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Wang F, Chen Z, Zhou Q, Xie L, Zheng N, Chen Z, Lin J, Li B, Li L. Implications of Liquid-Liquid Phase Separation and Ferroptosis in Alzheimer's Disease. Neuropharmacology 2024:110083. [PMID: 39043267 DOI: 10.1016/j.neuropharm.2024.110083] [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: 05/18/2024] [Revised: 07/04/2024] [Accepted: 07/15/2024] [Indexed: 07/25/2024]
Abstract
Neuronal cell demise represents a prevalent occurrence throughout the advancement of Alzheimer's disease (AD). However, the mechanism of triggering the death of neuronal cells remains unclear. Its potential mechanisms include aggregation of soluble amyloid-beta (Aβ) to form insoluble amyloid plaques, abnormal phosphorylation of tau protein and formation of intracellular neurofibrillary tangles (NFTs), neuroinflammation, ferroptosis, oxidative stress, liquid-liquid phase separation (LLPS) and metal ion disorders. Among them, ferroptosis is an iron-dependent lipid peroxidation-driven cell death and emerging evidences have demonstrated the involvement of ferroptosis in the pathological process of AD. The sensitivity to ferroptosis is tightly linked to numerous biological processes. Moreover, emerging evidences indicate that LLPS has great impacts on regulating human health and diseases, especially AD. Soluble Aβ can undergo LLPS to form liquid-like droplets, which can lead to the formation of insoluble amyloid plaques. Meanwhile, tau has a high propensity to condensate via the mechanism of LLPS, which can lead to the formation of NFTs. In this review, we summarize the most recent advancements pertaining to LLPS and ferroptosis in AD. Our primary focus is on expounding the influence of Aβ, tau protein, iron ions, and lipid oxidation on the intricate mechanisms underlying ferroptosis and LLPS within the domain of AD pathology. Additionally, we delve into the intricate cross-interactions that occur between LLPS and ferroptosis in the context of AD. Our findings are expected to serve as a theoretical and experimental foundation for clinical research and targeted therapy for AD.
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Affiliation(s)
- Fuwei Wang
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Zihao Chen
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Qiong Zhou
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Lihua Xie
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Nan Zheng
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Ziwen Chen
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Jiantao Lin
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China.
| | - Baohong Li
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China.
| | - Li Li
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China.
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2
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Li P, Chen P, Qi F, Shi J, Zhu W, Li J, Zhang P, Xie H, Li L, Lei M, Ren X, Wang W, Zhang L, Xiang X, Zhang Y, Gao Z, Feng X, Du W, Liu X, Xia L, Liu BF, Li Y. High-throughput and proteome-wide discovery of endogenous biomolecular condensates. Nat Chem 2024; 16:1101-1112. [PMID: 38499848 DOI: 10.1038/s41557-024-01485-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/23/2024] [Indexed: 03/20/2024]
Abstract
Phase separation inside mammalian cells regulates the formation of the biomolecular condensates that are related to gene expression, signalling, development and disease. However, a large population of endogenous condensates and their candidate phase-separating proteins have yet to be discovered in a quantitative and high-throughput manner. Here we demonstrate that endogenously expressed biomolecular condensates can be identified across a cell's proteome by sorting proteins across varying oligomeric states. We employ volumetric compression to modulate the concentrations of intracellular proteins and the degree of crowdedness, which are physical regulators of cellular biomolecular condensates. The changes in degree of the partition of proteins into condensates or phase separation led to varying oligomeric states of the proteins, which can be detected by coupling density gradient ultracentrifugation and quantitative mass spectrometry. In total, we identified 1,518 endogenous condensate proteins, of which 538 have not been reported before. Furthermore, we demonstrate that our strategy can identify condensate proteins that respond to specific biological processes.
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Affiliation(s)
- Pengjie Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Fukang Qi
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Jinyun Shi
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Wenjie Zhu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Jiashuo Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Peng Zhang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Han Xie
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Lina Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Mengcheng Lei
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xueqing Ren
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Wenhui Wang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Liang Zhang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xufu Xiang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yiwei Zhang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Zhaolong Gao
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xiaojun Feng
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Wei Du
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xin Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Limin Xia
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China.
| | - Yiwei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China.
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3
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Laakko T, Korkealaakso A, Yildirir BF, Batys P, Liljeström V, Hokkanen A, Nonappa, Penttilä M, Laukkanen A, Miserez A, Södergård C, Mohammadi P. Accelerated Engineering of ELP-Based Materials through Hybrid Biomimetic-De Novo Predictive Molecular Design. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2312299. [PMID: 38710202 DOI: 10.1002/adma.202312299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/28/2024] [Indexed: 05/08/2024]
Abstract
Efforts to engineer high-performance protein-based materials inspired by nature have mostly focused on altering naturally occurring sequences to confer the desired functionalities, whereas de novo design lags significantly behind and calls for unconventional innovative approaches. Here, using partially disordered elastin-like polypeptides (ELPs) as initial building blocks this work shows that de novo engineering of protein materials can be accelerated through hybrid biomimetic design, which this work achieves by integrating computational modeling, deep neural network, and recombinant DNA technology. This generalizable approach involves incorporating a series of de novo-designed sequences with α-helical conformation and genetically encoding them into biologically inspired intrinsically disordered repeating motifs. The new ELP variants maintain structural conformation and showed tunable supramolecular self-assembly out of thermal equilibrium with phase behavior in vitro. This work illustrates the effective translation of the predicted molecular designs in structural and functional materials. The proposed methodology can be applied to a broad range of partially disordered biomacromolecules and potentially pave the way toward the discovery of novel structural proteins.
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Affiliation(s)
- Timo Laakko
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
| | | | - Burcu Firatligil Yildirir
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 6, Tampere, FI-33720, Finland
| | - Piotr Batys
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, Krakow, PL-30239, Poland
| | - Ville Liljeström
- Department of Applied Physics, School of Science, Aalto University, Aalto, FI-00076, Finland
| | - Ari Hokkanen
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
| | - Nonappa
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 6, Tampere, FI-33720, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
| | - Anssi Laukkanen
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
| | - Ali Miserez
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore, 637553, Singapore
- School of Biological Sciences, NTU, Singapore, 637551, Singapore
| | - Caj Södergård
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
| | - Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
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4
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Latham AP, Zhu L, Sharon DA, Ye S, Willard AP, Zhang X, Zhang B. Microphase Separation Produces Interfacial Environment within Diblock Biomolecular Condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.30.534967. [PMID: 37034777 PMCID: PMC10081284 DOI: 10.1101/2023.03.30.534967] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The phase separation of intrinsically disordered proteins is emerging as an important mechanism for cellular organization. However, efforts to connect protein sequences to the physical properties of condensates, i.e., the molecular grammar, are hampered by a lack of effective approaches for probing high-resolution structural details. Using a combination of multiscale simulations and fluorescence lifetime imaging microscopy experiments, we systematically explored a series of systems consisting of diblock elastin-like polypeptides (ELP). The simulations succeeded in reproducing the variation of condensate stability upon amino acid substitution and revealed different microenvironments within a single condensate, which we verified with environmentally sensitive fluorophores. The interspersion of hydrophilic and hydrophobic residues and a lack of secondary structure formation result in an interfacial environment, which explains both the strong correlation between ELP condensate stability and interfacial hydrophobicity scales, as well as the prevalence of protein-water hydrogen bonds. Our study uncovers new mechanisms for condensate stability and organization that may be broadly applicable.
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Affiliation(s)
- Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Longchen Zhu
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Dina A Sharon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Songtao Ye
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Adam P Willard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Xin Zhang
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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5
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Kozak F, Brandis D, Pötzl C, Epasto LM, Reichinger D, Obrist D, Peterlik H, Polyansky A, Zagrovic B, Daus F, Geyer A, Becker CF, Kurzbach D. An Atomistic View on the Mechanism of Diatom Peptide-Guided Biomimetic Silica Formation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401239. [PMID: 38874418 DOI: 10.1002/advs.202401239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/23/2024] [Indexed: 06/15/2024]
Abstract
Deciphering nature's remarkable way of encoding functions in its biominerals holds the potential to enable the rational development of nature-inspired materials with tailored properties. However, the complex processes that convert solution-state precursors into solid biomaterials remain largely unknown. In this study, an unconventional approach is presented to characterize these precursors for the diatom-derived peptides R5 and synthetic Silaffin-1A1 (synSil-1A1). These molecules can form defined supramolecular assemblies in solution, which act as templates for solid silica structures. Using a tailored structural biology toolbox, the structure-function relationships of these self-assemblies are unveiled. NMR-derived constraints are employed to enable a recently developed fractal-cluster formalism and then reveal the architecture of the peptide assemblies in atomistic detail. Finally, by monitoring the self-assembly activities during silica formation at simultaneous high temporal and residue resolution using real-time spectroscopy, the mechanism is elucidated underlying template-driven silica formation. Thus, it is demonstrated how to exercise morphology control over bioinorganic solids by manipulating the template architectures. It is found that the morphology of the templates is translated into the shape of bioinorganic particles via a mechanism that includes silica nucleation on the solution-state complexes' surfaces followed by complete surface coating and particle precipitation.
