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Ruan K, Bai G, Fang Y, Li D, Li T, Liu X, Lu B, Lu Q, Songyang Z, Sun S, Wang Z, Zhang X, Zhou W, Zhang H. Biomolecular condensates and disease pathogenesis. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2661-3. [PMID: 39037698 DOI: 10.1007/s11427-024-2661-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 06/21/2024] [Indexed: 07/23/2024]
Abstract
Biomolecular condensates or membraneless organelles (MLOs) formed by liquid-liquid phase separation (LLPS) divide intracellular spaces into discrete compartments for specific functions. Dysregulation of LLPS or aberrant phase transition that disturbs the formation or material states of MLOs is closely correlated with neurodegeneration, tumorigenesis, and many other pathological processes. Herein, we summarize the recent progress in development of methods to monitor phase separation and we discuss the biogenesis and function of MLOs formed through phase separation. We then present emerging proof-of-concept examples regarding the disruption of phase separation homeostasis in a diverse array of clinical conditions including neurodegenerative disorders, hearing loss, cancers, and immunological diseases. Finally, we describe the emerging discovery of chemical modulators of phase separation.
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Affiliation(s)
- Ke Ruan
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Ge Bai
- Nanhu Brain-computer Interface Institute, Hangzhou, 311100, China.
- Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Yanshan Fang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
| | - Xingguo Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 510000, China.
| | - Boxun Lu
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai, 200433, China.
| | - Qing Lu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Zhou Songyang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Shuguo Sun
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Zheng Wang
- The Second Affiliated Hospital, School of Basic Medical Sciences, Institute of Biomedical Innovation, Jiangxi Medical College, Nanchang University, Nanchang, 330031, China.
| | - Xin Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China.
| | - Wen Zhou
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Hong Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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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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3
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Ibrahim KA, Naidu AS, Miljkovic H, Radenovic A, Yang W. Label-Free Techniques for Probing Biomolecular Condensates. ACS NANO 2024; 18:10738-10757. [PMID: 38609349 DOI: 10.1021/acsnano.4c01534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Biomolecular condensates play important roles in a wide array of fundamental biological processes, such as cellular compartmentalization, cellular regulation, and other biochemical reactions. Since their discovery and first observations, an extensive and expansive library of tools has been developed to investigate various aspects and properties, encompassing structural and compositional information, material properties, and their evolution throughout the life cycle from formation to eventual dissolution. This Review presents an overview of the expanded set of tools and methods that researchers use to probe the properties of biomolecular condensates across diverse scales of length, concentration, stiffness, and time. In particular, we review recent years' exciting development of label-free techniques and methodologies. We broadly organize the set of tools into 3 categories: (1) imaging-based techniques, such as transmitted-light microscopy (TLM) and Brillouin microscopy (BM), (2) force spectroscopy techniques, such as atomic force microscopy (AFM) and the optical tweezer (OT), and (3) microfluidic platforms and emerging technologies. We point out the tools' key opportunities, challenges, and future perspectives and analyze their correlative potential as well as compatibility with other techniques. Additionally, we review emerging techniques, namely, differential dynamic microscopy (DDM) and interferometric scattering microscopy (iSCAT), that have huge potential for future applications in studying biomolecular condensates. Finally, we highlight how some of these techniques can be translated for diagnostics and therapy purposes. We hope this Review serves as a useful guide for new researchers in this field and aids in advancing the development of new biophysical tools to study biomolecular condensates.
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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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Ray S, Buell AK. Emerging experimental methods to study the thermodynamics of biomolecular condensate formation. J Chem Phys 2024; 160:091001. [PMID: 38445729 DOI: 10.1063/5.0190160] [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: 12/04/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024] Open
Abstract
The formation of biomolecular condensates in vivo is increasingly recognized to underlie a multitude of crucial cellular functions. Furthermore, the evolution of highly dynamic protein condensates into progressively less reversible assemblies is thought to be involved in a variety of disorders, from cancer over neurodegeneration to rare genetic disorders. There is an increasing need for efficient experimental methods to characterize the thermodynamics of condensate formation and that can be used in screening campaigns to identify and rationally design condensate modifying compounds. Theoretical advances in the field are also identifying the key parameters that need to be measured in order to obtain a comprehensive understanding of the underlying interactions and driving forces. Here, we review recent progress in the development of efficient and quantitative experimental methods to study the driving forces behind and the temporal evolution of biomolecular condensates.
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Affiliation(s)
- Soumik Ray
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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6
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Wu X, Sun Y, Yu J, Miserez A. Tuning the viscoelastic properties of peptide coacervates by single amino acid mutations and salt kosmotropicity. Commun Chem 2024; 7:5. [PMID: 38177438 PMCID: PMC10766971 DOI: 10.1038/s42004-023-01094-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024] Open
Abstract
Coacervation, or liquid-liquid phase separation (LLPS) of biomacromolecules, is increasingly recognized to play an important role both intracellularly and in the extracellular space. Central questions that remain to be addressed are the links between the material properties of coacervates (condensates) and both the primary and the secondary structures of their constitutive building blocks. Short LLPS-prone peptides, such as GY23 variants explored in this study, are ideal model systems to investigate these links because simple sequence modifications and the chemical environment strongly affect the viscoelastic properties of coacervates. Herein, a systematic investigation of the structure/property relationships of peptide coacervates was conducted using GY23 variants, combining biophysical characterization (plate rheology and surface force apparatus, SFA) with secondary structure investigations by infrared (IR) and circular dichroism (CD) spectroscopy. Mutating specific residues into either more hydrophobic or more hydrophilic residues strongly regulates the viscoelastic properties of GY23 coacervates. Furthermore, the ionic strength and kosmotropic characteristics (Hofmeister series) of the buffer in which LLPS is induced also significantly impact the properties of formed coacervates. Structural investigations by CD and IR indicate a direct correlation between variations in properties induced by endogenous (peptide sequence) or exogenous (ionic strength, kosmotropic characteristics, aging) factors and the β-sheet content within coacervates. These findings provide valuable insights to rationally design short peptide coacervates with programmable materials properties that are increasingly used in biomedical applications.
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Affiliation(s)
- Xi Wu
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore, 637553, Singapore
| | - Yue Sun
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore, 637553, Singapore
| | - Jing Yu
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 637553, Singapore.
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore, 637553, Singapore.
| | - Ali Miserez
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore, 637553, Singapore.
- School of Biological Sciences, 60 Nanyang Drive, NTU, Singapore, 636921, Singapore.
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7
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Sun Y, Hiew SH, Miserez A. Bioinspired Squid Peptides─A Tale of Curiosity-Driven Research Leading to Unforeseen Biomedical Applications. Acc Chem Res 2024; 57:164-174. [PMID: 38117659 DOI: 10.1021/acs.accounts.3c00685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The molecular design of many peptide-based materials originates from structural proteins identified in living organisms. Prominent examples that have garnered broad interdisciplinary research interest (chemistry, materials science, bioengineering, etc.) include elastin, silk, or mussel adhesive proteins. The critical first steps in this type of research are to identify a convenient model system of interest followed by sequencing the prevailing proteins from which these biological structures are assembled. In our laboratory, the main model systems for many years have been the hard biotools of cephalopods, particularly their parrot-like tough beak and their sucker ring teeth (SRT) embedded within the sucker cuptions that line the interior surfaces of their arms and tentacles. Unlike the majority of biological hard tissues, these structures are devoid of biominerals and consist of protein/polysaccharide biomolecular composites (the beak) or, in the case of SRT, are entirely made of proteins that are assembled by supramolecular interactions.In this Account, we chronicle our journey into the discovery of these intriguing biological materials. We initially focus on their excellent mechanical robustness followed by the identification and sequencing of the structural proteins from which they are built, using the latest "omics" techniques including next-generation sequencing and high-throughput proteomics. A common feature of these proteins is their modular architecture at the molecular level consisting of short peptide repeats. We describe the molecular design of these peptide building blocks, highlighting the consensus motifs identified to play a key role in biofabrication and in regulating the mechanical properties of the macroscopic biological material. Structure/property relationships unveiled through advanced spectroscopic and scattering techniques, including Raman, infrared, circular dichroism, and NMR spectroscopies as well as wide-angle and small-angle X-ray scattering, are also discussed.We then present recent developments in exploiting the discovered molecular designs to engineer peptides and their conjugates for promising biomedical applications. One example includes short peptide hydrogels that self-assemble entirely under aqueous conditions and simultaneously encapsulate large macromolecules during the gelation process. A second example involves peptide coacervate microdroplets produced by liquid-liquid phase separation. These microdroplets are capable of recruiting and delivering large macromolecular therapeutics (genes, mRNA, proteins, peptides, CRISPR/Cas 9 modalities, etc.) into mammalian cells, which introduces exciting prospects in cancer, gene, and immune therapies.This Account also serves as a testament to how curiosity-driven explorations, which may lack an obvious practical goal initially, can lead to discoveries with unexpected and promising translational potential.
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Affiliation(s)
- Yue Sun
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 637553, Singapore
| | - Shu Hui Hiew
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 637553, Singapore
| | - Ali Miserez
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 637553, Singapore
- School of Biological Sciences, NTU, 637551, Singapore
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8
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Edwards CER, Lakkis KL, Luo Y, Helgeson ME. Coacervate or precipitate? Formation of non-equilibrium microstructures in coacervate emulsions. SOFT MATTER 2023; 19:8849-8862. [PMID: 37947798 DOI: 10.1039/d3sm00901g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Non-equilibrium processing of aqueous polyelectrolyte complex (PEC) coacervates is critical to many applications. In particular, many coacervate-forming systems are known to become trapped in out-of-equilibrium states (e.g., precipitation). The mechanism and conditions under which these states form, and whether they age, is not clearly understood. Here, we elucidate the influence of processing on the PEC coarsening mechanism as it varies with flow during mixing for a model system of poly(allylamine hydrochloride) and poly(acrylic acid sodium salt) in water. We demonstrate that flow conditions can be used to toggle the formation of rough, precipitate-like aggregates of micron-scale PEC structures. These structures form at compositions with viscous-dominant equilibrium rheology, and observations of their formation via optical microscopy suggest that they comprise colloidal aggregates of PEC coacervate droplets. We further show that these aggregates exhibit micron-scale coarsening, with a mixing time-dependent characteristic aging time scale. The results show that the formation of precipitate-like structures is not solely determined by composition, but is instead highly sensitive to mass transport and colloidal instability effects. Our observations suggest that the details of mixing flow can provide non-equilibrium structural control of a broad range of PEC coacervate materials orthogonally to structure-property inspired polymeric design. We anticipate that these findings will open the door for future studies on the control of non-equilibrium PEC formation and structure.
