1
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Driver MD, Postema J, Onck PR. The Effect of Dipeptide Repeat Proteins on FUS/TDP43-RNA Condensation in C9orf72 ALS/FTD. J Phys Chem B 2024; 128:9405-9417. [PMID: 39311028 DOI: 10.1021/acs.jpcb.4c04663] [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: 10/04/2024]
Abstract
Condensation of RNA binding proteins (RBPs) with RNA is essential for cellular function. The most common familial cause of the diseases ALS and FTD is C9orf72 repeat expansion disorders that produce dipeptide repeat proteins (DPRs). We explore the hypothesis that DPRs disrupt the native condensation behavior of RBPs and RNA through molecular interactions resulting in toxicity. FUS and TDP43 are two RBPs known to be affected in ALS/FTD. We use our previously developed 1-bead-per-amino acid and a newly developed 3-bead-per-nucleotide molecular dynamics model to explore ternary phase diagrams of FUS/TDP43-RNA-DPR systems. We show that the most toxic arginine containing DPRs (R-DPRs) can disrupt the RBP condensates through cation-π interactions and can strongly sequester RNA through electrostatic interactions. The native droplet morphologies are already modified at small additions of R-DPRs leading to non-native FUS/TDP43-encapsulated condensates with a marbled RNA/DPR core.
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Affiliation(s)
- Mark D Driver
- Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747AG, the Netherlands
| | - Jasper Postema
- Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747AG, the Netherlands
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747AG, the Netherlands
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2
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Santamaria A, Hutin S, Doucet CM, Zubieta C, Milhiet PE, Costa L. Quantifying surface tension and viscosity in biomolecular condensates by FRAP-ID. Biophys J 2024; 123:3366-3374. [PMID: 39113361 DOI: 10.1016/j.bpj.2024.07.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/01/2024] [Accepted: 07/31/2024] [Indexed: 08/22/2024] Open
Abstract
Many proteins with intrinsically disordered regions undergo liquid-liquid phase separation under specific conditions in vitro and in vivo. These complex biopolymers form a metastable phase with distinct mechanical properties defining the timescale of their biological functions. However, determining these properties is nontrivial, even in vitro, and often requires multiple techniques. Here we report the measurement of both viscosity and surface tension of biomolecular condensates via correlative fluorescence microscopy and atomic force microscopy (AFM) in a single experiment (fluorescence recovery after probe-induced dewetting, FRAP-ID). Upon surface tension evaluation via regular AFM-force spectroscopy, controlled AFM indentations induce dry spots in fluorescent condensates on a glass coverslip. The subsequent rewetting exhibits a contact line velocity that is used to quantify the condensed-phase viscosity. Therefore, in contrast with fluorescence recovery after photobleaching (FRAP), where molecular diffusion is observed, in FRAP-ID fluorescence recovery is obtained through fluid rewetting and the subsequent morphological relaxation. We show that the latter can be used to cross-validate viscosity values determined during the rewetting regime. Making use of fluid mechanics, FRAP-ID is a valuable tool to evaluate the mechanical properties that govern the dynamics of biomolecular condensates and determine how these properties impact the temporal aspects of condensate functionality.
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Affiliation(s)
- Andreas Santamaria
- Center for Structural Biology (CBS), CNRS, INSERM, Montpellier University, Montpellier, France
| | - Stephanie Hutin
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, Grenoble, France
| | - Christine M Doucet
- Center for Structural Biology (CBS), CNRS, INSERM, Montpellier University, Montpellier, France
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, Grenoble, France
| | - Pierre-Emmanuel Milhiet
- Center for Structural Biology (CBS), CNRS, INSERM, Montpellier University, Montpellier, France
| | - Luca Costa
- Center for Structural Biology (CBS), CNRS, INSERM, Montpellier University, Montpellier, France.
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3
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Wang H, Hoffmann C, Tromm JV, Su X, Elliott J, Wang H, Baum J, Pang ZP, Milovanovic D, Shi Z. Live-Cell Quantification Reveals Viscoelastic Regulation of Synapsin Condensates by α-Synuclein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.28.605529. [PMID: 39211102 PMCID: PMC11361170 DOI: 10.1101/2024.07.28.605529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Synapsin and α-synuclein represent a growing list of condensate-forming proteins where the material states of condensates are directly linked to cellular functions (e.g., neurotransmission) and pathology (e.g., neurodegeneration). However, quantifying condensate material properties in living systems has been a significant challenge. To address this, we develop MAPAC (micropipette aspiration and whole-cell patch clamp), a platform that allows direct material quantification of condensates in live cells. We find 10,000-fold variations in the viscoelasticity of synapsin condensates, regulated by the partitioning of α-synuclein, a marker for synucleinopathies. Through in vitro reconstitutions, we identify 4 molecular factors that distinctly regulate the viscosity and interfacial tension of synapsin condensates, verifying the cellular effects of α-synuclein. Overall, our study provides unprecedented quantitative insights into the material properties of neuronal condensates and reveals a crucial role of α-synuclein in regulating condensate viscoelasticity. Furthermore, we envision MAPAC applicable to study a broad range of condensates in vivo. .
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4
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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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5
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Chuang HY, He RY, Huang YA, Hsu WT, Cheng YJ, Guo ZR, Wali N, Hwang IS, Shie JJ, Huang JJT. Engineered droplet-forming peptide as photocontrollable phase modulator for fused in sarcoma protein. Nat Commun 2024; 15:5686. [PMID: 38971830 PMCID: PMC11227587 DOI: 10.1038/s41467-024-50025-5] [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: 10/19/2023] [Accepted: 06/27/2024] [Indexed: 07/08/2024] Open
Abstract
The assembly and disassembly of biomolecular condensates are crucial for the subcellular compartmentalization of biomolecules in the control of cellular reactions. Recently, a correlation has been discovered between the phase transition of condensates and their maturation (aggregation) process in diseases. Therefore, modulating the phase of condensates to unravel the roles of condensation has become a matter of interest. Here, we create a peptide-based phase modulator, JSF1, which forms droplets in the dark and transforms into amyloid-like fibrils upon photoinitiation, as evidenced by their distinctive nanomechanical and dynamic properties. JSF1 is found to effectively enhance the condensation of purified fused in sarcoma (FUS) protein and, upon light exposure, induce its fibrilization. We also use JSF1 to modulate the biophysical states of FUS condensates in live cells and elucidate the relationship between FUS phase transition and FUS proteinopathy, thereby shedding light on the effect of protein phase transition on cellular function and malfunction.
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Affiliation(s)
- Hao-Yu Chuang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Ruei-Yu He
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Yung-An Huang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Wan-Ting Hsu
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Ya-Jen Cheng
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, 115, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Zheng-Rong Guo
- Institute of Physics, Academia Sinica, Taipei, 115, Taiwan
| | - Niaz Wali
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | | | - Jiun-Jie Shie
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Joseph Jen-Tse Huang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan.
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, 115, Taiwan.
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan.
- Department of Applied Chemistry, National Chiayi University, Chiayi City, 600, Taiwan.
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6
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Zacco E, Broglia L, Kurihara M, Monti M, Gustincich S, Pastore A, Plath K, Nagakawa S, Cerase A, Sanchez de Groot N, Tartaglia GG. RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding. Chem Rev 2024; 124:4734-4777. [PMID: 38579177 PMCID: PMC11046439 DOI: 10.1021/acs.chemrev.3c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 04/07/2024]
Abstract
This comprehensive Review delves into the chemical principles governing RNA-mediated crowding events, commonly referred to as granules or biological condensates. We explore the pivotal role played by RNA sequence, structure, and chemical modifications in these processes, uncovering their correlation with crowding phenomena under physiological conditions. Additionally, we investigate instances where crowding deviates from its intended function, leading to pathological consequences. By deepening our understanding of the delicate balance that governs molecular crowding driven by RNA and its implications for cellular homeostasis, we aim to shed light on this intriguing area of research. Our exploration extends to the methodologies employed to decipher the composition and structural intricacies of RNA granules, offering a comprehensive overview of the techniques used to characterize them, including relevant computational approaches. Through two detailed examples highlighting the significance of noncoding RNAs, NEAT1 and XIST, in the formation of phase-separated assemblies and their influence on the cellular landscape, we emphasize their crucial role in cellular organization and function. By elucidating the chemical underpinnings of RNA-mediated molecular crowding, investigating the role of modifications, structures, and composition of RNA granules, and exploring both physiological and aberrant phase separation phenomena, this Review provides a multifaceted understanding of the intriguing world of RNA-mediated biological condensates.
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Affiliation(s)
- Elsa Zacco
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Laura Broglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Misuzu Kurihara
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Michele Monti
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Stefano Gustincich
- Central
RNA Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Annalisa Pastore
- UK
Dementia Research Institute at the Maurice Wohl Institute of King’s
College London, London SE5 9RT, U.K.
| | - Kathrin Plath
- Department
of Biological Chemistry, David Geffen School
of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Shinichi Nagakawa
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Andrea Cerase
- Blizard
Institute,
Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, U.K.
