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Aguilar OA, Fong LK, Lanier LL. ITAM-based receptors in natural killer cells. Immunol Rev 2024; 323:40-53. [PMID: 38411263 PMCID: PMC11102329 DOI: 10.1111/imr.13313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
The ability of cells of the immune system to acquire features such as increased longevity and enhanced secondary responses was long thought to be restricted to cells of the adaptive immune system. Natural killer (NK) cells have challenged this notion by demonstrating that they can also gain adaptive features. This has been observed in both humans and mice during infection with cytomegalovirus (CMV). The generation of adaptive NK cells requires antigen-specific recognition of virally infected cells through stimulatory NK receptors. These receptors lack the ability to signal on their own and rather rely on adaptor molecules that contain ITAMs for driving signals. Here, we highlight our understanding of how these receptors influence the production of adaptive NK cells and propose areas in the field that merit further investigation.
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Affiliation(s)
- Oscar A. Aguilar
- Dept. of Microbiology and Immunology, University of California - San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, University of California - San Francisco, San Francisco, CA, USA
| | - Lam-Kiu Fong
- Dept. of Pharmaceutical Chemistry, University of California – San Francisco, San Francisco, CA
| | - Lewis L. Lanier
- Dept. of Microbiology and Immunology, University of California - San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, University of California - San Francisco, San Francisco, CA, USA
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2
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Uversky VN. Functional unfoldomics: Roles of intrinsic disorder in protein (multi)functionality. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:179-210. [PMID: 38220424 DOI: 10.1016/bs.apcsb.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Intrinsically disordered proteins (IDPs), which are functional proteins without stable tertiary structure, and hybrid proteins containing ordered domains and intrinsically disordered regions (IDRs) constitute prominent parts of all proteomes collectively known as unfoldomes. IDPs/IDRs exist as highly dynamic structural ensembles of rapidly interconverting conformations and are characterized by the exceptional structural heterogeneity, where their different parts are (dis)ordered to different degree, and their overall structure represents a complex mosaic of foldons, inducible foldons, inducible morphing foldons, non-foldons, semifoldons, and even unfoldons. Despite their lack of unique 3D structures, IDPs/IDRs play crucial roles in the control of various biological processes and the regulation of different cellular pathways and are commonly involved in recognition and signaling, indicating that the disorder-based functional repertoire is complementary to the functions of ordered proteins. Furthermore, IDPs/IDRs are frequently multifunctional, and this multifunctionality is defined by their structural flexibility and heterogeneity. Intrinsic disorder phenomenon is at the roots of the structure-function continuum model, where the structure continuum is defined by the presence of differently (dis)ordered regions, and the function continuum arises from the ability of all these differently (dis)ordered parts to have different functions. In their everyday life, IDPs/IDRs utilize a broad spectrum of interaction mechanisms thereby acting as interaction specialists. They are crucial for the biogenesis of numerous proteinaceous membrane-less organelles driven by the liquid-liquid phase separation. This review introduces functional unfoldomics by representing some aspects of the intrinsic disorder-based functionality.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
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3
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Rinaldi DA, Kanagy WK, Kaye HC, Grattan RM, Lucero SR, Pérez MP, Wester MJ, Lidke KA, Wilson BS, Lidke DS. Antigen Geometry Tunes Mast Cell Signaling Through Distinct FcεRI Aggregation and Structural Changes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552060. [PMID: 37609336 PMCID: PMC10441289 DOI: 10.1101/2023.08.04.552060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Immunoreceptor tyrosine-based activation motif (ITAM)-containing Fc receptors are critical components of the innate and adaptive immune systems. FcεRI mediates the allergic response via crosslinking of IgE-bound receptors by multivalent antigens. Yet, the underlying molecular mechanisms that govern the response of FcεRI to specific antigens remain poorly understood. We compared responses induced by two antigens with distinct geometries, high valency DNP-BSA and trivalent DF3, and found unique secretion and receptor phosphorylation profiles that are due to differential recruitment of Lyn and SHIP1. To understand how these two antigens can cause such markedly different outcomes, we used direct stochastic optical reconstruction microscopy (dSTORM) super-resolution imaging combined with Bayesian Grouping of Localizations (BaGoL) analysis to compare the nanoscale characteristics of FcεRI aggregates. DF3 aggregates were found to be smaller and more densely packed than DNP-BSA aggregates. Using lifetime-based Förster resonance energy transfer (FRET) measurements, we discovered that FcεRI subunits undergo structural rearrangements upon crosslinking with either antigen, and in response to interaction with monovalent antigen presented on a supported lipid bilayer. The extent of conformational change is positively correlated with signaling efficiency. Finally, we provide evidence for forces in optimizing FcεRI signaling, such that immobilizing DF3 on a rigid surface promoted degranulation while increasing DNP-BSA flexibility lowered degranulation. These results provide a link between the physical attributes of allergens, including size, shape, valency, and flexibility, and FcεRI signaling strength. Thus, the antigen modulates mast cell outcomes by creating unique aggregate geometries that tune FcεRI conformation, phosphorylation and signaling partner recruitment.
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Affiliation(s)
- Derek A. Rinaldi
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
| | - William K. Kanagy
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Present address: Department of Immunology, University of Minnesota, Minneapolis, MN 55455
| | - Hannah C. Kaye
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
| | - Rachel M. Grattan
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
| | - Shayna R. Lucero
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
| | | | - Michael J. Wester
- Department Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131
| | - Keith A. Lidke
- Department Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - Bridget S. Wilson
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - Diane S. Lidke
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
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4
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Uceda AB, Frau J, Vilanova B, Adrover M. On the effect of methionine oxidation on the interplay between α-synuclein and synaptic-like vesicles. Int J Biol Macromol 2023; 229:92-104. [PMID: 36584779 DOI: 10.1016/j.ijbiomac.2022.12.262] [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: 09/14/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022]
Abstract
Human alpha-synuclein (αS) is an intrinsically disordered protein highly expressed in dopaminergic neurons. Its amyloid aggregates are the major component of Lewy bodies, which are considered a hallmark of Parkinson's disease (PD). αS has four different Met, which are particularly sensitive to oxidation, as most of them are found as Met sulfoxide (MetO) in the αS deposits. Consequently, researchers have invested mounting efforts trying to elucidate the molecular mechanisms underlying the links between oxidative stress, αS aggregation and PD. However, it has not been described yet the effect of Met oxidation on the physiological function of αS. Trying to shed light on this aspect, we have here studied a synthetic αS that displayed all its Met replaced by MetO moieties (αS-MetO). Our study has allowed to prove that MetO diminishes the affinity of αS towards anionic micelles (SDS), although the micelle-bound fraction of αS-MetO still adopts an α-helical folding resembling that of the lipid-bound αS. MetO also diminishes the affinity of αS towards synaptic-like vesicles, and its hindering effect is much more pronounced than that displayed on the αS-micelle affinity. Additionally, we have also demonstrated that MetO impairs the physiological function of αS as a catalyst of the clustering and the fusion of synaptic vesicles (SVs). Our findings provide a new understanding on how Met oxidation affects one of the most relevant biological functions attributed to αS that is to bind and cluster SVs along the neurotransmission.
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Affiliation(s)
- Ana Belén Uceda
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - Juan Frau
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - Bartolomé Vilanova
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - Miquel Adrover
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain.
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5
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Liang W, Yi R, Wang W, Shi Y, Zhang J, Xu X, Wang Q, Liu M, Wang F. Enhancing the Antitumor Immunity of T Cells by Engineering the Lipid-Regulatory Site of the TCR/CD3 Complex. Cancer Immunol Res 2023; 11:93-108. [PMID: 36265009 DOI: 10.1158/2326-6066.cir-21-1118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/24/2022] [Accepted: 10/13/2022] [Indexed: 01/05/2023]
Abstract
The engagement of the T-cell receptor (TCR) by a specific peptide-MHC ligand initiates transmembrane signaling to induce T-cell activation, a key step in most adaptive immune responses. Previous studies have indicated that TCR signaling is tightly regulated by cholesterol and its sulfate metabolite, cholesterol sulfate (CS), on the membrane. Here, we report a novel mechanism by which CS modulates TCR signaling through a conformational change of CD3 subunits. We found that the negatively charged CS interacted with the positively charged cytoplasmic domain of CD3ε (CD3εCD) to enhance its binding to the cell membrane and induce a stable secondary structure. This secondary structure suppressed the release of CD3εCD from the membrane in the presence of Ca2+, which in turn inhibited TCR phosphorylation and signaling. When a point mutation (I/A) was introduced to the intracellular immunoreceptor tyrosine-based activation motifs (YxxI-x6-8-YxxL) of CD3ε subunit, it reduced the stability of the secondary structure and regained sensitivity to Ca2+, which abolished CS-mediated inhibition and enhanced the signaling of the TCR complex. Notably, the I/A mutation could be applied to both murine and human TCR-T cell therapy to improve the antitumor efficacy. Our study reveals insights into the regulatory mechanism of TCR signaling and provides a strategy to functionally engineer the TCR/CD3 complex for T cell-based cancer immunotherapy.
