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Wang F, Chen Z, Zhou Q, Sun Q, Zheng N, Chen Z, Lin J, Li B, Li L. Implications of liquid-liquid phase separation and ferroptosis in Alzheimer's disease. Neuropharmacology 2024; 259:110083. [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] [MESH Headings] [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, The Affiliated Dongguan Songshan Lake Central Hospital, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Zihao Chen
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, The Affiliated Dongguan Songshan Lake Central Hospital, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Qiong Zhou
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, The Affiliated Dongguan Songshan Lake Central Hospital, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Qiang Sun
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, The Affiliated Dongguan Songshan Lake Central Hospital, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Nan Zheng
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, The Affiliated Dongguan Songshan Lake Central Hospital, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Ziwen Chen
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, The Affiliated Dongguan Songshan Lake Central Hospital, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Jiantao Lin
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, The Affiliated Dongguan Songshan Lake Central Hospital, School of Pharmacy, Guangdong Medical University, Dongguan, China.
| | - Baohong Li
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, The Affiliated Dongguan Songshan Lake Central Hospital, School of Pharmacy, Guangdong Medical University, Dongguan, China.
| | - Li Li
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, The Affiliated Dongguan Songshan Lake Central Hospital, School of Pharmacy, Guangdong Medical University, Dongguan, China.
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2
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Oranges M, Jash C, Golani G, Seal M, Cohen SR, Rosenhek-Goldian I, Bogdanov A, Safran S, Goldfarb D. Core-shell model of the clusters of CPEB4 isoforms preceding liquid-liquid phase separation. Biophys J 2024; 123:2604-2622. [PMID: 38943248 PMCID: PMC11365225 DOI: 10.1016/j.bpj.2024.06.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/03/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024] Open
Abstract
Protein solutions can undergo liquid-liquid phase separation (LLPS), where a dispersed phase with a low protein concentration coexists with coacervates with a high protein concentration. We focus on the low complexity N-terminal domain of cytoplasmic polyadenylation element binding-4 protein, CPEB4NTD, and its isoform depleted of the Exon4, CPEB4Δ4NTD. They both exhibit LLPS, but in contrast to most systems undergoing LLPS, the single-phase regime preceding LLPS consists mainly of soluble protein clusters. We combine experimental and theoretical approaches to resolve the internal structure of the clusters and the basis for their formation. Dynamic light scattering and atomic force microscopy show that both isoforms exhibit clusters with diameters ranging from 35 to 80 nm. Electron paramagnetic resonance spectroscopy of spin-labeled CPEB4NTD and CPEB4Δ4NTD revealed that these proteins have two distinct dynamical properties in both the clusters and coacervates. Based on the experimental results, we propose a core-shell structure for the clusters, which is supported by the agreement of the dynamic light scattering data on cluster size distribution with a statistical model developed to describe the structure of clusters. This model treats clusters as swollen micelles (microemulsions) where the core and the shell regions comprise different protein conformations, in agreement with the electron paramagnetic resonance detection of two protein populations. The effects of ionic strength and the addition of 1,6-hexanediol were used to probe the interactions responsible for cluster formation. While both CPEB4NTD and CPEB4Δ4NTD showed phase separation with increasing temperature and formed clusters, differences were found in the properties of the clusters and the coacervates. The data also suggested that the coacervates may consist of aggregates of clusters.
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Affiliation(s)
- Maria Oranges
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Chandrima Jash
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Gonen Golani
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel; Department of Physics, University of Haifa, Haifa, Israel
| | - Manas Seal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Sidney R Cohen
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Irit Rosenhek-Goldian
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Alexey Bogdanov
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Samuel Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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3
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Qian D, Ausserwoger H, Sneideris T, Farag M, Pappu RV, Knowles TPJ. Dominance analysis to assess solute contributions to multicomponent phase equilibria. Proc Natl Acad Sci U S A 2024; 121:e2407453121. [PMID: 39102550 PMCID: PMC11331137 DOI: 10.1073/pnas.2407453121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 07/05/2024] [Indexed: 08/07/2024] Open
Abstract
Phase separation in aqueous solutions of macromolecules underlies the generation of biomolecular condensates in cells. Condensates are membraneless bodies, representing dense, macromolecule-rich phases that coexist with the dilute, macromolecule-deficient phases. In cells, condensates comprise hundreds of different macromolecular and small molecule solutes. How do different solutes contribute to the driving forces for phase separation? To answer this question, we introduce a formalism we term energy dominance analysis. This approach rests on analysis of shapes of the dilute phase boundaries, slopes of tie lines, and changes to dilute phase concentrations in response to perturbations of concentrations of different solutes. The framework is based solely on conditions for phase equilibria in systems with arbitrary numbers of macromolecules and solution components. Its practical application relies on being able to measure dilute phase concentrations of the components of interest. The dominance framework is both theoretically facile and experimentally applicable. We present the formalism that underlies dominance analysis and establish its accuracy and flexibility by deploying it to analyze phase diagrams probed in simulations and in experiments.
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Affiliation(s)
- Daoyuan Qian
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EWCambridge, United Kingdom
| | - Hannes Ausserwoger
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EWCambridge, United Kingdom
| | - Tomas Sneideris
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EWCambridge, United Kingdom
| | - Mina Farag
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO63130
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO63130
| | - Tuomas P. J. Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EWCambridge, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, CB3 0HECambridge, United Kingdom
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4
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Castelletto V, Seitsonen J, Pollitt A, Hamley IW. Minimal Peptide Sequences That Undergo Liquid-Liquid Phase Separation via Self-Coacervation or Complex Coacervation with ATP. Biomacromolecules 2024; 25:5321-5331. [PMID: 39066731 PMCID: PMC11323023 DOI: 10.1021/acs.biomac.4c00738] [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: 05/31/2024] [Revised: 07/23/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
The simple (self-)coacervation of the minimal tryptophan/arginine peptide sequences W2R2 and W3R3 was observed in salt-free aqueous solution. The phase diagrams were mapped using turbidimetry and optical microscopy, and the coacervate droplets were imaged using confocal microscopy complemented by cryo-TEM to image smaller droplets. The droplet size distribution and stability were probed using dynamic light scattering, and the droplet surface potential was obtained from zeta potential measurements. SAXS was used to elucidate the structure within the coacervate droplets, and circular dichroism spectroscopy was used to probe the conformation of the peptides, a characteristic signature for cation-π interactions being present under conditions of coacervation. These observations were rationalized using a simple model for the Rayleigh stability of charged coacervate droplets, along with atomistic molecular dynamics simulations which provide insight into stabilizing π-π stacking interactions of tryptophan as well as arginine-tryptophan cation-π interactions (which modulate the charge of the tryptophan π-electron system). Remarkably, the dipeptide WR did not show simple coacervation under the conditions examined, but complex coacervation was observed in mixtures with ATP (adenosine triphosphate). The electrostatically stabilized coacervation in this case provides a minimal model for peptide/nucleotide membraneless organelle formation. These are among the simplest model peptide systems observed to date able to undergo either simple or complex coacervation and are of future interest as protocell systems.
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Affiliation(s)
- Valeria Castelletto
- School
of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
| | - Jani Seitsonen
- Nanomicroscopy
Center, Aalto University, Puumiehenkuja 2, Espoo 02150, Finland
| | - Alice Pollitt
- Institute
for Cardiovascular and Metabolic Research, School of Biological Sciences, University of Reading, Reading RG6 6AS, U.K.
| | - Ian W. Hamley
- School
of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
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5
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Meyer K, Yserentant K, Cheloor-Kovilakam R, Ruff KM, Chung CI, Shu X, Huang B, Weiner OD. YAP charge patterning mediates signal integration through transcriptional co-condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.10.607443. [PMID: 39149273 PMCID: PMC11326239 DOI: 10.1101/2024.08.10.607443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Transcription factor dynamics are used to selectively engage gene regulatory programs. Biomolecular condensates have emerged as an attractive signaling substrate in this process, but the underlying mechanisms are not well-understood. Here, we probed the molecular basis of YAP signal integration through transcriptional condensates. Leveraging light-sheet single-molecule imaging and synthetic condensates, we demonstrate charge-mediated co-condensation of the transcriptional regulators YAP and Mediator into transcriptionally active condensates in stem cells. IDR sequence analysis and YAP protein engineering demonstrate that instead of the net charge, YAP signaling specificity is established through its negative charge patterning that interacts with Mediator's positive charge blocks. The mutual enhancement of YAP/Mediator co-condensation is counteracted by negative feedback from transcription, driving an adaptive transcriptional response that is well-suited for decoding dynamic inputs. Our work reveals a molecular framework for YAP condensate formation and sheds new light on the function of YAP condensates for emergent gene regulatory behavior.
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Affiliation(s)
- Kirstin Meyer
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Klaus Yserentant
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, 94143, CA, USA
| | - Rasmi Cheloor-Kovilakam
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, 94143, CA, USA
| | - Kiersten M. Ruff
- Department of Biomedical Engineering and Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Chan-I Chung
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, 94143, CA, USA
| | - Xiaokun Shu
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, 94143, CA, USA
| | - Bo Huang
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, 94158, CA, USA
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, 94143, CA, USA
| | - Orion D. Weiner
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
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6
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Patel CK, Mukherjee TK. Biomolecular Condensation of Trypsin Prevents Autolysis and Promotes Ca 2+-Mediated Activation of Esterase Activity. Biomacromolecules 2024. [PMID: 39116325 DOI: 10.1021/acs.biomac.4c00736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
The presence of Ca2+ ions is known to facilitate the activity of trypsin-like serine proteases via structural stabilization against thermal denaturation and autolysis. Herein, we report a new and hidden regulatory role of Ca2+ in the catalytic pathways of trypsin and α-chymotrypsin under physiological conditions. We discovered that macromolecular crowding promotes spontaneous homotypic condensation of trypsin via liquid-liquid phase separation to yield membraneless condensates over a broad range of concentrations, pH, and temperature, which are stabilized by multivalent hydrophobic interactions. Interestingly, we found that Ca2+ binding in the calcium binding loop reversibly regulates the condensation of trypsin and α-chymotrypsin. Spontaneous condensation effectively prevents autolysis of trypsin and preserves its native-like esterase activity for a prolonged period of time. It has also been found that phase-separated trypsin responds to Ca2+-dependent activation of its esterase activity even after 14 days of storage while free trypsin failed to do so. The present study highlights an important physiological aspect by which cells can spatiotemporally regulate the biocatalytic efficacy of trypsin-like serine proteases via Ca2+-signaling.
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Affiliation(s)
- Chinmaya Kumar Patel
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Simrol, Indore 453552, Madhya Pradesh, India
| | - Tushar Kanti Mukherjee
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Simrol, Indore 453552, Madhya Pradesh, India
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7
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Fuxreiter M. Context-dependent, fuzzy protein interactions: Towards sequence-based insights. Curr Opin Struct Biol 2024; 87:102834. [PMID: 38759297 DOI: 10.1016/j.sbi.2024.102834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/19/2024]
Abstract
Predicting protein interactions in the cellular environment still remains a challenge in the AlphaFold era. Protein interactions, similarly to their structures, sample a continuum from ordered to disordered states, with specific partners in many bound configurations. A multiplicity of binding modes (MBM) enables transition between these states under different cellular conditions. This review focuses on how the cellular environment affects protein interactions, highlighting the molecular mechanisms, biophysical origin, and sequence-based principles of context-dependent, fuzzy interactions. It summarises experimental and computational approaches to address the challenge of interaction heterogeneity and its contribution to a wide range of biological functions. These insights will help in understanding complex cellular processes, involving conversions between protein assembly states, such as from liquid-like droplet state to the amyloid state.