- Unit
of Cell and developmental Biology, Department of Biology, Università di Pisa, 56123 Pisa, Italy
| | - Natalia Sanchez de Groot
- Unitat
de Bioquímica, Departament de Bioquímica i Biologia
Molecular, Universitat Autònoma de
Barcelona, 08193 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
- Catalan
Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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7
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Ibrahim KA, Naidu AS, Miljkovic H, Radenovic A, Yang W. Label-Free Techniques for Probing Biomolecular Condensates. ACS NANO 2024; 18:10738-10757. [PMID: 38609349 DOI: 10.1021/acsnano.4c01534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Biomolecular condensates play important roles in a wide array of fundamental biological processes, such as cellular compartmentalization, cellular regulation, and other biochemical reactions. Since their discovery and first observations, an extensive and expansive library of tools has been developed to investigate various aspects and properties, encompassing structural and compositional information, material properties, and their evolution throughout the life cycle from formation to eventual dissolution. This Review presents an overview of the expanded set of tools and methods that researchers use to probe the properties of biomolecular condensates across diverse scales of length, concentration, stiffness, and time. In particular, we review recent years' exciting development of label-free techniques and methodologies. We broadly organize the set of tools into 3 categories: (1) imaging-based techniques, such as transmitted-light microscopy (TLM) and Brillouin microscopy (BM), (2) force spectroscopy techniques, such as atomic force microscopy (AFM) and the optical tweezer (OT), and (3) microfluidic platforms and emerging technologies. We point out the tools' key opportunities, challenges, and future perspectives and analyze their correlative potential as well as compatibility with other techniques. Additionally, we review emerging techniques, namely, differential dynamic microscopy (DDM) and interferometric scattering microscopy (iSCAT), that have huge potential for future applications in studying biomolecular condensates. Finally, we highlight how some of these techniques can be translated for diagnostics and therapy purposes. We hope this Review serves as a useful guide for new researchers in this field and aids in advancing the development of new biophysical tools to study biomolecular condensates.
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8
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Khorsand FR, Uversky VN. Liquid-liquid phase separation as triggering factor of fibril formation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:143-182. [PMID: 38811080 DOI: 10.1016/bs.pmbts.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Liquid-liquid phase separation (LLPS) refers to the phenomenon, where a homogeneous solution spontaneously undergoes a transition into two or more immiscible phases. Through transient weak multivalent macromolecular interactions, a homogeneous solution can spontaneously separate into two phases: one rich in biomolecules and the other poor in biomolecules. Phase separation is believed to serve as the physicochemical foundation for the formation of membrane-less organelles (MLOs) and bio-molecular condensates within cells. Moreover, numerous biological processes depend on LLPS, such as transcription, immunological response, chromatin architecture, DNA damage response, stress granule formation, viral infection, etc. Abnormalities in phase separation can lead to diseases, such as cancer, neurodegeneration, and metabolic disorders. LLPS is regulated by various factors, such as concentration of molecules undergoing LLPS, salt concentration, pH, temperature, post-translational modifications, and molecular chaperones. Recent research on LLPS of biomolecules has progressed rapidly and led to the development of databases containing information pertaining to various aspects of the biomolecule separation analysis. However, more comprehensive research is still required to fully comprehend the specific molecular mechanisms and biological effects of LLPS.
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Affiliation(s)
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Pushchino, Moscow, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
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9
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Alfano C, Fichou Y, Huber K, Weiss M, Spruijt E, Ebbinghaus S, De Luca G, Morando MA, Vetri V, Temussi PA, Pastore A. Molecular Crowding: The History and Development of a Scientific Paradigm. Chem Rev 2024; 124:3186-3219. [PMID: 38466779 PMCID: PMC10979406 DOI: 10.1021/acs.chemrev.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.
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Affiliation(s)
- Caterina Alfano
- Structural
Biology and Biophysics Unit, Fondazione
Ri.MED, 90100 Palermo, Italy
| | - Yann Fichou
- CNRS,
Bordeaux INP, CBMN UMR 5248, IECB, University
of Bordeaux, F-33600 Pessac, France
| | - Klaus Huber
- Department
of Chemistry, University of Paderborn, 33098 Paderborn, Germany
| | - Matthias Weiss
- Experimental
Physics I, Physics of Living Matter, University
of Bayreuth, 95440 Bayreuth, Germany
| | - Evan Spruijt
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Simon Ebbinghaus
- Lehrstuhl
für Biophysikalische Chemie and Research Center Chemical Sciences
and Sustainability, Research Alliance Ruhr, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Giuseppe De Luca
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Valeria Vetri
- Dipartimento
di Fisica e Chimica − Emilio Segrè, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Annalisa Pastore
- King’s
College London, Denmark
Hill Campus, SE5 9RT London, United Kingdom
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10
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Ramirez DA, Hough LE, Shirts MR. Coiled-coil domains are sufficient to drive liquid-liquid phase separation in protein models. Biophys J 2024; 123:703-717. [PMID: 38356260 PMCID: PMC10995412 DOI: 10.1016/j.bpj.2024.02.007] [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: 07/25/2023] [Revised: 12/09/2023] [Accepted: 02/09/2024] [Indexed: 02/16/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) is thought to be a main driving force in the formation of membraneless organelles. Examples of such organelles include the centrosome, central spindle, and stress granules. Recently, it has been shown that coiled-coil (CC) proteins, such as the centrosomal proteins pericentrin, spd-5, and centrosomin, might be capable of LLPS. CC domains have physical features that could make them the drivers of LLPS, but it is unknown if they play a direct role in the process. We developed a coarse-grained simulation framework for investigating the LLPS propensity of CC proteins, in which interactions that support LLPS arise solely from CC domains. We show, using this framework, that the physical features of CC domains are sufficient to drive LLPS of proteins. The framework is specifically designed to investigate how the number of CC domains, as well as the multimerization state of CC domains, can affect LLPS. We show that small model proteins with as few as two CC domains can phase separate. Increasing the number of CC domains up to four per protein can somewhat increase LLPS propensity. We demonstrate that trimer-forming and tetramer-forming CC domains have a dramatically higher LLPS propensity than dimer-forming coils, which shows that multimerization state has a greater effect on LLPS than the number of CC domains per protein. These data support the hypothesis of CC domains as drivers of protein LLPS, and have implications in future studies to identify the LLPS-driving regions of centrosomal and central spindle proteins.
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Affiliation(s)
- Dominique A Ramirez
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | - Loren E Hough
- Department of Physics and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado.
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11
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Rai S, Pramanik S, Mukherjee S. Deciphering the liquid-liquid phase separation induced modulation in the structure, dynamics, and enzymatic activity of an ordered protein β-lactoglobulin. Chem Sci 2024; 15:3936-3948. [PMID: 38487243 PMCID: PMC10935713 DOI: 10.1039/d3sc06802a] [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: 12/18/2023] [Accepted: 01/23/2024] [Indexed: 03/17/2024] Open
Abstract
Owing to the significant role in the subcellular organization of biomolecules, physiology, and the realm of biomimetic materials, studies related to biomolecular condensates formed through liquid-liquid phase separation (LLPS) have emerged as a growing area of research. Despite valuable contributions of prior research, there is untapped potential in exploring the influence of phase separation on the conformational dynamics and enzymatic activities of native proteins. Herein, we investigate the LLPS of β-lactoglobulin (β-LG), a non-intrinsically disordered protein, under crowded conditions. In-depth characterization through spectroscopic and microscopic techniques revealed the formation of dynamic liquid-like droplets, distinct from protein aggregates, driven by hydrophobic interactions. Our analyses revealed that phase separation can alter structural flexibility and photophysical properties. Importantly, the phase-separated β-LG exhibited efficient enzymatic activity as an esterase; a characteristic seemingly exclusive to β-LG droplets. The droplets acted as robust catalytic crucibles, providing an ideal environment for efficient ester hydrolysis. Further investigation into the catalytic mechanism suggested the involvement of specific amino acid residues, rather than general acid or base catalysis. Also, the alteration in conformational distribution caused by phase separation unveils the latent functionality. Our study delineates the understanding of protein phase separation and insights into the diverse catalytic strategies employed by proteins. It opens exciting possibilities for designing functional artificial compartments based on phase-separated biomolecules.
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Affiliation(s)
- Saurabh Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road Bhopal 462066 Madhya Pradesh India
| | - Srikrishna Pramanik
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road Bhopal 462066 Madhya Pradesh India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road Bhopal 462066 Madhya Pradesh India
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12
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Zhang Y, Li S, Gong X, Chen J. Toward Accurate Simulation of Coupling between Protein Secondary Structure and Phase Separation. J Am Chem Soc 2024; 146:342-357. [PMID: 38112495 PMCID: PMC10842759 DOI: 10.1021/jacs.3c09195] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Intrinsically disordered proteins (IDPs) frequently mediate phase separation that underlies the formation of a biomolecular condensate. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding the sequence-specific phase separation of IDPs. However, the widely used Cα-only models are limited in capturing the peptide nature of IDPs, particularly backbone-mediated interactions and effects of secondary structures, in phase separation. Here, we describe a hybrid resolution (HyRes) protein model toward a more accurate description of the backbone and transient secondary structures in phase separation. With an atomistic backbone and coarse-grained side chains, HyRes can semiquantitatively capture the residue helical propensity and overall chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for the direct simulation of spontaneous phase separation and, at the same time, appears accurate enough to resolve the effects of single His to Lys mutations. HyRes simulations also successfully predict increased β-structure formation in the condensate, consistent with available experimental CD data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate the phase separation propensity as measured by the saturation concentration. The simulations successfully recapitulate the effect of these mutants on the helicity and phase separation propensity of TDP-43 CR. Analyses reveal that the balance between backbone and side chain-mediated interactions, but not helicity itself, actually determines phase separation propensity. These results support that HyRes represents an effective protein model for molecular simulation of IDP phase separation and will help to elucidate the coupling between transient secondary structures and phase separation.