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Affiliation(s)
- Fanny Kozak
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Dörte Brandis
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Christopher Pötzl
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Ludovica M Epasto
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Daniela Reichinger
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Dominik Obrist
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Herwig Peterlik
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, Vienna, 1090, Austria
| | - Anton Polyansky
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, Vienna, A-1030, Austria
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, Vienna, A-1030, Austria
| | - Fabian Daus
- Faculty of Chemistry, Philipps-Universität Marburg, 35032, Marburg, Germany
| | - Armin Geyer
- Faculty of Chemistry, Philipps-Universität Marburg, 35032, Marburg, Germany
| | - Christian Fw Becker
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Dennis Kurzbach
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
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6
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Lau K, Reichheld S, Xian M, Sharpe SJ, Cerruti M. Directed Assembly of Elastic Fibers via Coacervate Droplet Deposition on Electrospun Templates. Biomacromolecules 2024; 25:3519-3531. [PMID: 38742604 DOI: 10.1021/acs.biomac.4c00180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Elastic fibers provide critical elasticity to the arteries, lungs, and other organs. Elastic fiber assembly is a process where soluble tropoelastin is coacervated into liquid droplets, cross-linked, and deposited onto and into microfibrils. While much progress has been made in understanding the biology of this process, questions remain regarding the timing of interactions during assembly. Furthermore, it is unclear to what extent fibrous templates are needed to guide coacervate droplets into the correct architecture. The organization and shaping of coacervate droplets onto a fiber template have never been previously modeled or employed as a strategy for shaping elastin fiber materials. Using an in vitro system consisting of elastin-like polypeptides (ELPs), genipin cross-linker, electrospun polylactic-co-glycolic acid (PLGA) fibers, and tannic acid surface coatings for fibers, we explored ELP coacervation, cross-linking, and deposition onto fiber templates. We demonstrate that integration of coacervate droplets into a fibrous template is primarily influenced by two factors: (1) the balance of coacervation and cross-linking and (2) the surface energy of the fiber templates. The success of this integration affects the mechanical properties of the final fiber network. Our resulting membrane materials exhibit highly tunable morphologies and a range of elastic moduli (0.8-1.6 MPa) comparable to native elastic fibers.
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Affiliation(s)
- Kirklann Lau
- Department of Mining and Materials Engineering, McGill University, 3610 University Street, Wong Building 2250, Montreal, Quebec H3A 0C5, Canada
| | - Sean Reichheld
- Molecular Medicine, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, 686 Bay Street, Room 20.9714, Toronto, Ontario M5G 1X8, Canada
| | - Mingqian Xian
- Department of Mining and Materials Engineering, McGill University, 3610 University Street, Wong Building 2250, Montreal, Quebec H3A 0C5, Canada
| | - Simon J Sharpe
- Molecular Medicine, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, 686 Bay Street, Room 20.9714, Toronto, Ontario M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Room 5207, Toronto, Ontario M5S 1A8, Canada
| | - Marta Cerruti
- Department of Mining and Materials Engineering, McGill University, 3610 University Street, Wong Building 2250, Montreal, Quebec H3A 0C5, Canada
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7
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König B, Pezzotti S, Ramos S, Schwaab G, Havenith M. Real-time measure of solvation free energy changes upon liquid-liquid phase separation of α-elastin. Biophys J 2024; 123:1367-1375. [PMID: 37515326 PMCID: PMC11163292 DOI: 10.1016/j.bpj.2023.07.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/16/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023] Open
Abstract
Biological condensates are known to retain a large fraction of water to remain in a liquid and reversible state. Local solvation contributions from water hydrating hydrophilic and hydrophobic protein surfaces were proposed to play a prominent role for the formation of condensates through liquid-liquid phase separation (LLPS). However, although the total free energy is accessible by calorimetry, the partial solvent contributions to the free energy changes upon LLPS remained experimentally inaccessible so far. Here, we show that the recently developed THz calorimetry approach allows to quantify local hydration enthalpy and entropy changes upon LLPS of α-elastin in real time, directly from experimental THz spectroscopy data. We find that hydrophobic solvation dominates the entropic solvation term, whereas hydrophilic solvation mainly contributes to the enthalpy. Both terms are in the order of hundreds of kJ/mol, which is more than one order of magnitude larger than the total free energy changes at play during LLPS. However, since we show that entropy/enthalpy mostly compensates, a small entropy/enthalpy imbalance is sufficient to tune LLPS. Theoretically, a balance was proposed before. Here we present experimental evidence based on our spectroscopic approach. We finally show that LLPS can be steered by inducing small changes of solvation entropy/enthalpy compensation via concentration or temperature in α-elastin.
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Affiliation(s)
- Benedikt König
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum, Germany
| | - Simone Pezzotti
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum, Germany
| | - Sashary Ramos
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum, Germany
| | - Gerhard Schwaab
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum, Germany
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum, Germany.
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8
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Wang SH, Zheng T, Fawzi NL. Structure and interactions of prion-like domains in transcription factor Efg1 phase separation. Biophys J 2024; 123:1481-1493. [PMID: 38297837 PMCID: PMC11163291 DOI: 10.1016/j.bpj.2024.01.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/08/2024] [Accepted: 01/25/2024] [Indexed: 02/02/2024] Open
Abstract
Candida albicans, a prominent member of the human microbiome, can make an opportunistic switch from commensal coexistence to pathogenicity accompanied by an epigenetic shift between the white and opaque cell states. This transcriptional switch is under precise regulation by a set of transcription factors (TFs), with Enhanced Filamentous Growth Protein 1 (Efg1) playing a central role. Previous research has emphasized the importance of Efg1's prion-like domain (PrLD) and the protein's ability to undergo phase separation for the white-to-opaque transition of C. albicans. However, the underlying molecular mechanisms of Efg1 phase separation have remained underexplored. In this study, we delved into the biophysical basis of Efg1 phase separation, revealing the significant contribution of both N-terminal (N) and C-terminal (C) PrLDs. Through NMR structural analysis, we found that Efg1 N-PrLD and C-PrLD are mostly disordered but have prominent partial α-helical secondary structures in both domains. NMR titration experiments suggest that the partially helical structures in N-PrLD act as hubs for self-interaction as well as Efg1 interaction with RNA. Using condensed-phase NMR spectroscopy, we uncovered diverse amino acid interactions underlying Efg1 phase separation. Particularly, we highlight the indispensable role of tyrosine residues within the transient α-helical structures of PrLDs particularly in the N-PrLD compared to the C-PrLD in stabilizing phase separation. Our study provides evidence that the transient α-helical structure is present in the phase-separated state and highlights the particular importance of aromatic residues within these structures for phase separation. Together, these results enhance the understanding of C. albicans transcription factor interactions that lead to virulence and provide a crucial foundation for potential antifungal therapies targeting the transcriptional switch.
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Affiliation(s)
- Szu-Huan Wang
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Tongyin Zheng
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island.
| | - Nicolas L Fawzi
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island.
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9
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Puertas-Bartolomé M, Venegas-Bustos D, Acosta S, Rodríguez-Cabello JC. Contribution of the ELRs to the development of advanced in vitro models. Front Bioeng Biotechnol 2024; 12:1363865. [PMID: 38650751 PMCID: PMC11033926 DOI: 10.3389/fbioe.2024.1363865] [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: 12/31/2023] [Accepted: 03/18/2024] [Indexed: 04/25/2024] Open
Abstract
Developing in vitro models that accurately mimic the microenvironment of biological structures or processes holds substantial promise for gaining insights into specific biological functions. In the field of tissue engineering and regenerative medicine, in vitro models able to capture the precise structural, topographical, and functional complexity of living tissues, prove to be valuable tools for comprehending disease mechanisms, assessing drug responses, and serving as alternatives or complements to animal testing. The choice of the right biomaterial and fabrication technique for the development of these in vitro models plays an important role in their functionality. In this sense, elastin-like recombinamers (ELRs) have emerged as an important tool for the fabrication of in vitro models overcoming the challenges encountered in natural and synthetic materials due to their intrinsic properties, such as phase transition behavior, tunable biological properties, viscoelasticity, and easy processability. In this review article, we will delve into the use of ELRs for molecular models of intrinsically disordered proteins (IDPs), as well as for the development of in vitro 3D models for regenerative medicine. The easy processability of the ELRs and their rational design has allowed their use for the development of spheroids and organoids, or bioinks for 3D bioprinting. Thus, incorporating ELRs into the toolkit of biomaterials used for the fabrication of in vitro models, represents a transformative step forward in improving the accuracy, efficiency, and functionality of these models, and opening up a wide range of possibilities in combination with advanced biofabrication techniques that remains to be explored.
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Affiliation(s)
- María Puertas-Bartolomé
- Technical Proteins Nanobiotechnology, S.L. (TPNBT), Valladolid, Spain
- Bioforge Lab (Group for Advanced Materials and Nanobiotechnology), CIBER's Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Edificio LUCIA, Universidad de Valladolid, Valladolid, Spain
| | - Desiré Venegas-Bustos
- Bioforge Lab (Group for Advanced Materials and Nanobiotechnology), CIBER's Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Edificio LUCIA, Universidad de Valladolid, Valladolid, Spain
| | - Sergio Acosta
- Bioforge Lab (Group for Advanced Materials and Nanobiotechnology), CIBER's Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Edificio LUCIA, Universidad de Valladolid, Valladolid, Spain
| | - José Carlos Rodríguez-Cabello
- Bioforge Lab (Group for Advanced Materials and Nanobiotechnology), CIBER's Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Edificio LUCIA, Universidad de Valladolid, Valladolid, Spain
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10
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Hu B, Zhang C, Zhu J, Yang J, Zheng Q, Zhang X, Cao J, Han L. Liquid-liquid biopolymers aqueous solution segregative phase separation in food: From fundamentals to applications-A review. Int J Biol Macromol 2024; 265:131044. [PMID: 38518933 DOI: 10.1016/j.ijbiomac.2024.131044] [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: 10/13/2023] [Revised: 03/07/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
As a result of the spontaneous movement of molecules, liquid-liquid biopolymer segregative phase separation takes place in an aqueous solution. The efficacy of this type of separation can be optimized under conditions where variables such as pH, temperature, and molecular concentrations have minimal impact on its dynamics. Recently, interest in the applications of biopolymers and their segregative phase separation-associated molecular stratification has increased, particularly in the food industry, where these methods permit the purification of specific particles and the embedding of microcapsules. The present review offers a comprehensive examination of the theoretical mechanisms that regulate the liquid-liquid biopolymers aqueous solution segregative phase separation, the factors that may exert an impact on this procedure, and the importance of this particular separation method in the context of food science. These discussion points also address existing difficulties and future possibilities related to the use of segregative phase separation in food applications. This highlights the potential for the design of novel functional foods and the enhancement of food properties.
