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Cóppola-Segovia V, Reggiori F. Molecular Insights into Aggrephagy: Their Cellular Functions in the Context of Neurodegenerative Diseases. J Mol Biol 2024; 436:168493. [PMID: 38360089 DOI: 10.1016/j.jmb.2024.168493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
Protein homeostasis or proteostasis is an equilibrium of biosynthetic production, folding and transport of proteins, and their timely and efficient degradation. Proteostasis is guaranteed by a network of protein quality control systems aimed at maintaining the proteome function and avoiding accumulation of potentially cytotoxic proteins. Terminal unfolded and dysfunctional proteins can be directly turned over by the ubiquitin-proteasome system (UPS) or first amassed into aggregates prior to degradation. Aggregates can also be disposed into lysosomes by a selective type of autophagy known as aggrephagy, which relies on a set of so-called selective autophagy receptors (SARs) and adaptor proteins. Failure in eliminating aggregates, also due to defects in aggrephagy, can have devastating effects as underscored by several neurodegenerative diseases or proteinopathies, which are characterized by the accumulation of aggregates mostly formed by a specific disease-associated, aggregate-prone protein depending on the clinical pathology. Despite its medical relevance, however, the process of aggrephagy is far from being understood. Here we review the findings that have helped in assigning a possible function to specific SARs and adaptor proteins in aggrephagy in the context of proteinopathies, and also highlight the interplay between aggrephagy and the pathogenesis of proteinopathies.
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Affiliation(s)
| | - Fulvio Reggiori
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, 8000 Aarhus C, Denmark; Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Høegh-Guldbergs Gade 6B, 8000 Aarhus C, Denmark.
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2
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Staderini T, Bigi A, Lagrève C, Marzi I, Bemporad F, Chiti F. Biophysical characterization of the phase separation of TDP-43 devoid of the C-terminal domain. Cell Mol Biol Lett 2024; 29:104. [PMID: 38997630 PMCID: PMC11245819 DOI: 10.1186/s11658-024-00615-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/25/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND Frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-TDP), amyotrophic lateral sclerosis (ALS) and limbic-predominant age-related TDP-43 encephalopathy (LATE) are associated with deposition of cytoplasmic inclusions of TAR DNA-binding protein 43 (TDP-43) in neurons. One complexity of this process lies in the ability of TDP-43 to form liquid-phase membraneless organelles in cells. Previous work has shown that the recombinant, purified, prion-like domain (PrLD) forms liquid droplets in vitro, but the behaviour of the complementary fragment is uncertain. METHODS We have purified such a construct without the PrLD (PrLD-less TDP-43) and have induced its phase separation using a solution-jump method and an array of biophysical techniques to study the morphology, state of matter and structure of the TDP-43 assemblies. RESULTS The fluorescent TMR-labelled protein construct, imaged using confocal fluorescence, formed rapidly (< 1 min) round, homogeneous and 0.5-1.0 µm wide assemblies which then coalesced into larger, yet round, species. When labelled with AlexaFluor488, they initially exhibited fluorescence recovery after photobleaching (FRAP), showing a liquid behaviour distinct from full-length TDP-43 and similar to PrLD. The protein molecules did not undergo major structural changes, as determined with circular dichroism and intrinsic fluorescence spectroscopies. This process had a pH and salt dependence distinct from those of full-length TDP-43 and its PrLD, which can be rationalized on the grounds of electrostatic forces. CONCLUSIONS Similarly to PrLD, PrLD-less TDP-43 forms liquid droplets in vitro through liquid-liquid phase separation (LLPS), unlike the full-length protein that rather undergoes liquid-solid phase separation (LSPS). These results offer a rationale of the complex electrostatic forces governing phase separation of full-length TDP-43 and its fragments. On the one hand, PrLD-less TDP-43 has a low pI and oppositively charged domains, and LLPS is inhibited by salts, which attenuate inter-domain electrostatic attractions. On the other hand, PrLD is positively charged due to a high isoionic point (pI) and LLPS is therefore promoted by salts and pH increases as they both reduce electrostatic repulsions. By contrast, full-length TDP-43 undergoes LSPS most favourably at its pI, with positive and negative salt dependences at lower and higher pH, respectively, depending on whether repulsive or attractive forces dominate, respectively.
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Affiliation(s)
- Tommaso Staderini
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134, Florence, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, 50019, Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, 50019, Florence, Italy
| | - Alessandra Bigi
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134, Florence, Italy
| | - Clément Lagrève
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134, Florence, Italy
- Chimie ParisTech-PSL, École Nationale Supérieur de Chimie de Paris, 11 rue Pierre et Marie Curie, 75231, Paris, France
| | - Isabella Marzi
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134, Florence, Italy
| | - Francesco Bemporad
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134, Florence, Italy
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134, Florence, Italy.
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3
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Liu D, Yang J, Cristea IM. Liquid-liquid phase separation in innate immunity. Trends Immunol 2024; 45:454-469. [PMID: 38762334 PMCID: PMC11247960 DOI: 10.1016/j.it.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 05/20/2024]
Abstract
Intrinsic and innate immune responses are essential lines of defense in the body's constant surveillance of pathogens. The discovery of liquid-liquid phase separation (LLPS) as a key regulator of this primal response to infection brings an updated perspective to our understanding of cellular defense mechanisms. Here, we review the emerging multifaceted role of LLPS in diverse aspects of mammalian innate immunity, including DNA and RNA sensing and inflammasome activity. We discuss the intricate regulation of LLPS by post-translational modifications (PTMs), and the subversive tactics used by viruses to antagonize LLPS. This Review, therefore, underscores the significance of LLPS as a regulatory node that offers rapid and plastic control over host immune signaling, representing a promising target for future therapeutic strategies.
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Affiliation(s)
- Dawei Liu
- Department of Molecular Biology, Princeton University; Princeton, NJ 08544, USA
| | - Jinhang Yang
- Department of Molecular Biology, Princeton University; Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University; Princeton, NJ 08544, USA.
