1
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Prikhodko IV, Guria GT. The method for assessing the specificity of developing CAR therapies. BIOPHYSICAL REPORTS 2024; 4:100172. [PMID: 39025235 PMCID: PMC11344002 DOI: 10.1016/j.bpr.2024.100172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024]
Abstract
The effectiveness of antitumor chimeric antigen receptor (CAR) therapy mainly dealt with an elevated sensitivity of CAR cells to target cells. However, CAR therapies are associated with nonspecific side effects: on-target off-tumor toxicity. Sensitivity and specificity of CAR cells are the most important properties of the recognition process of target cells among other cells. Current developments are mainly concentrated on exploring molecular biology methods for designing CAR cells with the highest sensitivity, while the problem of the CAR cell specificity is rarely considered. For the assessment of CAR cell specificity, we suggest that, in addition to an elevated level of CAR-antigen affinity, the ability of CARs for clustering should be taken into account. We assume that the CAR cell cytotoxicity is determined by CAR clustering. The latter is treated within the framework of nucleation theory. The master equation for the probability of CAR cell cytotoxicity is derived. The size of a critical CAR cluster is found to be one of two most essential parameters. The conditions for necessary sensitivity and sufficient specificity are explored. Relevant parametric diagrams are derived. Possible applications of the method for assessing the specificity of developing CAR therapies are discussed.
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Affiliation(s)
- Ivan V Prikhodko
- Laboratory for Mathematical Modelling of Biological Processes, National Medical Research Center for Hematology, Moscow, Russia
| | - Georgy Th Guria
- Laboratory for Mathematical Modelling of Biological Processes, National Medical Research Center for Hematology, Moscow, Russia; Chair of the Living Systems Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia.
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2
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Bagheri Y, Rouches M, Machta B, Veatch SL. Prewetting couples membrane and protein phase transitions to greatly enhance coexistence in models and cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.26.609758. [PMID: 39253471 PMCID: PMC11383005 DOI: 10.1101/2024.08.26.609758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Both membranes and biopolymers can individually separate into coexisting liquid phases. Here we explore biopolymer prewetting at membranes, a phase transition that emerges when these two thermodynamic systems are coupled. In reconstitution, we couple short poly-L-Lysine and poly-L-Glutamic Acid polyelectrolytes to membranes of saturated lipids, unsaturated lipids, and cholesterol, and detect coexisting prewet and dry surface phases well outside of the region of coexistence for each individual system. Notability, polyelectrolyte prewetting is highly sensitive to membrane lipid composition, occurring at 10 fold lower polymer concentration in a membrane close to its phase transition compared to one without a phase transition. In cells, protein prewetting is achieved using an optogenetic tool that enables titration of condensing proteins and tethering to the plasma membrane inner leaflet. Here we show that protein prewetting occurs for conditions well outside those where proteins condense in the cytoplasm, and that the stability of prewet domains is sensitive to perturbations of plasma membrane composition and structure. Our work presents an example of how thermodynamic phase transitions can impact cellular structure outside their individual coexistence regions, suggesting new possible roles for phase-separation-prone systems in cell biology.
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Affiliation(s)
- Yousef Bagheri
- Program in Biophysics, University of Michigan, Ann Arbor, MI USA
| | - Mason Rouches
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven CT USA
| | | | - Sarah L Veatch
- Program in Biophysics, University of Michigan, Ann Arbor, MI USA
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3
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Wilson ZS, Raya-Sandino A, Miranda J, Fan S, Brazil JC, Quiros M, Garcia-Hernandez V, Liu Q, Kim CH, Hankenson KD, Nusrat A, Parkos CA. Critical role of thrombospondin-1 in promoting intestinal mucosal wound repair. JCI Insight 2024; 9:e180608. [PMID: 39078701 PMCID: PMC11385097 DOI: 10.1172/jci.insight.180608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/18/2024] [Indexed: 09/11/2024] Open
Abstract
Thrombospondin-1 (TSP1) is a matricellular protein associated with the regulation of cell migration through direct binding interactions with integrin proteins and by associating with other receptors known to regulate integrin function, including CD47 and CD36. We previously demonstrated that deletion of an epithelial TSP1 receptor, CD47, attenuates epithelial wound repair following intestinal mucosal injury. However, the mechanisms by which TSP1 contributes to intestinal mucosal repair remain poorly understood. Our results show upregulated TSP1 expression in colonic mucosal wounds and impaired intestinal mucosal wound healing in vivo upon intestinal epithelium-specific loss of TSP1 (VillinCre/+ Thbs1fl/fl or Thbs1ΔIEC mice). We report that exposure to exogenous TSP1 enhanced migration of intestinal epithelial cells in a CD47- and TGF-β1-dependent manner and that deficiency of TSP1 in primary murine colonic epithelial cells resulted in impaired wound healing. Mechanistically, TSP1 modulated epithelial actin cytoskeletal dynamics through suppression of RhoA activity, activation of Rho family small GTPase (Rac1), and changes in filamentous-actin bundling. Overall, TSP1 was found to regulate intestinal mucosal wound healing via CD47 and TGF-β1, coordinate integrin-containing cell-matrix adhesion dynamics, and remodel the actin cytoskeleton in migrating epithelial cells to enhance cell motility and promote wound repair.
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Affiliation(s)
| | | | | | | | | | | | | | - Qingyang Liu
- Department of Pathology
- Mary H. Weiser Food Allergy Center, and
| | - Chang H Kim
- Department of Pathology
- Mary H. Weiser Food Allergy Center, and
| | - Kurt D Hankenson
- Department of Orthopedic Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
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4
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Lee CT, Bell M, Bonilla-Quintana M, Rangamani P. Biophysical Modeling of Synaptic Plasticity. Annu Rev Biophys 2024; 53:397-426. [PMID: 38382115 DOI: 10.1146/annurev-biophys-072123-124954] [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] [Indexed: 02/23/2024]
Abstract
Dendritic spines are small, bulbous compartments that function as postsynaptic sites and undergo intense biochemical and biophysical activity. The role of the myriad signaling pathways that are implicated in synaptic plasticity is well studied. A recent abundance of quantitative experimental data has made the events associated with synaptic plasticity amenable to quantitative biophysical modeling. Spines are also fascinating biophysical computational units because spine geometry, signal transduction, and mechanics work in a complex feedback loop to tune synaptic plasticity. In this sense, ideas from modeling cell motility can inspire us to develop multiscale approaches for predictive modeling of synaptic plasticity. In this article, we review the key steps in postsynaptic plasticity with a specific focus on the impact of spine geometry on signaling, cytoskeleton rearrangement, and membrane mechanics. We summarize the main experimental observations and highlight how theory and computation can aid our understanding of these complex processes.
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Affiliation(s)
- Christopher T Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Miriam Bell
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Mayte Bonilla-Quintana
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
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5
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Litschel T, Kelley CF, Cheng X, Babl L, Mizuno N, Case LB, Schwille P. Membrane-induced 2D phase separation of the focal adhesion protein talin. Nat Commun 2024; 15:4986. [PMID: 38862544 PMCID: PMC11166923 DOI: 10.1038/s41467-024-49222-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/22/2024] [Indexed: 06/13/2024] Open
Abstract
Focal adhesions form liquid-like assemblies around activated integrin receptors at the plasma membrane. How they achieve their flexible properties is not well understood. Here, we use recombinant focal adhesion proteins to reconstitute the core structural machinery in vitro. We observe liquid-liquid phase separation of the core focal adhesion proteins talin and vinculin for a spectrum of conditions and interaction partners. Intriguingly, we show that binding to PI(4,5)P2-containing membranes triggers phase separation of these proteins on the membrane surface, which in turn induces the enrichment of integrin in the clusters. We suggest a mechanism by which 2-dimensional biomolecular condensates assemble on membranes from soluble proteins in the cytoplasm: lipid-binding triggers protein activation and thus, liquid-liquid phase separation of these membrane-bound proteins. This could explain how early focal adhesions maintain a structured and force-resistant organization into the cytoplasm, while still being highly dynamic and able to quickly assemble and disassemble.