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Affiliation(s)
- Wenhua Liang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruirong Yi
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weifang Wang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiwei Shi
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiqin Zhang
- BRL Medicine, Inc., Shanghai, China.,Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xiang Xu
- BRL Medicine, Inc., Shanghai, China
| | | | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Feng Wang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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6
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KIR signaling is regulated by electrostatic interaction of its cytosolic tail with the plasma membrane despite being neutral polyampholyte. Proc Natl Acad Sci U S A 2023; 120:e2212987120. [PMID: 36574700 PMCID: PMC9910492 DOI: 10.1073/pnas.2212987120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Many receptors signal upon phosphorylation of tyrosine-based motifs in their cytosolic tail, with intrinsic disorder as a common feature. Studies on CD3ζ and CD3ε tails, which are disordered and polybasic, suggested regulation of phosphorylation through accessibility of tyrosines, governed by electrostatic interactions with membrane anionic lipids. We noticed characteristics of intrinsic disorder and previously unappreciated features in tyrosine-based motif-bearing cytosolic tails of many, especially, inhibitory receptors. They are neutral or acidic polyampholytes, with acidic and basic residues linearly segregated. To explore roles of these electrostatic features, we studied inhibitory killer-cell immunoglobulin-like receptor (KIR). Its cytosolic tail is a disordered neutrally charged polyampholyte, wherein juxtamembrane and membrane distal stretches are basic, and the intervening stretch is acidic. Despite lacking net charge, it interacted electrostatically with the plasma membrane. The juxtamembrane stretch was crucial for overall binding, which sequestered tyrosines in the lipid bilayer and restrained their constitutive phosphorylation. Human leukocyte antigen-C ligand binding to KIR released its tail from the plasma membrane to initiate signaling. Tail release occurred independently of KIR polymerization, clustering, or tyrosine phosphorylation, but required acidic residues of the acidic stretch. Tail interaction with the plasma membrane dictated signaling strength of KIR. These results revealed an electrostatic protein-lipid interaction that is unusual in being governed by segregated clusters of acidic and basic residues in polyampholytic disordered region of protein. In contrast to previously known, segregated distribution of oppositely charged residues made both binding and unbinding modules inherent to receptor tail, which could make the interaction an independent signaling switch.
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7
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Uceda AB, Frau J, Vilanova B, Adrover M. Glycation of α-synuclein hampers its binding to synaptic-like vesicles and its driving effect on their fusion. Cell Mol Life Sci 2022; 79:342. [PMID: 35662377 PMCID: PMC9167179 DOI: 10.1007/s00018-022-04373-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/08/2022] [Accepted: 05/11/2022] [Indexed: 12/24/2022]
Abstract
Parkinson's disease (PD) is one of the most prevalent neurodegenerative disorders affecting the worldwide population. One of its hallmarks is the intraneuronal accumulation of insoluble Lewy bodies (LBs), which cause the death of dopaminergic neurons. α-Synuclein (αS) is the main component of these LBs and in them, it commonly contains non-enzymatic post-translational modifications, such as those resulting from its reaction with reactive carbonyl species arising as side products of the intraneuronal glycolysis (mainly methylglyoxal). Consequently, lysines of the αS found in LBs of diabetic individuals are usually carboxyethylated. A precise comprehension of the effect of Nε-(carboxyethyl)lysine (CEL) on the aggregation of αS and on its physiological function becomes crucial to fully understand the molecular mechanisms underlying the development of diabetes-induced PD. Consequently, we have here used a synthetic αS where all its Lys have been replaced by CEL moieties (αS-CEL), and we have studied how these modifications could impact on the neurotransmission mechanism. This study allows us to describe how the non-enzymatic glycosylation (glycation) affects the function of a protein like αS, involved in the pathogenesis of PD. CEL decreases the ability of αS to bind micelles, although the micelle-bound fraction of αS-CEL still displays an α-helical fold resembling that of the lipid-bound αS. However, CEL completely abolishes the affinity of αS towards synaptic-like vesicles and, consequently, it hampers its physiological function as a catalyst of the clustering and the fusion of the synaptic vesicles.
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Affiliation(s)
- Ana Belén Uceda
- Departament de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Universitat de les Illes Balears, Ed. Mateu Orfila i Rotger, Ctra. Valldemossa km 7.5, 07122, Palma, Spain
| | - Juan Frau
- Departament de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Universitat de les Illes Balears, Ed. Mateu Orfila i Rotger, Ctra. Valldemossa km 7.5, 07122, Palma, Spain
| | - Bartolomé Vilanova
- Departament de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Universitat de les Illes Balears, Ed. Mateu Orfila i Rotger, Ctra. Valldemossa km 7.5, 07122, Palma, Spain
| | - Miquel Adrover
- Departament de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Universitat de les Illes Balears, Ed. Mateu Orfila i Rotger, Ctra. Valldemossa km 7.5, 07122, Palma, Spain.
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8
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T cell receptor (TCR) signaling in health and disease. Signal Transduct Target Ther 2021; 6:412. [PMID: 34897277 PMCID: PMC8666445 DOI: 10.1038/s41392-021-00823-w] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 12/18/2022] Open
Abstract
Interaction of the T cell receptor (TCR) with an MHC-antigenic peptide complex results in changes at the molecular and cellular levels in T cells. The outside environmental cues are translated into various signal transduction pathways within the cell, which mediate the activation of various genes with the help of specific transcription factors. These signaling networks propagate with the help of various effector enzymes, such as kinases, phosphatases, and phospholipases. Integration of these disparate signal transduction pathways is done with the help of adaptor proteins that are non-enzymatic in function and that serve as a scaffold for various protein-protein interactions. This process aids in connecting the proximal to distal signaling pathways, thereby contributing to the full activation of T cells. This review provides a comprehensive snapshot of the various molecules involved in regulating T cell receptor signaling, covering both enzymes and adaptors, and will discuss their role in human disease.
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9
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Per aspera ad chaos: a personal journey to the wonderland of intrinsic disorder. Biochem J 2021; 478:3015-3024. [PMID: 34375385 DOI: 10.1042/bcj20210146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/19/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
This perspective article describes some of the key points of my personal journey through the intriguing world of intrinsically disordered proteins (IDPs). It also shows the evolution of my perception of functional proteins from a standard lock-and-key theory, where a unique function is defined by a unique 3D structure, to the structure-function continuum model, where the structural heterogeneity and conformational plasticity of IDPs define their remarkable multifunctionality and binding promiscuity. These personal accounts of the difficult and lengthy transition from order to disorder paralleled the uneasy and challenging transition in the mind of the scientific community from disbelief in intrinsic disorder to acceptance of IDPs as real entities that play critical biological roles. I hope that this perspective will be of interest to the readers of this journal.
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10
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Intrinsically disordered proteins and membranes: a marriage of convenience for cell signalling? Biochem Soc Trans 2021; 48:2669-2689. [PMID: 33155649 PMCID: PMC7752083 DOI: 10.1042/bst20200467] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023]
Abstract
The structure-function paradigm has guided investigations into the molecules involved in cellular signalling for decades. The peripheries of this paradigm, however, start to unravel when considering the co-operation between proteins and the membrane in signalling processes. Intrinsically disordered regions hold distinct advantages over folded domains in terms of their binding promiscuity, sensitivity to their particular environment and their ease of modulation through post-translational modifications. Low sequence complexity and bias towards charged residues are also favourable for the multivalent electrostatic interactions that occur at the surfaces of lipid bilayers. This review looks at the principles behind the successful marriage between protein disorder and membranes in addition to the role of this partnership in modifying and regulating signalling in cellular processes. The HVR (hypervariable region) of small GTPases is highlighted as a well-studied example of the nuanced role a short intrinsically disordered region can play in the fine-tuning of signalling pathways.
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11
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Prakaash D, Cook GP, Acuto O, Kalli AC. Multi-scale simulations of the T cell receptor reveal its lipid interactions, dynamics and the arrangement of its cytoplasmic region. PLoS Comput Biol 2021; 17:e1009232. [PMID: 34280187 PMCID: PMC8321403 DOI: 10.1371/journal.pcbi.1009232] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/29/2021] [Accepted: 07/01/2021] [Indexed: 12/27/2022] Open
Abstract
The T cell receptor (TCR-CD3) initiates T cell activation by binding to peptides of Major Histocompatibility Complexes (pMHC). The TCR-CD3 topology is well understood but the arrangement and dynamics of its cytoplasmic tails remains unknown, limiting our grasp of the signalling mechanism. Here, we use molecular dynamics simulations and modelling to investigate the entire TCR-CD3 embedded in a model membrane. Our study demonstrates conformational changes in the extracellular and transmembrane domains, and the arrangement of the TCR-CD3 cytoplasmic tails. The cytoplasmic tails formed highly interlaced structures while some tyrosines within the immunoreceptor tyrosine-based activation motifs (ITAMs) penetrated the hydrophobic core of the membrane. Interactions between the cytoplasmic tails and phosphatidylinositol phosphate lipids in the inner membrane leaflet led to the formation of a distinct anionic lipid fingerprint around the TCR-CD3. These results increase our understanding of the TCR-CD3 dynamics and the importance of membrane lipids in regulating T cell activation.
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Affiliation(s)
- Dheeraj Prakaash
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, United Kingdom
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Graham P. Cook
- Leeds Institute of Medical Research at St James’s, School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Oreste Acuto
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Antreas C. Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, United Kingdom
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- * E-mail:
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12
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Clemens L, Dushek O, Allard J. Intrinsic Disorder in the T Cell Receptor Creates Cooperativity and Controls ZAP70 Binding. Biophys J 2020; 120:379-392. [PMID: 33285117 PMCID: PMC7840419 DOI: 10.1016/j.bpj.2020.11.2266] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/24/2020] [Accepted: 11/19/2020] [Indexed: 12/31/2022] Open
Abstract
Many immunoreceptors have cytoplasmic domains that are intrinsically disordered (i.e., have high configurational entropy), have multiple sites of posttranslational modification (e.g., tyrosine phosphorylation), and participate in nonlinear signaling pathways (e.g., exhibiting switch-like behavior). Several hypotheses to explain the origin of these nonlinearities fall under the broad hypothesis that modification at one site changes the immunoreceptor’s entropy, which in turn changes further modification dynamics. Here, we use coarse-grain simulation to study three scenarios, all related to the chains that constitute the T cell receptor (TCR). We find that first, if phosphorylation induces local changes in the flexibility of the TCR ζ-chain, this naturally leads to rate enhancements and cooperativity. Second, we find that TCR CD3ɛ can provide a switch by modulating its residence in the plasma membrane. By constraining our model to be consistent with the previous observation that both basic residues and phosphorylation control membrane residence, we find that there is only a moderate rate enhancement of 10% between first and subsequent phosphorylation events. Third, we find that volume constraints do not limit the number of ZAP70s that can bind the TCR but that entropic penalties lead to a 200-fold decrease in binding rate by the seventh ZAP70, potentially explaining the observation that each TCR has around six ZAP70 molecules bound after receptor triggering. In all three scenarios, our results demonstrate that phenomena that change an immunoreceptor chain’s entropy (stiffening, confinement to a membrane, and multiple simultaneous binding) can lead to nonlinearities (rate enhancement, switching, and negative cooperativity) in how the receptor participates in signaling. These polymer-entropy-driven nonlinearities may augment the nonlinearities that arise from, e.g., kinetic proofreading and cluster formation. They also suggest different design strategies for engineered receptors, e.g., whether or not to put signaling modules on one chain or multiple clustered chains.