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Affiliation(s)
| | | | - Xiping Gong
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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13
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Liu D, Riggi M, Lee HO, Currie SL, Goodsell DS, Iwasa JH, Rog O. Depicting a cellular space occupied by condensates. Mol Biol Cell 2023; 34:tp2. [PMID: 37590933 PMCID: PMC10551707 DOI: 10.1091/mbc.e22-11-0519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/20/2023] [Accepted: 07/10/2023] [Indexed: 08/19/2023] Open
Abstract
Condensates have emerged as a new way to understand how cells are organized, and have been invoked to play crucial roles in essentially all cellular processes. In this view, the cell is occupied by numerous assemblies, each composed of member proteins and nucleic acids that preferentially interact with each other. However, available visual representations of condensates fail to communicate the growing body of knowledge about how condensates form and function. The resulting focus on only a subset of the potential implications of condensates can skew interpretations of results and hinder the generation of new hypotheses. Here we summarize the discussion from a workshop that brought together cell biologists, visualization and computation specialists, and other experts who specialize in thinking about space and ways to represent it. We place the recent advances in condensate research in a historical perspective that describes evolving views of the cell; highlight different attributes of condensates that are not well-served by current visual conventions; and survey potential approaches to overcome these challenges. An important theme of these discussions is that the new understanding on the roles of condensates exposes broader challenges in visual representations that apply to cell biological research more generally.
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Affiliation(s)
- Daniel Liu
- Historisches Seminar, Abt. Wissenschaftsgeschichte, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | | | - Hyun O. Lee
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Simon L. Currie
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390
| | - David S. Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
- Institute for Quantitative Biomedicine and Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
| | | | - Ofer Rog
- School of Biological Sciences and Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112
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14
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Zhang Y, Li S, Gong X, Chen J. Accurate Simulation of Coupling between Protein Secondary Structure and Liquid-Liquid Phase Separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554378. [PMID: 37662293 PMCID: PMC10473686 DOI: 10.1101/2023.08.22.554378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Intrinsically disordered proteins (IDPs) frequently mediate liquid-liquid phase separation (LLPS) that underlies the formation of membraneless organelles. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding sequence-specific phase separation of IDPs. However, the widely-used Cα-only models are severely limited in capturing the peptide nature of IDPs, including backbone-mediated interactions and effects of secondary structures, in LLPS. Here, we describe a hybrid resolution (HyRes) protein model for accurate description of the backbone and transient secondary structures in LLPS. With an atomistic backbone and coarse-grained side chains, HyRes accurately predicts the residue helical propensity and chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for direct simulation of spontaneous phase separation, and at the same time accurate enough to resolve the effects of single mutations. HyRes simulations also successfully predict increased beta-sheet formation in the condensate, consistent with available experimental data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate LLPS propensity. The simulations successfully recapitulate the effect of these mutants on the helicity and LLPS propensity of TDP-43 CR. Analyses reveal that the balance between backbone and sidechain-mediated interactions, but not helicity itself, actually determines LLPS propensity. We believe that the HyRes model represents an important advance in the molecular simulation of LLPS and will help elucidate the coupling between IDP transient secondary structures and phase separation.
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Affiliation(s)
| | | | - Xiping Gong
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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15
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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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16
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Li Y, Xu M, Qi Z. Deciphering molecular mechanisms of phase separation in RNA biology by single-molecule biophysical technologies. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1034-1041. [PMID: 37337634 PMCID: PMC10415185 DOI: 10.3724/abbs.2023113] [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: 12/31/2022] [Accepted: 03/06/2023] [Indexed: 06/21/2023] Open
Abstract
Ribonucleic acid (RNA) biology has emerged as one of the most important areas in modern biology and biomedicine. RNA and RNA-binding proteins (RBPs) are involved in forming biomolecular condensates, which are crucial for RNA metabolism. To quantitively decipher the molecular mechanisms of RNP granules, researchers have turned to single-molecule biophysical techniques, such as single-molecule Förster resonance energy transfer (smFRET), in vivo single-molecule imaging technique with single particle tracking (SPT), DNA Curtains, optical tweezers, and atomic force microscopy (AFM). These methods are used to investigate the molecular biophysical properties within RNP granules, as well as the molecular interactions between RNA and RBPs and RBPs themselves, which are challenging to study using traditional experimental methods of the liquid-liquid phase separation (LLPS) field, such as fluorescence recovery after photobleaching (FRAP). In this work, we summarize the applications of single-molecule biophysical techniques in RNP granule studies and highlight how these methods can be used to reveal the molecular mechanisms of RNP granules.
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Affiliation(s)
- Yuchen Li
- Center for Quantitative Biology and Peking-Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
| | - Mengmeng Xu
- Tsinghua-Peking Center for Life SciencesTsinghua UniversityBeijing100084China
| | - Zhi Qi
- Center for Quantitative Biology and Peking-Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
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17
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Cerulo L, Pezzella N, Caruso FP, Parente P, Remo A, Giordano G, Forte N, Busselez J, Boschi F, Galiè M, Franco B, Pancione M. Single-cell proteo-genomic reveals a comprehensive map of centrosome-associated spliceosome components. iScience 2023; 26:106602. [PMID: 37250316 PMCID: PMC10214398 DOI: 10.1016/j.isci.2023.106602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 01/16/2023] [Accepted: 03/29/2023] [Indexed: 05/31/2023] Open
Abstract
Ribonucleoprotein (RNP) condensates are crucial for controlling RNA metabolism and splicing events in animal cells. We used spatial proteomics and transcriptomic to elucidate RNP interaction networks at the centrosome, the main microtubule-organizing center in animal cells. We found a number of cell-type specific centrosome-associated spliceosome interactions localized in subcellular structures involved in nuclear division and ciliogenesis. A component of the nuclear spliceosome BUD31 was validated as an interactor of the centriolar satellite protein OFD1. Analysis of normal and disease cohorts identified the cholangiocarcinoma as target of centrosome-associated spliceosome alterations. Multiplexed single-cell fluorescent microscopy for the centriole linker CEP250 and spliceosome components including BCAS2, BUD31, SRSF2 and DHX35 recapitulated bioinformatic predictions on the centrosome-associated spliceosome components tissue-type specific composition. Collectively, centrosomes and cilia act as anchor for cell-type specific spliceosome components, and provide a helpful reference for explore cytoplasmic condensates functions in defining cell identity and in the origin of rare diseases.
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Affiliation(s)
- Luigi Cerulo
- Bioinformatics Laboratory, BIOGEM scrl, Ariano Irpino, Avellino, Italy
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Nunziana Pezzella
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, Pozzuoli, 80078 Naples, Italy
- School for Advanced Studies, Genomics and Experimental Medicine Program, Naples, Italy
| | - Francesca Pia Caruso
- Bioinformatics Laboratory, BIOGEM scrl, Ariano Irpino, Avellino, Italy
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Paola Parente
- Unit of Pathology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Andrea Remo
- Pathology Unit, Mater Salutis Hospital AULSS9, “Scaligera”, 37122 Verona, Italy
| | - Guido Giordano
- Unit of Medical Oncology and Biomolecular Therapy, Department of Medical and Surgical Sciences, University of Foggia, Policlinico Riuniti, 71122 Foggia, Italy
| | - Nicola Forte
- Department of Clinical Pathology, Fatebenefratelli Hospital, 82100 Benevento, Italy
| | - Johan Busselez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Federico Boschi
- Department of Computer Science, University of Verona, Strada Le Grazie 8, Verona, Italy
| | - Mirco Galiè
- Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, Pozzuoli, 80078 Naples, Italy
- School for Advanced Studies, Genomics and Experimental Medicine Program, Naples, Italy
- Medical Genetics, Department of Translational Medicine, University of Naples “Federico II”, Via Sergio Pansini, 80131 Naples, Italy
| | - Massimo Pancione
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University Madrid, 28040 Madrid, Spain
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18
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Dong W, Tang C, Chu WT, Wang E, Wang J. Effects of Mass Change on Liquid–Liquid Phase Separation of the RNA-Binding Protein Fused in Sarcoma. Biomolecules 2023; 13:biom13040625. [PMID: 37189373 DOI: 10.3390/biom13040625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/13/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
In recent years, many experimental and theoretical studies of protein liquid–liquid phase separation (LLPS) have shown its important role in the processes of physiology and pathology. However, there is a lack of definite information on the regulation mechanism of LLPS in vital activities. Recently, we found that the intrinsically disordered proteins with the insertion/deletion of a non-interacting peptide segment or upon isotope replacement could form droplets, and the LLPS states are different from the proteins without those. We believed that there is an opportunity to decipher the LLPS mechanism with the mass change perspective. To investigate the effect of molecular mass on LLPS, we developed a coarse-grained model with different bead masses, including mass 1.0, mass 1.1, mass 1.2, mass 1.3, and mass 1.5 in atomic units or with the insertion of a non-interacting peptide (10 aa) and performed molecular dynamic simulations. Consequently, we found that the mass increase promotes the LLPS stability, which is based on decreasing the z motion rate and increasing the density and the inter-chain interaction of droplets. This insight into LLPS by mass change paves the way for the regulation and relevant diseases on LLPS.