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4
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Mukherjee S, Poudyal M, Dave K, Kadu P, Maji SK. Protein misfolding and amyloid nucleation through liquid-liquid phase separation. Chem Soc Rev 2024; 53:4976-5013. [PMID: 38597222 DOI: 10.1039/d3cs01065a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Liquid-liquid phase separation (LLPS) is an emerging phenomenon in cell physiology and diseases. The weak multivalent interaction prerequisite for LLPS is believed to be facilitated through intrinsically disordered regions, which are prevalent in neurodegenerative disease-associated proteins. These aggregation-prone proteins also exhibit an inherent property for phase separation, resulting in protein-rich liquid-like droplets. The very high local protein concentration in the water-deficient confined microenvironment not only drives the viscoelastic transition from the liquid to solid-like state but also most often nucleate amyloid fibril formation. Indeed, protein misfolding, oligomerization, and amyloid aggregation are observed to be initiated from the LLPS of various neurodegeneration-related proteins. Moreover, in these cases, neurodegeneration-promoting genetic and environmental factors play a direct role in amyloid aggregation preceded by the phase separation. These cumulative recent observations ignite the possibility of LLPS being a prominent nucleation mechanism associated with aberrant protein aggregation. The present review elaborates on the nucleation mechanism of the amyloid aggregation pathway and the possible early molecular events associated with amyloid-related protein phase separation. It also summarizes the recent advancement in understanding the aberrant phase transition of major proteins contributing to neurodegeneration focusing on the common disease-associated factors. Overall, this review proposes a generic LLPS-mediated multistep nucleation mechanism for amyloid aggregation and its implication in neurodegeneration.
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Affiliation(s)
- Semanti Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Manisha Poudyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Kritika Dave
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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5
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Ramirez DA, Hough LE, Shirts MR. Coiled-coil domains are sufficient to drive liquid-liquid phase separation in protein models. Biophys J 2024; 123:703-717. [PMID: 38356260 PMCID: PMC10995412 DOI: 10.1016/j.bpj.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/09/2023] [Accepted: 02/09/2024] [Indexed: 02/16/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) is thought to be a main driving force in the formation of membraneless organelles. Examples of such organelles include the centrosome, central spindle, and stress granules. Recently, it has been shown that coiled-coil (CC) proteins, such as the centrosomal proteins pericentrin, spd-5, and centrosomin, might be capable of LLPS. CC domains have physical features that could make them the drivers of LLPS, but it is unknown if they play a direct role in the process. We developed a coarse-grained simulation framework for investigating the LLPS propensity of CC proteins, in which interactions that support LLPS arise solely from CC domains. We show, using this framework, that the physical features of CC domains are sufficient to drive LLPS of proteins. The framework is specifically designed to investigate how the number of CC domains, as well as the multimerization state of CC domains, can affect LLPS. We show that small model proteins with as few as two CC domains can phase separate. Increasing the number of CC domains up to four per protein can somewhat increase LLPS propensity. We demonstrate that trimer-forming and tetramer-forming CC domains have a dramatically higher LLPS propensity than dimer-forming coils, which shows that multimerization state has a greater effect on LLPS than the number of CC domains per protein. These data support the hypothesis of CC domains as drivers of protein LLPS, and have implications in future studies to identify the LLPS-driving regions of centrosomal and central spindle proteins.
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Affiliation(s)
- Dominique A Ramirez
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | - Loren E Hough
- Department of Physics and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado.
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6
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Huang Y, Chen J, Hsiung CH, Bai Y, Tan Z, Ye S, Zhang X. Detecting protein-protein interaction during liquid-liquid phase separation using fluorogenic protein sensors. Mol Biol Cell 2024; 35:ar41. [PMID: 38231854 PMCID: PMC10916855 DOI: 10.1091/mbc.e23-11-0442] [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: 11/20/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 01/19/2024] Open
Abstract
The formation of cellular condensates, akin to membraneless organelles, is typically mediated by liquid-liquid phase separation (LLPS), during which proteins and RNA molecules interact with each other via multivalent interactions. Gaining a comprehensive understanding of these interactions holds significance in unraveling the mechanisms underlying condensate formation and the pathology of related diseases. In an attempt toward this end, fluorescence microscopy is often used to examine the colocalization of target proteins/RNAs. However, fluorescence colocalization is inadequate to reliably identify protein interaction due to the diffraction limit of traditional fluorescence microscopy. In this study, we achieve this goal through adopting a novel chemical biology approach via the dimerization-dependent fluorescent proteins (ddFPs). We succeeded in utilizing ddFPs to detect protein interaction during LLPS both in vitro and in living cells. The ddFPs allow us to investigate the interaction between two important LLPS-associated proteins, FUS and TDP-43, as cellular condensates formed. Importantly, we revealed that their interaction was associated with RNA binding upon LLPS, indicating that RNA plays a critical role in mediating interactions between RBPs. More broadly, we envision that utilization of ddFPs would reveal previously unknown protein-protein interaction and uncover their functional roles in the formation and disassembly of biomolecular condensates.
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Affiliation(s)
- Yanan Huang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou 310030, Zhejiang, China
| | - Junlin Chen
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou 310030, Zhejiang, China
| | - Chia-Heng Hsiung
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou 310030, Zhejiang, China
| | - Yulong Bai
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou 310030, Zhejiang, China
| | - Zizhu Tan
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou 310030, Zhejiang, China
| | - Songtao Ye
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou 310030, Zhejiang, China
| | - Xin Zhang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou 310030, Zhejiang, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang Province, China
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7
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Mohanty P, Rizuan A, Kim YC, Fawzi NL, Mittal J. A complex network of interdomain interactions underlies the conformational ensemble of monomeric TDP-43 and modulates its phase behavior. Protein Sci 2024; 33:e4891. [PMID: 38160320 PMCID: PMC10804676 DOI: 10.1002/pro.4891] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/07/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
TAR DNA-binding protein 43 (TDP-43) is a multidomain protein involved in the regulation of RNA metabolism, and its aggregates have been observed in neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Numerous studies indicate TDP-43 can undergo liquid-liquid phase separation (LLPS) in vitro and is a component of biological condensates. Homo-oligomerization via the folded N-terminal domain (aa:1-77) and the conserved helical region (aa:319-341) of the disordered, C-terminal domain is found to be an important driver of TDP-43 phase separation. However, a comprehensive molecular view of TDP-43 phase separation, particularly regarding the nature of heterodomain interactions, is lacking due to the challenges associated with its stability and purification. Here, we utilize all-atom and coarse-grained (CG) molecular dynamics (MD) simulations to uncover the network of interdomain interactions implicated in TDP-43 phase separation. All-atom simulations uncovered the presence of transient, interdomain interactions involving flexible linkers, RNA-recognition motif (RRM) domains and a charged segment of disordered C-terminal domain (CTD). CG simulations indicate these inter-domain interactions which affect the conformational landscape of TDP-43 in the dilute phase are also prevalent in the condensed phase. Finally, sequence and surface charge distribution analysis coupled with all-atom simulations (at high salt) confirmed that the transient interdomain contacts are predominantly electrostatic in nature. Overall, our findings from multiscale simulations lead to a greater appreciation of the complex interaction network underlying the structural landscape and phase separation of TDP-43.
