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de Souza Cardoso R, Murakami T, Jacobovitz B, Veatch SL, Ono A. PIP 2 promotes the incorporation of CD43, PSGL-1, and CD44 into nascent HIV-1 particles. SCIENCE ADVANCES 2025; 11:eads9711. [PMID: 40184445 PMCID: PMC11970457 DOI: 10.1126/sciadv.ads9711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Accepted: 02/28/2025] [Indexed: 04/06/2025]
Abstract
Determinants regulating sorting of host transmembrane proteins at sites of enveloped virus assembly on the plasma membrane (PM) remain poorly understood. Here, we demonstrate that the PM acidic phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2) regulates this sorting into an enveloped virus, HIV-1. Incorporation of CD43, PSGL-1, and CD44 into HIV-1 particles has profound effects on viral spread; however, the mechanisms promoting their incorporation were unknown. We found that depletion of cellular PIP2 blocks incorporation of CD43, PSGL-1, and CD44 into HIV-1 particles. Expansion microscopy revealed that PIP2 depletion diminishes nanoscale coclustering between viral structural protein Gag and the three transmembrane proteins at the PM and that Gag induces PIP2 enrichment at its vicinity. CD43, PSGL-1, and CD44 also increased local PIP2 density, revealing their PIP2 affinity. Together, these results support a previously unknown mechanism where local enrichment of an acidic phospholipid drives coclustering between viral structural and cellular transmembrane proteins, thereby modulating the content, and hence the fate, of progeny virus particles.
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Affiliation(s)
- Ricardo de Souza Cardoso
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tomoyuki Murakami
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Binyamin Jacobovitz
- BRCF Microscopy Core, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sarah L. Veatch
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Akira Ono
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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2
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Shi X, He X, Xu C. Charge-based immunoreceptor signalling in health and disease. Nat Rev Immunol 2025; 25:298-311. [PMID: 39528837 DOI: 10.1038/s41577-024-01105-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2024] [Indexed: 11/16/2024]
Abstract
Immunoreceptors have crucial roles in sensing environmental signals and initiating immune responses to protect the host. Dysregulation of immunoreceptor signalling can therefore lead to a range of diseases, making immunoreceptor-based therapies a promising frontier in biomedicine. A common feature of various immunoreceptors is the basic-residue-rich sequence (BRS), which is a largely unexplored aspect of immunoreceptor signalling. The BRS is typically located in the cytoplasmic juxtamembrane region of immunoreceptors, where it forms dynamic interactions with neighbouring charged molecules to regulate signalling. Loss or gain of the basic residues in an immunoreceptor BRS has been linked to severe human diseases, such as immunodeficiency and autoimmunity. In this Perspective, we describe the role of BRSs in various immunoreceptors, elucidating their signalling mechanisms and biological functions. Furthermore, we highlight pathogenic mutations in immunoreceptor BRSs and discuss the potential of leveraging BRS signalling in engineered T cell-based therapies.
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Affiliation(s)
- Xiaoshan Shi
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Xing He
- Key Laboratory of Multi-Cell Systems, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Chenqi Xu
- Key Laboratory of Multi-Cell Systems, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.
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3
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Yanova M, Stepanova E, Maltseva D, Tonevitsky A. CD44 variant exons induce chemoresistance by modulating cell death pathways. Front Cell Dev Biol 2025; 13:1508577. [PMID: 40114966 PMCID: PMC11924683 DOI: 10.3389/fcell.2025.1508577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Accepted: 02/03/2025] [Indexed: 03/22/2025] Open
Abstract
Cancer chemoresistance presents a challenge in oncology, often leading to treatment failure and disease progression. CD44, a multifunctional cell surface glycoprotein, has garnered attention for its involvement in various aspects of cancer biology. Through alternative splicing, CD44 can form isoforms with the inclusion of only standard exons, typical for normal tissue, or with the addition of variant exons, frequently expressed in cancer tissue and associated with chemoresistance. The functions of CD44 involved in regulation of cancer signaling pathways are being actively studied, and the significance of specific variant exons in modulating cell death pathways, central to the response of cancer cells to chemotherapy, begins to become apparent. This review provides a comprehensive analysis of the association of CD44 variant exons/total CD44 with clinical outcomes of patients undergoing chemotherapy. The role of CD44 variant exons v6, v9 and others with a significant effect on patient chemotherapy outcomes by means of key cellular death pathways such as apoptosis, ferroptosis and autophagy modulation is further identified, and their impact on drug resistance is highlighted. An overview of clinical trials aimed at targeting variant exon-containing isoforms is provided, and possible directions for further development of CD44-targeted therapeutic strategies are discussed.
