1
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Structural Dynamics of the Lipid Antigen-Binding Site of CD1d Protein. Biomolecules 2020; 10:biom10040532. [PMID: 32244759 PMCID: PMC7226365 DOI: 10.3390/biom10040532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/30/2020] [Accepted: 03/30/2020] [Indexed: 12/26/2022] Open
Abstract
CD1 molecules present lipid antigens to T-cells in early stages of immune responses. Whereas CD1‒lipid‒T-cell receptors interactions are reasonably understood, molecular details on initial trafficking and loading of lipids onto CD1 proteins are less complete. We present a molecular dynamics (MD) study of human CD1d, the isotype that activates iNKT cells. MD simulations and calculations of properties and Poisson-Boltzmann electrostatic potentials were used to explore the dynamics of the antigen-binding domain of the apo-form, CD1d complexes with three lipid–antigens that activate iNKT cells and CD1d complex with GM2AP, a protein that assists lipid loading onto CD1 molecules in endosomes/lysosomes. The study was done at pH 7 and 4.5, values representative of strongly acidic environments in endosomal compartments. Our findings revealed dynamic features of the entrance to the hydrophobic channels of CD1d modulated by two α helices with sensitivity to the type of lipid. We also found lipid- and pH-dependent dynamic changes in three exposed tryptophans unique to CD1d among the five human CD1 isotypes. On the basis of modelled structures, our data also revealed external effects produced by the helper protein GM2AP only when it interacts in its open form, thus suggesting that the own assistant protein also adapts conformation to association with CD1d.
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2
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Cuevas-Zuviría B, Mínguez-Toral M, Díaz-Perales A, Garrido-Arandia M, Pacios LF. Dynamic plasticity of the lipid antigen-binding site of CD1d is crucially favoured by acidic pH and helper proteins. Sci Rep 2020; 10:5714. [PMID: 32235847 PMCID: PMC7109084 DOI: 10.1038/s41598-020-62833-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/20/2020] [Indexed: 11/16/2022] Open
Abstract
CD1 molecules present lipid antigens for recognition by T-cell receptors (TCRs). Although a reasonably detailed picture of the CD1-lipid-TCR interaction exists, the initial steps regarding lipid loading onto and exchange between CD1 proteins remain elusive. The hydrophobic nature of lipids and the fact that CD1 molecules are unable to extract lipids from membranes raise the need for the assistance of helper proteins in lipid trafficking. However, the experimental study of this traffic in the endosomal compartments at which it occurs is so challenging that computational studies can help provide mechanistic insight into the associated processes. Here we present a multifaceted computational approach to obtain dynamic structural data on the human CD1d isotype. Conformational dynamics analysis shows an intrinsic flexibility associated with the protein architecture. Electrostatic properties together with molecular dynamics results for CD1d complexes with several lipids and helper proteins unravel the high dynamic plasticity of the antigen-binding site that is crucially favoured by acidic pH and the presence of helper proteins.
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Affiliation(s)
- Bruno Cuevas-Zuviría
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Marina Mínguez-Toral
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Araceli Díaz-Perales
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas (ETSIAAB), Universidad Politécnica de Madrid (UPM), 28040, Madrid, Spain
| | - María Garrido-Arandia
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Luis F Pacios
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain.
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas (ETSIAAB), Universidad Politécnica de Madrid (UPM), 28040, Madrid, Spain.
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3
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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4
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Teyton L. Role of lipid transfer proteins in loading CD1 antigen-presenting molecules. J Lipid Res 2018; 59:1367-1373. [PMID: 29559523 PMCID: PMC6071766 DOI: 10.1194/jlr.r083212] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 03/18/2018] [Indexed: 11/20/2022] Open
Abstract
Research to connect lipids with immunology is growing, but details about the specific roles of lipid transfer proteins (LTPs) in antigen presentation remain unclear. A single class of major histocompatibility class-like molecules, called CD1 molecules, can present lipids and glycolipids to the immune system. These molecules all have a common hydrophobic antigen-binding groove. The loading of this groove with various lipids throughout the life of a CD1 molecule defines the immune recognition of lipids by T cells. At each location of residence, CD1 molecules are exposed to particular physicochemical conditions, particular collections of lipids, and unique combinations of LTPs that will define which lipids bind to CD1 and which do not. The lipid transfer machinery that is used by CD1 molecules is entirely hijacked from the normal synthetic and catalytic pathways of lipids. The precise determinants that regulate the presentation of certain lipids over others with respect to chemistry, solubility, and abundance are still poorly defined and require investigation to allow the use of lipids as regular antigenic targets of immunotherapy and vaccine.