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Affiliation(s)
- Bing Hu
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China.
| | - Cunzhi Zhang
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
| | - Junzhe Zhu
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
| | - Jixin Yang
- Faculty of Social and Life Sciences, Wrexham University, Mold Road, Wrexham LL11 2AW, United Kingdom
| | - Qiuyue Zheng
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
| | - Xiaobo Zhang
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
| | - Jijuan Cao
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
| | - Lingyu Han
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China.
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11
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Ye S, Latham AP, Tang Y, Hsiung CH, Chen J, Luo F, Liu Y, Zhang B, Zhang X. Micropolarity governs the structural organization of biomolecular condensates. Nat Chem Biol 2024; 20:443-451. [PMID: 37973891 PMCID: PMC10978266 DOI: 10.1038/s41589-023-01477-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/11/2023] [Indexed: 11/19/2023]
Abstract
Membraneless organelles within cells have unique microenvironments that play a critical role in their functions. However, how microenvironments of biomolecular condensates affect their structure and function remains unknown. In this study, we investigated the micropolarity and microviscosity of model biomolecular condensates by fluorescence lifetime imaging coupling with environmentally sensitive fluorophores. Using both in vitro and in cellulo systems, we demonstrated that sufficient micropolarity difference is key to forming multilayered condensates, where the shells present more polar microenvironments than the cores. Furthermore, micropolarity changes were shown to be accompanied by conversions of the layered structures. Decreased micropolarities of the granular components, accompanied by the increased micropolarities of the dense fibrillar components, result in the relocation of different nucleolus subcompartments in transcription-stalled conditions. Our results demonstrate the central role of the previously overlooked micropolarity in the regulation of structures and functions of membraneless organelles.
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Affiliation(s)
- Songtao Ye
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Yuqi Tang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Chia-Heng Hsiung
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Junlin Chen
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Feng Luo
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xin Zhang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou, China.
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
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12
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Rai S, Pramanik S, Mukherjee S. Deciphering the liquid-liquid phase separation induced modulation in the structure, dynamics, and enzymatic activity of an ordered protein β-lactoglobulin. Chem Sci 2024; 15:3936-3948. [PMID: 38487243 PMCID: PMC10935713 DOI: 10.1039/d3sc06802a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/23/2024] [Indexed: 03/17/2024] Open
Abstract
Owing to the significant role in the subcellular organization of biomolecules, physiology, and the realm of biomimetic materials, studies related to biomolecular condensates formed through liquid-liquid phase separation (LLPS) have emerged as a growing area of research. Despite valuable contributions of prior research, there is untapped potential in exploring the influence of phase separation on the conformational dynamics and enzymatic activities of native proteins. Herein, we investigate the LLPS of β-lactoglobulin (β-LG), a non-intrinsically disordered protein, under crowded conditions. In-depth characterization through spectroscopic and microscopic techniques revealed the formation of dynamic liquid-like droplets, distinct from protein aggregates, driven by hydrophobic interactions. Our analyses revealed that phase separation can alter structural flexibility and photophysical properties. Importantly, the phase-separated β-LG exhibited efficient enzymatic activity as an esterase; a characteristic seemingly exclusive to β-LG droplets. The droplets acted as robust catalytic crucibles, providing an ideal environment for efficient ester hydrolysis. Further investigation into the catalytic mechanism suggested the involvement of specific amino acid residues, rather than general acid or base catalysis. Also, the alteration in conformational distribution caused by phase separation unveils the latent functionality. Our study delineates the understanding of protein phase separation and insights into the diverse catalytic strategies employed by proteins. It opens exciting possibilities for designing functional artificial compartments based on phase-separated biomolecules.
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Affiliation(s)
- Saurabh Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road Bhopal 462066 Madhya Pradesh India
| | - Srikrishna Pramanik
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road Bhopal 462066 Madhya Pradesh India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road Bhopal 462066 Madhya Pradesh India
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13
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Jamhawi NM, Koder RL, Wittebort RJ. Elastin recoil is driven by the hydrophobic effect. Proc Natl Acad Sci U S A 2024; 121:e2304009121. [PMID: 38442161 PMCID: PMC10945822 DOI: 10.1073/pnas.2304009121] [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: 03/28/2023] [Accepted: 02/01/2024] [Indexed: 03/07/2024] Open
Abstract
Elastin is an extracellular matrix material found in all vertebrates. Its reversible elasticity, robustness, and low stiffness are essential for the function of arteries, lungs, and skin. It is among the most resilient elastic materials known: During a human lifetime, arterial elastin undergoes in excess of 2 × 109 stretching/contracting cycles without replacement, and slow oxidative hardening has been identified as a limiting factor on human lifespan. For over 50 y, the mechanism of entropic recoil has been controversial. Herein, we report a combined NMR and thermomechanical study that establishes the hydrophobic effect as the primary driver of elastin function. Water ordering at the solvent:protein interface was observed as a function of stretch using double quantum 2H NMR, and the most extensive thermodynamic analysis performed to date was obtained by measuring elastin length and volume as a function of force and temperature in normal water, heavy water and with cosolvents. When stretched, elastin's heat capacity increases, water is ordered proportional to the degree of stretching, the internal energy decreases, and heat is released in excess of the work performed. These properties show that recoil in elastin under physiological conditions is primarily driven by the hydrophobic effect rather than by configurational entropy as is the case for rubber. Consistent with this conclusion are decreases in the thermodynamic signatures when cosolvents that alter the hydrophobic effect are introduced. We propose that hydrophobic effect-driven recoil, as opposed to a configurational entropy mechanism where hardening from crystallization can occur, is the origin of elastin's unusual resilience.
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Affiliation(s)
- Nour M. Jamhawi
- Department of Chemistry, University of Louisville, Louisville, KY40292
| | - Ronald L. Koder
- Department of Physics, The City College of New York, New York, NY10031
- Graduate Programs of Physics, Chemistry, Biology and Biochemistry, The Graduate Center City University of New York (CUNY), New York, NY10016
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14
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Basu T, Das S, Majumdar S. Elucidating the influence of electrostatic force on the re-arrangement of H-bonds of protein polymers in the presence of salts. SOFT MATTER 2024; 20:2361-2373. [PMID: 38372459 DOI: 10.1039/d3sm01440a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Polyampholytes/proteins have an intriguing network of hydrogen bonds (H-bonds), especially their secondary structure, which plays a crucial role in determining the conformational stability of the polymer. The changes in protein secondary structure in the protein-salt system have been extensively deciphered by researchers, yet their pathways for breakage and recreation are unknown. Understanding the mechanism of protein conformational changes towards their biological activities, like protein folding, remains one of the main challenges and requires multiscale analysis of this strongly correlated system. Herein, salts have been used to reveal the re-arrangement behavior in the H-bond network of proteins under the influence of electrostatic interactions, as the strength of electrostatic forces is much stronger than that of H-bonds. At lower salt concentrations, there are negligible changes in the secondary structures as the electrostatic forces induced by the salt ions are less. Later, the existing H-bonds break and reconstruct new H-bonds at higher salt concentrations due to the influence of the stronger electrostatic interaction induced by the large number of salt ions. Molecular dynamics (MD) simulations and FTIR studies have been used rigorously to decipher the reason behind the re-arrangement of the H-bonds within gelatin (protein). The re-arrangement in the H-bond has also been observed with time from simulations and experiments. Thus, this study could provide a fresh perspective on the conformational changes of polyampholytes/proteins and will also influence the studies of protein folding-unfolding interaction in the presence of salt ions.
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Affiliation(s)
- Tithi Basu
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Telangana, 502285, India.
| | - Sougat Das
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Telangana, 502285, India.
| | - Saptarshi Majumdar
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Telangana, 502285, India.
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15
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Li S, Zhang Y, Chen J. Backbone interactions and secondary structures in phase separation of disordered proteins. Biochem Soc Trans 2024; 52:319-329. [PMID: 38348795 DOI: 10.1042/bst20230618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/29/2024]
Abstract
Intrinsically disordered proteins (IDPs) are one of the major drivers behind the formation and characteristics of biomolecular condensates. Due to their inherent flexibility, the backbones of IDPs are significantly exposed, rendering them highly influential and susceptible to biomolecular phase separation. In densely packed condensates, exposed backbones have a heightened capacity to interact with neighboring protein chains, which might lead to strong coupling between the secondary structures and phase separation and further modulate the subsequent transitions of the condensates, such as aging and fibrillization. In this mini-review, we provide an overview of backbone-mediated interactions and secondary structures within biomolecular condensates to underscore the importance of protein backbones in phase separation. We further focus on recent advances in experimental techniques and molecular dynamics simulation methods for probing and exploring the roles of backbone interactions and secondary structures in biomolecular phase separation involving IDPs.
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Affiliation(s)
- Shanlong Li
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Yumeng Zhang
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, U.S.A
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16
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Sicoli G, Sieme D, Overkamp K, Khalil M, Backer R, Griesinger C, Willbold D, Rezaei-Ghaleh N. Large dynamics of a phase separating arginine-glycine-rich domain revealed via nuclear and electron spins. Nat Commun 2024; 15:1610. [PMID: 38383529 PMCID: PMC10881997 DOI: 10.1038/s41467-024-45788-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
Liquid-liquid phase separation is the key process underlying formation of membrane-less compartments in cells. A highly dynamic cellular body with rapid component exchange is Cajal body (CB), which supports the extensive compositional dynamics of the RNA splicing machinery, spliceosome. Here, we select an arginine-glycine (RG)-rich segment of coilin, the major component of CB, establish its RNA-induced phase separation, and through combined use of nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) probes, interrogate its dynamics within the crowded interior of formed droplets. Taking advantage of glycine-based singlet-states, we show that glycines retain a large level of sub-nanoseconds dynamics inside the coilin droplets. Furthermore, the continuous-wave (CW) and electron-electron dipolar (PELDOR) and electron-nucleus hyperfine coupling EPR data (HYSCORE) support the RNA-induced formation of dynamic coilin droplets with high coilin peptide concentrations. The combined NMR and EPR data reveal the high dynamics of the RG-rich coilin within droplets and suggest its potential role in the large dynamics of CBs.