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Affiliation(s)
- Maria Yanova
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow, Russia
| | - Evgeniya Stepanova
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow, Russia
| | - Diana Maltseva
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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4
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de Souza Cardoso R, Murakami T, Jacobovitz B, Veatch SL, Ono A. PIP2 promotes the incorporation of CD43, PSGL-1 and CD44 into nascent HIV-1 particles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.05.611432. [PMID: 39282414 PMCID: PMC11398503 DOI: 10.1101/2024.09.05.611432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/21/2024]
Abstract
Determinants regulating sorting of host transmembrane proteins at sites of enveloped virus assembly on the plasma membrane (PM) remain poorly understood. Here, we demonstrate for the first time that PM acidic phospholipid PIP2 regulates such sorting into an enveloped virus, HIV-1. Incorporation of CD43, PSGL-1, and CD44 into HIV-1 particles is known to have profound effects on viral spread; however, the mechanisms promoting their incorporation were unknown. We found that depletion of cellular PIP2 blocks the incorporation of CD43, PSGL-1, and CD44 into HIV-1 particles. Expansion microscopy revealed that PIP2 depletion diminishes nanoscale co-clustering between viral structural protein Gag and the three transmembrane proteins at PM and that Gag induces PIP2 enrichment around itself. CD43, PSGL-1, and CD44 also increased local PIP2 density, revealing their PIP2 affinity. Altogether, these results support a new mechanism where local enrichment of an acidic phospholipid drives co-clustering between viral structural and cellular transmembrane proteins, thereby modulating the content, and hence the fate, of progeny virus particles.
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Affiliation(s)
- Ricardo de Souza Cardoso
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Tomoyuki Murakami
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | | | - Sarah L Veatch
- BRCF Microscopy Core, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Akira Ono
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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5
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Zhao L, Wang Y, Zhang Y, Chen H, Sun F. Dynamic Simulations of Interaction of the PEG-DPPE Micelle-Encapsulated Short-Chain Ceramides with the Raft-Included Membrane. J Chem Inf Model 2024; 64:3874-3883. [PMID: 38652138 DOI: 10.1021/acs.jcim.4c00170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The lipid raft subdomains in cancer cell membranes play a key role in signal transduction, biomolecule recruitment, and drug transmembrane transport. Augmented membrane rigidity due to the formation of a lipid raft is unfavorable for the entry of drugs, a limiting factor in clinical oncology. The short-chain ceramide (CER) has been reported to promote drug entry into membranes and disrupt lipid raft formation, but the underlying mechanism is not well understood. We recently explored the carrier-membrane fusion dynamics of PEG-DPPE micelles in delivering doxorubicin (DOX). Based on the phase-segregated membrane model composed of DPPC/DIPC/CHOL/GM1/PIP2, we aim to explore the dynamic mechanism of the PEG-DPPE micelle-encapsulating DOXs in association with the raft-included cell membrane modulated by C8 acyl tail CERs. The results show that the lipid raft remains integrated and DOX-resistant subjected to free DOXs and the micelle-encapsulating ones. Addition of CERs disorganizes the lipid raft by pushing CHOL aside from DPPC. It subsequently allows for a good permeability for PEG-DPPE micelle-encapsulated DOXs, which penetrate deeper as CER concentration increases. GM1 is significant in guiding drugs' redistributing between bilayer phases, and the anionic PIP2 further helps DOXs attain the inner bilayer surface. These results elaborate on the perturbing effect of CERs on lipid raft stability, which provides a new comprehensive approach for further design of drug delivery systems.
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Affiliation(s)
- Lina Zhao
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Yanjiao Wang
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Yi Zhang
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Hao Chen
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Fude Sun
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
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6
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Wu S, Tan Y, Li F, Han Y, Zhang S, Lin X. CD44: a cancer stem cell marker and therapeutic target in leukemia treatment. Front Immunol 2024; 15:1354992. [PMID: 38736891 PMCID: PMC11082360 DOI: 10.3389/fimmu.2024.1354992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/11/2024] [Indexed: 05/14/2024] Open
Abstract
CD44 is a ubiquitous leukocyte adhesion molecule involved in cell-cell interaction, cell adhesion, migration, homing and differentiation. CD44 can mediate the interaction between leukemic stem cells and the surrounding extracellular matrix, thereby inducing a cascade of signaling pathways to regulate their various behaviors. In this review, we focus on the impact of CD44s/CD44v as biomarkers in leukemia development and discuss the current research and prospects for CD44-related interventions in clinical application.
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Affiliation(s)
- Shuang Wu
- Laboratory Animal Center, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Institute of Hematology, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yicheng Tan
- Laboratory Animal Center, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Institute of Hematology, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Wenzhou Key laboratory of Hematology, Wenzhou, Zhejiang, China
| | - Fanfan Li
- Institute of Hematology, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Wenzhou Key laboratory of Hematology, Wenzhou, Zhejiang, China
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yixiang Han
- Institute of Hematology, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Wenzhou Key laboratory of Hematology, Wenzhou, Zhejiang, China
- Central Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Shenghui Zhang
- Laboratory Animal Center, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Institute of Hematology, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Wenzhou Key laboratory of Hematology, Wenzhou, Zhejiang, China
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaofei Lin
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
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7
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Vogl DP, Mateos B, Migotti M, Felkl M, Conibear AC, Konrat R, Becker CFW. Semisynthesis of segmentally isotope-labeled and site-specifically palmitoylated CD44 cytoplasmic tail. Bioorg Med Chem 2024; 100:117617. [PMID: 38306881 DOI: 10.1016/j.bmc.2024.117617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/04/2024]
Abstract
CD44, a ubiquitously expressed transmembrane receptor, plays a crucial role in cell growth, migration, and tumor progression. Dimerization of CD44 is a key event in signal transduction and has emerged as a potential target for anti-tumor therapies. Palmitoylation, a posttranslational modification, disrupts CD44 dimerization and promotes CD44 accumulation in ordered membrane domains. However, the effects of palmitoylation on the structure and dynamics of CD44 at atomic resolution remain poorly understood. Here, we present a semisynthetic approach combining solid-phase peptide synthesis, recombinant expression, and native chemical ligation to investigate the impact of palmitoylation on the cytoplasmic domain (residues 669-742) of CD44 (CD44ct) by NMR spectroscopy. A segmentally isotope-labeled and site-specifically palmitoylated CD44 variant enabled NMR studies, which revealed chemical shift perturbations and indicated local and long-range conformational changes induced by palmitoylation. The long-range effects suggest altered intramolecular interactions and potential modulation of membrane association patterns. Semisynthetic, palmitoylated CD44ct serves as the basis for studying CD44 clustering, conformational changes, and localization within lipid rafts, and could be used to investigate its role as a tumor suppressor and to explore its therapeutic potential.
