi
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, 77204, USA
| | - Hasan Zerze
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, 77204, USA
| | - Aman Agrawal
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, 77204, USA
- Department of Chemistry and Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
| | - Alamgir Karim
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, 77204, USA
| | - Gül H Zerze
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, 77204, USA.
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4
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Akcay Ogur F, Mamasoglu S, Perry SL, Akin FA, Kayitmazer AB. Interactions between Hyaluronic Acid and Chitosan by Isothermal Titration Calorimetry: The Effect of Ionic Strength, pH, and Polymer Molecular Weight. J Phys Chem B 2024; 128:9022-9035. [PMID: 39248492 DOI: 10.1021/acs.jpcb.4c03930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
Abstract
Hyaluronic acid (HA)/chitosan (CHI) complex coacervates have recently gained interest due to the pH-dependent ionization and semiflexibility of the polymers as well as their applicability in tissue engineering. Here, we apply isothermal titration calorimetry (ITC) to understand the apparent thermodynamics of coacervation for HA/CHI as a function of the pH, ionic strength, and chain length. We couple these ITC experiments with the knowledge of the charge states of HA and CHI from potentiometric titration to understand the mechanistic aspects of complex formation. Our data demonstrate that the driving force for the complex coacervation of HA and CHI is entropic in nature and this driving force decreased with increasing ionic strength. We also observed a decrease in the stoichiometry for ion-pairing with increasing ionic strength, which we suggest is a consequence of the changing degree of ionization for HA at higher ionic strengths. An increase in the strength of interactions with pH was hypothesized to also be a result of changes in the degree of ionization of HA, though stronger interactions were observed at the lowest pH tested, likely due to contributions from hydrogen bonding between HA and CHI.
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Affiliation(s)
- Fatma Akcay Ogur
- Department of Chemistry, Bogazici University, Bebek, Istanbul 34342, Turkiye
| | - Sezin Mamasoglu
- Department of Chemistry, Bogazici University, Bebek, Istanbul 34342, Turkiye
| | - Sarah L Perry
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Fatma Ahu Akin
- Department of Chemistry, Bogazici University, Bebek, Istanbul 34342, Turkiye
| | - A Basak Kayitmazer
- Department of Chemistry, Bogazici University, Bebek, Istanbul 34342, Turkiye
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5
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Song S, Ivanov T, Yuan D, Wang J, da Silva LC, Xie J, Cao S. Peptide-Based Biomimetic Condensates via Liquid-Liquid Phase Separation as Biomedical Delivery Vehicles. Biomacromolecules 2024; 25:5468-5488. [PMID: 39178343 DOI: 10.1021/acs.biomac.4c00814] [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: 08/25/2024]
Abstract
Biomolecular condensates are dynamic liquid droplets through intracellular liquid-liquid phase separation that function as membraneless organelles, which are highly involved in various complex cellular processes and functions. Artificial analogs formed via similar pathways that can be integrated with biological complexity and advanced functions have received tremendous research interest in the field of synthetic biology. The coacervate droplet-based compartments can partition and concentrate a wide range of solutes, which are regarded as attractive candidates for mimicking phase-separation behaviors and biophysical features of biomolecular condensates. The use of peptide-based materials as phase-separating components has advantages such as the diversity of amino acid residues and customized sequence design, which allows for programming their phase-separation behaviors and the physicochemical properties of the resulting compartments. In this Perspective, we highlight the recent advancements in the design and construction of biomimicry condensates from synthetic peptides relevant to intracellular phase-separating protein, with specific reference to their molecular design, self-assembly via phase separation, and biorelated applications, to envisage the use of peptide-based droplets as emerging biomedical delivery vehicles.
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Affiliation(s)
- Siyu Song
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz 55128, Germany
| | | | - Dandan Yuan
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, China
| | - Jianqiang Wang
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, China
| | | | - Jing Xie
- Institute of Biomedical Engineering, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shoupeng Cao
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, China
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6
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Phillips M, Muthukumar M, Ghosh K. Beyond monopole electrostatics in regulating conformations of intrinsically disordered proteins. PNAS NEXUS 2024; 3:pgae367. [PMID: 39253398 PMCID: PMC11382291 DOI: 10.1093/pnasnexus/pgae367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 08/13/2024] [Indexed: 09/11/2024]
Abstract
Conformations and dynamics of an intrinsically disordered protein (IDP) depend on its composition of charged and uncharged amino acids, and their specific placement in the protein sequence. In general, the charge (positive or negative) on an amino acid residue in the protein is not a fixed quantity. Each of the ionizable groups can exist in an equilibrated distribution of fully ionized state (monopole) and an ion-pair (dipole) state formed between the ionizing group and its counterion from the background electrolyte solution. The dipole formation (counterion condensation) depends on the protein conformation, which in turn depends on the distribution of charges and dipoles on the molecule. Consequently, effective charges of ionizable groups in the IDP backbone may differ from their chemical charges in isolation-a phenomenon termed charge-regulation. Accounting for the inevitable dipolar interactions, that have so far been ignored, and using a self-consistent procedure, we present a theory of charge-regulation as a function of sequence, temperature, and ionic strength. The theory quantitatively agrees with both charge reduction and salt-dependent conformation data of Prothymosin-alpha and makes several testable predictions. We predict charged groups are less ionized in sequences where opposite charges are well mixed compared to sequences where they are strongly segregated. Emergence of dipolar interactions from charge-regulation allows spontaneous coexistence of two phases having different conformations and charge states, sensitively depending on the charge patterning. These findings highlight sequence dependent charge-regulation and its potential exploitation by biological regulators such as phosphorylation and mutations in controlling protein conformation and function.
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Affiliation(s)
- Michael Phillips
- Department of Physics and Astronomy, University of Denver, Denver, CO 80208, USA
| | - Murugappan Muthukumar
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, CO 80208, USA
- Molecular and Cellular Biophysics, University of Denver, Denver, CO 80208, USA
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7
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Wang Y, Zou R, Zhou Y, Zheng Y, Peng C, Liu Y, Tan H, Fu Q, Ding M. Unraveling mechanisms of protein encapsulation and release in coacervates via molecular dynamics and machine learning. Chem Sci 2024; 15:13442-13451. [PMID: 39183928 PMCID: PMC11339950 DOI: 10.1039/d4sc03061c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/22/2024] [Indexed: 08/27/2024] Open
Abstract
Coacervates play a pivotal role in protein-based drug delivery research, yet their drug encapsulation and release mechanisms remain poorly understood. Here, we utilized the Martini model to investigate bovine serum albumin (BSA) protein encapsulation and release within polylysine/polyglutamate (PLys/PGlu) coacervates. Our findings emphasize the importance of ingredient addition sequence in coacervate formation and encapsulation rates, attributed to preference contact between oppositely charged proteins and poly(amino acid)s. Notably, coacervates composed of β-sheet poly(amino acid)s demonstrate greater BSA encapsulation efficiency due to their reduced entropy and flexibility. Furthermore, we examined the pH responsiveness of coacervates, shedding light on the dissolution process driven by Coulomb forces. By leveraging machine learning algorithms to analyze simulation results, our research advances the understanding of coacervate-based drug delivery systems, with the ultimate goal of optimizing therapeutic outcomes.
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Affiliation(s)
- Yiwei Wang
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University Chengdu 610065 China
| | - Rongrong Zou
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University Chengdu 610065 China
| | - Yeqiang Zhou
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University Chengdu 610065 China
| | - Yi Zheng
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University Chengdu 610065 China
| | - Chuan Peng
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University Chengdu 610065 China
| | - Yang Liu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University Chengdu 610065 China
| | - Hong Tan
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University Chengdu 610065 China
| | - Qiang Fu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University Chengdu 610065 China
| | - Mingming Ding
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University Chengdu 610065 China
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8
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Hong Y, Yoo S, Han J, Kim J, Lee Y, Jho Y, Kim YS, Hwang DS. Influence of the backbone chemistry and ionic functional groups of five pairs of oppositely charged polyelectrolytes on complex coacervation. Commun Chem 2024; 7:182. [PMID: 39147800 PMCID: PMC11327326 DOI: 10.1038/s42004-024-01271-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 08/06/2024] [Indexed: 08/17/2024] Open
Abstract
Complex coacervation plays an important role in various fields. Here, the influences of the backbone chemistry and ionic functional groups of five pairs of oppositely charged polyelectrolytes on complex coacervation were investigated. These pairs include synthetic polymers with aliphatic hydrocarbon backbones, peptides with amide bonds, and carbohydrates with glycosidic linkages. Despite sharing identical charged groups, specific pairs displayed distinct liquid/liquid and liquid/solid phase separations depending on the polyelectrolyte mixing ratio, buffer, and ionic strength. The coacervate phase boundary broadened in the orders: glycosidic linkages > amide backbone > aliphatic hydrocarbon backbone, and Tris-phosphate > Tris-acetate > Tris-chloride buffers. Coacervates prepared from polyelectrolytes with lower solubilities in water resisted disassembly at high salt concentrations, and their merge rate was slow. These observations suggest that the hydrophobic segments in polyelectrolytes interfere with the formation of complex coacervates; however, following coacervate formation, the hydrophobic segments render the coacervates stable and elastic.
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Affiliation(s)
- Yuri Hong
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Surim Yoo
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Jihoon Han
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Junseong Kim
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- Department of Physics and and Research Institute of Molecular Alchemy, Gyeongsang National University (GNU), Jinju, Republic of Korea
| | - Yongjin Lee
- Department of Chemical Engineering, Seoul National University (SNU), Seoul, Republic of Korea
| | - YongSeok Jho
- Department of Physics and and Research Institute of Molecular Alchemy, Gyeongsang National University (GNU), Jinju, Republic of Korea
| | - Youn Soo Kim
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
| | - Dong Soo Hwang
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
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9
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Zhou HX, Kota D, Qin S, Prasad R. Fundamental Aspects of Phase-Separated Biomolecular Condensates. Chem Rev 2024; 124:8550-8595. [PMID: 38885177 PMCID: PMC11260227 DOI: 10.1021/acs.chemrev.4c00138] [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] [Indexed: 06/20/2024]
Abstract
Biomolecular condensates, formed through phase separation, are upending our understanding in much of molecular, cell, and developmental biology. There is an urgent need to elucidate the physicochemical foundations of the behaviors and properties of biomolecular condensates. Here we aim to fill this need by writing a comprehensive, critical, and accessible review on the fundamental aspects of phase-separated biomolecular condensates. We introduce the relevant theoretical background, present the theoretical basis for the computation and experimental measurement of condensate properties, and give mechanistic interpretations of condensate behaviors and properties in terms of interactions at the molecular and residue levels.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
- Department of Physics, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Divya Kota
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Sanbo Qin
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
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10
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Holkar A, Gao S, Villaseñor K, Lake M, Srivastava S. Quantitative turbidimetric characterization of stabilized complex coacervate dispersions. SOFT MATTER 2024; 20:5060-5070. [PMID: 38743276 DOI: 10.1039/d3sm01761c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Stabilizing complex coacervate microdroplets is desirable due to their various applications, such as bioreactors, drug delivery vehicles, and encapsulants. Here, we present quantitative characterization of complex coacervate dispersion stability inferred by turbidimetry measurements. The stability of the dispersions is shown to be modulated by the concentrations of comb polyelectrolyte (cPE) stabilizers and salt. We demonstrate cPEs as effective stabilizers for complex coacervate dispersions independent of the chemistry or length of the constituent polyelectrolytes, salts, or preparation routes. By monitoring the temporal evolution of dispersion turbidity, we show that cPEs suppress microdroplet coalescence with minimal change in microdroplet sizes over 48 hours, even at salt concentrations up to 300 mM. The number density and average microdroplet size are shown to be controlled by varying the cPE and salt concentrations. Lastly, turbidity maps, akin to binodal phase maps, depict an expansion of the turbid two-phase region and an increase in the salt resistance of the coacervates upon the introduction of cPEs. The coacervate salt resistance is shown to increase by >3×, and this increase is maintained for up to 15 days, demonstrating that cPEs impart higher salt resistance over extended durations.