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Affiliation(s)
- Thomas Litschel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany.
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
| | - Charlotte F Kelley
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Xiaohang Cheng
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Leon Babl
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Naoko Mizuno
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Laboratory of Structural Cell Biology, National Institutes of Health, Bethesda, MD, USA
| | - Lindsay B Case
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany.
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6
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Wang B, Pareek G, Kundu M. ULK/Atg1: phasing in and out of autophagy. Trends Biochem Sci 2024; 49:494-505. [PMID: 38565496 PMCID: PMC11162330 DOI: 10.1016/j.tibs.2024.03.004] [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: 12/15/2023] [Revised: 02/28/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Autophagy - a highly regulated intracellular degradation process - is pivotal in maintaining cellular homeostasis. Liquid-liquid phase separation (LLPS) is a fundamental mechanism regulating the formation and function of membrane-less compartments. Recent research has unveiled connections between LLPS and autophagy, suggesting that phase separation events may orchestrate the spatiotemporal organization of autophagic machinery and cargo sequestration. The Unc-51-like kinase (ULK)/autophagy-related 1 (Atg1) family of proteins is best known for its regulatory role in initiating autophagy, but there is growing evidence that the functional spectrum of ULK/Atg1 extends beyond autophagy regulation. In this review, we explore the spatial and temporal regulation of the ULK/Atg1 family of kinases, focusing on their recruitment to LLPS-driven compartments, and highlighting their multifaceted functions beyond their traditional role.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; Shenzhen Research Institute of Xiamen University, Shenzhen, 518057, China
| | - Gautam Pareek
- Department of Cell and Molecular Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mondira Kundu
- Department of Cell and Molecular Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA.
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7
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Murai T. Transmembrane signaling through single-spanning receptors modulated by phase separation at the cell surface. Eur J Cell Biol 2024; 103:151413. [PMID: 38631097 DOI: 10.1016/j.ejcb.2024.151413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024] Open
Abstract
A wide variety of transmembrane signals are transduced by cell-surface receptors that activate intracellular signaling molecules. In particular, receptor clustering in the plasma membrane plays a critical role in these processes. Single-spanning or single-pass transmembrane proteins are among the most significant types of membrane receptors, which include adhesion receptors, such as integrins, CD44, cadherins, and receptor tyrosine kinases. Elucidating the molecular mechanisms underlying the regulation of the activity of these receptors is of great significance. Liquid-liquid phase separation (LLPS) is a recently emerging paradigm in cellular physiology for the ubiquitous regulation of the spatiotemporal dynamics of various signaling pathways. This study describes the emerging features of transmembrane signaling through single-spanning receptors from the perspective of phase separation. Possible physicochemical modulations of LLPS-based transmembrane signaling are also discussed.
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Affiliation(s)
- Toshiyuki Murai
- Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan.
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8
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Lin CC, Suen KM, Lidster J, Ladbury JE. The emerging role of receptor tyrosine kinase phase separation in cancer. Trends Cell Biol 2024; 34:371-379. [PMID: 37777392 DOI: 10.1016/j.tcb.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/17/2023] [Accepted: 09/06/2023] [Indexed: 10/02/2023]
Abstract
Receptor tyrosine kinase (RTK)-mediated signal transduction is fundamental to cell function and drives important cellular outcomes which, when dysregulated, can lead to malignant tumour growth and metastasis. The initiation of signals from plasma membrane-bound RTKs is subjected to multiple regulatory mechanisms that control downstream effector protein recruitment and function. The high propensity of RTKs to condense via liquid-liquid phase separation (LLPS) into membraneless organelles with downstream effector proteins provides a further fundamental mechanism for signal regulation. Herein we highlight how this phenomenon contributes to cancer signalling and consider the potential impact of LLPS on outcomes for cancer patients.
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Affiliation(s)
- Chi-Chuan Lin
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Kin Man Suen
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Jessica Lidster
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - John E Ladbury
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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9
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Kumar A, Tanaka K, Schwartz MA. Focal adhesion-derived liquid-liquid phase separations regulate mRNA translation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.22.568289. [PMID: 38045367 PMCID: PMC10690234 DOI: 10.1101/2023.11.22.568289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Liquid-liquid phase separation (LLPS) has emerged as a major organizing principle in cells. Recent work showed that multiple components of integrin-mediated focal adhesions including p130Cas can form LLPS, which govern adhesion dynamics and related cell behaviors. In this study, we found that the focal adhesion protein p130Cas drives formation of structures with the characteristics of LLPS that bud from focal adhesions into the cytoplasm. Condensing concentrated cytoplasm around p130Cas-coated beads allowed their isolation, which were enriched in a subset of focal adhesion proteins, mRNAs and RNA binding proteins, including those implicated in inhibiting mRNA translation. Plating cells on very high concentrations of fibronectin to induce large focal adhesions inhibited message translation which required p130Cas and correlated with droplet formation. Photo-induction of p130Cas condensates using the Cry2 system also reduced translation. These results identify a novel regulatory mechanism in which high adhesion limits message translation via induction of p130Cas-dependent cytoplasmic LLPS. This mechanism may contribute to the quiescent state of very strongly adhesive myofibroblasts and senescent cells.
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Affiliation(s)
- Abhishek Kumar
- Yale Cardiovascular Research Center, Department of Internal Medicine (Division of Cardiovascular Medicine), 300 George St. New Haven CT 06511
| | - Keiichiro Tanaka
- Yale Cardiovascular Research Center, Department of Internal Medicine (Division of Cardiovascular Medicine), 300 George St. New Haven CT 06511
| | - Martin A Schwartz
- Yale Cardiovascular Research Center, Department of Internal Medicine (Division of Cardiovascular Medicine), 300 George St. New Haven CT 06511
- Department of Cell Biology, Yale School of Medicine
- Department of Biomedical Engineering, Yale University
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10
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Liang P, Wu Y, Zheng S, Zhang J, Yang S, Wang J, Ma S, Zhang M, Gu Z, Liu Q, Jiang W, Xing Q, Wang B. Paxillin phase separation promotes focal adhesion assembly and integrin signaling. J Cell Biol 2024; 223:e202209027. [PMID: 38466167 PMCID: PMC10926639 DOI: 10.1083/jcb.202209027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/04/2022] [Accepted: 02/27/2023] [Indexed: 03/12/2024] Open
Abstract
Focal adhesions (FAs) are transmembrane protein assemblies mediating cell-matrix connection. Although protein liquid-liquid phase separation (LLPS) has been tied to the organization and dynamics of FAs, the underlying mechanisms remain unclear. Here, we experimentally tune the LLPS of PXN/Paxillin, an essential scaffold protein of FAs, by utilizing a light-inducible Cry2 system in different cell types. In addition to nucleating FA components, light-triggered PXN LLPS potently activates integrin signaling and subsequently accelerates cell spreading. In contrast to the homotypic interaction-driven LLPS of PXN in vitro, PXN condensates in cells are associated with the plasma membrane and modulated by actomyosin contraction and client proteins of FAs. Interestingly, non-specific weak intermolecular interactions synergize with specific molecular interactions to mediate the multicomponent condensation of PXN and are efficient in promoting FA assembly and integrin signaling. Thus, our data establish an active role of the PXN phase transition into a condensed membrane-associated compartment in promoting the assembly/maturation of FAs.
