1
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Mukherjee S, Poudyal M, Dave K, Kadu P, Maji SK. Protein misfolding and amyloid nucleation through liquid-liquid phase separation. Chem Soc Rev 2024; 53:4976-5013. [PMID: 38597222 DOI: 10.1039/d3cs01065a] [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: 04/11/2024]
Abstract
Liquid-liquid phase separation (LLPS) is an emerging phenomenon in cell physiology and diseases. The weak multivalent interaction prerequisite for LLPS is believed to be facilitated through intrinsically disordered regions, which are prevalent in neurodegenerative disease-associated proteins. These aggregation-prone proteins also exhibit an inherent property for phase separation, resulting in protein-rich liquid-like droplets. The very high local protein concentration in the water-deficient confined microenvironment not only drives the viscoelastic transition from the liquid to solid-like state but also most often nucleate amyloid fibril formation. Indeed, protein misfolding, oligomerization, and amyloid aggregation are observed to be initiated from the LLPS of various neurodegeneration-related proteins. Moreover, in these cases, neurodegeneration-promoting genetic and environmental factors play a direct role in amyloid aggregation preceded by the phase separation. These cumulative recent observations ignite the possibility of LLPS being a prominent nucleation mechanism associated with aberrant protein aggregation. The present review elaborates on the nucleation mechanism of the amyloid aggregation pathway and the possible early molecular events associated with amyloid-related protein phase separation. It also summarizes the recent advancement in understanding the aberrant phase transition of major proteins contributing to neurodegeneration focusing on the common disease-associated factors. Overall, this review proposes a generic LLPS-mediated multistep nucleation mechanism for amyloid aggregation and its implication in neurodegeneration.
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Affiliation(s)
- Semanti Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Manisha Poudyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Kritika Dave
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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2
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Fuxreiter M. Context-dependent, fuzzy protein interactions: Towards sequence-based insights. Curr Opin Struct Biol 2024; 87:102834. [PMID: 38759297 DOI: 10.1016/j.sbi.2024.102834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/19/2024]
Abstract
Predicting protein interactions in the cellular environment still remains a challenge in the AlphaFold era. Protein interactions, similarly to their structures, sample a continuum from ordered to disordered states, with specific partners in many bound configurations. A multiplicity of binding modes (MBM) enables transition between these states under different cellular conditions. This review focuses on how the cellular environment affects protein interactions, highlighting the molecular mechanisms, biophysical origin, and sequence-based principles of context-dependent, fuzzy interactions. It summarises experimental and computational approaches to address the challenge of interaction heterogeneity and its contribution to a wide range of biological functions. These insights will help in understanding complex cellular processes, involving conversions between protein assembly states, such as from liquid-like droplet state to the amyloid state.
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Affiliation(s)
- Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, Padova, Italy; Department of Physics and Astronomy, University of Padova, Padova, Italy.
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3
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Dada ST, Toprakcioglu Z, Cali MP, Röntgen A, Hardenberg MC, Morris OM, Mrugalla LK, Knowles TPJ, Vendruscolo M. Pharmacological inhibition of α-synuclein aggregation within liquid condensates. Nat Commun 2024; 15:3835. [PMID: 38714700 PMCID: PMC11076612 DOI: 10.1038/s41467-024-47585-x] [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: 08/17/2023] [Accepted: 04/03/2024] [Indexed: 05/10/2024] Open
Abstract
Aggregated forms of α-synuclein constitute the major component of Lewy bodies, the proteinaceous aggregates characteristic of Parkinson's disease. Emerging evidence suggests that α-synuclein aggregation may occur within liquid condensates formed through phase separation. This mechanism of aggregation creates new challenges and opportunities for drug discovery for Parkinson's disease, which is otherwise still incurable. Here we show that the condensation-driven aggregation pathway of α-synuclein can be inhibited using small molecules. We report that the aminosterol claramine stabilizes α-synuclein condensates and inhibits α-synuclein aggregation within the condensates both in vitro and in a Caenorhabditis elegans model of Parkinson's disease. By using a chemical kinetics approach, we show that the mechanism of action of claramine is to inhibit primary nucleation within the condensates. These results illustrate a possible therapeutic route based on the inhibition of protein aggregation within condensates, a phenomenon likely to be relevant in other neurodegenerative disorders.
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Affiliation(s)
- Samuel T Dada
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Zenon Toprakcioglu
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Mariana P Cali
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Alexander Röntgen
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Maarten C Hardenberg
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Owen M Morris
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Lena K Mrugalla
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Michele Vendruscolo
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK.
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4
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Liang Q, Peng N, Xie Y, Kumar N, Gao W, Miao Y. MolPhase, an advanced prediction algorithm for protein phase separation. EMBO J 2024; 43:1898-1918. [PMID: 38565952 PMCID: PMC11065880 DOI: 10.1038/s44318-024-00090-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/27/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
We introduce MolPhase, an advanced algorithm for predicting protein phase separation (PS) behavior that improves accuracy and reliability by utilizing diverse physicochemical features and extensive experimental datasets. MolPhase applies a user-friendly interface to compare distinct biophysical features side-by-side along protein sequences. By additional comparison with structural predictions, MolPhase enables efficient predictions of new phase-separating proteins and guides hypothesis generation and experimental design. Key contributing factors underlying MolPhase include electrostatic pi-interactions, disorder, and prion-like domains. As an example, MolPhase finds that phytobacterial type III effectors (T3Es) are highly prone to homotypic PS, which was experimentally validated in vitro biochemically and in vivo in plants, mimicking their injection and accumulation in the host during microbial infection. The physicochemical characteristics of T3Es dictate their patterns of association for multivalent interactions, influencing the material properties of phase-separating droplets based on the surrounding microenvironment in vivo or in vitro. Robust integration of MolPhase's effective prediction and experimental validation exhibit the potential to evaluate and explore how biomolecule PS functions in biological systems.
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Affiliation(s)
- Qiyu Liang
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Nana Peng
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Yi Xie
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Nivedita Kumar
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Weibo Gao
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore, Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore.
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 636921, Singapore, Singapore.
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5
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Idrees S, Paudel KR, Sadaf T, Hansbro PM. Uncovering domain motif interactions using high-throughput protein-protein interaction detection methods. FEBS Lett 2024; 598:725-742. [PMID: 38439692 DOI: 10.1002/1873-3468.14841] [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: 10/17/2023] [Revised: 01/09/2024] [Accepted: 02/18/2024] [Indexed: 03/06/2024]
Abstract
Protein-protein interactions (PPIs) are often mediated by short linear motifs (SLiMs) in one protein and domain in another, known as domain-motif interactions (DMIs). During the past decade, SLiMs have been studied to find their role in cellular functions such as post-translational modifications, regulatory processes, protein scaffolding, cell cycle progression, cell adhesion, cell signalling and substrate selection for proteasomal degradation. This review provides a comprehensive overview of the current PPI detection techniques and resources, focusing on their relevance to capturing interactions mediated by SLiMs. We also address the challenges associated with capturing DMIs. Moreover, a case study analysing the BioGrid database as a source of DMI prediction revealed significant known DMI enrichment in different PPI detection methods. Overall, it can be said that current high-throughput PPI detection methods can be a reliable source for predicting DMIs.
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Affiliation(s)
- Sobia Idrees
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Centre for Inflammation, Centenary Institute and Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
| | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
| | - Tayyaba Sadaf
- Centre for Inflammation, Centenary Institute and Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
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6
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Duan C, Wang R. A Unified Description of Salt Effects on the Liquid-Liquid Phase Separation of Proteins. ACS CENTRAL SCIENCE 2024; 10:460-468. [PMID: 38435530 PMCID: PMC10906038 DOI: 10.1021/acscentsci.3c01372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 03/05/2024]
Abstract
Protein aggregation via liquid-liquid phase separation (LLPS) is ubiquitous in nature and is intimately connected to many human diseases. Although it is widely known that the addition of salt has crucial impacts on the LLPS of proteins, full understanding of the salt effects remains an outstanding challenge. Here, we develop a molecular theory that systematically incorporates the self-consistent field theory for charged macromolecules into the solution thermodynamics. The electrostatic interaction, hydrophobicity, ion solvation, and translational entropy are included in a unified framework. Our theory fully captures the long-standing puzzles of the nonmonotonic salt concentration dependence and the specific ion effect. We find that proteins show salting-out at low salt concentrations due to ionic screening. The solubility follows the inverse Hofmeister series. In the high salt concentration regime, protein continues salting-out for small ions but turns to salting-in for larger ions, accompanied by the reversal of the Hofmeister series. We reveal that the solubility at high salt concentrations is determined by the competition between the solvation energy and translational entropy of the ion. Furthermore, we derive an analytical criterion for determining the boundary between the salting-in and salting-out regimes, which is in good agreement with experimental results for various proteins and salt ions.
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Affiliation(s)
- Chao Duan
- Department
of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Rui Wang
- Department
of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
- Materials
Sciences Division, Lawrence Berkeley National
Lab, Berkeley, California 94720, United States
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7
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Rinauro DJ, Chiti F, Vendruscolo M, Limbocker R. Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases. Mol Neurodegener 2024; 19:20. [PMID: 38378578 PMCID: PMC10877934 DOI: 10.1186/s13024-023-00651-2] [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: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 02/22/2024] Open
Abstract
The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes.