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Affiliation(s)
- Priyesh Mohanty
- Artie McFerrin Department of Chemical EngineeringTexas A&M UniversityCollege StationTexasUSA
| | - Azamat Rizuan
- Artie McFerrin Department of Chemical EngineeringTexas A&M UniversityCollege StationTexasUSA
| | - Young C. Kim
- Naval Research LaboratoryCenter for Materials Physics and TechnologyWashingtonDistrict of ColumbiaUSA
| | - Nicolas L. Fawzi
- Department of Molecular Biology, Cell Biology and BiochemistryProvidenceRhode IslandUSA
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical EngineeringTexas A&M UniversityCollege StationTexasUSA
- Department of ChemistryTexas A&M UniversityCollege StationTexasUSA
- Interdisciplinary Graduate Program in Genetics and GenomicsTexas A&M UniversityCollege StationTexasUSA
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8
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Liu J, Chen Y, Nong B, Luo X, Cui K, Li Z, Zhang P, Tan W, Yang Y, Ma W, Liang P, Songyang Z. CRISPR-assisted transcription activation by phase-separation proteins. Protein Cell 2023; 14:874-887. [PMID: 36905356 PMCID: PMC10691850 DOI: 10.1093/procel/pwad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/11/2023] [Indexed: 03/12/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been widely used for genome engineering and transcriptional regulation in many different organisms. Current CRISPR-activation (CRISPRa) platforms often require multiple components because of inefficient transcriptional activation. Here, we fused different phase-separation proteins to dCas9-VPR (dCas9-VP64-P65-RTA) and observed robust increases in transcriptional activation efficiency. Notably, human NUP98 (nucleoporin 98) and FUS (fused in sarcoma) IDR domains were best at enhancing dCas9-VPR activity, with dCas9-VPR-FUS IDR (VPRF) outperforming the other CRISPRa systems tested in this study in both activation efficiency and system simplicity. dCas9-VPRF overcomes the target strand bias and widens gRNA designing windows without affecting the off-target effect of dCas9-VPR. These findings demonstrate the feasibility of using phase-separation proteins to assist in the regulation of gene expression and support the broad appeal of the dCas9-VPRF system in basic and clinical applications.
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Affiliation(s)
- Jiaqi Liu
- 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 University, Guangzhou 510275, China
| | - Yuxi Chen
- 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 University, Guangzhou 510275, China
| | - Baoting Nong
- 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 University, Guangzhou 510275, China
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiao Luo
- 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 University, Guangzhou 510275, China
| | - Kaixin Cui
- 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 University, Guangzhou 510275, China
| | - Zhan Li
- 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 University, Guangzhou 510275, China
| | - Pengfei Zhang
- 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 University, Guangzhou 510275, China
| | | | - Yue Yang
- 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 University, Guangzhou 510275, China
| | - Wenbin Ma
- 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 University, Guangzhou 510275, China
| | - Puping Liang
- 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 University, Guangzhou 510275, 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 University, Guangzhou 510275, China
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
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9
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Song J. Molecular mechanisms of phase separation and amyloidosis of ALS/FTD-linked FUS and TDP-43. Aging Dis 2023:AD.2023.1118. [PMID: 38029395 DOI: 10.14336/ad.2023.1118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/18/2023] [Indexed: 12/01/2023] Open
Abstract
FUS and TDP-43, two RNA-binding proteins from the heterogeneous nuclear ribonucleoprotein family, have gained significant attention in the field of neurodegenerative diseases due to their association with amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). They possess folded domains for binding ATP and various nucleic acids including DNA and RNA, as well as substantial intrinsically disordered regions (IDRs) including prion-like domains (PLDs) and RG-/RGG-rich regions. They play vital roles in various cellular processes, including transcription, splicing, microRNA maturation, RNA stability and transport and DNA repair. In particular, they are key components for forming ribonucleoprotein granules and stress granules (SGs) through homotypic or heterotypic liquid-liquid phase separation (LLPS). Strikingly, liquid-like droplets formed by FUS and TDP-43 may undergo aging to transform into less dynamic assemblies such as hydrogels, inclusions, and amyloid fibrils, which are the pathological hallmarks of ALS and FTD. This review aims to synthesize and consolidate the biophysical knowledge of the sequences, structures, stability, dynamics, and inter-domain interactions of FUS and TDP-43 domains, so as to shed light on the molecular mechanisms underlying their liquid-liquid phase separation (LLPS) and amyloidosis. The review further delves into the mechanisms through which ALS-causing mutants of the well-folded hPFN1 disrupt the dynamics of LLPS of FUS prion-like domain, providing key insights into a potential mechanism for misfolding/aggregation-prone proteins to cause neurodegenerative diseases and aging by gain of functions. With better understanding of different biophysical aspects of FUS and TDP-43, the ultimate goal is to develop drugs targeting LLPS and amyloidosis, which could mediate protein homeostasis within cells and lead to new treatments for currently intractable diseases, particularly neurodegenerative diseases such as ALS, FTD and aging. However, the study of membrane-less organelles and condensates is still in its infancy and therefore the review also highlights key questions that require future investigation.
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10
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Gu J, Zhou X, Sutherland L, Kato M, Jaczynska K, Rizo J, McKnight SL. Oxidative regulation of TDP-43 self-association by a β-to-α conformational switch. Proc Natl Acad Sci U S A 2023; 120:e2311416120. [PMID: 37782781 PMCID: PMC10576115 DOI: 10.1073/pnas.2311416120] [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: 07/10/2023] [Accepted: 09/04/2023] [Indexed: 10/04/2023] Open
Abstract
An evolutionarily conserved region of the TDP-43 low-complexity domain (LCD) twenty residues in length can adopt either an α-helical or β-strand conformation. When in the latter conformation, TDP-43 self-associates via the formation of a labile, cross-β structure. Self-association can be monitored via the formation of phase-separated protein droplets. Exposure of droplets to hydrogen peroxide leads to oxidation of conserved methionine residues distributed throughout the LCD. Oxidation disassembles the cross-β structure, thus eliminating both self-association and phase separation. Here, we demonstrate that this process reciprocally enables formation of α-helical structure in precisely the same region formerly functioning to facilitate β-strand-mediated self-association. We further observe that the α-helical conformation allows interaction with a lipid-like detergent and that exposure to lipids enhances the β-to-α conformational switch. We hypothesize that regulation of this oxidative switch will prove to be important to the control of localized translation within vertebrate cells. The experimental observations reported herein were heavily reliant on studies of 1,6-hexanediol, a chemical agent that selectively dissolves labile structures formed via the self-association of protein domains of low sequence complexity. This aliphatic alcohol is shown to exert its dissociative activity primarily via hydrogen-bonding interactions with carbonyl oxygen atoms of the polypeptide backbone. Such observations underscore the central importance of backbone-mediated protein:protein interactions that facilitate the self-association and phase separation of LCDs.