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Affiliation(s)
- Luc Teyton
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037
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5
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Mason S, Chen BY, Jagodzinski F. Exploring Protein Cavities through Rigidity Analysis. Molecules 2018; 23:molecules23020351. [PMID: 29414909 PMCID: PMC6017401 DOI: 10.3390/molecules23020351] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 01/25/2018] [Accepted: 01/31/2018] [Indexed: 12/23/2022] Open
Abstract
The geometry of cavities in the surfaces of proteins facilitates a variety of biochemical functions. To better understand the biochemical nature of protein cavities, the shape, size, chemical properties, and evolutionary nature of functional and nonfunctional surface cavities have been exhaustively surveyed in protein structures. The rigidity of surface cavities, however, is not immediately available as a characteristic of structure data, and is thus more difficult to examine. Using rigidity analysis for assessing and analyzing molecular rigidity, this paper performs the first survey of the relationships between cavity properties, such as size and residue content, and how they correspond to cavity rigidity. Our survey measured a variety of rigidity metrics on 120,323 cavities from 12,785 sequentially non-redundant protein chains. We used VASP-E, a volume-based algorithm for analyzing cavity geometry. Our results suggest that rigidity properties of protein cavities are dependent on cavity surface area.
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Affiliation(s)
- Stephanie Mason
- Department of Computer Science, Western Washington University, 516 High Street, Bellingham, WA 98225, USA.
| | - Brian Y Chen
- Department of Computer Science and Engineering, Lehigh University, 19 Memorial Drive West, Bethlehem, PA 18015, USA.
| | - Filip Jagodzinski
- Department of Computer Science, Western Washington University, 516 High Street, Bellingham, WA 98225, USA.
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6
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Shin C, Kim M, Han JA, Choi B, Hwang D, Do Y, Yun JH. Human periodontal ligament stem cells suppress T-cell proliferation via down-regulation of non-classical major histocompatibility complex-like glycoprotein CD1b on dendritic cells. J Periodontal Res 2016; 52:135-146. [PMID: 27021598 DOI: 10.1111/jre.12378] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND OBJECTIVE Periodontal ligament stem cells (PDLSCs) from the periodontal ligament tissue were recently identified as mesenchymal stem cells (MSCs). The capabilities of PDLSCs in periodontal tissue or bone regeneration have been reported, but their immunomodulatory role in T-cell immune responses via dendritic cells (DCs), known as the most potent antigen-presenting cell, has not been studied. The aim of this study is to understand the immunological function of homogeneous human STRO-1+ CD146+ PDLSCs in DC-mediated T-cell immune responses to modulate the periodontal disease process. MATERIAL AND METHODS We utilized highly purified (> 95%) human STRO-1+ CD146+ PDLSCs and human bone marrow mesenchymal stem cells (BMSCs). Each stem cell was co-cultured with human monocyte-derived DCs in the presence of lipopolysaccharide isolated from Porphyromonas gingivalis, a major pathogenic bacterium responsible for periodontal disease, in vitro to examine the immunological effect of each stem cell on DCs and DC-mediated T-cell proliferation. RESULTS We discovered that STRO-1+ CD146+ PDLSCs, as well as BMSCs, significantly decreased the level of non-classical major histocompatibility complex glycoprotein CD1b on DCs, resulting in defective T-cell proliferation, whereas most human leukocyte antigens and the co-stimulatory molecules CD80 and CD86 in/on DCs were not significantly affected by the presence of BMSCs or STRO-1+ CD146+ PDLSCs. CONCLUSIONS This study unveiled an immunomodulatory role of STRO-1+ CD146+ PDLSCs in negatively regulating DC-mediated T-cell immune responses, demonstrating their potential to be utilized in promising new stem cell therapies.
