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Doktorova M, Daum S, Ebenhan J, Neudorf S, Han B, Sharma S, Kasson P, Levental KR, Bacia K, Kenworthy AK, Levental I. Caveolin assemblies displace one bilayer leaflet to organize and bend membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.28.610209. [PMID: 39257813 PMCID: PMC11383982 DOI: 10.1101/2024.08.28.610209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Caveolin is a monotopic integral membrane protein, widely expressed in metazoa and responsible for constructing enigmatic membrane invaginations known as caveolae. Recently, the high-resolution structure of a purified human caveolin assembly, the CAV1-8S complex, revealed a unique organization of 11 protomers arranged in a tightly packed, radially symmetric spiral disc. One face and the outer rim of this disc are highly hydrophobic, suggesting that the complex incorporates into membranes by displacing hundreds of lipids from one leaflet. The feasibility of this unique molecular architecture and its biophysical and functional consequences are currently unknown. Using Langmuir film balance measurements, we find that CAV1-8S is highly surface active and intercalates into lipid monolayers. Molecular simulations of biomimetic bilayers support this 'leaflet replacement' model and reveal that while CAV1-8S effectively displaces phospholipids from one bilayer leaflet, it accumulates 40-70 cholesterol molecules into a disordered monolayer between the complex and its distal lipid leaflet. We find that CAV1-8S preferentially associates with positively curved membrane surfaces due to its influence on the conformations of distal leaflet lipids, and that these effects laterally sort lipids of the distal leaflet. Large-scale simulations of multiple caveolin assemblies confirmed their association with large, positively curved membrane morphologies, consistent with the shape of caveolae. Further, association with curved membranes regulates the exposure of caveolin residues implicated in protein-protein interactions. Altogether, the unique structure of CAV1-8S imparts unusual modes of membrane interaction with implications for membrane organization, morphology, and physiology.
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Affiliation(s)
- Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia, USA
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Sebastian Daum
- Department of Physical Chemistry, Martin Luther University Halle-Wittenberg, Germany
| | - Jan Ebenhan
- Department of Physical Chemistry, Martin Luther University Halle-Wittenberg, Germany
| | - Sarah Neudorf
- Department of Physical Chemistry, Martin Luther University Halle-Wittenberg, Germany
| | - Bing Han
- Department of Molecular Physiology and Biological Physics, University of Virginia, USA
| | - Satyan Sharma
- Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Peter Kasson
- Department of Cell and Molecular Biology, Uppsala University, Sweden
- Departments of Chemistry and Biochemistry and Biomedical Engineering, Georgia Institute of Technology, USA
| | - Kandice R Levental
- Department of Molecular Physiology and Biological Physics, University of Virginia, USA
| | - Kirsten Bacia
- Department of Physical Chemistry, Martin Luther University Halle-Wittenberg, Germany
| | - Anne K Kenworthy
- Department of Molecular Physiology and Biological Physics, University of Virginia, USA
| | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, University of Virginia, USA
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2
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Vasquez Rodriguez SY, Lazaridis T. Simulations suggest a scaffolding mechanism of membrane deformation by the caveolin 8S complex. Biophys J 2023; 122:4082-4090. [PMID: 37742070 PMCID: PMC10598286 DOI: 10.1016/j.bpj.2023.09.008] [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: 06/14/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023] Open
Abstract
Caveolins form complexes of various sizes that deform membranes into polyhedral shapes. However, the recent structure of the 8S complex was disk-like with a flat membrane-binding surface. How can a flat complex deform membranes into nonplanar structures? Molecular dynamics simulations revealed that the 8S complex rapidly takes the form of a suction cup. Simulations on implicit membrane vesicles determined that binding is stronger when E140 gets protonated. In that case, the complex binds much more strongly to 5- and 10-nm-radius vesicles. A concave membrane-binding surface readily explains the membrane-deforming ability of caveolins by direct scaffolding. We propose that the 8S complex sits at the vertices of the caveolar polyhedra, rather than at the center of the polyhedral faces.
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Affiliation(s)
| | - Themis Lazaridis
- Department of Chemistry, City College of New York/CUNY, New York, New York; Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, New York, New York.
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3
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Kenworthy AK. The building blocks of caveolae revealed: caveolins finally take center stage. Biochem Soc Trans 2023; 51:855-869. [PMID: 37082988 PMCID: PMC10212548 DOI: 10.1042/bst20221298] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 04/22/2023]
Abstract
The ability of cells to divide, migrate, relay signals, sense mechanical stimuli, and respond to stress all rely on nanoscale invaginations of the plasma membrane known as caveolae. The caveolins, a family of monotopic membrane proteins, form the inner layer of the caveolar coat. Caveolins have long been implicated in the generation of membrane curvature, in addition to serving as scaffolds for signaling proteins. Until recently, however, the molecular architecture of caveolins was unknown, making it impossible to understand how they operate at a mechanistic level. Over the past year, two independent lines of evidence - experimental and computational - have now converged to provide the first-ever glimpse into the structure of the oligomeric caveolin complexes that function as the building blocks of caveolae. Here, we summarize how these discoveries are transforming our understanding of this long-enigmatic protein family and their role in caveolae assembly and function. We present new models inspired by the structure for how caveolins oligomerize, remodel membranes, interact with their binding partners, and reorganize when mutated. Finally, we discuss emerging insights into structural differences among caveolin family members that enable them to support the proper functions of diverse tissues and organisms.