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Affiliation(s)
- Lara Clemens
- Center for Complex Biological Systems, University of California Irvine, Irvine, California
| | - Omer Dushek
- Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Jun Allard
- Center for Complex Biological Systems, University of California Irvine, Irvine, California; Department of Mathematics and Department of Physics and Astronomy, University of California Irvine, Irvine, California.
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13
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Ma Y, Lim YJ, Benda A, Lou J, Goyette J, Gaus K. Clustering of the ζ-Chain Can Initiate T Cell Receptor Signaling. Int J Mol Sci 2020; 21:ijms21103498. [PMID: 32429097 PMCID: PMC7279048 DOI: 10.3390/ijms21103498] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 11/16/2022] Open
Abstract
T cell activation is initiated when ligand binding to the T cell receptor (TCR) triggers intracellular phosphorylation of the TCR-CD3 complex. However, it remains unknown how biophysical properties of TCR engagement result in biochemical phosphorylation events. Here, we constructed an optogenetic tool that induces spatial clustering of ζ-chain in a light controlled manner. We showed that spatial clustering of the ζ-chain intracellular tail alone was sufficient to initialize T cell triggering including phosphorylation of ζ-chain, Zap70, PLCγ, ERK and initiated Ca2+ flux. In reconstituted COS-7 cells, only Lck expression was required to initiate ζ-chain phosphorylation upon ζ-chain clustering, which leads to the recruitment of tandem SH2 domain of Zap70 from cell cytosol to the newly formed ζ-chain clusters at the plasma membrane. Taken together, our data demonstrated the biophysical relevance of receptor clustering in TCR signaling.
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Affiliation(s)
- Yuanqing Ma
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, The University of New South Wales, 2052 Sydney, Australia; (J.L.); (J.G.)
- ARC Centre of Excellence in Advanced Molecular Imaging, The University of New South Wales, 2052 Sydney, Australia
- Correspondence: (Y.M.); (K.G.)
| | - Yean J. Lim
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, 2601 Canberra, Australia;
- Research School of Electrical, Energy and Materials Engineering, College of Engineering and Computer Science, The Australian National University, 31 North Road, 2601 Canberra, Australia
| | - Aleš Benda
- IMCF at BIOCEV, Faculty of Science, Charles University, Průmyslová 595, 25250 Vestec, Czech Republic;
| | - Jieqiong Lou
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, The University of New South Wales, 2052 Sydney, Australia; (J.L.); (J.G.)
- ARC Centre of Excellence in Advanced Molecular Imaging, The University of New South Wales, 2052 Sydney, Australia
- School of Physics, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jesse Goyette
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, The University of New South Wales, 2052 Sydney, Australia; (J.L.); (J.G.)
- ARC Centre of Excellence in Advanced Molecular Imaging, The University of New South Wales, 2052 Sydney, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, The University of New South Wales, 2052 Sydney, Australia; (J.L.); (J.G.)
- ARC Centre of Excellence in Advanced Molecular Imaging, The University of New South Wales, 2052 Sydney, Australia
- Correspondence: (Y.M.); (K.G.)
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14
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Schamel WW, Alarcon B, Minguet S. The TCR is an allosterically regulated macromolecular machinery changing its conformation while working. Immunol Rev 2020; 291:8-25. [PMID: 31402501 DOI: 10.1111/imr.12788] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 05/30/2019] [Indexed: 12/13/2022]
Abstract
The αβ T-cell receptor (TCR) is a multiprotein complex controlling the activation of T cells. Although the structure of the complete TCR is not known, cumulative evidence supports that the TCR cycles between different conformational states that are promoted either by thermal motion or by force. These structural transitions determine whether the TCR engages intracellular effectors or not, regulating TCR phosphorylation and signaling. As for other membrane receptors, ligand binding selects and stabilizes the TCR in active conformations, and/or switches the TCR to activating states that were not visited before ligand engagement. Here we review the main models of TCR allostery, that is, ligand binding at TCRαβ changes the structure at CD3 and ζ. (a) The ITAM and proline-rich sequence exposure model, in which the TCR's cytoplasmic tails shield each other and ligand binding exposes them for phosphorylation. (b) The membrane-ITAM model, in which the CD3ε and ζ tails are sequestered inside the membrane and again ligand binding exposes them. (c) The mechanosensor model in which ligand binding exerts force on the TCR, inducing structural changes that allow signaling. Since these models are complementary rather than competing, we propose a unified model that aims to incorporate all existing data.
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Affiliation(s)
- Wolfgang W Schamel
- Department of Immunology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Center of Chronic Immunodeficiency CCI, University Clinics and Medical Faculty, Freiburg, Germany
| | - Balbino Alarcon
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | - Susana Minguet
- Department of Immunology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Center of Chronic Immunodeficiency CCI, University Clinics and Medical Faculty, Freiburg, Germany
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15
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Dube N, Marzinek JK, Glen RC, Bond PJ. The structural basis for membrane assembly of immunoreceptor signalling complexes. J Mol Model 2019; 25:277. [PMID: 31456056 DOI: 10.1007/s00894-019-4165-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/15/2019] [Indexed: 11/25/2022]
Abstract
Immunoreceptors are TM complexes that consist of separate ligand-binding and signal-transducing modules. Mounting evidence suggests that interactions with the local environment may influence the architecture of these TM domains, which assemble via crucial sets of conserved ionisable residues, and also control the peripheral association of immunoreceptor tyrosine-based activation motifs (ITAMs) whose phosphorylation triggers cytoplasmic signalling cascades. We now report a molecular dynamics (MD) simulation study of the archetypal T cell receptor (TCR) and its cluster of differentiation 3 (CD3) signalling partners, along with the analogous DNAX-activation protein of 12 kDa (DAP12)/natural killer group 2C (NKG2C) complex. Based on > 15 μs of explicitly solvated, atomic-resolution sampling, we explore molecular aspects of immunoreceptor complex stability in different functionally relevant states. A novel alchemical approach is used to simulate the cytoplasmic CD3ε tail at different depths within lipid bilayer models, revealing that the conformation and cytoplasmic exposure of ITAMs are highly sensitive to local enrichment by different lipid species and to phosphorylation. Furthermore, simulations of the TCR and DAP12 TM domains in various states of oligomerisation suggest that, during the early stages of assembly, stable membrane insertion is facilitated by the interfacial lipid/solvent environment and/or partial ionisation of charged residues. Collectively, our results indicate that the architecture and mechanisms of signal transduction in immunoreceptor complexes are tightly regulated by interactions with the microenvironment.
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Affiliation(s)
- Namita Dube
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Tata Institute of Fundamental Research, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, 500107, India
| | - Jan K Marzinek
- Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, Singapore, 138671, Singapore
| | - Robert C Glen
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Division of Integrative Systems Medicine and Digestive Diseases, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Peter J Bond
- Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, Singapore, 138671, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
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16
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Connolly A, Gagnon E. Electrostatic interactions: From immune receptor assembly to signaling. Immunol Rev 2019; 291:26-43. [DOI: 10.1111/imr.12769] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Audrey Connolly
- Institut de Recherche en Immunologie et Cancérologie/Institute for Research in Immunology and Cancer Montréal Québec Canada
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine Université de Montréal Montréal Québec Canada
| | - Etienne Gagnon
- Institut de Recherche en Immunologie et Cancérologie/Institute for Research in Immunology and Cancer Montréal Québec Canada
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine Université de Montréal Montréal Québec Canada
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17
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Djulbegovic MB, Uversky VN. Ferroptosis - An iron- and disorder-dependent programmed cell death. Int J Biol Macromol 2019; 135:1052-1069. [PMID: 31175900 DOI: 10.1016/j.ijbiomac.2019.05.221] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 12/20/2022]
Abstract
Programmed cell death (PCD) is an integral component of both developmental and pathological features of an organism. Recently, ferroptosis, a new form of PCD that is dependent on reactive oxygen species and iron, has been described. As with apoptosis, necroptosis, and autophagy, ferroptosis is associated with a large set of proteins assembled in protein-protein interaction (PPI) networks, interactability of which is driven by the presence of intrinsically disordered proteins (IDPs) and IDP regions (IDPRs). Previous investigations have identified the prevalence and functionality of IDPs/IDPRs in non-ferroptosis PCD. The intrinsic disorder in protein structures is used to increase the regulatory powers of these processes. As uncontrolled PCD is associated with the onset of various pathological traits, uncovering the association between intrinsic disorder and ferroptosis-related proteins is crucial. To understand this association, 31 human ferroptosis-related proteins were analyzed via a multi-dimensional array of bioinformatics and computational techniques. In addition, a disorder meta-predictor (PONDR® FIT) was implored to look at the evolutionary conservation of intrinsic disorder in these proteins. This study presents evidence that IDPs and IDPRs are prevalent in ferroptosis. The intrinsic disorder found in ferroptosis has far-reaching functional implications related to ferroptosis-related PPIs and molecular interactions.
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Affiliation(s)
- Mak B Djulbegovic
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, 142290 Pushchino, Moscow region, Russia.