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Affiliation(s)
- Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, Padova, Italy; Department of Physics and Astronomy, University of Padova, Padova, Italy.
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8
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Kitamura K, Oshima A, Sasaki F, Shiramasa Y, Yamamoto R, Kameda T, Kitazawa S, Kitahara R. Modulation of Biomolecular Liquid-Liquid Phase Separation by Preferential Hydration and Interaction of Small Osmolytes with Proteins. J Phys Chem Lett 2024; 15:7620-7627. [PMID: 39029245 DOI: 10.1021/acs.jpclett.4c01365] [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: 07/21/2024]
Abstract
We examined the effects of trimethylamine N-oxide (TMAO) and urea (known osmolytes) on the liquid-liquid phase separation (LLPS) of fused in sarcoma (FUS) and three FUS-LLPS states: LLPS states at atmospheric pressure with low- and high-salt concentrations and a re-entrant LLPS state above 2 kbar. Temperature- and pressure-scan turbidity measurements revealed that TMAO and urea contributed to stabilizing and destabilizing LLPS, respectively. These results can be attributed to the excluded volume effect of TMAO (preferential hydration) and preferential interaction of urea with proteins. Additionally, TMAO counteracted the effects of equimolar urea on LLPS, a phenomenon not previously reported. The concept of the m-value for osmolyte-induced protein folding and unfolding can be applied to the osmolyte's effects on LLPS. In conclusion, biomolecular LLPS can be modulated by preferential hydration and the interaction of small osmolytes with proteins, thereby facilitating LLPS formation, even in extreme environments characterized by high-salt, high-urea, and high-pressure conditions.
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Affiliation(s)
- Keiji Kitamura
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Ayano Oshima
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Fuka Sasaki
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Yutaro Shiramasa
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Ryu Yamamoto
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Soichiro Kitazawa
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Ryo Kitahara
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
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9
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Joshi A, Avni A, Walimbe A, Rai SK, Sarkar S, Mukhopadhyay S. Hydrogen-Bonded Network of Water in Phase-Separated Biomolecular Condensates. J Phys Chem Lett 2024; 15:7724-7734. [PMID: 39042834 DOI: 10.1021/acs.jpclett.4c01153] [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: 07/25/2024]
Abstract
Biomolecular condensates formed via phase separation of intrinsically disordered proteins/regions (IDPs/IDRs) and nucleic acids are associated with cell physiology and disease. Water makes up for ∼60-70% of the condensate volume and is thought to influence the complex interplay of chain-chain and chain-solvent interactions, modulating the mesoscale properties of condensates. The behavior of water in condensates and the key roles of protein hydration water in driving the phase separation remain elusive. Here, we employ single-droplet vibrational Raman spectroscopy to illuminate the structural redistribution within protein hydration water during the phase separation of neuronal IDPs. Our Raman measurements reveal the changes in the water hydrogen bonding network during homotypic and heterotypic phase separation governed by various molecular drivers. Such single-droplet water Raman measurements offer a potent generic tool to unmask the intriguing interplay of sequence-encoded chain-chain and chain-solvent interactions governing macromolecular phase separation into membraneless organelles, synthetic condensates, and protocells.
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10
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Chen F, Jacobs WM. Emergence of Multiphase Condensates from a Limited Set of Chemical Building Blocks. J Chem Theory Comput 2024. [PMID: 39078082 DOI: 10.1021/acs.jctc.4c00323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Biomolecules composed of a limited set of chemical building blocks can colocalize into distinct, spatially segregated compartments known as biomolecular condensates. While many condensates are known to form spontaneously via phase separation, it has been unclear how immiscible condensates with precisely controlled molecular compositions assemble from a small number of chemical building blocks. We address this question by establishing a connection between the specificity of biomolecular interactions and the thermodynamic stability of coexisting condensates. By computing the minimum interaction specificity required to assemble condensates with target molecular compositions, we show how to design heteropolymer mixtures that produce compositionally complex condensates by using only a small number of monomer types. Our results provide insight into how compositional specificity arises in naturally occurring multicomponent condensates and demonstrate a rational algorithm for engineering complex artificial condensates from simple chemical building blocks.
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Affiliation(s)
- Fan Chen
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - William M Jacobs
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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11
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De Luca G, Sancataldo G, Militello B, Vetri V. Surface-catalyzed liquid-liquid phase separation and amyloid-like assembly in microscale compartments. J Colloid Interface Sci 2024; 676:569-581. [PMID: 39053405 DOI: 10.1016/j.jcis.2024.07.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/24/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
Liquid-liquid phase separation is a key phenomenon in the formation of membrane-less structures within the cell, appearing as liquid biomolecular condensates. Protein condensates are the most studied for their biological relevance, and their tendency to evolve, resulting in the formation of aggregates with a high level of order called amyloid. In this study, it is demonstrated that Human Insulin forms micrometric, round amyloid-like structures at room temperature within sub-microliter scale aqueous compartments. These distinctive particles feature a solid core enveloped by a fluid-like corona and form at the interface between the aqueous compartment and the glass coverslip upon which they are cast. Quantitative fluorescence microscopy is used to study in real-time the formation of amyloid-like superstructures. Their formation results driven by liquid-liquid phase separation process that arises from spatially heterogeneous distribution of nuclei at the glass-water interface. The proposed experimental setup allows modifying the surface-to-volume ratio of the aqueous compartments, which affects the aggregation rate and particle size, while also inducing fine alterations in the molecular structures of the final assemblies. These findings enhance the understanding of the factors governing amyloid structure formation, shedding light on the catalytic role of surfaces in this process.
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Affiliation(s)
- Giuseppe De Luca
- Department Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, 16, 90128, Palermo, Italy; Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, 90128, Palermo, Italy.
| | - Giuseppe Sancataldo
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, 90128, Palermo, Italy.
| | - Benedetto Militello
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, 90128, Palermo, Italy; INFN Sezione di Catania, Via Santa Sofia 64, 95123 Catania, Italy.
| | - Valeria Vetri
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, 90128, Palermo, Italy.
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12
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Staderini T, Bigi A, Lagrève C, Marzi I, Bemporad F, Chiti F. Biophysical characterization of the phase separation of TDP-43 devoid of the C-terminal domain. Cell Mol Biol Lett 2024; 29:104. [PMID: 38997630 PMCID: PMC11245819 DOI: 10.1186/s11658-024-00615-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/25/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND Frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-TDP), amyotrophic lateral sclerosis (ALS) and limbic-predominant age-related TDP-43 encephalopathy (LATE) are associated with deposition of cytoplasmic inclusions of TAR DNA-binding protein 43 (TDP-43) in neurons. One complexity of this process lies in the ability of TDP-43 to form liquid-phase membraneless organelles in cells. Previous work has shown that the recombinant, purified, prion-like domain (PrLD) forms liquid droplets in vitro, but the behaviour of the complementary fragment is uncertain. METHODS We have purified such a construct without the PrLD (PrLD-less TDP-43) and have induced its phase separation using a solution-jump method and an array of biophysical techniques to study the morphology, state of matter and structure of the TDP-43 assemblies. RESULTS The fluorescent TMR-labelled protein construct, imaged using confocal fluorescence, formed rapidly (< 1 min) round, homogeneous and 0.5-1.0 µm wide assemblies which then coalesced into larger, yet round, species. When labelled with AlexaFluor488, they initially exhibited fluorescence recovery after photobleaching (FRAP), showing a liquid behaviour distinct from full-length TDP-43 and similar to PrLD. The protein molecules did not undergo major structural changes, as determined with circular dichroism and intrinsic fluorescence spectroscopies. This process had a pH and salt dependence distinct from those of full-length TDP-43 and its PrLD, which can be rationalized on the grounds of electrostatic forces. CONCLUSIONS Similarly to PrLD, PrLD-less TDP-43 forms liquid droplets in vitro through liquid-liquid phase separation (LLPS), unlike the full-length protein that rather undergoes liquid-solid phase separation (LSPS). These results offer a rationale of the complex electrostatic forces governing phase separation of full-length TDP-43 and its fragments. On the one hand, PrLD-less TDP-43 has a low pI and oppositively charged domains, and LLPS is inhibited by salts, which attenuate inter-domain electrostatic attractions. On the other hand, PrLD is positively charged due to a high isoionic point (pI) and LLPS is therefore promoted by salts and pH increases as they both reduce electrostatic repulsions. By contrast, full-length TDP-43 undergoes LSPS most favourably at its pI, with positive and negative salt dependences at lower and higher pH, respectively, depending on whether repulsive or attractive forces dominate, respectively.
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Affiliation(s)
- Tommaso Staderini
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134, Florence, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, 50019, Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, 50019, Florence, Italy
| | - Alessandra Bigi
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134, Florence, Italy
| | - Clément Lagrève
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134, Florence, Italy
- Chimie ParisTech-PSL, École Nationale Supérieur de Chimie de Paris, 11 rue Pierre et Marie Curie, 75231, Paris, France
| | - Isabella Marzi
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134, Florence, Italy
| | - Francesco Bemporad
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134, Florence, Italy
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134, Florence, Italy.
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13
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Zhou HX, Kota D, Qin S, Prasad R. Fundamental Aspects of Phase-Separated Biomolecular Condensates. Chem Rev 2024; 124:8550-8595. [PMID: 38885177 PMCID: PMC11260227 DOI: 10.1021/acs.chemrev.4c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Biomolecular condensates, formed through phase separation, are upending our understanding in much of molecular, cell, and developmental biology. There is an urgent need to elucidate the physicochemical foundations of the behaviors and properties of biomolecular condensates. Here we aim to fill this need by writing a comprehensive, critical, and accessible review on the fundamental aspects of phase-separated biomolecular condensates. We introduce the relevant theoretical background, present the theoretical basis for the computation and experimental measurement of condensate properties, and give mechanistic interpretations of condensate behaviors and properties in terms of interactions at the molecular and residue levels.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
- Department of Physics, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Divya Kota
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Sanbo Qin
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
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14
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Liu J, Jiang Y, Liu R, Jin J, Wei S, Ji W, He X, Wu F, Yu P, Mao L. Vitamin C Drives Reentrant Actin Phase Transition: Biphasic Exocytosis Regulation Revealed by Single-Vesicle Electrochemistry. J Am Chem Soc 2024; 146:17747-17756. [PMID: 38889317 DOI: 10.1021/jacs.4c02710] [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: 06/20/2024]
Abstract
Unveiling molecular mechanisms that dominate protein phase dynamics has been a pressing need for deciphering the intricate intracellular modulation machinery. While ions and biomacromolecules have been widely recognized for modulating protein phase separations, effects of small molecules that essentially constitute the cytosolic chemical atmosphere on the protein phase behaviors are rarely understood. Herein, we report that vitamin C (VC), a key small molecule for maintaining a reductive intracellular atmosphere, drives reentrant phase transitions of myosin II/F-actin (actomyosin) cytoskeletons. The actomyosin bundle condensates dissemble in the low-VC regime and assemble in the high-VC regime in vitro or inside neuronal cells, through a concurrent myosin II protein aggregation-dissociation process with monotonic VC concentration increase. Based on this finding, we employ in situ single-cell and single-vesicle electrochemistry to demonstrate the quantitative modulation of catecholamine transmitter vesicle exocytosis by intracellular VC atmosphere, i.e., exocytotic release amount increases in the low-VC regime and decreases in the high-VC regime. Furthermore, we show how VC regulates cytomembrane-vesicle fusion pore dynamics through counteractive or synergistic effects of actomyosin phase transitions and the intracellular free calcium level on membrane tensions. Our work uncovers the small molecule-based reversive protein phase regulatory mechanism, paving a new way to chemical neuromodulation and therapeutic repertoire expansion.