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Affiliation(s)
- Anne K. Kenworthy
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA, U.S.A
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, U.S.A
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4
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Molecular Mechanisms Underlying Caveolin-1 Mediated Membrane Curvature. J Membr Biol 2022; 255:225-236. [PMID: 35467110 DOI: 10.1007/s00232-022-00236-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/22/2022] [Indexed: 10/18/2022]
Abstract
Caveolin-1 is one of the main protein components of caveolae that acts as a mechanosensor at the cell membrane. The interactions of caveolin-1 with membranes have been shown to lead to complex effects such as curvature and the clustering of specific lipids. Here, we review the emerging concepts on the molecular interactions of caveolin-1, with a focus on insights from coarse-grain molecular dynamics simulations. Consensus structural models of caveolin-1 report a helix-turn-helix core motif with flanking domains of higher disorder that could be membrane composition dependent. Caveolin-1 appears to be mainly surface-bound and does not embed very deep in the membrane to which it is bound. The most interesting aspect of caveolin-1 membrane binding is the interplay of cholesterol clustering and membrane curvature. Although cholesterol has been reported to cluster in the vicinity of caveolin-1 by several approaches, simulations show that the clustering is maximal in membrane leaflet opposing the surface-bound caveolin-1. The intrinsic negative curvature of cholesterol appears to stabilize the negative curvature in the opposing leaflet. In fact, the simulations show that blocking cholesterol clustering (through artificial position restraints) blocks membrane curvature, and vice versa. Concomitant with cholesterol clustering is sphingomyelin clustering, again in the opposing leaflet, but in a concentration-dependent manner. The differential stress due to caveolin-1 binding and the inherent asymmetry of the membrane leaflets could be the determinant for membrane curvature and needs to be further probed. The review is an important step to reconcile the molecular level details emerging from simulations with the mesoscopic details provided by state of the art experimental approaches.
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5
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Prakash S, Krishna A, Sengupta D. Caveolin induced membrane curvature and lipid clustering: two sides of the same coin? Faraday Discuss 2021; 232:218-235. [PMID: 34545870 DOI: 10.1039/d0fd00062k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Caveolin-1 (cav-1) is a multi-domain membrane protein that is a key player in cell signaling, endocytosis and mechanoprotection. It is the principle component of cholesterol-rich caveolar domains and has been reported to induce membrane curvature. The molecular mechanisms underlying the interactions of cav-1 with complex membranes, leading to modulation of membrane topology and the formation of cholesterol-rich domains, remain elusive. In this study, we aim to understand the effect of lipid composition by analyzing the interactions of cav-1 with complex membrane bilayers comprised of about sixty lipid types. We have performed a series of coarse-grain molecular dynamics simulations using the Martini force-field with a cav-1 protein construct (residue 82-136) that includes the membrane binding domains and a palmitoyl tail. We observe that cav-1 induces curvature in this complex membrane, though it is restricted to a nanometer length scale. Concurrently, we observe a clustering of cholesterol, sphingolipids and other lipid molecules leading to the formation of nanodomains. Direct microsecond timescale interactions are observed for specific lipids such as cholesterol, phosphatidylserine and phosphatidylethanolamine lipid types. The results indicate that there is an interplay between membrane topology and lipid species. Our work is a step toward understanding how lipid composition and organization regulate the formation of caveolae, in the context of endocytosis and cell signaling.
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Affiliation(s)
- Shikha Prakash
- National Chemical Laboratory, Council of Scientific and Industrial Research, Dr. Homi Bhabha Road, Pune 411008, India.
| | - Anjali Krishna
- National Chemical Laboratory, Council of Scientific and Industrial Research, Dr. Homi Bhabha Road, Pune 411008, India.
| | - Durba Sengupta
- National Chemical Laboratory, Council of Scientific and Industrial Research, Dr. Homi Bhabha Road, Pune 411008, India.
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6
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Hojo H, Takei T, Asahina Y, Okumura N, Takao T, So M, Suetake I, Sato T, Kawamoto A, Hirabayashi Y. Total Synthesis and Structural Characterization of Caveolin‐1. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Hironobu Hojo
- Institute for Protein Research Osaka University Osaka 565-0871 Japan
| | - Toshiki Takei
- Institute for Protein Research Osaka University Osaka 565-0871 Japan
| | - Yuya Asahina
- Institute for Protein Research Osaka University Osaka 565-0871 Japan
| | - Nobuaki Okumura
- Institute for Protein Research Osaka University Osaka 565-0871 Japan
| | - Toshifumi Takao
- Institute for Protein Research Osaka University Osaka 565-0871 Japan
| | - Masatomo So
- Institute for Protein Research Osaka University Osaka 565-0871 Japan
| | - Isao Suetake
- Nakamura Gakuen University Fukuoka 814-0198 Japan
| | - Takeshi Sato
- Kyoto Pharmaceutical University Kyoto 607-8414 Japan
| | - Akihiro Kawamoto
- Institute for Protein Research Osaka University Osaka 565-0871 Japan
| | - Yoshio Hirabayashi
- RIKEN Cluster for Pioneering Research Saitama 351-0198 Japan
- Institute for Environmental and Gender-Specific Medicine Juntendo University Graduate School of Medicine Chiba 279-0021 Japan
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7
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Hojo H, Takei T, Asahina Y, Okumura N, Takao T, So M, Suetake I, Sato T, Kawamoto A, Hirabayashi Y. Total Synthesis and Structural Characterization of Caveolin-1. Angew Chem Int Ed Engl 2021; 60:13900-13905. [PMID: 33825275 DOI: 10.1002/anie.202100826] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Indexed: 11/06/2022]
Abstract
Caveolin-1, which is an essential protein for caveola formation, was chemically synthesized. It is composed of 177 amino acid residues, is triply palmitoylated at the C-terminal region, and is inserted into the lipid bilayer to form a V-shaped structure in the middle of the polypeptide chain. The entire sequence was divided into five peptide segments, each of which was synthesized by the solid-phase method. To improve the solubility of the C-terminal region, O-acyl isopeptide structures were incorporated. After ligation by the thioester method and the introduction of the palmitoyl groups, all the protecting groups were removed and the isopeptide structures were converted into the native peptide bond. Finally, the obtained polypeptide was successfully inserted into bicelles, thus showing the success of the synthesis.