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Affiliation(s)
- Peigang Liang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuchen Wu
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shanyuan Zheng
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jiaqi Zhang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shuo Yang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jinfang Wang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Suibin Ma
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mengjun Zhang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Zhuang Gu
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Qingfeng Liu
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Wenxue Jiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Qiong Xing
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Bo Wang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
- Shenzhen Research Institute of Xiamen University, Shenzhen, China
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11
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Mondal S, Cui Q. Sequence Sensitivity in Membrane Remodeling by Polyampholyte Condensates. J Phys Chem B 2024; 128:2087-2099. [PMID: 38407041 DOI: 10.1021/acs.jpcb.3c08149] [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: 02/27/2024]
Abstract
Intrinsically disordered peptides (IDPs) have been found to undergo liquid-liquid phase separation (LLPS) and produce complex coacervates that play numerous regulatory roles in the cell. Recent experimental studies have discovered that LLPS at or near the membrane surface helps in the biomolecular organization during signaling events and can significantly alter the membrane morphology. However, the molecular mechanism and microscopic details of such processes still remain unclear. Here we study the effect of polyampholyte and polyelectrolyte condensation on two different anionic membranes, as they represent a majority of naturally occurring IDPs. The polyampholytes are fifty-residue polymers, made of glutamate(E) and lysine(K) with different charge patterns. The polyelectrolytes are separate chains of E25 and K25. We first calibrate the MARTINI v3.0 force field and then perform long-time-scale coarse-grained molecular dynamics simulations. We find that condensates formed by all the polyampholytes get adsorbed on the membrane. However, the strong polyampholytes (i.e., blocky sequences) can remodel the membranes more prominently than the weaker ones (i.e., scrambled sequences). Condensates formed by the blocky sequences induce a significant negative curvature (∼0.1 nm-1) and local demixing of lipids, whereas those by the scrambled sequences tend to wet the membrane to a greater extent without generating significant curvature or demixing. We perform several microscopic analyses to characterize the nature of the interaction between membranes and these condensates. Our analyses of interaction energetics reveal that membrane remodeling and/or wetting are favored by enhanced interactions between polyampholytes with lipids and the counterions.
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Affiliation(s)
- Sayantan Mondal
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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12
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Liu M, Wu C, Wang R, Qiu J, She Z, Qu J, Xia J. Modulating Liquid-Liquid Phase Separation of Nck Adaptor Protein against Enteropathogenic Escherichia coli Infection. ACS CENTRAL SCIENCE 2023; 9:2358-2368. [PMID: 38161366 PMCID: PMC10755736 DOI: 10.1021/acscentsci.3c01068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/21/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024]
Abstract
Signaling proteins often form biomolecular condensates through liquid-liquid phase separation (LLPS) during intracellular signal transduction. Modulating the LLPS property of intracellular protein condensates will redirect intracellular signals and provide a potential way to regulate cellular physiology. Phosphorylation of multiple tyrosine residues of the transmembrane receptor nephrin is known to drive the LLPS of the adaptor protein Nck and neuronal Wiskott-Aldrich Syndrome protein (N-WASP) and form the Nck signaling complex. Phosphorylation of the translocated intimin receptor (Tir) in the host cell may recruit this enteropathogenic Escherichia coli (EPEC) virulence factor to the Nck signaling complex and lead to the entry of EPEC into the intestine cell. In this work, we first identified a phosphotyrosine (pY)-containing peptide 3pY based on the sequence similarity of nephrin and Tir; 3pY promoted the LLPS of Nck and N-WASP, mimicking the role of phosphorylated nephrin. Next, we designed a covalent blocker of Nck, peptide p1 based on the selected pY peptides, which site-selectively reacted with the SH2 domain of Nck (Nck-SH2) at Lys331 through a proximity-induced reaction. The covalent reaction of p1 with Nck blocked the protein binding site of Nck-SH2 and disintegrated the 3pY/Nck/N-WASP condensates. In the presence of membrane-translocating peptide L17E, p1 entered Caco-2 cells in the cytosol, reduced the number of Nck puncta, and rendered Caco-2 cells resistant to EPEC infection. Site-selective covalent blockage of Nck thereby disintegrates intracellular Nck condensates, inhibits actin reorganization, and shuts down the entrance pathway of EPEC. This work showcases the promotion or inhibition of protein phase separation by synthetic peptides and the use of reactive peptides as LLPS disruptors and signal modulators.
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Affiliation(s)
- Min Liu
- Department
of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Chunjian Wu
- Department
of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Rui Wang
- Pingshan
Translational Medicine Center, Shenzhen
Bay Laboratory, Shenzhen 518118, China
| | - Jiaming Qiu
- Department
of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Zhentao She
- Departments
of Electronic and Computer Engineering, Center of Systems Biology
and Human Health, School of Science and Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Jianan Qu
- Departments
of Electronic and Computer Engineering, Center of Systems Biology
and Human Health, School of Science and Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Jiang Xia
- Department
of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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13
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Aryan F, Detrés D, Luo CC, Kim SX, Shah AN, Bartusel M, Flynn RA, Calo E. Nucleolus activity-dependent recruitment and biomolecular condensation by pH sensing. Mol Cell 2023; 83:4413-4423.e10. [PMID: 37979585 PMCID: PMC10803072 DOI: 10.1016/j.molcel.2023.10.031] [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: 11/15/2022] [Revised: 06/20/2023] [Accepted: 10/23/2023] [Indexed: 11/20/2023]
Abstract
DEAD-box ATPases are major regulators of biomolecular condensates and orchestrate diverse biochemical processes that are critical for the functioning of cells. How DEAD-box proteins are selectively recruited to their respective biomolecular condensates is unknown. We explored this in the context of the nucleolus and DEAD-box protein DDX21. We find that the pH of the nucleolus is intricately linked to the transcriptional activity of the organelle and facilitates the recruitment and condensation of DDX21. We identify an evolutionarily conserved feature of the C terminus of DDX21 responsible for nucleolar localization. This domain is essential for zebrafish development, and its intrinsically disordered and isoelectric properties are necessary and sufficient for the ability of DDX21 to respond to changes in pH and form condensates. Molecularly, the enzymatic activities of poly(ADP-ribose) polymerases contribute to maintaining the nucleolar pH and, consequently, DDX21 recruitment and nucleolar partitioning. These observations reveal an activity-dependent physicochemical mechanism for the selective recruitment of biochemical activities to biomolecular condensates.
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Affiliation(s)
- Fardin Aryan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Diego Detrés
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Claire C Luo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Skylar X Kim
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arish N Shah
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michaela Bartusel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Eliezer Calo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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14
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Cheng X, Case LB. Phase separation in chemical and mechanical signal transduction. Curr Opin Cell Biol 2023; 85:102243. [PMID: 37788587 DOI: 10.1016/j.ceb.2023.102243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/09/2023] [Accepted: 09/03/2023] [Indexed: 10/05/2023]
Abstract
Signal transduction enables cells to sense and respond to chemical and mechanical information in the extracellular environment. Recently, phase separation has emerged as a physical mechanism that can influence the spatial organization of signaling molecules and regulate downstream signaling. Although many molecular components of signaling pathways, including receptors, kinases, and transcription factors, have been observed to undergo phase separation, understanding the functional consequences of their phase separation in signal transduction remains an ongoing area of research. In this review, we will discuss recent studies investigating how cells potentially use phase separation to regulate different signaling pathways by initiating signaling, amplifying signaling, or inhibiting signaling. We will also discuss recent observations that suggest a role for phase separation in mechanosensing in the Hippo pathway and at focal adhesions.