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Affiliation(s)
- Advait Holkar
- Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Shang Gao
- Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Kathleen Villaseñor
- Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Michael Lake
- NSF BioPACIFIC MIP, University of California, Los Angeles, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Samanvaya Srivastava
- Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
- NSF BioPACIFIC MIP, University of California, Los Angeles, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute for Carbon Management, University of California, Los Angeles, Los Angeles, CA 90095, USA
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11
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Laakko T, Korkealaakso A, Yildirir BF, Batys P, Liljeström V, Hokkanen A, Nonappa, Penttilä M, Laukkanen A, Miserez A, Södergård C, Mohammadi P. Accelerated Engineering of ELP-Based Materials through Hybrid Biomimetic-De Novo Predictive Molecular Design. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2312299. [PMID: 38710202 DOI: 10.1002/adma.202312299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/28/2024] [Indexed: 05/08/2024]
Abstract
Efforts to engineer high-performance protein-based materials inspired by nature have mostly focused on altering naturally occurring sequences to confer the desired functionalities, whereas de novo design lags significantly behind and calls for unconventional innovative approaches. Here, using partially disordered elastin-like polypeptides (ELPs) as initial building blocks this work shows that de novo engineering of protein materials can be accelerated through hybrid biomimetic design, which this work achieves by integrating computational modeling, deep neural network, and recombinant DNA technology. This generalizable approach involves incorporating a series of de novo-designed sequences with α-helical conformation and genetically encoding them into biologically inspired intrinsically disordered repeating motifs. The new ELP variants maintain structural conformation and showed tunable supramolecular self-assembly out of thermal equilibrium with phase behavior in vitro. This work illustrates the effective translation of the predicted molecular designs in structural and functional materials. The proposed methodology can be applied to a broad range of partially disordered biomacromolecules and potentially pave the way toward the discovery of novel structural proteins.
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Affiliation(s)
- Timo Laakko
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
| | | | - Burcu Firatligil Yildirir
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 6, Tampere, FI-33720, Finland
| | - Piotr Batys
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, Krakow, PL-30239, Poland
| | - Ville Liljeström
- Department of Applied Physics, School of Science, Aalto University, Aalto, FI-00076, Finland
| | - Ari Hokkanen
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
| | - Nonappa
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 6, Tampere, FI-33720, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
| | - Anssi Laukkanen
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
| | - Ali Miserez
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore, 637553, Singapore
- School of Biological Sciences, NTU, Singapore, 637551, Singapore
| | - Caj Södergård
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
| | - Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
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12
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Zhang L, Chen M, Wang Z, Zhong M, Chen H, Li T, Wang L, Zhao Z, Zhang XB, Ke G, Liu Y, Tan W. Spatiotemporal Regulation of Cell Fate in Living Systems Using Photoactivatable Artificial DNA Membraneless Organelles. ACS CENTRAL SCIENCE 2024; 10:1201-1210. [PMID: 38947212 PMCID: PMC11212128 DOI: 10.1021/acscentsci.4c00380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/17/2024] [Accepted: 05/08/2024] [Indexed: 07/02/2024]
Abstract
Coacervates formed by liquid-liquid phase separation emerge as important biomimetic models for studying the dynamic behaviors of membraneless organelles and synchronously motivating the creation of smart architectures with the regulation of cell fate. Despite continuous progress, it remains challenging to balance the trade-offs among structural stability, versatility, and molecular communication for regulation of cell fate and systemic investigation in a complex physiological system. Herein, we present a self-stabilizing and fastener-bound gain-of-function methodology to create a new type of synthetic DNA membraneless organelle (MO) with high stability and controlled bioactivity on the basis of DNA coacervates. Specifically, long single-strand DNA generated by rolling circle amplification (RCA) is selected as the scaffold that assembles into membraneless coacervates via phase separation. Intriguingly, the as-formed DNA MO can recruit RCA byproducts and other components to achieve self-stabilization, nanoscale condensation, and function encoding. As a proof of concept, photoactivatable DNA MO is constructed and successfully employed for time-dependent accumulation and spatiotemporal management of cancer in a mouse model. This study offers new, important insights into synthetic membraneless organelles for the basic understanding and manipulation of important life processes.
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Affiliation(s)
- Lili Zhang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Mei Chen
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Materials Science and Engineering, Aptamer
Engineering Center of Hunan Province, Hunan
University, Changsha, Hunan 410082, China
| | - Zhiqiang Wang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Minjuan Zhong
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Hong Chen
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Ting Li
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Linlin Wang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Zhihui Zhao
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Xiao-Bing Zhang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Guoliang Ke
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Yanlan Liu
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute
of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University
School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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13
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Stevens KC, Tirrell MV. Impact of a Lightly Branched Star Polyelectrolyte Architecture on Polyelectrolyte Complexes. ACS Macro Lett 2024; 13:688-694. [PMID: 38780149 DOI: 10.1021/acsmacrolett.4c00167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
The effect of charge density in blocky and statistical linear polyelectrolytes on polyelectrolyte complex (PEC) properties has been studied with the finding that increased charge density in a polyelectrolyte tends to increase the salt resistance and modulus of a PEC across various polyelectrolyte pairs. Here, we demonstrate the ability to orthogonally alter PEC salt resistance while maintaining rheological properties and internal structure by going from linear to lightly branched architectures with similar total degrees of polymerization. Using a model system built around glycidyl methacrylate (GMA) and thiol-epoxy "click" functionalization, we create a library of homologous linear, 4-armed, 6-armed, and 8-armed star polyelectrolytes. The PECs formed from these model polyelectrolyte pairs are then characterized via optical microscopy, rheology, and small-angle X-ray scattering to evaluate their salt resistance, mechanical properties, and internal structure. We argue that our results are due to the difference between linear charge density or charge per unit length along backbone segments for each polyelectrolyte and spatial charge density, the number of charges per unit volume of the polyelectrolyte prior to complexation. Our findings suggest that linear charge density is the dominant factor in determining intermolecular interactions of the complex, leading to identical rheological and structural behavior, whereas the spatial charge density primarily influences the stability of the complexes. These distinct mechanisms for altering various sought-after PEC properties offer greater potential applications in precision design of polyelectrolyte complex materials.
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Affiliation(s)
- Kaden C Stevens
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
| | - Matthew V Tirrell
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
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14
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Miglani C, Ralhan J, Banoo M, Nath D, Sil S, Pal SK, Gautam UK, Pal A. Stimuli-Responsive Control over Self-Assembled Nanostructures in Sequence-Specific Functional Block Copolymers. ACS POLYMERS AU 2024; 4:255-265. [PMID: 38882035 PMCID: PMC11177304 DOI: 10.1021/acspolymersau.4c00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 06/18/2024]
Abstract
The precise sequence of a protein's primary structure is essential in determining its folding pathways. To emulate the complexity of these biomolecules, functional block copolymers consisting of segmented triblocks with distinct functionalities positioned in a sequence-specific manner are designed to control the polymer chain compaction. Triblock polymers P- b -C- b -F and P- b -F- b -C and random diblock copolymer P- b -C- r -F consist of a hydrophilic poly(ethylene oxide) (PEO) block and a hydrophobic block with coumarin (C) and ferrocene (F) moieties that are grafted in a sequence-specific or random manner onto the hydrophilic block. External stimuli such as UVB light, redox, and chemical cues influence the functional hydrophobic block to alter the packing parameters that are monitored with spectroscopic and scattering techniques. Interestingly, the positioning of the stimuli-responsive moiety within the hydrophobic block of P- b -C- b -F, P- b -F- b -C, and P- b -C- r -F affects the extent of the hydrophobic-hydrophilic balance in block copolymers that renders orthogonal control in stimuli-responsive transformation of self-assembled vesicles to micelles.
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Affiliation(s)
- Chirag Miglani
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab 140306, India
| | - Jahanvi Ralhan
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab 140306, India
| | - Maqsuma Banoo
- Department of Chemical Sciences, IISER Mohali, Knowledge City, Sector 81, Mohali, Punjab 140306, India
| | - Debasish Nath
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab 140306, India
| | - Soma Sil
- Department of Chemical Sciences, IISER Mohali, Knowledge City, Sector 81, Mohali, Punjab 140306, India
| | - Santanu K Pal
- Department of Chemical Sciences, IISER Mohali, Knowledge City, Sector 81, Mohali, Punjab 140306, India
| | - Ujjal K Gautam
- Department of Chemical Sciences, IISER Mohali, Knowledge City, Sector 81, Mohali, Punjab 140306, India
| | - Asish Pal
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab 140306, India
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15
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Koyama T, Iso N, Norizoe Y, Sakaue T, Yoshimura SH. Charge block-driven liquid-liquid phase separation - mechanism and biological roles. J Cell Sci 2024; 137:jcs261394. [PMID: 38855848 DOI: 10.1242/jcs.261394] [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: 06/11/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) has increasingly been found to play pivotal roles in a number of intracellular events and reactions, and has introduced a new paradigm in cell biology to explain protein-protein and enzyme-ligand interactions beyond conventional molecular and biochemical theories. LLPS is driven by the cumulative effects of weak and promiscuous interactions, including electrostatic, hydrophobic and cation-π interactions, among polypeptides containing intrinsically disordered regions (IDRs) and describes the macroscopic behaviours of IDR-containing proteins in an intracellular milieu. Recent studies have revealed that interactions between 'charge blocks' - clusters of like charges along the polypeptide chain - strongly induce LLPS and play fundamental roles in its spatiotemporal regulation. Introducing a new parameter, termed 'charge blockiness', into physicochemical models of disordered polypeptides has yielded a better understanding of how the intrinsic amino acid sequence of a polypeptide determines the spatiotemporal occurrence of LLPS within a cell. Charge blockiness might also explain why some post-translational modifications segregate within IDRs and how they regulate LLPS. In this Review, we summarise recent progress towards understanding the mechanism and biological roles of charge block-driven LLPS and discuss how this new characteristic parameter of polypeptides offers new possibilities in the fields of structural biology and cell biology.