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Affiliation(s)
- Hironobu Hojo
- Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Toshiki Takei
- Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Yuya Asahina
- Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Nobuaki Okumura
- Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Toshifumi Takao
- Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Masatomo So
- Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Isao Suetake
- Nakamura Gakuen University, Fukuoka, 814-0198, Japan
| | - Takeshi Sato
- Kyoto Pharmaceutical University, Kyoto, 607-8414, Japan
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Yoshio Hirabayashi
- RIKEN Cluster for Pioneering Research, Saitama, 351-0198, Japan.,Institute for Environmental and Gender-Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, 279-0021, Japan
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8
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Prasad S, Simmonett AC, Meana-Pañeda R, Brooks BR. The Extended Eighth-Shell method for periodic boundary conditions with rotational symmetry. J Comput Chem 2021; 42:1373-1383. [PMID: 33977553 DOI: 10.1002/jcc.26545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/18/2021] [Accepted: 03/25/2021] [Indexed: 11/07/2022]
Abstract
The Eighth-Shell method for parallelization of molecular dynamics simulations has previously been shown to be the most optimal for efficiency at large process counts. However, in its current formulation only the P1 space group is supported for periodic boundary conditions (PBC) and thus reflection and/or rotational crystal symmetries are not supported. In this work, we outline the development and implementation of the Extended Eighth-Shell (EES) method that allows rotational symmetry by using an extended import region compared to the ES method. It simulates only the asymmetric unit and communicates coordinates and forces with images that correspond to P21 PBC. The P21 PBC has application in lipid bilayer simulations as it can be used to allow lipids to switch leaftlets, thus rapidly balancing the chemical potential difference between the two layers. Our results show that the EES method scales efficiently over large number of processes and can be used for simulations with P21 symmetry in an orthorhombic crystal.
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Affiliation(s)
- Samarjeet Prasad
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Rubén Meana-Pañeda
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland, USA
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9
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Structural Interplays in the Flexible N-Terminus and Scaffolding Domain of Human Membrane Protein Caveolin 3. MEMBRANES 2021; 11:membranes11020082. [PMID: 33499357 PMCID: PMC7912387 DOI: 10.3390/membranes11020082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/21/2021] [Accepted: 01/21/2021] [Indexed: 11/28/2022]
Abstract
Caveolins are critical for the formation of caveolae, which are small invaginations of the plasma membrane involved in a variety of biological processes. Caveolin 3 (Cav3), one of three caveolin isoforms, is an integral membrane protein mainly expressed in muscle tissues. Although various human diseases associated with Cav3 have been reported, structural characterization of Cav3 in the membrane has not been investigated in enough depth to understand the structure–function relationship. Here, using solution NMR, we characterized membrane association, structural communications, and molecular dynamics of the monomeric Cav3 in detergent micelle environment, particularly focused on the whole N-terminal part that is composed of the flexible N-terminus and the scaffolding domain. The results revealed a complicated structural interplay of the individual segments composing the whole N-terminal part, including the pH-dependent helical region, signature motif-like region, signature motif, and scaffolding domain. Collectively, the present study provides novel structural insights into the whole N-terminal part of Cav3 that plays important biological roles in cellular processes and diseases. In particular, given that several disease-related mutations are located at the whole N-terminal part of Cav3, the sophisticated communications in the whole N-terminal segments are likely to have relevance to the molecular basis of Cav3-related disease.
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10
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Krishna A, Prakash S, Sengupta D. Sphingomyelin Effects in Caveolin-1 Mediated Membrane Curvature. J Phys Chem B 2020; 124:5177-5185. [DOI: 10.1021/acs.jpcb.0c02962] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Anjali Krishna
- National Chemical Laboratory, Council of Scientific and Industrial Research, Dr. Homi Bhabha Road, Pune 411008, India
| | - Shikha Prakash
- National Chemical Laboratory, Council of Scientific and Industrial Research, Dr. Homi Bhabha Road, Pune 411008, India
| | - Durba Sengupta
- National Chemical Laboratory, Council of Scientific and Industrial Research, Dr. Homi Bhabha Road, Pune 411008, India
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11
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Samson GPB, Legler DF. Membrane Compartmentalization and Scaffold Proteins in Leukocyte Migration. Front Cell Dev Biol 2020; 8:285. [PMID: 32411706 PMCID: PMC7198906 DOI: 10.3389/fcell.2020.00285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/02/2020] [Indexed: 01/14/2023] Open
Abstract
Leukocyte migration across vessels into and within peripheral and lymphoid tissues is essential for host defense against invading pathogens. Leukocytes are specialized in sensing a variety of guidance cues and to integrate environmental stimuli to navigate in a timely and spatially controlled manner. These extracellular signals must be transmitted across the leukocyte’s plasma membrane in a way that intracellular signaling cascades enable directional cell movement. Therefore, the composition of the membrane in concert with proteins that influence the compartmentalization of the plasma membrane or contribute to delineate intracellular signaling molecules are key in controlling leukocyte navigation. This becomes evident by the fact that mislocalization of membrane proteins is known to deleteriously affect cellular functions that may cause diseases. In this review we summarize recent advances made in the understanding of how membrane cholesterol levels modulate chemokine receptor signaling and hence leukocyte trafficking. Moreover, we provide an overview on the role of membrane scaffold proteins, particularly tetraspanins, flotillins/reggies, and caveolins in controlling leukocyte migration both in vitro and in vivo.