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Affiliation(s)
- Dominik P Vogl
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria; University of Vienna, Vienna Doctoral School in Chemistry (DoSChem), Währinger Str. 42, 1090 Vienna, Austria
| | - Borja Mateos
- Max Perutz Laboratories, Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Mario Migotti
- Max Perutz Laboratories, Vienna Biocenter Campus 5, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030 Vienna, Austria
| | - Manuel Felkl
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria
| | - Anne C Conibear
- TU Wien, Institute of Applied Synthetic Chemistry, Getreidemarkt 9, 1060 Vienna, Austria
| | - Robert Konrat
- Max Perutz Laboratories, Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Christian F W Becker
- University of Vienna, Vienna Doctoral School in Chemistry (DoSChem), Währinger Str. 42, 1090 Vienna, Austria.
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8
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Gao C, Koko MY, Hong W, Gankhuyag J, Hui M, Gantumur MA, Dong N. Protective Properties of Intestinal Alkaline Phosphatase Supplementation on the Intestinal Barrier: Interactions and Effects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:27-45. [PMID: 37964463 DOI: 10.1021/acs.jafc.3c05119] [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: 11/16/2023]
Abstract
The intestinal barrier is critical for maintaining intestinal homeostasis, and its dysfunction is associated with various diseases. Recent findings have revealed the multifunctional role of intestinal alkaline phosphatase (IAP) in diverse biological processes, including gut health maintenance and function. This review summarizes the protective effects of IAP on intestinal barrier integrity, encompassing the physical, chemical, microbial, and immune barriers. We discuss the results and insights from in vitro, animal model, and clinical studies as well as the available evidence regarding the impact of diet on IAP activity and expression. IAP can also be used as an indicator to assess intestinal-barrier-related diseases. Further research into the mechanisms of action and long-term health effects of IAP in maintaining overall intestinal health is essential for its future use as a dietary supplement or functional component in medical foods.
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Affiliation(s)
- Chenzhe Gao
- Laboratory of Molecular Nutrition and Immunity, College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China 150030
- College of Food, Northeast Agricultural University, Harbin, People's Republic of China 150030
| | - Marwa Yagoub Koko
- College of Food, Northeast Agricultural University, Harbin, People's Republic of China 150030
| | - Weichen Hong
- Laboratory of Molecular Nutrition and Immunity, College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China 150030
| | - Javzan Gankhuyag
- College of Food, Northeast Agricultural University, Harbin, People's Republic of China 150030
| | - Mizhou Hui
- College of Food, Northeast Agricultural University, Harbin, People's Republic of China 150030
| | - Munkh-Amgalan Gantumur
- College of Food, Northeast Agricultural University, Harbin, People's Republic of China 150030
| | - Na Dong
- Laboratory of Molecular Nutrition and Immunity, College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China 150030
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9
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Pérez S. Computational modeling of protein-carbohydrate interactions: Current trends and future challenges. Adv Carbohydr Chem Biochem 2023; 83:133-149. [PMID: 37968037 DOI: 10.1016/bs.accb.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The article leads the reader through an up-to-date presentation of the concepts, developments, and main applications of computational modeling to study protein-carbohydrate interactions. It follows with the presentation of some current issues and perspectives arising from the expected evolution of generic methodological developments in deep learning, immersive analytics, and virtual reality for molecular visualization and data management. Such methodological developments for macromolecular interactions would greatly benefit a wide range of scientific endeavors in the field of carbohydrate chemistry and biochemistry, including the following interrelated efforts dealing with highly crowded media, with examples concerning glycoside transferases, the extracellular matrix, and the exploration of interactions between complex carbohydrates and intrinsically disordered proteins.
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Affiliation(s)
- Serge Pérez
- Centre de Recherches sur les Macromolécules Végétales, CNRS, Université Grenoble Alpes, Grenoble, France.
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10
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Borges-Araújo L, Patmanidis I, Singh AP, Santos LHS, Sieradzan AK, Vanni S, Czaplewski C, Pantano S, Shinoda W, Monticelli L, Liwo A, Marrink SJ, Souza PCT. Pragmatic Coarse-Graining of Proteins: Models and Applications. J Chem Theory Comput 2023; 19:7112-7135. [PMID: 37788237 DOI: 10.1021/acs.jctc.3c00733] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The molecular details involved in the folding, dynamics, organization, and interaction of proteins with other molecules are often difficult to assess by experimental techniques. Consequently, computational models play an ever-increasing role in the field. However, biological processes involving large-scale protein assemblies or long time scale dynamics are still computationally expensive to study in atomistic detail. For these applications, employing coarse-grained (CG) modeling approaches has become a key strategy. In this Review, we provide an overview of what we call pragmatic CG protein models, which are strategies combining, at least in part, a physics-based implementation and a top-down experimental approach to their parametrization. In particular, we focus on CG models in which most protein residues are represented by at least two beads, allowing these models to retain some degree of chemical specificity. A description of the main modern pragmatic protein CG models is provided, including a review of the most recent applications and an outlook on future perspectives in the field.