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19
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Zernia S, Stigler J. DNA curtains for studying phase separation mechanisms of DNA-organizing proteins. Methods Cell Biol 2023; 182:95-108. [PMID: 38359990 DOI: 10.1016/bs.mcb.2023.02.006] [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: 03/29/2023]
Abstract
Phase separation is one key mechanism to organize chromatin into compartments and to regulate the activity of the genome. The formation of liquid-like droplets within the nucleus is driven by protein association to the DNA via multivalent binding and the recruitment of other proteins building a concentrated reaction environment. Common methods to study phase separation and its liquid-like nature are based on microscopy of the formed droplets but lack the resolution to obtain information on the molecular level. Here, we describe the application of the DNA curtain technique for studying protein-mediated phase separation on DNA. For this, multiple lipid-anchored DNA strands are flow-stretched across a nanobarrier to allow single-molecule studies of protein-DNA interactions in a high-throughput approach. Our protocol describes how protein-induced DNA compaction can be observed in real-time and which wash protocols are suitable to characterize the interactions that promote condensate formation. Furthermore, we demonstrate how fluorescently labeled tracer proteins can serve as orientation points to examine the DNA compaction mechanism in detail.
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Affiliation(s)
- Sarah Zernia
- Gene Center Munich, Ludwig Maximilian University, Munich, Germany
| | - Johannes Stigler
- Gene Center Munich, Ludwig Maximilian University, Munich, Germany.
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20
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Magazzù A, Marcuello C. Investigation of Soft Matter Nanomechanics by Atomic Force Microscopy and Optical Tweezers: A Comprehensive Review. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:963. [PMID: 36985857 PMCID: PMC10053849 DOI: 10.3390/nano13060963] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 05/17/2023]
Abstract
Soft matter exhibits a multitude of intrinsic physico-chemical attributes. Their mechanical properties are crucial characteristics to define their performance. In this context, the rigidity of these systems under exerted load forces is covered by the field of biomechanics. Moreover, cellular transduction processes which are involved in health and disease conditions are significantly affected by exogenous biomechanical actions. In this framework, atomic force microscopy (AFM) and optical tweezers (OT) can play an important role to determine the biomechanical parameters of the investigated systems at the single-molecule level. This review aims to fully comprehend the interplay between mechanical forces and soft matter systems. In particular, we outline the capabilities of AFM and OT compared to other classical bulk techniques to determine nanomechanical parameters such as Young's modulus. We also provide some recent examples of nanomechanical measurements performed using AFM and OT in hydrogels, biopolymers and cellular systems, among others. We expect the present manuscript will aid potential readers and stakeholders to fully understand the potential applications of AFM and OT to soft matter systems.
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Affiliation(s)
- Alessandro Magazzù
- CNR-IPCF, Istituto per i Processi Chimico-Fisici, 98158 Mesina, Italy
- NLHT-Lab, Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
- Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, 50018 Zaragoza, Spain
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21
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Ji J, Wang W, Chen C. Single-molecule techniques to visualize and to characterize liquid-liquid phase separation and phase transition. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1023-1033. [PMID: 36876423 PMCID: PMC10415186 DOI: 10.3724/abbs.2023028] [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: 11/24/2022] [Accepted: 01/09/2023] [Indexed: 02/23/2023] Open
Abstract
Biomolecules forming membraneless structures via liquid-liquid phase separation (LLPS) is a common event in living cells. Some liquid-like condensates can convert into solid-like aggregations, and such a phase transition process is related to some neurodegenerative diseases. Liquid-like condensates and solid-like aggregations usually exhibit distinctive fluidity and are commonly distinguished via their morphology and dynamic properties identified through ensemble methods. Emerging single-molecule techniques are a group of highly sensitive techniques, which can offer further mechanistic insights into LLPS and phase transition at the molecular level. Here, we summarize the working principles of several commonly used single-molecule techniques and demonstrate their unique power in manipulating LLPS, examining mechanical properties at the nanoscale, and monitoring dynamic and thermodynamic properties at the molecular level. Thus, single-molecule techniques are unique tools to characterize LLPS and liquid-to-solid phase transition under close-to-physiological conditions.
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Affiliation(s)
- Jinyao Ji
- School of Life SciencesBeijing Advanced Innovation Center for Structural BiologyBeijing Frontier Research Center of Biological StructureTsinghua UniversityBeijing100084China
| | - Wenjuan Wang
- School of Life SciencesTechnology Center for Protein SciencesTsinghua UniversityBeijing100084China
| | - Chunlai Chen
- School of Life SciencesBeijing Advanced Innovation Center for Structural BiologyBeijing Frontier Research Center of Biological StructureTsinghua UniversityBeijing100084China
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22
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Haghizadeh A, Iftikhar M, Dandpat SS, Simpson T. Looking at Biomolecular Interactions through the Lens of Correlated Fluorescence Microscopy and Optical Tweezers. Int J Mol Sci 2023; 24:2668. [PMID: 36768987 PMCID: PMC9916863 DOI: 10.3390/ijms24032668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/19/2022] [Accepted: 01/26/2023] [Indexed: 02/01/2023] Open
Abstract
Understanding complex biological events at the molecular level paves the path to determine mechanistic processes across the timescale necessary for breakthrough discoveries. While various conventional biophysical methods provide some information for understanding biological systems, they often lack a complete picture of the molecular-level details of such dynamic processes. Studies at the single-molecule level have emerged to provide crucial missing links to understanding complex and dynamic pathways in biological systems, which are often superseded by bulk biophysical and biochemical studies. Latest developments in techniques combining single-molecule manipulation tools such as optical tweezers and visualization tools such as fluorescence or label-free microscopy have enabled the investigation of complex and dynamic biomolecular interactions at the single-molecule level. In this review, we present recent advances using correlated single-molecule manipulation and visualization-based approaches to obtain a more advanced understanding of the pathways for fundamental biological processes, and how this combination technique is facilitating research in the dynamic single-molecule (DSM), cell biology, and nanomaterials fields.
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23
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André AAM, Yewdall NA, Spruijt E. Crowding-induced phase separation and gelling by co-condensation of PEG in NPM1-rRNA condensates. Biophys J 2023; 122:397-407. [PMID: 36463407 PMCID: PMC9892608 DOI: 10.1016/j.bpj.2022.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/11/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
The crowdedness of the cell calls for adequate intracellular organization. Biomolecular condensates, formed by liquid-liquid phase separation of intrinsically disordered proteins and nucleic acids, are important organizers of cellular fluids. To underpin the molecular mechanisms of protein condensation, cell-free studies are often used where the role of crowding is not investigated in detail. Here, we investigate the effects of macromolecular crowding on the formation and material properties of a model heterotypic biomolecular condensate, consisting of nucleophosmin (NPM1) and ribosomal RNA (rRNA). We studied the effect of the macromolecular crowding agent poly(ethylene glycol) (PEG), which is often considered an inert crowding agent. We observed that PEG could induce both homotypic and heterotypic phase separation of NPM1 and NPM1-rRNA, respectively. Crowding increases the condensed concentration of NPM1 and decreases its equilibrium dilute phase concentration, although no significant change in the concentration of rRNA in the dilute phase was observed. Interestingly, the crowder itself is concentrated in the condensates, suggesting that co-condensation rather than excluded volume interactions underlie the enhanced phase separation by PEG. Fluorescence recovery after photobleaching measurements indicated that both NPM1 and rRNA become immobile at high PEG concentrations, indicative of a liquid-to-gel transition. Together, these results provide more insight into the role of synthetic crowding agents in phase separation and demonstrate that condensate properties determined in vitro depend strongly on the addition of crowding agents.
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Affiliation(s)
- Alain A M André
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - N Amy Yewdall
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
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24
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Zong W, Shao X, Li J, Chai Y, Hu X, Zhang X. Synthetic Intracellular Environments: From Basic Science to Applications. Anal Chem 2023; 95:535-549. [PMID: 36625127 DOI: 10.1021/acs.analchem.2c04199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Wei Zong
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China
| | - Xiaotong Shao
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China
| | - Jinlong Li
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China.,Heilongjiang Provincial Key Laboratory of Catalytic Synthesis for Fine Chemicals, Qiqihar University, Qiqihar161006, China
| | - Yunhe Chai
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China
| | - Xinyu Hu
- Key Laboratory of Micro-Nano Optoelectronic Devices (Wenzhou), College of Electrical and Electronic Engineering, Wenzhou University, Wenzhou325035, China
| | - Xunan Zhang
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China
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25
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Félix SS, Laurents DV, Oroz J, Cabrita EJ. Fused in sarcoma undergoes cold denaturation: Implications for phase separation. Protein Sci 2023; 32:e4521. [PMID: 36453011 PMCID: PMC9793971 DOI: 10.1002/pro.4521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/04/2022]
Abstract
The mediation of liquid-liquid phase separation (LLPS) for fused in sarcoma (FUS) protein is generally attributed to the low-complexity, disordered domains and is enhanced at low temperature. The role of FUS folded domains on the LLPS process remains relatively unknown since most studies are mainly based on fragmented FUS domains. Here, we investigate the effect of metabolites on full-length (FL) FUS LLPS using turbidity assays and differential interference contrast (DIC) microscopy, and explore the behavior of the folded domains by nuclear magnetic resonance (NMR) spectroscopy. FL FUS LLPS is maximal at low concentrations of glucose and glutamate, moderate concentrations of NaCl, Zn2+ , and Ca2+ and at the isoelectric pH. The FUS RNA recognition motif (RRM) and zinc-finger (ZnF) domains are found to undergo cold denaturation above 0°C at a temperature that is determined by the conformational stability of the ZnF domain. Cold unfolding exposes buried nonpolar residues that can participate in LLPS-promoting hydrophobic interactions. Therefore, these findings constitute the first evidence that FUS globular domains may have an active role in LLPS under cold stress conditions and in the assembly of stress granules, providing further insight into the environmental regulation of LLPS.