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Affiliation(s)
- Guerric P B Samson
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland
| | - Daniel F Legler
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland.,Faculty of Biology, University of Konstanz, Konstanz, Germany.,Theodor Kocher Institute, University of Bern, Bern, Switzerland
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12
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Secondary structure of caveolins: a mini review. Biochem Soc Trans 2019; 47:1489-1498. [DOI: 10.1042/bst20190375] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/19/2019] [Accepted: 08/27/2019] [Indexed: 01/28/2023]
Abstract
Abstract
Caveolae are 50–100 nm invaginations found within the plasma membrane of cells. Caveolae are involved in many processes that are essential for homeostasis, most notably endocytosis, mechano-protection, and signal transduction. Within these invaginations, the most important proteins are caveolins, which in addition to participating in the aforementioned processes are structural proteins responsible for caveolae biogenesis. When caveolin is misregulated or mutated, many disease states can arise which include muscular dystrophy, cancers, and heart disease. Unlike most integral membrane proteins, caveolin does not have a transmembrane orientation; instead, it is postulated to adopt an unusual topography where both the N- and C-termini lie on the cytoplasmic side of the membrane, and the hydrophobic span adopts an intramembrane loop conformation. While knowledge concerning the biology of caveolin has progressed apace, fundamental structural information has proven more difficult to obtain. In this mini-review, we curate as well as critically assess the structural data that have been obtained on caveolins to date in order to build a robust and compelling model of the caveolin secondary structure.
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13
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Cell Intrinsic and Extrinsic Mechanisms of Caveolin-1-Enhanced Metastasis. Biomolecules 2019; 9:biom9080314. [PMID: 31362353 PMCID: PMC6723107 DOI: 10.3390/biom9080314] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/17/2019] [Accepted: 07/25/2019] [Indexed: 12/19/2022] Open
Abstract
Caveolin-1 (CAV1) is a scaffolding protein with a controversial role in cancer. This review will initially discuss earlier studies focused on the role as a tumor suppressor before elaborating subsequently on those relating to function of the protein as a promoter of metastasis. Different mechanisms are summarized illustrating how CAV1 promotes such traits upon expression in cancer cells (intrinsic mechanisms). More recently, it has become apparent that CAV1 is also a secreted protein that can be included into exosomes where it plays a significant role in determining cargo composition. Thus, we will also discuss how CAV1 containing exosomes from metastatic cells promote malignant traits in more benign recipient cells (extrinsic mechanisms). This ability appears, at least in part, attributable to the transfer of specific cargos present due to CAV1 rather than the transfer of CAV1 itself. The evolution of how our perception of CAV1 function has changed since its discovery is summarized graphically in a time line figure.
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14
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Park S, Glover KJ, Im W. U-shaped caveolin-1 conformations are tightly regulated by hydrogen bonds with lipids. J Comput Chem 2019; 40:1570-1577. [PMID: 30828836 PMCID: PMC6458063 DOI: 10.1002/jcc.25807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/22/2019] [Accepted: 02/10/2019] [Indexed: 12/26/2022]
Abstract
The structure and dynamics of a truncated (residues 82-136) caveolin-1 (Cav1) construct having a helix-break-helix motif are explored by both all-atom free energy and molecular dynamics (MD) simulations in an explicit bilayer membrane. Two stable Cav1 conformations with small (LB-Cav1) and large hinge angles (RB-Cav1) between two helices are identified although their relative free energy cannot be reliably estimated due to the sampling issues. RB-Cav1s contain one or two lipids residing between the helices that are hydrogen bonded (h-bonded) to both helices in a multidentate fashion. LB-Cav1s show the helices with mono-dentate lipid h-bond interactions or multidentate interactions limited to a single helix at most. The two conformational states of Cav1 remain their initial state during 2-μs MD simulation, suggesting that there is a significant hidden barrier (other than the insertion depth of Cav1 and its hinge angle) and the Cav1 conformational states are tightly regulated by the h-bonds between Cav1 and lipids along with the associated lipid rearrangement during the course of Cav1 conformational changes. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Soohyung Park
- Department of Biological Sciences and Bioengineering, Lehigh University, 111 Research Dr. Bethlehem, Pennsylvania, United States, 18015
| | - Kerney Jebrell Glover
- Department of Chemistry, Lehigh University, 6 E. Packer Ave. Bethlehem, Pennsylvania, United States, 18015
| | - Wonpil Im
- Department of Biological Sciences and Bioengineering, Lehigh University, 111 Research Dr. Bethlehem, Pennsylvania, United States, 18015
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15
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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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Krishna A, Sengupta D. Interplay between Membrane Curvature and Cholesterol: Role of Palmitoylated Caveolin-1. Biophys J 2018; 116:69-78. [PMID: 30579563 DOI: 10.1016/j.bpj.2018.11.3127] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/14/2018] [Accepted: 11/01/2018] [Indexed: 01/07/2023] Open
Abstract
Caveolin-1 (cav-1) is an important player in cell signaling and endocytosis that has been shown to colocalize with cholesterol-rich membrane domains. Experimental studies with varying cav-1 constructs have suggested that it can induce both cholesterol clustering and membrane curvature. Here, we probe the molecular origin of membrane curvature and cholesterol clustering by cav-1 by using coarse-grain molecular dynamics simulations. We have performed a series of simulations of a functionally important cav-1 construct, comprising the membrane-interacting domains and a C-terminal palmitoyl tail. Our results suggest that cav-1 is able to induce cholesterol clustering in the membrane leaflet to which it is bound as well as the opposing leaflet. A positive membrane curvature is observed upon cav-1 binding in cholesterol-containing bilayers. Interestingly, we observe an interplay between cholesterol clustering and membrane curvature such that cav-1 is able to induce higher membrane curvature in cholesterol-rich membranes. The role of the cav-1 palmitoyl tail is less clear and appears to increase the membrane contacts. Further, we address the importance of the secondary structure of cav-1 domains and show that it could play an important role in membrane curvature and cholesterol clustering. Our work is an important step toward a molecular picture of caveolae and vesicular endocytosis.