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Affiliation(s)
- Luís Borges-Araújo
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Ilias Patmanidis
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Akhil P Singh
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
| | - Lucianna H S Santos
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, Inserm, CNRS, 06560 Valbonne, France
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita, Okayama 700-8530, Japan
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Adam Liwo
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
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11
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Ren M, Ma Z, Zhao L, Wang Y, An H, Sun F. Self-Association of ACE-2 with Different RBD Amounts: A Dynamic Simulation Perspective on SARS-CoV-2 Infection. J Chem Inf Model 2023; 63:4423-4432. [PMID: 37382878 DOI: 10.1021/acs.jcim.3c00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Transmissibility of SARS-CoV-2 initially relies on its trimeric Spike-RBDs to tether the ACE-2 on host cells, and enhanced self-association of ACE-2 engaged with Spike facilitates the viral infection. Two primary packing modes of Spike-ACE2 heteroproteins exist potentially due to discrepant amounts of RBDs loading on ACE-2, but the resultant self-association difference is inherently unclear. We used extensive coarse-grained dynamic simulations to characterize the self-association efficiency, the conformation relevance, and the molecular mechanism of ACE-2 with different RBD amounts. It was revealed that the ACE-2 hanging two/full RBDs (Mode-A) rapidly dimerized into the heteroprotein complex in a compact "linear" conformation, while the bare ACE-2 showed weakened self-association and a protein complex. The RBD-tethered ectodomains of ACE-2 presented a more upright conformation relative to the membrane, and the intermolecular ectodomains were predominantly packed by the neck domains, which was obligated to the rapid protein self-association in a compact pattern. Noted is the fact that the ACE-2 tethered by a single RBD (Mode-B) retained considerable self-association efficiency and clustering capability, which unravels the interrelation of ACE-2 colocalization and protein cross-linkage. The molecular perspectives in this study expound the self-association potency of ACE-2 with different RBD amounts and the viral activity implications, which can greatly enhance our comprehension of SARS-CoV-2 infection details.
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Affiliation(s)
- Meina Ren
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Ziyi Ma
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Lina Zhao
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Yanjiao Wang
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Hailong An
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Fude Sun
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
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12
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Ren M, Zhao L, Ma Z, An H, Marrink SJ, Sun F. Molecular basis of PIP2-dependent conformational switching of phosphorylated CD44 in binding FERM. Biophys J 2023; 122:2675-2685. [PMID: 37218130 PMCID: PMC10397572 DOI: 10.1016/j.bpj.2023.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 05/07/2023] [Accepted: 05/18/2023] [Indexed: 05/24/2023] Open
Abstract
Association of the cellular adhesive protein CD44 and the N-terminal (FERM) domain of cytoskeleton adaptors is critical for cell proliferation, migration, and signaling. Phosphorylation of the cytoplasmic domain (CTD) of CD44 acts as an important regulator of the protein association, but the structural transformation and dynamics mechanism remain enigmatic. In this study, extensive coarse-grained simulations were employed to explore the molecular details in the formation of CD44-FERM complex under S291 and S325 phosphorylation, a modification path known to exert reciprocal effects on the protein association. We find that phosphorylation of S291 inhibits complexation by causing the CTD of CD44 to adopt a more closed structure. In contrast, S325 phosphorylation liberates the CD44-CTD from the membrane surface and promotes the linkage with FERM. The phosphorylation-driven transformation is found to occur in a PIP2-dependent manner, with PIP2 effecting the relative stability of the closed and open conformation, and a replacement of PIP2 by POPS greatly abrogates this effect. The revealed interdependent regulation mechanism by phosphorylation and PIP2 in the association of CD44 and FERM further strengthens our understanding of the molecular basis of cellular signaling and migration.
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Affiliation(s)
- Meina Ren
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, China
| | - Lina Zhao
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, China
| | - Ziyi Ma
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, China
| | - Hailong An
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, China.
| | - Siewert Jan Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
| | - Fude Sun
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, China.
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13
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Das O, Masid A, Chakraborty M, Gope A, Dutta S, Bhaumik M. Butyrate driven raft disruption trots off enteric pathogen invasion: possible mechanism of colonization resistance. Gut Pathog 2023; 15:19. [PMID: 37085870 PMCID: PMC10122309 DOI: 10.1186/s13099-023-00545-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 04/09/2023] [Indexed: 04/23/2023] Open
Abstract
The gut microbiome derived short chain fatty acids perform multitude of functions to maintain gut homeostasis. Here we studied how butyrate stymie enteric bacterial invasion in cell using a simplistic binary model. The surface of the mammalian cells is enriched with microdomains rich in cholesterol that are known as rafts and act as entry points for pathogens. We showed that sodium butyrate treated RAW264.7 cells displayed reduced membrane cholesterol and less cholera-toxin B binding coupled with increased membrane fluidity compared to untreated cells indicating that reduced membrane cholesterol caused disruption of lipid rafts. The implication of such cellular biophysical changes on the invasion of enteric pathogenic bacteria was assessed. Our study showed, in comparison to untreated cells, butyrate-treated cells significantly reduced the invasion of Shigella and Salmonella, and these effects were found to be reversed by liposomal cholesterol treatment, increasing the likelihood that the rafts' function against bacterial invasion. The credence of ex vivo studies found to be in concordance in butyrate fed mouse model as evident from the significant drift towards a protective phenotype against virulent enteric pathogen invasion as compared to untreated mice. To produce a cytokine balance towards anti-inflammation, butyrate-treated mice produced more of the gut tissue anti-inflammatory cytokine IL-10 and less of the pro-inflammatory cytokines TNF-α, IL-6, and IFN-γ. In histological studies of Shigella infected gut revealed a startling observation where number of neutrophils infiltration was noted which was correlated with the pathology and was essentially reversed by butyrate treatment. Our results ratchet up a new dimension of our understanding how butyrate imparts resistance to pathogen invasion in the gut.