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Affiliation(s)
- Jinge Gu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75235
| | - Xiaoming Zhou
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75235
| | - Lillian Sutherland
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75235
| | - Masato Kato
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75235
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Inage-ku, Chiba263-8555, Japan
| | - Klaudia Jaczynska
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75235
| | - Josep Rizo
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75235
| | - Steven L. McKnight
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75235
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11
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Gu J, Zhou X, Sutherland L, Kato M, Jaczynska K, Rizo J, McKnight SL. Oxidative regulation of TDP-43 self-association by a β-to-α conformational switch. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555361. [PMID: 37693418 PMCID: PMC10491227 DOI: 10.1101/2023.08.29.555361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
An evolutionarily conserved region of the TDP-43 low complexity domain twenty residues in length can adopt either an α-helical or β-strand conformation. When in the latter conformation, TDP-43 self-associates via the formation of a labile, cross-β structure. Self-association can be monitored via the formation of phase separated protein droplets. Exposure of droplets to hydrogen peroxide leads to oxidation of conserved methionine residues distributed throughout the low complexity domain. Oxidation disassembles the cross-β structure, thus eliminating both self-association and phase separation. Here we demonstrate that this process reciprocally enables formation of α-helical structure in precisely the same region formerly functioning to facilitate β-strand mediated self-association. We further observe that the α-helical conformation allows interaction with a lipid-like detergent, and that exposure to lipids enhances the β-to-α conformational switch. We hypothesize that regulation of this oxidative switch will prove to be important to the control of localized translation within vertebrate cells. The experimental observations reported herein were heavily reliant on studies of 1,6-hexanediol, a chemical agent that selectively dissolves labile structures formed via the self-association of protein domains of low sequence complexity. This aliphatic alcohol is shown to exert its dissociative activity primarily via hydrogen bonding interactions with carbonyl oxygen atoms of the polypeptide backbone. Such observations underscore the central importance of backbone-mediated protein:protein interactions that facilitate the self-association and phase separation of low complexity domains. Significance Statement The TDP-43 protein is a constituent of RNA granules involved in regulated translation. TDP-43 contains a C-terminal domain of 150 amino acids of low sequence complexity conspicuously decorated with ten methionine residues. An evolutionarily conserved region (ECR) of 20 residues within this domain can adopt either of two forms of labile secondary structure. Under normal conditions wherein methionine residues are reduced, the ECR forms a labile cross-β structure that enables RNA granule condensation. Upon methionine oxidation, the ECR undergoes a conformational switch to become an α-helix incompatible with self-association and granule integrity. Oxidation of the TDP-43 low complexity domain is hypothesized to occur proximal to mitochondria, thus facilitating dissolution of RNA granules and activation of localized translation.
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Affiliation(s)
- Jinge Gu
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75235
| | - Xiaoming Zhou
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75235
| | - Lillian Sutherland
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75235
| | - Masato Kato
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75235
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology (QST) 4-9-1, Anagawa, Inage-ku, Chiba, JAPAN 263-8555
| | - Klaudia Jaczynska
- Department of Biophysics, UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75235
| | - Josep Rizo
- Department of Biophysics, UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75235
| | - Steven L. McKnight
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75235
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12
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Ramirez DA, Hough LE, Shirts MR. Coiled-coil domains are sufficient to drive liquid-liquid phase separation of proteins in molecular models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543124. [PMID: 37398035 PMCID: PMC10312653 DOI: 10.1101/2023.05.31.543124] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Liquid-liquid phase separation (LLPS) is thought to be a main driving force in the formation of membraneless organelles. Examples of such organelles include the centrosome, central spindle, and stress granules. Recently, it has been shown that coiled-coil (CC) proteins, such as the centrosomal proteins pericentrin, spd-5, and centrosomin, might be capable of LLPS. CC domains have physical features that could make them the drivers of LLPS, but it is unknown if they play a direct role in the process. We developed a coarse-grained simulation framework for investigating the LLPS propensity of CC proteins, in which interactions which support LLPS arise solely from CC domains. We show, using this framework, that the physical features of CC domains are sufficient to drive LLPS of proteins. The framework is specifically designed to investigate how the number of CC domains, as well as multimerization state of CC domains, can affect LLPS. We show that small model proteins with as few as two CC domains can phase separate. Increasing the number of CC domains up to four per protein can somewhat increase LLPS propensity. We demonstrate that trimer-forming and tetramer-forming CC domains have a dramatically higher LLPS propensity than dimer-forming coils, which shows that multimerization state has a greater effect on LLPS than the number of CC domains per protein. These data support the hypothesis of CC domains as drivers of protein LLPS, and has implications in future studies to identify the LLPS-driving regions of centrosomal and central spindle proteins.