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Affiliation(s)
- Chelsea E R Edwards
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106-5080, USA.
- Materials Research Laboratory, University of California, Santa Barbara, USA
| | - Kareem L Lakkis
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106-5080, USA.
| | - Yimin Luo
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106-5080, USA.
- Materials Research Laboratory, University of California, Santa Barbara, USA
| | - Matthew E Helgeson
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106-5080, USA.
- Materials Research Laboratory, University of California, Santa Barbara, USA
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Mekonnen G, Djaja N, Yuan X, Myong S. Advanced imaging techniques for studying protein phase separation in living cells and at single-molecule level. Curr Opin Chem Biol 2023; 76:102371. [PMID: 37523989 PMCID: PMC10528199 DOI: 10.1016/j.cbpa.2023.102371] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/04/2023] [Accepted: 06/24/2023] [Indexed: 08/02/2023]
Abstract
Protein-protein and protein-RNA interactions are essential for cell function and survival. These interactions facilitate the formation of ribonucleoprotein complexes and biomolecular condensates via phase separation. Such assembly is involved in transcription, splicing, translation and stress response. When dysregulated, proteins and RNA can undergo irreversible aggregation which can be cytotoxic and pathogenic. Despite technical advances in investigating biomolecular condensates, achieving the necessary spatiotemporal resolution to deduce the parameters that govern their assembly and behavior has been challenging. Many laboratories have applied advanced microscopy methods for imaging condensates. For example, single molecule imaging methods have enabled the detection of RNA-protein interaction, protein-protein interaction, protein conformational dynamics, and diffusional motion of molecules that report on the intrinsic molecular interactions underlying liquid-liquid phase separation. This review will outline advances in both microscopy and spectroscopy techniques which allow single molecule detection and imaging, and how these techniques can be used to probe unique aspects of biomolecular condensates.
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Affiliation(s)
- Gemechu Mekonnen
- Program in Cellular Molecular Developmental Biology and Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Nathalie Djaja
- Program in Cellular Molecular Developmental Biology and Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Xincheng Yuan
- Program in Cellular Molecular Developmental Biology and Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Sua Myong
- Program in Cellular Molecular Developmental Biology and Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA; Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
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Li M, Mirshafian R, Wang J, Mohanram H, Ahn KA, Hosseinzadeh S, Pervushin KV, Waite JH, Yu J. Compliant Clients: Catechols Exhibit Enhanced Solubility and Stability in Diverse Complex Coacervates. Biomacromolecules 2023; 24:4190-4198. [PMID: 37603820 DOI: 10.1021/acs.biomac.3c00519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Polyelectrolyte coacervates, with their greater-than-water density, low interfacial energy, shear thinning viscosity, and ability to undergo structural arrest, mediate the formation of diverse load-bearing macromolecular materials in living organisms as well as in industrial material fabrication. Coacervates, however, have other useful attributes that are challenging to study given the metastability of coacervate colloidal droplets and a lack of suitable analytical methods. We adopt solution electrochemistry and nuclear magnetic resonance measurements to obtain remarkable insights about coacervates as solvent media for low-molecular-weight catechols. When catechols are added to dispersions of coacervated polyelectrolytes, there are two significant consequences: (1) catechols preferentially partition up to 260-fold into the coacervate phase, and (2) coacervates stabilize catechol redox potentials by up to +200 mV relative to the equilibrium solution. The results suggest that the relationship between phase-separated polyelectrolytes and their client molecules is distinct from that existing in aqueous solution and has the potential for insulating many redox-unstable chemicals.
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Affiliation(s)
- Meng Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, P. R. China
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Razieh Mirshafian
- Marine Science Institute, University of California, Santa Barbara, California 93106, United States
- Department of Molecular, Cell & Developmental Biology, University of California, Santa Barbara, California 93106, United States
| | - Jining Wang
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
- Singapore Membrane Technology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
| | - Harini Mohanram
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Kollbe Ando Ahn
- Marine Science Institute, University of California, Santa Barbara, California 93106, United States
| | - Shayan Hosseinzadeh
- Marine Science Institute, University of California, Santa Barbara, California 93106, United States
| | - Konstantin V Pervushin
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - J Herbert Waite
- Marine Science Institute, University of California, Santa Barbara, California 93106, United States
- Department of Molecular, Cell & Developmental Biology, University of California, Santa Barbara, California 93106, United States
| | - Jing Yu
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore 637553, Singapore
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11
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Ray S, Mason TO, Boyens-Thiele L, Farzadfard A, Larsen JA, Norrild RK, Jahnke N, Buell AK. Mass photometric detection and quantification of nanoscale α-synuclein phase separation. Nat Chem 2023; 15:1306-1316. [PMID: 37337111 DOI: 10.1038/s41557-023-01244-8] [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: 07/11/2022] [Accepted: 05/19/2023] [Indexed: 06/21/2023]
Abstract
Protein liquid-liquid phase separation can lead to disease-related amyloid fibril formation. The mechanisms of conversion of monomeric protein into condensate droplets and of the latter into fibrils remain elusive. Here, using mass photometry, we demonstrate that the Parkinson's disease-related protein, α-synuclein, can form dynamic nanoscale clusters at physiologically relevant, sub-saturated concentrations. Nanoclusters nucleate in bulk solution and promote amyloid fibril formation of the dilute-phase monomers upon ageing. Their formation is instantaneous, even under conditions where macroscopic assemblies appear only after several days. The slow growth of the nanoclusters can be attributed to a kinetic barrier, probably due to an interfacial penalty from the charged C terminus of α-synuclein. Our findings reveal that α-synuclein phase separation occurs at much wider ranges of solution conditions than reported so far. Importantly, we establish mass photometry as a promising methodology to detect and quantify nanoscale precursors of phase separation. We also demonstrate its general applicability by probing the existence of nanoclusters of a non-amyloidogenic protein, Ddx4n1.
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Affiliation(s)
- Soumik Ray
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thomas O Mason
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Lars Boyens-Thiele
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Azad Farzadfard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Jacob Aunstrup Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Rasmus K Norrild
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Nadin Jahnke
- Novo Nordisk A/S, Novo Nordisk Park, Måløv, Denmark
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
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12
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Kubota R, Hiroi T, Ikuta Y, Liu Y, Hamachi I. Visualizing Formation and Dynamics of a Three-Dimensional Sponge-like Network of a Coacervate in Real Time. J Am Chem Soc 2023; 145:18316-18328. [PMID: 37562059 DOI: 10.1021/jacs.3c03793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Coacervates, which are formed by liquid-liquid phase separation, have been extensively explored as models for synthetic cells and membraneless organelles, so their in-depth structural analysis is crucial. However, both the inner structure dynamics and formation mechanism of coacervates remain elusive. Herein, we demonstrate real-time confocal observation of a three-dimensional sponge-like network in a dipeptide-based coacervate. In situ generation of the dipeptide allowed us to capture the emergence of the sponge-like network via unprecedented membrane folding of vesicle-shaped intermediates. We also visualized dynamic fluctuation of the network, including reversible engagement/disengagement of cross-links and a stochastic network kissing event. Photoinduced transient formation of a multiphase coacervate was achieved with a thermally responsive phase transition. Our findings expand the fundamental understanding of synthetic coacervates and provide opportunities to manipulate their physicochemical properties by engineering the inner network for potential applications in development of artificial cells and life-like material fabrication.
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Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Taro Hiroi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuriki Ikuta
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuchong Liu
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto University, Nishikyo-ku, Katsura 615-8530, Japan
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13
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Sárkány Z, Rocha F, Bratek‐Skicki A, Tompa P, Macedo‐Ribeiro S, Martins PM. Quantification of Surface Tension Effects and Nucleation-and-Growth Rates during Self-Assembly of Biological Condensates. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301501. [PMID: 37279376 PMCID: PMC10427409 DOI: 10.1002/advs.202301501] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/12/2023] [Indexed: 06/08/2023]
Abstract
Liquid-solid and liquid-liquid phase separation (PS) drives the formation of functional and disease-associated biological assemblies. Principles of phase equilibrium are here employed to derive a general kinetic solution that predicts the evolution of the mass and size of biological assemblies. Thermodynamically, protein PS is determined by two measurable concentration limits: the saturation concentration and the critical solubility. Due to surface tension effects, the critical solubility can be higher than the saturation concentration for small, curved nuclei. Kinetically, PS is characterized by the primary nucleation rate constant and a combined rate constant accounting for growth and secondary nucleation. It is demonstrated that the formation of a limited number of large condensates is possible without active mechanisms of size control and in the absence of coalescence phenomena. The exact analytical solution can be used to interrogate how the elementary steps of PS are affected by candidate drugs.