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Affiliation(s)
- Sara S. Félix
- UCIBIO, Department of ChemistryNOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Instituto de Química Física Rocasolano (IQFR), CSICMadridSpain
| | | | - Javier Oroz
- Instituto de Química Física Rocasolano (IQFR), CSICMadridSpain
| | - Eurico J. Cabrita
- UCIBIO, Department of ChemistryNOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal
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26
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Ghosh A, Kota D, Zhou HX. Determining Thermodynamic and Material Properties of Biomolecular Condensates by Confocal Microscopy and Optical Tweezers. Methods Mol Biol 2023; 2563:237-260. [PMID: 36227477 PMCID: PMC9577454 DOI: 10.1007/978-1-0716-2663-4_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
While the roles of biomolecular condensates in health and disease are being intensely studied, it is equally important that their physical properties are characterized in order to achieve mechanistic understanding. Here we share some of the protocols developed in our lab for measuring thermodynamic and materials properties of condensates. These include a simple method for determining the droplet-phase concentrations of condensate components on a confocal microscope, and a method for determining the viscoelasticity of condensates by optical tweezers. These protocols are either generally applicable to biomolecular condensates or are unique for their characterization.
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Affiliation(s)
- Archishman Ghosh
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Divya Kota
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Physics, University of Illinois at Chicago, Chicago, IL, USA.
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27
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Erkamp NA, Qi R, Welsh TJ, Knowles TPJ. Microfluidics for multiscale studies of biomolecular condensates. LAB ON A CHIP 2022; 23:9-24. [PMID: 36269080 PMCID: PMC9764808 DOI: 10.1039/d2lc00622g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/04/2022] [Indexed: 05/12/2023]
Abstract
Membraneless organelles formed through condensation of biomolecules in living cells have become the focus of sustained efforts to elucidate their mechanisms of formation and function. These condensates perform a range of vital functions in cells and are closely connected to key processes in functional and aberrant biology. Since these systems occupy a size scale intermediate between single proteins and conventional protein complexes on the one hand, and cellular length scales on the other hand, they have proved challenging to probe using conventional approaches from either protein science or cell biology. Additionally, condensate can form, solidify and perform functions on various time-scales. From a physical point of view, biomolecular condensates are colloidal soft matter systems, and microfluidic approaches, which originated in soft condensed matter research, have successfully been used to study biomolecular condensates. This review explores how microfluidics have aided condensate research into the thermodynamics, kinetics and other properties of condensates, by offering high-throughput and novel experimental setups.
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Affiliation(s)
- Nadia A Erkamp
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Runzhang Qi
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Timothy J Welsh
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge, CB3 0HE, UK
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28
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Ji Y, Li F, Qiao Y. Modulating liquid-liquid phase separation of FUS: mechanisms and strategies. J Mater Chem B 2022; 10:8616-8628. [PMID: 36268634 DOI: 10.1039/d2tb01688e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Liquid-liquid phase separation (LLPS) of biomolecules inspires the construction of protocells and drives the formation of cellular membraneless organelles. The resulting biomolecular condensates featuring dynamic assembly, disassembly, and phase transition play significant roles in a series of biological processes, including RNA metabolism, DNA damage response, signal transduction and neurodegenerative disease. Intensive investigations have been conducted for understanding and manipulating intracellular phase-separated disease-related proteins (e.g., FUS, tau and TDP-43). Herein, we review current studies on the regulation strategies of intracellular LLPS focusing on FUS, which are categorized into physical stimuli, biochemical modulators, and protein structural modifications, with summarized molecular mechanisms. This review is expected to provide a sketch of the modulation of FUS LLPS with its pros and cons, and an outlook for the potential clinical treatments of neurodegenerative diseases.
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Affiliation(s)
- Yanglimin Ji
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fen Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Qiao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China
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29
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van Tartwijk FW, Kaminski CF. Protein Condensation, Cellular Organization, and Spatiotemporal Regulation of Cytoplasmic Properties. Adv Biol (Weinh) 2022; 6:e2101328. [PMID: 35796197 DOI: 10.1002/adbi.202101328] [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: 12/31/2021] [Revised: 05/15/2022] [Indexed: 01/28/2023]
Abstract
The cytoplasm is an aqueous, highly crowded solution of active macromolecules. Its properties influence the behavior of proteins, including their folding, motion, and interactions. In particular, proteins in the cytoplasm can interact to form phase-separated assemblies, so-called biomolecular condensates. The interplay between cytoplasmic properties and protein condensation is critical in a number of functional contexts and is the subject of this review. The authors first describe how cytoplasmic properties can affect protein behavior, in particular condensate formation, and then describe the functional implications of this interplay in three cellular contexts, which exemplify how protein self-organization can be adapted to support certain physiological phenotypes. The authors then describe the formation of RNA-protein condensates in highly polarized cells such as neurons, where condensates play a critical role in the regulation of local protein synthesis, and describe how different stressors trigger extensive reorganization of the cytoplasm, both through signaling pathways and through direct stress-induced changes in cytoplasmic properties. Finally, the authors describe changes in protein behavior and cytoplasmic properties that may occur in extremophiles, in particular organisms that have adapted to inhabit environments of extreme temperature, and discuss the implications and functional importance of these changes.
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Affiliation(s)
- Francesca W van Tartwijk
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
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30
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Quinn SD, Dresser L, Graham S, Conteduca D, Shepherd J, Leake MC. Crowding-induced morphological changes in synthetic lipid vesicles determined using smFRET. Front Bioeng Biotechnol 2022; 10:958026. [PMID: 36394015 PMCID: PMC9650091 DOI: 10.3389/fbioe.2022.958026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/13/2022] [Indexed: 12/02/2022] Open
Abstract
Lipid vesicles are valuable mesoscale molecular confinement vessels for studying membrane mechanics and lipid-protein interactions, and they have found utility among bio-inspired technologies, including drug delivery vehicles. While vesicle morphology can be modified by changing the lipid composition and introducing fusion or pore-forming proteins and detergents, the influence of extramembrane crowding on vesicle morphology has remained under-explored owing to a lack of experimental tools capable of capturing morphological changes on the nanoscale. Here, we use biocompatible polymers to simulate molecular crowding in vitro, and through combinations of FRET spectroscopy, lifetime analysis, dynamic light scattering, and single-vesicle imaging, we characterize how crowding regulates vesicle morphology. We show that both freely diffusing and surface-tethered vesicles fluorescently tagged with the DiI and DiD FRET pair undergo compaction in response to modest concentrations of sorbitol, polyethylene glycol, and Ficoll. A striking observation is that sorbitol results in irreversible compaction, whereas the influence of high molecular weight PEG-based crowders was found to be reversible. Regulation of molecular crowding allows for precise control of the vesicle architecture in vitro, with vast implications for drug delivery and vesicle trafficking systems. Furthermore, our observations of vesicle compaction may also serve to act as a mechanosensitive readout of extramembrane crowding.
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Affiliation(s)
- Steven D. Quinn
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom
| | - Lara Dresser
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
| | - Sarah Graham
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
| | - Donato Conteduca
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
| | - Jack Shepherd
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- Department of Biology, University of York, York, United Kingdom
| | - Mark C. Leake
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom
- Department of Biology, University of York, York, United Kingdom
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31
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Dyer OT, Ball RC. Surfactancy in a tadpole model of proteins. J R Soc Interface 2022; 19:20220172. [PMID: 36195115 PMCID: PMC9532023 DOI: 10.1098/rsif.2022.0172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/16/2022] [Indexed: 11/07/2022] Open
Abstract
We model the environment of eukaryotic nuclei by representing macromolecules by only their entropic properties, with globular molecules represented by spherical colloids and flexible molecules by polymers. We put particular focus on proteins with both globular and intrinsically disordered regions, which we represent with 'tadpole' constructed by grafting single polymers and colloids together. In Monte Carlo simulations, we find these tadpoles support phase separation via depletion flocculation, and demonstrate several surfactant behaviours, including being found preferentially at interfaces and forming micelles in single phase solution. Furthermore, the model parameters can be tuned to give a tadpole a preference for either bulk phase. However, we find entropy too weak to drive these behaviours by itself at likely biological concentrations.