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Affiliation(s)
- Xiaohang Cheng
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lindsay B Case
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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15
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Guo K, Zhang J, Huang P, Xu Y, Pan W, Li K, Chen L, Luo L, Yu W, Chen S, He S, Wei Z, Yu C. KANK1 shapes focal adhesions by orchestrating protein binding, mechanical force sensing, and phase separation. Cell Rep 2023; 42:113321. [PMID: 37874676 DOI: 10.1016/j.celrep.2023.113321] [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: 04/26/2023] [Revised: 08/27/2023] [Accepted: 10/05/2023] [Indexed: 10/26/2023] Open
Abstract
Focal adhesions (FAs) are dynamic protein assemblies that connect cytoskeletons to the extracellular matrix and are crucial for cell adhesion and migration. KANKs are scaffold proteins that encircle FAs and act as key regulators of FA dynamics, but the molecular mechanism underlying their specified localization and functions remains poorly understood. Here, we determine the KANK1 structures in complex with talin and liprin-β, respectively. These structures, combined with our biochemical and cellular analyses, demonstrate how KANK1 scaffolds the FA core and associated proteins to modulate the FA shape in response to mechanical force. Additionally, we find that KANK1 undergoes liquid-liquid phase separation (LLPS), which is important for its localization at the FA edge and cytoskeleton connections to FAs. Our findings not only indicate the molecular basis of KANKs in bridging the core and periphery of FAs but also provide insights into the LLPS-mediated dynamic regulation of FA morphology.
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Affiliation(s)
- Kaitong Guo
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, and Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen 518055, Guangdong, China
| | - Jing Zhang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, and Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen 518055, Guangdong, China; Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Pei Huang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, and Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen 518055, Guangdong, China
| | - Yuqun Xu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Wenfei Pan
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Kaiyue Li
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Lu Chen
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, and Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen 518055, Guangdong, China
| | - Li Luo
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Weichun Yu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, and Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen 518055, Guangdong, China
| | - Shuai Chen
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Sicong He
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Zhiyi Wei
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Cong Yu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, and Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen 518055, Guangdong, China.
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16
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Liang P, Zhang J, Wu Y, Zheng S, Xu Z, Yang S, Wang J, Ma S, Xiao L, Hu T, Jiang W, Huang C, Xing Q, Kundu M, Wang B. An ULK1/2-PXN mechanotransduction pathway suppresses breast cancer cell migration. EMBO Rep 2023; 24:e56850. [PMID: 37846507 PMCID: PMC10626438 DOI: 10.15252/embr.202356850] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 09/09/2023] [Accepted: 09/27/2023] [Indexed: 10/18/2023] Open
Abstract
The remodeling and stiffening of the extracellular matrix (ECM) is a well-recognized modulator of breast cancer progression. How changes in the mechanical properties of the ECM are converted into biochemical signals that direct tumor cell migration and metastasis remain poorly characterized. Here, we describe a new role for the autophagy-inducing serine/threonine kinases ULK1 and ULK2 in mechanotransduction. We show that ULK1/2 activity inhibits the assembly of actin stress fibers and focal adhesions (FAs) and as a consequence impedes cell contraction and migration, independent of its role in autophagy. Mechanistically, we identify PXN/paxillin, a key component of the mechanotransducing machinery, as a direct binding partner and substrate of ULK1/2. ULK-mediated phosphorylation of PXN at S32 and S119 weakens homotypic interactions and liquid-liquid phase separation of PXN, impairing FA assembly, which in turn alters the mechanical properties of breast cancer cells and their response to mechanical stimuli. ULK1/2 and the well-characterized PXN regulator, FAK/Src, have opposing functions on mechanotransduction and compete for phosphorylation of adjacent serine and tyrosine residues. Taken together, our study reveals ULK1/2 as important regulator of PXN-dependent mechanotransduction.
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Affiliation(s)
- Peigang Liang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life SciencesXiamen UniversityXiamenChina
| | - Jiaqi Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life SciencesXiamen UniversityXiamenChina
| | - Yuchen Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life SciencesXiamen UniversityXiamenChina
| | - Shanyuan Zheng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life SciencesXiamen UniversityXiamenChina
| | - Zhaopeng Xu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life SciencesXiamen UniversityXiamenChina
| | - Shuo Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life SciencesXiamen UniversityXiamenChina
| | - Jinfang Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life SciencesXiamen UniversityXiamenChina
| | - Suibin Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life SciencesXiamen UniversityXiamenChina
| | - Li Xiao
- Department of OncologyZhongshan Hospital of Xiamen UniversityXiamenChina
| | - Tianhui Hu
- Cancer Research Center, School of MedicineXiamen UniversityXiamenChina
| | - Wenxue Jiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life SciencesHubei UniversityWuhanChina
| | - Chaoqun Huang
- Central LaboratoryThe Fifth Hospital of XiamenXiamenChina
| | - Qiong Xing
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life SciencesHubei UniversityWuhanChina
| | - Mondira Kundu
- Department of Cell and Molecular BiologySt. Jude Children's Research HospitalMemphisTNUSA
| | - Bo Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life SciencesXiamen UniversityXiamenChina
- Shenzhen Research Institute of Xiamen UniversityShenzhenChina
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17
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Galbraith JA, Galbraith CG. Using single molecule imaging to explore intracellular heterogeneity. Int J Biochem Cell Biol 2023; 163:106455. [PMID: 37586643 PMCID: PMC10528986 DOI: 10.1016/j.biocel.2023.106455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
Despite more than 100 years of study, it is unclear if the movement of proteins inside the cell is best described as a mosh pit or an exquisitely choreographed dance. Recent studies suggest the latter. Local interactions induce molecular condensates such as liquid-liquid phase separations (LLPSs) or non-liquid, functionally significant molecular aggregates, including synaptic densities, nucleoli, and Amyloid fibrils. Molecular condensates trigger intracellular signaling and drive processes ranging from gene expression to cell division. However, the descriptions of condensates tend to be qualitative and correlative. Here, we indicate how single-molecule imaging and analyses can be applied to quantify condensates. We discuss the pros and cons of different techniques for measuring differences between transient molecular behaviors inside and outside condensates. Finally, we offer suggestions for how imaging and analyses from different time and space regimes can be combined to identify molecular behaviors indicative of condensates within the dynamic high-density intracellular environment.
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Affiliation(s)
- James A Galbraith
- Oregon Health and Science University, Quantitative and Systems Biology Program in BME and The Knight Cancer Institute, Portland, OR 97239, USA.
| | - Catherine G Galbraith
- Oregon Health and Science University, Quantitative and Systems Biology Program in BME and The Knight Cancer Institute, Portland, OR 97239, USA.
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18
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Li R, Feng D, Han S, Zhai X, Yu X, Fu Y, Jin F. Macrophages and fibroblasts in foreign body reactions: How mechanical cues drive cell functions? Mater Today Bio 2023; 22:100783. [PMID: 37701130 PMCID: PMC10494263 DOI: 10.1016/j.mtbio.2023.100783] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/14/2023] Open
Abstract
Biomaterials, when implanted in the human body, can induce a series of cell- and cytokine-related reactions termed foreign body reactions (FBRs). In the progression of FBRs, macrophages regulate inflammation and healing by polarizing to either a pro-inflammatory or pro-healing phenotype and recruit fibroblasts by secreting cytokines. Stimulated by the biomaterials, fibrotic capsule is formed eventually. The implant, along with its newly formed capsule, introduces various mechanical cues that influence cellular functions. Mechanosensing proteins, such as integrins or ion channels, transduce extracellular mechanical signals into cytoplasm biochemical signals in response to mechanical stimuli. Consequently, the morphology, migration mode, function, and polarization state of the cells are affected. Modulated by different intracellular signaling pathways and their crosstalk, the expression of fibrotic genes increases with fibroblast activation and fibroblast to myofibroblast transition under stiff or force stimuli. However, summarized in most current studies, the outcomes of macrophage polarization in the effect of different mechanical cues are inconsistent. The underlying mechanisms should be investigated with more advanced technology and considering more interfering aspects. Further research is needed to determine how to modulate the progression of fibrotic capsule formation in FBR artificially.