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Affiliation(s)
- Zsuzsa Sárkány
- IBMC − Instituto de Biologia Molecular e CelularUniversidade do PortoPorto4150–180Portugal
- i3S − Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPorto4150–180Portugal
| | - Fernando Rocha
- LEPABE − Laboratory for Process Engineering Environment Biotechnology and EnergyFaculdade de Engenharia da Universidade do PortoPorto4200‐465Portugal
| | - Anna Bratek‐Skicki
- Jerzy Haber Institute of Catalysis and Surface ChemistryPolish Academy of SciencesNiezapominajek 8KrakowPL30239Poland
- VIB‐VUB Center for Structural BiologyVlaams Instituut voor BiotechnologyBrussels1050 IxellesBelgium
- Structural Biology Brussels (SBB)Bioengineering Sciences DepartmentVrije Universiteit Brussel (VUB)BrusselsB‐1050Belgium
| | - Peter Tompa
- VIB‐VUB Center for Structural BiologyVlaams Instituut voor BiotechnologyBrussels1050 IxellesBelgium
- Structural Biology Brussels (SBB)Bioengineering Sciences DepartmentVrije Universiteit Brussel (VUB)BrusselsB‐1050Belgium
- Institute of EnzymologyResearch Centre for Natural SciencesBudapest1117Hungary
| | - Sandra Macedo‐Ribeiro
- IBMC − Instituto de Biologia Molecular e CelularUniversidade do PortoPorto4150–180Portugal
- i3S − Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPorto4150–180Portugal
| | - Pedro M. Martins
- IBMC − Instituto de Biologia Molecular e CelularUniversidade do PortoPorto4150–180Portugal
- i3S − Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPorto4150–180Portugal
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14
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Guo X, Zhu K, Zhu X, Zhao W, Miao Y. Two-dimensional molecular condensation in cell signaling and mechanosensing. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1064-1074. [PMID: 37475548 PMCID: PMC10423693 DOI: 10.3724/abbs.2023132] [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: 01/28/2023] [Accepted: 05/21/2023] [Indexed: 07/22/2023] Open
Abstract
Membraneless organelles (MLO) regulate diverse biological processes in a spatiotemporally controlled manner spanning from inside to outside of the cells. The plasma membrane (PM) at the cell surface serves as a central platform for forming multi-component signaling hubs that sense mechanical and chemical cues during physiological and pathological conditions. During signal transduction, the assembly and formation of membrane-bound MLO are dynamically tunable depending on the physicochemical properties of the surrounding environment and partitioning biomolecules. Biomechanical properties of MLO-associated membrane structures can control the microenvironment for biomolecular interactions and assembly. Lipid-protein complex interactions determine the catalytic region's assembly pattern and assembly rate and, thereby, the amplitude of activities. In this review, we will focus on how cell surface microenvironments, including membrane curvature, surface topology and tension, lipid-phase separation, and adhesion force, guide the assembly of PM-associated MLO for cell signal transductions.
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Affiliation(s)
- Xiangfu Guo
- School of ChemistryChemical Engineering and BiotechnologyNanyang Technological UniversitySingapore637457Singapore
| | - Kexin Zhu
- School of Biological SciencesNanyang Technological UniversitySingapore637551Singapore
| | - Xinlu Zhu
- School of Biological SciencesNanyang Technological UniversitySingapore637551Singapore
| | - Wenting Zhao
- School of ChemistryChemical Engineering and BiotechnologyNanyang Technological UniversitySingapore637457Singapore
- Institute for Digital Molecular Analytics and ScienceNanyang Technological UniversitySingapore636921Singapore
| | - Yansong Miao
- School of Biological SciencesNanyang Technological UniversitySingapore637551Singapore
- Institute for Digital Molecular Analytics and ScienceNanyang Technological UniversitySingapore636921Singapore
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15
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Zhang Z, Huang G, Song Z, Gatch AJ, Ding F. Amyloid Aggregation and Liquid-Liquid Phase Separation from the Perspective of Phase Transitions. J Phys Chem B 2023; 127:6241-6250. [PMID: 37414583 PMCID: PMC10404378 DOI: 10.1021/acs.jpcb.3c01426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Amyloid aggregation describes the aberrant self-assembly of peptides into ordered fibrils characterized by cross-β spine cores and is associated with many neurodegenerative diseases and Type 2 diabetes. Oligomers, populated during the early stage of aggregation, are found to be more cytotoxic than mature fibrils. Recently, many amyloidogenic peptides have been reported to undergo liquid-liquid phase separation (LLPS)─a biological process important for the compartmentalization of biomolecules in living cells─prior to fibril formation. Understanding the relationship between LLPS and amyloid aggregation, especially the formation of oligomers, is essential for uncovering disease mechanisms and mitigating amyloid toxicity. In this Perspective, available theories and models of amyloid aggregation and LLPS are first briefly reviewed. By drawing analogies to gas, liquid, and solid phases in thermodynamics, a phase diagram of protein monomer, droplet, and fibril states separated by coexistence lines can be inferred. Due to the high free energy barrier of fibrillization kinetically delaying the formation of fibril seeds out of the droplets, a "hidden" monomer-droplet coexistence line extends into the fibril phase. Amyloid aggregation can then be described as the equilibration process from the initial "out-of-equilibrium" state of a homogeneous solution of monomers to the final equilibrium state of stable amyloid fibrils coexisting with monomers and/or droplets via the formation of metastable or stable droplets as the intermediates. The relationship between droplets and oligomers is also discussed. We suggest that the droplet formation of LLPS should be considered in future studies of amyloid aggregation, which may help to better understand the aggregation process and develop therapeutic strategies to mitigate amyloid toxicity.
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Affiliation(s)
- Zhenzhen Zhang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Gangtong Huang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Zhiyuan Song
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Adam J. Gatch
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, United States
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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16
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Zeng F, Jiang Y, He N, Guo T, Zhao T, Qu M, Sun Y, Chen S, Wang D, Luo Y, Chu G, Chen J, Sun SG, Liao HG. Real-time imaging of sulfhydryl single-stranded DNA aggregation. Commun Chem 2023; 6:86. [PMID: 37130956 PMCID: PMC10154300 DOI: 10.1038/s42004-023-00886-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 04/18/2023] [Indexed: 05/04/2023] Open
Abstract
The structure and functionality of biomacromolecules are often regulated by chemical bonds, however, the regulation process and underlying mechanisms have not been well understood. Here, by using in situ liquid-phase transmission electron microscopy (LP-TEM), we explored the function of disulfide bonds during the self-assembly and structural evolution of sulfhydryl single-stranded DNA (SH-ssDNA). Sulfhydryl groups could induce self-assembly of SH-ssDNA into circular DNA containing disulfide bonds (SS-cirDNA). In addition, the disulfide bond interaction triggered the aggregation of two SS-cirDNA macromolecules along with significant structural changes. This visualization strategy provided structure information at nanometer resolution in real time and space, which could benefit future biomacromolecules research.
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Affiliation(s)
- Fanwei Zeng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Youhong Jiang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Nana He
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Tiantian Guo
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Tiqing Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Mi Qu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Yue Sun
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Shuting Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Dan Wang
- State Key Laboratory of Organic-Inorganic Composites and Research Center of the Ministry of Education for High Gravity Engineering and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yong Luo
- State Key Laboratory of Organic-Inorganic Composites and Research Center of the Ministry of Education for High Gravity Engineering and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Guangwen Chu
- State Key Laboratory of Organic-Inorganic Composites and Research Center of the Ministry of Education for High Gravity Engineering and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jianfeng Chen
- State Key Laboratory of Organic-Inorganic Composites and Research Center of the Ministry of Education for High Gravity Engineering and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shi-Gang Sun
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Hong-Gang Liao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen, China.
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17
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Vratsanos M, Xue W, Rosenmann ND, Zarzar LD, Gianneschi NC. Ouzo Effect Examined at the Nanoscale via Direct Observation of Droplet Nucleation and Morphology. ACS CENTRAL SCIENCE 2023; 9:457-465. [PMID: 36968532 PMCID: PMC10037490 DOI: 10.1021/acscentsci.2c01194] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Indexed: 06/12/2023]
Abstract
Herein, we present the direct observation via liquid-phase transmission electron microscopy (LPTEM) of the nucleation and growth pathways of structures formed by the so-called "ouzo effect", which is a classic example of surfactant-free, spontaneous emulsification. Such liquid-liquid phase separation occurs in ternary systems with an appropriate cosolvent such that the addition of the third component extracts the cosolvent and makes the other component insoluble. Such droplets are homogeneously sized, stable, and require minimal energy to disperse compared to conventional emulsification methods. Thus, ouzo precipitation processes are an attractive, straightforward, and energy-efficient technique for preparing dispersions, especially those made on an industrial scale. While this process and the resulting emulsions have been studied by numerous indirect techniques (e.g., X-ray and light scattering), direct observation of such structures and their formation at the nanoscale has remained elusive. Here, we employed the nascent technique of LPTEM to simultaneously evaluate droplet growth and nanostructure. Observation of such emulsification and its rate dependence is a promising indication that similar LPTEM methodologies may be used to investigate emulsion formation and kinetics.
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Affiliation(s)
- Maria
A. Vratsanos
- Department
of Materials Science & Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Wangyang Xue
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Nathan D. Rosenmann
- Department
of Materials Science & Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Lauren D. Zarzar
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department
of Materials Science and Engineering, The
Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Materials
Research Institute, The Pennsylvania State
University, University Park, Pennsylvania 16802, United States
| | - Nathan C. Gianneschi
- Department
of Materials Science & Engineering, Northwestern University, Evanston, Illinois 60208, United States
- International
Institute for Nanotechnology, Simpson Querrey Institute, Chemistry
of Life Processes Institute, Northwestern
University, Evanston, Illinois 60208, United
States
- Department
of Chemistry, Department of Biomedical Engineering, Department of
Pharmacology, Northwestern University, Evanston, Illinois 60208, United States
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18
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Miserez A, Yu J, Mohammadi P. Protein-Based Biological Materials: Molecular Design and Artificial Production. Chem Rev 2023; 123:2049-2111. [PMID: 36692900 PMCID: PMC9999432 DOI: 10.1021/acs.chemrev.2c00621] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Polymeric materials produced from fossil fuels have been intimately linked to the development of industrial activities in the 20th century and, consequently, to the transformation of our way of living. While this has brought many benefits, the fabrication and disposal of these materials is bringing enormous sustainable challenges. Thus, materials that are produced in a more sustainable fashion and whose degradation products are harmless to the environment are urgently needed. Natural biopolymers─which can compete with and sometimes surpass the performance of synthetic polymers─provide a great source of inspiration. They are made of natural chemicals, under benign environmental conditions, and their degradation products are harmless. Before these materials can be synthetically replicated, it is essential to elucidate their chemical design and biofabrication. For protein-based materials, this means obtaining the complete sequences of the proteinaceous building blocks, a task that historically took decades of research. Thus, we start this review with a historical perspective on early efforts to obtain the primary sequences of load-bearing proteins, followed by the latest developments in sequencing and proteomic technologies that have greatly accelerated sequencing of extracellular proteins. Next, four main classes of protein materials are presented, namely fibrous materials, bioelastomers exhibiting high reversible deformability, hard bulk materials, and biological adhesives. In each class, we focus on the design at the primary and secondary structure levels and discuss their interplays with the mechanical response. We finally discuss earlier and the latest research to artificially produce protein-based materials using biotechnology and synthetic biology, including current developments by start-up companies to scale-up the production of proteinaceous materials in an economically viable manner.