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Affiliation(s)
- O. T. Dyer
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - R. C. Ball
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
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32
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Multivalent interactions between molecular components involved in fast endophilin mediated endocytosis drive protein phase separation. Nat Commun 2022; 13:5017. [PMID: 36028485 PMCID: PMC9418313 DOI: 10.1038/s41467-022-32529-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 08/03/2022] [Indexed: 11/30/2022] Open
Abstract
A specific group of transmembrane receptors, including the β1-adrenergic receptor (β1-AR), is internalized through a non-clathrin pathway known as Fast Endophilin Mediated Endocytosis (FEME). A key question is: how does the endocytic machinery assemble and how is it modulated by activated receptors during FEME. Here we show that endophilin, a major regulator of FEME, undergoes a phase transition into liquid-like condensates, which facilitates the formation of multi-protein assemblies by enabling the phase partitioning of endophilin binding proteins. The phase transition can be triggered by specific multivalent binding partners of endophilin in the FEME pathway such as the third intracellular loop (TIL) of the β1-AR, and the C-terminal domain of lamellipodin (LPD). Other endocytic accessory proteins can either partition into, or target interfacial regions of, these condensate droplets, and LPD also phase separates with the actin polymerase VASP. On the membrane, TIL promotes protein clustering in the presence of endophilin and LPD C-terminal domain. Our results demonstrate how the multivalent interactions between endophilin, LPD, and TIL regulate protein assembly formation on the membrane, providing mechanistic insights into the priming and initiation steps of FEME. Here the authors show that protein phase separation is a key mechanism in cellular receptor internalization via fast endophilin mediated endocytosis (FEME). Phase separation facilitates multivalent FEME-protein assembly in this clathrin-independent pathway.
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33
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Angert I, Karuka SR, Mansky LM, Mueller JD. Partitioning of ribonucleoprotein complexes from the cellular actin cortex. SCIENCE ADVANCES 2022; 8:eabj3236. [PMID: 35984883 PMCID: PMC9390997 DOI: 10.1126/sciadv.abj3236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
The cell cortex plays a crucial role in cell mechanics, signaling, and development. However, little is known about the influence of the cortical meshwork on the spatial distribution of cytoplasmic biomolecules. Here, we describe a fluorescence microscopy method with the capacity to infer the intracellular distribution of labeled biomolecules with subresolution accuracy. Unexpectedly, we find that RNA binding proteins are partially excluded from the cytoplasmic volume adjacent to the plasma membrane that corresponds to the actin cortex. Complementary diffusion measurements of RNA-protein complexes suggest that a rudimentary model based on excluded volume interactions can explain this partitioning effect. Our results suggest the actin cortex meshwork may play a role in regulating the biomolecular content of the volume immediately adjacent to the plasma membrane.
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Affiliation(s)
- Isaac Angert
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
- Institute of Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Siddarth Reddy Karuka
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Louis M. Mansky
- Institute of Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Joachim D. Mueller
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
- Institute of Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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34
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Michieletto D, Marenda M. Rheology and Viscoelasticity of Proteins and Nucleic Acids Condensates. JACS AU 2022; 2:1506-1521. [PMID: 35911447 PMCID: PMC9326828 DOI: 10.1021/jacsau.2c00055] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Phase separation is as familiar as watching vinegar separating from oil in vinaigrette. The observation that phase separation of proteins and nucleic acids is widespread in living cells has opened an entire field of research into the biological significance and the biophysical mechanisms of phase separation and protein condensation in biology. Recent evidence indicates that certain proteins and nucleic acids condensates are not simple liquids and instead display both viscous and elastic behaviors, which in turn may have biological significance. The aim of this Perspective is to review the state-of-the-art of this quickly emerging field focusing on the material and rheological properties of protein condensates. Finally, we discuss the different techniques that can be employed to quantify the viscoelasticity of condensates and highlight potential future directions and opportunities for interdisciplinary cross-talk between chemists, physicists, and biologists.
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Affiliation(s)
- Davide Michieletto
- School
of Physics and Astronomy, University of
Edinburgh, Peter Guthrie
Tait Road, Edinburgh EH9
3FD, U.K.
- MRC
Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, U.K.
| | - Mattia Marenda
- School
of Physics and Astronomy, University of
Edinburgh, Peter Guthrie
Tait Road, Edinburgh EH9
3FD, U.K.
- MRC
Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, U.K.
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35
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Kota D, Zhou HX. Macromolecular Regulation of the Material Properties of Biomolecular Condensates. J Phys Chem Lett 2022; 13:5285-5290. [PMID: 35674796 PMCID: PMC9729394 DOI: 10.1021/acs.jpclett.2c00824] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Biomolecular condensates inside cells contain dozens to hundreds of macromolecular components and are surrounded by many others. Our computational studies predicted that macromolecular regulators have matching effects on the phase equilibrium and interfacial tension of condensates. Here we validate this prediction experimentally and characterize the effects of macromolecular regulators on other material properties, including viscoelasticity and fusion speed. Local melting due to the heating of a laser beam and turbidity assay both show that Ficoll70 raises the melting temperature of condensates formed by polylysine:heparin mixtures, whereas optical-tweezer measurements reveal parallel increases in interfacial tension. Additional optical-tweezer experiments report elevations in viscosity and shear relaxation time but also fusion speed by Ficoll70. The fusion speed is higher than predicted by modeling the condensates as purely viscous, demonstrating viscoelasticity and shear thinning. These results illustrate the ample opportunities for macromolecular regulators to tune material properties for proper functions of biomolecular condensates.
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Affiliation(s)
- Divya Kota
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, United State
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, United State
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, United State
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36
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Jonchhe S, Pan W, Pokhrel P, Mao H. Small Molecules Modulate Liquid-to-Solid Transitions in Phase-Separated Tau Condensates. Angew Chem Int Ed Engl 2022; 61:e202113156. [PMID: 35320624 PMCID: PMC9156559 DOI: 10.1002/anie.202113156] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Indexed: 11/08/2022]
Abstract
In Tau protein condensates formed by the Liquid-Liquid Phase Separation (LLPS) process, liquid-to-solid transitions lead to the formation of fibrils implicated in Alzheimer's disease. Here, by tracking two contacting Tau-rich droplets using a simple and nonintrusive video microscopy, we found that the halftime of the liquid-to-solid transition in the Tau condensate is affected by the Hofmeister series according to the solvation energy of anions. After dissecting functional groups of physiologically relevant small molecules using a multivariate approach, we found that charged groups facilitate the liquid-to-solid transition in a manner similar to the Hofmeister effect, whereas hydrophobic alkyl chains and aromatic rings inhibit the transition. Our results not only elucidate the driving force of the liquid-to-solid transition in Tau condensates, but also provide guidelines to design small molecules to modulate this important transition for many biological functions for the first time.
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Affiliation(s)
- Sagun Jonchhe
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Wei Pan
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Pravin Pokhrel
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Hanbin Mao
- Department of Chemistry & Biochemistry, Advanced Materials and Liquid Crystal Institute, Department of Biomedical Sciences, Kent State University, Kent, OH 44242, USA
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37
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Tomares DT, Whitlock S, Mann M, DiBernardo E, Childers WS. Repurposing Peptide Nanomaterials as Synthetic Biomolecular Condensates in Bacteria. ACS Synth Biol 2022; 11:2154-2162. [PMID: 35658421 DOI: 10.1021/acssynbio.2c00078] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide nanomaterials exhibit diverse applications in vitro, such as drug delivery. Here, we consider the utility of de novo peptide nanomaterials to organize biochemistry within the bacterial cytoplasm. Toward this goal, we discovered that ABC coiled-coil triblock peptides form gel-like biomolecular condensates with a csat of 10 μM in addition to their well-known hydrogel-forming capabilities. Expression of the coiled-coil triblock peptides in bacteria leads to cell pole accumulation via a nucleoid occlusion mechanism. We then provide a proof of principle that these synthetic biomolecular condensates could sequester clients at the cell pole. Finally, we demonstrate that triblock peptides and another biomolecular condensate, RNase E, phase-separate as distinct protein-rich assemblies in vitro and in vivo. These results reveal the potential of using peptide nanomaterials to divide the bacterial cytoplasm into distinct subcellular zones with future metabolic engineering and synthetic biology applications.
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Affiliation(s)
- Dylan T Tomares
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sara Whitlock
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Matthew Mann
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Emma DiBernardo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - W Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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38
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Linsenmeier M, Hondele M, Grigolato F, Secchi E, Weis K, Arosio P. Dynamic arrest and aging of biomolecular condensates are modulated by low-complexity domains, RNA and biochemical activity. Nat Commun 2022; 13:3030. [PMID: 35641495 PMCID: PMC9156751 DOI: 10.1038/s41467-022-30521-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/27/2022] [Indexed: 11/18/2022] Open
Abstract
Biomolecular condensates require suitable control of material properties for their function. Here we apply Differential Dynamic Microscopy (DDM) to probe the material properties of an in vitro model of processing bodies consisting of out-of-equilibrium condensates formed by the DEAD-box ATPase Dhh1 in the presence of ATP and RNA. By applying this single-droplet technique we show that condensates within the same population exhibit a distribution of material properties, which are regulated on several levels. Removal of the low-complexity domains (LCDs) of the protein decreases the fluidity of the condensates. Structured RNA leads to a larger fraction of dynamically arrested condensates with respect to unstructured polyuridylic acid (polyU). Promotion of the enzymatic ATPase activity of Dhh1 reduces aging of the condensates and the formation of arrested structures, indicating that biochemical activity and material turnover can maintain fluid-like properties over time.