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Affiliation(s)
- Anjali Krishna
- CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Durba Sengupta
- CSIR-National Chemical Laboratory, Pune, Maharashtra, India.
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17
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Pezeshkian W, Chevrot G, Khandelia H. The role of caveolin-1 in lipid droplets and their biogenesis. Chem Phys Lipids 2018; 211:93-99. [DOI: 10.1016/j.chemphyslip.2017.11.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 10/03/2017] [Accepted: 11/09/2017] [Indexed: 12/21/2022]
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Alcalá AC, Hernández-Bravo R, Medina F, Coll DS, Zambrano JL, del Angel RM, Ludert JE. The dengue virus non-structural protein 1 (NS1) is secreted from infected mosquito cells via a non-classical caveolin-1-dependent pathway. J Gen Virol 2017; 98:2088-2099. [DOI: 10.1099/jgv.0.000881] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Affiliation(s)
- Ana C. Alcalá
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), CDMX, Mexico
| | - Raiza Hernández-Bravo
- Exploration and Production Research Office, Mexican Petroleum Institute (IMP), Mexico City, Mexico
| | - Fernando Medina
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), CDMX, Mexico
| | - David S. Coll
- Center of Chemistry, Venezuelan Institute for Scientific Research (IVIC), Caracas, Venezuela
| | - Jose L. Zambrano
- Center of Microbiology and Cell Biology, Venezuelan Institute for Scientific Research (IVIC), Caracas, Venezuela
| | - Rosa M. del Angel
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), CDMX, Mexico
| | - Juan E. Ludert
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), CDMX, Mexico
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A pH-Mediated Topological Switch within the N-Terminal Domain of Human Caveolin-3. Biophys J 2017; 110:2475-2485. [PMID: 27276265 DOI: 10.1016/j.bpj.2016.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 04/27/2016] [Accepted: 05/02/2016] [Indexed: 11/22/2022] Open
Abstract
Caveolins mediate the formation of caveolae, which are small omega-shaped membrane invaginations involved in a variety of cellular processes. There are three caveolin isoforms, the third of which (Cav3) is expressed in smooth and skeletal muscles. Mutations in Cav3 cause a variety of human muscular diseases. In this work, we characterize the secondary structure, dynamics, and topology of the monomeric form of the full-length lipidated protein. Cav3 consists of a series of membrane-embedded or surface-associated helical elements connected by extramembrane connecting loops or disordered domains. Our results also reveal that the N-terminal domain undergoes a large scale pH-mediated topological rearrangement between soluble and membrane-anchored forms. Considering that roughly one-third of pathogenic mutations in Cav3 influence charged residues located in this domain, we hypothesize that this transition is likely to be relevant to the molecular basis of Cav3-linked diseases. These results provide insight into the structure of Cav3 and set the stage for mechanistic investigations of the effects of pathogenic mutations.
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20
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Busija AR, Patel HH, Insel PA. Caveolins and cavins in the trafficking, maturation, and degradation of caveolae: implications for cell physiology. Am J Physiol Cell Physiol 2017; 312:C459-C477. [PMID: 28122734 DOI: 10.1152/ajpcell.00355.2016] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 01/09/2023]
Abstract
Caveolins (Cavs) are ~20 kDa scaffolding proteins that assemble as oligomeric complexes in lipid raft domains to form caveolae, flask-shaped plasma membrane (PM) invaginations. Caveolae ("little caves") require lipid-lipid, protein-lipid, and protein-protein interactions that can modulate the localization, conformational stability, ligand affinity, effector specificity, and other functions of proteins that are partners of Cavs. Cavs are assembled into small oligomers in the endoplasmic reticulum (ER), transported to the Golgi for assembly with cholesterol and other oligomers, and then exported to the PM as an intact coat complex. At the PM, cavins, ~50 kDa adapter proteins, oligomerize into an outer coat complex that remodels the membrane into caveolae. The structure of caveolae protects their contents (i.e., lipids and proteins) from degradation. Cellular changes, including signal transduction effects, can destabilize caveolae and produce cavin dissociation, restructuring of Cav oligomers, ubiquitination, internalization, and degradation. In this review, we provide a perspective of the life cycle (biogenesis, degradation), composition, and physiologic roles of Cavs and caveolae and identify unanswered questions regarding the roles of Cavs and cavins in caveolae and in regulating cell physiology.1.
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Affiliation(s)
- Anna R Busija
- Department of Anesthesiology, University of California, San Diego, La Jolla, California.,Department of Pharmacology, University of California, San Diego, La Jolla, California
| | - Hemal H Patel
- Department of Anesthesiology, University of California, San Diego, La Jolla, California
| | - Paul A Insel
- Department of Medicine, University of California, San Diego, La Jolla, California; and .,Department of Pharmacology, University of California, San Diego, La Jolla, California
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21
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22
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Park S, Beaven AH, Klauda JB, Im W. How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets? J Chem Theory Comput 2016; 11:3466-77. [PMID: 26575780 PMCID: PMC4685941 DOI: 10.1021/acs.jctc.5b00232] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Difficulties in estimating the correct
number of lipids in each
leaflet of complex bilayer membrane simulation systems make it inevitable
to introduce a mismatch in lipid packing (i.e., area per lipid) and
thus alter the lateral pressure of each leaflet. To investigate potential
impacts of such mismatch on simulation results, we performed molecular
dynamics simulations of saturated and monounsaturated lipid bilayers
with and without gramicidin A or WALP23 at various mismatches by adjusting
the number of lipids in the lower leaflet from no mismatch to a 25%
reduction compared to that in the upper leaflet. All simulations were
stable under the constant pressure barostat, but the mismatch induces
asymmetric lipid packing between the leaflets, so that the upper leaflet
becomes more ordered, and the lower leaflet becomes less ordered.