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Affiliation(s)
- Tetsu Koyama
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Naoki Iso
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Yuki Norizoe
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Shige H Yoshimura
- Graduate School of Biostudies , Kyoto University, Yoshida-konoe, Sakyo-ku, Kyoto, 606-8501, Japan
- Center for Living Systems Information Science (CeLiSIS) , Kyoto University, Yoshida-Konoe-Cho, Sakyo-ku, Kyoto, 606-8501, Japan
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16
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King MR, Ruff KM, Lin AZ, Pant A, Farag M, Lalmansingh JM, Wu T, Fossat MJ, Ouyang W, Lew MD, Lundberg E, Vahey MD, Pappu RV. Macromolecular condensation organizes nucleolar sub-phases to set up a pH gradient. Cell 2024; 187:1889-1906.e24. [PMID: 38503281 DOI: 10.1016/j.cell.2024.02.029] [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] [Received: 07/18/2023] [Revised: 01/02/2024] [Accepted: 02/22/2024] [Indexed: 03/21/2024]
Abstract
Nucleoli are multicomponent condensates defined by coexisting sub-phases. We identified distinct intrinsically disordered regions (IDRs), including acidic (D/E) tracts and K-blocks interspersed by E-rich regions, as defining features of nucleolar proteins. We show that the localization preferences of nucleolar proteins are determined by their IDRs and the types of RNA or DNA binding domains they encompass. In vitro reconstitutions and studies in cells showed how condensation, which combines binding and complex coacervation of nucleolar components, contributes to nucleolar organization. D/E tracts of nucleolar proteins contribute to lowering the pH of co-condensates formed with nucleolar RNAs in vitro. In cells, this sets up a pH gradient between nucleoli and the nucleoplasm. By contrast, juxta-nucleolar bodies, which have different macromolecular compositions, featuring protein IDRs with very different charge profiles, have pH values that are equivalent to or higher than the nucleoplasm. Our findings show that distinct compositional specificities generate distinct physicochemical properties for condensates.
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Affiliation(s)
- Matthew R King
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Kiersten M Ruff
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrew Z Lin
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Avnika Pant
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Mina Farag
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Jared M Lalmansingh
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Tingting Wu
- Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Department of Electrical and Systems Engineering, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Martin J Fossat
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Wei Ouyang
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA; Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Matthew D Lew
- Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Department of Electrical and Systems Engineering, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Emma Lundberg
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA; Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Michael D Vahey
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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17
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Morrison C, Chan EP, Lee T, Deming TJ. Switchable Coacervate Formation via Amino Acid Functionalization of Poly(dehydroalanine). Biomacromolecules 2024; 25:2554-2562. [PMID: 38426942 PMCID: PMC11005011 DOI: 10.1021/acs.biomac.4c00048] [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: 01/15/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
Our group recently developed a family of side-chain amino acid-functionalized poly(S-alkyl-l-homocysteines), Xaa-CH (Xaa = generic amino acid), which possess the ability to form environmentally responsive coacervates in water. In an effort to further study how the molecular structure affects polypeptide coacervate formation, we prepared side-chain amino acid-functionalized poly(S-alkyl-rac-cysteines), Xaa-rac-C, via post-polymerization modification of poly(dehydroalanine), ADH. The use of the ADH platform allowed straightforward synthesis of a diverse range of side-chain amino acid-functionalized polypeptides via direct reaction of unprotected l-amino acid 2-mercaptoethylamides with ADH. Despite their differences in the main-chain structure, we found that Xaa-rac-C can form coacervates with properties similar to those seen with Xaa-CH. These results suggest that the incorporation of side-chain amino acids onto polypeptides may be a way to generally favor coacervation. The incorporation of l-methionine in Met-rac-C allowed the preparation of coacervates with improved stability against high ionic strength media. Further, the presence of additional thioether groups in Met-rac-C resulted in an increased solubility change upon oxidation allowing facile reversible redox switching of coacervate formation in aqueous media.
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Affiliation(s)
- Casey
A. Morrison
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Ethan P. Chan
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Thatcher Lee
- Department
of Chemistry, Smith College, Northampton, Massachusetts 01063, United States
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Timothy J. Deming
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
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18
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Zhu Q, Wu Y, Luo R. Understanding and fine tuning the propensity of ATP-driven liquid-liquid phase separation with oligolysine. Phys Chem Chem Phys 2024; 26:10568-10578. [PMID: 38512104 PMCID: PMC11056285 DOI: 10.1039/d4cp00761a] [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] [Indexed: 03/22/2024]
Abstract
Liquid-liquid phase separation (LLPS) plays a pivotal role in the organization and functionality of living cells. It is imperative to understand the underlying driving forces behind LLPS and to control its occurrence. In this study, we employed coarse-grained (CG) simulations as a research tool to investigate systems comprising oligolysine and adenosine triphosphate (ATP) under conditions of various ionic concentrations and oligolysine lengths. Consistent with experimental observations, our CG simulations captured the formation of LLPS upon the addition of ATP and tendency of dissociating under high ionic concentration. The electrostatic interaction between oligolysine and ATP is of great importance in forming LLPS. An in-depth analysis on the structural properties of LLPS was conducted, where the oligolysine structure remained unchanged with increased ionic concentration and the addition of ATP led to a more pronounced curvature, aligning with the observed enhancement of α-helical secondary structure in experiments. In terms of the dynamic properties, the introduction of ATP led to a significant reduction in translational and vibrational degrees of freedom but not rotational degrees of freedom. Through keeping the total number of charged residues constant and varying their entropic effects, we constructed two systems of similar biochemical significance and further validated the entropy effects on the LLPS formation. These findings provide a deeper understanding of LLPS formation and shed lights on the development of novel bioreactor and primitive artificial cells for synthesizing key chemicals for certain diseases.
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Affiliation(s)
- Qiang Zhu
- Department of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, California 92697, USA.
| | - Yongxian Wu
- Department of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, California 92697, USA.
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, California 92697, USA.
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19
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Abeysinghe AADT, Young EJ, Rowland AT, Dunshee LC, Urandur S, Sullivan MO, Kerfeld CA, Keating CD. Interfacial Assembly of Bacterial Microcompartment Shell Proteins in Aqueous Multiphase Systems. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308390. [PMID: 38037673 DOI: 10.1002/smll.202308390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/13/2023] [Indexed: 12/02/2023]
Abstract
Compartments are a fundamental feature of life, based variously on lipid membranes, protein shells, or biopolymer phase separation. Here, this combines self-assembling bacterial microcompartment (BMC) shell proteins and liquid-liquid phase separation (LLPS) to develop new forms of compartmentalization. It is found that BMC shell proteins assemble at the liquid-liquid interfaces between either 1) the dextran-rich droplets and PEG-rich continuous phase of a poly(ethyleneglycol)(PEG)/dextran aqueous two-phase system, or 2) the polypeptide-rich coacervate droplets and continuous dilute phase of a polylysine/polyaspartate complex coacervate system. Interfacial protein assemblies in the coacervate system are sensitive to the ratio of cationic to anionic polypeptides, consistent with electrostatically-driven assembly. In both systems, interfacial protein assembly competes with aggregation, with protein concentration and polycation availability impacting coating. These two LLPS systems are then combined to form a three-phase system wherein coacervate droplets are contained within dextran-rich phase droplets. Interfacial localization of BMC hexameric shell proteins is tunable in a three-phase system by changing the polyelectrolyte charge ratio. The tens-of-micron scale BMC shell protein-coated droplets introduced here can accommodate bioactive cargo such as enzymes or RNA and represent a new synthetic cell strategy for organizing biomimetic functionality.
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Affiliation(s)
| | - Eric J Young
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Andrew T Rowland
- Department of Chemistry, Pennsylvania State University, State College, PA, 16801, USA
| | - Lucas C Dunshee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Sandeep Urandur
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Cheryl A Kerfeld
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Christine D Keating
- Department of Chemistry, Pennsylvania State University, State College, PA, 16801, USA
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20
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Xie S, Yue C, Ye S, Li Z. Probing the hierarchical dynamics of DNA-sperm nuclear transition protein complexes through fuzzy interaction and mesoscale condensation. Phys Chem Chem Phys 2024; 26:10408-10418. [PMID: 38502252 DOI: 10.1039/d3cp05957j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Nuclear transition protein TNP1 is a crucial player mediating histone-protamine exchange in condensing spermatids. A unique combination of intrinsic disorder and multivalent properties turns TNP1 into an ideal agent for orchestrating the formation of versatile TNP-DNA assemblies. Despite its significance, the physicochemical property and the molecular mechanism followed by TNP1 for histone replacement and DNA condensation are still poorly understood. This study reports the first-time in vitro expression and purification of human TNP1 and investigates the hierarchical dynamics of TNP1-DNA interaction using a combination of computational simulations, biochemical assays, fluorescence imaging, and atomic force microscopy. We explored three crucial facets of TNP1-DNA interactions. Initially, we delve into the molecular binding process that entails fuzzy interactions between TNP1 and DNA at the atomistic scale. Subsequently, we analyze how TNP1 binding affects the electrostatic and mechanical characteristics of DNA and influences its morphology. Finally, we study the biomolecular condensation of TNP1-DNA when subjected to high concentrations. The findings of our study set the foundation for comprehending the potential involvement of TNP1 in histone replacement and DNA condensation in spermatogenesis.
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Affiliation(s)
- Shangqiang Xie
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
| | - Congran Yue
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
| | - Sheng Ye
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Zhenlu Li
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, 92 Weijin Road, Tianjin 300072, China
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21
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Lei M, Liao H, Wang S, Zhou H, Zhu J, Wan H, Payne GF, Liu C, Qu X. Electro-Sorting Create Heterogeneity: Constructing A Multifunctional Janus Film with Integrated Compositional and Microstructural Gradients for Guided Bone Regeneration. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307606. [PMID: 38225697 DOI: 10.1002/advs.202307606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/25/2023] [Indexed: 01/17/2024]
Abstract
Biology remains the envy of flexible soft matter fabrication because it can satisfy multiple functional needs by organizing a small set of proteins and polysaccharides into hierarchical systems with controlled heterogeneity in composition and microstructure. Here, it is reported that controlled, mild electronic inputs (<10 V; <20 min) induce a homogeneous gelatin-chitosan mixture to undergo sorting and bottom-up self-assembly into a Janus film with compositional gradient (i.e., from chitosan-enriched layer to chitosan/gelatin-contained layer) and tunable dense-porous gradient microstructures (e.g., porosity, pore size, and ratio of dense to porous layers). This Janus film performs is shown multiple functions for guided bone regeneration: the integration of compositional and microstructural features confers flexible mechanics, asymmetric properties for interfacial wettability, molecular transport (directional growth factor release), and cellular responses (prevents fibroblast infiltration but promotes osteoblast growth and differentiation). Overall, this work demonstrates the versatility of electrofabrication for the customized manufacturing of functional gradient soft matter.