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Affiliation(s)
- Jing Liu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
- Institute of Analysis and Testing, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Ying Jiang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ran Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jing Jin
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Shiyi Wei
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Wenliang Ji
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xiulan He
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Fei Wu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Lanqun Mao
- College of Chemistry, Beijing Normal University, Beijing 100875, China
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15
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Maraldo A, Rnjak-Kovacina J, Marquis C. Tyrosine - a structural glue for hierarchical protein assembly. Trends Biochem Sci 2024; 49:633-648. [PMID: 38653686 DOI: 10.1016/j.tibs.2024.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
Protein self-assembly, guided by the interplay of sequence- and environment-dependent liquid-liquid phase separation (LLPS), constitutes a fundamental process in the assembly of numerous intrinsically disordered proteins. Heuristic examination of these proteins has underscored the role of tyrosine residues, evident in their conservation and pivotal involvement in initiating LLPS and subsequent liquid-solid phase transitions (LSPT). The development of tyrosine-templated constructs, designed to mimic their natural counterparts, emerges as a promising strategy for creating adaptive, self-assembling systems with diverse applications. This review explores the central role of tyrosine in orchestrating protein self-assembly, delving into key interactions and examining its potential in innovative applications, including responsive biomaterials and bioengineering.
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Affiliation(s)
- Anton Maraldo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Jelena Rnjak-Kovacina
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, Australia.
| | - Christopher Marquis
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.
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16
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Zhu R, Wang R, Li J, Chen M, Qiu L, Bai S. An artificial liquid-liquid phase separation-driven silk fibroin-based adhesive for rapid hemostasis and wound sealing. Acta Biomater 2024; 182:14-27. [PMID: 38750918 DOI: 10.1016/j.actbio.2024.05.024] [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: 01/12/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/24/2024]
Abstract
The powerful adhesion systems of marine organisms have inspired the development of artificial protein-based bioadhesives. However, achieving robust wet adhesion using artificial bioadhesives remains technically challenging because the key element of liquid-liquid phase separation (LLPS)-driven complex coacervation in natural adhesion systems is often ignored. In this study, mimicking the complex coacervation phenomenon of marine organisms, an artificial protein-based adhesive hydrogel (SFG hydrogel) was developed by adopting the LLPS-mediated coacervation of the natural protein silk fibroin (SF) and the anionic surfactant sodium dodecylbenzene sulfonate (SDBS). The assembled SF/SDBS complex coacervate enabled precise spatial positioning and easy self-adjustable deposition on irregular substrate surfaces, allowing for tight contact. Spontaneous liquid-to-solid maturation promoted the phase transition of the SF/SDBS complex coacervate to form the SFG hydrogel in situ, enhancing its bulk cohesiveness and interfacial adhesion. The formed SFG hydrogel exhibited intrinsic advantages as a new type of artificial protein-based adhesive, including good biocompatibility, robust wet adhesion, rapid blood-clotting capacity, and easy operation. In vitro and in vivo experiments demonstrated that the SFG hydrogel not only achieved instant and effective hemostatic sealing of tissue injuries but also promoted wound healing and tissue regeneration, thus advancing its clinical applications. STATEMENT OF SIGNIFICANCE: Marine mussels utilize the liquid-liquid phase separation (LLPS) strategy to induce the supramolecular assembly of mussel foot proteins, which plays a critical role in strong underwater adhesion of mussel foot proteins. Herein, an artificial protein-based adhesive hydrogel (named SFG hydrogel) was reported by adopting the LLPS-mediated coacervation of natural protein silk fibroin (SF) and anionic surfactant sodium dodecylbenzene sulfonate (SDBS). The assembled SFG hydrogel enabled the precise spatial positioning and easy self-adjustable deposition on substrate surfaces with irregularities, allowing tight interfacial adhesion and cohesiveness. The SFG hydrogel not only achieved instant and effective hemostatic sealing of tissue injuries but also promoted wound healing and tissue regeneration, exhibiting intrinsic advantages as a new type of artificial protein-based bioadhesives.
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Affiliation(s)
- Rui Zhu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Ruiheng Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Jie Li
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Minghui Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Lingyu Qiu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Shumeng Bai
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People's Republic of China.
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17
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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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18
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Tsoi PS, Ferreon JC, Ferreon ACM. Initiation of hnRNPA1 Low-Complexity Domain Condensation Monitored by Dynamic Light Scattering. Int J Mol Sci 2024; 25:6825. [PMID: 38999934 PMCID: PMC11241569 DOI: 10.3390/ijms25136825] [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: 05/10/2024] [Revised: 06/14/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024] Open
Abstract
Biomolecular condensates (BMCs) exhibit physiological and pathological relevance in biological systems. Both liquid and solid condensates play significant roles in the spatiotemporal regulation and organization of macromolecules and their biological activities. Some pathological solid condensates, such as Lewy Bodies and other fibrillar aggregates, have been hypothesized to originate from liquid condensates. With the prevalence of BMCs having functional and dysfunctional roles, it is imperative to understand the mechanism of biomolecular condensate formation and initiation. Using the low-complexity domain (LCD) of heterogenous ribonuclear protein A1 (hnRNPA1) as our model, we monitored initial assembly events using dynamic light scattering (DLS) while modulating pH and salt conditions to perturb macromolecule and condensate properties. We observed the formation of nanometer-sized BMCs (nano-condensates) distinct from protein monomers and micron-sized condensates. We also observed that conditions that solubilize micron-sized protein condensates do not solubilize nano-condensates, indicating that the balance of forces that stabilize nano-condensates and micron-sized condensates are distinct. These findings provide insight into the forces that drive protein phase separation and potential nucleation structures of macromolecular condensation.
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Affiliation(s)
| | - Josephine C. Ferreon
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Allan Chris M. Ferreon
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
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19
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Kitamura A, Fujimoto A, Kawashima R, Lyu Y, Sasaki K, Hamada Y, Moriya K, Kurata A, Takahashi K, Brielmann R, Bott LC, Morimoto RI, Kinjo M. Hetero-oligomerization of TDP-43 carboxy-terminal fragments with cellular proteins contributes to proteotoxicity. Commun Biol 2024; 7:743. [PMID: 38902525 PMCID: PMC11190292 DOI: 10.1038/s42003-024-06410-3] [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: 06/22/2022] [Accepted: 06/03/2024] [Indexed: 06/22/2024] Open
Abstract
Carboxy terminal fragments (CTFs) of TDP-43 contain an intrinsically disordered region (IDR) and form cytoplasmic condensates containing amyloid fibrils. Such condensates are toxic and associated with pathogenicity in amyotrophic lateral sclerosis. However, the molecular details of how the domain of TDP-43 CTFs leads to condensation and cytotoxicity remain elusive. Here, we show that truncated RNA/DNA-recognition motif (RRM) at the N-terminus of TDP-43 CTFs leads to the structural transition of the IDR, whereas the IDR itself of TDP-43 CTFs is difficult to assemble even if they are proximate intermolecularly. Hetero-oligomers of TDP-43 CTFs that have recruited other proteins are more toxic than homo-oligomers, implicating loss-of-function of the endogenous proteins by such oligomers is associated with cytotoxicity. Furthermore, such toxicity of TDP-43 CTFs was cell-nonautonomously affected in the nematodes. Therefore, misfolding and oligomeric characteristics of the truncated RRM at the N-terminus of TDP-43 CTFs define their condensation properties and toxicity.
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Affiliation(s)
- Akira Kitamura
- Laboratory of Cellular and Molecular Sciences, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan.
- PRIME, Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo, 100-0004, Japan.
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan.
| | - Ai Fujimoto
- Laboratory of Cellular and Molecular Sciences, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Rei Kawashima
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Yidan Lyu
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Kotetsu Sasaki
- Laboratory of Cellular and Molecular Sciences, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Yuta Hamada
- Laboratory of Cellular and Molecular Sciences, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Kanami Moriya
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Ayumi Kurata
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Kazuho Takahashi
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Reneé Brielmann
- Department of Molecular Bioscience, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL, 60208, USA
| | - Laura C Bott
- Department of Molecular Bioscience, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL, 60208, USA
| | - Richard I Morimoto
- Department of Molecular Bioscience, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL, 60208, USA
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
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20
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Robinson JL, Suh E, Xu Y, Hurtig HI, Elman L, McMillan CT, Irwin DJ, Porta S, Van Deerlin VM, Lee EB. Annexin A11 aggregation in FTLD-TDP type C and related neurodegenerative disease proteinopathies. Acta Neuropathol 2024; 147:104. [PMID: 38896345 PMCID: PMC11186923 DOI: 10.1007/s00401-024-02753-7] [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: 04/16/2024] [Revised: 06/09/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
TAR DNA-binding protein 43 (TDP-43) is an RNA binding protein found within ribonucleoprotein granules tethered to lysosomes via annexin A11. TDP-43 protein forms inclusions in many neurodegenerative diseases including amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP) and limbic predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC). Annexin A11 is also known to form aggregates in ALS cases with pathogenic variants in ANXA11. Annexin A11 aggregation has not been described in sporadic ALS, FTLD-TDP or LATE-NC cases. To explore the relationship between TDP-43 and annexin A11, genetic analysis of 822 autopsy cases was performed to identify rare ANXA11 variants. In addition, an immunohistochemical study of 368 autopsy cases was performed to identify annexin A11 aggregates. Insoluble annexin A11 aggregates which colocalize with TDP-43 inclusions were present in all FTLD-TDP Type C cases. Annexin A11 inclusions were also seen in a small proportion (3-6%) of sporadic and genetic forms of FTLD-TDP types A and B, ALS, and LATE-NC. In addition, we confirm the comingling of annexin A11 and TDP-43 aggregates in an ALS case with the pathogenic ANXA11 p.G38R variant. Finally, we found abundant annexin A11 inclusions as the primary pathologic finding in a case of progressive supranuclear palsy-like frontotemporal dementia with prominent striatal vacuolization due to a novel variant, ANXA11 p.P75S. By immunoblot, FTLD-TDP with annexinopathy and ANXA11 variant cases show accumulation of insoluble ANXA11 including a truncated fragment. These results indicate that annexin A11 forms a diverse and heterogeneous range of aggregates in both sporadic and genetic forms of TDP-43 proteinopathies. In addition, the finding of a primary vacuolar annexinopathy due to ANXA11 p.P75S suggests that annexin A11 aggregation is sufficient to cause neurodegeneration.