The mismatch impacts on various bilayer properties are mild up to
5–10% mismatch, and bilayers with fully saturated chains appear
to be more prone to these impacts than those with unsaturated tails.
The nonvanishing leaflet surface tensions and the free energy derivatives
with respect to the bilayer curvature indicate that the bilayer would
be energetically unstable in the presence of mismatch. We propose
a quantitative criterion for allowable mismatch based on the energetics
derived from a continuum elastic model, which grows as a square root
of the number of the lipids in the system. On the basis of this criterion,
we infer that the area per lipid mismatch up to 5% would be tolerable
in various membrane simulations of reasonable all-atom system sizes
(40–160 lipids per leaflet).
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Affiliation(s)
| | | | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Program, University of Maryland , College Park, Maryland 20742, United States
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23
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Probing the structure and dynamics of caveolin-1 in a caveolae-mimicking asymmetric lipid bilayer model. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 45:511-21. [DOI: 10.1007/s00249-016-1118-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 12/09/2015] [Accepted: 02/10/2016] [Indexed: 01/28/2023]
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24
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Cheng X, Jo S, Qi Y, Marassi FM, Im W. Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes. Biophys J 2016; 108:1954-62. [PMID: 25902435 DOI: 10.1016/j.bpj.2015.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/05/2015] [Accepted: 03/10/2015] [Indexed: 10/23/2022] Open
Abstract
Solid-state NMR has been used to determine the structures of membrane proteins in native-like lipid bilayer environments. Most structure calculations based on solid-state NMR observables are performed using simulated annealing with restrained molecular dynamics and an energy function, where all nonbonded interactions are represented by a single, purely repulsive term with no contributions from van der Waals attractive, electrostatic, or solvation energy. To our knowledge, this is the first application of an ensemble dynamics technique performed in explicit membranes that uses experimental solid-state NMR observables to obtain the refined structure of a membrane protein together with information about its dynamics and its interactions with lipids. Using the membrane-bound form of the fd coat protein as a model membrane protein and its experimental solid-state NMR data, we performed restrained ensemble dynamics simulations with different ensemble sizes in explicit membranes. For comparison, a molecular dynamics simulation of fd coat protein was also performed without any restraints. The average orientation of each protein helix is similar to a structure determined by traditional single-conformer approaches. However, their variations are limited in the resulting ensemble of structures with one or two replicas, as they are under the strong influence of solid-state NMR restraints. Although highly consistent with all solid-state NMR observables, the ensembles of more than two replicas show larger orientational variations similar to those observed in the molecular dynamics simulation without restraints. In particular, in these explicit membrane simulations, Lys(40), residing at the C-terminal side of the transmembrane helix, is observed to cause local membrane curvature. Therefore, compared to traditional single-conformer approaches in implicit environments, solid-state NMR restrained ensemble simulations in explicit membranes readily characterize not only protein dynamics but also protein-lipid interactions in detail.
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Affiliation(s)
- Xi Cheng
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Sunhwan Jo
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Yifei Qi
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | | | - Wonpil Im
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas.
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25
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Root KT, Glover KJ. Reconstitution and spectroscopic analysis of caveolin-1 residues 62-178 reveals that proline 110 governs its structure and solvent exposure. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:682-8. [PMID: 26775739 DOI: 10.1016/j.bbamem.2016.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 12/04/2015] [Accepted: 01/06/2016] [Indexed: 12/21/2022]
Abstract
Caveolin-1 is a membrane protein that possesses an unusual topology where both N- and C-termini are cytoplasmic as a result of a membrane-embedded turn. In particular, proline 110 has been postulated to be the linchpin of this unusual motif. Using a caveolin-1 construct (residues 62-178) reconstituted into dodecylphosphocholine micelles with and without a cholesterol mimic, the changes that occurred upon P110A mutation were probed. Using far UV circular dichroism spectroscopy it was shown that cholesterol attenuated the helicity of caveolin-1, and that mutation of P110 to alanine caused a significant increase in the α-helicity of the protein. Near UV circular dichroism spectroscopy showed significant changes in structure and/or environment upon mutation that again were modulated by the presence of cholesterol. Stern-Volmer quenching and λ(max) analysis of tryptophan residues showed that the proline mutation caused W85 to become more exposed, W98 and W115 to become less exposed, and W128 showed no change. This finding provided evidence that regions proximal and far away from the proline are buried differentially upon its mutation and therefore this residue is strongly tied to maintaining the hydrophobic coverage along the caveolin-1 sequence. In the presence of cholesterol, the accessibilities of the two tryptophan residues that proceeded position 110 were altered much more significantly upon P110A mutation than the two tryptophans aft P110. Overall, this work provides strong evidence that proline 110 is critical for maintaining both the structure and hydrophobic coverage of caveolin-1 and that cholesterol also plays a significant role in modulating these parameters.
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Affiliation(s)
- Kyle T Root
- Department of Chemistry, Lehigh University, 6 E. Packer Ave., Bethlehem, PA 18015, USA
| | - Kerney Jebrell Glover
- Department of Chemistry, Lehigh University, 6 E. Packer Ave., Bethlehem, PA 18015, USA.