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Affiliation(s)
- Miao Lei
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Haitao Liao
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Shijia Wang
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Hang Zhou
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jianwei Zhu
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Haoran Wan
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Gregory F Payne
- Institute for Bioscience and Biotechnology Research and Robert E. Fischell Biomedical Device Institute, 5118 A. James Clark Hall, College Park, Maryland, 20742, USA
| | - Changsheng Liu
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xue Qu
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
- Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China
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22
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Alshareedah I, Singh A, Yang S, Ramachandran V, Quinn A, Potoyan DA, Banerjee PR. Determinants of viscoelasticity and flow activation energy in biomolecular condensates. SCIENCE ADVANCES 2024; 10:eadi6539. [PMID: 38363841 PMCID: PMC10871536 DOI: 10.1126/sciadv.adi6539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/17/2024] [Indexed: 02/18/2024]
Abstract
The form and function of biomolecular condensates are intimately linked to their material properties. Here, we integrate microrheology with molecular simulations to dissect the physical determinants of condensate fluid phase dynamics. By quantifying the timescales and energetics of network relaxation in a series of heterotypic viscoelastic condensates, we uncover distinctive roles of sticker motifs, binding energy, and chain length in dictating condensate dynamical properties. We find that the mechanical relaxation times of condensate-spanning networks are determined by both intermolecular interactions and chain length. We demonstrate, however, that the energy barrier for network reconfiguration, termed flow activation energy, is independent of chain length and only varies with the strengths of intermolecular interactions. Biomolecular diffusion in the dense phase depends on a complex interplay between viscoelasticity and flow activation energy. Our results illuminate distinctive roles of chain length and sequence-specific multivalent interactions underlying the complex material and transport properties of biomolecular condensates.
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Affiliation(s)
| | - Anurag Singh
- Department of Physics, University at Buffalo, Buffalo, NY 14260, USA
| | - Sean Yang
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | | | - Alexander Quinn
- Department of Physics, University at Buffalo, Buffalo, NY 14260, USA
| | - Davit A. Potoyan
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | - Priya R. Banerjee
- Department of Physics, University at Buffalo, Buffalo, NY 14260, USA
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23
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Staňo R, van Lente J, Lindhoud S, Košovan P. Sequestration of Small Ions and Weak Acids and Bases by a Polyelectrolyte Complex Studied by Simulation and Experiment. Macromolecules 2024; 57:1383-1398. [PMID: 38370910 PMCID: PMC10867894 DOI: 10.1021/acs.macromol.3c01209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 02/20/2024]
Abstract
Mixing of oppositely charged polyelectrolytes can result in phase separation into a polymer-poor supernatant and a polymer-rich polyelectrolyte complex (PEC). We present a new coarse-grained model for the Grand-reaction method that enables us to determine the composition of the coexisting phases in a broad range of pH and salt concentrations. We validate the model by comparing it to recent simulations and experimental studies, as well as our own experiments on poly(acrylic acid)/poly(allylamine hydrochloride) complexes. The simulations using our model predict that monovalent ions partition approximately equally between both phases, whereas divalent ones accumulate in the PEC phase. On a semiquantitative level, these results agree with our own experiments, as well as with other experiments and simulations in the literature. In the sequel, we use the model to study the partitioning of a weak diprotic acid at various pH values of the supernatant. Our results show that the ionization of the acid is enhanced in the PEC phase, resulting in its preferential accumulation in this phase, which monotonically increases with the pH. Currently, this effect is still waiting to be confirmed experimentally. We explore how the model parameters (particle size, charge density, permittivity, and solvent quality) affect the measured partition coefficients, showing that fine-tuning of these parameters can make the agreement with the experiments almost quantitative. Nevertheless, our results show that charge regulation in multivalent solutes can potentially be exploited in engineering the partitioning of charged molecules in PEC-based systems at various pH values.
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Affiliation(s)
- Roman Staňo
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
- Vienna
Doctoral School in Physics, University of
Vienna, Boltzmanngasse
5, 1090 Vienna, Austria
| | - Jéré
J. van Lente
- Department
of Molecules & Materials, University
of Twente, Drienerlolaan 5, 7522 NB Enschede, The Netherlands
| | - Saskia Lindhoud
- Department
of Molecules & Materials, University
of Twente, Drienerlolaan 5, 7522 NB Enschede, The Netherlands
| | - Peter Košovan
- Department
of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 40 Prague 2, Czech Republic
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24
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Joshi P, Decker C, Zeng X, Sathyavageeswaran A, Perry SL, Heldt CL. Design Rules for the Sequestration of Viruses into Polypeptide Complex Coacervates. Biomacromolecules 2024; 25:741-753. [PMID: 38103178 PMCID: PMC10866146 DOI: 10.1021/acs.biomac.3c00938] [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: 09/05/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023]
Abstract
Encapsulation is a strategy that has been used to facilitate the delivery and increase the stability of proteins and viruses. Here, we investigate the encapsulation of viruses via complex coacervation, which is a liquid-liquid phase separation resulting from the complexation of oppositely charged polymers. In particular, we utilized polypeptide-based coacervates and explored the effects of peptide chemistry, chain length, charge patterning, and hydrophobicity to better understand the effects of the coacervating polypeptides on virus incorporation. Our study utilized two nonenveloped viruses, porcine parvovirus (PPV) and human rhinovirus (HRV). PPV has a higher charge density than HRV, and they both appear to be relatively hydrophobic. These viruses were compared to characterize how the charge, hydrophobicity, and patterning of chemistry on the surface of the virus capsid affects encapsulation. Consistent with the electrostatic nature of complex coacervation, our results suggest that electrostatic effects associated with the net charge of both the virus and polypeptide dominated the potential for incorporating the virus into a coacervate, with clustering of charges also playing a significant role. Additionally, the hydrophobicity of a virus appears to determine the degree to which increasing the hydrophobicity of the coacervating peptides can enhance virus uptake. Nonintuitive trends in uptake were observed with regard to both charge patterning and polypeptide chain length, with these parameters having a significant effect on the range of coacervate compositions over which virus incorporation was observed. These results provide insights into biophysical mechanisms, where sequence effects can control the uptake of proteins or viruses into biological condensates and provide insights for use in formulation strategies.
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Affiliation(s)
- Pratik
U. Joshi
- Department
of Chemical Engineering, Michigan Technological
University, Houghton, Michigan 49931, United States
- Health
Research Institute, Michigan Technological
University, Houghton, Michigan 49931, United States
| | - Claire Decker
- Department
of Chemical Engineering, Michigan Technological
University, Houghton, Michigan 49931, United States
| | - Xianci Zeng
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Arvind Sathyavageeswaran
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Sarah L. Perry
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
- Institute
for Applied Life Sciences, University of
Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Caryn L. Heldt
- Department
of Chemical Engineering, Michigan Technological
University, Houghton, Michigan 49931, United States
- Health
Research Institute, Michigan Technological
University, Houghton, Michigan 49931, United States
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25
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Truong HP, Saleh OA. Magnetic tweezers characterization of the entropic elasticity of intrinsically disordered proteins and peptoids. Methods Enzymol 2024; 694:209-236. [PMID: 38492952 DOI: 10.1016/bs.mie.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
Understanding the conformational behavior of biopolymers is essential to unlocking knowledge of their biophysical mechanisms and functional roles. Single-molecule force spectroscopy can provide a unique perspective on this by exploiting entropic elasticity to uncover key biopolymer structural parameters. A particularly powerful approach involves the use of magnetic tweezers, which can easily generate lower stretching forces (0.1-20 pN). For forces at the low end of this range, the elastic response of biopolymers is sensitive to excluded volume effects, and they can be described by Pincus blob elasticity model that allow robust extraction of the Flory polymer scaling exponent. Here, we detail protocols for the use of magnetic tweezers for force-extension measurements of intrinsically disordered proteins and peptoids. We also discuss procedures for fitting low-force elastic curves to the predictions of polymer physics models to extract key conformational parameters.
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Affiliation(s)
- Hoang P Truong
- Materials Department, University of California, Santa Barbara, CA, United States
| | - Omar A Saleh
- Materials Department, University of California, Santa Barbara, CA, United States; Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, CA, United States; Physics Department, University of California, Santa Barbara, CA, United States.
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26
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Sathyavageeswaran A, Bonesso Sabadini J, Perry SL. Self-Assembling Polypeptides in Complex Coacervation. Acc Chem Res 2024; 57:386-398. [PMID: 38252962 DOI: 10.1021/acs.accounts.3c00689] [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] [Indexed: 01/24/2024]
Abstract
Intracellular compartmentalization plays a pivotal role in cellular function, with membrane-bound organelles and membrane-less biomolecular "condensates" playing key roles. These condensates, formed through liquid-liquid phase separation (LLPS), enable selective compartmentalization without the barrier of a lipid bilayer, thereby facilitating rapid formation and dissolution in response to stimuli. Intrinsically disordered proteins (IDPs) or proteins with intrinsically disordered regions (IDRs), which are often rich in charged and polar amino acid sequences, scaffold many condensates, often in conjunction with RNA.Comprehending the impact of IDP/IDR sequences on phase separation poses a challenge due to the extensive chemical diversity resulting from the myriad amino acids and post-translational modifications. To tackle this hurdle, one approach has been to investigate LLPS in simplified polypeptide systems, which offer a narrower scope within the chemical space for exploration. This strategy is supported by studies that have demonstrated how IDP function can largely be understood based on general chemical features, such as clusters or patterns of charged amino acids, rather than residue-level effects, and the ways in which these kinds of motifs give rise to an ensemble of conformations.Our laboratory has utilized complex coacervates assembled from oppositely charged polypeptides as a simplified material analogue to the complexity of liquid-liquid phase separated biological condensates. Complex coacervation is an associative LLPS that occurs due to the electrostatic complexation of oppositely charged macro-ions. This process is believed to be driven by the entropic gains resulting from the release of bound counterions and the reorganization of water upon complex formation. Apart from their direct applicability to IDPs, polypeptides also serve as excellent model polymers for investigating molecular interactions due to the wide range of available side-chain functionalities and the capacity to finely regulate their sequence, thus enabling precise control over interactions with guest molecules.Here, we discuss fundamental studies examining how charge patterning, hydrophobicity, chirality, and architecture affect the phase separation of polypeptide-based complex coacervates. These efforts have leveraged a combination of experimental and computational approaches that provide insight into molecular level interactions. We also examine how these parameters affect the ability of complex coacervates to incorporate globular proteins and viruses. These efforts couple directly with our fundamental studies into coacervate formation, as such "guest" molecules should not be considered as experiencing simple encapsulation and are instead active participants in the electrostatic assembly of coacervate materials. Interestingly, we observed trends in the incorporation of proteins and viruses into coacervates formed using different chain length polypeptides that are not well explained by simple electrostatic arguments and may be the result of more complex interactions between globular and polymeric species. Additionally, we describe experimental evidence supporting the potential for complex coacervates to improve the thermal stability of embedded biomolecules, such as viral vaccines.Ultimately, peptide-based coacervates have the potential to help unravel the physics behind biological condensates, while paving the way for innovative methods in compartmentalization, purification, and biomolecule stabilization. These advancements could have implications spanning medicine to biocatalysis.