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Affiliation(s)
- John L Robinson
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Institute On Aging, Perelman School of Medicine, University of Pennsylvania, 613A Stellar Chance Laboratories, 422 Curie Blvd, Philadelphia, PA, 19104, USA
| | - EunRan Suh
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Institute On Aging, Perelman School of Medicine, University of Pennsylvania, 613A Stellar Chance Laboratories, 422 Curie Blvd, Philadelphia, PA, 19104, USA
| | - Yan Xu
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Institute On Aging, Perelman School of Medicine, University of Pennsylvania, 613A Stellar Chance Laboratories, 422 Curie Blvd, Philadelphia, PA, 19104, USA
| | - Howard I Hurtig
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lauren Elman
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Corey T McMillan
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David J Irwin
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sílvia Porta
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Institute On Aging, Perelman School of Medicine, University of Pennsylvania, 613A Stellar Chance Laboratories, 422 Curie Blvd, Philadelphia, PA, 19104, USA.
| | - Vivianna M Van Deerlin
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Institute On Aging, Perelman School of Medicine, University of Pennsylvania, 613A Stellar Chance Laboratories, 422 Curie Blvd, Philadelphia, PA, 19104, USA.
| | - Edward B Lee
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Institute On Aging, Perelman School of Medicine, University of Pennsylvania, 613A Stellar Chance Laboratories, 422 Curie Blvd, Philadelphia, PA, 19104, USA.
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21
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Yang X, Wang Y, Yang G. Molecular dynamics simulation on regulation of liquid-liquid phase separation of repetitive peptides. Sci Rep 2024; 14:13382. [PMID: 38862770 PMCID: PMC11167010 DOI: 10.1038/s41598-024-64327-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 06/07/2024] [Indexed: 06/13/2024] Open
Abstract
Understanding the intricate interactions governing protein and peptide behavior in liquid-liquid phase separation (LLPS) is crucial for unraveling biological functions and dysfunctions. This study employs a residue-leveled coarse-grained molecular dynamics approach to simulate the phase separation of repetitive polyproline and polyarginine peptides (poly PR) with varying lengths and sequences in solution, considering different concentrations and temperatures. Our findings highlight the crucial role of sequence order in promoting LLPS in peptides with identical lengths of repetitive sequences. Interestingly, repetitive peptides containing fewer than 10 polyarginine repeats exhibit no LLPS, even at salt concentrations up to 3 M. Notably, our simulations align with experimental observations, pinpointing a salt concentration of 2.7 M for PR25-induced LLPS. Utilizing the same methodology, we predict the required salt concentrations for LLPS induction as 1.2 M, 1.5 M, and 2.7 M for PR12, PR15, and PR35, respectively. These predictions demonstrate good agreement with experimental results. Extending our investigation to include the peptide glutamine and arginine (GR15) in DNA solution, our simulations mirror experimental observations of phase separation. To unveil the molecular forces steering peptide phase separation, we introduce a dielectric constant modifier and hydrophobicity disruptor into poly PR systems. Our coarse-grained analysis includes an examination of temperature effects, leading to the inference that both hydrophobic and electrostatic interactions drive phase separation in peptide systems.
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Affiliation(s)
- Xiaojun Yang
- Department of Physics, Wenzhou University, Wenzhou, 325035, China
| | - Yanwei Wang
- Department of Physics, Wenzhou University, Wenzhou, 325035, China.
| | - Guangcan Yang
- Department of Physics, Wenzhou University, Wenzhou, 325035, China.
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22
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Ryder BD, Ustyantseva E, Boyer DR, Mendoza-Oliva A, Kuska MI, Wydorski PM, Macierzyńska P, Morgan N, Sawaya MR, Diamond MI, Kampinga HH, Joachimiak LA. DNAJB8 oligomerization is mediated by an aromatic-rich motif that is dispensable for substrate activity. Structure 2024; 32:662-678.e8. [PMID: 38508190 PMCID: PMC11162344 DOI: 10.1016/j.str.2024.02.015] [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: 05/01/2023] [Revised: 01/17/2024] [Accepted: 02/22/2024] [Indexed: 03/22/2024]
Abstract
J-domain protein (JDP) molecular chaperones have emerged as central players that maintain a healthy proteome. The diverse members of the JDP family function as monomers/dimers and a small subset assemble into micron-sized oligomers. The oligomeric JDP members have eluded structural characterization due to their low-complexity, intrinsically disordered middle domains. This in turn, obscures the biological significance of these larger oligomers in protein folding processes. Here, we identified a short, aromatic motif within DNAJB8 that drives self-assembly through π-π stacking and determined its X-ray structure. We show that mutations in the motif disrupt DNAJB8 oligomerization in vitro and in cells. DNAJB8 variants that are unable to assemble bind to misfolded tau seeds more specifically and retain capacity to reduce protein aggregation in vitro and in cells. We propose a new model for DNAJB8 function in which the sequences in the low-complexity domains play distinct roles in assembly and substrate activity.
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Affiliation(s)
- Bryan D Ryder
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elizaveta Ustyantseva
- Department of Biomedical Sciences of Cells & Systems, University Medical Center Groningen, University of Groningen, Groningen 9713 AV, The Netherlands
| | - David R Boyer
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ayde Mendoza-Oliva
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mikołaj I Kuska
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Paweł M Wydorski
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Paulina Macierzyńska
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nabil Morgan
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael R Sawaya
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Harm H Kampinga
- Department of Biomedical Sciences of Cells & Systems, University Medical Center Groningen, University of Groningen, Groningen 9713 AV, The Netherlands
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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23
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Kamatar A, Bravo JPK, Yuan F, Wang L, Lafer EM, Taylor DW, Stachowiak JC, Parekh SH. Lipid droplets as substrates for protein phase separation. Biophys J 2024; 123:1494-1507. [PMID: 38462838 PMCID: PMC11163294 DOI: 10.1016/j.bpj.2024.03.015] [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: 11/21/2023] [Revised: 01/26/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024] Open
Abstract
Membrane-associated protein phase separation plays critical roles in cell biology, driving essential cellular phenomena from immune signaling to membrane traffic. Importantly, by reducing dimensionality from three to two dimensions, lipid bilayers can nucleate phase separation at far lower concentrations compared with those required for phase separation in solution. How might other intracellular lipid substrates, such as lipid droplets, contribute to nucleation of phase separation? Distinct from bilayer membranes, lipid droplets consist of a phospholipid monolayer surrounding a core of neutral lipids, and they are energy storage organelles that protect cells from lipotoxicity and oxidative stress. Here, we show that intrinsically disordered proteins can undergo phase separation on the surface of synthetic and cell-derived lipid droplets. Specifically, we find that the model disordered domains FUS LC and LAF-1 RGG separate into protein-rich and protein-depleted phases on the surfaces of lipid droplets. Owing to the hydrophobic nature of interactions between FUS LC proteins, increasing ionic strength drives an increase in its phase separation on droplet surfaces. The opposite is true for LAF-1 RGG, owing to the electrostatic nature of its interprotein interactions. In both cases, protein-rich phases on the surfaces of synthetic and cell-derived lipid droplets demonstrate molecular mobility indicative of a liquid-like state. Our results show that lipid droplets can nucleate protein condensates, suggesting that protein phase separation could be key in organizing biological processes involving lipid droplets.
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Affiliation(s)
- Advika Kamatar
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas
| | - Jack P K Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas
| | - Feng Yuan
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas
| | - Liping Wang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Eileen M Lafer
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas; Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, Texas; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas; LIVESTRONG Cancer Institutes, Dell Medical School, Austin, Texas
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas; McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas.
| | - Sapun H Parekh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas.
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24
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Chew PY, Joseph JA, Collepardo-Guevara R, Reinhardt A. Aromatic and arginine content drives multiphasic condensation of protein-RNA mixtures. Biophys J 2024; 123:1342-1355. [PMID: 37408305 PMCID: PMC11163273 DOI: 10.1016/j.bpj.2023.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/20/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023] Open
Abstract
Multiphasic architectures are found ubiquitously in biomolecular condensates and are thought to have important implications for the organization of multiple chemical reactions within the same compartment. Many of these multiphasic condensates contain RNA in addition to proteins. Here, we investigate the importance of different interactions in multiphasic condensates comprising two different proteins and RNA using computer simulations with a residue-resolution coarse-grained model of proteins and RNA. We find that in multilayered condensates containing RNA in both phases, protein-RNA interactions dominate, with aromatic residues and arginine forming the key stabilizing interactions. The total aromatic and arginine content of the two proteins must be appreciably different for distinct phases to form, and we show that this difference increases as the system is driven toward greater multiphasicity. Using the trends observed in the different interaction energies of this system, we demonstrate that we can also construct multilayered condensates with RNA preferentially concentrated in one phase. The "rules" identified can thus enable the design of synthetic multiphasic condensates to facilitate further study of their organization and function.
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Affiliation(s)
- Pin Yu Chew
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jerelle A Joseph
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom; Department of Physics, University of Cambridge, Cambridge, United Kingdom; Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
| | - Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
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25
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Evangelista NN, Micheletto MC, Kava E, Mendes LFS, Costa-Filho AJ. Biomolecular condensates of Chlorocatechol 1,2-Dioxygenase as prototypes of enzymatic microreactors for the degradation of polycyclic aromatic hydrocarbons. Int J Biol Macromol 2024; 270:132294. [PMID: 38735602 DOI: 10.1016/j.ijbiomac.2024.132294] [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: 09/08/2023] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are molecules with two or more fused aromatic rings that occur naturally in the environment due to incomplete combustion of organic substances. However, the increased demand for fossil fuels in recent years has increased anthropogenic activity, contributing to the environmental concentration of PAHs. The enzyme chlorocatechol 1,2-dioxygenase from Pseudomonas putida (Pp 1,2-CCD) is responsible for the breakdown of the aromatic ring of catechol, making it a potential player in bioremediation strategies. Pp 1,2-CCD can tolerate a broader range of substrates, including halogenated compounds, than other dioxygenases. Here, we report the construction of a chimera protein able to form biomolecular condensates with potential application in bioremediation. The chimera protein was built by conjugating Pp 1,2-CCD to low complex domains (LCDs) derived from the DEAD-box protein Dhh1. We showed that the chimera could undergo liquid-liquid phase separation (LLPS), forming a protein-rich liquid droplet under different conditions (variable protein and PEG8000 concentrations and pH values), in which the protein maintained its structure and main biophysical properties. The condensates were active against 4-chlorocatechol, showing that the chimera droplets preserved the enzymatic activity of the native protein. Therefore, it constitutes a prototype of a microreactor with potential use in bioremediation.