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Affiliation(s)
- Ali Miserez
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore637553.,School of Biological Sciences, NTU, Singapore637551
| | - Jing Yu
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore637553.,Institute for Digital Molecular Analytics and Science (IDMxS), NTU, 50 Nanyang Avenue, Singapore637553
| | - Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd., Espoo, UusimaaFI-02044, Finland
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19
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Hiew SH, Lu Y, Han H, Gonçalves RA, Alfarano SR, Mezzenga R, Parikh AN, Mu Y, Miserez A. Modulation of Mechanical Properties of Short Bioinspired Peptide Materials by Single Amino-Acid Mutations. J Am Chem Soc 2023; 145:3382-3393. [PMID: 36730942 DOI: 10.1021/jacs.2c09853] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The occurrence of modular peptide repeats in load-bearing (structural) proteins is common in nature, with distinctive peptide sequences that often remain conserved across different phylogenetic lineages. These highly conserved peptide sequences endow specific mechanical properties to the material, such as toughness or elasticity. Here, using bioinformatic tools and phylogenetic analysis, we have identified the GX8 peptide with the sequence GLYGGYGX (where X can be any residue) in a wide range of organisms. By simple mutation of the X residue, we demonstrate that GX8 can be self-assembled into various supramolecular structures, exhibiting vastly different physicochemical and viscoelastic properties, from liquid-like coacervate microdroplets to hydrogels to stiff solid materials. A combination of spectroscopic, electron microscopy, mechanical, and molecular dynamics studies is employed to obtain insights into molecular scale interactions driving self-assembly of GX8 peptides, underscoring that π-π stacking and hydrophobic interactions are the drivers of peptide self-assembly, whereas the X residue determines the extent of hydrogen bonding that regulates the macroscopic mechanical response. This study highlights the ability of single amino-acid polymorphism to tune the supramolecular assembly and bulk material properties of GX8 peptides, enabling us to cover a broad range of potential biomedical applications such as hydrogels for tissue engineering or coacervates for drug delivery.
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Affiliation(s)
- Shu Hui Hiew
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Yang Lu
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Hao Han
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Rui A Gonçalves
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Serena Rosa Alfarano
- Department of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Atul N Parikh
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore.,Departments of Biomedical Engineering and Materials Science & Engineering, University of California, Davis, California 95616, United States
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Ali Miserez
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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20
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Erkamp NA, Qi R, Welsh TJ, Knowles TPJ. Microfluidics for multiscale studies of biomolecular condensates. LAB ON A CHIP 2022; 23:9-24. [PMID: 36269080 PMCID: PMC9764808 DOI: 10.1039/d2lc00622g] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/04/2022] [Indexed: 05/12/2023]
Abstract
Membraneless organelles formed through condensation of biomolecules in living cells have become the focus of sustained efforts to elucidate their mechanisms of formation and function. These condensates perform a range of vital functions in cells and are closely connected to key processes in functional and aberrant biology. Since these systems occupy a size scale intermediate between single proteins and conventional protein complexes on the one hand, and cellular length scales on the other hand, they have proved challenging to probe using conventional approaches from either protein science or cell biology. Additionally, condensate can form, solidify and perform functions on various time-scales. From a physical point of view, biomolecular condensates are colloidal soft matter systems, and microfluidic approaches, which originated in soft condensed matter research, have successfully been used to study biomolecular condensates. This review explores how microfluidics have aided condensate research into the thermodynamics, kinetics and other properties of condensates, by offering high-throughput and novel experimental setups.
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Affiliation(s)
- Nadia A Erkamp
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Runzhang Qi
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Timothy J Welsh
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge, CB3 0HE, UK
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21
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Luo L, Wu Q, Ji S, Liu Y, Cheng K, Liu M, Jiang L, Li C. Liquid-Liquid Phase Separation of an Intrinsically Disordered Region of a Germ Cell-Specific Protein Modulates the Stability and Conformational Exchange Rate of SH3 Domain. J Phys Chem Lett 2022; 13:7804-7808. [PMID: 35975930 DOI: 10.1021/acs.jpclett.2c01920] [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: 06/15/2023]
Abstract
The phenomenon of liquid-liquid phase separation is found in numerous biological processes. The biomolecules enveloped in the phase-separated droplets experience an obviously different environment from those in cellular or aqueous solution. Herein, we quantitatively characterized the thermodynamics and exchange kinetics of a model protein SH3 domain in the condensed phase of an intrinsically disordered region of a germ cell-specific protein DDX4N1 by using 19F-NMR spectroscopy. The stability and exchange rate of the SH3 domain are different from those in buffer and macromolecular crowding conditions. Our finding indicates that the local transient ordered microstructure and heterogeneity in the condensates play significant roles in modulating the biophysical properties of the enveloped proteins, and this finding may be essential to further our understanding how phase separation regulates the function of proteins in cells.
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Affiliation(s)
- Liang Luo
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Science, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiong Wu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Science, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shixia Ji
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China
| | - Yixiang Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Science, Wuhan, 430071, China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Science, Wuhan, 430071, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Science, Wuhan, 430071, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China
| | - Ling Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Science, Wuhan, 430071, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Science, Wuhan, 430071, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China
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22
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Cai H, Vernon RM, Forman-Kay JD. An Interpretable Machine-Learning Algorithm to Predict Disordered Protein Phase Separation Based on Biophysical Interactions. Biomolecules 2022; 12:biom12081131. [PMID: 36009025 PMCID: PMC9405563 DOI: 10.3390/biom12081131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/21/2022] Open
Abstract
Protein phase separation is increasingly understood to be an important mechanism of biological organization and biomaterial formation. Intrinsically disordered protein regions (IDRs) are often significant drivers of protein phase separation. A number of protein phase-separation-prediction algorithms are available, with many being specific for particular classes of proteins and others providing results that are not amenable to the interpretation of the contributing biophysical interactions. Here, we describe LLPhyScore, a new predictor of IDR-driven phase separation, based on a broad set of physical interactions or features. LLPhyScore uses sequence-based statistics from the RCSB PDB database of folded structures for these interactions, and is trained on a manually curated set of phase-separation-driving proteins with different negative training sets including the PDB and human proteome. Competitive training for a variety of physical chemical interactions shows the greatest contribution of solvent contacts, disorder, hydrogen bonds, pi–pi contacts, and kinked beta-structures to the score, with electrostatics, cation–pi contacts, and the absence of a helical secondary structure also contributing. LLPhyScore has strong phase-separation-prediction recall statistics and enables a breakdown of the contribution from each physical feature to a sequence’s phase-separation propensity, while recognizing the interdependence of many of these features. The tool should be a valuable resource for guiding experiments and providing hypotheses for protein function in normal and pathological states, as well as for understanding how specificity emerges in defining individual biomolecular condensates.
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Affiliation(s)
- Hao Cai
- Molecular Medicine Program, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Robert M. Vernon
- Molecular Medicine Program, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Julie D. Forman-Kay
- Molecular Medicine Program, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Correspondence:
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23
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Shen Y, Zhao X, Gong R, Ngo E, Maurice JL, Roca i Cabarrocas P, Chen W. Influence of the Electron Beam and the Choice of Heating Membrane on the Evolution of Si Nanowires’ Morphology in In Situ TEM. MATERIALS 2022; 15:ma15155244. [PMID: 35955179 PMCID: PMC9369465 DOI: 10.3390/ma15155244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/23/2022] [Accepted: 07/27/2022] [Indexed: 01/25/2023]
Abstract
We used in situ transmission electron microscopy (TEM) to observe the dynamic changes of Si nanowires under electron beam irradiation. We found evidence of structural evolutions under TEM observation due to a combination of electron beam and thermal effects. Two types of heating holders were used: a carbon membrane, and a silicon nitride membrane. Different evolution of Si nanowires on these membranes was observed. Regarding the heating of Si nanowires on a C membrane at 800 °C and above, a serious degradation dependent on the diameter of the Si nanowire was observed under the electron beam, with the formation of Si carbide. When the membrane was changed to Si nitride, a reversible sectioning and welding of the Si nanowire was observed.
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Affiliation(s)
- Ya Shen
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China; (Y.S.); (X.Z.); (R.G.)
| | - Xuechun Zhao
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China; (Y.S.); (X.Z.); (R.G.)
| | - Ruiling Gong
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China; (Y.S.); (X.Z.); (R.G.)
| | - Eric Ngo
- Laboratoire de Physique des Interfaces et des Couches Minces (LPICM), Centre National de la Recherche Scientifique (CNRS), Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France; (E.N.); (J.-L.M.); (P.R.i.C.)
| | - Jean-Luc Maurice
- Laboratoire de Physique des Interfaces et des Couches Minces (LPICM), Centre National de la Recherche Scientifique (CNRS), Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France; (E.N.); (J.-L.M.); (P.R.i.C.)
| | - Pere Roca i Cabarrocas
- Laboratoire de Physique des Interfaces et des Couches Minces (LPICM), Centre National de la Recherche Scientifique (CNRS), Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France; (E.N.); (J.-L.M.); (P.R.i.C.)
| | - Wanghua Chen
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China; (Y.S.); (X.Z.); (R.G.)