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Affiliation(s)
- Arvind Sathyavageeswaran
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 10003, United States
| | - Júlia Bonesso Sabadini
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 10003, United States
- Institute of Chemistry, University of Campinas (UNICAMP), Campinas, SP 13083-970, Brazil
| | - Sarah L Perry
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 10003, United States
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27
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Cook AB, Gonzalez BD, van Hest JCM. Tuning of Cationic Polymer Functionality in Complex Coacervate Artificial Cells for Optimized Enzyme Activity. Biomacromolecules 2024; 25:425-435. [PMID: 38064593 PMCID: PMC10777345 DOI: 10.1021/acs.biomac.3c01063] [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: 10/05/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024]
Abstract
Complex coacervates are a versatile platform to mimic the structure of living cells. In both living systems and artificial cells, a macromolecularly crowded condensate phase has been shown to be able to modulate enzyme activity. Yet, how enzyme activity is affected by interactions (particularly with cationic charges) inside coacervates is not well studied. Here, we synthesized a series of amino-functional polymers to investigate the effect of the type of amine and charge density on coacervate formation, stability, protein partitioning, and enzyme function. The polymers were prepared by RAFT polymerization using as monomers aminoethyl methacrylate (AEAM), 2-(dimethylamino)ethyl methacrylate (DMAEMA), imidazolepropyl methacrylamide (IPMAm), and [2-(methacryloyloxy)ethyl] trimethylammonium chloride (TMAEMA). Membranized complex coacervate artificial cells were formed with these polycations and an anionic amylose derivative. Results show that polycations with reduced charge density result in higher protein mobility in the condensates and also higher enzyme activity. Insights described here could help guide the use of coacervate artificial cells in applications such as sensing, catalysis, and therapeutic formulations.
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Affiliation(s)
- Alexander B Cook
- Bio-Organic
Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven 5600 MB, Netherlands
| | - Bruno Delgado Gonzalez
- Departamento
de Química Orgánica, Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, Santiago de Compostela 15782, Spain
| | - Jan C M van Hest
- Bio-Organic
Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven 5600 MB, Netherlands
- Biomedical
Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven 5600 MB, Netherlands
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28
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Wu X, Sun Y, Yu J, Miserez A. Tuning the viscoelastic properties of peptide coacervates by single amino acid mutations and salt kosmotropicity. Commun Chem 2024; 7:5. [PMID: 38177438 PMCID: PMC10766971 DOI: 10.1038/s42004-023-01094-y] [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: 09/08/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024] Open
Abstract
Coacervation, or liquid-liquid phase separation (LLPS) of biomacromolecules, is increasingly recognized to play an important role both intracellularly and in the extracellular space. Central questions that remain to be addressed are the links between the material properties of coacervates (condensates) and both the primary and the secondary structures of their constitutive building blocks. Short LLPS-prone peptides, such as GY23 variants explored in this study, are ideal model systems to investigate these links because simple sequence modifications and the chemical environment strongly affect the viscoelastic properties of coacervates. Herein, a systematic investigation of the structure/property relationships of peptide coacervates was conducted using GY23 variants, combining biophysical characterization (plate rheology and surface force apparatus, SFA) with secondary structure investigations by infrared (IR) and circular dichroism (CD) spectroscopy. Mutating specific residues into either more hydrophobic or more hydrophilic residues strongly regulates the viscoelastic properties of GY23 coacervates. Furthermore, the ionic strength and kosmotropic characteristics (Hofmeister series) of the buffer in which LLPS is induced also significantly impact the properties of formed coacervates. Structural investigations by CD and IR indicate a direct correlation between variations in properties induced by endogenous (peptide sequence) or exogenous (ionic strength, kosmotropic characteristics, aging) factors and the β-sheet content within coacervates. These findings provide valuable insights to rationally design short peptide coacervates with programmable materials properties that are increasingly used in biomedical applications.
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Affiliation(s)
- Xi Wu
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore, 637553, Singapore
| | - Yue Sun
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore, 637553, Singapore
| | - Jing Yu
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 637553, Singapore.
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore, 637553, Singapore.
| | - Ali Miserez
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore, 637553, Singapore.
- School of Biological Sciences, 60 Nanyang Drive, NTU, Singapore, 636921, Singapore.
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29
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Yamaguchi T, Chong SH, Yoshida N. Coexistence of two coacervate phases of polyglycine in water suggested by polymer reference interaction site model theory. J Chem Phys 2023; 159:245101. [PMID: 38131487 DOI: 10.1063/5.0185157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
Mixing Gibbs energy and phase equilibria of aqueous solutions of polyglycine were studied theoretically by means of polymer reference interaction site model integral equation theory combined with the Gibbs-Duhem method. In addition to the ordinary liquid-liquid phase separation between dilute and concentrated solutions, the theoretical calculation predicted the coexistence of two coacervate phases, namely, the lower- and higher-density coacervates. The relative thermodynamic stabilities of these two phases change with the polymerization degree of polyglycine. The higher-density coacervate phase was rapidly stabilized by increasing the polymer length, and the lower-density phase became metastable at large polymers. The hydrogen bonds between the peptide chains were strengthened, and water was thermodynamically destabilized in the higher-density coacervate. A possible relation with the formation of amyloid fibril within a liquid droplet is also discussed.
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Affiliation(s)
- Tsuyoshi Yamaguchi
- Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Song-Ho Chong
- Global Center for Natural Resources Sciences, Faculty of Life Sciences, Kumamoto University, Oe-honmachi 5-1, Chuo-ku, Kumamoto 862-0973, Japan
| | - Norio Yoshida
- Graduate School of Informatics, Nagoya University, Chikusa, Nagoya 464-8601, Japan
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30
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Rumyantsev AM, Zhulina EB, Borisov OV. Surface-Immobilized Interpolyelectrolyte Complexes Formed by Polyelectrolyte Brushes. ACS Macro Lett 2023; 12:1727-1732. [PMID: 38061050 DOI: 10.1021/acsmacrolett.3c00548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
A scaling theory of interaction and complex formation between planar polyelectrolyte (PE) brush and oppositely charged mobile linear PEs is developed. Counterion release is found to be the main driving force for the complexation. An interpolyelectrolyte coacervate complex (IPEC) between the brush and oppositely charged mobile PEs is formed at moderate grafting density and low salt concentration. At higher grafting density mobile chains penetrate the brush, but the brush structure is controlled by the balance between entropic elasticity and nonelectrostatic short-range interactions, as happens in a neutral brush. An increase in salt concentration beyond the theoretically predicted threshold leads to the release of the guest polyions from the brush. For brushes with moderate grafting density, complexation with oppositely charged guest polyions is predicted to trigger lateral microphase separation and formation of the finite-size surface IPEC clusters. Power law dependencies for the cluster dimensions on the brush grafting density, PE length, and salt concentration are provided.
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Affiliation(s)
- Artem M Rumyantsev
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Ekaterina B Zhulina
- Institute of Macromolecular Compounds of the Russian Academy of Sciences, 199004 St. Petersburg, Russia
| | - Oleg V Borisov
- Institute of Macromolecular Compounds of the Russian Academy of Sciences, 199004 St. Petersburg, Russia
- CNRS, Université de Pau et des Pays de l'Adour UMR 5254, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux, 64053 Pau, France
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31
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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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32
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Lin T, Zhou Y, Dadmohammadi Y, Yaghoobi M, Meletharayil G, Kapoor R, Abbaspourrad A. Encapsulation and stabilization of lactoferrin in polyelectrolyte ternary complexes. Food Hydrocoll 2023; 145:109064. [PMID: 37545760 PMCID: PMC10399645 DOI: 10.1016/j.foodhyd.2023.109064] [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] [Indexed: 08/08/2023]
Abstract
Effective delivery of the bioactive protein, lactoferrin (LF), remains a challenge as it is sensitive to environmental changes and easily denatured during heating, restricting its application in functional food products. To overcome these challenges, we formulated novel polyelectrolyte ternary complexes of LF with gelatin (G) and negatively charged polysaccharides, to improve the thermal stability of LF with retained antibacterial activity. Linear, highly charged polysaccharides were able to form interpolymeric complexes with LF and G, while coacervates were formed with branched polysaccharides. A unique multiphase coacervate was observed in the gum Arabic GA-LF-G complex, where a special coacervate-in-coacervate structure was found. The ternary complexes made with GA, soy soluble polysaccharide (SSP), or high methoxyl pectin (HMP) preserved the protein structures and demonstrated enhanced thermal stability of LF. The GA-LF-G complex was especially stable with >90% retention of the native LF after treatment at 90 °C for 2 min in a water bath or at 145 °C for 30 s, while the LF control had only ~ 7% undenatured LF under both conditions. In comparison to untreated LF, LF in ternary complex retained significant antibacterial activity on both Gram-positive and Gram-negative bacteria, even after heat treatment. These ternary complexes of LF maintain the desired functionality of LF, thermal stability and antibacterial activity, in the final products. The ternary complex structure, particularly the multiphase coacervate, may serve as a template for the encapsulation and stabilization of other bioactives and peptides.
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Affiliation(s)
- Tiantian Lin
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Yufeng Zhou
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Younas Dadmohammadi
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Mohammad Yaghoobi
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | | | | | - Alireza Abbaspourrad
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
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33
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Chen C, Wu S, Wang Y, Cao J, Tian L. Reversible modulation of protocell volume via collective response of functional protein in its membrane. J Colloid Interface Sci 2023; 651:182-190. [PMID: 37542893 DOI: 10.1016/j.jcis.2023.07.184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/07/2023]
Abstract
Volume change plays an important role in biological cells to regulate their internal microenvironment. To adapt to the rapid variation of the surface area during the volume change, the lipid membrane is dynamically modulated via membrane folding invagination, or spontaneous uptake or release of lipid molecules under osmotic pressure. Here, we demonstrate an alternative approach to design a functional protocellular system capable of dynamically adjusting its volume and intracellular microenvironment in response to the alteration of pH. By assembling and subsequently cross-linking pH-responsive caseinate at the water-oil interface, the caseinate-based protocell with more than ten thousand caseinate units in its membrane was established and showed a reversible volume and pore size change to pH variation due to the collective response of the caseinate in the membrane, which could be used to control the spatial distribution of proto-organelle by regulating of the viscosity inside the protocell.