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Affiliation(s)
- Giuseppe Sicoli
- CNRS UMR 8516, University of Lille, LASIRE, C4 Building, Avenue Paul Langevin, F-59655, Villeneuve d'Ascq, France
| | - Daniel Sieme
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077, Göttingen, Germany
| | - Kerstin Overkamp
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077, Göttingen, Germany
| | - Mahdi Khalil
- CNRS UMR 8516, University of Lille, LASIRE, C4 Building, Avenue Paul Langevin, F-59655, Villeneuve d'Ascq, France
| | - Robin Backer
- Heinrich Heine University (HHU) Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077, Göttingen, Germany
| | - Dieter Willbold
- Heinrich Heine University (HHU) Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-52428, Jülich, Germany
| | - Nasrollah Rezaei-Ghaleh
- Heinrich Heine University (HHU) Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Universitätsstrasse 1, D-40225, Düsseldorf, Germany.
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-52428, Jülich, Germany.
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17
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Fang Z, Zhu YJ, Qian ZG, Xia XX. Designer protein compartments for microbial metabolic engineering. Curr Opin Biotechnol 2024; 85:103062. [PMID: 38199036 DOI: 10.1016/j.copbio.2023.103062] [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: 10/02/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
Protein compartments are distinct structures assembled in living cells via self-assembly or phase separation of specific proteins. Significant efforts have been made to discover their molecular structures and formation mechanisms, as well as their fundamental roles in spatiotemporal control of cellular metabolism. Here, we review the design and construction of synthetic protein compartments for spatial organization of target metabolic pathways toward increased efficiency and specificity. In particular, we highlight the compartmentalization strategies and recent examples to speed up desirable metabolic reactions, to reduce the accumulation of toxic metabolic intermediates, and to switch competing metabolic pathways. We also identify the most important challenges that need to be addressed for exploitation of these designer compartments as a versatile toolkit in metabolic reprogramming.
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Affiliation(s)
- Zhen Fang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Ya-Jiao Zhu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Zhi-Gang Qian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China.
| | - Xiao-Xia Xia
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China.
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18
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Das S, Basu T, Majumdar S. Electrostatic-Dominated Conformational Fluctuations and Transition States of Phase Separation in Charge-Balanced Protein Polymer. ACS Macro Lett 2024; 13:34-39. [PMID: 38109356 DOI: 10.1021/acsmacrolett.3c00625] [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: 12/20/2023]
Abstract
Hydration of the protein/polymer is the most important aspect of stability. It is well-known that salts alter the charged polymer's electrostatic forces, ultimately impacting its conformations in solution. The solvent effects lead to certain conformational fluctuations. Previous studies have shown the screening of electrostatic repulsion within the charge-imbalanced protein following charge inversion owing to counterion condensation and phase separation. This article studies conformation stability and phase separation of charge-balanced gelatin (a protein polymer at the isoelectric point) with the addition of different salts. A phenomenon has been reported where the electrostatic effect of salts results in conformational fluctuations in gelatin due to its insufficient hydrations (termed as starvation), which scales with salt concentration. This article also presents different transition states for charge-balanced proteins prior to phase separation. It is concluded that phase separation of a charge-balanced protein passes through a stable state followed by an unstable transition state, where certain unique interactions with salts occur.
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Affiliation(s)
- Sougat Das
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad 502285, India
| | - Tithi Basu
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad 502285, India
| | - Saptarshi Majumdar
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad 502285, India
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19
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Zhang Y, Li S, Gong X, Chen J. Toward Accurate Simulation of Coupling between Protein Secondary Structure and Phase Separation. J Am Chem Soc 2024; 146:342-357. [PMID: 38112495 PMCID: PMC10842759 DOI: 10.1021/jacs.3c09195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Intrinsically disordered proteins (IDPs) frequently mediate phase separation that underlies the formation of a biomolecular condensate. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding the sequence-specific phase separation of IDPs. However, the widely used Cα-only models are limited in capturing the peptide nature of IDPs, particularly backbone-mediated interactions and effects of secondary structures, in phase separation. Here, we describe a hybrid resolution (HyRes) protein model toward a more accurate description of the backbone and transient secondary structures in phase separation. With an atomistic backbone and coarse-grained side chains, HyRes can semiquantitatively capture the residue helical propensity and overall chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for the direct simulation of spontaneous phase separation and, at the same time, appears accurate enough to resolve the effects of single His to Lys mutations. HyRes simulations also successfully predict increased β-structure formation in the condensate, consistent with available experimental CD data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate the phase separation propensity as measured by the saturation concentration. The simulations successfully recapitulate the effect of these mutants on the helicity and phase separation propensity of TDP-43 CR. Analyses reveal that the balance between backbone and side chain-mediated interactions, but not helicity itself, actually determines phase separation propensity. These results support that HyRes represents an effective protein model for molecular simulation of IDP phase separation and will help to elucidate the coupling between transient secondary structures and phase separation.
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Affiliation(s)
| | | | - Xiping Gong
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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20
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Gao G, Sumrall ES, Pitchiaya S, Bitzer M, Alberti S, Walter NG. Biomolecular condensates in kidney physiology and disease. Nat Rev Nephrol 2023; 19:756-770. [PMID: 37752323 DOI: 10.1038/s41581-023-00767-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2023] [Indexed: 09/28/2023]
Abstract
The regulation and preservation of distinct intracellular and extracellular solute microenvironments is crucial for the maintenance of cellular homeostasis. In mammals, the kidneys control bodily salt and water homeostasis. Specifically, the urine-concentrating mechanism within the renal medulla causes fluctuations in extracellular osmolarity, which enables cells of the kidney to either conserve or eliminate water and electrolytes, depending on the balance between intake and loss. However, relatively little is known about the subcellular and molecular changes caused by such osmotic stresses. Advances have shown that many cells, including those of the kidney, rapidly (within seconds) and reversibly (within minutes) assemble membraneless, nano-to-microscale subcellular assemblies termed biomolecular condensates via the biophysical process of hyperosmotic phase separation (HOPS). Mechanistically, osmotic cell compression mediates changes in intracellular hydration, concentration and molecular crowding, rendering HOPS one of many related phase-separation phenomena. Osmotic stress causes numerous homo-multimeric proteins to condense, thereby affecting gene expression and cell survival. HOPS rapidly regulates specific cellular biochemical processes before appropriate protective or corrective action by broader stress response mechanisms can be initiated. Here, we broadly survey emerging evidence for, and the impact of, biomolecular condensates in nephrology, where initial concentration buffering by HOPS and its subsequent cellular escalation mechanisms are expected to have important implications for kidney physiology and disease.
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Affiliation(s)
- Guoming Gao
- Biophysics Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | - Emily S Sumrall
- Biophysics Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Markus Bitzer
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Simon Alberti
- Technische Universität Dresden, Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Engineering (CMCB), Dresden, Germany
| | - Nils G Walter
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA.
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21
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Suyama K, Murashima M, Maeda I, Nose T. Enhancement of Aggregate Formation Through Aromatic Compound Adsorption in Elastin-like Peptide (FPGVG) 5 Analogs. Biomacromolecules 2023; 24:5265-5276. [PMID: 37865930 DOI: 10.1021/acs.biomac.3c00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Elastin-like peptides (ELPs) exhibit temperature-dependent reversible self-assembly. Repetitive sequences derived from elastin, such as Val-Pro-Gly-Val-Gly (VPGVG), are essential for the self-assembly of ELPs. Previously, we developed (FPGVG)5 (F5), in which the first valine residue in the VPGVG sequence was replaced with phenylalanine, which showed strong self-aggregation ability. This suggests that interactions through the aromatic amino acid residues of ELPs could play an important role in self-assembly. In this study, we investigated the thermoresponsive behavior of F5 analogs in the presence of aromatic compounds. Turbidimetry, spectroscopy, and fluorescence measurements demonstrated that aromatic compounds interacted with F5 analogs below the transition temperature and enhanced the self-assembly ability of ELPs by stabilizing amyloid-like structures. Furthermore, quantitative high-performance liquid chromatography analyses showed that the F5 analogs could adsorb and remove hydrophobic aromatic compounds from aqueous solutions during aggregate formation. These results suggested that the F5 analogs can be applicable as scavengers of aromatic compounds.
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Affiliation(s)
- Keitaro Suyama
- Faculty of Arts and Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Masayuki Murashima
- Department of Chemistry, Faculty and Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Iori Maeda
- Department of Physics and Information Technology, Kyushu Institute of Technology, Iizuka 820-8502, Fukuoka, Japan
| | - Takeru Nose
- Faculty of Arts and Science, Kyushu University, Fukuoka 819-0395, Japan
- Department of Chemistry, Faculty and Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
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22
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Wang SH, Zheng T, Fawzi NL. Structure and position-specific interactions of prion-like domains in transcription factor Efg1 phase separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566450. [PMID: 37986834 PMCID: PMC10659382 DOI: 10.1101/2023.11.09.566450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Candida albicans, a prominent member of the human microbiome, can make an opportunistic switch from commensal coexistence to pathogenicity accompanied by an epigenetic shift between the white and opaque cell states. This transcriptional switch is under precise regulation by a set of transcription factors (TFs), with Enhanced Filamentous Growth Protein 1 (Efg1) playing a central role. Previous research has emphasized the importance of Egf1's prion-like domain (PrLD) and the protein's ability to undergo phase separation for the white-to-opaque transition of C. albicans. However, the underlying molecular mechanisms of Efg1 phase separation have remained underexplored. In this study, we delved into the biophysical basis of Efg1 phase separation, revealing the significant contribution of both N-terminal (N) and C-terminal (C) PrLDs. Through NMR structural analysis, we found that Efg1 N-PrLD and C-PrLD are mostly disordered though have prominent partial α-helical secondary structures in both domains. NMR titration experiments suggest that the partially helical structures in N-PrLD act as hubs for self-interaction as well as Efg1 interaction with RNA. Using condensed-phase NMR spectroscopy, we uncovered diverse amino acid interactions underlying Efg1 phase separation. Particularly, we highlight the indispensable role of tyrosine residues within the transient α-helical structures of PrLDs particularly in the N-PrLD compared to the C-PrLD in stabilizing phase separation. Our study provides evidence that the transient α-helical structure is present in the phase separated state and highlights the particular importance of aromatic residues within these structures for phase separation. Together, these results enhance the understanding of C. albicans TF interactions that lead to virulence and provide a crucial foundation for potential antifungal therapies targeting the transcriptional switch.
