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Joshi O, Skóra T, Yarema A, Rabbitt RD, Bidone TC. Contributions of the individual domains of α IIbβ 3 integrin to its extension: Insights from multiscale modeling. Cytoskeleton (Hoboken) 2024. [PMID: 38682753 DOI: 10.1002/cm.21865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 05/01/2024]
Abstract
The platelet integrin αIIbβ3 undergoes long-range conformational transitions between bent and extended conformations to regulate platelet aggregation during hemostasis and thrombosis. However, how exactly αIIbβ3 transitions between conformations remains largely elusive. Here, we studied how transitions across bent and extended-closed conformations of αIIbβ3 integrin are regulated by effective interactions between its functional domains. We first carried out μs-long equilibrium molecular dynamics (MD) simulations of full-length αIIbβ3 integrins in bent and intermediate conformations, the latter characterized by an extended headpiece and closed legs. Then, we built heterogeneous elastic network models, perturbed inter-domain interactions, and evaluated their relative contributions to the energy barriers between conformations. Results showed that integrin extension emerges from: (i) changes in interfaces between functional domains; (ii) allosteric coupling of the head and upper leg domains with flexible lower leg domains. Collectively, these results provide new insights into integrin conformational activation based on short- and long-range interactions between its functional domains and highlight the importance of the lower legs in the regulation of integrin allostery.
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Affiliation(s)
- Onkar Joshi
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah, USA
| | - Tomasz Skóra
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah, USA
| | - Anna Yarema
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah, USA
| | - Richard D Rabbitt
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah, USA
| | - Tamara C Bidone
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah, USA
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, Utah, USA
- Department of Biochemistry, University of Utah, Salt Lake City, Utah, USA
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Rodríguez de Francisco B, Bezault A, Xu XP, Hanein D, Volkmann N. MEPSi: A tool for simulating tomograms of membrane-embedded proteins. J Struct Biol 2022; 214:107921. [PMID: 36372192 DOI: 10.1016/j.jsb.2022.107921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 10/27/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022]
Abstract
The throughput and fidelity of cryogenic cellular electron tomography (cryo-ET) is constantly increasing through advances in cryogenic electron microscope hardware, direct electron detection devices, and powerful image processing algorithms. However, the need for careful optimization of sample preparations and for access to expensive, high-end equipment, make cryo-ET a costly and time-consuming technique. Generally, only after the last step of the cryo-ET workflow, when reconstructed tomograms are available, it becomes clear whether the chosen imaging parameters were suitable for a specific type of sample in order to answer a specific biological question. Tools for a-priory assessment of the feasibility of samples to answer biological questions and how to optimize imaging parameters to do so would be a major advantage. Here we describe MEPSi (Membrane Embedded Protein Simulator), a simulation tool aimed at rapid and convenient evaluation and optimization of cryo-ET data acquisition parameters for studies of transmembrane proteins in their native environment. We demonstrate the utility of MEPSi by showing how to detangle the influence of different data collection parameters and different orientations in respect to tilt axis and electron beam for two examples: (1) simulated plasma membranes with embedded single-pass transmembrane αIIbβ3 integrin receptors and (2) simulated virus membranes with embedded SARS-CoV-2 spike proteins.
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Affiliation(s)
- Borja Rodríguez de Francisco
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Image Analysis Unit, Paris, France
| | - Armel Bezault
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Image Analysis Unit, Paris, France
| | | | - Dorit Hanein
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, Paris, France; Scintillon Institute, San Diego, CA 92121, USA
| | - Niels Volkmann
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Image Analysis Unit, Paris, France.