- Correspondence:
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24
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Garg DK, Bhat R. Modulation of assembly of TDP-43 low-complexity domain by heparin: From droplets to amyloid fibrils. Biophys J 2022; 121:2568-2582. [PMID: 35644946 PMCID: PMC9300664 DOI: 10.1016/j.bpj.2022.05.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 09/03/2021] [Accepted: 05/25/2022] [Indexed: 11/02/2022] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is an RNA-regulating protein that carries out many cellular functions through liquid-liquid phase separation (LLPS). The LLPS of TDP-43 is mediated by its C-terminal low-complexity domain (TDP43-LCD) corresponding to the region 267-414. In neurodegenerative disorders amyotrophic lateral sclerosis and frontotemporal dementia, pathological inclusions of the TDP-43 are found that are rich in the C-terminal fragments of ∼25 and ∼35 kDa, of which TDP43-LCD is a part. Thus, understanding the assembly process of TDP43-LCD is essential, given its involvement in the formation of both functional liquid-like assemblies and solid- or gel-like pathological aggregates. Here, we show that the solution pH and salt modulate TDP43-LCD LLPS. A gradual reduction in the pH below its isoelectric point of 9.8 results in a monotonic decrease of TDP43-LCD LLPS due to charge-charge repulsion between monomers, while at pH 6 and below no LLPS was observed. The addition of heparin to TDP43-LCD solution at pH 6, at a 1:2 heparin-to-TDP43-LCD molar ratio, promotes TDP43-LCD LLPS, while at higher concentration, it disrupts LLPS through a reentrant phase transition. Upon incubation at pH 6, TDP43-LCD undergoes gelation without phase separation. However, in the reentrant regime in the presence of a high heparin concentration, it forms thick amyloid aggregates that are significantly more SDS resistant than the gel. The results indicate that the material nature of the TDP43-LCD assembly products can be modulated by heparin which is significant in the context of liquid-to-solid phase transition observed in TDP-43 proteinopathies. Our findings are also crucial in relation to similar transitions that could occur due to alteration in the molecular level interactions among various multivalent biomolecules involving other LCDs and RNAs.
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Affiliation(s)
| | - Rajiv Bhat
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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25
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Antifeeva IA, Fonin AV, Fefilova AS, Stepanenko OV, Povarova OI, Silonov SA, Kuznetsova IM, Uversky VN, Turoverov KK. Liquid-liquid phase separation as an organizing principle of intracellular space: overview of the evolution of the cell compartmentalization concept. Cell Mol Life Sci 2022; 79:251. [PMID: 35445278 PMCID: PMC11073196 DOI: 10.1007/s00018-022-04276-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/24/2022] [Accepted: 03/27/2022] [Indexed: 12/14/2022]
Abstract
At the turn of the twenty-first century, fundamental changes took place in the understanding of the structure and function of proteins and then in the appreciation of the intracellular space organization. A rather mechanistic model of the organization of living matter, where the function of proteins is determined by their rigid globular structure, and the intracellular processes occur in rigidly determined compartments, was replaced by an idea that highly dynamic and multifunctional "soft matter" lies at the heart of all living things. According this "new view", the most important role in the spatio-temporal organization of the intracellular space is played by liquid-liquid phase transitions of biopolymers. These self-organizing cellular compartments are open dynamic systems existing at the edge of chaos. They are characterized by the exceptional structural and compositional dynamics, and their multicomponent nature and polyfunctionality provide means for the finely tuned regulation of various intracellular processes. Changes in the external conditions can cause a disruption of the biogenesis of these cellular bodies leading to the irreversible aggregation of their constituent proteins, followed by the transition to a gel-like state and the emergence of amyloid fibrils. This work represents a historical overview of changes in our understanding of the intracellular space compartmentalization. It also reflects methodological breakthroughs that led to a change in paradigms in this area of science and discusses modern ideas about the organization of the intracellular space. It is emphasized here that the membrane-less organelles have to combine a certain resistance to the changes in their environment and, at the same time, show high sensitivity to the external signals, which ensures the normal functioning of the cell.
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Affiliation(s)
- Iuliia A Antifeeva
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Anna S Fefilova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Olga I Povarova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Sergey A Silonov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL, 33612, USA.
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia.
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The crystallization of decanoic acid/dopamine supramolecular self-assemblies in the presence of coacervates. J Colloid Interface Sci 2022; 615:759-767. [PMID: 35176542 DOI: 10.1016/j.jcis.2022.02.016] [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: 01/10/2022] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 11/20/2022]
Abstract
HYPOTHESIS Supramolecular self-assemblies involving non-covalent interactions play important roles in material science as well as living systems as they result in unique properties and/or functions. However, understanding of their self-assembly mechanism and crystallization has remained rudimentary. EXPERIMENT Here, we focus on biomolecular fatty acid and dopamine, which commonly exist in biological systems and closely related to neurodegenerative diseases, and investigate their self-assembly pathway by optical and fluorescence microscopy, DLS, SAXS, TEM, 2D-NMR, etc. FINDINGS: It is found that they could form the crystalline plates in solution or via a metastable liquid - liquid phase separation (LLPS). The nucleation and growth of crystalline plates observed occurs in solution or the dilute phase of LLPS, and not within the concentrated coacervate phase. This is because in coacervate, dopamine intercalates into fatty acid through hydrophobic and electrostatic interaction, which hinders the rearrangement of molecules and nucleation process, whereas in solution or dilute phase, they have the mobility to arrange into ordered structures to maximize electrostatic, hydrogen bonding and π-π interactions, leading to nucleation and crystallization. Moreover, the transitions between the coacervates and crystalline phase can be realized by adjusting the temperature. Our results shed light on the multistep nucleation in the presence of LLPS, as well as molecular mechanisms involved, thus further extending the nucleation-growth mechanisms.
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Ramos R, Bernard J, Ganachaud F, Miserez A. Protein‐Based Encapsulation Strategies: Toward Micro‐ and Nanoscale Carriers with Increased Functionality. SMALL SCIENCE 2022. [DOI: 10.1002/smsc.202100095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Ricardo Ramos
- Université de Lyon INSA Lyon CNRS IMP 5223 Villeurbanne Cedex 69621 France
- INSA-Lyon, IMP Villeurbanne F-69621 France
- CNRS, UMR 5223 Ingénierie des Matériaux Polymères Villeurbanne F-69621 France
| | - Julien Bernard
- Université de Lyon INSA Lyon CNRS IMP 5223 Villeurbanne Cedex 69621 France
- INSA-Lyon, IMP Villeurbanne F-69621 France
- CNRS, UMR 5223 Ingénierie des Matériaux Polymères Villeurbanne F-69621 France
| | - François Ganachaud
- Université de Lyon INSA Lyon CNRS IMP 5223 Villeurbanne Cedex 69621 France
- INSA-Lyon, IMP Villeurbanne F-69621 France
- CNRS, UMR 5223 Ingénierie des Matériaux Polymères Villeurbanne F-69621 France
| | - Ali Miserez
- Biological and Biomimetic Material Laboratory Center for Sustainable Materials (SusMat), School of Materials Science and Engineering Nanyang Technological University (NTU) 50 Nanyang Avenue Singapore 637 553 Singapore
- School of Biological Sciences NTU 59 Nanyang Drive Singapore 636921 Singapore
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28
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Titus AR, Kooijman EE. Current methods for studying intracellular liquid-liquid phase separation. CURRENT TOPICS IN MEMBRANES 2021; 88:55-73. [PMID: 34862032 DOI: 10.1016/bs.ctm.2021.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Liquid-liquid phase separation (LLPS) is a ubiquitous process that drives the formation of membrane-less intracellular compartments. This compartmentalization contains vastly different protein/RNA/macromolecule concentrations compared to the surrounding cytosol despite the absence of a lipid boundary. Because of this, LLPS is important for many cellular signaling processes and may play a role in their dysregulation. This chapter highlights recent advances in the understanding of intracellular phase transitions along with current methods used to identify LLPS in vitro and model LLPS in situ.
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Affiliation(s)
- Amber R Titus
- Department of Biological Sciences, Kent State University, Kent, OH, United States.
| | - Edgar E Kooijman
- Department of Biological Sciences, Kent State University, Kent, OH, United States
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29
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Tom JK, Deniz AA. Complex dynamics of multicomponent biological coacervates. Curr Opin Colloid Interface Sci 2021. [DOI: 10.1016/j.cocis.2021.101488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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30
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Sheng T, Guan X, Liu C, Su Y. De Novo Approach to Encapsulating Biocatalysts into Synthetic Matrixes: From Enzymes to Microbial Electrocatalysts. ACS APPLIED MATERIALS & INTERFACES 2021; 13:52234-52249. [PMID: 34352175 DOI: 10.1021/acsami.1c09708] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biocatalysts hold great promise in chemical and electrochemical reactions. However, biocatalysts are prone to inhospitable physiochemical conditions. Encapsulating biocatalysts into a synthetic host matrix can improve their stability and activity, and broaden their operational conditions. In this Review, we summarize the emerging de novo approaches to encapsulating biocatalysts into synthetic matrixes. Here, de novo means that embedding of biocatalysts and construction of matrixes take place simultaneously. We discuss the advantages and limitations of the de novo approach. On the basis of the nature of the biocatalysts and the synthetic frameworks, we specifically focus on two aspects: (1) encapsulation of enzymes (in vitro) in metal-organic frameworks and (2) encapsulation of microbial electrocatalysts (in vivo) on the electrode. For both cases, we discuss how the encapsulation improves biocatalysts' performance (stability, viability, activity, and etc.). We also highlight the benefit of encapsulation in facilitating the transport of charge carriers in microbial electrocatalysis.