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Affiliation(s)
- Szu-Huan Wang
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence Rhode Island, 02912, USA
- These authors contributed equally to this work
| | - Tongyin Zheng
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence Rhode Island, 02912, USA
- These authors contributed equally to this work
| | - Nicolas L. Fawzi
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence Rhode Island, 02912, USA
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23
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Shukla VK, Heller GT, Hansen DF. Biomolecular NMR spectroscopy in the era of artificial intelligence. Structure 2023; 31:1360-1374. [PMID: 37848030 DOI: 10.1016/j.str.2023.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/19/2023]
Abstract
Biomolecular nuclear magnetic resonance (NMR) spectroscopy and artificial intelligence (AI) have a burgeoning synergy. Deep learning-based structural predictors have forever changed structural biology, yet these tools currently face limitations in accurately characterizing protein dynamics, allostery, and conformational heterogeneity. We begin by highlighting the unique abilities of biomolecular NMR spectroscopy to complement AI-based structural predictions toward addressing these knowledge gaps. We then highlight the direct integration of deep learning approaches into biomolecular NMR methods. AI-based tools can dramatically improve the acquisition and analysis of NMR spectra, enhancing the accuracy and reliability of NMR measurements, thus streamlining experimental processes. Additionally, deep learning enables the development of novel types of NMR experiments that were previously unattainable, expanding the scope and potential of biomolecular NMR spectroscopy. Ultimately, a combination of AI and NMR promises to further revolutionize structural biology on several levels, advance our understanding of complex biomolecular systems, and accelerate drug discovery efforts.
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Affiliation(s)
- Vaibhav Kumar Shukla
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Gabriella T Heller
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK.
| | - D Flemming Hansen
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK.
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24
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de Souza JP, Stone HA. Protein condensation regulates water availability in cells. Nature 2023; 623:698-699. [PMID: 37853191 DOI: 10.1038/d41586-023-03098-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
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25
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Gallo R, Rai AK, McIntyre ABR, Meyer K, Pelkmans L. DYRK3 enables secretory trafficking by maintaining the liquid-like state of ER exit sites. Dev Cell 2023; 58:1880-1897.e11. [PMID: 37643612 DOI: 10.1016/j.devcel.2023.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/16/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023]
Abstract
The dual-specificity kinase DYRK3 controls the formation and dissolution of multiple biomolecular condensates, regulating processes including stress recovery and mitotic progression. Here, we report that DYRK3 functionally interacts with proteins associated with endoplasmic reticulum (ER) exit sites (ERESs) and that inhibition of DYRK3 perturbs the organization of the ERES-Golgi interface and secretory trafficking. DYRK3-mediated regulation of ERES depends on the N-terminal intrinsically disordered region (IDR) of the peripheral membrane protein SEC16A, which co-phase separates with ERES components to form liquid-like condensates on the surface of the ER. By modulating the liquid-like properties of ERES, we show that their physical state is essential for functional cargo trafficking through the early secretory pathway. Our findings support a mechanism whereby phosphorylation by DYRK3 and its reversal by serine-threonine phosphatases regulate the material properties of ERES to create a favorable physicochemical environment for directional membrane traffic in eukaryotic cells.
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Affiliation(s)
- Raffaella Gallo
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Arpan Kumar Rai
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland.
| | - Alexa B R McIntyre
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Katrina Meyer
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland.
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26
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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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27
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Hazra M, Levy Y. Cross-Talk of Cation-π Interactions with Electrostatic and Aromatic Interactions: A Salt-Dependent Trade-off in Biomolecular Condensates. J Phys Chem Lett 2023; 14:8460-8469. [PMID: 37721444 PMCID: PMC10544028 DOI: 10.1021/acs.jpclett.3c01642] [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: 06/15/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
Biomolecular condensates are essential for cellular functionality, yet the complex interplay among the diverse molecular interactions that mediate their formation remains poorly understood. Here, using coarse-grained molecular dynamics simulations, we address the contribution of cation-π interactions to the stability of condensates formed via liquid-liquid phase separation. We found greater stabilization of up to 80% via cation-π interactions in condensates formed from peptides with higher aromatic residue content or less charge clustering. The contribution of cation-π interactions to droplet stability increases with increasing ionic strength, suggesting a trade-off between cation-π and electrostatic interactions. Cation-π interactions, therefore, can compensate for reduced electrostatic interactions, such as occurs at higher salt concentrations and in sequences with less charged residue content or clustering. Designing condensates with desired biophysical characteristics therefore requires quantification not only of the individual interactions but also cross-talks involving charge-charge, π-π, and cation-π interactions.
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Affiliation(s)
- Milan
Kumar Hazra
- Department of Chemical and
Structural Biology, Weizmann Institute of
Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Chemical and
Structural Biology, Weizmann Institute of
Science, Rehovot 76100, Israel
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28
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Lipiński WP, Zehnder J, Abbas M, Güntert P, Spruijt E, Wiegand T. Fibrils Emerging from Droplets: Molecular Guiding Principles behind Phase Transitions of a Short Peptide-Based Condensate Studied by Solid-State NMR. Chemistry 2023; 29:e202301159. [PMID: 37310801 DOI: 10.1002/chem.202301159] [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: 04/12/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/15/2023]
Abstract
Biochemical reactions occurring in highly crowded cellular environments require different means of control to ensure productivity and specificity. Compartmentalization of reagents by liquid-liquid phase separation is one of these means. However, extremely high local protein concentrations of up to 400 mg/ml can result in pathological aggregation into fibrillar amyloid structures, a phenomenon that has been linked to various neurodegenerative diseases. Despite its relevance, the process of liquid-to-solid transition inside condensates is still not well understood at the molecular level. We thus herein use small peptide derivatives that can undergo both liquid-liquid and subsequent liquid-to-solid phase transition as model systems to study both processes. Using solid-state nuclear magnetic resonance (NMR) and transmission electron microscopy (TEM), we compare the structure of condensed states of leucine, tryptophan and phenylalanine containing derivatives, distinguishing between liquid-like condensates, amorphous aggregates and fibrils, respectively. A structural model for the fibrils formed by the phenylalanine derivative was obtained by an NMR-based structure calculation. The fibrils are stabilised by hydrogen bonds and side-chain π-π interactions, which are likely much less pronounced or absent in the liquid and amorphous state. Such noncovalent interactions are equally important for the liquid-to-solid transition of proteins, particularly those related to neurodegenerative diseases.
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Affiliation(s)
- Wojciech P Lipiński
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Johannes Zehnder
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Manzar Abbas
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Peter Güntert
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
- Institute of Biophysical Chemistry Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji-shi, 192-0397, Tokyo, Japan
| | - Evan Spruijt
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Thomas Wiegand
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
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29
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Zhang Y, Li S, Gong X, Chen J. Accurate Simulation of Coupling between Protein Secondary Structure and Liquid-Liquid Phase Separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554378. [PMID: 37662293 PMCID: PMC10473686 DOI: 10.1101/2023.08.22.554378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Intrinsically disordered proteins (IDPs) frequently mediate liquid-liquid phase separation (LLPS) that underlies the formation of membraneless organelles. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding sequence-specific phase separation of IDPs. However, the widely-used Cα-only models are severely limited in capturing the peptide nature of IDPs, including backbone-mediated interactions and effects of secondary structures, in LLPS. Here, we describe a hybrid resolution (HyRes) protein model for accurate description of the backbone and transient secondary structures in LLPS. With an atomistic backbone and coarse-grained side chains, HyRes accurately predicts the residue helical propensity and chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for direct simulation of spontaneous phase separation, and at the same time accurate enough to resolve the effects of single mutations. HyRes simulations also successfully predict increased beta-sheet formation in the condensate, consistent with available experimental data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate LLPS propensity. The simulations successfully recapitulate the effect of these mutants on the helicity and LLPS propensity of TDP-43 CR. Analyses reveal that the balance between backbone and sidechain-mediated interactions, but not helicity itself, actually determines LLPS propensity. We believe that the HyRes model represents an important advance in the molecular simulation of LLPS and will help elucidate the coupling between IDP transient secondary structures and phase separation.
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Affiliation(s)
| | | | - Xiping Gong
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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30
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Silva JL, Foguel D, Ferreira VF, Vieira TCRG, Marques MA, Ferretti GDS, Outeiro TF, Cordeiro Y, de Oliveira GAP. Targeting Biomolecular Condensation and Protein Aggregation against Cancer. Chem Rev 2023. [PMID: 37379327 DOI: 10.1021/acs.chemrev.3c00131] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Biomolecular condensates, membrane-less entities arising from liquid-liquid phase separation, hold dichotomous roles in health and disease. Alongside their physiological functions, these condensates can transition to a solid phase, producing amyloid-like structures implicated in degenerative diseases and cancer. This review thoroughly examines the dual nature of biomolecular condensates, spotlighting their role in cancer, particularly concerning the p53 tumor suppressor. Given that over half of the malignant tumors possess mutations in the TP53 gene, this topic carries profound implications for future cancer treatment strategies. Notably, p53 not only misfolds but also forms biomolecular condensates and aggregates analogous to other protein-based amyloids, thus significantly influencing cancer progression through loss-of-function, negative dominance, and gain-of-function pathways. The exact molecular mechanisms underpinning the gain-of-function in mutant p53 remain elusive. However, cofactors like nucleic acids and glycosaminoglycans are known to be critical players in this intersection between diseases. Importantly, we reveal that molecules capable of inhibiting mutant p53 aggregation can curtail tumor proliferation and migration. Hence, targeting phase transitions to solid-like amorphous and amyloid-like states of mutant p53 offers a promising direction for innovative cancer diagnostics and therapeutics.