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Affiliation(s)
- Dillon J Rinauro
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA.
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8
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Zhang J, Vincenzetti S, Polidori P, Polzonetti V, Di Michele A, Perinelli DR, Liu G, Li L, Pucciarelli S. The effects of pH, temperature, and buffer concentration on the self-assembling behavior, secondary structure, and surface hydrophobicity of donkey and bovine β-casein. Food Chem 2024; 433:137285. [PMID: 37683474 DOI: 10.1016/j.foodchem.2023.137285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023]
Abstract
The self-assembling behavior, secondary structure, and surface hydrophobicity of purified donkey β-casein in terms of pH, temperature, and buffer concentration were investigated in comparison with commercial bovine β-casein. Critical micelle concentration of both β-caseins decreased with the lowering of pH (pH 8.0-6.0) and the increasing temperatures (25-50 °C). Critical micelle temperature of both β-caseins increased moving from pH 6.0 to 8.0 and aggregates larger than micelles formed at pH 6.0 that is close to their isoelectric point. Fluorescence spectroscopy analysis demonstrated that the maximum surface hydrophobicity was achieved at pH 6.0. The secondary structure was examined using circular dichroism spectroscopy, highlighting an increase of α-helix content and a decrease of unordered structures with the decrease of pH and increase of temperature. This work provides insights on parameters promoting molecular interactions involved in donkey β-CN self-association, useful to develop nanocarriers for encapsulating bioactive compounds in pharmaceutical and nutraceutical applications.
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Affiliation(s)
- Jingjing Zhang
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032 Camerino, MC, Italy; College of Agronomy, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of Black Donkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng University, 252000 Liaocheng, Shandong, China.
| | - Silvia Vincenzetti
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032 Camerino, MC, Italy.
| | - Paolo Polidori
- School of Pharmacy, University of Camerino, Via Gentile da Varano, 62032 Camerino, MC, Italy.
| | - Valeria Polzonetti
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032 Camerino, MC, Italy.
| | - Alessandro Di Michele
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, PG, Italy.
| | - Diego Romano Perinelli
- School of Pharmacy, University of Camerino, Via Gentile da Varano, 62032 Camerino, MC, Italy.
| | - Guiqin Liu
- College of Agronomy, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of Black Donkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng University, 252000 Liaocheng, Shandong, China.
| | - Lanjie Li
- College of Agronomy, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of Black Donkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng University, 252000 Liaocheng, Shandong, China.
| | - Stefania Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032 Camerino, MC, Italy.
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Fedorov D, Roas-Escalona N, Tolmachev D, Harmat AL, Scacchi A, Sammalkorpi M, Aranko AS, Linder MB. Triblock Proteins with Weakly Dimerizing Terminal Blocks and an Intrinsically Disordered Region for Rational Design of Condensate Properties. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2306817. [PMID: 37964343 DOI: 10.1002/smll.202306817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/20/2023] [Indexed: 11/16/2023]
Abstract
Condensates are molecular assemblies that are formed through liquid-liquid phase separation and play important roles in many biological processes. The rational design of condensate formation and their properties is central to applications, such as biosynthetic materials, synthetic biology, and for understanding cell biology. Protein engineering is used to make a triblock structure with varying terminal blocks of folded proteins on both sides of an intrinsically disordered mid-region. Dissociation constants are determined in the range of micromolar to millimolar for a set of proteins suitable for use as terminal blocks. Varying the weak dimerization of terminal blocks leads to an adjustable tendency for condensate formation while keeping the intrinsically disordered region constant. The dissociation constants of the terminal domains correlate directly with the tendency to undergo liquid-liquid phase separation. Differences in physical properties, such as diffusion rate are not directly correlated with the strength of dimerization but can be understood from the properties and interplay of the constituent blocks. The work demonstrates the importance of weak interactions in condensate formation and shows a principle for protein design that will help in fabricating functional condensates in a predictable and rational way.
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Affiliation(s)
- Dmitrii Fedorov
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - Nelmary Roas-Escalona
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - Dmitry Tolmachev
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - Adam L Harmat
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - Alberto Scacchi
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Department of Applied Physics, Aalto University, P.O. Box 11000, Aalto, FI-00076, Finland
| | - Maria Sammalkorpi
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - A Sesilja Aranko
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - Markus B Linder
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
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10
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Marcato D, Giacometti A, Maritan A, Rosa A. Phase behaviour of semiflexible lattice polymers in poor-solvent solution: Mean-field theory and Monte Carlo simulations. J Chem Phys 2023; 159:154901. [PMID: 37843062 DOI: 10.1063/5.0171911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/22/2023] [Indexed: 10/17/2023] Open
Abstract
We study a solution of interacting semiflexible polymers with curvature energy in poor-solvent conditions on the d-dimensional cubic lattice using mean-field theory and Monte Carlo computer simulations. Building upon past studies on a single chain, we construct a field-theory representation of the system and solve it within a mean-field approximation supported by Monte Carlo simulations in d = 3. A gas-liquid transition is found in the temperature-density plane that is then interpreted in terms of real systems. Interestingly, we find this transition to be independent of the bending rigidity. Past classical Flory-Huggins and Flory mean-field results are shown to be particular cases of this more general framework. Perspectives in terms of guiding experimental results towards optimal conditions are also proposed.
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Affiliation(s)
- Davide Marcato
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, 30123 Venezia, Italy
- European Centre for Living Technology (ECLT) Ca' Bottacin, 3911 Dorsoduro Calle Crosera, 30123 Venezia, Italy
| | - Amos Maritan
- Laboratory of Interdisciplinary Physics, Department of Physics and Astronomy "G. Galilei," University of Padova, Padova, Italy and INFN, Sezione di Padova, Via Marzolo 8, 35131 Padova, Italy
| | - Angelo Rosa
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
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11
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Poudyal M, Patel K, Gadhe L, Sawner AS, Kadu P, Datta D, Mukherjee S, Ray S, Navalkar A, Maiti S, Chatterjee D, Devi J, Bera R, Gahlot N, Joseph J, Padinhateeri R, Maji SK. Intermolecular interactions underlie protein/peptide phase separation irrespective of sequence and structure at crowded milieu. Nat Commun 2023; 14:6199. [PMID: 37794023 PMCID: PMC10550955 DOI: 10.1038/s41467-023-41864-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) has emerged as a crucial biological phenomenon underlying the sequestration of macromolecules (such as proteins and nucleic acids) into membraneless organelles in cells. Unstructured and intrinsically disordered domains are known to facilitate multivalent interactions driving protein LLPS. We hypothesized that LLPS could be an intrinsic property of proteins/polypeptides but with distinct phase regimes irrespective of their sequence and structure. To examine this, we studied many (a total of 23) proteins/polypeptides with different structures and sequences for LLPS study in the presence and absence of molecular crowder, polyethylene glycol (PEG-8000). We showed that all proteins and even highly charged polypeptides (under study) can undergo liquid condensate formation, however with different phase regimes and intermolecular interactions. We further demonstrated that electrostatic, hydrophobic, and H-bonding or a combination of such intermolecular interactions plays a crucial role in individual protein/peptide LLPS.
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Affiliation(s)
- Manisha Poudyal
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Komal Patel
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, IIT Bombay, Powai, Mumbai, 400076, India
| | - Laxmikant Gadhe
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Ajay Singh Sawner
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Debalina Datta
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Semanti Mukherjee
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Soumik Ray
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Siddhartha Maiti
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
- Department of Bioengineering, VIT Bhopal University, Bhopal-Indore Highway, Kothrikalan, Sehore, Madhya Pradesh, 466114, India
| | - Debdeep Chatterjee
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Jyoti Devi
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Riya Bera
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Nitisha Gahlot
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Jennifer Joseph
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, IIT Bombay, Powai, Mumbai, 400076, India.
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12
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Lim CM, González Díaz A, Fuxreiter M, Pun FW, Zhavoronkov A, Vendruscolo M. Multiomic prediction of therapeutic targets for human diseases associated with protein phase separation. Proc Natl Acad Sci U S A 2023; 120:e2300215120. [PMID: 37774095 PMCID: PMC10556643 DOI: 10.1073/pnas.2300215120] [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: 01/05/2023] [Accepted: 08/02/2023] [Indexed: 10/01/2023] Open
Abstract
The phenomenon of protein phase separation (PPS) underlies a wide range of cellular functions. Correspondingly, the dysregulation of the PPS process has been associated with numerous human diseases. To enable therapeutic interventions based on the regulation of this association, possible targets should be identified. For this purpose, we present an approach that combines the multiomic PandaOmics platform with the FuzDrop method to identify PPS-prone disease-associated proteins. Using this approach, we prioritize candidates with high PandaOmics and FuzDrop scores using a profiling method that accounts for a wide range of parameters relevant for disease mechanism and pharmacological intervention. We validate the differential phase separation behaviors of three predicted Alzheimer's disease targets (MARCKS, CAMKK2, and p62) in two cell models of this disease. Overall, the approach that we present generates a list of possible therapeutic targets for human diseases associated with the dysregulation of the PPS process.