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Affiliation(s)
- Rihan Li
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, 110000, China
- Department of Breast and Reconstructive Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, 110000, China
| | - Dongdong Feng
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, 110000, China
- Department of Breast and Reconstructive Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, 110000, China
| | - Siyuan Han
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, 110000, China
- Department of Breast and Reconstructive Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, 110000, China
| | - Xiaoyue Zhai
- Department of Histology and Embryology, Basic Medical College, China Medical University, Shenyang, Liaoning, 110000, China
| | - Xinmiao Yu
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, 110000, China
- Department of Breast and Reconstructive Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, 110000, China
| | - Yuanyuan Fu
- Department of Histology and Embryology, Basic Medical College, China Medical University, Shenyang, Liaoning, 110000, China
| | - Feng Jin
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, 110000, China
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19
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Grudtsyna V, Packirisamy S, Bidone TC, Swaminathan V. Extracellular matrix sensing via modulation of orientational order of integrins and F-actin in focal adhesions. Life Sci Alliance 2023; 6:e202301898. [PMID: 37463754 PMCID: PMC10355215 DOI: 10.26508/lsa.202301898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
Specificity of cellular responses to distinct cues from the ECM requires precise and sensitive decoding of physical information. However, how known mechanisms of mechanosensing like force-dependent catch bonds and conformational changes in FA proteins can confer that this sensitivity is not known. Using polarization microscopy and computational modeling, we identify dynamic changes in an orientational order of FA proteins as a molecular organizational mechanism that can fine-tune cell sensitivity to the ECM. We find that αV integrins and F-actin show precise changes in the orientational order in an ECM-mediated integrin activation-dependent manner. These changes are sensitive to ECM density and are regulated independent of myosin-II activity though contractility can enhance this sensitivity. A molecular-clutch model demonstrates that the orientational order of integrin-ECM binding coupled to directional catch bonds can capture cellular responses to changes in ECM density. This mechanism also captures decoupling of ECM density sensing from stiffness sensing thus elucidating specificity. Taken together, our results suggest relative geometric organization of FA molecules as an important molecular architectural feature and regulator of mechanotransduction.
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Affiliation(s)
- Valeriia Grudtsyna
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Swathi Packirisamy
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Tamara C Bidone
- Department of Biomedical Engineering, The University of Utah, Salt Lake City, UT, USA
| | - Vinay Swaminathan
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden
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20
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Galbraith JA, Galbraith CG. Using Single Molecule Imaging to Explore Intracellular Heterogeneity. ARXIV 2023:arXiv:2308.01431v1. [PMID: 37576125 PMCID: PMC10418527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Despite more than 100 years of study, it is unclear if the movement of proteins inside the cell is best described as a mosh pit or an exquisitely choreographed dance. Recent studies suggest the latter. Local interactions induce molecular condensates such as liquid-liquid phase separations (LLPSs) or non-liquid, functionally significant molecular aggregates, including synaptic densities, nucleoli, and Amyloid fibrils. Molecular condensates trigger intracellular signaling and drive processes ranging from gene expression to cell division. However, the descriptions of condensates tend to be qualitative and correlative. Here, we indicate how single-molecule imaging and analyses can be applied to quantify condensates. We discuss the pros and cons of different techniques for measuring differences between transient molecular behaviors inside and outside condensates. Finally, we offer suggestions for how imaging and analyses from different time and space regimes can be combined to identify molecular behaviors indicative of condensates within the dynamic high-density intracellular environment.
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Affiliation(s)
- James A Galbraith
- Oregon Health and Science University, Quantitative and Systems Biology Program in BME and The Knight Cancer Institute, Portland, OR 97239
| | - Catherine G Galbraith
- Oregon Health and Science University, Quantitative and Systems Biology Program in BME and The Knight Cancer Institute, Portland, OR 97239
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21
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López-Palacios TP, Andersen JL. Kinase regulation by liquid-liquid phase separation. Trends Cell Biol 2023; 33:649-666. [PMID: 36528418 PMCID: PMC10267292 DOI: 10.1016/j.tcb.2022.11.009] [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: 09/26/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022]
Abstract
Liquid-liquid phase separation (LLPS) is emerging as a mechanism of spatiotemporal regulation that could answer long-standing questions about how order is achieved in biochemical signaling. In this review we discuss how LLPS orchestrates kinase signaling, either by creating condensate structures that are sensed by kinases or by direct LLPS of kinases, cofactors, and substrates - thereby acting as a mechanism to compartmentalize kinase-substrate relationships, and in some cases also sequestering the kinase away from inhibitory factors. We also examine the possibility that selective pressure promotes genomic rearrangements that fuse pro-growth kinases to LLPS-prone protein sequences, which in turn drives aberrant kinase activation through LLPS.
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Affiliation(s)
- Tania P López-Palacios
- Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Joshua L Andersen
- Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
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22
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Kumar S, Stainer A, Dubrulle J, Simpkins C, Cooper JA. Cas phosphorylation regulates focal adhesion assembly. eLife 2023; 12:e90234. [PMID: 37489578 PMCID: PMC10435235 DOI: 10.7554/elife.90234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023] Open
Abstract
Integrin-mediated cell attachment rapidly induces tyrosine kinase signaling. Despite years of research, the role of this signaling in integrin activation and focal adhesion assembly is unclear. We provide evidence that the Src-family kinase (SFK) substrate Cas (Crk-associated substrate, p130Cas, BCAR1) is phosphorylated and associated with its Crk/CrkL effectors in clusters that are precursors of focal adhesions. The initial phospho-Cas clusters contain integrin β1 in its inactive, bent closed, conformation. Later, phospho-Cas and total Cas levels decrease as integrin β1 is activated and core focal adhesion proteins including vinculin, talin, kindlin, and paxillin are recruited. Cas is required for cell spreading and focal adhesion assembly in epithelial and fibroblast cells on collagen and fibronectin. Cas cluster formation requires Cas, Crk/CrkL, SFKs, and Rac1 but not vinculin. Rac1 provides positive feedback onto Cas through reactive oxygen, opposed by negative feedback from the ubiquitin proteasome system. The results suggest a two-step model for focal adhesion assembly in which clusters of phospho-Cas, effectors and inactive integrin β1 grow through positive feedback prior to integrin activation and recruitment of core focal adhesion proteins.
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Affiliation(s)
- Saurav Kumar
- Fred Hutchinson Cancer CenterSeattleUnited States
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23
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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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24
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Lee YRJ, Yamada S, Lo SH. Phase transition of tensin-1 during the focal adhesion disassembly and cell division. Proc Natl Acad Sci U S A 2023; 120:e2303037120. [PMID: 37011205 PMCID: PMC10104483 DOI: 10.1073/pnas.2303037120] [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: 02/23/2023] [Accepted: 03/09/2023] [Indexed: 04/05/2023] Open
Abstract
Biomolecular condensates are nonmembranous structures that are mainly formed through liquid-liquid phase separation. Tensins are focal adhesion (FA) proteins linking the actin cytoskeleton to integrin receptors. Here, we report that GFP-tagged tensin-1 (TNS1) proteins phase-separate to form biomolecular condensates in cells. Live-cell imaging showed that new TNS1 condensates are budding from the disassembling ends of FAs, and the presence of these condensates is cell cycle dependent. TNS1 condensates dissolve immediately prior to mitosis and rapidly reappear while postmitotic daughter cells establish new FAs. TNS1 condensates contain selected FA proteins and signaling molecules such as pT308Akt but not pS473Akt, suggesting previously unknown roles of TNS1 condensates in disassembling FAs, as the storage of core FA components and the signaling intermediates.