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Affiliation(s)
- Nathan N Evangelista
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Mariana C Micheletto
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Emanuel Kava
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Luis F S Mendes
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil; Grupo de Biofísica Molecular Sérgio Mascarenhas, Departamento de Física e Ciência Interdisciplinar, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Antonio J Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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26
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Yoshioka D, Nakamura T, Kubota Y, Takekawa M. Formation of the NLRP3 inflammasome inhibits stress granule assembly by multiple mechanisms. J Biochem 2024; 175:629-641. [PMID: 38299728 PMCID: PMC11155693 DOI: 10.1093/jb/mvae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/21/2024] [Accepted: 01/30/2024] [Indexed: 02/02/2024] Open
Abstract
Proper regulation of cellular response to environmental stress is crucial for maintaining biological homeostasis and is achieved by the balance between cell death processes, such as the formation of the pyroptosis-inducing NLRP3 inflammasome, and pro-survival processes, such as stress granule (SG) assembly. However, the functional interplay between these two stress-responsive organelles remains elusive. Here, we identified DHX33, a viral RNA sensor for the NLRP3 inflammasome, as a SG component, and the SG-nucleating protein G3BP as an NLRP3 inflammasome component. We also found that a decrease in intracellular potassium (K+) concentration, a key 'common' step in NLRP3 inflammasome activation, markedly inhibited SG assembly. Therefore, when macrophages are exposed to stress stimuli with the potential to induce both SGs and the NLRP3 inflammasome, such as cytoplasmic poly(I:C) stimulation, they preferentially form the NLRP3 inflammasome but avoid SG assembly by sequestering G3BP into the inflammasome and by inducing a reduction in intracellular K+ levels. Thus, under such conditions, DHX33 is primarily utilized as a viral RNA sensor for the inflammasome. Our data reveal the functional crosstalk between NLRP3 inflammasome-mediated pyroptosis and SG-mediated cell survival pathways and delineate a molecular mechanism that regulates cell-fate decisions and anti-viral innate immunity under stress.
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Affiliation(s)
- Daisuke Yoshioka
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Takanori Nakamura
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yuji Kubota
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Mutsuhiro Takekawa
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
- Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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27
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Yang X, Huang Y, Xia P. The property and function of proteins undergoing liquid-liquid phase separation in plants. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38808958 DOI: 10.1111/pce.14988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/16/2024] [Accepted: 05/19/2024] [Indexed: 05/30/2024]
Abstract
A wide variety of membrane-less organelles in cells play an essential role in regulating gene expression, RNA processing, plant growth and development, and helping organisms cope with changing external environments. In biology, liquid-liquid phase separation (LLPS) usually refers to a reversible process in which one or more specific molecular components are spontaneously separated from the bulk environment, producing two distinct liquid phases: concentrated and dilute. LLPS may be a powerful cellular compartmentalisation mechanism whereby biocondensates formed via LLPS when biomolecules exceed critical or saturating concentrations in the environment where they are found will be generated. It has been widely used to explain the formation of membrane-less organelles in organisms. LLPS studies in the context of plant physiology are now widespread, but most of the research is still focused on non-plant systems; the study of phase separation in plants needs to be more thorough. Proteins and nucleic acids are the main components involved in LLPS. This review summarises the specific features and properties of biomolecules undergoing LLPS in plants. We describe in detail these biomolecules' structural characteristics, the mechanism of formation of condensates, and the functions of these condensates. Finally, We summarised the phase separation mechanisms in plant growth, development, and stress adaptation.
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Affiliation(s)
- Xuejiao Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yang Huang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Pengguo Xia
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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28
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Kar M, Vogel LT, Chauhan G, Felekyan S, Ausserwöger H, Welsh TJ, Dar F, Kamath AR, Knowles TPJ, Hyman AA, Seidel CAM, Pappu RV. Solutes unmask differences in clustering versus phase separation of FET proteins. Nat Commun 2024; 15:4408. [PMID: 38782886 PMCID: PMC11116469 DOI: 10.1038/s41467-024-48775-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Phase separation and percolation contribute to phase transitions of multivalent macromolecules. Contributions of percolation are evident through the viscoelasticity of condensates and through the formation of heterogeneous distributions of nano- and mesoscale pre-percolation clusters in sub-saturated solutions. Here, we show that clusters formed in sub-saturated solutions of FET (FUS-EWSR1-TAF15) proteins are affected differently by glutamate versus chloride. These differences on the nanoscale, gleaned using a suite of methods deployed across a wide range of protein concentrations, are prevalent and can be unmasked even though the driving forces for phase separation remain unchanged in glutamate versus chloride. Strikingly, differences in anion-mediated interactions that drive clustering saturate on the micron-scale. Beyond this length scale the system separates into coexisting phases. Overall, we find that sequence-encoded interactions, mediated by solution components, make synergistic and distinct contributions to the formation of pre-percolation clusters in sub-saturated solutions, and to the driving forces for phase separation.
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Affiliation(s)
- Mrityunjoy Kar
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany
| | - Laura T Vogel
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Gaurav Chauhan
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Suren Felekyan
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Hannes Ausserwöger
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Timothy J Welsh
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Furqan Dar
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Anjana R Kamath
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Anthony A Hyman
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany.
| | - Claus A M Seidel
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany.
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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29
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Zhu L, Pan Y, Hua Z, Liu Y, Zhang X. Ionic Effect on the Microenvironment of Biomolecular Condensates. J Am Chem Soc 2024; 146:14307-14317. [PMID: 38722189 DOI: 10.1021/jacs.4c04036] [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: 05/23/2024]
Abstract
Biomolecules such as proteins and RNA could organize to form condensates with distinct microenvironments through liquid-liquid phase separation (LLPS). Recent works have demonstrated that the microenvironment of biomolecular condensates plays a crucial role in mediating biological activities, such as the partition of biomolecules, and the subphase organization of the multiphasic condensates. Ions could influence the phase transition point of LLPS, following the Hofmeister series. However, the ion-specific effect on the microenvironment of biomolecular condensates remains unknown. In this study, we utilized fluorescence lifetime imaging microscopy (FLIM), fluorescence recovery after photobleaching (FRAP), and microrheology techniques to investigate the ion effect on the microenvironment of condensates. We found that ions significantly affect the microenvironment of biomolecular condensates: salting-in ions increase micropolarity and reduce the microviscosity of the condensate, while salting-out ions induce opposing effects. Furthermore, we manipulate the miscibility and multilayering behavior of condensates through ion-specific effects. In summary, our work provides the first quantitative survey of the microenvironment of protein condensates in the presence of ions from the Hofmeister series, demonstrating how ions impact micropolarity, microviscosity, and viscoelasticity of condensates. Our results bear implications on how membrane-less organelles would exhibit varying microenvironments in the presence of continuously changing cellular conditions.
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Affiliation(s)
- Longchen Zhu
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, P. R. China
| | - Yifei Pan
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, P. R. China
| | - Ziyi Hua
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, P. R. China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Xin Zhang
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, P. R. China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, P. R. China
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30
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Dinic J, Tirrell MV. Effects of Charge Sequence Pattern and Lysine-to-Arginine Substitution on the Structural Stability of Bioinspired Polyampholytes. Biomacromolecules 2024; 25:2838-2851. [PMID: 38567844 PMCID: PMC11094733 DOI: 10.1021/acs.biomac.4c00002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 05/14/2024]
Abstract
A comprehensive study focusing on the combined influence of the charge sequence pattern and the type of positively charged amino acids on the formation of secondary structures in sequence-specific polyampholytes is presented. The sequences of interest consisting exclusively of ionizable amino acids (lysine, K; arginine, R; and glutamic acid, E) are (EKEK)5, (EKKE)5, (ERER)5, (ERRE)5, and (EKER)5. The stability of the secondary structure was examined at three pH values in the presence of urea and NaCl. The results presented here underscore the combined prominent effects of the charge sequence pattern and the type of positively charged monomers on secondary structure formation. Additionally, (ERRE)5 readily aggregated across a wide range of pH. In contrast, sequences with the same charge pattern, (EKKE)5, as well as the sequences with the equivalent amino acid content, (ERER)5, exhibited no aggregate formation under equivalent pH and concentration conditions.
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Affiliation(s)
- Jelena Dinic
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
- Center
for Molecular Engineering and Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Matthew V. Tirrell
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
- Center
for Molecular Engineering and Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
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31
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Liang Q, Peng N, Xie Y, Kumar N, Gao W, Miao Y. MolPhase, an advanced prediction algorithm for protein phase separation. EMBO J 2024; 43:1898-1918. [PMID: 38565952 PMCID: PMC11065880 DOI: 10.1038/s44318-024-00090-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/27/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
We introduce MolPhase, an advanced algorithm for predicting protein phase separation (PS) behavior that improves accuracy and reliability by utilizing diverse physicochemical features and extensive experimental datasets. MolPhase applies a user-friendly interface to compare distinct biophysical features side-by-side along protein sequences. By additional comparison with structural predictions, MolPhase enables efficient predictions of new phase-separating proteins and guides hypothesis generation and experimental design. Key contributing factors underlying MolPhase include electrostatic pi-interactions, disorder, and prion-like domains. As an example, MolPhase finds that phytobacterial type III effectors (T3Es) are highly prone to homotypic PS, which was experimentally validated in vitro biochemically and in vivo in plants, mimicking their injection and accumulation in the host during microbial infection. The physicochemical characteristics of T3Es dictate their patterns of association for multivalent interactions, influencing the material properties of phase-separating droplets based on the surrounding microenvironment in vivo or in vitro. Robust integration of MolPhase's effective prediction and experimental validation exhibit the potential to evaluate and explore how biomolecule PS functions in biological systems.
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Affiliation(s)
- Qiyu Liang
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Nana Peng
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Yi Xie
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Nivedita Kumar
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Weibo Gao
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore, Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore.
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 636921, Singapore, Singapore.
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32
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Bagchi D, Maity A, Chakraborty A. Metal Ion-Induced Unusual Stability of the Metastable Vesicle-like Intermediates Evolving during the Self-Assembly of Phenylalanine: Prominent Role of Surface Charge Inversion. J Phys Chem Lett 2024; 15:4468-4476. [PMID: 38631022 DOI: 10.1021/acs.jpclett.4c00444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
The underlying mechanism and intermediate formation in the self-assembly of aromatic amino acids, peptides, and proteins remain elusive despite numerous reports. We, for the first time, report that one can stabilize the intermediates by tuning the metal ion-amino acid interaction. Microscopic and spectroscopic investigations of the self-assembly of carboxybenzyl (Z)-protected phenylalanine (ZF) reveal that the bivalent metal ions eventually lead to the formation of fibrillar networks similar to blank ZF whereas the trivalent ions develop vesicle-like intermediates that do not undergo fibrillation for a prolonged time. The time-lapse measurement of surface charge reveals that the surface charge of blank ZF and in the presence of bivalent metal ions changes from a negative value to zero, implying unstable intermediates leading to the fibril network. Strikingly, a prominent charge inversion from an initial negative value to a positive value in the presence of trivalent metal ions imparts unusual stability to the metastable intermediates.