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Jin L, Han X, Zhang X, Zhao Z, Ulrich J, Syrovets T, Simmet T. Identification of Oleanolic Acid as Allosteric Agonist of Integrin α M by Combination of In Silico Modeling and In Vitro Analysis. Front Pharmacol 2021; 12:702529. [PMID: 34603018 PMCID: PMC8484648 DOI: 10.3389/fphar.2021.702529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/31/2021] [Indexed: 12/31/2022] Open
Abstract
Oleanolic acid is a widely distributed natural product, which possesses promising antitumor, antiviral, antihyperlipidemic, and anti-inflammatory activities. A heterodimeric complex formed by integrin αM (CD11b) and integrin β2 (CD18) is highly expressed on monocytes and macrophages. In the current study, we demonstrate that the I domain of αM (αM-I domain) might present a potential cellular target for oleanolic acid. In vitro data show that oleanolic acid induces clustering of αM on macrophages and reduces their non-directional migration. In accordance with experimental data, molecular docking revealed that oleanolic acid binds to the αM-I domain in its extended-open form, the dominant conformation found in αM clusters. Molecular dynamics simulation revealed that oleanolic acid can increase the flexibility of the α7 helix and promote its movement away from the N-terminus, indicating that oleanolic acid may facilitate the conversion of the αM-I domain from the extended-closed to the extended-open conformation. As demonstrated by metadynamics simulation, oleanolic acid can destabilize the local minimum of the αM-I domain in the open conformation partially through disturbance of the interactions between α1 and α7 helices. In summary, we demonstrate that oleanolic acid might function as an allosteric agonist inducing clustering of αM on macrophages by shifting the balance from the closed to the extended-open conformation. The molecular target identified in this study might hold potential for a purposeful use of oleanolic acid to modulate chronic inflammatory responses.
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Affiliation(s)
- Lu Jin
- Institute of Pharmacology of Natural Products and Clinical Pharmacology, Ulm University, Ulm, Germany.,School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xiaoyu Han
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xinlei Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Zhimin Zhao
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Judith Ulrich
- Institute of Pharmacology of Natural Products and Clinical Pharmacology, Ulm University, Ulm, Germany
| | - Tatiana Syrovets
- Institute of Pharmacology of Natural Products and Clinical Pharmacology, Ulm University, Ulm, Germany
| | - Thomas Simmet
- Institute of Pharmacology of Natural Products and Clinical Pharmacology, Ulm University, Ulm, Germany
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Sorrentino S, Conesa JJ, Cuervo A, Melero R, Martins B, Fernandez-Gimenez E, de Isidro-Gomez FP, de la Morena J, Studt JD, Sorzano COS, Eibauer M, Carazo JM, Medalia O. Structural analysis of receptors and actin polarity in platelet protrusions. Proc Natl Acad Sci U S A 2021; 118:e2105004118. [PMID: 34504018 DOI: 10.1073/pnas.2105004118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2021] [Indexed: 11/18/2022] Open
Abstract
During activation the platelet cytoskeleton is reorganized, inducing adhesion to the extracellular matrix and cell spreading. These processes are critical for wound healing and clot formation. Initially, this task relies on the formation of strong cellular-extracellular matrix interactions, exposed in subendothelial lesions. Despite the medical relevance of these processes, there is a lack of high-resolution structural information on the platelet cytoskeleton controlling cell spreading and adhesion. Here, we present in situ structural analysis of membrane receptors and the underlying cytoskeleton in platelet protrusions by applying cryoelectron tomography to intact platelets. We utilized three-dimensional averaging procedures to study receptors at the plasma membrane. Analysis of substrate interaction-free receptors yielded one main structural class resolved to 26 Å, resembling the αIIbβ3 integrin folded conformation. Furthermore, structural analysis of the actin network in pseudopodia indicates a nonuniform polarity of filaments. This organization would allow generation of the contractile forces required for integrin-mediated cell adhesion.
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Janke U, Mitlehner A, Weide A, Gutmann T, Delcea M. Reconstitution of Functional Integrin αIIbβ3 and Its Activation in Plasma Membrane-Mimetic Lipid Environments. Membranes (Basel) 2021; 11:499. [PMID: 34209233 DOI: 10.3390/membranes11070499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/26/2021] [Accepted: 06/29/2021] [Indexed: 11/29/2022]
Abstract
The study of the platelet receptor integrin αIIbβ3 in a membrane-mimetic environment without interfering signalling pathways is crucial to understand protein structure and dynamics. Our understanding of this receptor and its sequential activation steps has been tremendously progressing using structural and reconstitution approaches in model membranes, such as liposomes or supported-lipid bilayers. For most αIIbβ3 reconstitution approaches, saturated short-chain lipids have been used, which is not reflecting the native platelet cell membrane composition. We report here on the reconstitution of label-free full-length αIIbβ3 in liposomes containing cholesterol, sphingomyelin, and unsaturated phosphatidylcholine mimicking the plasma membrane that formed supported-lipid bilayers for quartz-crystal microbalance with dissipation (QCM-D) experiments. We demonstrate the relevance of the lipid environment and its resulting physicochemical properties on integrin reconstitution efficiency and its conformational dynamics. We present here an approach to investigate αIIbβ3 in a biomimetic membrane system as a useful platform do dissect disease-relevant integrin mutations and effects on ligand binding in a lipid-specific context, which might be applicable for drug screening.