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Affiliation(s)
- Oishika Das
- ICMR-National Institute of Cholera and Enteric Diseases, P-33 C.I. T Road, Beleghata, Kolkata, West Bengal, 700010, India
| | - Aaheli Masid
- ICMR-National Institute of Cholera and Enteric Diseases, P-33 C.I. T Road, Beleghata, Kolkata, West Bengal, 700010, India
| | - Mainak Chakraborty
- ICMR-National Institute of Cholera and Enteric Diseases, P-33 C.I. T Road, Beleghata, Kolkata, West Bengal, 700010, India
| | - Animesh Gope
- ICMR-National Institute of Cholera and Enteric Diseases, P-33 C.I. T Road, Beleghata, Kolkata, West Bengal, 700010, India
| | - Shanta Dutta
- ICMR-National Institute of Cholera and Enteric Diseases, P-33 C.I. T Road, Beleghata, Kolkata, West Bengal, 700010, India
| | - Moumita Bhaumik
- ICMR-National Institute of Cholera and Enteric Diseases, P-33 C.I. T Road, Beleghata, Kolkata, West Bengal, 700010, India.
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14
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Buhr J, Franz F, Gräter F. Intrinsically disordered region of talin's FERM domain functions as an initial PIP 2 recognition site. Biophys J 2023; 122:1277-1286. [PMID: 36814383 PMCID: PMC10111347 DOI: 10.1016/j.bpj.2023.02.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/01/2023] [Accepted: 02/15/2023] [Indexed: 02/23/2023] Open
Abstract
Focal adhesions (FAs) mediate the interaction of the cytoskeleton with the extracellular matrix in a highly dynamic fashion. Talin is a central regulator, adaptor protein, and mechano-sensor of FA complexes. For recruitment and firm attachment at FAs, talin's N-terminal FERM domain binds to phosphatidylinositol 4,5-bisphosphate (PIP2)-enriched membranes. A newly published autoinhibitory structure of talin-1, where the known PIP2 interaction sites are covered up, lead us to hypothesize that a hitherto less examined loop insertion of the FERM domain acts as an additional and initial site of contact. We evaluated direct interactions of talin-1 with a PIP2 membrane by means of atomistic molecular dynamics simulations. We show that this unstructured, 33-residue-long loop strongly interacts with PIP2 and can facilitate further membrane contacts, including the canonical PIP2 interactions, by serving as a flexible membrane anchor. Under force as present at FAs, the extensible FERM loop ensures talin maintains membrane contacts when pulled away from the membrane by up to 7 nm. We identify key basic residues of the anchor mediating the highly dynamic talin-membrane interaction. Our results put forward an intrinsically disordered loop as a key and highly adaptable PIP2 recognition site of talin and potentially other PIP2-binding mechano-proteins.
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Affiliation(s)
- Jannik Buhr
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
| | - Florian Franz
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany.
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15
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Ozturk TN, Coumoundouros C, Culham DE, Wood JM. Structural Determinants and Functional Significance of Dimerization for Osmosensing Transporter ProP in Escherichia coli. Biochemistry 2023; 62:118-133. [PMID: 36516499 DOI: 10.1021/acs.biochem.2c00393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Osmosensing transporter ProP forestalls cellular dehydration by detecting environments with high osmotic pressure and mediating the accumulation of organic osmolytes by bacterial cells. It is composed of 12 transmembrane helices with cytoplasmic N- and C-termini. In Escherichia coli, dimers form when the C-terminal domains of ProP molecules form homodimeric, antiparallel, α-helical coiled coils. No dominant negative effect was detected when inactive and active ProP molecules formed heterodimers in vivo. Purification of ProP in detergent dodecylmaltoside yielded monomers, which were functional after reconstitution in proteoliposomes. With other evidence, this suggests that ProP monomers function independently whether in the monomeric or dimeric state. Amino acid replacements that disrupted or reversed the coiled coil did not prevent in vivo dimerization of ProP detected with a bacterial two-hybrid system. Maleimide labeling detected no osmolality-dependent variation in the reactivities of cysteine residues introduced to transmembrane helix (TM) XII. In contrast, coarse-grained molecular dynamic simulations detected deformation of the lipid around TMs III and VI, on the lipid-exposed protein surface opposite to TM XII. This suggests that the dimer interface of ProP includes the surfaces of TMs III and VI, not of TM XII as previously suggested by crosslinking data. Homology modeling suggested that coiled-coil formation and dimerization via such an interface are not mutually exclusive. In previous work, alterations to the C-terminal coiled coil blocked co-localization of ProP with phospholipid cardiolipin at E. coli cell poles. Thus, dimerization may contribute to ProP targeting, adjust its lipid environment, and hence indirectly modify its osmotic stress response.