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Affiliation(s)
- Christine M. Lim
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Alicia González Díaz
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, Padova35131, Italy
| | - Frank W. Pun
- Insilico Medicine, Hong Kong Science and Technology Park, Hong Kong, China
| | - Alex Zhavoronkov
- Insilico Medicine, Hong Kong Science and Technology Park, Hong Kong, China
| | - Michele Vendruscolo
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
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13
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Negri ML, D'Annunzio S, Vitali G, Zippo A. May the force be with you: Nuclear condensates function beyond transcription control: Potential nongenetic functions of nuclear condensates in physiological and pathological conditions. Bioessays 2023; 45:e2300075. [PMID: 37530178 DOI: 10.1002/bies.202300075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/03/2023] [Accepted: 07/13/2023] [Indexed: 08/03/2023]
Abstract
Over the past decade, research has revealed biomolecular condensates' relevance in diverse cellular functions. Through a phase separation process, they concentrate macromolecules in subcompartments shaping the cellular organization and physiology. In the nucleus, biomolecular condensates assemble relevant biomolecules that orchestrate gene expression. We here hypothesize that chromatin condensates can also modulate the nongenetic functions of the genome, including the nuclear mechanical properties. The importance of chromatin condensates is supported by the genetic evidence indicating that mutations in their members are causative of a group of rare Mendelian diseases named chromatinopathies (CPs). Despite a broad spectrum of clinical features and the perturbations of the epigenetic machinery characterizing the CPs, recent findings highlighted negligible changes in gene expression. These data argue in favor of possible noncanonical functions of chromatin condensates in regulating the genome's spatial organization and, consequently, the nuclear mechanics. In this review, we discuss how condensates may impact nuclear mechanical properties, thus affecting the cellular response to mechanical cues and, eventually, cell fate and identity. Chromatin condensates organize macromolecules in the nucleus orchestrating the transcription regulation and mutations in their members are responsible for rare diseases named chromatinopathies. We argue that chromatin condensates, in concert with the nuclear lamina, may also govern the nuclear mechanical properties affecting the cellular response to external cues.
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Affiliation(s)
- Maria Luce Negri
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Sarah D'Annunzio
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Giulia Vitali
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessio Zippo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
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14
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Luchsinger C, Lee K, Mardones GA, KewalRamani VN, Diaz-Griffero F. Formation of nuclear CPSF6/CPSF5 biomolecular condensates upon HIV-1 entry into the nucleus is important for productive infection. Sci Rep 2023; 13:10974. [PMID: 37414787 PMCID: PMC10325960 DOI: 10.1038/s41598-023-37364-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/20/2023] [Indexed: 07/08/2023] Open
Abstract
The early events of HIV-1 infection involve the transport of the viral core into the nucleus. This event triggers the translocation of CPSF6 from paraspeckles into nuclear speckles forming puncta-like structures. Our investigations revealed that neither HIV-1 integration nor reverse transcription is required for the formation of puncta-like structures. Moreover, HIV-1 viruses without viral genome are competent for the induction of CPSF6 puncta-like structures. In agreement with the notion that HIV-1 induced CPSF6 puncta-like structures are biomolecular condensates, we showed that osmotic stress and 1,6-hexanediol induced the disassembly of CPSF6 condensates. Interestingly, replacing the osmotic stress by isotonic media re-assemble CPSF6 condensates in the cytoplasm of the cell. To test whether CPSF6 condensates were important for infection we utilized hypertonic stress, which prevents formation of CPSF6 condensates, during infection. Remarkably, preventing the formation of CPSF6 condensates inhibits the infection of wild type HIV-1 but not of HIV-1 viruses bearing the capsid changes N74D and A77V, which do not form CPSF6 condensates during infection1,2. We also investigated whether the functional partners of CPSF6 are recruited to the condensates upon infection. Our experiments revealed that CPSF5, but not CPSF7, co-localized with CPSF6 upon HIV-1 infection. We found condensates containing CPSF6/CPSF5 in human T cells and human primary macrophages upon HIV-1 infection. Additionally, we observed that the integration cofactor LEDGF/p75 changes distribution upon HIV-1 infection and surrounds the CPSF6/CPSF5 condensates. Overall, our work demonstrated that CPSF6 and CPSF5 are forming biomolecular condensates that are important for infection of wild type HIV-1 viruses.
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Affiliation(s)
- Charlotte Luchsinger
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1301 Morris Park - Price Center 501, Bronx, NY, 10461, USA
| | - KyeongEun Lee
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Gonzalo A Mardones
- Facultad de Medicina Y Ciencia, Universidad San Sebastian, Arturo Prat 154, Valdivia, Chile
| | - Vineet N KewalRamani
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1301 Morris Park - Price Center 501, Bronx, NY, 10461, USA.
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15
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Vendruscolo M. Thermodynamic and kinetic approaches for drug discovery to target protein misfolding and aggregation. Expert Opin Drug Discov 2023:1-11. [PMID: 37276120 DOI: 10.1080/17460441.2023.2221024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/30/2023] [Indexed: 06/07/2023]
Abstract
INTRODUCTION Protein misfolding diseases, including Alzheimer's and Parkinson's diseases, are characterized by the aberrant aggregation of proteins. These conditions are still largely untreatable, despite having a major impact on our healthcare systems and societies. AREAS COVERED We describe drug discovery strategies to target protein misfolding and aggregation. We compare thermodynamic approaches, which are based on the stabilization of the native states of proteins, with kinetic approaches, which are based on the slowing down of the aggregation process. This comparison is carried out in terms of the current knowledge of the process of protein misfolding and aggregation, the mechanisms of disease and the therapeutic targets. EXPERT OPINION There is an unmet need for disease-modifying treatments that target protein misfolding and aggregation for the over 50 human disorders known to be associated with this phenomenon. With the approval of the first drugs that can prevent misfolding or inhibit aggregation, future efforts will be focused on the discovery of effective compounds with these mechanisms of action for a wide range of conditions.
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Affiliation(s)
- Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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16
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Li P, Chen J, Wang X, Su Z, Gao M, Huang Y. Liquid - liquid phase separation of tau: Driving forces, regulation, and biological implications. Neurobiol Dis 2023; 183:106167. [PMID: 37230179 DOI: 10.1016/j.nbd.2023.106167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/16/2023] [Accepted: 05/21/2023] [Indexed: 05/27/2023] Open
Abstract
The past 15 years have witnessed an explosion in the studies of biomolecular condensates that are implicated in numerous biological processes and play vital roles in human health and diseases. Recent findings demonstrate that the microtubule-associated protein tau forms liquid condensates through liquid-liquid phase separation (LLPS) in in vitro experiments using purified recombinant proteins and cell-based experiments. Although in vivo studies are lacking, liquid condensates have emerged as an important assembly state of physiological and pathological tau and LLPS can regulate the function of microtubules, mediate stress granule formation, and accelerate tau amyloid aggregation. In this review, we summarize recent advances in tau LLPS, aiming to unveiling the delicate interactions driving tau LLPS. We further discuss the association of tau LLPS with physiology and disease in the context of the sophisticated regulation of tau LLPS. Deciphering the mechanisms underlying tau LLPS and the liquid-to-solid transition enables rational design of molecules that inhibit or delay the formation of tau solid species, thus providing novel targeted therapeutic strategies for tauopathies.
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Affiliation(s)
- Ping Li
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan 430068, China; Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China; Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Jingxin Chen
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan 430068, China; Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China; Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Xi Wang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan 430068, China; Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China; Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Zhengding Su
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan 430068, China; Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China; Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Meng Gao
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan 430068, China; Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China; Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China.
| | - Yongqi Huang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan 430068, China; Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China; Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China.
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17
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Vendruscolo M, Fuxreiter M. Towards sequence-based principles for protein phase separation predictions. Curr Opin Chem Biol 2023; 75:102317. [PMID: 37207400 DOI: 10.1016/j.cbpa.2023.102317] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/21/2023]
Abstract
The phenomenon of protein phase separation, which underlies the formation of biomolecular condensates, has been associated with numerous cellular functions. Recent studies indicate that the amino acid sequences of most proteins may harbour not only the code for folding into the native state but also for condensing into the liquid-like droplet state and the solid-like amyloid state. Here we review the current understanding of the principles for sequence-based methods for predicting the propensity of proteins for phase separation. A guiding concept is that entropic contributions are generally more important to stabilise the droplet state than they are for the native and amyloid states. Although estimating these entropic contributions has proven difficult, we describe some progress that has been recently made in this direction. To conclude, we discuss the challenges ahead to extend sequence-based prediction methods of protein phase separation to include quantitative in vivo characterisations of this process.
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Affiliation(s)
- Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
| | - Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, PD 35131, Italy; Department of Physics and Astronomy, University of Padova, PD 35131, Italy.