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Affiliation(s)
- Chong Chen
- Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China; Innovation Center for Smart Medical Technologies & Devices, Binjiang Institute of Zhejiang University, Hangzhou 310053, China
| | - Shuqi Wu
- Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China
| | - Ying Wang
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, China.
| | - Jinxuan Cao
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Liangfei Tian
- Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China; Innovation Center for Smart Medical Technologies & Devices, Binjiang Institute of Zhejiang University, Hangzhou 310053, China; Department of Ultrasound, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310027, China.
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34
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Papageorgiou AC, Pospisilova M, Cibulka J, Ashraf R, Waudby CA, Kadeřávek P, Maroz V, Kubicek K, Prokop Z, Krejci L, Tripsianes K. Recognition and coacervation of G-quadruplexes by a multifunctional disordered region in RECQ4 helicase. Nat Commun 2023; 14:6751. [PMID: 37875529 PMCID: PMC10598209 DOI: 10.1038/s41467-023-42503-z] [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] [Received: 02/09/2022] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
Biomolecular polyelectrolyte complexes can be formed between oppositely charged intrinsically disordered regions (IDRs) of proteins or between IDRs and nucleic acids. Highly charged IDRs are abundant in the nucleus, yet few have been functionally characterized. Here, we show that a positively charged IDR within the human ATP-dependent DNA helicase Q4 (RECQ4) forms coacervates with G-quadruplexes (G4s). We describe a three-step model of charge-driven coacervation by integrating equilibrium and kinetic binding data in a global numerical model. The oppositely charged IDR and G4 molecules form a complex in the solution that follows a rapid nucleation-growth mechanism leading to a dynamic equilibrium between dilute and condensed phases. We also discover a physical interaction with Replication Protein A (RPA) and demonstrate that the IDR can switch between the two extremes of the structural continuum of complexes. The structural, kinetic, and thermodynamic profile of its interactions revealed a dynamic disordered complex with nucleic acids and a static ordered complex with RPA protein. The two mutually exclusive binding modes suggest a regulatory role for the IDR in RECQ4 function by enabling molecular handoffs. Our study extends the functional repertoire of IDRs and demonstrates a role of polyelectrolyte complexes involved in G4 binding.
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Affiliation(s)
- Anna C Papageorgiou
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michaela Pospisilova
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jakub Cibulka
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Raghib Ashraf
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Pavel Kadeřávek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Volha Maroz
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Karel Kubicek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic
| | - Lumir Krejci
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic.
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35
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Chowdhury A, Borgia A, Ghosh S, Sottini A, Mitra S, Eapen RS, Borgia MB, Yang T, Galvanetto N, Ivanović MT, Łukijańczuk P, Zhu R, Nettels D, Kundagrami A, Schuler B. Driving forces of the complex formation between highly charged disordered proteins. Proc Natl Acad Sci U S A 2023; 120:e2304036120. [PMID: 37796987 PMCID: PMC10576128 DOI: 10.1073/pnas.2304036120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/22/2023] [Indexed: 10/07/2023] Open
Abstract
Highly disordered complexes between oppositely charged intrinsically disordered proteins present a new paradigm of biomolecular interactions. Here, we investigate the driving forces of such interactions for the example of the highly positively charged linker histone H1 and its highly negatively charged chaperone, prothymosin α (ProTα). Temperature-dependent single-molecule Förster resonance energy transfer (FRET) experiments and isothermal titration calorimetry reveal ProTα-H1 binding to be enthalpically unfavorable, and salt-dependent affinity measurements suggest counterion release entropy to be an important thermodynamic driving force. Using single-molecule FRET, we also identify ternary complexes between ProTα and H1 in addition to the heterodimer at equilibrium and show how they contribute to the thermodynamics observed in ensemble experiments. Finally, we explain the observed thermodynamics quantitatively with a mean-field polyelectrolyte theory that treats counterion release explicitly. ProTα-H1 complex formation resembles the interactions between synthetic polyelectrolytes, and the underlying principles are likely to be of broad relevance for interactions between charged biomolecules in general.
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Affiliation(s)
- Aritra Chowdhury
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Alessandro Borgia
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Souradeep Ghosh
- Department of Physical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur741246, India
| | - Andrea Sottini
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Soumik Mitra
- Department of Physical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur741246, India
| | - Rohan S. Eapen
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | | | - Tianjin Yang
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Nicola Galvanetto
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
- Department of Physics, University of Zurich, Zurich8057, Switzerland
| | - Miloš T. Ivanović
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Paweł Łukijańczuk
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Ruijing Zhu
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Arindam Kundagrami
- Department of Physical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur741246, India
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
- Department of Physics, University of Zurich, Zurich8057, Switzerland
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36
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Himanshu, Chakraborty K, Patra TK. Developing efficient deep learning model for predicting copolymer properties. Phys Chem Chem Phys 2023; 25:25166-25176. [PMID: 37712405 DOI: 10.1039/d3cp03100d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Deep learning models are gaining popularity and potency in predicting polymer properties. These models can be built using pre-existing data and are useful for the rapid prediction of polymer properties. However, the performance of a deep learning model is intricately connected to its topology and the volume of training data. There is no facile protocol available to select a deep learning architecture, and there is a lack of a large volume of homogeneous sequence-property data of polymers. These two factors are the primary bottleneck for the efficient development of deep learning models for polymers. Here we assess the severity of these factors and propose strategies to address them. We show that a linear layer-by-layer expansion of a neural network can help in identifying the best neural network topology for a given problem. Moreover, we map the discrete sequence space of a polymer to a continuous one-dimensional latent space using a feature extraction technique to identify minimal data points for training a deep learning model. We implement these approaches for two representative cases of building sequence-property surrogate models, viz., the single-molecule radius of gyration of a copolymer and copolymer compatibilizer. This work demonstrates efficient methods for building deep learning models with minimal data and hyperparameters for predicting sequence-defined properties of polymers.
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Affiliation(s)
- Himanshu
- Department of Chemical Engineering and Center for Atomistic Modeling and Materials Design, Indian Institute of Technology Madras, Chennai, TN 600036, India.
| | - Kaushik Chakraborty
- Department of Chemical Engineering and Center for Atomistic Modeling and Materials Design, Indian Institute of Technology Madras, Chennai, TN 600036, India.
| | - Tarak K Patra
- Department of Chemical Engineering and Center for Atomistic Modeling and Materials Design, Indian Institute of Technology Madras, Chennai, TN 600036, India.
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37
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Yu B, Liang H, Nealey PF, Tirrell MV, Rumyantsev AM, de Pablo JJ. Structure and Dynamics of Hybrid Colloid-Polyelectrolyte Coacervates: Insights from Molecular Simulations. Macromolecules 2023; 56:7256-7270. [PMID: 37781214 PMCID: PMC10538443 DOI: 10.1021/acs.macromol.3c01079] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/08/2023] [Indexed: 10/03/2023]
Abstract
Electrostatic interactions in polymeric systems are responsible for a wide range of liquid-liquid phase transitions that are of importance for biology and materials science. Such transitions are referred to as complex coacervation, and recent studies have sought to understand the underlying physics and chemistry. Most theoretical and simulation efforts to date have focused on oppositely charged linear polyelectrolytes, which adopt nearly ideal-coil conformations in the condensed phase. However, when one of the coacervate components is a globular protein, a better model of complexation should replace one of the species with a spherical charged particle or colloid. In this work, we perform coarse-grained simulations of colloid-polyelectrolyte coacervation using a spherical model for the colloid. Simulation results indicate that the electroneutral cell of the resulting (hybrid) coacervates consists of a polyelectrolyte layer adsorbed on the colloid. Power laws for the structure and the density of the condensed phase, which are extracted from simulations, are found to be consistent with the adsorption-based scaling theory of hybrid coacervation. The coacervates remain amorphous (disordered) at a moderate colloid charge, Q, while an intra-coacervate colloidal crystal is formed above a certain threshold, at Q > Q*. In the disordered coacervate, if Q is sufficiently low, colloids diffuse as neutral nonsticky nanoparticles in the semidilute polymer solution. For higher Q, adsorption is strong and colloids become effectively sticky. Our findings are relevant for the coacervation of polyelectrolytes with proteins, spherical micelles of ionic surfactants, and solid organic or inorganic nanoparticles.
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Affiliation(s)
- Boyuan Yu
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
| | - Heyi Liang
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
| | - Paul F. Nealey
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
| | - Matthew V. Tirrell
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
- Center
for Molecular Engineering, Argonne National
Laboratory, Lemont, Illinois 60439, United States
| | - Artem M. Rumyantsev
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
- Department
of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Juan J. de Pablo
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
- Center
for Molecular Engineering, Argonne National
Laboratory, Lemont, Illinois 60439, United States
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38
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Muthukumar M. Fluctuations, structure, and size inside coacervates. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:79. [PMID: 37682368 DOI: 10.1140/epje/s10189-023-00335-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023]
Abstract
Aqueous solutions of oppositely charged macromolecules exhibit the ubiquitous phenomenon of coacervation. This subject is of considerable current interest due to numerous biotechnological applications of coacervates and the general premise of biomolecular condensates. Towards a theoretical foundation of structural features of coacervates, we present a field-theoretic treatment of coacervates formed by uniformly charged flexible polycations and polyanions in an electrolyte solution. We delineate different regimes of polymer concentration fluctuations and structural features of coacervates based on the concentrations of polycation and polyanion, salt concentration, and experimentally observable length scales. We present closed-form formulas for correlation length of polymer concentration fluctuations, scattering structure factor, and radius of gyration of a labelled polyelectrolyte chain inside a concentrated coacervate. Using random phase approximation suitable for concentrated polymer systems, we show that the inter-monomer electrostatic interaction is screened by interpenetration of all charged polymer chains and that the screening length depends on the individual concentrations of the polycation and the polyanion, as well as the salt concentration. Our calculations show that the scattering intensity decreases monotonically with scattering wave vector at higher salt concentrations, while it exhibits a peak at intermediate scattering wave vector at lower salt concentrations. Furthermore, we predict that the dependence of the radius of gyration of a labelled chain on its degree of polymerization generally obeys the Gaussian chain statistics. However, the chain is modestly swollen, the extent of which depending on polyelectrolyte composition, salt concentration, and the electrostatic features of the polycation and polyanion such as the degree of ionization.
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Affiliation(s)
- Murugappan Muthukumar
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA, 01003, USA.