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Affiliation(s)
- Tugba N Ozturk
- Department of Biochemistry and Molecular Biophysics, Washington University in Saint Louis, Saint Louis, Missouri63110, United States.,Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland20814, United States
| | - Chelsea Coumoundouros
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, CanadaN1G 2 W1
| | - Doreen E Culham
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, CanadaN1G 2 W1
| | - Janet M Wood
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, CanadaN1G 2 W1
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16
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Thallmair V, Schultz L, Zhao W, Marrink SJ, Oliver D, Thallmair S. Two cooperative binding sites sensitize PI(4,5)P 2 recognition by the tubby domain. SCIENCE ADVANCES 2022; 8:eabp9471. [PMID: 36070381 PMCID: PMC9451155 DOI: 10.1126/sciadv.abp9471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/20/2022] [Indexed: 05/22/2023]
Abstract
Phosphoinositides (PIs) are lipid signaling molecules that operate by recruiting proteins to cellular membranes via PI recognition domains. The dominant PI of the plasma membrane is phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]. One of only two PI(4,5)P2 recognition domains characterized in detail is the tubby domain. It is essential for targeting proteins into cilia involving reversible membrane association. However, the PI(4,5)P2 binding properties of tubby domains have remained enigmatic. Here, we used coarse-grained molecular dynamics simulations to explore PI(4,5)P2 binding by the prototypic tubby domain. The comparatively low PI(4,5)P2 affinity of the previously described canonical binding site is underpinned in a cooperative manner by a previously unknown, adjacent second binding site. Mutations in the previously unknown site impaired PI(4,5)P2-dependent plasma membrane localization in living cells and PI(4,5)P2 interaction in silico, emphasizing its importance for PI(4,5)P2 affinity. The two-ligand binding mode may serve to sharpen the membrane association-dissociation cycle of tubby-like proteins that underlies delivery of ciliary cargo.
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Affiliation(s)
- Veronika Thallmair
- Institute for Physiology and Pathophysiology, Philipps University Marburg, Deutschhausstr. 1-2, 35037 Marburg, Germany
- DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps University Marburg, Marburg, Germany
| | - Lea Schultz
- Institute for Physiology and Pathophysiology, Philipps University Marburg, Deutschhausstr. 1-2, 35037 Marburg, Germany
- DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps University Marburg, Marburg, Germany
| | - Wencai Zhao
- Institute for Physiology and Pathophysiology, Philipps University Marburg, Deutschhausstr. 1-2, 35037 Marburg, Germany
- DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps University Marburg, Marburg, Germany
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Dominik Oliver
- Institute for Physiology and Pathophysiology, Philipps University Marburg, Deutschhausstr. 1-2, 35037 Marburg, Germany
- DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps University Marburg, Marburg, Germany
- Corresponding author. (S.T.); (D.O.)
| | - Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, 60438 Frankfurt am Main, Germany
- Corresponding author. (S.T.); (D.O.)
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17
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Distel JS, Flores RMO, Bienvenu A, Aguilera MO, Bonazzi M, Berón W. Ezrin and CD44 participate in the internalization process of
Coxiella burnetii
into non‐phagocytic cells. Biol Cell 2022; 114:237-253. [DOI: 10.1111/boc.202100096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 07/11/2022] [Accepted: 07/15/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Jesús S. Distel
- Instituto de Histología y Embriología Facultad de Ciencias Médicas Universidad Nacional de Cuyo ‐ CONICET Mendoza 5500 Argentina
| | - Rodolfo M. Ortiz Flores
- Instituto de Histología y Embriología Facultad de Ciencias Médicas Universidad Nacional de Cuyo ‐ CONICET Mendoza 5500 Argentina
- Cátedra de Microbiología Parasitología e Inmunología Facultad de Odontología Universidad Nacional de Cuyo Mendoza Argentina
| | - Arthur Bienvenu
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004 CNRS Université de Montpellier Montpellier France
| | - Milton O. Aguilera
- Instituto de Histología y Embriología Facultad de Ciencias Médicas Universidad Nacional de Cuyo ‐ CONICET Mendoza 5500 Argentina
- Cátedra de Microbiología Parasitología e Inmunología Facultad de Odontología Universidad Nacional de Cuyo Mendoza Argentina
| | - Matteo Bonazzi
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004 CNRS Université de Montpellier Montpellier France
| | - Walter Berón
- Instituto de Histología y Embriología Facultad de Ciencias Médicas Universidad Nacional de Cuyo ‐ CONICET Mendoza 5500 Argentina
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18
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Marrink SJ, Monticelli L, Melo MN, Alessandri R, Tieleman DP, Souza PCT. Two decades of Martini: Better beads, broader scope. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials University of Groningen Groningen The Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras Portugal
| | - Riccardo Alessandri
- Pritzker School of Molecular Engineering University of Chicago Chicago Illinois USA
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences University of Calgary Alberta Canada
| | - Paulo C. T. Souza
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
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19
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Ma Z, Shi S, Ren M, Pang C, Zhan Y, An H, Sun F. Molecular Mechanism of CD44 Homodimerization Modulated by Palmitoylation and Membrane Environments. Biophys J 2022; 121:2671-2683. [PMID: 35733341 DOI: 10.1016/j.bpj.2022.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/21/2022] [Accepted: 06/16/2022] [Indexed: 11/15/2022] Open
Abstract
The homodimerization of CD44 plays a key role in an intercellular-to-extracellular signal transduction and tumor progression. Acylated modification and specific membrane environments have been reported to mediate translocation and oligomerization of CD44, however, the underlying molecular mechanism remains elusive. In this study, extensive molecular dynamics simulations are performed to characterize the dimerization of palmitoylated CD44 variants in different bilayer environments. CD44 forms homodimer depending on the cysteines on the juxta-membrane domains, and the dimerization efficiency and packing configurations are defected by their palmitoylated modifications. In the phase-segregated (raft included) membrane, homodimerization of the palmitoylated CD44 is hardly observed, whereas PIP2 addition compensates to realize dimerization. However, the structure of CD44 homodimer formed in the phase-segregated bilayer turns susceptive and PIP2 addition allows for an extensive conformation of the cytoplasmic domain, a proposal prerequisite to access the cytoskeleton linker proteins. The results unravel a delicate competitive relationship between PIP2, lipid raft and palmitoylation in mediating protein homodimerization, which helps to clarify the dynamic dimer conformations and involved cellular signaling of the CD44 likewise proteins.