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18
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The Structural and Functional Diversity of Intrinsically Disordered Regions in Transmembrane Proteins. J Membr Biol 2019; 252:273-292. [DOI: 10.1007/s00232-019-00069-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/17/2019] [Indexed: 10/26/2022]
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19
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Cheng H, Schwell V, Curtis BR, Fazlieva R, Roder H, Campbell KS. Conformational Changes in the Cytoplasmic Region of KIR3DL1 upon Interaction with SHP-2. Structure 2019; 27:639-650.e2. [PMID: 30773397 DOI: 10.1016/j.str.2019.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/07/2018] [Accepted: 01/18/2019] [Indexed: 12/29/2022]
Abstract
KIR3DL1 is an inhibitory killer cell immunoglobulin-like receptor (KIR) that negatively regulates natural killer cell cytotoxicity. The KIR3DL1 cytoplasmic region (3DL1-cyto) is disordered and can be dissected into three segments: (I) H340-V351; (II) M352-D371; and (III) P372-P423. NMR studies indicate that segment II can dynamically adopt a loop-like conformation, and segments I and III can form dynamic helices that may mediate binding to membranes, particularly in the region around the N-terminal (N) immunoreceptor tyrosine-based inhibitory motif (ITIM), consistent with its role in signaling. Furthermore, individual SH2 domains of SHP-2 strongly engage with the unphosphorylated N-ITIM of 3DL1-cyto, while binding of the tandem SHP-2 SH2 domains to the bis-phosphorylated ITIMs results in more extensive conformational changes in segments I and III. The findings enhance our understanding of KIR function and how ITIMs in a target receptor operate in concert to engage the tandem SH2 domains of SHP-2.
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Affiliation(s)
- Hong Cheng
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
| | - Vered Schwell
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Brett R Curtis
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Ruzaliya Fazlieva
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Heinrich Roder
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Kerry S Campbell
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
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20
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Targeting Intramembrane Protein-Protein Interactions: Novel Therapeutic Strategy of Millions Years Old. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 111:61-99. [PMID: 29459036 PMCID: PMC7102818 DOI: 10.1016/bs.apcsb.2017.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Intramembrane protein-protein interactions (PPIs) are involved in transmembrane signal transduction mediated by cell surface receptors and play an important role in health and disease. Recently, receptor-specific modulatory peptides rationally designed using a general platform of transmembrane signaling, the signaling chain homooligomerization (SCHOOL) model, have been proposed to therapeutically target these interactions in a variety of serious diseases with unmet needs including cancer, sepsis, arthritis, retinopathy, and thrombosis. These peptide drug candidates use ligand-independent mechanisms of action (SCHOOL mechanisms) and demonstrate potent efficacy in vitro and in vivo. Recent studies surprisingly revealed that in order to modify and/or escape the host immune response, human viruses use similar mechanisms and modulate cell surface receptors by targeting intramembrane PPIs in a ligand-independent manner. Here, I review these intriguing mechanistic similarities and discuss how the viral strategies optimized over a billion years of the coevolution of viruses and their hosts can help to revolutionize drug discovery science and develop new, disruptive therapies. Examples are given.
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21
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Uversky VN. The roles of intrinsic disorder-based liquid-liquid phase transitions in the "Dr. Jekyll-Mr. Hyde" behavior of proteins involved in amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Autophagy 2017; 13:2115-2162. [PMID: 28980860 DOI: 10.1080/15548627.2017.1384889] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pathological developments leading to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are associated with misbehavior of several key proteins, such as SOD1 (superoxide dismutase 1), TARDBP/TDP-43, FUS, C9orf72, and dipeptide repeat proteins generated as a result of the translation of the intronic hexanucleotide expansions in the C9orf72 gene, PFN1 (profilin 1), GLE1 (GLE1, RNA export mediator), PURA (purine rich element binding protein A), FLCN (folliculin), RBM45 (RNA binding motif protein 45), SS18L1/CREST, HNRNPA1 (heterogeneous nuclear ribonucleoprotein A1), HNRNPA2B1 (heterogeneous nuclear ribonucleoprotein A2/B1), ATXN2 (ataxin 2), MAPT (microtubule associated protein tau), and TIA1 (TIA1 cytotoxic granule associated RNA binding protein). Although these proteins are structurally and functionally different and have rather different pathological functions, they all possess some levels of intrinsic disorder and are either directly engaged in or are at least related to the physiological liquid-liquid phase transitions (LLPTs) leading to the formation of various proteinaceous membrane-less organelles (PMLOs), both normal and pathological. This review describes the normal and pathological functions of these ALS- and FTLD-related proteins, describes their major structural properties, glances at their intrinsic disorder status, and analyzes the involvement of these proteins in the formation of normal and pathological PMLOs, with the ultimate goal of better understanding the roles of LLPTs and intrinsic disorder in the "Dr. Jekyll-Mr. Hyde" behavior of those proteins.
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Affiliation(s)
- Vladimir N Uversky
- a Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute , Morsani College of Medicine , University of South Florida , Tampa , FL , USA.,b Institute for Biological Instrumentation of the Russian Academy of Sciences , Pushchino, Moscow region , Russia
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22
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Zimmermann K, Eells R, Heinrich F, Rintoul S, Josey B, Shekhar P, Lösche M, Stern LJ. The cytosolic domain of T-cell receptor ζ associates with membranes in a dynamic equilibrium and deeply penetrates the bilayer. J Biol Chem 2017; 292:17746-17759. [PMID: 28893902 PMCID: PMC5663876 DOI: 10.1074/jbc.m117.794370] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/21/2017] [Indexed: 11/06/2022] Open
Abstract
Interactions between lipid bilayers and the membrane-proximal regions of membrane-associated proteins play important roles in regulating membrane protein structure and function. The T-cell antigen receptor is an assembly of eight single-pass membrane-spanning subunits on the surface of T lymphocytes that initiates cytosolic signaling cascades upon binding antigens presented by MHC-family proteins on antigen-presenting cells. Its ζ-subunit contains multiple cytosolic immunoreceptor tyrosine-based activation motifs involved in signal transduction, and this subunit by itself is sufficient to couple extracellular stimuli to intracellular signaling events. Interactions of the cytosolic domain of ζ (ζcyt) with acidic lipids have been implicated in the initiation and regulation of transmembrane signaling. ζcyt is unstructured in solution. Interaction with acidic phospholipids induces structure, but its disposition when bound to lipid bilayers is controversial. Here, using surface plasmon resonance and neutron reflection, we characterized the interaction of ζcyt with planar lipid bilayers containing mixtures of acidic and neutral lipids. We observed two binding modes of ζcyt to the bilayers in dynamic equilibrium: one in which ζcyt is peripherally associated with lipid headgroups and one in which it penetrates deeply into the bilayer. Such an equilibrium between the peripherally bound and embedded forms of ζcyt apparently controls accessibility of the immunoreceptor tyrosine-based activation signal transduction pathway. Our results reconcile conflicting findings of the ζ structure reported in previous studies and provide a framework for understanding how lipid interactions regulate motifs to tyrosine kinases and may regulate the T-cell antigen receptor biological activities for this cell-surface receptor system.
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Affiliation(s)
| | | | - Frank Heinrich
- the Departments of Physics and
- the National Institute of Standards and Technology (NIST) Center for Neutron Research, Gaithersburg, Maryland 20899
| | | | | | | | - Mathias Lösche
- the Departments of Physics and
- the National Institute of Standards and Technology (NIST) Center for Neutron Research, Gaithersburg, Maryland 20899
- Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, and
| | - Lawrence J Stern
- From the Departments of Pathology and
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
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23
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Uversky VN. Intrinsic Disorder, Protein-Protein Interactions, and Disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 110:85-121. [PMID: 29413001 DOI: 10.1016/bs.apcsb.2017.06.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
It is recognized now that biologically active proteins without stable tertiary structure (known as intrinsically disordered proteins, IDPs) and hybrid proteins containing ordered domains and intrinsically disordered protein regions (IDPRs) are important players found in any given proteome. These IDPs/IDPRs possess functions that complement functional repertoire of their ordered counterparts, being commonly related to recognition, as well as control and regulation of various signaling pathways. They are interaction masters, being able to utilize a wide spectrum of interaction mechanisms, ranging from induced folding to formation of fuzzy complexes where significant levels of disorder are preserved, to polyvalent stochastic interactions playing crucial roles in the liquid-liquid phase transitions leading to the formation of proteinaceous membrane-less organelles. IDPs/IDPRs are tightly controlled themselves via various means, including alternative splicing, precisely controlled expression and degradation, binding to specific partners, and posttranslational modifications. Distortions in the regulation and control of IDPs/IDPRs, as well as their aberrant interactivity are commonly associated with various human diseases. This review presents some aspects of the intrinsic disorder-based functionality and dysfunctionality, paying special attention to the normal and pathological protein-protein interactions.
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Affiliation(s)
- Vladimir N Uversky
- USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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24
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Ionic CD3-Lck interaction regulates the initiation of T-cell receptor signaling. Proc Natl Acad Sci U S A 2017; 114:E5891-E5899. [PMID: 28659468 DOI: 10.1073/pnas.1701990114] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Antigen-triggered T-cell receptor (TCR) phosphorylation is the first signaling event in T cells to elicit adaptive immunity against invading pathogens and tumor cells. Despite its physiological importance, the underlying mechanism of TCR phosphorylation remains elusive. Here, we report a key mechanism regulating the initiation of TCR phosphorylation. The major TCR kinase Lck shows high selectivity on the four CD3 signaling proteins of TCR. CD3ε is the only CD3 chain that can efficiently interact with Lck, mainly through the ionic interactions between CD3ε basic residue-rich sequence (BRS) and acidic residues in the Unique domain of Lck. We applied a TCR reconstitution system to explicitly study the initiation of TCR phosphorylation. The ionic CD3ε-Lck interaction controls the phosphorylation level of the whole TCR upon antigen stimulation. CD3ε BRS is sequestered in the membrane, and antigen stimulation can unlock this motif. Dynamic opening of CD3ε BRS and its subsequent recruitment of Lck thus can serve as an important switch of the initiation of TCR phosphorylation.