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Affiliation(s)
- Yuh-Ru Julie Lee
- Department of Plant Biology, University of California, Davis, CA95616
| | - Soichiro Yamada
- Department of Biomedical Engineering, University of California, Davis, CA95616
| | - Su Hao Lo
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA95817
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25
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Liu Z, Yethiraj A, Cui Q. Sensitive and selective polymer condensation at membrane surface driven by positive co-operativity. Proc Natl Acad Sci U S A 2023; 120:e2212516120. [PMID: 37018196 PMCID: PMC10104518 DOI: 10.1073/pnas.2212516120] [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: 07/20/2022] [Accepted: 03/06/2023] [Indexed: 04/06/2023] Open
Abstract
Biomolecular phase separation has emerged as an essential mechanism for cellular organization. How cells respond to environmental stimuli in a robust and sensitive manner to build functional condensates at the proper time and location is only starting to be understood. Recently, lipid membranes have been recognized as an important regulatory center for biomolecular condensation. However, how the interplay between the phase behaviors of cellular membranes and surface biopolymers may contribute to the regulation of surface condensation remains to be elucidated. Using simulations and a mean-field theoretical model, we show that two key factors are the membrane's tendency to phase-separate and the surface polymer's ability to reorganize local membrane composition. Surface condensate forms with high sensitivity and selectivity in response to features of biopolymer when positive co-operativity is established between coupled growth of the condensate and local lipid domains. This effect relating the degree of membrane-surface polymer co-operativity and condensate property regulation is shown to be robust by different ways of tuning the co-operativity, such as varying membrane protein obstacle concentration, lipid composition, and the affinity between lipid and polymer. The general physical principle emerged from the current analysis may have implications in other biological processes and beyond.
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Affiliation(s)
- Zhuang Liu
- Department of Physics, Boston University, Boston, MA02215
| | - Arun Yethiraj
- Department of Chemistry, University of Wisconsin, Madison, WI53706
| | - Qiang Cui
- Department of Physics, Boston University, Boston, MA02215
- Department of Chemistry, Boston University, Boston, MA02215
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26
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Shil S, Tsuruta M, Kawauchi K, Miyoshi D. Biomolecular Liquid-Liquid Phase Separation for Biotechnology. BIOTECH 2023; 12:26. [PMID: 37092470 PMCID: PMC10123627 DOI: 10.3390/biotech12020026] [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: 03/09/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
The liquid-liquid phase separation (LLPS) of biomolecules induces condensed assemblies called liquid droplets or membrane-less organelles. In contrast to organelles with lipid membrane barriers, the liquid droplets induced by LLPS do not have distinct barriers (lipid bilayer). Biomolecular LLPS in cells has attracted considerable attention in broad research fields from cellular biology to soft matter physics. The physical and chemical properties of LLPS exert a variety of functions in living cells: activating and deactivating biomolecules involving enzymes; controlling the localization, condensation, and concentration of biomolecules; the filtration and purification of biomolecules; and sensing environmental factors for fast, adaptive, and reversible responses. The versatility of LLPS plays an essential role in various biological processes, such as controlling the central dogma and the onset mechanism of pathological diseases. Moreover, biomolecular LLPS could be critical for developing new biotechnologies such as the condensation, purification, and activation of a series of biomolecules. In this review article, we introduce some fundamental aspects and recent progress of biomolecular LLPS in living cells and test tubes. Then, we discuss applications of biomolecular LLPS toward biotechnologies.
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Affiliation(s)
| | | | | | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Hyogo, Japan
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27
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Graham K, Chandrasekaran A, Wang L, Ladak A, Lafer EM, Rangamani P, Stachowiak JC. Liquid-like VASP condensates drive actin polymerization and dynamic bundling. NATURE PHYSICS 2023; 19:574-585. [PMID: 38405682 PMCID: PMC10887402 DOI: 10.1038/s41567-022-01924-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 12/15/2022] [Indexed: 02/27/2024]
Abstract
The organization of actin filaments into bundles is required for cellular processes such as motility, morphogenesis, and cell division. Filament bundling is controlled by a network of actin-binding proteins. Recently, several proteins that comprise this network have been found to undergo liquid-liquid phase separation. How might liquid-like condensates contribute to filament bundling? Here, we show that the processive actin polymerase and bundling protein, VASP, forms liquid-like droplets under physiological conditions. As actin polymerizes within VASP droplets, elongating filaments partition to the edges of the droplet to minimize filament curvature, forming an actin-rich ring within the droplet. The rigidity of this ring is balanced by the droplet's surface tension, as predicted by a continuum-scale computational model. However, as actin polymerizes and the ring grows thicker, its rigidity increases and eventually overcomes the surface tension of the droplet, deforming into a linear bundle. The resulting bundles contain long, parallel actin filaments that grow from their tips. Significantly, the fluid nature of the droplets is critical for bundling, as more solid droplets resist deformation, preventing filaments from rearranging to form bundles. Once the parallel arrangement of filaments is created within a VASP droplet, it propagates through the addition of new actin monomers to achieve a length that is many times greater than the initial droplet. This droplet-based mechanism of bundling may be relevant to the assembly of cellular architectures rich in parallel actin filaments, such as filopodia, stress fibers, and focal adhesions.
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Affiliation(s)
- Kristin Graham
- University of Texas at Austin, Department of Biomedical Engineering
| | | | - Liping Wang
- University of Texas Health Science Center at San Antonio, Department of Biochemistry and Structural Biology
| | - Aly Ladak
- University of Texas at Austin, Department of Biomedical Engineering
| | - Eileen M Lafer
- University of Texas Health Science Center at San Antonio, Department of Biochemistry and Structural Biology
| | - Padmini Rangamani
- University of California San Diego, Department of Mechanical and Aerospace Engineering
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28
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Ullo MF, Case LB. How cells sense and integrate information from different sources. WIREs Mech Dis 2023:e1604. [PMID: 36781396 DOI: 10.1002/wsbm.1604] [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: 06/24/2022] [Revised: 01/06/2023] [Accepted: 01/24/2023] [Indexed: 02/15/2023]
Abstract
Cell signaling is a fundamental cellular process that enables cells to sense and respond to information in their surroundings. At the molecular level, signaling is primarily carried out by transmembrane protein receptors that can initiate complex downstream signal transduction cascades to alter cellular behavior. In the human body, different cells can be exposed to a wide variety of environmental conditions, and cells express diverse classes of receptors capable of sensing and integrating different signals. Furthermore, different receptors and signaling pathways can crosstalk with each other to calibrate the cellular response. Crosstalk occurs through multiple mechanisms at different levels of signaling pathways. In this review, we discuss how cells sense and integrate different chemical, mechanical, and spatial signals as well as the mechanisms of crosstalk between pathways. To illustrate these concepts, we use a few well-studied signaling pathways, including receptor tyrosine kinases and integrin receptors. Finally, we discuss the implications of dysregulated cellular sensing on driving diseases such as cancer. This article is categorized under: Cancer > Molecular and Cellular Physiology Metabolic Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Maria F Ullo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Lindsay B Case
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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29
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Sánchez MF, Tampé R. Ligand-independent receptor clustering modulates transmembrane signaling: a new paradigm. Trends Biochem Sci 2023; 48:156-171. [PMID: 36115755 DOI: 10.1016/j.tibs.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/22/2022] [Accepted: 08/02/2022] [Indexed: 01/25/2023]
Abstract
Cell-surface receptors mediate communication between cells and their environment. Lateral membrane organization and dynamic receptor cluster formation are fundamental in signal transduction and cell signaling. However, it is not yet fully understood how receptor clustering modulates a wide variety of physiologically relevant processes. Recent growing evidence indicates that biological responses triggered by membrane receptors can be modulated even in the absence of the natural receptor ligand. We review the most recent findings on how ligand-independent receptor clustering can regulate transmembrane signaling. We discuss the latest technologies to control receptor assembly, such as DNA nanotechnology, optogenetics, and optochemistry, focusing on the biological relevance and unraveling of ligand-independent signaling.
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Affiliation(s)
- M Florencia Sánchez
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany.