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Affiliation(s)
| | - Loren E. Hough
- Department of Physics and BioFrontiers Institute, University of Colorado Boulder, Boulder CO, 80309
| | - Michael R. Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder CO, 80309
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13
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Whitman BT, Wang Y, Murray CRA, Glover MJN, Owttrim GW. Liquid-Liquid Phase Separation of the DEAD-Box Cyanobacterial RNA Helicase Redox (CrhR) into Dynamic Membraneless Organelles in Synechocystis sp. Strain PCC 6803. Appl Environ Microbiol 2023; 89:e0001523. [PMID: 36920190 PMCID: PMC10132119 DOI: 10.1128/aem.00015-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/17/2023] [Indexed: 03/16/2023] Open
Abstract
Compartmentalization of macromolecules into discrete non-lipid-bound bodies by liquid-liquid phase separation (LLPS) is a well-characterized regulatory mechanism frequently associated with the cellular stress response in eukaryotes. In contrast, the formation and importance of similar complexes is just becoming evident in bacteria. Here, we identify LLPS as the mechanism by which the DEAD-box RNA helicase, cyanobacterial RNA helicase redox (CrhR), compartmentalizes into dynamic membraneless organelles in a temporal and spatial manner in response to abiotic stress in the cyanobacterium Synechocystis sp. strain PCC 6803. Stress conditions induced CrhR to form a single crescent localized exterior to the thylakoid membrane, indicating that this region is a crucial domain in the cyanobacterial stress response. These crescents rapidly dissipate upon alleviation of the stress conditions. Furthermore, CrhR aggregation was mediated by LLPS in an RNA-dependent reaction. We propose that dynamic CrhR condensation performs crucial roles in RNA metabolism, enabling rapid adaptation of the photosynthetic apparatus to environmental stresses. These results expand our understanding of the role that functional compartmentalization of RNA helicases and thus RNA processing in membraneless organelles by LLPS-mediated protein condensation performs in the bacterial response to environmental stress. IMPORTANCE Oxygen-evolving photosynthetic cyanobacteria evolved ~3 billion years ago, performing fundamental roles in the biogeochemical evolution of the early Earth and continue to perform fundamental roles in nutrient cycling and primary productivity today. The phylum consists of diverse species that flourish in heterogeneous environments. A prime driver for survival is the ability to alter photosynthetic performance in response to the shifting environmental conditions these organisms continuously encounter. This study demonstrated that diverse abiotic stresses elicit dramatic changes in localization and structural organization of the RNA helicase CrhR associated with the photosynthetic thylakoid membrane. These dynamic changes, mediated by a liquid-liquid phase separation (LLPS)-mediated mechanism, reveal a novel mechanism by which cyanobacteria can compartmentalize the activity of ribonucleoprotein complexes in membraneless organelles. The results have significant consequences for understanding bacterial adaptation and survival in response to changing environmental conditions.
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Affiliation(s)
- Brendan T. Whitman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Yixiong Wang
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Cameron R. A. Murray
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mark J. N. Glover
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - George W. Owttrim
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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14
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Jung KH, Sun J, Hsiung CH, Lance Lian X, Liu Y, Zhang X. Nuclear bodies protect phase separated proteins from degradation in stressed proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537522. [PMID: 37131610 PMCID: PMC10153235 DOI: 10.1101/2023.04.19.537522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
RNA-binding proteins (RBPs) containing intrinsically disordered domains undergo liquid-liquid phase separation to form nuclear bodies under stress conditions. This process is also connected to the misfolding and aggregation of RBPs, which are associated with a series of neurodegenerative diseases. However, it remains elusive how folding states of RBPs changes upon the formation and maturation of nuclear bodies. Here, we describe SNAP-tag based imaging methods to visualize the folding states of RBPs in live cells via time-resolved quantitative microscopic analyses of their micropolarity and microviscosity. Using these imaging methods in conjunction with immunofluorescence imaging, we demonstrate that RBPs, represented by TDP-43, initially enters the PML nuclear bodies in its native state upon transient proteostasis stress, albeit it begins to misfolded during prolonged stress. Furthermore, we show that heat shock protein 70 co-enters the PML nuclear bodies to prevent the degradation of TDP-43 from the proteotoxic stress, thus revealing a previously unappreciated protective role of the PML nuclear bodies in the prevention of stress-induced degradation of TDP-43. In summary, our imaging methods described in the manuscript, for the first time, reveal the folding states of RBPs, which were previously challenging to study with conventional methods in nuclear bodies of live cells. This study uncovers the mechanistic correlations between the folding states of a protein and functions of nuclear bodies, in particular PML bodies. We envision that the imaging methods can be generally applied to elucidating the structural aspects of other proteins that exhibit granular structures under biological stimulus.
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Affiliation(s)
- Kwan Ho Jung
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Jiarui Sun
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Chia-Heng Hsiung
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
- Present address: Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China; Westlake Laboratory of Life Sciences and Biomedicine; 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Department of Biomedical Engineering, The Huck Institute of Life Sciences, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Xiaojun Lance Lian
- Department of Biomedical Engineering, The Huck Institute of Life Sciences, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Yu Liu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Xin Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
- Present address: Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China; Westlake Laboratory of Life Sciences and Biomedicine; 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Department of Biomedical Engineering, The Huck Institute of Life Sciences, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
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15
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Doke AA, Jha SK. Shapeshifter TDP-43: Molecular mechanism of structural polymorphism, aggregation, phase separation and their modulators. Biophys Chem 2023; 295:106972. [PMID: 36812677 DOI: 10.1016/j.bpc.2023.106972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023]
Abstract
TDP-43 is a nucleic acid-binding protein that performs physiologically essential functions and is known to undergo phase separation and aggregation during stress. Initial observations have shown that TDP-43 forms heterogeneous assemblies, including monomer, dimer, oligomers, aggregates, phase-separated assemblies, etc. However, the significance of each assembly of TDP-43 concerning its function, phase separation, and aggregation is poorly known. Furthermore, how different assemblies of TDP-43 are related to each other is unclear. In this review, we focus on the various assemblies of TDP-43 and discuss the plausible origin of the structural heterogeneity of TDP-43. TDP-43 is involved in multiple physiological processes like phase separation, aggregation, prion-like seeding, and performing physiological functions. However, the molecular mechanism behind the physiological process performed by TDP-43 is not well understood. The current review discusses the plausible molecular mechanism of phase separation, aggregation, and prion-like propagation of TDP-43.
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Affiliation(s)
- Abhilasha A Doke
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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16
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Herrera MG, Amundarain MJ, Santos J. Biophysical evaluation of the oligomerization and conformational properties of the N-terminal domain of TDP-43. Arch Biochem Biophys 2023; 737:109533. [PMID: 36740035 DOI: 10.1016/j.abb.2023.109533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 01/08/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023]
Abstract
TDP-43 is an RNA-binding protein that presents four domains comprising an N-terminal region, two RNA recognition motifs and a C-terminal region. The N-terminal domain (NTD) has a relevant role in the oligomerization and splicing activity of TDP-43. In this work, we have expressed, purified and biophysically characterized the region that includes residues 1 to 102 that contains the nuclear localization signal (residues 80-102, NLS). Furthermore, we have evaluated the oligomerization equilibrium for this protein fragment. Also, we have determined changes in the tertiary structure and its stability in a broad range of pH values by means of different spectroscopic methods. Additionally, we compared this fragment with the one that lacks the NLS employing experimental and computational methods. Finally, we evaluated the motion of dimeric forms to get insights into the conformational flexibility of this TDP-43 module in an oligomeric state. Our results suggest that this domain has a conformational plasticity in the vicinity of the single tryptophan of this domain (Trp68), which is enhanced by the presence of the nuclear localization signal. All these results help to understand the molecular features of the NTD of TDP-43.