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Affiliation(s)
- Ziyi Ma
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Sai Shi
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China; State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China
| | - Meina Ren
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Chunli Pang
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Yong Zhan
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China; State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China
| | - Hailong An
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China; State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China.
| | - Fude Sun
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China.
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20
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Qin X, Tieleman DP, Liang Q. Effects of Cholesterol and PIP2 on Interactions between Glycophorin A and Band 3 in Lipid Bilayers. Biophys J 2022; 121:2069-2077. [PMID: 35524411 DOI: 10.1016/j.bpj.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/17/2022] [Accepted: 05/02/2022] [Indexed: 11/02/2022] Open
Abstract
In the erythrocyte membrane, the interactions between Glycophorin A (GPA) and Band 3 are associated strongly with the biological function of the membrane and several blood disorders. In this work, using coarse-grained molecular dynamics simulation, we systematically investigate the effects of cholesterol and phosphatidylinositol-4,5-bisphosphate (PIP2) on the interactions of GPA with Band 3 in the model erythrocyte membranes. We examine the dynamics of the interactions of GPA with Band 3 in different lipid bilayers on the microsecond time scale and calculate the binding free energy between GPA and Band 3. The results indicate that cholesterols thermodynamically favor the binding of GPA to Band 3 by increasing the thickness of the lipid bilayer and by producing an effective attraction between the proteins due to the depletion effect. Cholesterols also slow the kinetics of the binding of GPA to Band 3 by reducing the lateral mobility of the lipids and proteins and may influence the binding sites between the proteins. The anionic PIP2 lipids prefer binding to the surface of the proteins through electrostatic attraction between the PIP2 headgroup and the positively charged residues on the protein surface. Ions in the solvent facilitate the PIP2 aggregation which promotes the binding of GPA to Band 3.
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Affiliation(s)
- Xiaoxue Qin
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China
| | - D Peter Tieleman
- Centre for Molecular Simulations and Department of Biological Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
| | - Qing Liang
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China.
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21
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Shen H, Wu Z, Lu C. Extension of the CAVS model to the simulation of helical peptides in a membrane environment. Phys Chem Chem Phys 2021; 23:12850-12863. [PMID: 34060579 DOI: 10.1039/d1cp01238j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Considering the effect of peptide insertion on the dipole potential of the lipid membrane, we extend the CAVS coarse-grained (CG) model to the simulation of helical peptides in a membrane environment. In this approach, the CG scheme for a peptide backbone is similar to the treatment in the united-atom model, while we treated the side chain of an amino acid by grouping 1-3 heavy atoms into a CG unit. The CAVS CG force field for peptides is optimized by reproducing the experimental results for the backbone (φ, ψ) distribution and predicting the PMF profiles of transferring organic molecules in a lipid bilayer membrane obtained from all-atom simulations. The CAVS simulation of a helical peptide in a phosphatidylcholine (PC) lipid bilayer revealed that the insertion of a peptide increases the dipole potential of the PC lipid bilayer, in which the peptide and its neutralized ions make a significant contribution. Finally, we carried out the CAVS simulation for five different helical peptides in the PC lipid bilayer to explore the behavior of peptide tilt, showing excellent agreement with the all-atom simulations. Our work suggests that the peptide tilt should relieve the deformation stress from the lipid bilayer, and the peptide aggregation could reduce the peptide tilt by resisting the deformation stress from the surrounding lipids.
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Affiliation(s)
- Hujun Shen
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang, Guizhou 550018, P. R. China.
| | - Zhenhua Wu
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, P. R. China
| | - Chan Lu
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang, Guizhou 550018, P. R. China.