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Affiliation(s)
- Miriam Linsenmeier
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology, 8093, Zurich, Switzerland
| | - Maria Hondele
- Department of Biology, Institute for Biochemistry, Swiss Federal Institute of Technology, 8093, Zurich, Switzerland
- Biozentrum, Center for Molecular Life Sciences, University of Basel, 4056, Basel, Switzerland
| | - Fulvio Grigolato
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology, 8093, Zurich, Switzerland
| | - Eleonora Secchi
- Department of Civil, Environmental and Geomatic Engineering, Swiss Federal Institute of Technology, 8093, Zurich, Switzerland
| | - Karsten Weis
- Department of Biology, Institute for Biochemistry, Swiss Federal Institute of Technology, 8093, Zurich, Switzerland.
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology, 8093, Zurich, Switzerland.
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39
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Liu J, Zhorabek F, Dai X, Huang J, Chau Y. Minimalist Design of an Intrinsically Disordered Protein-Mimicking Scaffold for an Artificial Membraneless Organelle. ACS CENTRAL SCIENCE 2022; 8:493-500. [PMID: 35505868 PMCID: PMC9052801 DOI: 10.1021/acscentsci.1c01021] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Indexed: 05/05/2023]
Abstract
Liquid-liquid phase separation (LLPS) is an emerging and universal mechanism for intracellular organization, particularly, by forming membraneless organelles (MLOs) hosting intrinsically disordered proteins (IDPs) as scaffolds. Genetic engineering is generally applied to reconstruct IDPs harboring over 100 amino acid residues. Here, we report the first design of synthetic hybrids consisting of short oligopeptides of fewer than 10 residues as "stickers" and dextran as a "spacer" to recapitulate the characteristics of IDPs, as exemplified by the multivalent FUS protein. Hybrids undergo LLPS into micron-sized liquid droplets resembling LLPS in vitro and in living cells. Moreover, the droplets formed are capable of recruiting proteins and RNAs and providing a favorable environment for a biochemical reaction with highly enriched components, thereby mimicking the function of natural MLOs. This simple yet versatile model system can help elucidate the molecular interactions implicated in MLOs and pave ways to a new type of biomimetic materials.
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Affiliation(s)
- Jianhui Liu
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Fariza Zhorabek
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Xin Dai
- Department
of Chemistry, The Hong Kong University of
Science and Technology, Clear Water
Bay, Kowloon, Hong Kong SAR, China
| | - Jinqing Huang
- Department
of Chemistry, The Hong Kong University of
Science and Technology, Clear Water
Bay, Kowloon, Hong Kong SAR, China
| | - Ying Chau
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
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40
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Cubuk J, Soranno A. Macromolecular crowding and intrinsically disordered proteins: a polymer physics perspective. CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202100051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jasmine Cubuk
- Washington University in St Louis Biochemistry and Molecular Biophysics UNITED STATES
| | - Andrea Soranno
- Washington University in St Louis Biochemistry and Molecular Biophysics 660 St Euclid Ave 63110 St Louis UNITED STATES
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41
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Phase separation on cell surface facilitates bFGF signal transduction with heparan sulphate. Nat Commun 2022; 13:1112. [PMID: 35236856 PMCID: PMC8891335 DOI: 10.1038/s41467-022-28765-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 02/09/2022] [Indexed: 12/29/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) plays important roles in various cellular processes, facilitating membrane-less organelles construction, chromatin condensation, signal transduction on inner membrane and many other processes. Current perception is that LLPS relies on weak multivalent interactions and crowded environments intracellularly. In this study, we demonstrate that heparan sulfate can serve as a platform to induce the phase separation of basic fibroblast growth factor on cell surface. The phase separation model provides an alternative mechanism how bFGF is enriched to its receptors, therefore triggering the signaling transduction. The research provides insights on the mechanism how growth factors can be recruited to cell surface by heparan sulfate and execute their functions, extending people’s view on phase separation from intracellular to extracellular proteins at cellular level. Liquid-liquid phase separation (LLPS) is reported to occur in the intracellular environment. Here the authors show that heparan sulphate serves as a platform for basic fibroblast growth factor to undergo LLPS on the cell surface, therefore facilitating downstream signalling
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42
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Wang Z, Lou J, Zhang H. Essence determines phenomenon: Assaying the material properties of biological condensates. J Biol Chem 2022; 298:101782. [PMID: 35245500 PMCID: PMC8958544 DOI: 10.1016/j.jbc.2022.101782] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 01/02/2023] Open
Abstract
Intracellular spaces are partitioned into separate compartments to ensure that numerous biochemical reactions and cellular functions take place in a spatiotemporally controlled manner. Biomacromolecules including proteins and RNAs undergo liquid–liquid phase separation and subsequent phase transition to form biological condensates with diverse material states. The material/physical properties of biological condensates are crucial for fulfilling their distinct physiological functions, and abnormal material properties can cause deleterious effects under pathological conditions. Here, we review recent studies showing the role of the material properties of biological condensates in their physiological functions. We also summarize several classic methods as well as newly emerging techniques for characterization and/or measurement of the material properties of biological condensates.
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Affiliation(s)
- Zheng Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Jizhong Lou
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
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43
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Ronceray P, Zhang Y, Liu X, Wingreen NS. Stoichiometry Controls the Dynamics of Liquid Condensates of Associative Proteins. PHYSICAL REVIEW LETTERS 2022; 128:038102. [PMID: 35119898 PMCID: PMC10497325 DOI: 10.1103/physrevlett.128.038102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 01/04/2022] [Indexed: 05/12/2023]
Abstract
Multivalent associative proteins with strong complementary interactions play a crucial role in phase separation of intracellular liquid condensates. We study the internal dynamics of such "bond-network" condensates comprising two complementary proteins via scaling analysis and molecular dynamics. We find that when stoichiometry is balanced, relaxation slows down dramatically due to a scarcity of alternative binding partners following bond breakage. This microscopic slow-down strongly affects the bulk diffusivity, viscosity, and mixing, which provides a means to experimentally test this prediction.
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Affiliation(s)
- Pierre Ronceray
- Center for the Physics of Biological Function, Princeton University, Princeton, New Jersey 08544, USA
- Aix Marseille Univ, CNRS, CINAM, Turing Center for Living Systems, Marseille, France
| | - Yaojun Zhang
- Center for the Physics of Biological Function, Princeton University, Princeton, New Jersey 08544, USA
- Department of Physics and Astronomy and Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xichong Liu
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
- Stanford University School of Medicine, Stanford, California 94305, USA
| | - Ned S. Wingreen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
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44
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Rhine K, Skanchy S, Myong S. Single-molecule and ensemble methods to probe RNP nucleation and condensate properties. Methods 2022; 197:74-81. [PMID: 33610691 PMCID: PMC8374000 DOI: 10.1016/j.ymeth.2021.02.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/02/2021] [Accepted: 02/13/2021] [Indexed: 01/03/2023] Open
Abstract
Biomolecular condensates often consist of intrinsically disordered protein and RNA molecules, which together promote the formation of membraneless organelles in cells. The nucleation, condensation, and maturation of condensates is a critical yet poorly understood process. Here, we present single-molecule and accompanying ensemble methods to quantify these processes more comprehensively. In particular, we focus on how to properly design and execute a single-molecule nucleation assay, in which we detect signals arising from individual units of fluorescently labeled RNA-binding proteins associating with an RNA substrate. The analysis of this data allows one to determine the kinetics involved with each step of nucleation. Complemented with meso-scale techniques that measure the biophysical properties of ribonucleoprotein condensates, the methods described herein are powerful tools that can be adopted for studying any protein-RNA interactions that promote phase separation.
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Affiliation(s)
- Kevin Rhine
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218,Department of Biology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218
| | - Sophie Skanchy
- Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218
| | - Sua Myong
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218,Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218,Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, 506 S Wright St, Urbana, IL 61801,Corresponding Author;
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45
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Jo Y, Jang J, Song D, Park H, Jung Y. Determinants for intrinsically disordered protein recruitment into phase-separated protein condensates. Chem Sci 2022; 13:522-530. [PMID: 35126984 PMCID: PMC8729795 DOI: 10.1039/d1sc05672g] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/10/2021] [Indexed: 12/21/2022] Open
Abstract
Multivalent interactions between amino acid residues of intrinsically disordered proteins (IDPs) drive phase separation of these proteins into liquid condensates, forming various membrane-less organelles in cells. These interactions between often biased residues of IDPs are also likely involved in selective recruitment of many other IDPs into condensates. However, determining factors for this IDP recruitment into protein condensates are not understood yet. Here, we quantitatively examined recruitment tendencies of various IDPs with different sequence compositions into IDP-clustered condensates both in vitro as well as in cells. Condensate-forming IDP scaffolds, recruited IDP clients, and phase separation conditions were carefully varied to find key factors for selective IDP partitioning in protein condensates. Regardless of scaffold sequences, charged residues in client IDPs assured potent IDP recruitment, likely via strong electrostatic interactions, where positive residues could further enhance recruitment, possibly with cation–pi interactions. Notably, poly-ethylene glycol, a widely used crowding reagent for in vitro phase separation, abnormally increased IDP recruitment, indicating the need for careful use of crowding conditions. Tyrosines of IDP clients also strongly participated in recruitment both in vitro and in cells. Lastly, we measured recruitment degrees by more conventional interactions between folded proteins instead of disordered proteins. Surprisingly, recruitment forces by an even moderate protein interaction (Kd ∼ 5 μM) were substantially stronger than those by natural IDP–IDP interactions. The present data offer valuable information on how cells might organize protein partitioning on various protein condensates. Diverse interactions between folded and disordered proteins collectively dictate selective protein recruitment into bimolecular condensates.![]()
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Affiliation(s)
- Yongsang Jo
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jinyoung Jang
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Daesun Song
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyoin Park
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yongwon Jung
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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46
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Samanta N, Ribeiro SS, Becker M, Laborie E, Pollak R, Timr S, Sterpone F, Ebbinghaus S. Sequestration of Proteins in Stress Granules Relies on the In-Cell but Not the In Vitro Folding Stability. J Am Chem Soc 2021; 143:19909-19918. [PMID: 34788540 DOI: 10.1021/jacs.1c09589] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Stress granules (SGs) are among the most studied membraneless organelles that form upon heat stress (HS) to sequester unfolded, misfolded, or aggregated protein, supporting protein quality control (PQC) clearance. The folding states that are primarily associated with SGs, as well as the function of the phase separated environment in adjusting the energy landscapes, remain unknown. Here, we investigate the association of superoxide dismutase 1 (SOD1) proteins with different folding stabilities and aggregation propensities with condensates in cells, in vitro and by simulation. We find that irrespective of aggregation the folding stability determines the association of SOD1 with SGs in cells. In vitro and in silico experiments however suggest that the increased flexibility of the unfolded state constitutes only a minor driving force to associate with the dynamic biomolecular network of the condensate. Specific protein-protein interactions in the cytoplasm in comparison to SGs determine the partitioning of folding states between the respective phases during HS.