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Affiliation(s)
- Tianran Sheng
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, China
| | - Xun Guan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Chong Liu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Yude Su
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, China
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31
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Lin K, Jing B, Zhu Y. pH-Dependent complexation and polyelectrolyte chain conformation of polyzwitterion-polycation coacervates in salted water. SOFT MATTER 2021; 17:8937-8949. [PMID: 34549769 DOI: 10.1039/d1sm00880c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The phase behavior and chain conformational structure of biphasic polyzwitterion-polyelectrolyte coacervates in salted aqueous solution are investigated with a model weak cationic polyelectrolyte, poly(2-vinylpyridine) (P2VP), whose charge fraction can be effectively tuned by pH. It is observed that increasing the pH leads to the increase of the yielding volume fraction and the water content of dense coacervates formed between net neutral polybetaine and cationic P2VP in contrast to the decrease of critical salt concentration for the onset of coacervation, where the P2VP charge fraction is reduced correspondingly. Surprisingly, a single-molecule fluorescence spectroscopic study suggests that P2VP chains upon coacervation seem to adopt a swollen or an even more expanded conformational structure at higher pH. As the hydrophobicity of P2VP chains is accompanied by a reduced charge fraction by increasing the pH, a strong pH-dependent phase and conformational behaviors suggest the shift of entropic and enthalpic contribution to the underlying thermodynamic energy landscape and chain structural dynamics of polyelectrolyte coacervation involving weak polyelectrolytes in aqueous solution.
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Affiliation(s)
- Kehua Lin
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202, USA.
| | - Benxin Jing
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202, USA.
| | - Yingxi Zhu
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202, USA.
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32
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Tyukalova E, Vimal Vas J, Ignatans R, Mueller AD, Medwal R, Imamura M, Asada H, Fukuma Y, Rawat RS, Tileli V, Duchamp M. Challenges and Applications to Operando and In Situ TEM Imaging and Spectroscopic Capabilities in a Cryogenic Temperature Range. Acc Chem Res 2021; 54:3125-3135. [PMID: 34339603 DOI: 10.1021/acs.accounts.1c00078] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
ConspectusIn this Account, we describe the challenges and promising applications of transmission electron microscopy (TEM) imaging and spectroscopy at cryogenic temperatures. Our work focuses on two areas of application: the delay of electron-beam-induced degradation and following low-temperature phenomena in a continuous and variable temperature range. For the former, we present a study of LiMn1.5Ni0.5O4 lithium ion battery cathode material that undergoes electron beam-induced degradation when studied at room temperature by TEM. Cryogenic imaging reveals the true structure of LiMn1.5Ni0.5O4 nanoparticles in their discharged state. Improved stability under electron beam irradiation was confirmed by following the evolution of the O K-edge fine structure by electron energy-loss spectroscopy. Our results demonstrate that the effect of radiation damage on discharged LiMn1.5Ni0.5O4 was previously underestimated and that atomic-resolution imaging at cryogenic temperature has a potential to be generalized to most of the Li-based materials and beyond. For the latter, we present two studies in the imaging of low-temperature phenomena on the local scale, namely, the evolution of ferroelectric and ferromagnetic domains walls, in BaTiO3 and Y3Fe5O12 systems, respectively, in a continuous and variable temperature range. Continuous imaging of the phase transition in BaTiO3, a prototypical ferroelectric system, from the low-temperature orthorhombic phase continuously up to the centrosymmetric high-temperature phase is shown to be possible inside a TEM. Similarly, the propagation of domain walls in Y3Fe5O12, a magnetic insulator, is studied from ∼120 to ∼400 K and combined with the application of a magnetic field and electrical current pulses to mimic the operando conditions as in domain wall memory and logic devices for information technology. Such studies are promising for studying the pinning of the ferroelectric and magnetic domains versus temperature, spin-polarized current, and externally applied magnetic field to better manipulate the domain walls. The capability of combining operando TEM stimuli such as current, voltage, and/or magnetic field with in situ TEM imaging in a continuous cryogenic temperature range will allow the uncovering of fundamental phenomena on the nanometer scale. These studies were made possible using a MEMS-based TEM holder that allowed an electron-transparent sample to be transferred and electrically contacted on a MEMS chip. The six-contact double-tilt holder allows the alignment of the specimen into its zone axis while simultaneously using four electrical contacts to regulate the temperature and two contacts to apply the electrical stimuli, i.e., operando TEM imaging. This Account leads to the demonstration of (i) the high-resolution imaging and spectroscopy of nanoparticles oriented in the desired [110] zone-axis direction at cryogenic temperatures to mitigate the electron beam degradation, (ii) imaging of low-temperature transitions with accurate and continuous control of the temperature that allowed single-frame observation of the presence of both the orthorhombic and tetragonal phases in the BaTiO3 system, and (iii) magnetic domain wall propagation as a function of temperature, magnetic field, and current pulses (100 ns with a 100 kHz repetition rate) in the Y3Fe5O12 system.
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Affiliation(s)
| | | | - Reinis Ignatans
- Institute of Materials, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | | | | | - Masaaki Imamura
- Department of Electrical Engineering, Fukuoka Institute of Technology, Fukuoka 811-0295, Japan
| | - Hironori Asada
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan
| | - Yasuhiro Fukuma
- Department of Physics and Information Technology, Kyushu Institute of Technology, Iizuka 820-8502, Japan
- Research Center for Neuromorphic AI Hardwares, Kyushu Institute of Technology, Kitakyushu 808-0196, Japan
| | | | - Vasiliki Tileli
- Institute of Materials, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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33
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Rizvi A, Mulvey JT, Carpenter BP, Talosig R, Patterson JP. A Close Look at Molecular Self-Assembly with the Transmission Electron Microscope. Chem Rev 2021; 121:14232-14280. [PMID: 34329552 DOI: 10.1021/acs.chemrev.1c00189] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Molecular self-assembly is pervasive in the formation of living and synthetic materials. Knowledge gained from research into the principles of molecular self-assembly drives innovation in the biological, chemical, and materials sciences. Self-assembly processes span a wide range of temporal and spatial domains and are often unintuitive and complex. Studying such complex processes requires an arsenal of analytical and computational tools. Within this arsenal, the transmission electron microscope stands out for its unique ability to visualize and quantify self-assembly structures and processes. This review describes the contribution that the transmission electron microscope has made to the field of molecular self-assembly. An emphasis is placed on which TEM methods are applicable to different structures and processes and how TEM can be used in combination with other experimental or computational methods. Finally, we provide an outlook on the current challenges to, and opportunities for, increasing the impact that the transmission electron microscope can have on molecular self-assembly.
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Affiliation(s)
- Aoon Rizvi
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Justin T Mulvey
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Brooke P Carpenter
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Rain Talosig
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Joseph P Patterson
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
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34
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Wohl S, Jakubowski M, Zheng W. Salt-Dependent Conformational Changes of Intrinsically Disordered Proteins. J Phys Chem Lett 2021; 12:6684-6691. [PMID: 34259536 DOI: 10.1021/acs.jpclett.1c01607] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The flexible structure of an intrinsically disordered protein (IDP) is known to be perturbed by salt concentrations, which can be understood by electrostatic screening on charged amino acids. However, an IDP usually contains more uncharged residues that are influenced by the salting-out effect. Here we have parametrized the salting-out effect into a coarse-grained model using a set of Förster resonance energy transfer data and verified with experimental salt-dependent liquid-liquid phase separation (LLPS) of 17 proteins. The new model can correctly capture the behavior of 6 more sequences, resulting in a total of 13 when varying salt concentrations. Together with a survey of more than 500 IDP sequences, we conclude that the salting-out effect, which was considered to be secondary to electrostatic screening, is important for IDP sequences with moderately charged residues at physiological salt concentrations. The presented scheme is generally applicable to other computational models for capturing salt-dependent IDP conformations.
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Affiliation(s)
- Samuel Wohl
- Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Matthew Jakubowski
- College of Integrative Sciences and Arts, Arizona State University, Mesa, Arizona 85212, United States
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, Arizona 85212, United States
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35
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Lim J, Kumar A, Low K, Verma CS, Mu Y, Miserez A, Pervushin K. Liquid-Liquid Phase Separation of Short Histidine- and Tyrosine-Rich Peptides: Sequence Specificity and Molecular Topology. J Phys Chem B 2021; 125:6776-6790. [PMID: 34106723 DOI: 10.1021/acs.jpcb.0c11476] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The increasing realization of the prevalence of liquid-liquid phase separation (LLPS) across multiple length scales of biological constructs, from intracellular membraneless organelles to extracellular load-bearing tissues, has raised intriguing questions about intermolecular interactions regulating LLPS at the atomic level. Squid-beak derived histidine (His)- and tyrosine (Tyr)-rich peptides (HBpeps) have recently emerged as suitable short model peptides to precisely assess the roles of peptide motifs and single residues on the phase behavior and material properties of microdroplets obtained by LLPS. In this study, by systematically introducing single mutations in an HBpep, we have identified specific sticker residues that attract peptide chains together. We find that His and Tyr residues located near the sequence termini drive phase separation, forming interaction nodes that stabilize microdroplets. Combining quantum chemistry simulations with NMR studies, we predict atomic-level bond geometries and uncover inter-residue supramolecular interactions governing LLPS. These results are subsequently used to propose possible topological arrangements of the peptide chains, which upon expansion can help explain the three-dimensional network of microdroplets. The stability of the proposed topologies carried out through all-atom molecular dynamics simulations predicts chain topologies that are more likely to stabilize the microdroplets. Overall, this study provides useful guidelines for the de novo design of peptide coacervates with tunable phase behavior and material properties. In addition, the analysis of nanoscale topologies may pave the way to understand how client molecules can be trapped within microdroplets, with direct implications for the encapsulation and controlled release of therapeutics for drug delivery applications.