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Affiliation(s)
- Maria Georgina Herrera
- Faculty of Exact and Natural Sciences, Institute of Biosciences, Biotechnology and Translational Biology (iB3), University of Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina; Institute of Biochemistry and Pathobiochemistry, Ruhr-Universität Bochum, Gebäude MA 2/143, Universitätsstraße 150, 44801, Bochum, Germany.
| | - Maria Julia Amundarain
- Faculty of Chemistry, OCIII, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Javier Santos
- Faculty of Exact and Natural Sciences, Institute of Biosciences, Biotechnology and Translational Biology (iB3), University of Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina
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17
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Liquid-liquid Phase Separation of α-Synuclein: A New Mechanistic Insight for α-Synuclein Aggregation Associated with Parkinson's Disease Pathogenesis. J Mol Biol 2023; 435:167713. [PMID: 35787838 DOI: 10.1016/j.jmb.2022.167713] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 02/04/2023]
Abstract
Aberrant aggregation of the misfolded presynaptic protein, α-Synuclein (α-Syn) into Lewy body (LB) and Lewy neuritis (LN) is a major pathological hallmark of Parkinson's disease (PD) and other synucleinopathies. Numerous studies have suggested that prefibrillar and fibrillar species of the misfolded α-Syn aggregates are responsible for cell death in PD pathogenesis. However, the precise molecular events during α-Syn aggregation, especially in the early stages, remain elusive. Emerging evidence has demonstrated that liquid-liquid phase separation (LLPS) of α-Syn occurs in the nucleation step of α-Syn aggregation, which offers an alternate non-canonical aggregation pathway in the crowded microenvironment. The liquid-like α-Syn droplets gradually undergo an irreversible liquid-to-solid phase transition into amyloid-like hydrogel entrapping oligomers and fibrils. This new mechanism of α-Syn LLPS and gel formation might represent the molecular basis of cellular toxicity associated with PD. This review aims to demonstrate the recent development of α-Syn LLPS, the underlying mechanism along with the microscopic events of aberrant phase transition. This review further discusses how several intrinsic and extrinsic factors regulate the thermodynamics and kinetics of α-Syn LLPS and co-LLPS with other proteins, which might explain the pathophysiology of α-Syn in various neurodegenerative diseases.
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18
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Mohanty P, Kapoor U, Sundaravadivelu Devarajan D, Phan TM, Rizuan A, Mittal J. Principles Governing the Phase Separation of Multidomain Proteins. Biochemistry 2022; 61:2443-2455. [PMID: 35802394 PMCID: PMC9669140 DOI: 10.1021/acs.biochem.2c00210] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A variety of membraneless organelles, often termed "biological condensates", play an important role in the regulation of cellular processes such as gene transcription, translation, and protein quality control. On the basis of experimental and theoretical investigations, liquid-liquid phase separation (LLPS) has been proposed as a possible mechanism for the origin of biological condensates. LLPS requires multivalent macromolecules that template the formation of long-range, intermolecular interaction networks and results in the formation of condensates with defined composition and material properties. Multivalent interactions driving LLPS exhibit a wide range of modes from highly stereospecific to nonspecific and involve both folded and disordered regions. Multidomain proteins serve as suitable macromolecules for promoting phase separation and achieving disparate functions due to their potential for multivalent interactions and regulation. Here, we aim to highlight the influence of the domain architecture and interdomain interactions on the phase separation of multidomain protein condensates. First, the general principles underlying these interactions are illustrated on the basis of examples of multidomain proteins that are predominantly associated with nucleic acid binding and protein quality control and contain both folded and disordered regions. Next, the examples showcase how LLPS properties of folded and disordered regions can be leveraged to engineer multidomain constructs that form condensates with the desired assembly and functional properties. Finally, we highlight the need for improvements in coarse-grained computational models that can provide molecular-level insights into multidomain protein condensates in conjunction with experimental efforts.
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Affiliation(s)
- Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Utkarsh Kapoor
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | | | - Tien Minh Phan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
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19
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Phase separation and other forms of α-Synuclein self-assemblies. Essays Biochem 2022; 66:987-1000. [DOI: 10.1042/ebc20220055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022]
Abstract
Abstract
α-Synuclein (α-Syn) is a natively unstructured protein, which self-assembles into higher-order aggregates possessing serious pathophysiological implications. α-Syn aberrantly self-assembles into protein aggregates, which have been widely implicated in Parkinson’s disease (PD) pathogenesis and other synucleinopathies. The self-assembly of α-Syn involves the structural conversion of soluble monomeric protein into oligomeric intermediates and eventually fibrillar aggregates of amyloids with cross-β-sheet rich conformation. These aggregated α-Syn species majorly constitute the intraneuronal inclusions, which is a hallmark of PD neuropathology. Self-assembly/aggregation of α-Syn is not a single-state conversion process as unfolded protein can access multiple conformational states through the formation of metastable, transient pre-fibrillar intermediate species. Recent studies have indicated that soluble oligomers are the potential neurotoxic species responsible for cell death in PD pathogenesis. The heterogeneous and transient nature of oligomers formed during the early stage of aggregation pathway limit their detailed study in understanding the structure–toxicity relationship. Moreover, the precise molecular events occurring in the early stage of α-Syn aggregation process majorly remain unsolved. Recently, liquid–liquid phase separation (LLPS) of α-Syn has been designated as an alternate nucleation mechanism, which occurs in the early lag phase of the aggregation pathway leading to the formation of dynamic supramolecular assemblies. The stronger self-association among the protein molecules triggers the irreversible liquid-to-solid transition of these supramolecular assemblies into the amyloid-like hydrogel, which may serve as a reservoir entrapping toxic oligomeric intermediates and fibrils. This review strives to provide insights into different modes of α-Syn self-assemblies including LLPS-mediated self-assembly and its recent advancements.