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30
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Li X, Heng BC, Bai Y, Wang Q, Gao M, He Y, Zhang X, Deng X, Zhang X. Electrical charge on ferroelectric nanocomposite membranes enhances SHED neural differentiation. Bioact Mater 2023; 20:81-92. [PMID: 35633875 PMCID: PMC9131252 DOI: 10.1016/j.bioactmat.2022.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022] Open
Abstract
Stem cells from human exfoliated deciduous teeth (SHED) uniquely exhibit high proliferative and neurogenic potential. Charged biomaterials have been demonstrated to promote neural differentiation of stem cells, but the dose-response effect of electrical stimuli from these materials on neural differentiation of SHED remains to be elucidated. Here, by utilizing different annealing temperatures prior to corona poling treatment, BaTiO3/P(VDF-TrFE) ferroelectric nanocomposite membranes with varying charge polarization intensity (d33 ≈ 0, 4, 12 and 19 pC N−1) were fabricated. Enhanced expression of neural markers, increased cell elongation and more prominent neurite outgrowths were observed with increasing surface charge of the nanocomposite membrane indicating a dose-response effect of surface electrical charge on SHED neural differentiation. Further investigations of the underlying molecular mechanisms revealed that intracellular calcium influx, focal adhesion formation, FAK-ERK mechanosensing pathway and neurogenic-related ErbB signaling pathway were implicated in the enhancement of SHED neural differentiation by surface electrical charge. Hence, this study confirms the dose-response effect of biomaterial surface charge on SHED neural differentiation and provides preliminary insights into the molecular mechanisms and signaling pathways involved. Membrane surface charge can be precisely controlled by adjusting annealing temperature and corona poling parameters. Both earlier and later neurogenic differentiation of SHED appear to be dose-dependently enhanced by surface charge. Underlying molecular mechanisms may involve intracellular Ca2+ influx, focal adhesion formation, FAK-ERK and ErbB signaling.
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Affiliation(s)
- Xiaochan Li
- Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, PR China
- Department of Dental Materials & Dental Medical Devices Testing Center, Peking University School and Hospital of Stomatology, Beijing, 100081, PR China
- Department of Prosthodontics, Peking University School and Hospital of Stomatology, Beijing, 100081, PR China
| | - Boon Chin Heng
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, 100081, PR China
| | - Yunyang Bai
- Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, PR China
| | - Qianqian Wang
- Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, PR China
| | - Min Gao
- Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, PR China
| | - Ying He
- Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, PR China
| | - Xinwen Zhang
- Center of Implant Dentistry, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, 110002, PR China
- Corresponding author.
| | - Xuliang Deng
- Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, PR China
- National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, NMPA Key Laboratory for Dental Materials, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology, Beijing, 100081, PR China
- Corresponding author. Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, PR China.
| | - Xuehui Zhang
- Department of Dental Materials & Dental Medical Devices Testing Center, Peking University School and Hospital of Stomatology, Beijing, 100081, PR China
- National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, NMPA Key Laboratory for Dental Materials, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology, Beijing, 100081, PR China
- Corresponding author. Department of Dental Materials & Dental Medical Devices Testing Center, Peking University School and Hospital of Stomatology, Beijing, 100081, PR China.
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31
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Kanchanawong P, Calderwood DA. Organization, dynamics and mechanoregulation of integrin-mediated cell-ECM adhesions. Nat Rev Mol Cell Biol 2023; 24:142-161. [PMID: 36168065 PMCID: PMC9892292 DOI: 10.1038/s41580-022-00531-5] [Citation(s) in RCA: 104] [Impact Index Per Article: 104.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2022] [Indexed: 02/04/2023]
Abstract
The ability of animal cells to sense, adhere to and remodel their local extracellular matrix (ECM) is central to control of cell shape, mechanical responsiveness, motility and signalling, and hence to development, tissue formation, wound healing and the immune response. Cell-ECM interactions occur at various specialized, multi-protein adhesion complexes that serve to physically link the ECM to the cytoskeleton and the intracellular signalling apparatus. This occurs predominantly via clustered transmembrane receptors of the integrin family. Here we review how the interplay of mechanical forces, biochemical signalling and molecular self-organization determines the composition, organization, mechanosensitivity and dynamics of these adhesions. Progress in the identification of core multi-protein modules within the adhesions and characterization of rearrangements of their components in response to force, together with advanced imaging approaches, has improved understanding of adhesion maturation and turnover and the relationships between adhesion structures and functions. Perturbations of adhesion contribute to a broad range of diseases and to age-related dysfunction, thus an improved understanding of their molecular nature may facilitate therapeutic intervention in these conditions.
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Affiliation(s)
- Pakorn Kanchanawong
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore.
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore.
| | - David A Calderwood
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.
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32
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Wu X, Qiu H, Zhang M. Interactions between Membraneless Condensates and Membranous Organelles at the Presynapse: A Phase Separation View of Synaptic Vesicle Cycle. J Mol Biol 2023; 435:167629. [PMID: 35595170 DOI: 10.1016/j.jmb.2022.167629] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 02/04/2023]
Abstract
Action potential-induced neurotransmitter release in presynaptic boutons involves coordinated actions of a large list of proteins that are associated directly or indirectly with membrane structures including synaptic vesicles and plasma membranes. These proteins are often highly abundant in different synaptic bouton sub-compartments, and they rarely act alone. Instead, these proteins interact with each other forming intricate and distinct molecular complexes. Many of these complexes form condensed clusters on membrane surfaces. This review summarizes findings in recent years showing that many of presynaptic protein complex assemblies are formed via phase separation. These protein condensates extensively interact with lipid membranes via distinct modes, forming various mesoscale structures by different mode of organizations between membraneless condensates and membranous organelles. We discuss that such mesoscale interactions could have deep implications on mobilization, exocytosis, and retrieval of synaptic vesicles.
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Affiliation(s)
- Xiandeng Wu
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Hua Qiu
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Mingjie Zhang
- Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen 518036, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
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33
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Bhattacharjee R, Hall AR, Mangione MC, Igarashi MG, Roberts-Galbraith RH, Chen JS, Vavylonis D, Gould KL. Multiple polarity kinases inhibit phase separation of F-BAR protein Cdc15 and antagonize cytokinetic ring assembly in fission yeast. eLife 2023; 12:83062. [PMID: 36749320 PMCID: PMC9904764 DOI: 10.7554/elife.83062] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/16/2022] [Indexed: 02/08/2023] Open
Abstract
The F-BAR protein Cdc15 is essential for cytokinesis in Schizosaccharomyces pombe and plays a key role in attaching the cytokinetic ring (CR) to the plasma membrane (PM). Cdc15's abilities to bind to the membrane and oligomerize via its F-BAR domain are inhibited by phosphorylation of its intrinsically disordered region (IDR). Multiple cell polarity kinases regulate Cdc15 IDR phosphostate, and of these the DYRK kinase Pom1 phosphorylation sites on Cdc15 have been shown in vivo to prevent CR formation at cell tips. Here, we compared the ability of Pom1 to control Cdc15 phosphostate and cortical localization to that of other Cdc15 kinases: Kin1, Pck1, and Shk1. We identified distinct but overlapping cohorts of Cdc15 phosphorylation sites targeted by each kinase, and the number of sites correlated with each kinases' abilities to influence Cdc15 PM localization. Coarse-grained simulations predicted that cumulative IDR phosphorylation moves the IDRs of a dimer apart and toward the F-BAR tips. Further, simulations indicated that the overall negative charge of phosphorylation masks positively charged amino acids necessary for F-BAR oligomerization and membrane interaction. Finally, simulations suggested that dephosphorylated Cdc15 undergoes phase separation driven by IDR interactions. Indeed, dephosphorylated but not phosphorylated Cdc15 undergoes liquid-liquid phase separation to form droplets in vitro that recruit Cdc15 binding partners. In cells, Cdc15 phosphomutants also formed PM-bound condensates that recruit other CR components. Together, we propose that a threshold of Cdc15 phosphorylation by assorted kinases prevents Cdc15 condensation on the PM and antagonizes CR assembly.