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18
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Sahin C, Motso A, Gu X, Feyrer H, Lama D, Arndt T, Rising A, Gese GV, Hällberg BM, Marklund EG, Schafer NP, Petzold K, Teilum K, Wolynes PG, Landreh M. Mass Spectrometry of RNA-Binding Proteins during Liquid-Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures. J Am Chem Soc 2023; 145:10659-10668. [PMID: 37145883 DOI: 10.1021/jacs.3c00932] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Liquid-liquid phase separation (LLPS) of heterogeneous ribonucleoproteins (hnRNPs) drives the formation of membraneless organelles, but structural information about their assembled states is still lacking. Here, we address this challenge through a combination of protein engineering, native ion mobility mass spectrometry, and molecular dynamics simulations. We used an LLPS-compatible spider silk domain and pH changes to control the self-assembly of the hnRNPs FUS, TDP-43, and hCPEB3, which are implicated in neurodegeneration, cancer, and memory storage. By releasing the proteins inside the mass spectrometer from their native assemblies, we could monitor conformational changes associated with liquid-liquid phase separation. We find that FUS monomers undergo an unfolded-to-globular transition, whereas TDP-43 oligomerizes into partially disordered dimers and trimers. hCPEB3, on the other hand, remains fully disordered with a preference for fibrillar aggregation over LLPS. The divergent assembly mechanisms revealed by ion mobility mass spectrometry of soluble protein species that exist under LLPS conditions suggest structurally distinct complexes inside liquid droplets that may impact RNA processing and translation depending on biological context.
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Affiliation(s)
- Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Aikaterini Motso
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
| | - Xinyu Gu
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Hannes Feyrer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
| | - Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
| | - Tina Arndt
- Department of Biosciences and Nutrition, Karolinska Institutet, S-141 57 Huddinge, Sweden
| | - Anna Rising
- Department of Biosciences and Nutrition, Karolinska Institutet, S-141 57 Huddinge, Sweden
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Box 7011, S-750 07 Uppsala, Sweden
| | - Genis Valentin Gese
- Department of Cell and Molecular Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 171 65 Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 171 65 Stockholm, Sweden
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Nicholas P Schafer
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 24 Uppsala, Sweden
| | - Kaare Teilum
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
- Department of Cell- and Molecular Biology, Uppsala University, Box 596, 751 24 Uppsala, Sweden
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19
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Schulte T, Panas MD, Han X, Williams L, Kedersha N, Fleck JS, Tan TJC, Dopico XC, Olsson A, Morro AM, Hanke L, Nilvebrant J, Giang KA, Nygren PÅ, Anderson P, Achour A, McInerney GM. Caprin-1 binding to the critical stress granule protein G3BP1 is influenced by pH. Open Biol 2023; 13:220369. [PMID: 37161291 PMCID: PMC10170197 DOI: 10.1098/rsob.220369] [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: 12/19/2022] [Accepted: 03/28/2023] [Indexed: 05/11/2023] Open
Abstract
G3BP is the central node within stress-induced protein-RNA interaction networks known as stress granules (SGs). The SG-associated proteins Caprin-1 and USP10 bind mutually exclusively to the NTF2 domain of G3BP1, promoting and inhibiting SG formation, respectively. Herein, we present the crystal structure of G3BP1-NTF2 in complex with a Caprin-1-derived short linear motif (SLiM). Caprin-1 interacts with His-31 and His-62 within a third NTF2-binding site outside those covered by USP10, as confirmed using biochemical and biophysical-binding assays. Nano-differential scanning fluorimetry revealed reduced thermal stability of G3BP1-NTF2 at acidic pH. This destabilization was counterbalanced significantly better by bound USP10 than Caprin-1. The G3BP1/USP10 complex immunoprecipated from human U2OS cells was more resistant to acidic buffer washes than G3BP1/Caprin-1. Acidification of cellular condensates by approximately 0.5 units relative to the cytosol was detected by ratiometric fluorescence analysis of pHluorin2 fused to G3BP1. Cells expressing a Caprin-1/FGDF chimera with higher G3BP1-binding affinity had reduced Caprin-1 levels and slightly reduced condensate sizes. This unexpected finding may suggest that binding of the USP10-derived SLiM to NTF2 reduces the propensity of G3BP1 to enter condensates.
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Affiliation(s)
- Tim Schulte
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, 171 77, Sweden
| | - Marc D. Panas
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Xiao Han
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, 171 77, Sweden
| | - Lucy Williams
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Nancy Kedersha
- Division of Rheumatology, Immunity, and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jonas Simon Fleck
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, 171 77, Sweden
| | - Timothy J. C. Tan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Anders Olsson
- Protein Expression and Characterization, AlbaNova University Center, Royal Institute of Technology, 114 21, Stockholm
| | - Ainhoa Moliner Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Johan Nilvebrant
- Division of Protein Engineering, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology, 114 21, Stockholm
- Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Sweden
| | - Kim Anh Giang
- Division of Protein Engineering, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology, 114 21, Stockholm
- Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Sweden
| | - Per-Åke Nygren
- Division of Protein Engineering, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology, 114 21, Stockholm
- Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Sweden
| | - Paul Anderson
- Division of Rheumatology, Immunity, and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, 171 77, Sweden
| | - Gerald M. McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
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20
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Leppert A, Chen G, Lama D, Sahin C, Railaite V, Shilkova O, Arndt T, Marklund EG, Lane DP, Rising A, Landreh M. Liquid-Liquid Phase Separation Primes Spider Silk Proteins for Fiber Formation via a Conditional Sticker Domain. NANO LETTERS 2023. [PMID: 37084706 DOI: 10.1021/acs.nanolett.3c00773] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Many protein condensates can convert to fibrillar aggregates, but the underlying mechanisms are unclear. Liquid-liquid phase separation (LLPS) of spider silk proteins, spidroins, suggests a regulatory switch between both states. Here, we combine microscopy and native mass spectrometry to investigate the influence of protein sequence, ions, and regulatory domains on spidroin LLPS. We find that salting out-effects drive LLPS via low-affinity stickers in the repeat domains. Interestingly, conditions that enable LLPS simultaneously cause dissociation of the dimeric C-terminal domain (CTD), priming it for aggregation. Since the CTD enhances LLPS of spidroins but is also required for their conversion into amyloid-like fibers, we expand the stickers and spacers-model of phase separation with the concept of folded domains as conditional stickers that represent regulatory units.
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Affiliation(s)
- Axel Leppert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, S-17165 Solna, Sweden
| | - Gefei Chen
- Department of Biosciences and Nutrition, Karolinska Institutet, S-14157 Huddinge, Sweden
| | - Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, S-17165 Solna, Sweden
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, S-17165 Solna, Sweden
- Linderstro̷m-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Vaida Railaite
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, S-17165 Solna, Sweden
| | - Olga Shilkova
- Department of Biosciences and Nutrition, Karolinska Institutet, S-14157 Huddinge, Sweden
| | - Tina Arndt
- Department of Biosciences and Nutrition, Karolinska Institutet, S-14157 Huddinge, Sweden
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, S-75123 Uppsala, Sweden
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, S-17165 Solna, Sweden
| | - Anna Rising
- Department of Biosciences and Nutrition, Karolinska Institutet, S-14157 Huddinge, Sweden
- Department of Anatomy Physiology and Biochemistry, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, S-17165 Solna, Sweden
- Department of Cell and Molecular Biology, Uppsala University, S-75124 Uppsala, Sweden
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21
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Duan C, Wang R. Electrostatics-Induced Nucleated Conformational Transition of Protein Aggregation. PHYSICAL REVIEW LETTERS 2023; 130:158401. [PMID: 37115902 DOI: 10.1103/physrevlett.130.158401] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Despite the wide existence of protein aggregation in nature and its intimate connection to many human diseases, the underlying mechanism remains unclear. Here, we develop a molecular theory by systematically incorporating the self-consistent field theory for charged macromolecules into the dilute solution thermodynamics. The kinetic pathway is tracked without any restriction on the morphology of the aggregates. We find that protein aggregation at low salt concentrations is via a two-step nucleated process involving a conformational transition from metastable spherical oligomer to elongated fibril. The scaling analysis elucidates the electrostatic origin of the conformational transition: the fibril enters the screening region much earlier than the spherical aggregate. As salt concentration increases, the classical mode of one-step nucleation corresponding to macroscopic liquid-liquid phase separation is recovered. Our results reveal that the screened electrostatic interaction is essential for the existence of the metastable oligomer and its subsequent conformational transition to fibril. The theoretical predictions of the kinetic pathway and the morphology of the aggregates are in good agreement with the experimental observations of real proteins.
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Affiliation(s)
- Chao Duan
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, California 94720, USA
| | - Rui Wang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, California 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Lab, Berkeley, California 94720, USA
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22
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Gupta A, Joshi A, Arora K, Mukhopadhyay S, Guptasarma P. The bacterial nucleoid-associated proteins, HU, and Dps, condense DNA into context-dependent biphasic or multiphasic complex coacervates. J Biol Chem 2023; 299:104637. [PMID: 36963493 PMCID: PMC10141540 DOI: 10.1016/j.jbc.2023.104637] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/27/2023] [Accepted: 03/08/2023] [Indexed: 03/26/2023] Open
Abstract
The bacterial chromosome, known as its nucleoid, is an amorphous assemblage of globular nucleoprotein domains. It exists in a state of phase separation from the cell's cytoplasm, as an irregularly-shaped, membrane-less, intracellular compartment. This state (the nature of which remains largely unknown) is maintained through bacterial generations ad infinitum. Here, we show that HU, and Dps, two of the most abundant nucleoid-associated proteins (NAPs) of Escherichia coli, undergo spontaneous complex coacervation with different forms of DNA/RNA, both individually and in each other's presence, to cause accretion and compaction of DNA/RNA into liquid-liquid phase separated (LLPS) condensates in vitro. Upon mixing with nucleic acids, HU-A and HU-B form (a) bi-phasic heterotypic mixed condensates in which HU-B helps to lower the Csat of HU-A; and also (b) multi-phasic heterotypic condensates, with Dps, in which de-mixed domains display different contents of HU and Dps. We believe that these modes of complex coacervation that are seen in vitro can serve as models for the in vivo relationships amongst NAPs in nucleoids, involving local and global variations in the relative abundances of the different NAPs, especially in de-mixed sub-domains that are characterized by differing grades of phase separation. Our results clearly demonstrate some quantitative, and some qualitative, differences in the coacervating abilities of different NAPs with DNA, potentially explaining (i) why E. coli has two isoforms of HU, and (ii) why changes in the abundances of HU and Dps facilitate the lag, logarithmic and stationary phases of E. coli growth.