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25
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Lipid-dependent conformational dynamics underlie the functional versatility of T-cell receptor. Cell Res 2017; 27:505-525. [PMID: 28337984 DOI: 10.1038/cr.2017.42] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 01/19/2017] [Accepted: 02/09/2017] [Indexed: 01/11/2023] Open
Abstract
T-cell receptor-CD3 complex (TCR) is a versatile signaling machine that can initiate antigen-specific immune responses based on various biochemical changes of CD3 cytoplasmic domains, but the underlying structural basis remains elusive. Here we developed biophysical approaches to study the conformational dynamics of CD3ε cytoplasmic domain (CD3εCD). At the single-molecule level, we found that CD3εCD could have multiple conformational states with different openness of three functional motifs, i.e., ITAM, BRS and PRS. These conformations were generated because different regions of CD3εCD had heterogeneous lipid-binding properties and therefore had heterogeneous dynamics. Live-cell imaging experiments demonstrated that different antigen stimulations could stabilize CD3εCD at different conformations. Lipid-dependent conformational dynamics thus provide structural basis for the versatile signaling property of TCR.
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26
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Abstract
Triggering of cell-mediated immunity is largely dependent on the recognition of foreign or abnormal molecules by a myriad of cell surface-bound receptors. Many activating immune receptors do not possess any intrinsic signaling capacity but instead form noncovalent complexes with one or more dimeric signaling modules that communicate with a common set of kinases to initiate intracellular information-transfer pathways. This modular architecture, where the ligand binding and signaling functions are detached from one another, is a common theme that is widely employed throughout the innate and adaptive arms of immune systems. The evolutionary advantages of this highly adaptable platform for molecular recognition are visible in the variety of ligand-receptor interactions that can be linked to common signaling pathways, the diversification of receptor modules in response to pathogen challenges, and the amplification of cellular responses through incorporation of multiple signaling motifs. Here we provide an overview of the major classes of modular activating immune receptors and outline the current state of knowledge regarding how these receptors assemble, recognize their ligands, and ultimately trigger intracellular signal transduction pathways that activate immune cell effector functions.
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Affiliation(s)
- Richard Berry
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University , Clayton, Victoria 3800, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University , Clayton, Victoria 3800, Australia
| | - Matthew E Call
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research , Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne , Parkville, Victoria 3052, Australia
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27
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Banerjee PR, Moosa MM, Deniz AA. Two-Dimensional Crowding Uncovers a Hidden Conformation of α-Synuclein. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Priya R. Banerjee
- Department of Integrative Structural and Computational Biology; The Scripps Research Institute; La Jolla CA 92037 USA
| | - Mahdi Muhammad Moosa
- Department of Integrative Structural and Computational Biology; The Scripps Research Institute; La Jolla CA 92037 USA
| | - Ashok A. Deniz
- Department of Integrative Structural and Computational Biology; The Scripps Research Institute; La Jolla CA 92037 USA
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28
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Banerjee PR, Moosa MM, Deniz AA. Two-Dimensional Crowding Uncovers a Hidden Conformation of α-Synuclein. Angew Chem Int Ed Engl 2016; 55:12789-12792. [PMID: 27612332 DOI: 10.1002/anie.201606963] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Indexed: 11/09/2022]
Abstract
The intrinsically disordered protein (IDP), α-synuclein (αS), is well-known for phospholipid membrane binding-coupled folding into tunable helical conformers. Here, using single-molecule experiments in conjunction with ensemble assays and a theoretical model, we present a unique case demonstrating that the interaction-folding landscape of αS can be tuned by two-dimensional (2D) crowding through simultaneous binding of a second protein on the bilayer surface. Unexpectedly, the experimental data show a clear deviation from a simple competitive inhibition model, but are consistent with a bimodal inhibition mechanism wherein membrane binding of a second protein (a membrane interacting chaperone, Hsp27, in this case) differentially inhibits two distinct modules of αS-membrane interaction. As a consequence, αS molecules are forced to access a hidden conformational state on the phospholipid bilayer in which only the higher-affinity module remains membrane-bound. Our results demonstrate that macromolecular crowding in two dimensions can play a significant role in shaping the conformational landscape of membrane-binding IDPs with multiple binding modes.
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Affiliation(s)
- Priya R Banerjee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Mahdi Muhammad Moosa
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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29
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Shaban H, Na I, Kislichkina AA, Dentovskaya SV, Anisimov AP, Uversky VN. Effect of natural polymorphism on structure and function of the Yersinia pestis outer membrane porin F (OmpF protein): a computational study. J Biomol Struct Dyn 2016; 35:2588-2603. [PMID: 27593697 DOI: 10.1080/07391102.2016.1224734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The Yersinia pestis outer membrane porin F (OmpF) is a transmembrane protein located in the outer membrane of this Gram-negative bacterium which is the causative agent of plague, where it plays a significant role in controlling the selective permeability of the membrane. The amino acid sequences of OmpF proteins from 48 Y. pestis strains representing all currently available phylogenetic groups of this Gram-negative bacterium were recently deduced. Comparison of these amino acid sequences revealed that the OmpF can be present in four isoforms, the pestis-pestis type, and the pestis-microtus types I, II, and III. OmpF of the most recent pestis-pestis type has an alanine residue at the position 148, where all the pestis-microtus types have threonine there (T148A polymorphism). The variability of different pestis-microtus types is caused by an additional polymorphism at the 193rd position, where the OmpFs of the pestis-microtus type II and type III have isoleucine-glycine (IG+193) or isoleucine-glycine-isoleucine-glycine (IGIG+193) insertions, respectively (IG+193 and IGIG+193 polymorphism). To investigate potential effects of these sequence polymorphisms on the structural properties of the OmpF protein, we conducted multi-level computational analysis of its isoforms. Analysis of the I-TASSER-generated 3D-models revealed that the Yersinia OmpF is very similar to other non-specific enterobacterial porins. The T148A polymorphism affected a loop located in the external vestibule of the OmpF channel, whereas IG+193 and IGIG+193 polymorphisms affected one of its β-strands. Our analysis also suggested that polymorphism has moderate effect on the predicted local intrinsic disorder predisposition of OmpF, but might have some functional implementations.
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Affiliation(s)
- Hiba Shaban
- a Department of Molecular Medicine, Morsani College of Medicine , University of South Florida , Tampa 33612 , FL , USA
| | - Insing Na
- a Department of Molecular Medicine, Morsani College of Medicine , University of South Florida , Tampa 33612 , FL , USA
| | - Angelina A Kislichkina
- b State Research Center for Applied Microbiology and Biotechnology , Obolensk 142279 , Moscow Region , Russia
| | - Svetlana V Dentovskaya
- b State Research Center for Applied Microbiology and Biotechnology , Obolensk 142279 , Moscow Region , Russia
| | - Andrey P Anisimov
- b State Research Center for Applied Microbiology and Biotechnology , Obolensk 142279 , Moscow Region , Russia
| | - Vladimir N Uversky
- a Department of Molecular Medicine, Morsani College of Medicine , University of South Florida , Tampa 33612 , FL , USA.,c USF Health Byrd Alzheimer's Research Institute , Morsani College of Medicine, University of South Florida , Tampa 33612 , FL , USA.,d Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg 194064 , Russia
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Deng W, Li R. Juxtamembrane contribution to transmembrane signaling. Biopolymers 2016; 104:317-22. [PMID: 25846274 DOI: 10.1002/bip.22651] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/23/2015] [Accepted: 03/30/2015] [Indexed: 12/11/2022]
Abstract
Signaling across the cell membrane mediated by transmembrane receptors plays an important role in diverse biological processes. Recent studies have indicated that, in a number of single-span transmembrane receptors, the intracellular juxtamembrane (JM) sequence linking the transmembrane helix with the rest of the cytoplasmic domain participates directly in the signaling process via several novel mechanisms. This review briefly highlights several modes of JM dynamics in the context of signal transduction that are shared by different types of transmembrane receptors.
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Affiliation(s)
- Wei Deng
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Emory University School of Medicine, Atlanta, GA, 30322
| | - Renhao Li
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Emory University School of Medicine, Atlanta, GA, 30322
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Structural biology of intrinsically disordered proteins: Revisiting unsolved mysteries. Biochimie 2016; 125:112-8. [PMID: 27004461 DOI: 10.1016/j.biochi.2016.03.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/17/2016] [Indexed: 01/30/2023]
Abstract
The emergence of intrinsically disordered proteins (IDPs) has challenged the classical protein structure-function paradigm by introducing a new paradigm of "coupled binding and folding". This paradigm suggests that IDPs fold upon binding to their partners. Further studies, however, revealed a novel and previously unrecognized phenomenon of "uncoupled binding and folding" suggesting that IDPs do not necessarily fold upon interaction with their lipid and protein partners. The complex and often unusual biophysics of IDPs makes structural characterization of these proteins and their complexes not only challenging but often resulting in opposite conclusions. For this reason, some crucial questions in this field remain unsolved for well over a decade. Considering an important role of IDPs in cellular regulation, signaling and control in health and disease, more efforts are needed to solve these mysteries. Here, I focus on two long-standing contradictions in the literature concerning dimerization and membrane-binding activities of IDPs. Molecular explanation of these discrepancies is provided. I also demonstrate how resolution of these critical issues in the field of IDPs results in our expanded understanding of cell function and has multiple applications in biology and medicine.