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Affiliation(s)
- Rahul Bhattacharjee
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Aaron R Hall
- Department of Physics, Lehigh UniversityBethlehemUnited States
| | - MariaSanta C Mangione
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Maya G Igarashi
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Rachel H Roberts-Galbraith
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Dimitrios Vavylonis
- Department of Physics, Lehigh UniversityBethlehemUnited States,Center for Computational Biology, Flatiron InstituteNew YorkUnited States
| | - Kathleen L Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
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34
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Rahman SK, Ampah KK, Roy P. Role of NS2 specific RNA binding and phosphorylation in liquid-liquid phase separation and virus assembly. Nucleic Acids Res 2022; 50:11273-11284. [PMID: 36259663 DOI: 10.1093/nar/gkac904] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/28/2022] [Accepted: 10/08/2022] [Indexed: 11/13/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) has assumed a prominent role in biological cell systems, where it underpins the formation of subcellular compartments necessary for cell function. We investigated the underlying mechanism of LLPS in virus infected cells, where virus inclusion bodies are formed by an RNA-binding phosphoprotein (NS2) of Bluetongue virus to serve as sites for subviral particle assembly and virus maturation. We show that NS2 undergoes LLPS that is dependent on protein phosphorylation and RNA-binding and that LLPS occurrence is accompanied by a change in protein secondary structure. Site-directed mutagenesis identified two critical arginine residues in NS2 responsible for specific RNA binding and thus for NS2-RNA complex driven LLPS. Reverse genetics identified the same residues as essential for VIB assembly in infected cells and virus viability. Our findings suggest that a specific arginine-RNA interaction in the context of a phosphorylated state drives LLPS in this, and possibly other, virus infections.
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Affiliation(s)
- Shah Kamranur Rahman
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT UK
| | - Khamal Kwesi Ampah
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT UK
| | - Polly Roy
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT UK
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35
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Le Coq J, Acebrón I, Rodrigo Martin B, López Navajas P, Lietha D. New insights into FAK structure and function in focal adhesions. J Cell Sci 2022; 135:277381. [PMID: 36239192 DOI: 10.1242/jcs.259089] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Focal adhesion kinase (FAK; also known as PTK2) was discovered three decades ago and is now recognised as a key player in the regulation of cell-matrix adhesion and mesenchymal cell migration. Although it is essential during development, FAK also drives invasive cancer progression and metastasis. On a structural level, the basic building blocks of FAK have been described for some time. However, a picture of how FAK integrates into larger assemblies in various cellular environments, including one of its main cellular locations, the focal adhesion (FA) complex, is only beginning to emerge. Nano-resolution data from cellular studies, as well as atomic structures from reconstituted systems, have provided first insights, but also point to challenges that remain for obtaining a full structural understanding of how FAK is integrated in the FA complex and the structural changes occurring at different stages of FA maturation. In this Review, we discuss the known structural features of FAK, the interactions with its partners within the FA environment on the cell membrane and propose how its initial assembly in nascent FAs might change during FA maturation under force.
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Affiliation(s)
- Johanne Le Coq
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Iván Acebrón
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Bárbara Rodrigo Martin
- Structural and Chemical Biology, Margarita Salas Center for Biological Research (CIB), Spanish National Research Council (CSIC), 28040 Madrid, Spain
| | - Pilar López Navajas
- Structural and Chemical Biology, Margarita Salas Center for Biological Research (CIB), Spanish National Research Council (CSIC), 28040 Madrid, Spain
| | - Daniel Lietha
- Structural and Chemical Biology, Margarita Salas Center for Biological Research (CIB), Spanish National Research Council (CSIC), 28040 Madrid, Spain
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36
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Cheng X, Ullo MF, Case LB. Reconstitution of Phase-Separated Signaling Clusters and Actin Polymerization on Supported Lipid Bilayers. Front Cell Dev Biol 2022; 10:932483. [PMID: 35959492 PMCID: PMC9361016 DOI: 10.3389/fcell.2022.932483] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Liquid-liquid phase separation driven by weak interactions between multivalent molecules contributes to the cellular organization by promoting the formation of biomolecular condensates. At membranes, phase separation can promote the assembly of transmembrane proteins with their cytoplasmic binding partners into micron-sized membrane-associated condensates. For example, phase separation promotes clustering of nephrin, a transmembrane adhesion molecule, resulting in increased Arp2/3 complex-dependent actin polymerization. In vitro reconstitution is a powerful approach to understand phase separation in biological systems. With a bottom-up approach, we can determine the molecules necessary and sufficient for phase separation, map the phase diagram by quantifying de-mixing over a range of molecular concentrations, assess the material properties of the condensed phase using fluorescence recovery after photobleaching (FRAP), and even determine how phase separation impacts downstream biochemical activity. Here, we describe a detailed protocol to reconstitute nephrin clusters on supported lipid bilayers with purified recombinant protein. We also describe how to measure Arp2/3 complex-dependent actin polymerization on bilayers using fluorescence microscopy. These different protocols can be performed independently or combined as needed. These general techniques can be applied to reconstitute and study phase-separated signaling clusters of many different receptors or to generally understand how actin polymerization is regulated at membranes.
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Affiliation(s)
| | | | - Lindsay B. Case
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
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37
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Mondal S, Cui Q. Coacervation of poly-electrolytes in the presence of lipid bilayers: mutual alteration of structure and morphology. Chem Sci 2022; 13:7933-7946. [PMID: 35865903 PMCID: PMC9258347 DOI: 10.1039/d2sc02013k] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/13/2022] [Indexed: 11/21/2022] Open
Abstract
Many intrinsically disordered peptides have been shown to undergo liquid-liquid phase separation and form complex coacervates, which play various regulatory roles in the cell. Recent experimental studies found that such phase separation processes may also occur at the lipid membrane surface and help organize biomolecules during signaling events; in some cases, phase separation of proteins at the membrane surface was also observed to lead to significant remodeling of the membrane morphology. The molecular mechanisms that govern the interactions between complex coacervates and lipid membranes and the impacts of such interactions on their structure and morphology, however, remain unclear. Here we study the coacervation of poly-glutamate (E30) and poly-lysine (K30) in the presence of lipid bilayers of different compositions. We carry out explicit-solvent coarse-grained molecular dynamics simulations by using the MARTINI (v3.0) force-field. We find that more than 20% anionic lipids are required for the coacervate to form stable contact with the bilayer. Upon wetting, the coacervate induces negative curvature to the bilayer and facilitates local lipid demixing, without any peptide insertion. The magnitude of negative curvature, extent of lipid demixing, and asphericity of the coacervate increase with the concentration of anionic lipids. Overall, we observe a decrease in the number of contacts among the polyelectrolytes as the droplet spreads over the bilayer. Therefore, unlike previous suggestions, interactions among polyelectrolytes do not constitute a driving force for the membrane bending upon wetting by the coacervate. Rather, analysis of interaction energy components suggests that bending of the membrane is favored by enhanced interactions between polyelectrolytes with lipids as well as with counterions. Kinetic studies reveal that, at the studied polyelectrolyte concentrations, the coacervate formation precedes bilayer wetting.
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Affiliation(s)
- Sayantan Mondal
- Department of Chemistry, Boston University 590 Commonwealth Avenue Boston MA 02215 USA (+1)-617-353-6189
| | - Qiang Cui
- Department of Chemistry, Boston University 590 Commonwealth Avenue Boston MA 02215 USA (+1)-617-353-6189
- Department of Physics, Boston University 590 Commonwealth Avenue Boston MA 02215 USA
- Department of Biomedical Engineering, Boston University 44 Cummington Mall Boston MA 02215 USA
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