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Affiliation(s)
- Archit Gupta
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India.
| | - Ashish Joshi
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India
| | - Kanika Arora
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Chemical Sciences; Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India
| | - Purnananda Guptasarma
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India.
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23
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Garg N, Štibler UK, Eismann B, Mercker M, Bergheim BG, Linn A, Tuchscherer P, Engel U, Redl S, Marciniak-Czochra A, Holstein TW, Hess MW, Özbek S. Non-muscle myosin II drives critical steps of nematocyst morphogenesis. iScience 2023; 26:106291. [PMID: 36936784 PMCID: PMC10014300 DOI: 10.1016/j.isci.2023.106291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/04/2022] [Accepted: 02/20/2023] [Indexed: 03/02/2023] Open
Abstract
Nematocysts are generated by secretion of proteins into a post-Golgi compartment. They consist of a capsule that elongates into a long tube, which is coiled inside the capsule matrix and expelled during its nano-second discharge deployed for prey capture. The driving force for discharge is an extreme osmotic pressure of 150 bar. The complex processes of tube elongation and invagination under these biomechanical constraints have so far been elusive. Here, we show that a non-muscle myosin II homolog (HyNMII) is essential for nematocyst formation in Hydra. In early nematocysts, HyNMII assembles to a collar around the neck of the protruding tube. HyNMII then facilitates tube outgrowth by compressing it along the longitudinal axis as evidenced by inhibitor treatment and genetic knockdown. In addition, live imaging of a NOWA::NOWA-GFP transgenic line, which re-defined NOWA as a tube component facilitating invagination, allowed us to analyze the impact of HyNMII on tube maturation.
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Affiliation(s)
- Niharika Garg
- University of Heidelberg, Centre for Organismal Studies, Department of Molecular Evolution and Genomics, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Urška Knez Štibler
- University of Heidelberg, Centre for Organismal Studies, Department of Molecular Evolution and Genomics, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Björn Eismann
- University of Heidelberg, Centre for Organismal Studies, Department of Molecular Evolution and Genomics, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Moritz Mercker
- Institute for Applied Mathematics, Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Bruno Gideon Bergheim
- University of Heidelberg, Centre for Organismal Studies, Department of Molecular Evolution and Genomics, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Anna Linn
- University of Heidelberg, Centre for Organismal Studies, Department of Molecular Evolution and Genomics, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Patrizia Tuchscherer
- University of Heidelberg, Centre for Organismal Studies, Department of Molecular Evolution and Genomics, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Ulrike Engel
- University of Heidelberg, Centre for Organismal Studies, Department of Molecular Evolution and Genomics, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
- Nikon Imaging Center at the University of Heidelberg, Bioquant, Heidelberg University, 69120 Heidelberg, Germany
| | - Stefan Redl
- Institute of Neuroanatomy, Medical University of Innsbruck, Müllerstrasse 59, 6020 Innsbruck, Austria
- Institute of Zoology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Anna Marciniak-Czochra
- Institute for Applied Mathematics, Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Thomas W. Holstein
- University of Heidelberg, Centre for Organismal Studies, Department of Molecular Evolution and Genomics, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Michael W. Hess
- Institute of Histology and Embryology, Medical University of Innsbruck, Müllerstrasse 59, 6020 Innsbruck, Austria
| | - Suat Özbek
- University of Heidelberg, Centre for Organismal Studies, Department of Molecular Evolution and Genomics, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
- Corresponding author
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24
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Alternatively spliced exon regulates context-dependent MEF2D higher-order assembly during myogenesis. Nat Commun 2023; 14:1329. [PMID: 36898987 PMCID: PMC10006080 DOI: 10.1038/s41467-023-37017-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 02/24/2023] [Indexed: 03/12/2023] Open
Abstract
During muscle cell differentiation, the alternatively spliced, acidic β-domain potentiates transcription of Myocyte-specific Enhancer Factor 2 (Mef2D). Sequence analysis by the FuzDrop method indicates that the β-domain can serve as an interaction element for Mef2D higher-order assembly. In accord, we observed Mef2D mobile nuclear condensates in C2C12 cells, similar to those formed through liquid-liquid phase separation. In addition, we found Mef2D solid-like aggregates in the cytosol, the presence of which correlated with higher transcriptional activity. In parallel, we observed a progress in the early phase of myotube development, and higher MyoD and desmin expression. In accord with our predictions, the formation of aggregates was promoted by rigid β-domain variants, as well as by a disordered β-domain variant, capable of switching between liquid-like and solid-like higher-order states. Along these lines, NMR and molecular dynamics simulations corroborated that the β-domain can sample both ordered and disordered interactions leading to compact and extended conformations. These results suggest that β-domain fine-tunes Mef2D higher-order assembly to the cellular context, which provides a platform for myogenic regulatory factors and the transcriptional apparatus during the developmental process.
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25
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Joshi A, Mukhopadhyay S. Biophysics of biomolecular condensates. Biophys J 2023; 122:737-740. [PMID: 36791720 PMCID: PMC10027443 DOI: 10.1016/j.bpj.2023.02.002] [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: 01/15/2023] [Revised: 01/28/2023] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
The formation of biomolecular condensates has emerged as a new biophysical principle for subcellular compartmentalization within cells to facilitate the spatiotemporal regulation of a multitude of complex biomolecular reactions. In this Research Highlight, we summarize the findings that were published in Biophysical Journal during the past two years (2021 and 2022). These papers provided biophysical insights into the formation of biomolecular condensates via phase separation of proteins with or without nucleic acids.
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Affiliation(s)
- Ashish Joshi
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
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26
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Hiew SH, Lu Y, Han H, Gonçalves RA, Alfarano SR, Mezzenga R, Parikh AN, Mu Y, Miserez A. Modulation of Mechanical Properties of Short Bioinspired Peptide Materials by Single Amino-Acid Mutations. J Am Chem Soc 2023; 145:3382-3393. [PMID: 36730942 DOI: 10.1021/jacs.2c09853] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The occurrence of modular peptide repeats in load-bearing (structural) proteins is common in nature, with distinctive peptide sequences that often remain conserved across different phylogenetic lineages. These highly conserved peptide sequences endow specific mechanical properties to the material, such as toughness or elasticity. Here, using bioinformatic tools and phylogenetic analysis, we have identified the GX8 peptide with the sequence GLYGGYGX (where X can be any residue) in a wide range of organisms. By simple mutation of the X residue, we demonstrate that GX8 can be self-assembled into various supramolecular structures, exhibiting vastly different physicochemical and viscoelastic properties, from liquid-like coacervate microdroplets to hydrogels to stiff solid materials. A combination of spectroscopic, electron microscopy, mechanical, and molecular dynamics studies is employed to obtain insights into molecular scale interactions driving self-assembly of GX8 peptides, underscoring that π-π stacking and hydrophobic interactions are the drivers of peptide self-assembly, whereas the X residue determines the extent of hydrogen bonding that regulates the macroscopic mechanical response. This study highlights the ability of single amino-acid polymorphism to tune the supramolecular assembly and bulk material properties of GX8 peptides, enabling us to cover a broad range of potential biomedical applications such as hydrogels for tissue engineering or coacervates for drug delivery.
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Affiliation(s)
- Shu Hui Hiew
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Yang Lu
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Hao Han
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Rui A Gonçalves
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Serena Rosa Alfarano
- Department of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Atul N Parikh
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore.,Departments of Biomedical Engineering and Materials Science & Engineering, University of California, Davis, California 95616, United States
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Ali Miserez
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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27
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Fukuchi S, Noguchi T, Anbo H, Homma K. Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor. Mol Biol Evol 2022; 40:6931801. [PMID: 36529689 PMCID: PMC9825244 DOI: 10.1093/molbev/msac272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/06/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Most prokaryotic proteins consist of a single structural domain (SD) with little intrinsically disordered regions (IDRs) that by themselves do not adopt stable structures, whereas the typical eukaryotic protein comprises multiple SDs and IDRs. How eukaryotic proteins evolved to differ from prokaryotic proteins has not been fully elucidated. Here, we found that the longer the internal exons are, the more frequently they encode IDRs in eight eukaryotes including vertebrates, invertebrates, a fungus, and plants. Based on this observation, we propose the "small bang" model from the proteomic viewpoint: the protoeukaryotic genes had no introns and mostly encoded one SD each, but a majority of them were subsequently divided into multiple exons (step 1). Many exons unconstrained by SDs elongated to encode IDRs (step 2). The elongated exons encoding IDRs frequently facilitated the acquisition of multiple SDs to make the last common ancestor of eukaryotes (step 3). One prediction of the model is that long internal exons are mostly unconstrained exons. Analytical results of the eight eukaryotes are consistent with this prediction. In support of the model, we identified cases of internal exons that elongated after the rat-mouse divergence and discovered that the expanded sections are mostly in unconstrained exons and preferentially encode IDRs. The model also predicts that SDs followed by long internal exons tend to have other SDs downstream. This prediction was also verified in all the eukaryotic species analyzed. Our model accounts for the dichotomy between prokaryotic and eukaryotic proteins and proposes a selective advantage conferred by IDRs.