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39
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Nguyen M, Shen K, Sherck N, Köhler S, Gupta R, Delaney KT, Shell MS, Fredrickson GH. A molecularly informed field-theoretic study of the complexation of polycation PDADMA with mixed micelles of sodium dodecyl sulfate and ethoxylated surfactants. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:75. [PMID: 37665423 DOI: 10.1140/epje/s10189-023-00332-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/11/2023] [Indexed: 09/05/2023]
Abstract
The self-assembly and phase separation of mixtures of polyelectrolytes and surfactants are important to a range of applications, from formulating personal care products to drug encapsulation. In contrast to systems of oppositely charged polyelectrolytes, in polyelectrolyte-surfactant systems the surfactants micellize into structures that are highly responsive to solution conditions. In this work, we examine how the morphology of micelles and degree of polyelectrolyte adsorption dynamically change upon varying the mixing ratio of charged and neutral surfactants. Specifically, we consider a solution of the cationic polyelectrolyte polydiallyldimethylammonium, anionic surfactant sodium dodecyl sulfate, neutral ethoxylated surfactants (C[Formula: see text]EO[Formula: see text]), sodium chloride salt, and water. To capture the chemical specificity of these species, we leverage recent developments in constructing molecularly informed field theories via coarse-graining from all-atom simulations. Our results show how changing the surfactant mixing ratios and the identity of the nonionic surfactant modulates micelle size and surface charge, and as a result dictates the degree of polyelectrolyte adsorption. These results are in semi-quantitative agreement with experimental observations on the same system.
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Affiliation(s)
- My Nguyen
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Kevin Shen
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
- Materials Research Laboratory, University of California, Santa Barbara, CA, 93106, USA
| | | | | | - Rohini Gupta
- California Research Alliance (CARA) by BASF, Berkeley, CA, 94720, USA
| | - Kris T Delaney
- Materials Research Laboratory, University of California, Santa Barbara, CA, 93106, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA.
| | - Glenn H Fredrickson
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA.
- Materials Research Laboratory, University of California, Santa Barbara, CA, 93106, USA.
- Department of Materials, University of California, Santa Barbara, CA, 93106, USA.
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40
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Viola G, Floriani F, Barracchia CG, Munari F, D'Onofrio M, Assfalg M. Ultrasmall Gold Nanoparticles as Clients of Biomolecular Condensates. Chemistry 2023; 29:e202301274. [PMID: 37293933 DOI: 10.1002/chem.202301274] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/29/2023] [Accepted: 06/09/2023] [Indexed: 06/10/2023]
Abstract
Liquid-liquid phase separation (LLPS) of biopolymers to form condensates is a widespread phenomenon in living cells. Agents that target or alter condensation can help uncover elusive physiological and pathological mechanisms. Owing to their unique material properties and modes of interaction with biomolecules, nanoparticles represent attractive condensate-targeting agents. Our work focused on elucidating the interaction between ultrasmall gold nanoparticles (usGNPs) and diverse types of condensates of tau, a representative phase-separating protein associated with neurodegenerative disorders. usGNPs attract considerable interest in the biomedical community due to unique features, including emergent optical properties and good cell penetration. We explored the interaction of usGNPs with reconstituted self-condensates of tau, two-component tau/polyanion and three-component tau/RNA/alpha-synuclein coacervates. The usGNPs were found to concentrate into condensed liquid droplets, consistent with the formation of dynamic client (nanoparticle) - scaffold (tau) interactions, and were observable thanks to their intrinsic luminescence. Furthermore, usGNPs were capable to promote LLPS of a protein domain which is unable to phase separate on its own. Our study demonstrates the ability of usGNPs to interact with and illuminate protein condensates. We anticipate that nanoparticles will have broad applicability as nanotracers to interrogate phase separation, and as nanoactuators controlling the formation and dissolution of condensates.
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Affiliation(s)
- Giovanna Viola
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Fulvio Floriani
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | | | - Francesca Munari
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | | | - Michael Assfalg
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
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41
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Alston JJ, Soranno A. Condensation Goes Viral: A Polymer Physics Perspective. J Mol Biol 2023; 435:167988. [PMID: 36709795 PMCID: PMC10368797 DOI: 10.1016/j.jmb.2023.167988] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
Abstract
The past decade has seen a revolution in our understanding of how the cellular environment is organized, where an incredible body of work has provided new insights into the role played by membraneless organelles. These rapid advancements have been made possible by an increasing awareness of the peculiar physical properties that give rise to such bodies and the complex biology that enables their function. Viral infections are not extraneous to this. Indeed, in host cells, viruses can harness existing membraneless compartments or, even, induce the formation of new ones. By hijacking the cellular machinery, these intracellular bodies can assist in the replication, assembly, and packaging of the viral genome as well as in the escape of the cellular immune response. Here, we provide a perspective on the fundamental polymer physics concepts that may help connect and interpret the different observed phenomena, ranging from the condensation of viral genomes to the phase separation of multicomponent solutions. We complement the discussion of the physical basis with a description of biophysical methods that can provide quantitative insights for testing and developing theoretical and computational models.
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Affiliation(s)
- Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA.
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42
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Zhang M, Liu Y, Zuo X, Qian S, Pingali SV, Gillilan RE, Huang Q, Zhang D. pH-Dependent Solution Micellar Structure of Amphoteric Polypeptoid Block Copolymers with Positionally Controlled Ionizable Sites. Biomacromolecules 2023; 24:3700-3715. [PMID: 37478325 PMCID: PMC10428163 DOI: 10.1021/acs.biomac.3c00407] [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: 04/20/2023] [Revised: 07/09/2023] [Indexed: 07/23/2023]
Abstract
While solution micellization of ionic block copolymers (BCP) with randomly distributed ionization sites along the hydrophilic segments has been extensively studied, the roles of positionally controlled ionization sites along the BCP chains in their micellization and resulting micellar structure remain comparatively less understood. Herein, three amphoteric polypeptoid block copolymers carrying two oppositely charged ionizable sites, with one fixed at the hydrophobic terminus and the other varyingly positioned along the hydrophilic segment, have been synthesized by sequential ring-opening polymerization method. The presence of the ionizable site at the hydrophobic segment terminus is expected to promote polymer association toward equilibrium micellar structures in an aqueous solution. The concurrent presence of oppositely charged ionizable sites on the polymer chains allows the polymer association to be electrostatically modulated in a broad pH range (ca. 2-12). Micellization of the amphoteric polypeptoid BCP in dilute aqueous solution and the resulting micellar structure at different solution pHs was investigated by a combination of scattering and microscopic methods. Negative-stain transmission-electron microscopy (TEM), small-angle neutron scattering (SANS), and small-angle X-ray scattering (SAXS) analyses revealed the dominant presence of core-shell-type spherical micelles and occasional rod-like micelles with liquid crystalline (LC) domains in the micellar core. The micellar structures (e.g., aggregation number, radius of gyration, chain packing in the micelle) were found to be dependent on the solution pH and the position of the ionizable site along the chain. This study has highlighted the potential of controlling the position of ionizable sites along the BCP polymer to modulate the electrostatic and LC interactions, thus tailoring the micellar structure at different solution pH values in water.
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Affiliation(s)
- Meng Zhang
- Department
of Chemistry and Macromolecular Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Yun Liu
- Center
for Neutron Research, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Xiaobing Zuo
- X-ray
Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Shuo Qian
- Neutron
Scattering Division and Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Sai Venkatesh Pingali
- Neutron
Scattering Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Richard E. Gillilan
- MacCHESS
(Macromolecular Diffraction Facility at CHESS), Cornell University, Ithaca, New York 14850, United States
| | - Qingqiu Huang
- MacCHESS
(Macromolecular Diffraction Facility at CHESS), Cornell University, Ithaca, New York 14850, United States
| | - Donghui Zhang
- Department
of Chemistry and Macromolecular Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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43
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Abstract
Multivalent proteins and nucleic acids, collectively referred to as multivalent associative biomacromolecules, provide the driving forces for the formation and compositional regulation of biomolecular condensates. Here, we review the key concepts of phase transitions of aqueous solutions of associative biomacromolecules, specifically proteins that include folded domains and intrinsically disordered regions. The phase transitions of these systems come under the rubric of coupled associative and segregative transitions. The concepts underlying these processes are presented, and their relevance to biomolecular condensates is discussed.
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Affiliation(s)
- Rohit V Pappu
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Samuel R Cohen
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Furqan Dar
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mina Farag
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mrityunjoy Kar
- Max Planck Institute of Cell Biology and Genetics, 01307 Dresden, Germany
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44
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Stevens K, Marras AE, Campagna TR, Ting JM, Tirrell MV. Effect of Charged Block Length Mismatch on Double Diblock Polyelectrolyte Complex Micelle Cores. Macromolecules 2023; 56:5557-5566. [PMID: 37521249 PMCID: PMC10373519 DOI: 10.1021/acs.macromol.3c00555] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/23/2023] [Indexed: 08/01/2023]
Abstract
Polyelectrolyte complex micelles are hydrophilic nanoparticles that self-assemble in aqueous environments due to associative microphase separation between oppositely charged blocky polyelectrolytes. In this work, we employ a suite of physical characterization tools to examine the effect of charged block length mismatch on the equilibrium structure of double diblock polyelectrolyte complex micelles (D-PCMs) by mixing a diverse library of peptide and synthetic charged-neutral block polyelectrolytes with a wide range of charged block lengths (25-200 units) and chemistries. Early work on D-PCMs suggested that this class of micelles can only be formed from blocky polyelectrolytes with identical charged block lengths, a phenomenon referred to as chain length recognition. Here, we use salt annealing to create PCMs at equilibrium, which shows that chain length recognition, a longstanding hurdle to repeatable self-assembly from mismatched polyelectrolytes, can be overcome. Interestingly, D-PCM structure-property relationships display a range of values that vary systematically with the charged block lengths and chemical identity of constituent polyelectrolyte pairings and cannot be described by generalizable scaling laws. We discuss the interdependent growth behavior of the radius, ionic pair aggregation number, and density in the micelle core for three chemically distinct diblock pairings and suggest a potential physical mechanism that leads to this unique behavior. By comparing the results of these D-PCMs to the scaling laws recently developed for single diblock polyelectrolyte complex micelles (S-PCMs: diblock + homopolymer), we observe that D-PCM design schemes reduce the size and aggregation number and restrict their growth to a function of charged block length relative to S-PCMs. Understanding these favorable attributes enables more predictive use of a wider array of charged molecular building blocks to anticipate and control macroscopic properties of micelles spanning countless storage and delivery applications.