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Affiliation(s)
- Jessica Lim
- School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637 551
| | - Akshita Kumar
- Biological and Biomimetic Material Laboratory, Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, NTU, 50 Nanyang Avenue, Singapore 637 553.,Bioinformatics Institute, A*STAR, 30 Biopolis Street, 07-01 Matrix, Singapore 138 671
| | - Kimberly Low
- School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637 551
| | - Chandra S Verma
- School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637 551.,Bioinformatics Institute, A*STAR, 30 Biopolis Street, 07-01 Matrix, Singapore 138 671.,Department of Biological Sciences, National University of Singapore (NUS), 16 Science Drive 4, Singapore 117 558
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637 551
| | - Ali Miserez
- School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637 551.,Biological and Biomimetic Material Laboratory, Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, NTU, 50 Nanyang Avenue, Singapore 637 553
| | - Konstantin Pervushin
- School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637 551
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36
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Ohtani R, Anegawa Y, Watanabe H, Tajima Y, Kinoshita M, Matsumori N, Kawano K, Yanaka S, Kato K, Nakamura M, Ohba M, Hayami S. Metal Complex Lipids for Fluid–Fluid Phase Separation in Coassembled Phospholipid Membranes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ryo Ohtani
- Department of Chemistry Faculty of Science Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Yuka Anegawa
- Department of Chemistry Graduate School of Science Kumamoto University 2-39-1 Kurokami, Chuo-ku Kumamoto 860-8555 Japan
| | - Hikaru Watanabe
- Department of Chemistry Faculty of Science Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Yutaro Tajima
- Department of Chemistry Faculty of Science Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Masanao Kinoshita
- Department of Chemistry Faculty of Science Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Nobuaki Matsumori
- Department of Chemistry Faculty of Science Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Kenichi Kawano
- Institute for Chemical Research Kyoto University Uji Kyoto 611-0011 Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS) National Institutes of Natural Sciences 5-1 Higashiyama Myodaiji Okazaki 444-8787 Japan
- Graduate School of Pharmaceutical Sciences Nagoya City University 3-1 Tanabe-dori, Mizuho-ku Nagoya Aichi 467-8603 Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS) National Institutes of Natural Sciences 5-1 Higashiyama Myodaiji Okazaki 444-8787 Japan
- Graduate School of Pharmaceutical Sciences Nagoya City University 3-1 Tanabe-dori, Mizuho-ku Nagoya Aichi 467-8603 Japan
| | - Masaaki Nakamura
- Department of Chemistry Graduate School of Science Kumamoto University 2-39-1 Kurokami, Chuo-ku Kumamoto 860-8555 Japan
| | - Masaaki Ohba
- Department of Chemistry Faculty of Science Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Shinya Hayami
- Department of Chemistry Graduate School of Science Kumamoto University 2-39-1 Kurokami, Chuo-ku Kumamoto 860-8555 Japan
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37
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Ohtani R, Anegawa Y, Watanabe H, Tajima Y, Kinoshita M, Matsumori N, Kawano K, Yanaka S, Kato K, Nakamura M, Ohba M, Hayami S. Metal Complex Lipids for Fluid-Fluid Phase Separation in Coassembled Phospholipid Membranes. Angew Chem Int Ed Engl 2021; 60:13603-13608. [PMID: 33723910 DOI: 10.1002/anie.202102774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Indexed: 11/08/2022]
Abstract
We demonstrate a fluid-fluid phase separation in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) membranes using a metal complex lipid of type [Mn(L1)] (1; HL1=1-(2-hydroxybenzamide)-2-(2-hydroxy-3-formyl-5-hexadecyloxybenzylideneamino)ethane). Small amount of 1 produces two separated domains in DMPC, whose phase transition temperatures of lipids (Tc ) are both lower than that of the pristine DMPC. Variable temperature fluorescent microscopy for giant-unilamellar vesicles of DMPC/1 hybrids demonstrates that visible phase separations remain in fluid phases up to 37 °C, which is clearly over the Tc of DMPC. This provides a new dimension for the application of metal complex lipids toward controlling lipid distributions in fluid membranes.
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Affiliation(s)
- Ryo Ohtani
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yuka Anegawa
- Department of Chemistry, Graduate School of Science, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Hikaru Watanabe
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yutaro Tajima
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Masanao Kinoshita
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kenichi Kawano
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Masaaki Nakamura
- Department of Chemistry, Graduate School of Science, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Masaaki Ohba
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Shinya Hayami
- Department of Chemistry, Graduate School of Science, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
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38
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Kashin AS, Boiko DA, Ananikov VP. Neural Network Analysis of Electron Microscopy Video Data Reveals the Temperature-Driven Microphase Dynamics in the Ions/Water System. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2007726. [PMID: 33938144 DOI: 10.1002/smll.202007726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/17/2021] [Indexed: 06/12/2023]
Abstract
Real-time field-emission scanning electron microscopy (FE-SEM) measurements and neural network analysis were successfully merged to observe the temperature-induced behavior of soft liquid microdomains in mixtures of different ionic liquids with water. The combination of liquid FE-SEM and in situ heating techniques revealed temperature-driven solution restructuring for ions/water systems with different water states and their critical point behavior expressed in a rapid switch between thermal expansion and shrinkage of liquid microphases at temperatures of ≈100-130 °C, which was directly recorded on electron microscopy videos. Automation of FE-SEM video analysis by a neural network approach allowed quantification of the morphological changes in ions/water systems during heating on the basis of thousands of images processed with a speed almost equal to the frame rate of original electron microscopy videos. Tracking and evolution of the micro-heterogeneous domains, hypothesized in the Ioliomics concept, was mapped and quantified for the first time. The present study describes the concept for quick acquisition of big data in electron microscopy, develops rapid neural network analysis and shows how to link microscopic data to fundamental molecular properties.
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Affiliation(s)
- Alexey S Kashin
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, 119991, Russian Federation
| | - Daniil A Boiko
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, 119991, Russian Federation
| | - Valentine P Ananikov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, 119991, Russian Federation
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39
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Kubota R, Tanaka W, Hamachi I. Microscopic Imaging Techniques for Molecular Assemblies: Electron, Atomic Force, and Confocal Microscopies. Chem Rev 2021; 121:14281-14347. [DOI: 10.1021/acs.chemrev.0c01334] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Wataru Tanaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8530, Japan
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40
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Liang CQ, Wang L, Luo YY, Li QQ, Li YM. Capturing protein droplets: label-free visualization and detection of protein liquid-liquid phase separation with an aggregation-induced emission fluorogen. Chem Commun (Camb) 2021; 57:3805-3808. [PMID: 33876127 DOI: 10.1039/d1cc00947h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We developed a new method for protein droplet visualization by means of a droplet probe (DroProbe) based on an aggregation-induced emission (AIE) fluorogen. A simple method for viscosity comparison of the protein condensed phase based on the lifetime of the DroProbe was also developed.
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Affiliation(s)
- Chu-Qiao Liang
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University Beijing, 100084, P. R. China.
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41
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Heymann D, Mohanram H, Kumar A, Verma CS, Lescar J, Miserez A. Structure of a consensus chitin-binding domain revealed by solution NMR. J Struct Biol 2021; 213:107725. [PMID: 33744410 DOI: 10.1016/j.jsb.2021.107725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/10/2021] [Accepted: 03/14/2021] [Indexed: 11/29/2022]
Abstract
Chitin-binding proteins (CBPs) are a versatile group of proteins found in almost every organism on earth. CBPs are involved in enzymatic carbohydrate degradation and also serve as templating scaffolds in the exoskeleton of crustaceans and insects. One specific chitin-binding motif found across a wide range of arthropods' exoskeletons is the "extended Rebers and Riddiford" consensus (R&R), whose mechanism of chitin binding remains unclear. Here, we report the 3D structure and molecular level interactions of a chitin-binding domain (CBD-γ) located in a CBP from the beak of the jumbo squid Dosidicus gigas. This CBP is one of four chitin-binding proteins identified in the beak mouthpart of D. gigas and is believed to interact with chitin to form a scaffold network that is infiltrated with a second set of structural proteins during beak maturation. We used solution state NMR spectroscopy to elucidate the molecular interactions between CBD-γ and the soluble chitin derivative pentaacetyl-chitopentaose (PCP), and find that folding of CBD-γ is triggered upon its interaction with PCP. To our knowledge, this is the first experimental 3D structure of a CBP containing the R&R consensus motif, which can be used as a template to understand in more details the role of the R&R motif found in a wide range of CBP-chitin complexes. The present structure also provides molecular information for biomimetic synthesis of graded biomaterials using aqueous-based chemistry and biopolymers.
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Affiliation(s)
- Dario Heymann
- Biological and Biomimetic Material Laboratory, Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore 637553, Singapore; NTU Institute of Structural Biology, Experimental Medicine Building (EMB), 59 Nanyang Drive, Level 06-01, Singapore 636921, Singapore
| | - Harini Mohanram
- Biological and Biomimetic Material Laboratory, Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore 637553, Singapore
| | - Akshita Kumar
- Biological and Biomimetic Material Laboratory, Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore 637553, Singapore; Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Chandra S Verma
- School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore 637551, Singapore; Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; Department of Biological Sciences, National University of Singapore (NUS), 16 Science Drive 4, Singapore 117558, Singapore
| | - Julien Lescar
- School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Experimental Medicine Building (EMB), 59 Nanyang Drive, Level 06-01, Singapore 636921, Singapore.
| | - Ali Miserez
- Biological and Biomimetic Material Laboratory, Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore 637553, Singapore; School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Experimental Medicine Building (EMB), 59 Nanyang Drive, Level 06-01, Singapore 636921, Singapore.
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42
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Yan Z, Xue J, Zhou M, Wang J, Zhang Y, Wang Y, Qiao J, He Y, Li P, Zhang S, Zhang X. Dynamic Monitoring of Phase-Separated Biomolecular Condensates by Photoluminescence Lifetime Imaging. Anal Chem 2021; 93:2988-2995. [PMID: 33512148 DOI: 10.1021/acs.analchem.0c05011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The formation of biomolecular condensates is driven by liquid-liquid phase separation, which is prevalent in cells to govern crucial cellular functions. However, understanding the properties of phase-separated condensates remains very challenging for the lack of suitable techniques. Here, we report a photoluminescence lifetime imaging method for real-time monitoring of phase-separated condensates, both in vitro and in living cells, using a microsecond-scale photoluminescence lifetime probe based on iridium complex. The probe has a large Stokes shift, excellent cell permeability, and minimal cell autofluorescence interference. With this method, the dynamic process of phase separation of fused in sarcoma protein has been well explored, showing high spatiotemporal resolution and high throughput. Beginning with initial formation, the protein droplets get bigger and more viscous, and then a final maturation to solidified aggregates has been characterized. This study paves the path for a deeper understanding of the properties of phase-separated biomolecular condensates.