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Affiliation(s)
- Debanjan Bagchi
- Indian Institute of Technology Indore, Department of Chemistry, Indore 453552, Madhya Pradesh, India
| | - Avijit Maity
- Indian Institute of Technology Indore, Department of Chemistry, Indore 453552, Madhya Pradesh, India
| | - Anjan Chakraborty
- Indian Institute of Technology Indore, Department of Chemistry, Indore 453552, Madhya Pradesh, India
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33
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Shiramasa Y, Yamamoto R, Kashiwagi N, Sasaki F, Imai S, Ike M, Kitazawa S, Kameda T, Kitahara R. An aberrant fused in sarcoma liquid droplet of amyotrophic lateral sclerosis pathological variant, R495X, accelerates liquid-solid phase transition. Sci Rep 2024; 14:8914. [PMID: 38632300 PMCID: PMC11024109 DOI: 10.1038/s41598-024-59604-4] [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: 11/14/2023] [Accepted: 04/12/2024] [Indexed: 04/19/2024] Open
Abstract
Intracellular aggregation of fused in sarcoma (FUS) is associated with the pathogenesis of familial amyotrophic lateral sclerosis (ALS). Under stress, FUS forms liquid droplets via liquid-liquid phase separation (LLPS). Two types of wild-type FUS LLPS exist in equilibrium: low-pressure LLPS (LP-LLPS) and high-pressure LLPS (HP-LLPS); the former dominates below 2 kbar and the latter over 2 kbar. Although several disease-type FUS variants have been identified, the molecular mechanism underlying accelerated cytoplasmic granule formation in ALS patients remains poorly understood. Herein, we report the reversible formation of the two LLPS states and the irreversible liquid-solid transition, namely droplet aging, of the ALS patient-type FUS variant R495X using fluorescence microscopy and ultraviolet-visible absorption spectroscopy combined with perturbations in pressure and temperature. Liquid-to-solid phase transition was accelerated in the HP-LLPS of R495X than in the wild-type variant; arginine slowed the aging of droplets at atmospheric conditions by inhibiting the formation of HP-LLPS more selectively compared to that of LP-LLPS. Our findings provide new insight into the mechanism by which R495X readily forms cytoplasmic aggregates. Targeting the aberrantly formed liquid droplets (the HP-LLPS state) of proteins with minimal impact on physiological functions could be a novel therapeutic strategy for LLPS-mediated protein diseases.
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Affiliation(s)
- Yutaro Shiramasa
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Ryu Yamamoto
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Norika Kashiwagi
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Fuka Sasaki
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Sawaka Imai
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Mikihito Ike
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Soichiro Kitazawa
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Ryo Kitahara
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
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34
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Zhang H, Guo H, Li D, Zhang Y, Zhang S, Kang W, Liu C, Le W, Wang L, Li D, Dai B. Halogen doped graphene quantum dots modulate TDP-43 phase separation and aggregation in the nucleus. Nat Commun 2024; 15:2980. [PMID: 38582774 PMCID: PMC10998863 DOI: 10.1038/s41467-024-47167-x] [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: 09/04/2023] [Accepted: 03/22/2024] [Indexed: 04/08/2024] Open
Abstract
TDP-43 is implicated in the dynamic formation of nuclear bodies and stress granules through phase separation. In diseased states, it can further condense into pathological aggregates in the nucleus and cytoplasm, contributing to the onset of amyotrophic lateral sclerosis. In this study, we evaluate the effect of graphene quantum dots (GQDs) with different functional groups on TDP-43's phase separation and aggregation in various cellular locations. We find that halogen atom-doped GQDs (GQDs-Cl, Cl-GQDs-OH) penetrate the nuclear envelope, inhibiting the assembly of TDP-43 nuclear bodies and stress granules under oxidative stress or hyperosmotic environments, and reduce amyloid aggregates and disease-associated phosphorylation of TDP-43. Mechanistic analysis reveals GQDs-Cl and Cl-GQDs-OH modulate TDP-43 phase separation through hydrophobic and electrostatic interactions. Our findings highlight the potential of GQDs-Cl and Cl-GQDs-OH in modulating nuclear protein condensation and pathological aggregation, offering direction for the innovative design of GQDs to modulate protein phase separation and aggregation.
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Affiliation(s)
- Hong Zhang
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Huazhang Guo
- Institute of Nanochemistry and Nanobiology, School of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Baoshan District, Shanghai, 200444, PR China
| | - Danni Li
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yiling Zhang
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Wenyan Kang
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Department of Neurology, Ruijin Hainan Hospital, Shanghai Jiao Tong University School of Medicine (Boao Research Hospital), Hainan, 571434, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Weidong Le
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, 201318, China
- Center for Clinical and Translational Medicine, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Liang Wang
- Institute of Nanochemistry and Nanobiology, School of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Baoshan District, Shanghai, 200444, PR China.
| | - Dan Li
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200030, China.
- Bio-X-Renji Hospital Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Bin Dai
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
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35
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Ahn SY, Obermeyer AC. Selectivity of Complex Coacervation in Multi-Protein Mixtures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587643. [PMID: 38617366 PMCID: PMC11014547 DOI: 10.1101/2024.04.02.587643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Liquid-liquid phase separation of biomolecules is increasingly recognized as relevant to various cellular functions, and complex coacervation of biomacromolecules, particularly proteins, is emerging as a key mechanism for this phenomenon. Complex coacervation is also being explored as a potential protein purification method due to its potential scalability, aqueous operation, and ability to produce a highly concentrated product. However, to date most studies of complex coacervation have evaluated the phase behavior of a binary mixture of two oppositely charged macromolecules. Therefore, a comprehensive understanding of the phase behavior of complex biological mixtures has yet to be established. To address this, a panel of engineered proteins was designed to allow for quantitative analysis of the complex coacervation of individual proteins within a multi-component mixture. The behavior of individual proteins was evaluated using a defined mixture of proteins that mimics the charge profile of the E. coli proteome. To allow for direct quantification of proteins in each phase, spectrally separated fluorescent proteins were used to construct the protein mixture. From this quantitative analysis, we observed that the coacervation behavior of individual proteins in the mixture was consistent with each other, which was distinctive from the behavior when each protein was evaluated in a single-protein system. Subtle differences in biophysical properties between the proteins became noticeable in the mixture, which allowed us to elucidate parameters for protein complex coacervation. With this understanding, we successfully designed methods to enrich a range of proteins of interest from a mixture of proteins.
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Affiliation(s)
- So Yeon Ahn
- Department of Chemical Engineering, Columbia University, New York, NY
| | - Allie C Obermeyer
- Department of Chemical Engineering, Columbia University, New York, NY
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36
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Kovács ZJ, Harami GM, Pálinkás J, Kuljanishvili N, Hegedüs J, Harami‐Papp H, Mahmudova L, Khamisi L, Szakács G, Kovács M. DNA-dependent phase separation by human SSB2 (NABP1/OBFC2A) protein points to adaptations to eukaryotic genome repair processes. Protein Sci 2024; 33:e4959. [PMID: 38511671 PMCID: PMC10955726 DOI: 10.1002/pro.4959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/04/2024] [Accepted: 02/21/2024] [Indexed: 03/22/2024]
Abstract
Single-stranded DNA binding proteins (SSBs) are ubiquitous across all domains of life and play essential roles via stabilizing and protecting single-stranded (ss) DNA as well as organizing multiprotein complexes during DNA replication, recombination, and repair. Two mammalian SSB paralogs (hSSB1 and hSSB2 in humans) were recently identified and shown to be involved in various genome maintenance processes. Following our recent discovery of the liquid-liquid phase separation (LLPS) propensity of Escherichia coli (Ec) SSB, here we show that hSSB2 also forms LLPS condensates under physiologically relevant ionic conditions. Similar to that seen for EcSSB, we demonstrate the essential contribution of hSSB2's C-terminal intrinsically disordered region (IDR) to condensate formation, and the selective enrichment of various genome metabolic proteins in hSSB2 condensates. However, in contrast to EcSSB-driven LLPS that is inhibited by ssDNA binding, hSSB2 phase separation requires single-stranded nucleic acid binding, and is especially facilitated by ssDNA. Our results reveal an evolutionarily conserved role for SSB-mediated LLPS in the spatiotemporal organization of genome maintenance complexes. At the same time, differential LLPS features of EcSSB and hSSB2 point to functional adaptations to prokaryotic versus eukaryotic genome metabolic contexts.
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Affiliation(s)
- Zoltán J. Kovács
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
- HUN‐REN–ELTE Motor Pharmacology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Gábor M. Harami
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - János Pálinkás
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Natalie Kuljanishvili
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - József Hegedüs
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Hajnalka Harami‐Papp
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Lamiya Mahmudova
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Lana Khamisi
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Gergely Szakács
- HUN‐REN Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Hungarian Academy of SciencesBudapestHungary
- Center for Cancer ResearchMedical University of ViennaWienAustria
| | - Mihály Kovács
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
- HUN‐REN–ELTE Motor Pharmacology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
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37
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Li Z, Shen Q, Usher ET, Anderson AP, Iburg M, Lin R, Zimmer B, Meyer MD, Holehouse AS, You L, Chilkoti A, Dai Y, Lu GJ. Phase transition of GvpU regulates gas vesicle clustering in bacteria. Nat Microbiol 2024; 9:1021-1035. [PMID: 38553608 DOI: 10.1038/s41564-024-01648-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 02/20/2024] [Indexed: 04/06/2024]
Abstract
Gas vesicles (GVs) are microbial protein organelles that support cellular buoyancy. GV engineering has multiple applications, including reporter gene imaging, acoustic control and payload delivery. GVs often cluster into a honeycomb pattern to minimize occupancy of the cytosol. The underlying molecular mechanism and the influence on cellular physiology remain unknown. Using genetic, biochemical and imaging approaches, here we identify GvpU from Priestia megaterium as a protein that regulates GV clustering in vitro and upon expression in Escherichia coli. GvpU binds to the C-terminal tail of the core GV shell protein and undergoes a phase transition to form clusters in subsaturated solution. These properties of GvpU tune GV clustering and directly modulate bacterial fitness. GV variants can be designed with controllable sensitivity to GvpU-mediated clustering, enabling design of genetically tunable biosensors. Our findings elucidate the molecular mechanisms and functional roles of GV clustering, enabling its programmability for biomedical applications.
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Affiliation(s)
- Zongru Li
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Qionghua Shen
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Emery T Usher
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO, USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, Saint Louis, MO, USA
| | | | - Manuel Iburg
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Richard Lin
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Brandon Zimmer
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Matthew D Meyer
- Shared Equipment Authority, Rice University, Houston, TX, USA
| | - Alex S Holehouse
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO, USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, Saint Louis, MO, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Quantitative BioDesign, Duke University, Durham, NC, USA.
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
| | - Yifan Dai
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO, USA.
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
| | - George J Lu
- Department of Bioengineering, Rice University, Houston, TX, USA.