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Affiliation(s)
- Kaden
C. Stevens
- Pritzker
School of Molecular Engineering, The University
of Chicago, Chicago, Illinois 60637, United States
| | - Alexander E. Marras
- Walker
Department of Mechanical Engineering, The
University of Texas at Austin, Austin, Texas 78712, United States
- Texas
Materials Institute, The University of Texas
at Austin, Austin, Texas 78712, United States
| | - Trinity R. Campagna
- Pritzker
School of Molecular Engineering, The University
of Chicago, Chicago, Illinois 60637, United States
| | | | - Matthew V. Tirrell
- Pritzker
School of Molecular Engineering, The University
of Chicago, Chicago, Illinois 60637, United States
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45
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K C B, Nii T, Mori T, Katayama Y. Dynamic frustrated charge hotspots created by charge density modulation sequester globular proteins into complex coacervates. Chem Sci 2023; 14:6608-6620. [PMID: 37350836 PMCID: PMC10283495 DOI: 10.1039/d3sc00993a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/19/2023] [Indexed: 06/24/2023] Open
Abstract
This study presents a simple strategy for the sequestration of globular proteins as clients into synthetic polypeptide-based complex coacervates as a scaffold, thereby recapitulating the scaffold-client interaction found in biological condensates. Considering the low net charges of scaffold proteins participating in biological condensates, the linear charge density (σ) on the polyanion, polyethylene glycol-b-poly(aspartic acids), was reduced by introducing hydroxypropyl or butyl moieties as a charge-neutral pendant group. Complex coacervate prepared from the series of reduced-σ polyanions and the polycation, homo-poly-l-lysine, could act as a scaffold that sequestered various globular proteins with high encapsulation efficiency (>80%), which sometimes involved further agglomerations in the coacervates. The sequestration of proteins was basically driven by electrostatic interaction, and therefore depended on the ionic strength and charges of the proteins. However, based on the results of polymer partitioning in the coacervate in the presence or absence of proteins, charge ratios between cationic and anionic polymers were maintained at the charge ratio of unity. Therefore, the origin of the electrostatic interaction with proteins is considered to be dynamic frustrated charges in the complex coacervates created by non-neutralized charges on polymer chains. Furthermore, fluorescence recovery after photobleaching (FRAP) measurements showed that the interaction of side-chains and proteins changed the dynamic property of coacervates. It also suggested that the physical properties of the condensate are tunable before and after the sequestration of globular proteins. The present rational design approach of the scaffold-client interaction is helpful for basic life-science research and the applied frontier of artificial organelles.
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Affiliation(s)
- Biplab K C
- Graduate School of Systems Life Sciences, Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Teruki Nii
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Takeshi Mori
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
- Center for Future Chemistry, Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Yoshiki Katayama
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
- Center for Future Chemistry, Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
- Center for Molecular Systems, Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
- Center for Advanced Medical Open Innovation, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
- Department of Biomedical Engineering, Chung Yuan Christian University 200 Chung Pei Rd. Chung Li Taiwan 32023 ROC
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Miyagi T, Ueda K, Sugimoto M, Yagi T, Ito D, Yamazaki R, Narumi S, Hayamizu Y, Uji-i H, Kuroda M, Kanekura K. Differential toxicity and localization of arginine-rich C9ORF72 dipeptide repeat proteins depend on de-clustering of positive charges. iScience 2023; 26:106957. [PMID: 37332605 PMCID: PMC10275993 DOI: 10.1016/j.isci.2023.106957] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023] Open
Abstract
Arginine-rich dipeptide repeat proteins (R-DPRs), poly(PR) and poly(GR), translated from the hexanucleotide repeat expansion in the amyotrophic lateral sclerosis (ALS)-causative C9ORF72 gene, contribute significantly to pathogenesis of ALS. Although both R-DPRs share many similarities, there are critical differences in their subcellular localization, phase separation, and toxicity mechanisms. We analyzed localization, protein-protein interactions, and phase separation of R-DPR variants and found that sufficient segregation of arginine charges is necessary for nucleolar distribution. Proline not only efficiently separated the charges, but also allowed for weak, but highly multivalent binding. In contrast, because of its high flexibility, glycine cannot fully separate the charges, and poly(GR) behaves similarly to the contiguous arginines, being trapped in the cytoplasm. We conclude that the amino acid that spaces the arginine charges determines the strength and multivalency of the binding, leading to differences in localization and toxicity mechanisms.
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Affiliation(s)
- Tamami Miyagi
- Department of Molecular Pathology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
- Department of Pharmacology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Masahiro Sugimoto
- Research and Development Center for Minimally Invasive Therapies, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
- Institute for Advanced Biosciences, KEIO University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Takuya Yagi
- Department of Neurology, KEIO University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Daisuke Ito
- Department of Physiology, KEIO University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Rio Yamazaki
- Department of Molecular Pathology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
- Department of Pharmacology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| | - Satoshi Narumi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Yuhei Hayamizu
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Hiroshi Uji-i
- Department of Nanomaterials and Nanoscopy, Research Institute for Electronic Science, Hokkaido University, Kita 10 Nishi 20, North Ward, Sapporo, Hokkaido 001-0020, Japan
- Department of Chemistry, KU Leuven Celestijnenlaan 200F, Heverlee, 3001 Leuven, Belgium
| | - Masahiko Kuroda
- Department of Molecular Pathology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| | - Kohsuke Kanekura
- Department of Molecular Pathology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
- Department of Pharmacology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
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Melnikova D, Khisravashirova C, Smotrina T, Skirda V. Interaction of Hyaluronan Acid with Some Proteins in Aqueous Solution as Studied by NMR. MEMBRANES 2023; 13:436. [PMID: 37103863 PMCID: PMC10141478 DOI: 10.3390/membranes13040436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/09/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
Abstract
According to actual literature data, hyaluronic acid (HA) that is presented in the extracellular matrix can interact with proteins and thereby affect several important functions of the cell membrane. The purpose of this work was to reveal the features of the interaction of HA with proteins using the PFG NMR method by sampling two systems: aqueous solutions of HA with bovine serum albumin (BSA) and aqueous solutions of HA with hen egg-white lysozyme (HEWL). It was found that the presence of BSA in the HA aqueous solution initiates a certain additional mechanism; as a result, the population of HA molecules in the gel structure increases to almost 100%. At the same time, for an aqueous solution of HA/HEWL, even in the range of low (0.01-0.2%) HEWL contents, strong signs of degradation (depolymerization) of some HA macromolecules were observed such that they lost the ability to form a gel. Moreover, lysozyme molecules form a strong complex with degraded HA molecules and lose their enzymatic function. Thus, the presence of HA molecules in the intercellular matrix, as well as in the state associated with the surface of the cell membrane, can, in addition to the known ones, perform one more important function: the function of protecting the cell membrane from the destructive action of lysozymes. The obtained results are important for understanding the mechanism and features of the interaction of extracellular matrix glycosaminoglycan with cell membrane proteins.
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Affiliation(s)
- Daria Melnikova
- Department of Molecular Physics, Institute of Physics, Kazan Federal University, Kazan 420011, Russia
| | - Catherine Khisravashirova
- Department of Molecular Physics, Institute of Physics, Kazan Federal University, Kazan 420011, Russia
| | - Tatiana Smotrina
- Department of Chemistry, Mari State University, Yoshkar-Ola 424002, Russia
| | - Vladimir Skirda
- Department of Molecular Physics, Institute of Physics, Kazan Federal University, Kazan 420011, Russia
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48
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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: 14] [Impact Index Per Article: 14.0] [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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Michna A, Pomorska A, Ozcan O. Biocompatible Macroion/Growth Factor Assemblies for Medical Applications. Biomolecules 2023; 13:biom13040609. [PMID: 37189357 DOI: 10.3390/biom13040609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/24/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023] Open
Abstract
Growth factors are a class of proteins that play a role in the proliferation (the increase in the number of cells resulting from cell division) and differentiation (when a cell undergoes changes in gene expression becoming a more specific type of cell) of cells. They can have both positive (accelerating the normal healing process) and negative effects (causing cancer) on disease progression and have potential applications in gene therapy and wound healing. However, their short half-life, low stability, and susceptibility to degradation by enzymes at body temperature make them easily degradable in vivo. To improve their effectiveness and stability, growth factors require carriers for delivery that protect them from heat, pH changes, and proteolysis. These carriers should also be able to deliver the growth factors to their intended destination. This review focuses on the current scientific literature concerning the physicochemical properties (such as biocompatibility, high affinity for binding growth factors, improved bioactivity and stability of the growth factors, protection from heat, pH changes or appropriate electric charge for growth factor attachment via electrostatic interactions) of macroions, growth factors, and macroion-growth factor assemblies, as well as their potential uses in medicine (e.g., diabetic wound healing, tissue regeneration, and cancer therapy). Specific attention is given to three types of growth factors: vascular endothelial growth factors, human fibroblast growth factors, and neurotrophins, as well as selected biocompatible synthetic macroions (obtained through standard polymerization techniques) and polysaccharides (natural macroions composed of repeating monomeric units of monosaccharides). Understanding the mechanisms by which growth factors bind to potential carriers could lead to more effective delivery methods for these proteins, which are of significant interest in the diagnosis and treatment of neurodegenerative and civilization diseases, as well as in the healing of chronic wounds.
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50
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Sato Y, Takinoue M. Sequence-dependent fusion dynamics and physical properties of DNA droplets. NANOSCALE ADVANCES 2023; 5:1919-1925. [PMID: 36998664 PMCID: PMC10044877 DOI: 10.1039/d3na00073g] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/12/2023] [Indexed: 06/19/2023]
Abstract
Liquid-liquid phase separation (LLPS) of biopolymer molecules generates liquid-like droplets. Physical properties such as viscosity and surface tension play important roles in the functions of these droplets. DNA-nanostructure-based LLPS systems provide useful model tools to investigate the influence of molecular design on the physical properties of the droplets, which has so far remained unclear. Herein, we report changes in the physical properties of DNA droplets by sticky end (SE) design in DNA nanostructures. We used a Y-shaped DNA nanostructure (Y-motif) with three SEs as a model structure. Seven different SE designs were used. The experiments were performed at the phase transition temperature where the Y-motifs self-assembled into droplets. We found that the DNA droplets assembled from the Y-motifs with longer SEs exhibited a longer coalescence period. In addition, the Y-motifs with the same length but different sequence SEs showed slight variations in the coalescence period. Our results suggest that the SE length greatly affected the surface tension at the phase transition temperature. We believe that these findings will accelerate our understanding of the relationship between molecular design and the physical properties of droplets formed via LLPS.
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Affiliation(s)
- Yusuke Sato
- Department of Computer Science, Tokyo Institute of Technology 4259, Nagatsuta-cho, Midori-ku Yokoham Kanagawa 226-8502 Japan
- Department of Intelligent and Control Systems, Kyushu Institute of Technology 680-4 Kawazu, IIzuka Fukuoka 820-8502 Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology 4259, Nagatsuta-cho, Midori-ku Yokoham Kanagawa 226-8502 Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8501 Japan
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