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Affiliation(s)
- C Shin
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - M Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Korea
| | - J-A Han
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - B Choi
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - D Hwang
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Korea.,Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Korea
| | - Y Do
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - J-H Yun
- Department of Periodontology, School of Dentistry and Institute of Oral Bioscience, Chonbuk National University, Jeonju, Korea.,Research Institute of Clinical Medicine of Chonbuk National University-Biomedical Research Institute of Chonbuk National University Hospital, Jeonju, Korea
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7
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Ortiz-Suarez M, Bond P. The Structural Basis for Lipid and Endotoxin Binding in RP105-MD-1, and Consequences for Regulation of Host Lipopolysaccharide Sensitivity. Structure 2016; 24:200-211. [DOI: 10.1016/j.str.2015.10.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 09/09/2015] [Accepted: 10/12/2015] [Indexed: 12/22/2022]
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8
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Abstract
Over two decades ago, it was discovered that the human T-cell repertoire contains T cells that do not recognize peptide antigens in the context of MHC molecules but instead respond to lipid antigens presented by CD1 antigen-presenting molecules. The ability of T cells to 'see' lipid antigens bound to CD1 enables these lymphocytes to sense changes in the lipid composition of cells and tissues as a result of infections, inflammation, or malignancies. Although foreign lipid antigens have been shown to function as antigens for CD1-restricted T cells, many CD1-restricted T cells do not require foreign antigens for activation but instead can be activated by self-lipids presented by CD1. This review highlights recent developments in the field, including the identification of common mammalian lipids that function as autoantigens for αβ and γδ T cells, a novel mode of T-cell activation whereby CD1a itself rather than lipids serves as the autoantigen, and various mechanisms by which the activation of CD1-autoreactive T cells is regulated. As CD1 can induce T-cell effector functions in the absence of foreign antigens, multiple mechanisms are in place to regulate this self-reactivity, and stimulatory CD1-lipid complexes appear to be tightly controlled in space and time.
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9
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Malinina L, Simanshu DK, Zhai X, Samygina VR, Kamlekar R, Kenoth R, Ochoa-Lizarralde B, Malakhova ML, Molotkovsky JG, Patel DJ, Brown RE. Sphingolipid transfer proteins defined by the GLTP-fold. Q Rev Biophys 2015; 48:281-322. [PMID: 25797198 PMCID: PMC4691851 DOI: 10.1017/s003358351400016x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Glycolipid transfer proteins (GLTPs) originally were identified as small (~24 kDa), soluble, amphitropic proteins that specifically accelerate the intermembrane transfer of glycolipids. GLTPs and related homologs now are known to adopt a unique, helically dominated, two-layer 'sandwich' architecture defined as the GLTP-fold that provides the structural underpinning for the eukaryotic GLTP superfamily. Recent advances now provide exquisite insights into structural features responsible for lipid headgroup selectivity as well as the adaptability of the hydrophobic compartment for accommodating hydrocarbon chains of differing length and unsaturation. A new understanding of the structural versatility and evolutionary premium placed on the GLTP motif has emerged. Human GLTP-motifs have evolved to function not only as glucosylceramide binding/transferring domains for phosphoinositol 4-phosphate adaptor protein-2 during glycosphingolipid biosynthesis but also as selective binding/transfer proteins for ceramide-1-phosphate. The latter, known as ceramide-1-phosphate transfer protein, recently has been shown to form GLTP-fold while critically regulating Group-IV cytoplasmic phospholipase A2 activity and pro-inflammatory eicosanoid production.
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Affiliation(s)
- Lucy Malinina
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
- Structural Biology Unit, CICbioGUNE, Technology Park of Bizkaia, 48160 Derio-Bilbao, Spain
| | - Dhirendra K. Simanshu
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Xiuhong Zhai
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Valeria R. Samygina
- Structural Biology Unit, CICbioGUNE, Technology Park of Bizkaia, 48160 Derio-Bilbao, Spain
| | | | - Roopa Kenoth
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Borja Ochoa-Lizarralde
- Structural Biology Unit, CICbioGUNE, Technology Park of Bizkaia, 48160 Derio-Bilbao, Spain
| | | | - Julian G. Molotkovsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dinshaw J. Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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10
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Siddiqui S, Visvabharathy L, Wang CR. Role of Group 1 CD1-Restricted T Cells in Infectious Disease. Front Immunol 2015; 6:337. [PMID: 26175733 PMCID: PMC4484338 DOI: 10.3389/fimmu.2015.00337] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/16/2015] [Indexed: 12/12/2022] Open
Abstract
The evolutionarily conserved CD1 family of antigen-presenting molecules presents lipid antigens rather than peptide antigens to T cells. CD1 molecules, unlike classical MHC molecules, display limited polymorphism, making CD1-restricted lipid antigens attractive vaccine targets that could be recognized in a genetically diverse human population. Group 1 CD1 (CD1a, CD1b, and CD1c)-restricted T cells have been implicated to play critical roles in a variety of autoimmune and infectious diseases. In this review, we summarize current knowledge and recent discoveries on the development of group 1 CD1-restricted T cells and their function in different infection models. In particular, we focus on (1) newly identified microbial and self-lipid antigens, (2) kinetics, phenotype, and unique properties of group 1 CD1-restricted T cells during infection, and (3) the similarities of group 1 CD1-restricted T cells to the closely related group 2 CD1-restricted T cells.