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Affiliation(s)
- Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Debora Foguel
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Vitor F Ferreira
- Faculty of Pharmacy, Fluminense Federal University (UFF), Rio de Janeiro, RJ 21941-902, Brazil
| | - Tuane C R G Vieira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Mayra A Marques
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Giulia D S Ferretti
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center, 37075 Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne NE2 4HH, U.K
- Scientific employee with an honorary contract at Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 37075 Göttingen, Germany
| | - Yraima Cordeiro
- Faculty of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
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31
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Guo C, Alfaro-Aco R, Zhang C, Russell RW, Petry S, Polenova T. Structural basis of protein condensation on microtubules underlying branching microtubule nucleation. Nat Commun 2023; 14:3682. [PMID: 37344496 PMCID: PMC10284871 DOI: 10.1038/s41467-023-39176-z] [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: 09/13/2022] [Accepted: 06/01/2023] [Indexed: 06/23/2023] Open
Abstract
Targeting protein for Xklp2 (TPX2) is a key factor that stimulates branching microtubule nucleation during cell division. Upon binding to microtubules (MTs), TPX2 forms condensates via liquid-liquid phase separation, which facilitates recruitment of microtubule nucleation factors and tubulin. We report the structure of the TPX2 C-terminal minimal active domain (TPX2α5-α7) on the microtubule lattice determined by magic-angle-spinning NMR. We demonstrate that TPX2α5-α7 forms a co-condensate with soluble tubulin on microtubules and binds to MTs between two adjacent protofilaments and at the intersection of four tubulin heterodimers. These interactions stabilize the microtubules and promote the recruitment of tubulin. Our results reveal that TPX2α5-α7 is disordered in solution and adopts a folded structure on MTs, indicating that TPX2α5-α7 undergoes structural changes from unfolded to folded states upon binding to microtubules. The aromatic residues form dense interactions in the core, which stabilize folding of TPX2α5-α7 on microtubules. This work informs on how the phase-separated TPX2α5-α7 behaves on microtubules and represents an atomic-level structural characterization of a protein that is involved in a condensate on cytoskeletal filaments.
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Affiliation(s)
- Changmiao Guo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Raymundo Alfaro-Aco
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Chunting Zhang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Ryan W Russell
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Sabine Petry
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
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32
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Rangachari V. Biomolecular condensates - extant relics or evolving microcompartments? Commun Biol 2023; 6:656. [PMID: 37344557 PMCID: PMC10284869 DOI: 10.1038/s42003-023-04963-3] [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: 03/13/2023] [Accepted: 05/22/2023] [Indexed: 06/23/2023] Open
Abstract
Unprecedented discoveries during the past decade have unearthed the ubiquitous presence of biomolecular condensates (BCs) in diverse organisms and their involvement in a plethora of biological functions. A predominant number of BCs involve coacervation of RNA and proteins that demix from homogenous solutions by a process of phase separation well described by liquid-liquid phase separation (LLPS), which results in a phase with higher concentration and density from the bulk solution. BCs provide a simple and effective means to achieve reversible spatiotemporal control of cellular processes and adaptation to environmental stimuli in an energy-independent manner. The journey into the past of this phenomenon provides clues to the evolutionary origins of life itself. Here I assemble some current and historic discoveries on LLPS to contemplate whether BCs are extant biological hubs or evolving microcompartments. I conclude that BCs in biology could be extant as a phenomenon but are co-evolving as functionally and compositionally complex microcompartments in cells alongside the membrane-bound organelles.
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Affiliation(s)
- Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences and Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS, 39402, USA.
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33
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Guseva S, Schnapka V, Adamski W, Maurin D, Ruigrok RWH, Salvi N, Blackledge M. Liquid-Liquid Phase Separation Modifies the Dynamic Properties of Intrinsically Disordered Proteins. J Am Chem Soc 2023; 145:10548-10563. [PMID: 37146977 DOI: 10.1021/jacs.2c13647] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Liquid-liquid phase separation of flexible biomolecules has been identified as a ubiquitous phenomenon underlying the formation of membraneless organelles that harbor a multitude of essential cellular processes. We use nuclear magnetic resonance (NMR) spectroscopy to compare the dynamic properties of an intrinsically disordered protein (measles virus NTAIL) in the dilute and dense phases at atomic resolution. By measuring 15N NMR relaxation at different magnetic field strengths, we are able to characterize the dynamics of the protein in dilute and crowded conditions and to compare the amplitude and timescale of the different motional modes to those present in the membraneless organelle. Although the local backbone conformational sampling appears to be largely retained, dynamics occurring on all detectable timescales, including librational, backbone dihedral angle dynamics and segmental, chainlike motions, are considerably slowed down. Their relative amplitudes are also drastically modified, with slower, chain-like motions dominating the dynamic profile. In order to provide additional mechanistic insight, we performed extensive molecular dynamics simulations of the protein under self-crowding conditions at concentrations comparable to those found in the dense liquid phase. Simulation broadly reproduces the impact of formation of the condensed phase on both the free energy landscape and the kinetic interconversion between states. In particular, the experimentally observed reduction in the amplitude of the fastest component of backbone dynamics correlates with higher levels of intermolecular contacts or entanglement observed in simulations, reducing the conformational space available to this mode under strongly self-crowding conditions.
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Affiliation(s)
- Serafima Guseva
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Vincent Schnapka
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Wiktor Adamski
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Damien Maurin
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Rob W H Ruigrok
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Nicola Salvi
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Martin Blackledge
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
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34
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Miserez A, Yu J, Mohammadi P. Protein-Based Biological Materials: Molecular Design and Artificial Production. Chem Rev 2023; 123:2049-2111. [PMID: 36692900 PMCID: PMC9999432 DOI: 10.1021/acs.chemrev.2c00621] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Polymeric materials produced from fossil fuels have been intimately linked to the development of industrial activities in the 20th century and, consequently, to the transformation of our way of living. While this has brought many benefits, the fabrication and disposal of these materials is bringing enormous sustainable challenges. Thus, materials that are produced in a more sustainable fashion and whose degradation products are harmless to the environment are urgently needed. Natural biopolymers─which can compete with and sometimes surpass the performance of synthetic polymers─provide a great source of inspiration. They are made of natural chemicals, under benign environmental conditions, and their degradation products are harmless. Before these materials can be synthetically replicated, it is essential to elucidate their chemical design and biofabrication. For protein-based materials, this means obtaining the complete sequences of the proteinaceous building blocks, a task that historically took decades of research. Thus, we start this review with a historical perspective on early efforts to obtain the primary sequences of load-bearing proteins, followed by the latest developments in sequencing and proteomic technologies that have greatly accelerated sequencing of extracellular proteins. Next, four main classes of protein materials are presented, namely fibrous materials, bioelastomers exhibiting high reversible deformability, hard bulk materials, and biological adhesives. In each class, we focus on the design at the primary and secondary structure levels and discuss their interplays with the mechanical response. We finally discuss earlier and the latest research to artificially produce protein-based materials using biotechnology and synthetic biology, including current developments by start-up companies to scale-up the production of proteinaceous materials in an economically viable manner.
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Affiliation(s)
- Ali Miserez
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore637553.,School of Biological Sciences, NTU, Singapore637551
| | - Jing Yu
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore637553.,Institute for Digital Molecular Analytics and Science (IDMxS), NTU, 50 Nanyang Avenue, Singapore637553
| | - Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd., Espoo, UusimaaFI-02044, Finland
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35
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Morozova TI, García NA, Matsarskaia O, Roosen-Runge F, Barrat JL. Structural and Dynamical Properties of Elastin-Like Peptides near Their Lower Critical Solution Temperature. Biomacromolecules 2023; 24:1912-1923. [PMID: 36877869 DOI: 10.1021/acs.biomac.3c00124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Elastin-like peptides (ELPs) are artificially derived intrinsically disordered proteins (IDPs) mimicking the hydrophobic repeat unit in the protein elastin. ELPs are characterized by a lower critical solution temperature (LCST) in aqueous media. Here, we investigate the sequence GVG(VPGVG)3 over a wide range of temperatures (below, around, and above the LCST) and peptide concentrations employing all-atom molecular dynamics simulations, where we focus on the role of intra- and interpeptide interactions. We begin by investigating the structural properties of a single peptide that demonstrates a hydrophobic collapse with temperature, albeit moderate, because the sequence length is short. We observe a change in the interaction between two peptides from repulsive to attractive with temperature by evaluating the potential of mean force, indicating an LCST-like behavior. Next, we explore dynamical and structural properties of peptides in multichain systems. We report the formation of dynamical aggregates with coil-like conformation, in which valine central residues play an important role. Moreover, the lifetime of contacts between chains strongly depends on the temperature and can be described by a power-law decay that is consistent with the LCST-like behavior. Finally, the peptide translational and internal motion are slowed by an increase in the peptide concentration and temperature.