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22
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Souza PCT, Limongelli V, Wu S, Marrink SJ, Monticelli L. Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations. Front Mol Biosci 2021; 8:657222. [PMID: 33855050 PMCID: PMC8039319 DOI: 10.3389/fmolb.2021.657222] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/05/2021] [Indexed: 01/12/2023] Open
Abstract
Molecular docking is central to rational drug design. Current docking techniques suffer, however, from limitations in protein flexibility and solvation models and by the use of simplified scoring functions. All-atom molecular dynamics simulations, on the other hand, feature a realistic representation of protein flexibility and solvent, but require knowledge of the binding site. Recently we showed that coarse-grained molecular dynamics simulations, based on the most recent version of the Martini force field, can be used to predict protein/ligand binding sites and pathways, without requiring any a priori information, and offer a level of accuracy approaching all-atom simulations. Given the excellent computational efficiency of Martini, this opens the way to high-throughput drug screening based on dynamic docking pipelines. In this opinion article, we sketch the roadmap to achieve this goal.
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Affiliation(s)
- Paulo C. T. Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
- PharmCADD, Busan, South Korea
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, Lyon, France
| | - Vittorio Limongelli
- Faculty of Biomedical Sciences, Institute of Computational Science, Università della Svizzera Italiana (USI), Lugano, Switzerland
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
| | - Sangwook Wu
- PharmCADD, Busan, South Korea
- Department of Physics, Pukyong National University, Busan, South Korea
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, Lyon, France
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23
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Medrano-González PA, Rivera-Ramírez O, Montaño LF, Rendón-Huerta EP. Proteolytic Processing of CD44 and Its Implications in Cancer. Stem Cells Int 2021; 2021:6667735. [PMID: 33505471 PMCID: PMC7811561 DOI: 10.1155/2021/6667735] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/04/2020] [Accepted: 12/24/2020] [Indexed: 01/16/2023] Open
Abstract
CD44 is a transmembrane glycoprotein expressed in several healthy and tumor tissues. Modifications in its structure contribute differently to the activity of this molecule. One modification that has provoked interest is the consecutive cleavage of the CD44 extracellular ectodomain by enzymes that belong mainly to the family of metalloproteases. This process releases biologically active substrates, via alternative splice forms of CD44, that generate CD44v3 or v6 isoforms which participate in the transcriptional regulation of genes and proteins associated to signaling pathways involved in the development of cancer. These include the protooncogene tyrosine-protein kinase Src (c-Src)/signal transducer and activator of transcription 3 (STAT3), the epithelial growth factor receptor, the estrogen receptor, Wnt/βcatenin, or Hippo signaling pathways all of which are associated to cell proliferation, differentiation, or cancer progression. Whereas CD44 still remains as a very useful prognostic cell marker in different pathologies, the main topic is that the generation of CD44 intracellular fragments assists the regulation of transcriptional proteins involved in the cell cycle, cell metabolism, and most importantly, the regulation of some stem cell-associated markers.
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Affiliation(s)
- Priscila Anhel Medrano-González
- Lab. Inmunobiología, Depto. Biología Celular y Tisular, Facultad de Medicina, UNAM, Mexico, Mexico
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edif. D, 1 piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, 04510 Mexico, Mexico
| | - Osmar Rivera-Ramírez
- Lab. Inmunobiología, Depto. Biología Celular y Tisular, Facultad de Medicina, UNAM, Mexico, Mexico
| | - Luis Felipe Montaño
- Lab. Inmunobiología, Depto. Biología Celular y Tisular, Facultad de Medicina, UNAM, Mexico, Mexico
| | - Erika P. Rendón-Huerta
- Lab. Inmunobiología, Depto. Biología Celular y Tisular, Facultad de Medicina, UNAM, Mexico, Mexico
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24
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Greenlee JD, Subramanian T, Liu K, King MR. Rafting Down the Metastatic Cascade: The Role of Lipid Rafts in Cancer Metastasis, Cell Death, and Clinical Outcomes. Cancer Res 2021; 81:5-17. [PMID: 32999001 PMCID: PMC7952000 DOI: 10.1158/0008-5472.can-20-2199] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/01/2020] [Accepted: 09/21/2020] [Indexed: 11/16/2022]
Abstract
Lipid rafts are tightly packed, cholesterol- and sphingolipid-enriched microdomains within the plasma membrane that play important roles in many pathophysiologic processes. Rafts have been strongly implicated as master regulators of signal transduction in cancer, where raft compartmentalization can promote transmembrane receptor oligomerization, shield proteins from enzymatic degradation, and act as scaffolds to enhance intracellular signaling cascades. Cancer cells have been found to exploit these mechanisms to initiate oncogenic signaling and promote tumor progression. This review highlights the roles of lipid rafts within the metastatic cascade, specifically within tumor angiogenesis, cell adhesion, migration, epithelial-to-mesenchymal transition, and transendothelial migration. In addition, the interplay between lipid rafts and different modes of cancer cell death, including necrosis, apoptosis, and anoikis, will be described. The clinical role of lipid raft-specific proteins, caveolin and flotillin, in assessing patient prognosis and evaluating metastatic potential of various cancers will be presented. Collectively, elucidation of the complex roles of lipid rafts and raft components within the metastatic cascade may be instrumental for therapeutic discovery to curb prometastatic processes.
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Affiliation(s)
- Joshua D Greenlee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - Tejas Subramanian
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - Kevin Liu
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - Michael R King
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee.
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Gök C, Fuller W. Topical review: Shedding light on molecular and cellular consequences of NCX1 palmitoylation. Cell Signal 2020; 76:109791. [DOI: 10.1016/j.cellsig.2020.109791] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 01/21/2023]
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