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Affiliation(s)
- Sarah Siddiqui
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine , Chicago, IL , USA
| | - Lavanya Visvabharathy
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine , Chicago, IL , USA
| | - Chyung-Ru Wang
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine , Chicago, IL , USA
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11
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Laurent X, Renault N, Farce A, Chavatte P, Hénon E. Relationships between Th1 or Th2 iNKT cell activity and structures of CD1d-antigen complexes: meta-analysis of CD1d-glycolipids dynamics simulations. PLoS Comput Biol 2014; 10:e1003902. [PMID: 25376021 PMCID: PMC4222593 DOI: 10.1371/journal.pcbi.1003902] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 08/22/2014] [Indexed: 01/17/2023] Open
Abstract
A number of potentially bioactive molecules can be found in nature. In particular, marine organisms are a valuable source of bioactive compounds. The activity of an α-galactosylceramide was first discovered in 1993 via screening of a Japanese marine sponge (Agelas mauritanius). Very rapidly, a synthetic glycololipid analogue of this natural molecule was discovered, called KRN7000. Associated with the CD1d protein, this α-galactosylceramide 1 (KRN7000) interacts with the T-cell antigen receptor to form a ternary complex that yields T helper (Th) 1 and Th2 responses with opposing effects. In our work, we carried out molecular dynamics simulations (11.5 µs in total) involving eight different ligands (conducted in triplicate) in an effort to find out correlation at the molecular level, if any, between chemical modulation of 1 and the orientation of the known biological response, Th1 or Th2. Comparative investigations of human versus mouse and Th1 versus Th2 data have been carried out. A large set of analysis tools was employed including free energy landscapes. One major result is the identification of a specific conformational state of the sugar polar head, which could be correlated, in the present study, to the biological Th2 biased response. These theoretical tools provide a structural basis for predicting the very different dynamical behaviors of α-glycosphingolipids in CD1d and might aid in the future design of new analogues of 1.
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Affiliation(s)
- Xavier Laurent
- Intestinal Biotech Development, Faculté de Médecine, Lille, France
- Laboratoire de Chimie Thérapeutique EA4481, Université Lille 2, Lille, France
| | - Nicolas Renault
- Laboratoire de Chimie Thérapeutique EA4481, Université Lille 2, Lille, France
| | - Amaury Farce
- Laboratoire de Chimie Thérapeutique EA4481, Université Lille 2, Lille, France
| | - Philippe Chavatte
- Laboratoire de Chimie Thérapeutique EA4481, Université Lille 2, Lille, France
- Institut de Chimie Pharmaceutique Albert Lespagnol EA4481, Université Lille 2, Lille, France
| | - Eric Hénon
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, University of Reims Champagne-Ardenne, Reims, France
- * E-mail:
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12
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The CD1 size problem: lipid antigens, ligands, and scaffolds. Cell Mol Life Sci 2014; 71:3069-79. [PMID: 24658584 DOI: 10.1007/s00018-014-1603-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 02/10/2014] [Accepted: 03/06/2014] [Indexed: 01/17/2023]
Abstract
Whereas research on CD1d has emphasized a few glycosyl ceramides, the broader family of four human CD1 antigen-presenting molecules binds hundreds of distinct self-lipids. Individual lipid types bind within CD1 grooves in different ways, such that they partially fill the groove, match the groove volume, or protrude substantially from the groove. These differing modes of binding can now be connected to differing immunological functions, as individual lipids can act as stimulatory antigens, inhibitory ligands, or space-filling scaffolds. Because each type of CD1 protein folds to produce antigen-binding grooves with differing sizes and shapes, CD1a, CD1b, CD1c, CD1d, and CD1e have distinct mechanisms of capturing self-lipids and exchanging them for foreign lipids. The size discrepancy between endogeneous lipids and groove volume is most pronounced for CD1b. Recent studies show that the large CD1b cavity can simultaneously bind two self-lipids, the antigen, and its scaffold lipid, which can be exchanged for one large bacterial lipid. In this review, we will highlight recent studies showing how cells regulate lipid antigen loading and the roles CD1 groove structures have in control of the presentation of chemically diverse lipids to T cells.