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26
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Kraehling JR, Hao Z, Lee MY, Vinyard DJ, Velazquez H, Liu X, Stan RV, Brudvig GW, Sessa WC. Uncoupling Caveolae From Intracellular Signaling In Vivo. Circ Res 2015; 118:48-55. [PMID: 26602865 DOI: 10.1161/circresaha.115.307767] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 11/24/2015] [Indexed: 11/16/2022]
Abstract
RATIONALE Caveolin-1 (Cav-1) negatively regulates endothelial nitric oxide (NO) synthase-derived NO production, and this has been mapped to several residues on Cav-1, including F92. Herein, we reasoned that endothelial expression of an F92ACav-1 transgene would let us decipher the mechanisms and relationships between caveolae structure and intracellular signaling. OBJECTIVE This study was designed to separate caveolae formation from its downstream signaling effects. METHODS AND RESULTS An endothelial-specific doxycycline-regulated mouse model for the expression of Cav-1-F92A was developed. Blood pressure by telemetry and nitric oxide bioavailability by electron paramagnetic resonance and phosphorylation of vasodilator-stimulated phosphoprotein were determined. Caveolae integrity in the presence of Cav-1-F92A was measured by stabilization of caveolin-2, sucrose gradient, and electron microscopy. Histological analysis of heart and lung, echocardiography, and signaling were performed. CONCLUSIONS This study shows that mutant Cav-1-F92A forms caveolae structures similar to WT but leads to increases in NO bioavailability in vivo, thereby demonstrating that caveolae formation and downstream signaling events occur through independent mechanisms.
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Affiliation(s)
- Jan R Kraehling
- From the Vascular Biology and Therapeutics Program (J.R.K., Z.H., M.Y.L., W.C.S.) and Department of Pharmacology (J.R.K., Z.H., M.Y.L., W.C.S.), Yale University School of Medicine, New Haven, CT; Department of Chemistry, Yale University, New Haven, CT (D.J.V., G.W.B.); Department of Internal Medicine, VA Connecticut Healthcare System, West Haven, CT (H.V.); Department of Cell Biology, Yale University, School of Medicine, New Haven, CT (X.L.); and Department of Pathology, Dartmouth Medical School, Lebanon, NH (R.V.S.)
| | - Zhengrong Hao
- From the Vascular Biology and Therapeutics Program (J.R.K., Z.H., M.Y.L., W.C.S.) and Department of Pharmacology (J.R.K., Z.H., M.Y.L., W.C.S.), Yale University School of Medicine, New Haven, CT; Department of Chemistry, Yale University, New Haven, CT (D.J.V., G.W.B.); Department of Internal Medicine, VA Connecticut Healthcare System, West Haven, CT (H.V.); Department of Cell Biology, Yale University, School of Medicine, New Haven, CT (X.L.); and Department of Pathology, Dartmouth Medical School, Lebanon, NH (R.V.S.)
| | - Monica Y Lee
- From the Vascular Biology and Therapeutics Program (J.R.K., Z.H., M.Y.L., W.C.S.) and Department of Pharmacology (J.R.K., Z.H., M.Y.L., W.C.S.), Yale University School of Medicine, New Haven, CT; Department of Chemistry, Yale University, New Haven, CT (D.J.V., G.W.B.); Department of Internal Medicine, VA Connecticut Healthcare System, West Haven, CT (H.V.); Department of Cell Biology, Yale University, School of Medicine, New Haven, CT (X.L.); and Department of Pathology, Dartmouth Medical School, Lebanon, NH (R.V.S.)
| | - David J Vinyard
- From the Vascular Biology and Therapeutics Program (J.R.K., Z.H., M.Y.L., W.C.S.) and Department of Pharmacology (J.R.K., Z.H., M.Y.L., W.C.S.), Yale University School of Medicine, New Haven, CT; Department of Chemistry, Yale University, New Haven, CT (D.J.V., G.W.B.); Department of Internal Medicine, VA Connecticut Healthcare System, West Haven, CT (H.V.); Department of Cell Biology, Yale University, School of Medicine, New Haven, CT (X.L.); and Department of Pathology, Dartmouth Medical School, Lebanon, NH (R.V.S.)
| | - Heino Velazquez
- From the Vascular Biology and Therapeutics Program (J.R.K., Z.H., M.Y.L., W.C.S.) and Department of Pharmacology (J.R.K., Z.H., M.Y.L., W.C.S.), Yale University School of Medicine, New Haven, CT; Department of Chemistry, Yale University, New Haven, CT (D.J.V., G.W.B.); Department of Internal Medicine, VA Connecticut Healthcare System, West Haven, CT (H.V.); Department of Cell Biology, Yale University, School of Medicine, New Haven, CT (X.L.); and Department of Pathology, Dartmouth Medical School, Lebanon, NH (R.V.S.)
| | - Xinran Liu
- From the Vascular Biology and Therapeutics Program (J.R.K., Z.H., M.Y.L., W.C.S.) and Department of Pharmacology (J.R.K., Z.H., M.Y.L., W.C.S.), Yale University School of Medicine, New Haven, CT; Department of Chemistry, Yale University, New Haven, CT (D.J.V., G.W.B.); Department of Internal Medicine, VA Connecticut Healthcare System, West Haven, CT (H.V.); Department of Cell Biology, Yale University, School of Medicine, New Haven, CT (X.L.); and Department of Pathology, Dartmouth Medical School, Lebanon, NH (R.V.S.)
| | - Radu V Stan
- From the Vascular Biology and Therapeutics Program (J.R.K., Z.H., M.Y.L., W.C.S.) and Department of Pharmacology (J.R.K., Z.H., M.Y.L., W.C.S.), Yale University School of Medicine, New Haven, CT; Department of Chemistry, Yale University, New Haven, CT (D.J.V., G.W.B.); Department of Internal Medicine, VA Connecticut Healthcare System, West Haven, CT (H.V.); Department of Cell Biology, Yale University, School of Medicine, New Haven, CT (X.L.); and Department of Pathology, Dartmouth Medical School, Lebanon, NH (R.V.S.)