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Affiliation(s)
- Nirnay Samanta
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, D-38106 Braunschweig, Germany
| | - Sara S Ribeiro
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, D-38106 Braunschweig, Germany
| | - Mailin Becker
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, D-38106 Braunschweig, Germany
| | - Emeline Laborie
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, Paris 75005, France
| | - Roland Pollak
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, D-38106 Braunschweig, Germany
| | - Stepan Timr
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, Paris 75005, France.,J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejskova 2155/3, Prague 8 182 23, Czech Republic
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, Paris 75005, France
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, D-38106 Braunschweig, Germany
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47
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Hubatsch L, Jawerth LM, Love C, Bauermann J, Tang TD, Bo S, Hyman AA, Weber CA. Quantitative theory for the diffusive dynamics of liquid condensates. eLife 2021; 10:68620. [PMID: 34636323 PMCID: PMC8580480 DOI: 10.7554/elife.68620] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 10/11/2021] [Indexed: 12/02/2022] Open
Abstract
Key processes of biological condensates are diffusion and material exchange with their environment. Experimentally, diffusive dynamics are typically probed via fluorescent labels. However, to date, a physics-based, quantitative framework for the dynamics of labeled condensate components is lacking. Here, we derive the corresponding dynamic equations, building on the physics of phase separation, and quantitatively validate the related framework via experiments. We show that by using our framework, we can precisely determine diffusion coefficients inside liquid condensates via a spatio-temporal analysis of fluorescence recovery after photobleaching (FRAP) experiments. We showcase the accuracy and precision of our approach by considering space- and time-resolved data of protein condensates and two different polyelectrolyte-coacervate systems. Interestingly, our theory can also be used to determine a relationship between the diffusion coefficient in the dilute phase and the partition coefficient, without relying on fluorescence measurements in the dilute phase. This enables us to investigate the effect of salt addition on partitioning and bypasses recently described quenching artifacts in the dense phase. Our approach opens new avenues for theoretically describing molecule dynamics in condensates, measuring concentrations based on the dynamics of fluorescence intensities, and quantifying rates of biochemical reactions in liquid condensates.
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Affiliation(s)
- Lars Hubatsch
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Louise M Jawerth
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Celina Love
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jonathan Bauermann
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Ty Dora Tang
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Stefano Bo
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Christoph A Weber
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
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48
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Chauhan G, Simpson ML, Abel SM. Adsorption of semiflexible polymers in crowded environments. J Chem Phys 2021; 155:034904. [PMID: 34293868 DOI: 10.1063/5.0054797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Macromolecular crowding is a feature of cellular and cell-free systems that, through depletion effects, can impact the interactions of semiflexible biopolymers with surfaces. In this work, we use computer simulations to study crowding-induced adsorption of semiflexible polymers on otherwise repulsive surfaces. Crowding particles are modeled explicitly, and we investigate the interplay between the bending stiffness of the polymer and the volume fraction and size of crowding particles. Adsorption to flat surfaces is promoted by stiffer polymers, smaller crowding particles, and larger volume fractions of crowders. We characterize transitions from non-adsorbed to partially and strongly adsorbed states as a function of bending stiffness. The crowding-induced transitions occur at smaller values of the bending stiffness as the volume fraction of crowders increases. Concomitant effects on the size and shape of the polymer are reflected by crowding- and stiffness-dependent changes to the radius of gyration. For various polymer lengths, we identify a critical crowding fraction for adsorption and analyze its scaling behavior in terms of polymer stiffness. We also consider crowding-induced adsorption in spherical confinement and identify a regime in which increasing the bending stiffness induces desorption. The results of our simulations shed light on the interplay of crowding and bending stiffness on the spatial organization of biopolymers in encapsulated cellular and cell-free systems.
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Affiliation(s)
- Gaurav Chauhan
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Knoxville, Tennessee 37996, USA
| | - Michael L Simpson
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, Knoxville, Tennessee 37996, USA
| | - Steven M Abel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Knoxville, Tennessee 37996, USA
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49
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The kinetics of islet amyloid polypeptide phase-separated system and hydrogel formation are critically influenced by macromolecular crowding. Biochem J 2021; 478:3025-3046. [PMID: 34313292 PMCID: PMC8370757 DOI: 10.1042/bcj20210384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/19/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022]
Abstract
Many protein misfolding diseases (e.g. type II diabetes and Alzheimer's disease) are characterised by amyloid deposition. Human islet amyloid polypeptide (hIAPP, involved in type II diabetes) spontaneously undergoes liquid-liquid phase separation (LLPS) and a kinetically complex hydrogelation, both catalysed by hydrophobic-hydrophilic interfaces (e.g. air-water interface and/or phospholipids-water interfaces). Gelation of hIAPP phase-separated liquid droplets initiates amyloid aggregation and the formation of clusters of interconnected aggregates, which grow and fuse to eventually percolate the whole system. Droplet maturation into irreversible hydrogels via amyloid aggregation is thought to be behind the pathology of several diseases. Biological fluids contain a high volume fraction of macromolecules, leading to macromolecular crowding. Despite crowding agent addition in in vitro studies playing a significant role in changing protein phase diagrams, the mechanism underlying enhanced LLPS, and the effect(s) on stages beyond LLPS remain poorly or not characterised.We investigated the effect of macromolecular crowding and increased viscosity on the kinetics of hIAPP hydrogelation using rheology and the evolution of the system beyond LLPS by microscopy. We demonstrate that increased viscosity exacerbated the kinetic variability of hydrogelation and of the phase separated-aggregated system, whereas macromolecular crowding abolished heterogeneity. Increased viscosity also strengthened the gel meshwork and accelerated aggregate cluster fusion. In contrast, crowding either delayed cluster fusion onset (dextran) or promoted it (Ficoll). Our study highlights that an in vivo crowded environment would critically influence amyloid stages beyond LLPS and pathogenesis.
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50
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Vweza AO, Song CG, Chong KT. Liquid-Liquid Phase Separation in the Presence of Macromolecular Crowding and State-dependent Kinetics. Int J Mol Sci 2021; 22:6675. [PMID: 34206440 PMCID: PMC8268629 DOI: 10.3390/ijms22136675] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/13/2021] [Accepted: 06/14/2021] [Indexed: 12/27/2022] Open
Abstract
Biomolecular condensates formed via liquid-liquid phase separation (LLPS) are increasingly being shown to play major roles in cellular self-organization dynamics in health and disease. It is well established that macromolecular crowding has a profound impact on protein interactions, particularly those that lead to LLPS. Although synthetic crowding agents are used during in vitro LLPS experiments, they are considerably different from the highly crowded nucleo-/cytoplasm and the effects of in vivo crowding remain poorly understood. In this work, we applied computational modeling to investigate the effects of macromolecular crowding on LLPS. To include biologically relevant LLPS dynamics, we extended the conventional Cahn-Hilliard model for phase separation by coupling it to experimentally derived macromolecular crowding dynamics and state-dependent reaction kinetics. Through extensive field-theoretic computer simulations, we show that the inclusion of macromolecular crowding results in late-stage coarsening and the stabilization of relatively smaller condensates. At a high crowding concentration, there is an accelerated growth and late-stage arrest of droplet formation, effectively resulting in anomalous labyrinthine morphologies akin to protein gelation observed in experiments. These results not only elucidate the crowder effects observed in experiments, but also highlight the importance of including state-dependent kinetics in LLPS models, and may help in designing further experiments to probe the intricate roles played by LLPS in self-organization dynamics of cells.
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Affiliation(s)
- Alick-O. Vweza
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; (A.-O.V.); (C.-G.S.)
| | - Chul-Gyu Song
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; (A.-O.V.); (C.-G.S.)
- Advanced Biomedical Imaging Center, Jeonbuk National University, Jeonju 54896, Korea
| | - Kil-To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; (A.-O.V.); (C.-G.S.)
- Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, Korea
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