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Affiliation(s)
- Satoshi Fukuchi
- Program for Information Systems, Division of Informatics, Bioengineering and Bioscience, Maebashi Institute of Technology, Maebashi-shi, Japan
| | - Tamotsu Noguchi
- Pharmaceutical Education Research Center, Meiji Pharmaceutical University, Kiyose, Tokyo, Japan
| | - Hiroto Anbo
- Program for Information Systems, Division of Informatics, Bioengineering and Bioscience, Maebashi Institute of Technology, Maebashi-shi, Japan
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28
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Functional benefit of structural disorder for the replication of measles, Nipah and Hendra viruses. Essays Biochem 2022; 66:915-934. [PMID: 36148633 DOI: 10.1042/ebc20220045] [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] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 12/24/2022]
Abstract
Measles, Nipah and Hendra viruses are severe human pathogens within the Paramyxoviridae family. Their non-segmented, single-stranded, negative-sense RNA genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid that is the substrate used by the viral RNA-dependent-RNA-polymerase (RpRd) for transcription and replication. The RpRd is a complex made of the large protein (L) and of the phosphoprotein (P), the latter serving as an obligate polymerase cofactor and as a chaperon for N. Both the N and P proteins are enriched in intrinsically disordered regions (IDRs), i.e. regions devoid of stable secondary and tertiary structure. N possesses a C-terminal IDR (NTAIL), while P consists of a large, intrinsically disordered N-terminal domain (NTD) and a C-terminal domain (CTD) encompassing alternating disordered and ordered regions. The V and W proteins, two non-structural proteins that are encoded by the P gene via a mechanism of co-transcriptional edition of the P mRNA, are prevalently disordered too, sharing with P the disordered NTD. They are key players in the evasion of the host antiviral response and were shown to phase separate and to form amyloid-like fibrils in vitro. In this review, we summarize the available information on IDRs within the N, P, V and W proteins from these three model paramyxoviruses and describe their molecular partnership. We discuss the functional benefit of disorder to virus replication in light of the critical role of IDRs in affording promiscuity, multifunctionality, fine regulation of interaction strength, scaffolding functions and in promoting liquid-liquid phase separation and fibrillation.
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29
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Biological soft matter: intrinsically disordered proteins in liquid-liquid phase separation and biomolecular condensates. Essays Biochem 2022; 66:831-847. [PMID: 36350034 DOI: 10.1042/ebc20220052] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/10/2022]
Abstract
The facts that many proteins with crucial biological functions do not have unique structures and that many biological processes are compartmentalized into the liquid-like biomolecular condensates, which are formed via liquid-liquid phase separation (LLPS) and are not surrounded by the membrane, are revolutionizing the modern biology. These phenomena are interlinked, as the presence of intrinsic disorder represents an important requirement for a protein to undergo LLPS that drives biogenesis of numerous membrane-less organelles (MLOs). Therefore, one can consider these phenomena as crucial constituents of a new IDP-LLPS-MLO field. Furthermore, intrinsically disordered proteins (IDPs), LLPS, and MLOs represent a clear link between molecular and cellular biology and soft matter and condensed soft matter physics. Both IDP and LLPS/MLO fields are undergoing explosive development and generate the ever-increasing mountain of crucial data. These new data provide answers to so many long-standing questions that it is difficult to imagine that in the very recent past, protein scientists and cellular biologists operated without taking these revolutionary concepts into account. The goal of this essay is not to deliver a comprehensive review of the IDP-LLPS-MLO field but to provide a brief and rather subjective outline of some of the recent developments in these exciting fields.
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30
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Hu HY, Liu YJ. Sequestration of cellular native factors by biomolecular assemblies: Physiological or pathological? BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119360. [PMID: 36087810 DOI: 10.1016/j.bbamcr.2022.119360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
In addition to native-state structures, biomolecules often form condensed supramolecular assemblies or cellular membraneless organelles that are critical for cell life. These biomolecular assemblies, generally including liquid-like droplets (condensates) and amyloid-like aggregates, can sequester or recruit their interacting partners, so as to either modulate various cellular behaviors or even cause disorders. This review article summarizes recent advances in the sequestration of native factors by biomolecular assemblies and discusses their potential consequences on cellular function, homeostasis, and disease pathology.
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Affiliation(s)
- Hong-Yu Hu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, PR China.
| | - Ya-Jun Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
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31
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Protein interactions: anything new? Essays Biochem 2022; 66:821-830. [PMID: 36416856 PMCID: PMC9760424 DOI: 10.1042/ebc20220044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 11/24/2022]
Abstract
How do proteins interact in the cellular environment? Which interactions stabilize liquid-liquid phase separated condensates? Are the concepts, which have been developed for specific protein complexes also applicable to higher-order assemblies? Recent discoveries prompt for a universal framework for protein interactions, which can be applied across the scales of protein communities. Here, we discuss how our views on protein interactions have evolved from rigid structures to conformational ensembles of proteins and discuss the open problems, in particular related to biomolecular condensates. Protein interactions have evolved to follow changes in the cellular environment, which manifests in multiple modes of interactions between the same partners. Such cellular context-dependence requires multiplicity of binding modes (MBM) by sampling multiple minima of the interaction energy landscape. We demonstrate that the energy landscape framework of protein folding can be applied to explain this phenomenon, opening a perspective toward a physics-based, universal model for cellular protein behaviors.
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Sequence-Based Prediction of Protein Phase Separation: The Role of Beta-Pairing Propensity. Biomolecules 2022; 12:biom12121771. [PMID: 36551199 PMCID: PMC9775558 DOI: 10.3390/biom12121771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/10/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The formation of droplets of bio-molecular condensates through liquid-liquid phase separation (LLPS) of their component proteins is a key factor in the maintenance of cellular homeostasis. Different protein properties were shown to be important in LLPS onset, making it possible to develop predictors, which try to discriminate a positive set of proteins involved in LLPS against a negative set of proteins not involved in LLPS. On the other hand, the redundancy and multivalency of the interactions driving LLPS led to the suggestion that the large conformational entropy associated with non specific side-chain interactions is also a key factor in LLPS. In this work we build a LLPS predictor which combines the ability to form pi-pi interactions, with an unrelated feature, the propensity to stabilize the β-pairing interaction mode. The cross-β structure is formed in the amyloid aggregates, which are involved in degenerative diseases and may be the final thermodynamically stable state of protein condensates. Our results show that the combination of pi-pi and β-pairing propensity yields an improved performance. They also suggest that protein sequences are more likely to be involved in phase separation if the main chain conformational entropy of the β-pairing maintained droplet state is increased. This would stabilize the droplet state against the more ordered amyloid state. Interestingly, the entropic stabilization of the droplet state appears to proceed according to different mechanisms, depending on the fraction of "droplet-driving" proteins present in the positive set.
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33
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Qian ZG, Huang SC, Xia XX. Synthetic protein condensates for cellular and metabolic engineering. Nat Chem Biol 2022; 18:1330-1340. [DOI: 10.1038/s41589-022-01203-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/07/2022] [Indexed: 11/20/2022]
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34
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Horvath A, Vendruscolo M, Fuxreiter M. Sequence-based Prediction of the Cellular Toxicity Associated with Amyloid Aggregation within Protein Condensates. Biochemistry 2022; 61:2461-2469. [DOI: 10.1021/acs.biochem.2c00499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Attila Horvath
- John Curtin School of Medical Research, The Australian National University, Acton, ACT 2601, Canberra2600, Australia
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, UK
| | - Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, Padova, PD35131Italy
- Department of Physics and Astronomy, University of Padova, Padova, PD35131Italy
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35
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Gabryelczyk B, Sammalisto FE, Gandier JA, Feng J, Beaune G, Timonen JV, Linder MB. Recombinant protein condensation inside E. coli enables the development of building blocks for bioinspired materials engineering – Biomimetic spider silk protein as a case study. Mater Today Bio 2022; 17:100492. [DOI: 10.1016/j.mtbio.2022.100492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/05/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
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Abstract
Condensed states of proteins, including liquid-like membraneless organelles and solid-like aggregates, contribute in fundamental ways to the organisation and function of the cell. Perturbations of these states can lead to a variety of diseases through mechanisms that we are now beginning to understand. We define protein condensation diseases as conditions caused by the disruption of the normal behaviour of the condensed states of proteins. We analyze the problem of the identification of targets for pharmacological interventions for these diseases and explore opportunities for the regulation of the formation and organisation of aberrant condensed states of proteins. In this review, the authors define protein condensation diseases as conditions caused by aberrant liquid-like or solid-like states of proteins, and describe opportunities for therapeutic interventions to restore the normal phase behaviour of proteins. The review accompanies the related collection of articles published in Nature Communications focusing on possible therapeutic approaches involving liquid-liquid phase separation.