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20
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Kang K, Shi Q, Wang X, Chen YG. Dishevelled phase separation promotes Wnt signalosome assembly and destruction complex disassembly. J Cell Biol 2022; 221:213667. [PMID: 36342472 PMCID: PMC9811998 DOI: 10.1083/jcb.202205069] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/21/2022] [Accepted: 09/19/2022] [Indexed: 11/09/2022] Open
Abstract
The amplitude of Wnt/β-catenin signaling is precisely controlled by the assembly of the cell surface-localized Wnt receptor signalosome and the cytosolic β-catenin destruction complex. How these two distinct complexes are coordinately controlled remains largely unknown. Here, we demonstrated that the signalosome scaffold protein Dishevelled 2 (Dvl2) undergoes liquid-liquid phase separation (LLPS). Dvl2 LLPS is mediated by an intrinsically disordered region and facilitated by components of the signalosome, such as the receptor Fzd5. Assembly of the signalosome is initiated by rapid recruitment of Dvl2 to the membrane, followed by slow and dynamic recruitment of Axin1. Axin LLPS mediates assembly of the β-catenin destruction complex, and Dvl2 attenuates LLPS of Axin. Compared with the destruction complex, Axin partitions into the signalosome at a lower concentration and exhibits a higher mobility. Together, our results revealed that Dvl2 LLPS is crucial for controlling the assembly of the Wnt receptor signalosome and disruption of the phase-separated β-catenin destruction complex.
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Affiliation(s)
- Kexin Kang
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qiaoni Shi
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xu Wang
- Guangzhou Laboratory, Guangzhou, China
| | - Ye-Guang Chen
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China,Guangzhou Laboratory, Guangzhou, China,School of Basic Medicine, Nanchang University, Nanchang, China,Correspondence to Ye-Guang Chen:
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21
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Ng WS, Sielaff H, Zhao ZW. Phase Separation-Mediated Chromatin Organization and Dynamics: From Imaging-Based Quantitative Characterizations to Functional Implications. Int J Mol Sci 2022; 23:ijms23148039. [PMID: 35887384 PMCID: PMC9316379 DOI: 10.3390/ijms23148039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 12/14/2022] Open
Abstract
As an effective and versatile strategy to compartmentalize cellular components without the need for lipid membranes, phase separation has been found to underpin a wide range of intranuclear processes, particularly those involving chromatin. Many of the unique physico-chemical properties of chromatin-based phase condensates are harnessed by the cell to accomplish complex regulatory functions in a spatially and temporally controlled manner. Here, we survey key recent findings on the mechanistic roles of phase separation in regulating the organization and dynamics of chromatin-based molecular processes across length scales, packing states and intranuclear functions, with a particular emphasis on quantitative characterizations of these condensates enabled by advanced imaging-based approaches. By illuminating the complex interplay between chromatin and various chromatin-interacting molecular species mediated by phase separation, this review sheds light on an emerging multi-scale, multi-modal and multi-faceted landscape that hierarchically regulates the genome within the highly crowded and dynamic nuclear space. Moreover, deficiencies in existing studies also highlight the need for mechanism-specific criteria and multi-parametric approaches for the characterization of chromatin-based phase separation using complementary techniques and call for greater efforts to correlate the quantitative features of these condensates with their functional consequences in close-to-native cellular contexts.
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Affiliation(s)
- Woei Shyuan Ng
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore 119543, Singapore; (W.S.N.); (H.S.)
- Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore 117557, Singapore
| | - Hendrik Sielaff
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore 119543, Singapore; (W.S.N.); (H.S.)
- Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore 117557, Singapore
| | - Ziqing Winston Zhao
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore 119543, Singapore; (W.S.N.); (H.S.)
- Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore 117557, Singapore
- Mechanobiology Institute (MBI), National University of Singapore, Singapore 117411, Singapore
- Correspondence:
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22
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Duan L, Zaepfel BL, Aksenova V, Dasso M, Rothstein JD, Kalab P, Hayes LR. Nuclear RNA binding regulates TDP-43 nuclear localization and passive nuclear export. Cell Rep 2022; 40:111106. [PMID: 35858577 PMCID: PMC9345261 DOI: 10.1016/j.celrep.2022.111106] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/26/2022] [Accepted: 06/27/2022] [Indexed: 11/27/2022] Open
Abstract
Nuclear clearance of the RNA-binding protein TDP-43 is a hallmark of neurodegeneration and an important therapeutic target. Our current understanding of TDP-43 nucleocytoplasmic transport does not fully explain its predominantly nuclear localization or mislocalization in disease. Here, we show that TDP-43 exits nuclei by passive diffusion, independent of facilitated mRNA export. RNA polymerase II blockade and RNase treatment induce TDP-43 nuclear efflux, suggesting that nuclear RNAs sequester TDP-43 in nuclei and limit its availability for passive export. Induction of TDP-43 nuclear efflux by short, GU-rich oligomers (presumably by outcompeting TDP-43 binding to endogenous nuclear RNAs), and nuclear retention conferred by splicing inhibition, demonstrate that nuclear TDP-43 localization depends on binding to GU-rich nuclear RNAs. Indeed, RNA-binding domain mutations markedly reduce TDP-43 nuclear localization and abolish transcription blockade-induced nuclear efflux. Thus, the nuclear abundance of GU-RNAs, dictated by the balance of transcription, pre-mRNA processing, and RNA export, regulates TDP-43 nuclear localization.
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Affiliation(s)
- Lauren Duan
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Benjamin L Zaepfel
- Biochemistry, Cellular and Molecular Biology Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Vasilisa Aksenova
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Petr Kalab
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Lindsey R Hayes
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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23
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Conversion of the Native N-Terminal Domain of TDP-43 into a Monomeric Alternative Fold with Lower Aggregation Propensity. Molecules 2022; 27:molecules27134309. [PMID: 35807552 PMCID: PMC9268139 DOI: 10.3390/molecules27134309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/30/2022] [Accepted: 07/02/2022] [Indexed: 11/17/2022] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) forms intraneuronal cytoplasmic inclusions associated with amyotrophic lateral sclerosis and ubiquitin-positive frontotemporal lobar degeneration. Its N-terminal domain (NTD) can dimerise/oligomerise with the head-to-tail arrangement, which is essential for function but also favours liquid-liquid phase separation and inclusion formation of full-length TDP-43. Using various biophysical approaches, we identified an alternative conformational state of NTD in the presence of Sulfobetaine 3-10 (SB3-10), with higher content of α-helical structure and tryptophan solvent exposure. NMR shows a highly mobile structure, with partially folded regions and β-sheet content decrease, with a concomitant increase of α-helical structure. It is monomeric and reverts to native oligomeric NTD upon SB3-10 dilution. The equilibrium GdnHCl-induced denaturation shows a cooperative folding and a somewhat lower conformational stability. When the aggregation processes were compared with and without pre-incubation with SB3-10, but at the identical final SB3-10 concentration, a slower aggregation was found in the former case, despite the reversible attainment of the native conformation in both cases. This was attributed to protein monomerization and oligomeric seeds disruption by the conditions promoting the alternative conformation. Overall, the results show a high plasticity of TDP-43 NTD and identify strategies to monomerise TDP-43 NTD for methodological and biomedical applications.