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38
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Guo D, Xiong Y, Fu B, Sha Z, Li B, Wu H. Liquid-Liquid phase separation in bacteria. Microbiol Res 2024; 281:127627. [PMID: 38262205 DOI: 10.1016/j.micres.2024.127627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/16/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
Cells are the essential building blocks of living organisms, responsible for carrying out various biochemical reactions and performing specific functions. In eukaryotic cells, numerous membrane organelles have evolved to facilitate these processes by providing specific spatial locations. In recent years, it has also been discovered that membraneless organelles play a crucial role in the subcellular organization of bacteria, which are single-celled prokaryotic microorganisms characterized by their simple structure and small size. These membraneless organelles in bacteria have been found to undergo Liquid-Liquid phase separation (LLPS), a molecular mechanism that allows for their assembly. Through extensive research, the occurrence of LLPS and its role in the spatial organization of bacteria have been better understood. Various biomacromolecules have been identified to exhibit LLPS properties in different bacterial species. LLPS which is introduced into synthetic biology applies to bacteria has important implications, and three recent research reports have shed light on its potential applications in this field. Overall, this review investigates the molecular mechanisms of LLPS occurrence and its significance in bacteria while also considering the future prospects of implementing LLPS in synthetic biology.
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Affiliation(s)
- Dong Guo
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yan Xiong
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Beibei Fu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Zhou Sha
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Bohao Li
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Chongqing 401331, China.
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39
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Furuki T, Nobeyama T, Suetaka S, Matsui R, Fukuoka T, Arai M, Shiraki K. Reentrant condensation of a multicomponent cola/milk system induced by polyphosphate. Food Chem X 2024; 21:101165. [PMID: 38328695 PMCID: PMC10847600 DOI: 10.1016/j.fochx.2024.101165] [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: 11/04/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/09/2024] Open
Abstract
Reentrant condensation (RC) is a protein behavior in which the protein solution shifts between the one- and two-phase state more than twice by increasing a single parameter. Although RC would be a candidate mechanism for the physicochemical design of food additives, no realistic model has been established under diverse contaminants like food materials. Here, we found that a mixture of cola and milk yielded RC. At pH 3.2-3.6, cola induced milk condensation at 30-40%, while lower or higher concentrations of cola did not. Furthermore, we reduced this cola/milk system to two pure components, casein in milk and polyphosphate (polyP) in cola, and investigated the characteristics of casein concentration and zeta potential. This was the first experimental demonstration of RC occurrence in a multicomponent system. The well-characterized cola/milk system would explore both the universal nature of proteins and the industrial application of RC.
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Affiliation(s)
- Tomohiro Furuki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
- Department of Integrated Sciences, College of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
- Ishikawa Prefectural Nanao High School, E-1-1 Nishi-fujihashi, Nanao, Ishikawa 926-0817, Japan
| | - Tomohiro Nobeyama
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Shunji Suetaka
- Department of Integrated Sciences, College of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Ryokei Matsui
- Ishikawa Prefectural Nanao High School, E-1-1 Nishi-fujihashi, Nanao, Ishikawa 926-0817, Japan
| | - Tatsuhiko Fukuoka
- Ishikawa Prefectural Nanao High School, E-1-1 Nishi-fujihashi, Nanao, Ishikawa 926-0817, Japan
| | - Munehito Arai
- Department of Integrated Sciences, College of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
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40
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Haider R, Shipley B, Surewicz K, Hinczewski M, Surewicz WK. Pathological C-terminal phosphomimetic substitutions alter the mechanism of liquid-liquid phase separation of TDP-43 low complexity domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586202. [PMID: 38585945 PMCID: PMC10996529 DOI: 10.1101/2024.03.21.586202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
C-terminally phosphorylated TAR DNA-binding protein of 43 kDa (TDP-43) marks the proteinaceous inclusions that characterize a number of age-related neurodegenerative diseases, including amyotrophic lateral sclerosis, frontotemporal lobar degeneration and Alzheimer's disease. TDP-43 phosphorylation at S403/S404, and especially at S409/S410, is in fact accepted as a biomarker of proteinopathy. These residues are located within the low complexity domain (LCD), which also drives the protein's liquid-liquid phase separation (LLPS). The impact of phosphorylation at these LCD sites on phase separation of the protein is a topic of great interest, as these post-translational modifications and LLPS are both implicated in proteinopathies. Here, we employed a combination of experimental and simulation-based approaches to explore this question on a phosphomimetic model of the TDP-43 LCD. Our turbidity and fluorescence microscopy data show that Ser-to-Asp substitutions at residues S403, S404, S409 and S410 alter the LLPS behavior of TDP-43 LCD. In particular, in contrast to the unmodified protein, the phosphomimetic variants display a biphasic dependence on salt concentration. Through coarse-grained modeling, we find that this biphasic salt dependence is derived from an altered mechanism of phase separation, in which LLPS-driving short-range intermolecular hydrophobic interactions are modulated by long-range attractive electrostatic interactions. Overall, this in vitro and in silico study provides a physiochemical foundation for understanding the impact of pathologically-relevant C-terminal phosphorylation on the LLPS of the TDP-43 in a more complex cellular environment.
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Affiliation(s)
- Raza Haider
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, United States
| | - Brandon Shipley
- Department of Physics, Case Western Reserve University, Cleveland, United States
| | - Krystyna Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, United States
| | - Michael Hinczewski
- Department of Physics, Case Western Reserve University, Cleveland, United States
| | - Witold K Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, United States
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41
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Johnson CN, Sojitra KA, Sohn EJ, Moreno-Romero AK, Baudin A, Xu X, Mittal J, Libich DS. Insights into Molecular Diversity within the FUS/EWS/TAF15 Protein Family: Unraveling Phase Separation of the N-Terminal Low-Complexity Domain from RNA-Binding Protein EWS. J Am Chem Soc 2024; 146:8071-8085. [PMID: 38492239 PMCID: PMC11156192 DOI: 10.1021/jacs.3c12034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
The FET protein family, comprising FUS, EWS, and TAF15, plays crucial roles in mRNA maturation, transcriptional regulation, and DNA damage response. Clinically, they are linked to Ewing family tumors and neurodegenerative diseases such as amyotrophic lateral sclerosis. The fusion protein EWS::FLI1, the causative mutation of Ewing sarcoma, arises from a genomic translocation that fuses a portion of the low-complexity domain (LCD) of EWS (EWSLCD) with the DNA binding domain of the ETS transcription factor FLI1. This fusion protein modifies transcriptional programs and disrupts native EWS functions, such as splicing. The exact role of the intrinsically disordered EWSLCD remains a topic of active investigation, but its ability to phase separate and form biomolecular condensates is believed to be central to EWS::FLI1's oncogenic properties. Here, we used paramagnetic relaxation enhancement NMR, microscopy, and all-atom molecular dynamics (MD) simulations to better understand the self-association and phase separation tendencies of the EWSLCD. Our NMR data and mutational analysis suggest that a higher density and proximity of tyrosine residues amplify the likelihood of condensate formation. MD simulations revealed that the tyrosine-rich termini exhibit compact conformations with unique contact networks and provided critical input on the relationship between contacts formed within a single molecule (intramolecular) and inside the condensed phase (intermolecular). These findings enhance our understanding of FET proteins' condensate-forming capabilities and underline differences between EWS, FUS, and TAF15.
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Affiliation(s)
- Courtney N. Johnson
- Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
| | - Kandarp A Sojitra
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Erich J. Sohn
- Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
| | - Alma K. Moreno-Romero
- Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
| | - Antoine Baudin
- Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
| | - Xiaoping Xu
- Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843, United States
| | - David S. Libich
- Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
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42
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Qian D, Ausserwoger H, Sneideris T, Farag M, Pappu RV, Knowles TPJ. Dominance Analysis: A formalism to uncover dominant energetic contributions to biomolecular condensate formation in multicomponent systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.12.544666. [PMID: 38562796 PMCID: PMC10983860 DOI: 10.1101/2023.06.12.544666] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Phase separation in aqueous solutions of macromolecules is thought to underlie the generation of biomolecular condensates in cells. Condensates are membraneless bodies, representing dense, macromolecule-rich phases that coexist with the dilute, macromolecule-deficient phase. In cells, condensates comprise hundreds of different macromolecular and small molecule solutes. Do all components contribute equally or very differently to the driving forces for phase separation? Currently, we lack a coherent formalism to answer this question, a gap we remedy in this work through the introduction of a formalism we term energy dominance analysis. This approach rests on model-free analysis of shapes of the dilute arms of phase boundaries, slopes of tie lines, and changes to dilute phase concentrations in response to perturbations of concentrations of different solutes. We present the formalism that underlies dominance analysis, and establish its accuracy and flexibility by deploying it to analyse phase spaces probed in silico, in vitro , and in cellulo .
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43
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Liu HN, Wang T, Hu JJ, Chen L, Shi X, Li YM, Luo SZ. The disordered protein SERF promotes α-Synuclein aggregation through liquid-liquid phase separation. J Biol Chem 2024; 300:105667. [PMID: 38272228 PMCID: PMC10877630 DOI: 10.1016/j.jbc.2024.105667] [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: 03/01/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/27/2024] Open
Abstract
The aggregation of α-Synuclein (α-Syn) into amyloid fibrils is the hallmark of Parkinson's disease. Under stress or other pathological conditions, the accumulation of α-Syn oligomers is the main contributor to the cytotoxicity. A potential approach for treating Parkinson's disease involves preventing the accumulation of these α-Syn oligomers. In this study, we present a novel mechanism involving a conserved group of disorderly proteins known as small EDRK-rich factor (SERF), which promotes the aggregation of α-Syn through a cophase separation process. Using diverse methods like confocal microscopy, fluorescence recovery after photobleaching assays, solution-state NMR spectroscopy, and Western blot, we determined that the N-terminal domain of SERF1a plays a role in the interactions that occur during cophase separation. Within these droplets, α-Syn undergoes a gradual transformation from solid condensates to amyloid fibrils, while SERF1a is excluded from the condensates and dissolves into the solution. Notably, in vivo experiments show that SERF1a cophase separation with α-Syn significantly reduces the deposition of α-Syn oligomers and decreases its cellular toxicity under stress. These findings suggest that SERF1a accelerates the conversion of α-Syn from highly toxic oligomers to less toxic fibrils through cophase separation, thereby mitigating the biological damage of α-Syn aggregation.
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Affiliation(s)
- He-Ning Liu
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Ting Wang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jin-Jian Hu
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Long Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xiangyan Shi
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China.
| | - Yan-Mei Li
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China.
| | - Shi-Zhong Luo
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
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44
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Hirano A, Wada M, Sato TK, Kameda T. N-acetyl amino acid amide solubility in aqueous 1,6-hexanediol solutions: Insights into the protein droplet deformation mechanism. Int J Biol Macromol 2024; 261:129724. [PMID: 38272403 DOI: 10.1016/j.ijbiomac.2024.129724] [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: 10/11/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 01/27/2024]
Abstract
Proteinaceous liquid droplets, generated by liquid-liquid phase separation, function as membraneless compartments that are essential for diverse biological functions. Studies addressing droplet generation have used 1,6-hexanediol (1,6-HD) as a droplet-discerning agent owing to its capacity to induce droplet deformation. Despite the empirical utility of 1,6-HD, the mechanism underlying 1,6-HD-induced droplet deformation remains unknown. In this study, the solubilities of N-acetyl amino acid amides, which correspond to proteinogenic amino acid residues, were examined in the presence of 1,6-HD at 25 °C. Other solvents included ethanol, 1-propanol, and amides. Remarkably, 1,6-HD effectively solubilized hydrophobic species (particularly aromatic species) and exhibited reduced efficacy in solubilizing hydrophilic species and peptide bond moieties. These solubilizing effects are reflected in changes in protein solubility and structure. Specifically, 1,6-HD primarily targets the hydrophobic regions of a protein, increasing protein solubility without causing substantial structural changes. This solubilization mechanism is essential for elucidating the role of 1,6-HD as a droplet-discerning agent and recognizing its potential limitations.