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38
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Homodimeric complexes of the 90-231 human prion: a multilayered computational study based on FMO/GRID-DRY approach. J Mol Model 2022; 28:241. [PMID: 35918494 PMCID: PMC9345805 DOI: 10.1007/s00894-022-05244-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/25/2022] [Indexed: 12/25/2022]
Abstract
The molecular interaction properties and aggregation capabilities disclosed by PrP-E200K, a pathogenic mutant of the human prion protein, were investigated in detail using multilayered computational approaches. In a previous work, we reported that the electrostatic complementarity between region1 (negative) and region3 (positive) has been assumed to lead to a head-to tail interaction between 120 and 231 PrP-E200K units and to initiation of the aggregation process. In this work, we extended the PrP-E200K structure by including the unstructured 90–120 segment which was found to assume different conformations. Plausible models of 90–231 PrP-E200K dimers were calculated and analyzed in depth to identify the nature of the involved protein–protein interactions. The unstructured 90–120 segment was found to extend the positively charged region3 involved in the association of PrP-E200K units which resulted to be driven by hydrophobic interactions. The combination of molecular dynamics, protein–protein docking, grid-based mapping, and fragment molecular orbital approaches allowed us to provide a plausible mechanism of the early state of 90–231 PrP-E200K aggregation, considered a preliminary step of amyloid conversion.
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Avni A, Joshi A, Walimbe A, Pattanashetty SG, Mukhopadhyay S. Single-droplet surface-enhanced Raman scattering decodes the molecular determinants of liquid-liquid phase separation. Nat Commun 2022; 13:4378. [PMID: 35902591 PMCID: PMC9334365 DOI: 10.1038/s41467-022-32143-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022] Open
Abstract
Biomolecular condensates formed via liquid-liquid phase separation (LLPS) are involved in a myriad of critical cellular functions and debilitating neurodegenerative diseases. Elucidating the role of intrinsic disorder and conformational heterogeneity of intrinsically disordered proteins/regions (IDPs/IDRs) in these phase-separated membrane-less organelles is crucial to understanding the mechanism of formation and regulation of biomolecular condensates. Here we introduce a unique single-droplet surface-enhanced Raman scattering (SERS) methodology that utilizes surface-engineered, plasmonic, metal nanoparticles to unveil the inner workings of mesoscopic liquid droplets of Fused in Sarcoma (FUS) in the absence and presence of RNA. These highly sensitive measurements offer unprecedented sensitivity to capture the crucial interactions, conformational heterogeneity, and structural distributions within the condensed phase in a droplet-by-droplet manner. Such an ultra-sensitive single-droplet vibrational methodology can serve as a potent tool to decipher the key molecular drivers of biological phase transitions of a wide range of biomolecular condensates involved in physiology and disease. The authors introduce a unique single-droplet surface-enhanced Raman scattering (SERS) methodology that illuminates a wealth of molecular information within the mesoscopic liquid condensed phase of Fused in Sarcoma in the absence and presence of RNA.
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Affiliation(s)
- Anamika Avni
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Ashish Joshi
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Anuja Walimbe
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Swastik G Pattanashetty
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India. .,Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India. .,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
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40
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Horvath A, Fuxreiter M, Vendruscolo M, Holt C, Carver JA. Are casein micelles extracellular condensates formed by liquid-liquid phase separation? FEBS Lett 2022; 596:2072-2085. [PMID: 35815989 DOI: 10.1002/1873-3468.14449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/27/2022] [Indexed: 11/05/2022]
Abstract
Casein micelles are extracellular polydisperse assemblies of unstructured casein proteins. Caseins are the major component of milk. Within casein micelles, casein molecules are stabilised by binding to calcium phosphate nanoclusters and, by acting as molecular chaperones, through multivalent interactions. In light of such interactions, we discuss whether casein micelles can be considered as extracellular condensates formed by liquid-liquid phase separation. We analyse the sequence, structure and interactions of caseins in comparison to proteins forming intracellular condensates. Furthermore, we review the similarities between caseins and small heat-shock proteins whose chaperone activity is linked to phase separation of proteins. By bringing these observations together, we describe a regulatory mechanism for protein condensates, as exemplified by casein micelles.
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Affiliation(s)
- Attila Horvath
- John Curtin School of Medical Research, The Australian National University, Acton, ACT, 2601, Australia
| | - Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B 35131, Padova, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Carl Holt
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | - John A Carver
- Research School of Chemistry, The Australian National University, Acton, ACT, 2601, Australia
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41
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Basant A, Way M. The relative binding position of Nck and Grb2 adaptors impacts actin-based motility of Vaccinia virus. eLife 2022; 11:74655. [PMID: 35796545 PMCID: PMC9333988 DOI: 10.7554/elife.74655] [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: 10/12/2021] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
Phosphotyrosine (pTyr) motifs in unstructured polypeptides orchestrate important cellular processes by engaging SH2-containing adaptors to assemble complex signalling networks. The concept of phase separation has recently changed our appreciation of multivalent networks, however, the role of pTyr motif positioning in their function remains to be explored. We have now investigated this parameter in the operation of the signalling cascade driving actin-based motility and spread of Vaccinia virus. This network involves two pTyr motifs in the viral protein A36 that recruit the adaptors Nck and Grb2 upstream of N-WASP and Arp2/3 complex-mediated actin polymerisation. Manipulating the position of pTyr motifs in A36 and the unrelated p14 from Orthoreovirus, we find that only specific spatial arrangements of Nck and Grb2 binding sites result in robust N-WASP recruitment, Arp2/3 complex driven actin polymerisation and viral spread. This suggests that the relative position of pTyr adaptor binding sites is optimised for signal output. This finding may explain why the relative positions of pTyr motifs are frequently conserved in proteins from widely different species. It also has important implications for regulation of physiological networks, including those undergoing phase transitions.
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Affiliation(s)
- Angika Basant
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael Way
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
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Abstract
The number of (TTAGGG)n repeats at the ends of chromosomes is highly variable between individual chromosomes, between different cells and between species. Progressive loss of telomere repeats limits the proliferation of pre-malignant human cells but also contributes to aging by inducing apoptosis and senescence in normal cells. Despite enormous progress in understanding distinct pathways that result in loss and gain of telomeric DNA in different cell types, many questions remain. Further studies are needed to delineate the role of damage to telomeric DNA, replication errors, chromatin structure, liquid-liquid phase transition, telomeric transcripts (TERRA) and secondary DNA structures such as guanine quadruplex structures, R-loops and T-loops in inducing gains and losses of telomere repeats in different cell types. Limitations of current telomere length measurements techniques and differences in telomere biology between species and different cell types complicate generalizations about the role of telomeres in aging and cancer. Here some of the factors regulating the telomere length in embryonic and adult cells in mammals are discussed from a mechanistic and evolutionary perspective.
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Affiliation(s)
- Peter Lansdorp
- Terry Fox Laboratory, British Columbia (BC) Cancer Agency, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Peter Lansdorp,
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43
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Hatos A, Tosatto SCE, Vendruscolo M, Fuxreiter M. FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid-liquid phase separation and aggregation of proteins. Nucleic Acids Res 2022; 50:W337-W344. [PMID: 35610022 PMCID: PMC9252777 DOI: 10.1093/nar/gkac386] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/20/2022] [Accepted: 05/19/2022] [Indexed: 11/15/2022] Open
Abstract
Many proteins perform their functions within membraneless organelles, where they form a liquid-like condensed state, also known as droplet state. The FuzDrop method predicts the probability of spontaneous liquid-liquid phase separation of proteins and provides a sequence-based score to identify the regions that promote this process. Furthermore, the FuzDrop method estimates the propensity of conversion of proteins to the amyloid state, and identifies aggregation hot-spots, which can drive the irreversible maturation of the liquid-like droplet state. These predictions can also identify mutations that can induce formation of amyloid aggregates, including those implicated in human diseases. To facilitate the interpretation of the predictions, the droplet-promoting and aggregation-promoting regions can be visualized on protein structures generated by AlphaFold. The FuzDrop server (https://fuzdrop.bio.unipd.it) thus offers insights into the complex behavior of proteins in their condensed states and facilitates the understanding of the functional relationships of proteins.
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Affiliation(s)
- Andras Hatos
- Department of Biomedical Sciences, University of Padova, via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, via Ugo Bassi 58/B, 35131 Padova, Italy
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44
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Palaia I, Šarić A. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. J Chem Phys 2022; 156:194902. [PMID: 35597653 DOI: 10.1063/5.0087769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
By varying the concentration of molecules in the cytoplasm or on the membrane, cells can induce the formation of condensates and liquid droplets, similar to phase separation. Their thermodynamics, much studied, depends on the mutual interactions between microscopic constituents. Here, we focus on the kinetics and size control of 2D clusters, forming on membranes. Using molecular dynamics of patchy colloids, we model a system of two species of proteins, giving origin to specific heterotypic bonds. We find that concentrations, together with valence and bond strength, control both the size and the growth time rate of the clusters. In particular, if one species is in large excess, it gradually saturates the binding sites of the other species; the system then becomes kinetically arrested and cluster coarsening slows down or stops, thus yielding effective size selection. This phenomenology is observed both in solid and fluid clusters, which feature additional generic homotypic interactions and are reminiscent of the ones observed on biological membranes.