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Brazin KN, Mallis RJ, Das DK, Feng Y, Hwang W, Wang JH, Wagner G, Lang MJ, Reinherz EL. Structural Features of the αβTCR Mechanotransduction Apparatus That Promote pMHC Discrimination. Front Immunol 2015; 6:441. [PMID: 26388869 PMCID: PMC4558533 DOI: 10.3389/fimmu.2015.00441] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/14/2015] [Indexed: 12/20/2022] Open
Abstract
The αβTCR was recently revealed to function as a mechanoreceptor. That is, it leverages mechanical energy generated during immune surveillance and at the immunological synapse to drive biochemical signaling following ligation by a specific foreign peptide-MHC complex (pMHC). Here, we review the structural features that optimize this transmembrane (TM) receptor for mechanotransduction. Specialized adaptations include (1) the CβFG loop region positioned between Vβ and Cβ domains that allosterically gates both dynamic T cell receptor (TCR)-pMHC bond formation and lifetime; (2) the rigid super β-sheet amalgams of heterodimeric CD3εγ and CD3εδ ectodomain components of the αβTCR complex; (3) the αβTCR subunit connecting peptides linking the extracellular and TM segments, particularly the oxidized CxxC motif in each CD3 heterodimeric subunit that facilitates force transfer through the TM segments and surrounding lipid, impacting cytoplasmic tail conformation; and (4) quaternary changes in the αβTCR complex that accompany pMHC ligation under load. How bioforces foster specific αβTCR-based pMHC discrimination and why dynamic bond formation is a primary basis for kinetic proofreading are discussed. We suggest that the details of the molecular rearrangements of individual αβTCR subunit components can be analyzed utilizing a combination of structural biology, single-molecule FRET, optical tweezers, and nanobiology, guided by insightful atomistic molecular dynamic studies. Finally, we review very recent data showing that the pre-TCR complex employs a similar mechanobiology to that of the αβTCR to interact with self-pMHC ligands, impacting early thymic repertoire selection prior to the CD4(+)CD8(+) double positive thymocyte stage of development.
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Affiliation(s)
- Kristine N. Brazin
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Robert J. Mallis
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Dibyendu Kumar Das
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Yinnian Feng
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX, USA
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, South Korea
| | - Jia-huai Wang
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Matthew J. Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Ellis L. Reinherz
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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Wu W, Yan C, Shi X, Li L, Liu W, Xu C. Lipid in T-cell receptor transmembrane signaling. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 118:130-8. [DOI: 10.1016/j.pbiomolbio.2015.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 12/18/2022]
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López CA, Sethi A, Goldstein B, Wilson BS, Gnanakaran S. Membrane-mediated regulation of the intrinsically disordered CD3ϵ cytoplasmic tail of the TCR. Biophys J 2015; 108:2481-2491. [PMID: 25992726 PMCID: PMC4457001 DOI: 10.1016/j.bpj.2015.03.059] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 01/27/2015] [Accepted: 03/02/2015] [Indexed: 10/23/2022] Open
Abstract
The regulation of T-cell-mediated immune responses depends on the phosphorylation of immunoreceptor tyrosine-based activation motifs (ITAMs) on T-cell receptors. Although many details of the signaling cascades are well understood, the initial mechanism and regulation of ITAM phosphorylation remains unknown. We used molecular dynamics simulations to study the influence of different compositions of lipid bilayers on the membrane association of the CD3ϵ cytoplasmic tails of the T-cell receptors. Our results show that binding of CD3ϵ to membranes is modulated by both the presence of negatively charged lipids and the lipid order of the membrane. Free-energy calculations reveal that the protein-membrane interaction is favored by the presence of nearby basic residues and the ITAM tyrosines. Phosphorylation minimizes membrane association, rendering the ITAM motif more accessible to binding partners. In systems mimicking biological membranes, the CD3ϵ chain localization is modulated by different facilitator lipids (e.g., gangliosides or phosphoinositols), revealing a plausible regulatory effect on activation through the regulation of lipid composition in cell membranes.
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Affiliation(s)
- Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Anurag Sethi
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Byron Goldstein
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Bridget S Wilson
- Department of Pathology and Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico; New Mexico Consortium, Los Alamos, New Mexico.
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Uversky VN. Unreported intrinsic disorder in proteins: Disorder emergency room. INTRINSICALLY DISORDERED PROTEINS 2015; 3:e1010999. [PMID: 28232885 DOI: 10.1080/21690707.2015.1010999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/01/2014] [Accepted: 11/24/2014] [Indexed: 10/23/2022]
Abstract
This article continues an "Unreported Intrinsic Disorder in Proteins" series, the goal of which is to expose some interesting cases of missed (or overlooked, or ignored) disorder in proteins. The need for this series is justified by the observation that despite the fact that protein intrinsic disorder is widely accepted by the scientific community, there are still numerous instances when appreciation of this phenomenon is absent. This results in the avalanche of research papers which are talking about intrinsically disordered proteins (or hybrid proteins with ordered and disordered regions) not recognizing that they are talking about such proteins. Articles in the "Unreported Intrinsic Disorder in Proteins" series provide a fast fix for some of the recent noticeable disorder overlooks.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer Research Institute; Morsani College of Medicine, University of South Florida; Tampa, FL USA; Biology Department; Faculty of Science; King Abdulaziz University; Jeddah, Kingdom of Saudi Arabia; Laboratory of Structural Dynamics; Stability and Folding of Proteins; Institute of Cytology; Russian Academy of Sciences; St. Petersburg, Russia
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36
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Intrinsically disordered cytoplasmic domains of two cytokine receptors mediate conserved interactions with membranes. Biochem J 2015; 468:495-506. [PMID: 25846210 DOI: 10.1042/bj20141243] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 04/07/2015] [Indexed: 01/29/2023]
Abstract
Class 1 cytokine receptors regulate essential biological processes through complex intracellular signalling networks. However, the structural platform for understanding their functions is currently incomplete as structure-function studies of the intracellular domains (ICDs) are critically lacking. The present study provides the first comprehensive structural characterization of any cytokine receptor ICD and demonstrates that the human prolactin (PRL) receptor (PRLR) and growth hormone receptor (GHR) ICDs are intrinsically disordered throughout their entire lengths. We show that they interact specifically with hallmark lipids of the inner plasma membrane leaflet through conserved motifs resembling immuno receptor tyrosine-based activation motifs (ITAMs). However, contrary to the observations made for ITAMs, lipid association of the PRLR and GHR ICDs was shown to be unaccompanied by changes in transient secondary structure and independent of tyrosine phosphorylation. The results of the present study provide a new structural platform for studying class 1 cytokine receptors and may implicate the membrane as an active component regulating intracellular signalling.
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The proline-rich region of 18.5 kDa myelin basic protein binds to the SH3-domain of Fyn tyrosine kinase with the aid of an upstream segment to form a dynamic complex in vitro. Biosci Rep 2014; 34:e00157. [PMID: 25343306 PMCID: PMC4266924 DOI: 10.1042/bsr20140149] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The intrinsically disordered 18.5 kDa classic isoform of MBP (myelin basic protein) interacts with Fyn kinase during oligodendrocyte development and myelination. It does so primarily via a central proline-rich SH3 (Src homology 3) ligand (T92–R104, murine 18.5 kDa MBP sequence numbering) that is part of a molecular switch due to its high degree of conservation and modification by MAP (mitogen-activated protein) and other kinases, especially at residues T92 and T95. Here, we show using co-transfection experiments of an early developmental oligodendroglial cell line (N19) that an MBP segment upstream of the primary ligand is involved in MBP–Fyn–SH3 association in cellula. Using solution NMR spectroscopy in vitro, we define this segment to comprise MBP residues (T62–L68), and demonstrate further that residues (V83–P93) are the predominant SH3-target, assessed by the degree of chemical shift change upon titration. We show by chemical shift index analysis that there is no formation of local poly-proline type II structure in the proline-rich segment upon binding, and by NOE (nuclear Overhauser effect) and relaxation measurements that MBP remains dynamic even while complexed with Fyn–SH3. The association is a new example first of a non-canonical SH3-domain interaction and second of a fuzzy MBP complex. MBP interacts with Fyn kinase during oligodendrocyte development and myelination. We show that there is no binding-induced PPII formation in the primary ligand segment, and that a region upstream is required for in vitro interaction.
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Sigalov AB. Unusual biophysics of immune signaling-related intrinsically disordered proteins. SELF NONSELF 2014; 1:271-281. [PMID: 21487502 DOI: 10.4161/self.1.4.13641] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 09/15/2010] [Accepted: 09/15/2010] [Indexed: 11/19/2022]
Abstract
Intrinsically disordered (ID) regions, the regions that lack a well-defined three-dimensional structure under physiological conditions, are preferentially located in the cytoplasmic segments of plasma membrane proteins, many of which are known to be involved in cell signaling. This is in line with our studies that demonstrated that cytoplasmic domains of signaling subunits of immune receptors, including those of ζ, CD3ε, CD3δ and CD3γ chains of T cell receptor, Igα and Igβ chains of B cell receptor as well as the Fc receptor γ chain represent a novel class of ID proteins (IDPs). The domains all have one or more copies of an immunoreceptor tyrosine-based activation motif, tyrosine residues of which are phosphorylated upon receptor engagement in an early and obligatory event in the signaling cascade. Our studies of these IDPs revealed several unusual biophysical phenomena, including (1) the specific dimerization of disordered protein molecules, (2) the fast and slow dimerization equilibrium, depending on the protein, (3) no disorder-to-order transition and the lack of significant chemical shift and peak intensity changes upon dimerization or interaction with a well-folded partner protein and (4) the dual mode of binding to model membranes (with and without folding), depending on the lipid bilayer stability. Here, I highlight several of these studies that not only facilitate a rethinking process of the fundamental paradigms in protein biophysics but also open new perspectives on the molecular mechanisms involved in receptor signaling.