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13
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Paramo T, East A, Garzón D, Ulmschneider MB, Bond PJ. Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity. J Chem Theory Comput 2014; 10:2151-64. [DOI: 10.1021/ct401098b] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Teresa Paramo
- Unilever
Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Alexandra East
- Unilever
Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Diana Garzón
- Unilever
Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Martin B. Ulmschneider
- Department
of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Peter J. Bond
- Unilever
Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Bioinformatics Institute (A*STAR), 30
Biopolis Str, #07-01 Matrix, Singapore 138671
- Department
of Biological Sciences, National University of Singapore, 14 Science
Drive 4, 117543 Singapore
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14
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Dowds CM, Kornell SC, Blumberg RS, Zeissig S. Lipid antigens in immunity. Biol Chem 2014; 395:61-81. [PMID: 23999493 PMCID: PMC4128234 DOI: 10.1515/hsz-2013-0220] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 08/27/2013] [Indexed: 02/07/2023]
Abstract
Lipids are not only a central part of human metabolism but also play diverse and critical roles in the immune system. As such, they can act as ligands of lipid-activated nuclear receptors, control inflammatory signaling through bioactive lipids such as prostaglandins, leukotrienes, lipoxins, resolvins, and protectins, and modulate immunity as intracellular phospholipid- or sphingolipid-derived signaling mediators. In addition, lipids can serve as antigens and regulate immunity through the activation of lipid-reactive T cells, which is the topic of this review. We will provide an overview of the mechanisms of lipid antigen presentation, the biology of lipid-reactive T cells, and their contribution to immunity.
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Affiliation(s)
- C. Marie Dowds
- Department of Internal Medicine I, University Medical Center
Schleswig-Holstein, Schittenhelmstraße 12, D-24105 Kiel,
Germany
| | - Sabin-Christin Kornell
- Department of Internal Medicine I, University Medical Center
Schleswig-Holstein, Schittenhelmstraße 12, D-24105 Kiel,
Germany
| | - Richard S. Blumberg
- Division of Gastroenterology, Hepatology, and Endoscopy, Brigham
and Women’s Hospital, Harvard Medical School, 75 Francis Street,
Boston, MA 02115, USA
| | - Sebastian Zeissig
- Department of Internal Medicine I, University Medical Center
Schleswig-Holstein, Schittenhelmstraße 12, D-24105 Kiel,
Germany
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Paramo T, Piggot TJ, Bryant CE, Bond PJ. The structural basis for endotoxin-induced allosteric regulation of the Toll-like receptor 4 (TLR4) innate immune receptor. J Biol Chem 2013; 288:36215-25. [PMID: 24178299 DOI: 10.1074/jbc.m113.501957] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
As part of the innate immune system, Toll-like receptor 4 (TLR4) recognizes bacterial cell surface lipopolysaccharide (LPS) by forming a complex with a lipid-binding co-receptor, MD-2. In the presence of agonist, TLR4·MD-2 dimerizes to form an active receptor complex, leading to initiation of intracellular inflammatory signals. TLR4 is of great biomedical interest, but its pharmacological manipulation is complicated because even subtle variations in the structure of LPS can profoundly impact the resultant immunological response. Here, we use atomically detailed molecular simulations to gain insights into the nature of the molecular signaling mechanism. We first demonstrate that MD-2 is extraordinarily flexible. The "clamshell-like" motions of its β-cup fold enable it to sensitively match the volume of its hydrophobic cavity to the size and shape of the bound lipid moiety. We show that MD-2 allosterically transmits this conformational plasticity, in a ligand-dependent manner, to a phenylalanine residue (Phe-126) at the cavity mouth previously implicated in TLR4 activation. Remarkably, within the receptor complex, we observe spontaneous transitions between active and inactive signaling states of Phe-126, and we confirm that Phe-126 is indeed the "molecular switch" in endotoxic signaling.
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Affiliation(s)
- Teresa Paramo
- From the Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Tomasio SM, Harding HP, Ron D, Cross BCS, Bond PJ. Selective inhibition of the unfolded protein response: targeting catalytic sites for Schiff base modification. MOLECULAR BIOSYSTEMS 2013; 9:2408-16. [DOI: 10.1039/c3mb70234k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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