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Affiliation(s)
| | - Nicolás A García
- Instituto de Física del Sur (IFISUR), Departamento de Física, Universidad Nacional del Sur (UNS), CONICET, Av. L. N. Alem 1253, B8000CPB Bahía Blanca, Argentina
| | - Olga Matsarskaia
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Felix Roosen-Runge
- Department of Biomedical Science and Biofilms Research Center for Biointerfaces (BRCB), Malmö University, 20506 Malmö, Sweden
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36
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Mabuchi T, Kijima J, Yamashita Y, Miura E, Muraoka T. Coacervate Formation of Elastin-like Polypeptides in Explicit Aqueous Solution Using Coarse-Grained Molecular Dynamics Simulations. Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c02195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Takuya Mabuchi
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 2-1-1 Katahira,
Aoba-ku, Sendai, Miyagi980-8577, Japan
- Institute of Fluid Science, Tohoku University, 2-1-1 Katahira,
Aoba-ku, Sendai, Miyagi980-8577, Japan
| | - Junko Kijima
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 2-1-1 Katahira,
Aoba-ku, Sendai, Miyagi980-8577, Japan
| | - Yukino Yamashita
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho,
Koganei, Tokyo184-8588, Japan
| | - Erika Miura
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho,
Koganei, Tokyo184-8588, Japan
| | - Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho,
Koganei, Tokyo184-8588, Japan
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Hasenahuer MA, Sanchis-Juan A, Laskowski RA, Baker JA, Stephenson JD, Orengo CA, Raymond FL, Thornton JM. Mapping the Constrained Coding Regions in the Human Genome to Their Corresponding Proteins. J Mol Biol 2023; 435:167892. [PMID: 36410474 PMCID: PMC9875310 DOI: 10.1016/j.jmb.2022.167892] [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: 09/10/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022]
Abstract
Constrained Coding Regions (CCRs) in the human genome have been derived from DNA sequencing data of large cohorts of healthy control populations, available in the Genome Aggregation Database (gnomAD) [1]. They identify regions depleted of protein-changing variants and thus identify segments of the genome that have been constrained during human evolution. By mapping these DNA-defined regions from genomic coordinates onto the corresponding protein positions and combining this information with protein annotations, we have explored the distribution of CCRs and compared their co-occurrence with different protein functional features, previously annotated at the amino acid level in public databases. As expected, our results reveal that functional amino acids involved in interactions with DNA/RNA, protein-protein contacts and catalytic sites are the protein features most likely to be highly constrained for variation in the control population. More surprisingly, we also found that linear motifs, linear interacting peptides (LIPs), disorder-order transitions upon binding with other protein partners and liquid-liquid phase separating (LLPS) regions are also strongly associated with high constraint for variability. We also compared intra-species constraints in the human CCRs with inter-species conservation and functional residues to explore how such CCRs may contribute to the analysis of protein variants. As has been previously observed, CCRs are only weakly correlated with conservation, suggesting that intraspecies constraints complement interspecies conservation and can provide more information to interpret variant effects.
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Affiliation(s)
- Marcia A. Hasenahuer
- European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK,Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK,Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK,Corresponding author at: European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK. @MarHasenahuer
| | - Alba Sanchis-Juan
- Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge CB2 0XY, UK,NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Roman A. Laskowski
- European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - James A. Baker
- European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - James D. Stephenson
- European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Christine A. Orengo
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - F. Lucy Raymond
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK,NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Janet M. Thornton
- European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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Zhang M, Xue B, Li Q, Shi R, Cao Y, Wang W, Li J. Sequence Tendency for the Interaction between Low-Complexity Intrinsically Disordered Proteins. JACS AU 2023; 3:93-104. [PMID: 36711093 PMCID: PMC9875249 DOI: 10.1021/jacsau.2c00414] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 06/18/2023]
Abstract
Reversible interaction between intrinsically disordered proteins (IDPs) is considered as the driving force for liquid-liquid phase separation (LLPS), while the detailed description of such a transient interaction process still remains a challenge. And the mechanisms underlying the behavior of IDP interaction, for example, the possible relationship with its inherent conformational fluctuations and sequence features, remain elusive. Here, we use atomistic molecular dynamics (MD) simulation to investigate the reversible association of the LAF-1 RGG domain, the IDP with ultra-low LLPS concentration (0.06 mM). We find that the duration of the association between two RGG domains is highly heterogeneous, and the sustained associations essentially dominate the IDP interaction. More interestingly, such sustained associations are mediated by a finite region, that is, the C-terminal region 138-168 (denoted as a contact-prone region). We noticed that such sequence tendency is attributed to the extended conformation of the RGG domain during its inherent conformational fluctuations. Hence, our results suggest that there is a certain region in this low-complexity IDP which can essentially dominate their interaction and should be also important to the LLPS. And the inherent conformational fluctuations are actually essential for the emergence of such a hot region of IDP interaction. The importance of this hot region to LLPS is verified by experiment.
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Affiliation(s)
- Moxin Zhang
- Zhejiang
Province Key Laboratory of Quantum Technology and Device, School of
Physics, Zhejiang University, Hangzhou310058, China
| | - Bin Xue
- Collaborative
Innovation Center of Advanced Microstructures, National Laboratory
of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing210093, China
| | - Qingtai Li
- Collaborative
Innovation Center of Advanced Microstructures, National Laboratory
of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing210093, China
| | - Rui Shi
- Zhejiang
Province Key Laboratory of Quantum Technology and Device, School of
Physics, Zhejiang University, Hangzhou310058, China
| | - Yi Cao
- Collaborative
Innovation Center of Advanced Microstructures, National Laboratory
of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing210093, China
| | - Wei Wang
- Collaborative
Innovation Center of Advanced Microstructures, National Laboratory
of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing210093, China
| | - Jingyuan Li
- Zhejiang
Province Key Laboratory of Quantum Technology and Device, School of
Physics, Zhejiang University, Hangzhou310058, China
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39
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López
Barreiro D, Folch-Fortuny A, Muntz I, Thies JC, Sagt CM, Koenderink GH. Sequence Control of the Self-Assembly of Elastin-Like Polypeptides into Hydrogels with Bespoke Viscoelastic and Structural Properties. Biomacromolecules 2023; 24:489-501. [PMID: 36516874 PMCID: PMC9832484 DOI: 10.1021/acs.biomac.2c01405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The biofabrication of structural proteins with controllable properties via amino acid sequence design is interesting for biomedicine and biotechnology, yet a complete framework that connects amino acid sequence to material properties is unavailable, despite great progress to establish design rules for synthesizing peptides and proteins with specific conformations (e.g., unfolded, helical, β-sheets, or β-turns) and intermolecular interactions (e.g., amphipathic peptides or hydrophobic domains). Molecular dynamics (MD) simulations can help in developing such a framework, but the lack of a standardized way of interpreting the outcome of these simulations hinders their predictive value for the design of de novo structural proteins. To address this, we developed a model that unambiguously classifies a library of de novo elastin-like polypeptides (ELPs) with varying numbers and locations of hydrophobic/hydrophilic and physical/chemical-cross-linking blocks according to their thermoresponsiveness at physiological temperature. Our approach does not require long simulation times or advanced sampling methods. Instead, we apply (un)supervised data analysis methods to a data set of molecular properties from relatively short MD simulations (150 ns). We also experimentally investigate hydrogels of those ELPs from the library predicted to be thermoresponsive, revealing several handles to tune their mechanical and structural properties: chain hydrophilicity/hydrophobicity or block distribution control the viscoelasticity and thermoresponsiveness, whereas ELP concentration defines the network permeability. Our findings provide an avenue to accelerate the design of de novo ELPs with bespoke phase behavior and material properties.
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Affiliation(s)
- Diego López
Barreiro
- DSM
Biosciences and Process Innovation, DSM, Alexander Fleminglaan 1, 2613 AXDelft, The Netherlands
| | - Abel Folch-Fortuny
- DSM
Biodata and Translation, DSM, Alexander Fleminglaan 1, 2613 AXDelft, The Netherlands
| | - Iain Muntz
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZDelft, The Netherlands
| | - Jens C. Thies
- DSM
Biomedical, DSM, Urmonderbaan
22, 6160 BB, Geleen, The Netherlands,E-mail:
| | - Cees M.J. Sagt
- DSM
Biosciences and Process Innovation, DSM, Alexander Fleminglaan 1, 2613 AXDelft, The Netherlands,E-mail:
| | - Gijsje H. Koenderink
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZDelft, The Netherlands,E-mail:
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40
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Ginell GM, Holehouse AS. An Introduction to the Stickers-and-Spacers Framework as Applied to Biomolecular Condensates. Methods Mol Biol 2023; 2563:95-116. [PMID: 36227469 DOI: 10.1007/978-1-0716-2663-4_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Cellular organization is determined by a combination of membrane-bound and membrane-less biomolecular assemblies that range from clusters of tens of molecules to micrometer-sized cellular bodies. Over the last decade, membrane-less assemblies have come to be referred to as biomolecular condensates, reflecting their ability to condense specific molecules with respect to the remainder of the cell. In many cases, the physics of phase transitions provides a conceptual framework and a mathematical toolkit to describe the assembly, maintenance, and dissolution of biomolecular condensates. Among the various quantitative and qualitative models applied to understand intracellular phase transitions, the stickers-and-spacers framework offers an intuitive yet rigorous means to map biomolecular sequences and structure to the driving forces needed for higher-order assembly. This chapter introduces the fundamental concepts behind the stickers-and-spacers model, considers its application to different biological systems, and discusses limitations and misconceptions around the model.
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Affiliation(s)
- Garrett M Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA.
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41
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Tibble RW, Gross JD. A call to order: Examining structured domains in biomolecular condensates. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 346:107318. [PMID: 36657879 PMCID: PMC10878105 DOI: 10.1016/j.jmr.2022.107318] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/20/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
Diverse cellular processes have been observed or predicted to occur in biomolecular condensates, which are comprised of proteins and nucleic acids that undergo liquid-liquid phase separation (LLPS). Protein-driven LLPS often involves weak, multivalent interactions between intrinsically disordered regions (IDRs). Due to their inherent lack of defined tertiary structures, NMR has been a powerful resource for studying the behavior and interactions of IDRs in condensates. While IDRs in proteins are necessary for phase separation, core proteins enriched in condensates often contain structured domains that are essential for their function and contribute to phase separation. How phase separation can affect the structure and conformational dynamics of structured domains is critical for understanding how biochemical reactions can be effectively regulated in cellular condensates. In this perspective, we discuss the consequences phase separation can have on structured domains and outline NMR observables we believe are useful for assessing protein structure and dynamics in condensates.
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Affiliation(s)
- Ryan W Tibble
- Program in Chemistry and Chemical Biology, University of California, San Francisco, United States; Department of Pharmaceutical Chemistry, University of California, San Francisco, United States
| | - John D Gross
- Program in Chemistry and Chemical Biology, University of California, San Francisco, United States; Department of Pharmaceutical Chemistry, University of California, San Francisco, United States.