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Van Roey K, Uyar B, Weatheritt RJ, Dinkel H, Seiler M, Budd A, Gibson TJ, Davey NE. Short Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell Regulation. Chem Rev 2014; 114:6733-78. [DOI: 10.1021/cr400585q] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Kim Van Roey
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Bora Uyar
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Robert J. Weatheritt
- MRC
Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Holger Dinkel
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Markus Seiler
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Aidan Budd
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Toby J. Gibson
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Norman E. Davey
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department
of Physiology, University of California, San Francisco, San Francisco, California 94143, United States
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Rosenlöw J, Isaksson L, Mayzel M, Lengqvist J, Orekhov VY. Tyrosine phosphorylation within the intrinsically disordered cytosolic domains of the B-cell receptor: an NMR-based structural analysis. PLoS One 2014; 9:e96199. [PMID: 24769851 PMCID: PMC4000212 DOI: 10.1371/journal.pone.0096199] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 04/04/2014] [Indexed: 11/19/2022] Open
Abstract
Intrinsically disordered proteins are found extensively in cell signaling pathways where they often are targets of posttranslational modifications e.g. phosphorylation. Such modifications can sometimes induce or disrupt secondary structure elements present in the modified protein. CD79a and CD79b are membrane-spanning, signal-transducing components of the B-cell receptor. The cytosolic domains of these proteins are intrinsically disordered and each has an immunoreceptor tyrosine-based activation motif (ITAM). When an antigen binds to the receptor, conserved tyrosines located in the ITAMs are phosphorylated which initiate further downstream signaling. Here we use NMR spectroscopy to examine the secondary structure propensity of the cytosolic domains of CD79a and CD79b in vitro before and after phosphorylation. The phosphorylation patterns are identified through analysis of changes of backbone chemical shifts found for the affected tyrosines and neighboring residues. The number of the phosphorylated sites is confirmed by mass spectrometry. The secondary structure propensities are calculated using the method of intrinsic referencing, where the reference random coil chemical shifts are measured for the same protein under denaturing conditions. Our analysis revealed that CD79a and CD79b both have an overall propensity for α-helical structure that is greatest in the C-terminal region of the ITAM. Phosphorylation of CD79a caused a decrease in helical propensity in the C-terminal ITAM region. For CD79b, the opposite was observed and phosphorylation resulted in an increase of helical propensity in the C-terminal part.
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Affiliation(s)
- Joakim Rosenlöw
- The Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden
| | - Linnéa Isaksson
- The Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden
| | - Maxim Mayzel
- The Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden
| | - Johan Lengqvist
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Li Y, Yin Y, Mariuzza RA. Structural and biophysical insights into the role of CD4 and CD8 in T cell activation. Front Immunol 2013; 4:206. [PMID: 23885256 PMCID: PMC3717711 DOI: 10.3389/fimmu.2013.00206] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 07/08/2013] [Indexed: 11/19/2022] Open
Abstract
T cell receptors (TCRs) recognize peptides presented by MHC molecules (pMHC) on an antigen-presenting cell (APC) to discriminate foreign from self-antigens and initiate adaptive immune responses. In addition, T cell activation generally requires binding of this same pMHC to a CD4 or CD8 co-receptor, resulting in assembly of a TCR–pMHC–CD4 or TCR–pMHC–CD8 complex and recruitment of Lck via its association with the co-receptor. Here we review structural and biophysical studies of CD4 and CD8 interactions with MHC molecules and TCR–pMHC complexes. Crystal structures have been determined of CD8αα and CD8αβ in complex with MHC class I, of CD4 bound to MHC class II, and of a complete TCR–pMHC–CD4 ternary complex. Additionally, the binding of these co-receptors to pMHC and TCR–pMHC ligands has been investigated both in solution and in situ at the T cell–APC interface. Together, these studies have provided key insights into the role of CD4 and CD8 in T cell activation, and into how these co-receptors focus TCR on MHC to guide TCR docking on pMHC during thymic T cell selection.
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Affiliation(s)
- Yili Li
- W. M. Keck Laboratory for Structural Biology, Institute for Bioscience and Biotechnology Research, University of Maryland , Rockville, MD , USA ; Department of Cell Biology and Molecular Genetics, University of Maryland , College Park, MD , USA
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Popovic M, Zlatev V, Hodnik V, Anderluh G, Felli IC, Pongor S, Pintar A. Flexibility of the PDZ-binding motif in the micelle-bound form of Jagged-1 cytoplasmic tail. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1818:1706-16. [PMID: 22465068 DOI: 10.1016/j.bbamem.2012.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 01/07/2023]
Abstract
Human Jagged-1, one of the ligands of Notch receptors, is a transmembrane protein composed of a large extracellular region and a 125-residue cytoplasmic tail which bears a C-terminal PDZ recognition motif. To investigate the interaction between Jagged-1 cytoplasmic tail and the inner leaflet of the plasma membrane we determined, by solution NMR, the secondary structure and dynamics of the recombinant protein corresponding to the intracellular region of Jagged-1, J1_tmic, bound to negatively charged lysophospholipid micelles. NMR showed that the PDZ binding motif is preceded by four alpha-helical segments and that, despite the extensive interaction between J1_tmic and the micelle, the PDZ binding motif remains highly flexible. Binding of J1_tmic to negatively charged, but not to zwitterionic vesicles, was confirmed by surface plasmon resonance. To study the PDZ binding region in more detail, we prepared a peptide corresponding to the last 24 residues of Jagged-1, J1C24, and different phosphorylated variants of it. J1C24 displays a marked helical propensity and undergoes a coil-helix transition in the presence of negatively charged, but not zwitterionic, lysophospholipid micelles. Phosphorylation at different positions drastically decreases the helical propensity of the peptides and abolishes the coil-helix transition triggered by lysophospholipid micelles. We propose that phosphorylation of residues upstream of the PDZ binding motif may shift the equilibrium from an ordered, membrane-bound, interfacial form of Jagged-1 C-terminal region to a more disordered form with an increased accessibility of the PDZ recognition motif, thus playing an indirect role in the interaction between Jagged-1 and the PDZ-containing target protein.
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Affiliation(s)
- Matija Popovic
- International Centre for Genetic Engineering and Biotechnology, AREA Science Park Padriciano 99, 1-34149 Trieste, Italy
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43
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Uversky VN. A decade and a half of protein intrinsic disorder: biology still waits for physics. Protein Sci 2013; 22:693-724. [PMID: 23553817 PMCID: PMC3690711 DOI: 10.1002/pro.2261] [Citation(s) in RCA: 363] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 03/23/2013] [Accepted: 03/25/2013] [Indexed: 12/28/2022]
Abstract
The abundant existence of proteins and regions that possess specific functions without being uniquely folded into unique 3D structures has become accepted by a significant number of protein scientists. Sequences of these intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) are characterized by a number of specific features, such as low overall hydrophobicity and high net charge which makes these proteins predictable. IDPs/IDPRs possess large hydrodynamic volumes, low contents of ordered secondary structure, and are characterized by high structural heterogeneity. They are very flexible, but some may undergo disorder to order transitions in the presence of natural ligands. The degree of these structural rearrangements varies over a very wide range. IDPs/IDPRs are tightly controlled under the normal conditions and have numerous specific functions that complement functions of ordered proteins and domains. When lacking proper control, they have multiple roles in pathogenesis of various human diseases. Gaining structural and functional information about these proteins is a challenge, since they do not typically "freeze" while their "pictures are taken." However, despite or perhaps because of the experimental challenges, these fuzzy objects with fuzzy structures and fuzzy functions are among the most interesting targets for modern protein research. This review briefly summarizes some of the recent advances in this exciting field and considers some of the basic lessons learned from the analysis of physics, chemistry, and biology of IDPs.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, USA.
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Isaksson L, Mayzel M, Saline M, Pedersen A, Rosenlöw J, Brutscher B, Karlsson BG, Orekhov VY. Highly efficient NMR assignment of intrinsically disordered proteins: application to B- and T cell receptor domains. PLoS One 2013; 8:e62947. [PMID: 23667548 PMCID: PMC3647075 DOI: 10.1371/journal.pone.0062947] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 03/26/2013] [Indexed: 01/27/2023] Open
Abstract
We present an integrated approach for efficient characterization of intrinsically disordered proteins. Batch cell-free expression, fast data acquisition, automated analysis, and statistical validation with data resampling have been combined for achieving cost-effective protein expression, and rapid automated backbone assignment. The new methodology is applied for characterization of five cytosolic domains from T- and B-cell receptors in solution.
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MESH Headings
- Amino Acid Motifs
- Cytosol/metabolism
- Humans
- Intracellular Space/metabolism
- Intrinsically Disordered Proteins/chemistry
- Intrinsically Disordered Proteins/metabolism
- Ligands
- Nuclear Magnetic Resonance, Biomolecular/methods
- Protein Structure, Tertiary
- Receptors, Antigen, B-Cell/chemistry
- Receptors, Antigen, B-Cell/metabolism
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/metabolism
- Signal Transduction
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Affiliation(s)
- Linnéa Isaksson
- Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden
| | - Maxim Mayzel
- Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden
| | - Maria Saline
- Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden
| | - Anders Pedersen
- Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden
| | - Joakim Rosenlöw
- Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden
| | - Bernhard Brutscher
- Institut de Biologie Structurale, Université Grenoble CEA CNRS, Grenoble, France
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45
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Kuhns MS, Badgandi HB. Piecing together the family portrait of TCR-CD3 complexes. Immunol Rev 2013; 250:120-43. [PMID: 23046126 DOI: 10.1111/imr.12000] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The pre-T-cell receptor (TCR)-, αβTCR-, and γδTCR-CD3 complexes are members of a family of modular biosensors that are responsible for driving T-cell development, activation, and effector functions. They inform essential checkpoint decisions by relaying key information from their ligand-binding modules (TCRs) to their signaling modules (CD3γε + CD3δε and CD3ζζ) and on to the intracellular signaling apparatus. Their actions shape the T-cell repertoire, as well as T-cell-mediated immunity; yet, the mechanisms that underlie their activity remain an enigma. As with any molecular machine, understanding how they function depends upon understanding how their parts fit and work together. In the 30 years since the initial biochemical and genetic characterizations of the αβTCR, the structure and function of the individual components of these family members have been extensively characterized. Cumulatively, this information has allowed us to piece together a portrait of the αβTCR-CD3 complex and outline the form of the remaining family members. Here we review the known structural and functional characteristics of the components of these TCR-CD3 complex family members. We then discuss how these data have informed our understanding of the architecture of the αβTCR-CD3 complex as well as their implications for the other family members. The intent is to provide a framework for considering: (i) how these thematically similar complexes diverge to execute their specific functions and (ii) how our knowledge of the form and function of these distinct family members can cross-inform our understanding of the other family members.