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Niu J, Qiu C, Abbott NL, Gellman SH. Formation of versus Recruitment to RNA-Rich Condensates: Controlling Effects Exerted by Peptide Side Chain Identity. J Am Chem Soc 2022; 144:10386-10395. [PMID: 35639776 PMCID: PMC9746169 DOI: 10.1021/jacs.2c02222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Liquid-liquid phase separation (LLPS), the spontaneous formation of contiguous liquid phases with distinct compositions, has been long known in chemical systems and more recently recognized as a ubiquitous feature of cell biology. We describe a system involving biologically relevant components, synthetic peptides, and total yeast RNA, that has enabled us to explore factors that underlie phase separation. Coulombic complementarity between a cationic peptide and anionic RNA is necessary but not sufficient for formation of a condensed phase in our system. In addition to a net positive charge, the peptide must present the proper type of cationic moiety. Guanidinium groups, as found in the Arg side chain, support phase separation, but ammonium groups, as found in the Lys side chain, or dimethylguanidinium groups, as found in post-translationally modified Arg side chains, do not support phase separation in our system. However, the cationic groups that do not support phase separation via interaction with RNA can nevertheless enable recruitment to a condensed phase, which reveals that the network of forces governing condensed phase formation can differ from the network of forces governing recruitment to such a phase. We introduce a new method for measuring the concentrations of components in condensed phases based on fluorine-containing additives and 19F NMR.
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Affiliation(s)
- Jiani Niu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Cindy Qiu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, New York 14853, USA
| | - Nicholas L. Abbott
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, New York 14853, USA
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Carrettiero DC, Almeida MC, Longhini AP, Rauch JN, Han D, Zhang X, Najafi S, Gestwicki JE, Kosik KS. Stress routes clients to the proteasome via a BAG2 ubiquitin-independent degradation condensate. Nat Commun 2022; 13:3074. [PMID: 35654899 PMCID: PMC9163039 DOI: 10.1038/s41467-022-30751-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 05/16/2022] [Indexed: 02/06/2023] Open
Abstract
The formation of membraneless organelles can be a proteotoxic stress control mechanism that locally condenses a set of components capable of mediating protein degradation decisions. The breadth of mechanisms by which cells respond to stressors and form specific functional types of membraneless organelles, is incompletely understood. We found that Bcl2-associated athanogene 2 (BAG2) marks a distinct phase-separated membraneless organelle, triggered by several forms of stress, particularly hyper-osmotic stress. Distinct from well-known condensates such as stress granules and processing bodies, BAG2-containing granules lack RNA, lack ubiquitin and promote client degradation in a ubiquitin-independent manner via the 20S proteasome. These organelles protect the viability of cells from stress and can traffic to the client protein, in the case of Tau protein, on the microtubule. Components of these ubiquitin-independent degradation organelles include the chaperone HSP-70 and the 20S proteasome activated by members of the PA28 (PMSE) family. BAG2 condensates did not co-localize with LAMP-1 or p62/SQSTM1. When the proteasome is inhibited, BAG2 condensates and the autophagy markers traffic to an aggresome-like structure.
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Affiliation(s)
- Daniel C Carrettiero
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
- Center for Natural and Human Sciences, Federal University of ABC, São Bernardo do Campo, SP, Brazil
| | - Maria C Almeida
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
- Center for Natural and Human Sciences, Federal University of ABC, São Bernardo do Campo, SP, Brazil
| | - Andrew P Longhini
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Jennifer N Rauch
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Dasol Han
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Xuemei Zhang
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Saeed Najafi
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Jason E Gestwicki
- Institute for Neurodegenerative Disease, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Kenneth S Kosik
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.
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Lye YS, Chen YR. TAR DNA-binding protein 43 oligomers in physiology and pathology. IUBMB Life 2022; 74:794-811. [PMID: 35229461 DOI: 10.1002/iub.2603] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/19/2022] [Accepted: 01/28/2022] [Indexed: 11/08/2022]
Abstract
TAR DNA-binding protein 43 (TDP-43) is an RNA/DNA-binding protein involved in RNA regulation and diseases. In 2006, TDP-43 inclusions were found in the disease lesions of several neurodegenerative diseases. It is the pathological hallmark in both amyotrophic lateral sclerosis and frontotemporal lobar dementia. It also presents in a large portion of patients with Alzheimer's disease. TDP-43 is prone to aggregate; however, the role of TDP-43 oligomers remains poorly understood in both physiological and pathological conditions. In this review, we emphasize the role of oligomeric TDP-43 in both physiological and pathological conditions and discuss the potential mechanisms of oligomer formation. Finally, we suggest therapeutic strategies against the TDP-43 oligomers in neurodegenerative diseases.
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Affiliation(s)
- Yuh Shen Lye
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Cheng Kung University and Academia Sinica, Taipei, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Cheng Kung University and Academia Sinica, Taipei, Taiwan
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Dong X, Wan W, Zeng L, Jin W, Huang Y, Shen D, Bai Y, Zhao Q, Zhang L, Liu Y, Gao Z. Regulation of Fluorescence Solvatochromism To Resolve Cellular Polarity upon Protein Aggregation. Anal Chem 2021; 93:16447-16455. [PMID: 34859995 DOI: 10.1021/acs.analchem.1c03401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Common solvatochromic fluorophores exhibit a bathochromic fluorescence emission wavelength shift accompanied by intensity attenuation due to the presence of nonradiative decay pathways at the excited state. Such intrinsic but inevitable fluorescence quenching of solvatochromism impedes its applications to faithfully quantify local polarity, especially in a polar environment. Herein, we report a new donor-π-acceptor (D-π-A) type solvatochromic fluorophore scaffold containing a perfluorophenyl group that exhibits both a solvatochromic emission wavelength shift and a controllable emission intensity upon polarity fluctuation. The regulation of fluorescence solvatochromism and colors was achieved by tuning the aryl donors. We exploited such desired solvatochromism of these probes to monitor protein misfolding and aggregation via wavelength shift. Finally, the polarity of pathogenic aggregated proteins was quantified by HaloTag bioorthogonal labeling technology in live cells. While much effort has been devoted to resolving the morphology of pathogenic aggregated proteins, this work provides quantitative hints regarding the chemical information at this disease-related protein interphase.
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Affiliation(s)
- Xuepeng Dong
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, P. R. China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Lianggang Zeng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,University of the Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, P. R. China
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