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42
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Otis JB, Sharpe S. Sequence Context and Complex Hofmeister Salt Interactions Dictate Phase Separation Propensity of Resilin-like Polypeptides. Biomacromolecules 2022; 23:5225-5238. [PMID: 36378745 DOI: 10.1021/acs.biomac.2c01027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Resilin is an elastic material found in insects with exceptional durability, resilience, and extensibility, making it a promising biomaterial for tissue engineering. The monomeric precursor, pro-resilin, undergoes thermo-responsive self-assembly through liquid-liquid phase separation (LLPS). Understanding the molecular details of this assembly process is critical to developing complex biomaterials. The present study investigates the interplay between the solvent, sequence syntax, structure, and dynamics in promoting LLPS of resilin-like-polypeptides (RLPs) derived from domains 1 and 3 of Drosophila melanogaster pro-resilin. NMR, UV-vis, and microscopy data demonstrate that while kosmotropic salts and low pH promote LLPS, the effects of chaotropic salts with increasing pH are more complex. Subtle variations between the repeating amino acid motifs of resilin domain 1 and domain 3 lead to significantly different salt and pH dependence of LLPS, with domain 3 sequence motifs more strongly favoring phase separation under most conditions. These findings provide new insight into the molecular drivers of RLP phase separation and the complex roles of both RLP sequence and solution composition in fine-tuning assembly conditions.
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Affiliation(s)
- James Brandt Otis
- Molecular Medicine, Hospital for Sick Children, 686 Bay St, Toronto, ONM5G 0A4, Canada.,Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ONM5S 1A8, Canada
| | - Simon Sharpe
- Molecular Medicine, Hospital for Sick Children, 686 Bay St, Toronto, ONM5G 0A4, Canada.,Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ONM5S 1A8, Canada
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43
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Latham AP, Zhang B. Molecular Determinants for the Layering and Coarsening of Biological Condensates. AGGREGATE (HOBOKEN, N.J.) 2022; 3:e306. [PMID: 37065433 PMCID: PMC10101022 DOI: 10.1002/agt2.306] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Many membraneless organelles, or biological condensates, form through phase separation, and play key roles in signal sensing and transcriptional regulation. While the functional importance of these condensates has inspired many studies to characterize their stability and spatial organization, the underlying principles that dictate these emergent properties are still being uncovered. In this review, we examine recent work on biological condensates, especially multicomponent systems. We focus on connecting molecular factors such as binding energy, valency, and stoichiometry with the interfacial tension, explaining the nontrivial interior organization in many condensates. We further discuss mechanisms that arrest condensate coalescence by lowering the surface tension or introducing kinetic barriers to stabilize the multidroplet state.
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Affiliation(s)
- Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94143
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139
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44
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Molecular and environmental determinants of biomolecular condensate formation. Nat Chem Biol 2022; 18:1319-1329. [DOI: 10.1038/s41589-022-01175-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 09/15/2022] [Indexed: 11/21/2022]
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45
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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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46
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Ren J, Zhang Z, Zong Z, Zhang L, Zhou F. Emerging Implications of Phase Separation in Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202855. [PMID: 36117111 PMCID: PMC9631093 DOI: 10.1002/advs.202202855] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/26/2022] [Indexed: 05/19/2023]
Abstract
In eukaryotic cells, biological activities are executed in distinct cellular compartments or organelles. Canonical organelles with membrane-bound structures are well understood. Cells also inherently contain versatile membrane-less organelles (MLOs) that feature liquid or gel-like bodies. A biophysical process termed liquid-liquid phase separation (LLPS) elucidates how MLOs form through dynamic biomolecule assembly. LLPS-related molecules often have multivalency, which is essential for low-affinity inter- or intra-molecule interactions to trigger phase separation. Accumulating evidence shows that LLPS concentrates and organizes desired molecules or segregates unneeded molecules in cells. Thus, MLOs have tunable functional specificity in response to environmental stimuli and metabolic processes. Aberrant LLPS is widely associated with several hallmarks of cancer, including sustained proliferative signaling, growth suppressor evasion, cell death resistance, telomere maintenance, DNA damage repair, etc. Insights into the molecular mechanisms of LLPS provide new insights into cancer therapeutics. Here, the current understanding of the emerging concepts of LLPS and its involvement in cancer are comprehensively reviewed.
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Affiliation(s)
- Jiang Ren
- School of MedicineZhejiang University City CollegeHangzhou215123China
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Zhenyu Zhang
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan450003China
| | - Zhi Zong
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Long Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
- International Biomed‐X Research Center, Second Affiliated Hospital of Zhejiang University School of MedicineZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhou215123China
| | - Fangfang Zhou
- School of MedicineZhejiang University City CollegeHangzhou215123China
- Institutes of Biology and Medical SciencesSoochow UniversitySuzhou215123China
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A simple thermodynamic description of phase separation of Nup98 FG domains. Nat Commun 2022; 13:6172. [PMID: 36257947 PMCID: PMC9579204 DOI: 10.1038/s41467-022-33697-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022] Open
Abstract
The permeability barrier of nuclear pore complexes (NPCs) controls nucleocytoplasmic transport. It retains inert macromolecules but allows facilitated passage of nuclear transport receptors that shuttle cargoes into or out of nuclei. The barrier can be described as a condensed phase assembled from cohesive FG repeat domains, including foremost the charge-depleted FG domain of Nup98. We found that Nup98 FG domains show an LCST-type phase separation, and we provide comprehensive and orthogonal experimental datasets for a quantitative description of this behaviour. A derived thermodynamic model correlates saturation concentration with repeat number, temperature, and ionic strength. It allows estimating the enthalpy, entropy, and ΔG (0.2 kJ/mol, 0.1 kB·T) contributions per repeat to phase separation and inter-repeat cohesion. While changing the cohesion strength strongly impacts the strictness of barrier, these numbers provide boundary conditions for in-depth modelling not only of barrier assembly but also of NPC passage.
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Vazquez DS, Toledo PL, Gianotti AR, Ermácora MR. Protein conformation and biomolecular condensates. Curr Res Struct Biol 2022; 4:285-307. [PMID: 36164646 PMCID: PMC9508354 DOI: 10.1016/j.crstbi.2022.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 10/27/2022] Open
Abstract
Protein conformation and cell compartmentalization are fundamental concepts and subjects of vast scientific endeavors. In the last two decades, we have witnessed exciting advances that unveiled the conjunction of these concepts. An avalanche of studies highlighted the central role of biomolecular condensates in membraneless subcellular compartmentalization that permits the spatiotemporal organization and regulation of myriads of simultaneous biochemical reactions and macromolecular interactions. These studies have also shown that biomolecular condensation, driven by multivalent intermolecular interactions, is mediated by order-disorder transitions of protein conformation and by protein domain architecture. Conceptually, protein condensation is a distinct level in protein conformational landscape in which collective folding of large collections of molecules takes place. Biomolecular condensates arise by the physical process of phase separation and comprise a variety of bodies ranging from membraneless organelles to liquid condensates to solid-like conglomerates, spanning lengths from mesoscopic clusters (nanometers) to micrometer-sized objects. In this review, we summarize and discuss recent work on the assembly, composition, conformation, material properties, thermodynamics, regulation, and functions of these bodies. We also review the conceptual framework for future studies on the conformational dynamics of condensed proteins in the regulation of cellular processes.
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Affiliation(s)
- Diego S. Vazquez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Pamela L. Toledo
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Alejo R. Gianotti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Mario R. Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
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Liquid to solid transition of elastin condensates. Proc Natl Acad Sci U S A 2022; 119:e2202240119. [PMID: 36067308 PMCID: PMC9477396 DOI: 10.1073/pnas.2202240119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Liquid-liquid phase separation of tropoelastin has long been considered to be an important early step in the complex process of elastin fiber assembly in the body and has inspired the development of elastin-like peptides with a wide range of industrial and biomedical applications. Despite decades of study, the material state of the condensed liquid phase of elastin and its subsequent maturation remain poorly understood. Here, using a model minielastin that mimics the alternating domain structure of full-length tropoelastin, we examine the elastin liquid phase. We combine differential interference contrast (DIC), fluorescence, and scanning electron microscopy with particle-tracking microrheology to resolve the material transition occurring within elastin liquids over time in the absence of exogenous cross-linking. We find that this transition is accompanied by an intermediate stage marked by the coexistence of insoluble solid and dynamic liquid phases giving rise to significant spatial heterogeneities in material properties. We further demonstrate that varying the length of the terminal hydrophobic domains of minielastins can tune the maturation process. This work not only resolves an important step in the hierarchical assembly process of elastogenesis but further contributes mechanistic insight into the diverse repertoire of protein condensate maturation pathways with emerging importance across biology.
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50
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Yu L, Brüschweiler R. Quantitative prediction of ensemble dynamics, shapes and contact propensities of intrinsically disordered proteins. PLoS Comput Biol 2022; 18:e1010036. [PMID: 36084124 PMCID: PMC9491582 DOI: 10.1371/journal.pcbi.1010036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/21/2022] [Accepted: 08/03/2022] [Indexed: 12/29/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are highly dynamic systems that play an important role in cell signaling processes and their misfunction often causes human disease. Proper understanding of IDP function not only requires the realistic characterization of their three-dimensional conformational ensembles at atomic-level resolution but also of the time scales of interconversion between their conformational substates. Large sets of experimental data are often used in combination with molecular modeling to restrain or bias models to improve agreement with experiment. It is shown here for the N-terminal transactivation domain of p53 (p53TAD) and Pup, which are two IDPs that fold upon binding to their targets, how the latest advancements in molecular dynamics (MD) simulations methodology produces native conformational ensembles by combining replica exchange with series of microsecond MD simulations. They closely reproduce experimental data at the global conformational ensemble level, in terms of the distribution properties of the radius of gyration tensor, and at the local level, in terms of NMR properties including 15N spin relaxation, without the need for reweighting. Further inspection revealed that 10-20% of the individual MD trajectories display the formation of secondary structures not observed in the experimental NMR data. The IDP ensembles were analyzed by graph theory to identify dominant inter-residue contact clusters and characteristic amino-acid contact propensities. These findings indicate that modern MD force fields with residue-specific backbone potentials can produce highly realistic IDP ensembles sampling a hierarchy of nano- and picosecond time scales providing new insights into their biological function.
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Affiliation(s)
- Lei Yu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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