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Affiliation(s)
- Michael S Kuhns
- Department of Immunobiology, The University of Arizona College of Medicine, Tucson, USA.
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46
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Busman-Sahay K, Drake L, Sitaram A, Marks M, Drake JR. Cis and trans regulatory mechanisms control AP2-mediated B cell receptor endocytosis via select tyrosine-based motifs. PLoS One 2013; 8:e54938. [PMID: 23372794 PMCID: PMC3553015 DOI: 10.1371/journal.pone.0054938] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 12/18/2012] [Indexed: 12/20/2022] Open
Abstract
Following antigen recognition, B cell receptor (BCR)-mediated endocytosis is the first step of antigen processing and presentation to CD4+ T cells, a crucial component of the initiation and control of the humoral immune response. Despite this, the molecular mechanism of BCR internalization is poorly understood. Recently, studies of activated B cell-like diffuse large B cell lymphoma (ABC DLBCL) have shown that mutations within the BCR subunit CD79b leads to increased BCR surface expression, suggesting that CD79b may control BCR internalization. Adaptor protein 2 (AP2) is the major mediator of receptor endocytosis via clathrin-coated pits. The BCR contains five putative AP2-binding YxxØ motifs, including four that are present within two immunoreceptor tyrosine-based activation motifs (ITAMs). Using a combination of in vitro and in situ approaches, we establish that the sole mediator of AP2-dependent BCR internalization is the membrane proximal ITAM YxxØ motif in CD79b, which is a major target of mutation in ABC DLBCL. In addition, we establish that BCR internalization can be regulated at a minimum of two different levels: regulation of YxxØ AP2 binding in cis by downstream ITAM-embedded DCSM and QTAT regulatory elements and regulation in trans by the partner cytoplasmic domain of the CD79 heterodimer. Beyond establishing the basic rules governing BCR internalization, these results illustrate an underappreciated role for ITAM residues in controlling clathrin-dependent endocytosis and highlight the complex mechanisms that control the activity of AP2 binding motifs in this receptor system.
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Affiliation(s)
- Kathleen Busman-Sahay
- Center for Immunology and Microbial Disease, Albany Medical College, Albany, New York, United States of America
| | - Lisa Drake
- Center for Immunology and Microbial Disease, Albany Medical College, Albany, New York, United States of America
| | - Anand Sitaram
- Departments of Pathology and Laboratory Medicine and Physiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Michael Marks
- Departments of Pathology and Laboratory Medicine and Physiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - James R. Drake
- Center for Immunology and Microbial Disease, Albany Medical College, Albany, New York, United States of America
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47
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Tantos A, Szabo B, Lang A, Varga Z, Tsylonok M, Bokor M, Verebelyi T, Kamasa P, Tompa K, Perczel A, Buday L, Lee SH, Choo Y, Han KH, Tompa P. Multiple fuzzy interactions in the moonlighting function of thymosin-β4. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e26204. [PMID: 28516021 PMCID: PMC5424802 DOI: 10.4161/idp.26204] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 08/15/2013] [Accepted: 08/18/2013] [Indexed: 12/19/2022]
Abstract
Thymosine β4 (Tß4) is a 43 amino acid long intrinsically disordered protein (IDP), which was initially identified as an actin-binding and sequestering molecule. Later it was described to have multiple other functions, such as regulation of endothelial cell differentiation, blood vessel formation, wound repair, cardiac cell migration, and survival.1 The various functions of Tβ4 are mediated by interactions with distinct and structurally unrelated partners, such as PINCH, ILK, and stabilin-2, besides the originally identified G-actin. Although the cellular readout of these interactions and the formation of these complexes have been thoroughly described, no attempt was made to study these interactions in detail, and to elucidate the thermodynamic, kinetic, and structural underpinning of this range of moonlighting functions. Because Tβ4 is mostly disordered, and its 4 described partners are structurally unrelated (the CTD of stabilin-2 is actually fully disordered), it occurred to us that this system might be ideal to characterize the structural adaptability and ensuing moonlighting functions of IDPs. Unexpectedly, we found that Tβ4 engages in multiple weak, transient, and fuzzy interactions, i.e., it is capable of mediating distinct yet specific interactions without adapting stable folded structures.
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Affiliation(s)
- Agnes Tantos
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest, Hungary
| | - Beata Szabo
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest, Hungary
| | - Andras Lang
- Eötvös Loránd University; Institute of Chemistry; Budapest, Hungary
| | - Zoltan Varga
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest, Hungary
| | - Maksym Tsylonok
- VIB Department of Structural Biology; Vrije Universiteit Brussel; Brussels, Belgium
| | - Monika Bokor
- Institute for Solid State Physics and Optics; Wigner Research Centre for Physics of the Hungarian Academy of Sciences; Budapest, Hungary
| | - Tamas Verebelyi
- Institute for Solid State Physics and Optics; Wigner Research Centre for Physics of the Hungarian Academy of Sciences; Budapest, Hungary
| | - Pawel Kamasa
- Institute for Solid State Physics and Optics; Wigner Research Centre for Physics of the Hungarian Academy of Sciences; Budapest, Hungary
| | - Kalman Tompa
- Institute for Solid State Physics and Optics; Wigner Research Centre for Physics of the Hungarian Academy of Sciences; Budapest, Hungary
| | - Andras Perczel
- Eötvös Loránd University; Institute of Chemistry; Budapest, Hungary
| | - Laszlo Buday
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest, Hungary
| | - Si Hyung Lee
- Division of Biosystems Research; Korea Research Institute of Bioscience and Biotechnology; Daejeon, Republic of Korea
| | - Yejin Choo
- Division of Biosystems Research; Korea Research Institute of Bioscience and Biotechnology; Daejeon, Republic of Korea
| | - Kyou-Hoon Han
- Division of Biosystems Research; Korea Research Institute of Bioscience and Biotechnology; Daejeon, Republic of Korea
- Department of Bioinformatics; University of Science and Technology; Daejeon, Republic of Korea
| | - Peter Tompa
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest, Hungary
- VIB Department of Structural Biology; Vrije Universiteit Brussel; Brussels, Belgium
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48
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Gagnon E, Schubert DA, Gordo S, Chu HH, Wucherpfennig KW. Local changes in lipid environment of TCR microclusters regulate membrane binding by the CD3ε cytoplasmic domain. J Exp Med 2012; 209:2423-39. [PMID: 23166358 PMCID: PMC3526357 DOI: 10.1084/jem.20120790] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 10/05/2012] [Indexed: 12/19/2022] Open
Abstract
The CD3ε and ζ cytoplasmic domains of the T cell receptor bind to the inner leaflet of the plasma membrane (PM), and a previous nuclear magnetic resonance structure showed that both tyrosines of the CD3ε immunoreceptor tyrosine-based activation motif partition into the bilayer. Electrostatic interactions between acidic phospholipids and clusters of basic CD3ε residues were previously shown to be essential for CD3ε and ζ membrane binding. Phosphatidylserine (PS) is the most abundant negatively charged lipid on the inner leaflet of the PM and makes a major contribution to membrane binding by the CD3ε cytoplasmic domain. Here, we show that TCR triggering by peptide--MHC complexes induces dissociation of the CD3ε cytoplasmic domain from the plasma membrane. Release of the CD3ε cytoplasmic domain from the membrane is accompanied by a substantial focal reduction in negative charge and available PS in TCR microclusters. These changes in the lipid composition of TCR microclusters even occur when TCR signaling is blocked with a Src kinase inhibitor. Local changes in the lipid composition of TCR microclusters thus render the CD3ε cytoplasmic domain accessible during early stages of T cell activation.
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Affiliation(s)
- Etienne Gagnon
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
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49
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Shi X, Bi Y, Yang W, Guo X, Jiang Y, Wan C, Li L, Bai Y, Guo J, Wang Y, Chen X, Wu B, Sun H, Liu W, Wang J, Xu C. Ca2+ regulates T-cell receptor activation by modulating the charge property of lipids. Nature 2012. [DOI: 10.1038/nature11699] [Citation(s) in RCA: 172] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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50
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Abstract
Signal transduction by cell surface receptors in the context of heterogeneous and variable cellular environments plays a pivotal role in regulating many biological processes, including development, activation, and homeostasis of the immune system. In some receptors, extracellular ligand-binding and intracellular signaling domains are located on the same protein chain (single-chain receptors), while in the so-called multichain immune recognition receptors (MIRRs), recognition and signaling functions are separated between different protein chains. Why did nature separate recognition and signaling functions for MIRRs, thereby increasing the risk of malfunction and potential attack by pathogens? The risk is real: in order to escape the immune response, viruses are able to disrupt functional coupling between recognition and signaling aspects of MIRR machinery. Intrinsic disorder of intracellular signal-generating regions of MIRRs adds further intrigue to the story. Why did nature select protein disorder for MIRRs to translate recognition of distinct antigens into appropriate activation signals that would induce specific functional outcomes? Here, I suggest that nature takes the risks associated with intrareceptor separation of functions as well as with the chaos and indeterminacy of protein disorder in exchange for providing diversity and variability of signal transduction. Not only does this phenomenon serve as the molecular basis for the development and evolution of the immune and other complex biological systems, but it fits closely to Darwinian evolutionary biology.
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