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Obermann WMJ, Brockhaus K, Eble JA. Platelets, Constant and Cooperative Companions of Sessile and Disseminating Tumor Cells, Crucially Contribute to the Tumor Microenvironment. Front Cell Dev Biol 2021; 9:674553. [PMID: 33937274 PMCID: PMC8085416 DOI: 10.3389/fcell.2021.674553] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
Although platelets and the coagulation factors are components of the blood system, they become part of and contribute to the tumor microenvironment (TME) not only within a solid tumor mass, but also within a hematogenous micrometastasis on its way through the blood stream to the metastatic niche. The latter basically consists of blood-borne cancer cells which are in close association with platelets. At the site of the primary tumor, the blood components reach the TME via leaky blood vessels, whose permeability is increased by tumor-secreted growth factors, by incomplete angiogenic sprouts or by vasculogenic mimicry (VM) vessels. As a consequence, platelets reach the primary tumor via several cell adhesion molecules (CAMs). Moreover, clotting factor VII from the blood associates with tissue factor (TF) that is abundantly expressed on cancer cells. This extrinsic tenase complex turns on the coagulation cascade, which encompasses the activation of thrombin and conversion of soluble fibrinogen into insoluble fibrin. The presence of platelets and their release of growth factors, as well as fibrin deposition changes the TME of a solid tumor mass substantially, thereby promoting tumor progression. Disseminating cancer cells that circulate in the blood stream also recruit platelets, primarily by direct cell-cell interactions via different receptor-counterreceptor pairs and indirectly by fibrin, which bridges the two cell types via different integrin receptors. These tumor cell-platelet aggregates are hematogenous micrometastases, in which platelets and fibrin constitute a particular TME in favor of the cancer cells. Even at the distant site of settlement, the accompanying platelets help the tumor cell to attach and to grow into metastases. Understanding the close liaison of cancer cells with platelets and coagulation factors that change the TME during tumor progression and spreading will help to curb different steps of the metastatic cascade and may help to reduce tumor-induced thrombosis.
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Affiliation(s)
| | | | - Johannes A. Eble
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Münster, Germany
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Abstract
The composition and organization of the plasma membrane play important functional and regulatory roles in integrin signaling, which direct many physiological and pathological processes, such as development, wound healing, immunity, thrombosis, and cancer metastasis. Membranes are comprised of regions that are thick or thin owing to spontaneous partitioning of long-chain saturated lipids from short-chain polyunsaturated lipids into domains defined as ordered and liquid-disorder domains, respectively. Liquid-ordered domains are typically 100 nm in diameter and sometimes referred to as lipid rafts. We posit that integrin β senses membrane thickness and that mechanical force on the membrane regulates integrin activation through membrane thinning. This review examines what we know about the nature and mechanism of the interaction of integrins with the plasma membrane and its effects on regulating integrins and its binding partners.
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Affiliation(s)
- Daniel Lietha
- Cell Signaling and Adhesion Group, Structural and Chemical Biology, Margarita Salas Center for Biological Research (CIB-CSIC), E-28040 Madrid, Spain;
| | - Tina Izard
- Cell Adhesion Laboratory, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
- Correspondence:
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Abstract
The interactions between lipids and proteins are one of the most fundamental processes in living organisms, responsible for critical cellular events ranging from replication, cell division, signaling, and movement. Enabling the central coupling responsible for maintaining the functionality of the breadth of proteins, receptors, and enzymes that find their natural home in biological membranes, the fundamental mechanisms of recognition of protein for lipid, and vice versa, have been a focal point of biochemical and biophysical investigations for many decades. Complexes of lipids and proteins, such as the various lipoprotein factions, play central roles in the trafficking of important proteins, small molecules and metabolites and are often implicated in disease states. Recently an engineered lipoprotein particle, termed the nanodisc, a modified form of the human high density lipoprotein fraction, has served as a membrane mimetic for the investigation of membrane proteins and studies of lipid-protein interactions. In this review, we summarize the current knowledge regarding this self-assembling lipid-protein complex and provide examples for its utility in the investigation of a large number of biological systems.
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Affiliation(s)
- Yajun Zheng
- Pliant Therapeutics, South San Francisco, California 94080, United States
| | - Katerina Leftheris
- Pliant Therapeutics, South San Francisco, California 94080, United States
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