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Affiliation(s)
- Atsushi Hirano
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan.
| | - Momoyo Wada
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
| | - Takehiro K Sato
- Spiber, Inc., 234-1 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto, Tokyo 135-0064, Japan
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45
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Duan C, Wang R. A Unified Description of Salt Effects on the Liquid-Liquid Phase Separation of Proteins. ACS CENTRAL SCIENCE 2024; 10:460-468. [PMID: 38435530 PMCID: PMC10906038 DOI: 10.1021/acscentsci.3c01372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 03/05/2024]
Abstract
Protein aggregation via liquid-liquid phase separation (LLPS) is ubiquitous in nature and is intimately connected to many human diseases. Although it is widely known that the addition of salt has crucial impacts on the LLPS of proteins, full understanding of the salt effects remains an outstanding challenge. Here, we develop a molecular theory that systematically incorporates the self-consistent field theory for charged macromolecules into the solution thermodynamics. The electrostatic interaction, hydrophobicity, ion solvation, and translational entropy are included in a unified framework. Our theory fully captures the long-standing puzzles of the nonmonotonic salt concentration dependence and the specific ion effect. We find that proteins show salting-out at low salt concentrations due to ionic screening. The solubility follows the inverse Hofmeister series. In the high salt concentration regime, protein continues salting-out for small ions but turns to salting-in for larger ions, accompanied by the reversal of the Hofmeister series. We reveal that the solubility at high salt concentrations is determined by the competition between the solvation energy and translational entropy of the ion. Furthermore, we derive an analytical criterion for determining the boundary between the salting-in and salting-out regimes, which is in good agreement with experimental results for various proteins and salt ions.
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Affiliation(s)
- Chao Duan
- Department
of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Rui Wang
- Department
of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
- Materials
Sciences Division, Lawrence Berkeley National
Lab, Berkeley, California 94720, United States
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46
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Lao Z, Tang Y, Dong X, Tan Y, Li X, Liu X, Li L, Guo C, Wei G. Elucidating the reversible and irreversible self-assembly mechanisms of low-complexity aromatic-rich kinked peptides and steric zipper peptides. NANOSCALE 2024; 16:4025-4038. [PMID: 38347806 DOI: 10.1039/d3nr05130g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Many RNA-binding proteins such as fused-in sarcoma (FUS) can self-assemble into reversible liquid droplets and fibrils through the self-association of their low-complexity (LC) domains. Recent experiments have revealed that SYG-rich segments in the FUS LC domains play critical roles in the reversible self-assembly behaviors of FUS. These FUS LC segments alone can self-assemble into reversible kinked fibrils, which are markedly different from the canonical irreversible steric zipper β-sheet fibrils. However, the molecular determinants underlying the reversible and irreversible self-assembly are poorly understood. Herein we conducted extensive all-atom and coarse-grained molecular dynamics simulations of four representative hexapeptides: two low-complexity aromatic-rich kinked peptides from the amyotrophic lateral sclerosis-related FUS protein, FUS37-42 (SYSGYS) and FUS54-59 (SYSSYG); and two steric zipper peptides from Alzheimer's-associated Aβ and Tau proteins, Aβ16-21 (KLVFFA) and Tau306-311 (VQIVYK). We dissected their reversible and irreversible self-assembly dynamics, predicted their phase separation behaviors, and elucidated the underpinning molecular interactions. Our simulations showed that alternating stickers (Tyr) and spacers (Gly and Ser) in FUS37-42 and FUS54-59 facilitate the formation of highly dynamic coil-rich oligomers and lead to reversible self-assembly, while consecutive hydrophobic residues of LVFF in Aβ16-21 and IVY in Tau306-311 act as hydrophobic patches, favoring the formation of stable β-sheet-rich oligomers and driving the irreversible self-assembly. Intriguingly, we found that FUS37-42 and FUS54-59 peptides, possessing the same amino acid composition and the same number of sticker and spacer residues, display differential self-assembly propensities. This finding suggests that the self-assembly behaviors of FUS peptides are fine-tuned by the site-specific patterning of spacer residues (Ser and Gly). This study provides significant mechanistic insights into reversible and irreversible peptide self-assembly, which would be helpful for understanding the molecular mechanisms underlying the formation of biological liquid condensates and pathological solid amyloid fibrils.
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Affiliation(s)
- Zenghui Lao
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, China.
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, China.
| | - Xuewei Dong
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, Jiangsu, China
| | - Yuan Tan
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, China.
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xianshi Liu
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, China.
| | - Le Li
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, China.
| | - Cong Guo
- Department of Physics and International Centre for Quantum and Molecular Structures, College of Sciences, Shanghai University, Shanghai, China.
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, China.
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47
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Rozhkov S, Goryunov A, Rozhkova N. Molecular Serum Albumin Unmask Nanobio Properties of Molecular Graphenes in Shungite Carbon Nanoparticles. Int J Mol Sci 2024; 25:2465. [PMID: 38473711 DOI: 10.3390/ijms25052465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/11/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
Serum albumin is a popular macromolecule for studying the effect of proteins on the colloidal stability of nanoparticle (NP) dispersions, as well as the protein-nanoparticle interaction and protein corona formation. In this work, we analyze the specific conformation-dependent phase, redox, and fatty acid delivery properties of bovine albumin in the presence of shungite carbon (ShC) molecular graphenes stabilized in aqueous dispersions in the form of NPs in order to reveal the features of NP bioactivity. The formation of NP complexes with proteins (protein corona around NP) affects the transport properties of albumin for the delivery of fatty acids. Being acceptors of electrons and ligands, ShC NPs are capable of exhibiting both their own biological activity and significantly affecting conformational and phase transformations in protein systems.
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Affiliation(s)
- Sergey Rozhkov
- Institute of Biology, Karelian Research Centre RAS, 185910 Petrozavodsk, Russia
| | - Andrey Goryunov
- Institute of Biology, Karelian Research Centre RAS, 185910 Petrozavodsk, Russia
| | - Natalia Rozhkova
- Institute of Geology, Karelian Research Centre RAS, 185910 Petrozavodsk, Russia
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48
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Rinauro DJ, Chiti F, Vendruscolo M, Limbocker R. Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases. Mol Neurodegener 2024; 19:20. [PMID: 38378578 PMCID: PMC10877934 DOI: 10.1186/s13024-023-00651-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 02/22/2024] Open
Abstract
The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes.
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Affiliation(s)
- Dillon J Rinauro
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA.
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49
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Chappidi N, Quail T, Doll S, Vogel LT, Aleksandrov R, Felekyan S, Kühnemuth R, Stoynov S, Seidel CAM, Brugués J, Jahnel M, Franzmann TM, Alberti S. PARP1-DNA co-condensation drives DNA repair site assembly to prevent disjunction of broken DNA ends. Cell 2024; 187:945-961.e18. [PMID: 38320550 DOI: 10.1016/j.cell.2024.01.015] [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: 05/09/2023] [Revised: 10/27/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024]
Abstract
DNA double-strand breaks (DSBs) are repaired at DSB sites. How DSB sites assemble and how broken DNA is prevented from separating is not understood. Here we uncover that the synapsis of broken DNA is mediated by the DSB sensor protein poly(ADP-ribose) (PAR) polymerase 1 (PARP1). Using bottom-up biochemistry, we reconstitute functional DSB sites and show that DSB sites form through co-condensation of PARP1 multimers with DNA. The co-condensates exert mechanical forces to keep DNA ends together and become enzymatically active for PAR synthesis. PARylation promotes release of PARP1 from DNA ends and the recruitment of effectors, such as Fused in Sarcoma, which stabilizes broken DNA ends against separation, revealing a finely orchestrated order of events that primes broken DNA for repair. We provide a comprehensive model for the hierarchical assembly of DSB condensates to explain DNA end synapsis and the recruitment of effector proteins for DNA damage repair.
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Affiliation(s)
- Nagaraja Chappidi
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Thomas Quail
- Max Planck Institute of Cell Biology and Genetics (MPI-CBG), Pfotenhauerstr. 108, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany; Max Planck Institute for the Physics of Complex Systems (MPI-PKS), Nöthnitzer Str. 38, 01187 Dresden, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Simon Doll
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany
| | - Laura T Vogel
- Department of Molecular Physical Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Radoslav Aleksandrov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str, bl.21, 1113 Sofia, Bulgaria
| | - Suren Felekyan
- Department of Molecular Physical Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ralf Kühnemuth
- Department of Molecular Physical Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Stoyno Stoynov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str, bl.21, 1113 Sofia, Bulgaria
| | - Claus A M Seidel
- Department of Molecular Physical Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Jan Brugués
- Max Planck Institute of Cell Biology and Genetics (MPI-CBG), Pfotenhauerstr. 108, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany; Max Planck Institute for the Physics of Complex Systems (MPI-PKS), Nöthnitzer Str. 38, 01187 Dresden, Germany
| | - Marcus Jahnel
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany
| | - Titus M Franzmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany.
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50
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Wake N, Weng SL, Zheng T, Wang SH, Kirilenko V, Mittal J, Fawzi NL. Expanding the molecular grammar of polar residues and arginine in FUS prion-like domain phase separation and aggregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580391. [PMID: 38405719 PMCID: PMC10888811 DOI: 10.1101/2024.02.15.580391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
A molecular grammar governing low-complexity prion-like domains phase separation (PS) has been proposed based on mutagenesis experiments that identified tyrosine and arginine as primary drivers of phase separation via aromatic-aromatic and aromatic-arginine interactions. Here we show that additional residues make direct favorable contacts that contribute to phase separation, highlighting the need to account for these contributions in PS theories and models. We find that tyrosine and arginine make important contacts beyond only tyrosine-tyrosine and tyrosine-arginine, including arginine-arginine contacts. Among polar residues, glutamine in particular contributes to phase separation with sequence/position-specificity, making contacts with both tyrosine and arginine as well as other residues, both before phase separation and in condensed phases. For glycine, its flexibility, not its small solvation volume, favors phase separation by allowing favorable contacts between other residues and inhibits the liquid-to-solid (LST) transition. Polar residue types also make sequence-specific contributions to aggregation that go beyond simple rules, which for serine positions is linked to formation of an amyloid-core structure by the FUS low-complexity domain. Hence, here we propose a revised molecular grammar expanding the role of arginine and polar residues in prion-like domain protein phase separation and aggregation.
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Affiliation(s)
- Noah Wake
- Therapeutic Sciences Graduate Program, Brown University, Providence, RI 02912
| | - Shuo-Lin Weng
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Tongyin Zheng
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Szu-Huan Wang
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Valentin Kirilenko
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Jeetain Mittal
- Department of Chemistry, Texas A&M University, College Station, TX 77843
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843
| | - Nicolas L Fawzi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
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