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Affiliation(s)
- Ivan Palaia
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Anđela Šarić
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
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Caragliano E, Brune W, Bosse JB. Herpesvirus Replication Compartments: Dynamic Biomolecular Condensates? Viruses 2022; 14:960. [PMID: 35632702 PMCID: PMC9147375 DOI: 10.3390/v14050960] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/29/2022] [Accepted: 05/01/2022] [Indexed: 02/01/2023] Open
Abstract
Recent progress has provided clear evidence that many RNA-viruses form cytoplasmic biomolecular condensates mediated by liquid-liquid phase separation to facilitate their replication. In contrast, seemingly contradictory data exist for herpesviruses, which replicate their DNA genomes in nuclear membrane-less replication compartments (RCs). Here, we review the current literature and comment on nuclear condensate formation by herpesviruses, specifically with regard to RC formation. Based on data obtained with human cytomegalovirus (human herpesvirus 5), we propose that liquid and homogenous early RCs convert into more heterogeneous RCs with complex properties over the course of infection. We highlight how the advent of DNA replication leads to the maturation of these biomolecular condensates, likely by adding an additional DNA scaffold.
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Affiliation(s)
- Enrico Caragliano
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany;
- Centre for Structural Systems Biology, 22607 Hamburg, Germany
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - Wolfram Brune
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany;
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 38124 Braunschweig, Germany
| | - Jens B. Bosse
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany;
- Centre for Structural Systems Biology, 22607 Hamburg, Germany
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
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46
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Vendruscolo M. Lipid Homeostasis and Its Links With Protein Misfolding Diseases. Front Mol Neurosci 2022; 15:829291. [PMID: 35401104 PMCID: PMC8990168 DOI: 10.3389/fnmol.2022.829291] [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: 12/05/2021] [Accepted: 01/31/2022] [Indexed: 12/30/2022] Open
Abstract
The maintenance of lipid homeostasis is essential for the normal functioning of living organisms. Alterations of the lipid homeostasis system remodel the composition of the lipidome, potentially leading to the formation of toxic lipid species. In turn, lipidome changes can affect the protein homeostasis system by causing perturbations that elicit protein condensation phenomena such as protein liquid-liquid phase separation and protein aggregation. Lipids can also be more directly involved the formation of aberrant condensed states of proteins by facilitating the early events that initiate these processes and by stabilizing the condensed states themselves. These observations suggest that lipid-induced toxicity can contribute to protein misfolding diseases, including Alzheimer’s and Parkinson’s diseases. According to this view, an impairment of the lipid homeostasis system generates toxic states of lipids that disturb the protein homeostasis system and promote the formation of toxic states of proteins.
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47
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Spatiotemporal modulations in heterotypic condensates of prion and α-synuclein control phase transitions and amyloid conversion. Nat Commun 2022; 13:1154. [PMID: 35241680 PMCID: PMC8894376 DOI: 10.1038/s41467-022-28797-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 02/10/2022] [Indexed: 12/30/2022] Open
Abstract
Biomolecular condensation via liquid-liquid phase separation of proteins and nucleic acids is associated with a range of critical cellular functions and neurodegenerative diseases. Here, we demonstrate that complex coacervation of the prion protein and α-synuclein within narrow stoichiometry results in the formation of highly dynamic, reversible, thermo-responsive liquid droplets via domain-specific electrostatic interactions between the positively-charged intrinsically disordered N-terminal segment of prion and the acidic C-terminal tail of α-synuclein. The addition of RNA to these coacervates yields multiphasic, vesicle-like, hollow condensates. Picosecond time-resolved measurements revealed the presence of transient electrostatic nanoclusters that are stable on the nanosecond timescale and can undergo breaking-and-making of interactions on slower timescales giving rise to a liquid-like behavior in the mesoscopic regime. The liquid-to-solid transition drives a rapid conversion of complex coacervates into heterotypic amyloids. Our results suggest that synergistic prion-α-synuclein interactions within condensates provide mechanistic underpinnings of their physiological role and overlapping neuropathological features. The authors show that prion protein and α-synuclein undergo phase separation through domain-specific electrostatic interactions. These complex coacervates possess electrostatic nanoclusters and can convert into multiphasic condensates and amyloids.
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48
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Ma Y, Li H, Gong Z, Yang S, Wang P, Tang C. Nucleobase Clustering Contributes to the Formation and Hollowing of Repeat-Expansion RNA Condensate. J Am Chem Soc 2022; 144:4716-4720. [PMID: 35179357 DOI: 10.1021/jacs.1c12085] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA molecules with repeat expansion sequences can phase separate into gel-like condensate, which could lead to neurodegenerative diseases. Here, we report that, in the presence of Mg2+, RNA molecules containing 20× CAG repeats self-assemble into three morphologically distinct droplets. Using hyperspectral stimulated Raman microscopy, we show that RNA phase separation is accompanied by the clustering of nucleobases while forfeiting the canonical base-paired structure. As the RNA/Mg2+ ratio increases, the RNA droplets first expand and then shrink to adopt hollow vesicle-like structures. Significantly, for both large and vesicle-like RNA droplets, the nucleobase-clustered structure is more prominent at the rim, suggesting a continuously hardening process. This mechanism may be implicated in the general aging processes of RNA-containing membrane-less organelles.
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Affiliation(s)
- Yingxue Ma
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Haozheng Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Shuai Yang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Ping Wang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Chun Tang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Center for Computational Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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49
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Pesce G, Gondelaud F, Ptchelkine D, Nilsson JF, Bignon C, Cartalas J, Fourquet P, Longhi S. Experimental Evidence of Intrinsic Disorder and Amyloid Formation by the Henipavirus W Proteins. Int J Mol Sci 2022; 23:ijms23020923. [PMID: 35055108 PMCID: PMC8780864 DOI: 10.3390/ijms23020923] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Henipaviruses are severe human pathogens within the Paramyxoviridae family. Beyond the P protein, the Henipavirus P gene also encodes the V and W proteins which share with P their N-terminal, intrinsically disordered domain (NTD) and possess a unique C-terminal domain. Henipavirus W proteins antagonize interferon (IFN) signaling through NTD-mediated binding to STAT1 and STAT4, and prevent type I IFN expression and production of chemokines. Structural and molecular information on Henipavirus W proteins is lacking. By combining various bioinformatic approaches, we herein show that the Henipaviruses W proteins are predicted to be prevalently disordered and yet to contain short order-prone segments. Using limited proteolysis, differential scanning fluorimetry, analytical size exclusion chromatography, far-UV circular dichroism and small-angle X-ray scattering, we experimentally confirmed their overall disordered nature. In addition, using Congo red and Thioflavin T binding assays and negative-staining transmission electron microscopy, we show that the W proteins phase separate to form amyloid-like fibrils. The present study provides an additional example, among the few reported so far, of a viral protein forming amyloid-like fibrils, therefore significantly contributing to enlarge our currently limited knowledge of viral amyloids. In light of the critical role of the Henipavirus W proteins in evading the host innate immune response and of the functional role of phase separation in biology, these studies provide a conceptual asset to further investigate the functional impact of the phase separation abilities of the W proteins.
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Affiliation(s)
- Giulia Pesce
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Frank Gondelaud
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Denis Ptchelkine
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Juliet F. Nilsson
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Christophe Bignon
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Jérémy Cartalas
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Patrick Fourquet
- INSERM, Centre de Recherche en Cancérologie de Marseille (CRCM), Centre National de la Recherche Scientifique (CNRS), Marseille Protéomique, Institut Paoli-Calmettes, Aix Marseille University, 27 Bvd Leï Roure, CS 30059, 13273 Marseille, France;
| | - Sonia Longhi
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
- Correspondence:
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50
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Scholl D, Deniz AA. Conformational Freedom and Topological Confinement of Proteins in Biomolecular Condensates. J Mol Biol 2022; 434:167348. [PMID: 34767801 PMCID: PMC8748313 DOI: 10.1016/j.jmb.2021.167348] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 01/17/2023]
Abstract
The emergence of biomolecular condensation and liquid-liquid phase separation (LLPS) introduces a new layer of complexity into our understanding of cell and molecular biology. Evidence steadily grows indicating that condensates are not only implicated in physiology but also human disease. Macro- and mesoscale characterization of condensates as a whole have been instrumental in understanding their biological functions and dysfunctions. By contrast, the molecular level characterization of condensates and how condensates modify the properties of the molecules that constitute them thus far remain comparably scarce. In this minireview we summarize and discuss the findings of several recent studies that have focused on structure, dynamics, and interactions of proteins undergoing condensation. The mechanistic insights they provide help us identify the relevant properties nature and scientists can leverage to modulate the behavior of condensate systems. We also discuss the unique environment of the droplet surface and speculate on effects of topological constraints and physical exclusion on condensate properties.
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Affiliation(s)
- Daniel Scholl
- Department of Integrative and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, United States. https://twitter.com/@DanielScholl_be
| | - Ashok A Deniz
- Department of Integrative and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, United States.
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