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Affiliation(s)
- Zihe Yan
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jianfeng Xue
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Min Zhou
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
| | - Jinyu Wang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yanxin Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yuan Wang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
| | - Juan Qiao
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yan He
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
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43
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Yang Y, Xiong Y, Zeng R, Lu X, Krumov M, Huang X, Xu W, Wang H, DiSalvo FJ, Brock JD, Muller DA, Abruña HD. Operando Methods in Electrocatalysis. ACS Catal 2021. [DOI: 10.1021/acscatal.0c04789] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Yao Yang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Yin Xiong
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Rui Zeng
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Xinyao Lu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Mihail Krumov
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Xin Huang
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York 14853, United States
| | - Weixuan Xu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Hongsen Wang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Francis J. DiSalvo
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Joel. D. Brock
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York 14853, United States
| | - David A. Muller
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
- Kavli Institute at Cornell for Nanoscale Science, Ithaca, New York 14853, United States
| | - Héctor D. Abruña
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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44
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Jing B, Ferreira M, Lin K, Li R, Yavitt BM, Qiu J, Fukuto M, Zhu Y. Ultrastructure of Critical-Gel-like Polyzwitterion–Polyoxometalate Complex Coacervates: Effects of Temperature, Salt Concentration, and Shear. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Benxin Jing
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
| | - Manuela Ferreira
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
| | - Kehua Lin
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
| | - Ruipeng Li
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Benjamin M. Yavitt
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Jie Qiu
- School of Nuclear Science and Technology and State Key Laboratory of Multiphase Flow in Power Engineering, Xi’an Jiaotong University, Xi’an 710049, China
| | - Masafumi Fukuto
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Yingxi Zhu
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
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45
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Nakajima K, Yamazaki T, Kimura Y, So M, Goto Y, Ogi H. Time-Resolved Observation of Evolution of Amyloid-β Oligomer with Temporary Salt Crystals. J Phys Chem Lett 2020; 11:6176-6184. [PMID: 32687370 DOI: 10.1021/acs.jpclett.0c01487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The aggregation behavior of amyloid-β (Aβ) peptides remains unclarified despite the fact that it is closely related to the pathogenic mechanism of Alzheimer's disease. Aβ peptides form diverse oligomers with various diameters before nucleation, making clarification of the mechanism involved a complex problem with conventional macroscopic analysis methods. Time-resolved single-molecule level analysis in bulk solution is thus required to fully understand their early stage aggregation behavior. Here, we perform time-resolved observation of the aggregation dynamics of Aβ oligomers in bulk solution using liquid-state transmission electron microscopy. Our observations reveal previously unknown behaviors. The most important discovery is that a salt crystal can precipitate even with a concentration much lower than its solubility, and it then dissolves in a short time, during which the aggregation reaction of Aβ peptides is significantly accelerated. These findings will provide new insights in the evolution of the Aβ oligomer.
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Affiliation(s)
- Kichitaro Nakajima
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tomoya Yamazaki
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-8638, Japan
| | - Yuki Kimura
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-8638, Japan
| | - Masatomo So
- Institute of Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuji Goto
- Institute of Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hirotsugu Ogi
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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46
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Wu H, Friedrich H, Patterson JP, Sommerdijk NAJM, de Jonge N. Liquid-Phase Electron Microscopy for Soft Matter Science and Biology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2001582. [PMID: 32419161 DOI: 10.1002/adma.202001582] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/05/2020] [Accepted: 04/06/2020] [Indexed: 05/20/2023]
Abstract
Innovations in liquid-phase electron microscopy (LP-EM) have made it possible to perform experiments at the optimized conditions needed to examine soft matter. The main obstacle is conducting experiments in such a way that electron beam radiation can be used to obtain answers for scientific questions without changing the structure and (bio)chemical processes in the sample due to the influence of the radiation. By overcoming these experimental difficulties at least partially, LP-EM has evolved into a new microscopy method with nanometer spatial resolution and sub-second temporal resolution for analysis of soft matter in materials science and biology. Both experimental design and applications of LP-EM for soft matter materials science and biological research are reviewed, and a perspective of possible future directions is given.
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Affiliation(s)
- Hanglong Wu
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Heiner Friedrich
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Joseph P Patterson
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - Nico A J M Sommerdijk
- Department of Biochemistry, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Niels de Jonge
- INM - Leibniz Institute for New Materials, Saarbrücken, 66123, Germany
- Department of Physics, Saarland University, Saarbrücken, 66123, Germany
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47
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Zhou L, Shi H, Li Z, He C. Recent Advances in Complex Coacervation Design from Macromolecular Assemblies and Emerging Applications. Macromol Rapid Commun 2020; 41:e2000149. [DOI: 10.1002/marc.202000149] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/29/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Lili Zhou
- Department of Materials Science and Engineering National University of Singapore 9 Engineering Drive 1 Singapore 117576 Singapore
| | - Huihui Shi
- Department of Materials Science and Engineering National University of Singapore 9 Engineering Drive 1 Singapore 117576 Singapore
| | - Zibiao Li
- Institute of Materials Research and Engineering A:STAR (Agency for Science, Technology and Research) 2 Fusionopolis Way, Innovis, #08‐03 Singapore 138634 Singapore
| | - Chaobin He
- Department of Materials Science and Engineering National University of Singapore 9 Engineering Drive 1 Singapore 117576 Singapore
- Institute of Materials Research and Engineering A:STAR (Agency for Science, Technology and Research) 2 Fusionopolis Way, Innovis, #08‐03 Singapore 138634 Singapore
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48
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Walton F, Bolling J, Farrell A, MacEwen J, Syme CD, Jiménez MG, Senn HM, Wilson C, Cinque G, Wynne K. Polyamorphism Mirrors Polymorphism in the Liquid-Liquid Transition of a Molecular Liquid. J Am Chem Soc 2020; 142:7591-7597. [PMID: 32249557 PMCID: PMC7181258 DOI: 10.1021/jacs.0c01712] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
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Liquid–liquid
transitions between two amorphous phases in
a single-component liquid have courted controversy. All known examples
of liquid–liquid transitions in molecular liquids have been
observed in the supercooled state, suggesting an intimate connection
with vitrification and locally favored structures inhibiting crystallization.
However, there is precious little information about the local molecular
packing in supercooled liquids, meaning that the order parameter of
the transition is still unknown. Here, we investigate the liquid–liquid
transition in triphenyl phosphite and show that it is caused by the
competition between liquid structures that mirror two crystal polymorphs.
The liquid–liquid transition is found to be between a geometrically
frustrated liquid and a dynamically frustrated glass. These results
indicate a general link between polymorphism and polyamorphism and
will lead to a much greater understanding of the physical basis of
liquid–liquid transitions and allow the systematic discovery
of other examples.
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Affiliation(s)
- Finlay Walton
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
| | - John Bolling
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Andrew Farrell
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Jamie MacEwen
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
| | | | | | - Hans M Senn
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Claire Wilson
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Gianfelice Cinque
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, U.K
| | - Klaas Wynne
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
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49
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Miyagawa A, Harada M, Fukuhara G, Okada T. Space Size-Dependent Transformation of Tetraphenylethylene Carboxylate Aggregates by Ice Confinement. J Phys Chem B 2020; 124:2209-2217. [PMID: 32097006 DOI: 10.1021/acs.jpcb.9b11345] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tetraphenylethylene carboxylate (TPEC) aggregates are transformed by ice confinement, which is controlled by the initial concentration of sucrose employed as a cryoprotectant and temperature. The freezing of aqueous sucrose leads to the formation of micro- or nanoliquid phase confined in ice. Aggregation-induced emission (AIE) of tetraphenylethylene carboxylate (TPEC) in the ice-confined space is explored using fluorescence spectroscopy and lifetime measurements. The characteristics of AIE in the ice-confined space strongly depend on the initial sucrose concentration and temperature, which determine the size of the liquid phase. The AIE of TPEC in the ice-confined space can be classified into three regimes in terms of spectroscopic features. Loosely packed J aggregates of TPEC are formed in the microliquid phase (>2 μm). The fluorescence intensity increases, and the wavelength is hypsochromically shifted with a decrease in the size of the space, indicating that the molecular arrangement in the aggregate depends on the space size. The fluorescence lifetimes indicate polydisperse, loosely packed aggregation. No further change in aggregate structure is observed once the liquid phase size is decreased to ∼2 μm, and a spectroscopically identical structure is maintained upon further reduction of the space size to ∼0.5 μm. The molecular arrangement in the aggregate is independent of the space size in this regime. However, when the size of the space becomes smaller than ∼0.5 μm, the aggregate structure again starts to change into a more tightly packed aggregate and a hypsochromic shift of the fluorescence wavelength occurs again. The fluorescence lifetime indicates monodispersed aggregation in this submicrospace.
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Affiliation(s)
- Akihisa Miyagawa
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8551, Japan
| | - Makoto Harada
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8551, Japan
| | - Gaku Fukuhara
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8551, Japan.,JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Tetsuo Okada
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8551, Japan
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50
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Smith JW, Chen Q. Liquid-phase electron microscopy imaging of cellular and biomolecular systems. J Mater Chem B 2020; 8:8490-8506. [DOI: 10.1039/d0tb01300e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Liquid-phase electron microscopy, a new method for real-time nanoscopic imaging in liquid, makes it possible to study cells or biomolecules with a singular combination of spatial and temporal resolution. We review the state of the art in biological research in this growing and promising field.
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Affiliation(s)
- John W. Smith
- Department of Materials Science and Engineering, University of Illinois at Urbana–Champaign
- Urbana
- USA
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois at Urbana–Champaign
- Urbana
- USA
- Department of Chemistry
- University of Illinois at Urbana–Champaign
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