| | - Gary W Brudvig
- From the Vascular Biology and Therapeutics Program (J.R.K., Z.H., M.Y.L., W.C.S.) and Department of Pharmacology (J.R.K., Z.H., M.Y.L., W.C.S.), Yale University School of Medicine, New Haven, CT; Department of Chemistry, Yale University, New Haven, CT (D.J.V., G.W.B.); Department of Internal Medicine, VA Connecticut Healthcare System, West Haven, CT (H.V.); Department of Cell Biology, Yale University, School of Medicine, New Haven, CT (X.L.); and Department of Pathology, Dartmouth Medical School, Lebanon, NH (R.V.S.)
| | - William C Sessa
- From the Vascular Biology and Therapeutics Program (J.R.K., Z.H., M.Y.L., W.C.S.) and Department of Pharmacology (J.R.K., Z.H., M.Y.L., W.C.S.), Yale University School of Medicine, New Haven, CT; Department of Chemistry, Yale University, New Haven, CT (D.J.V., G.W.B.); Department of Internal Medicine, VA Connecticut Healthcare System, West Haven, CT (H.V.); Department of Cell Biology, Yale University, School of Medicine, New Haven, CT (X.L.); and Department of Pathology, Dartmouth Medical School, Lebanon, NH (R.V.S.)
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Kumar A, Baycin-Hizal D, Zhang Y, Bowen MA, Betenbaugh MJ. Cellular traffic cops: the interplay between lipids and proteins regulates vesicular formation, trafficking, and signaling in mammalian cells. Curr Opin Biotechnol 2015; 36:215-21. [PMID: 26540512 DOI: 10.1016/j.copbio.2015.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 08/18/2015] [Accepted: 09/17/2015] [Indexed: 11/30/2022]
Abstract
Protein secretion and vesicular trafficking in mammalian cells rely on several key lipids including sphingolipids, phospholipids, and neutral lipids crucial to protein processing and other intracellular events. Proteins interact with these lipids to alter the shape of lipid bilayer, thereby playing a pivotal role in cellular sorting. Although some efforts have elucidated the role of these components, extensive studies are needed to further decipher the protein-lipid interactions along with the effect of membrane curvature and rafts in sorting of proteins. The regulatory role of proteins in subcellular localization and metabolism of lipids also needs to be described. Recent studies on the role of lipid-protein interactions in modulating membrane shape, signal transduction, and vesicular trafficking are presented in this review.
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Affiliation(s)
- Amit Kumar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Deniz Baycin-Hizal
- Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, MD 20878, USA
| | - Yue Zhang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Michael A Bowen
- Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, MD 20878, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
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28
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Ariotti N, Rae J, Leneva N, Ferguson C, Loo D, Okano S, Hill MM, Walser P, Collins BM, Parton RG. Molecular Characterization of Caveolin-induced Membrane Curvature. J Biol Chem 2015; 290:24875-90. [PMID: 26304117 DOI: 10.1074/jbc.m115.644336] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Indexed: 01/07/2023] Open
Abstract
The generation of caveolae involves insertion of the cholesterol-binding integral membrane protein caveolin-1 (Cav1) into the membrane, however, the precise molecular mechanisms are as yet unknown. We have speculated that insertion of the caveolin scaffolding domain (CSD), a conserved amphipathic region implicated in interactions with signaling proteins, is crucial for caveola formation. We now define the core membrane-juxtaposed region of Cav1 and show that the oligomerization domain and CSD are protected by tight association with the membrane in both mature mammalian caveolae and a model prokaryotic system for caveola biogenesis. Cryoelectron tomography reveals the core membrane-juxtaposed domain to be sufficient to maintain oligomerization as defined by polyhedral distortion of the caveolar membrane. Through mutagenesis we demonstrate the importance of the membrane association of the oligomerization domain/CSD for defined caveola biogenesis and furthermore, highlight the functional significance of the intramembrane domain and the CSD for defined caveolin-induced membrane deformation. Finally, we define the core structural domain of Cav1, constituting only 66 amino acids and of great potential to nanoengineering applications, which is required for caveolin-induced vesicle formation in a bacterial system. These results have significant implications for understanding the role of Cav1 in caveola formation and in regulating cellular signaling events.
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Affiliation(s)
- Nicholas Ariotti
- From the University of Queensland, Institute for Molecular Bioscience, Queensland 4072, Australia
| | - James Rae
- From the University of Queensland, Institute for Molecular Bioscience, Queensland 4072, Australia
| | - Natalya Leneva
- From the University of Queensland, Institute for Molecular Bioscience, Queensland 4072, Australia
| | - Charles Ferguson
- From the University of Queensland, Institute for Molecular Bioscience, Queensland 4072, Australia
| | - Dorothy Loo
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Queensland,Australia, and
| | - Satomi Okano
- From the University of Queensland, Institute for Molecular Bioscience, Queensland 4072, Australia
| | - Michelle M Hill
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Queensland,Australia, and
| | - Piers Walser
- From the University of Queensland, Institute for Molecular Bioscience, Queensland 4072, Australia
| | - Brett M Collins
- From the University of Queensland, Institute for Molecular Bioscience, Queensland 4072, Australia
| | - Robert G Parton
- From the University of Queensland, Institute for Molecular Bioscience, Queensland 4072, Australia, the University of Queensland, Centre for Microscopy and Microanalysis, Brisbane, Queensland 4072, Australia
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29
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Root KT, Plucinsky SM, Glover KJ. Recent progress in the topology, structure, and oligomerization of caveolin: a building block of caveolae. CURRENT TOPICS IN MEMBRANES 2015; 75:305-36. [PMID: 26015287 DOI: 10.1016/bs.ctm.2015.03.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Caveolae are cholesterol-rich plasma membrane invaginations that are found in a plethora of cell types. They play many roles including signal transduction, endocytosis, and mechanoprotection. The most critical protein in caveolae is the integral membrane protein, caveolin, which has been shown to be necessary for caveolae formation, and governs the major functions attributed to caveolae. Caveolin is postulated to act as a scaffold in the high molecular weight striated coat that surrounds the caveolar bulb, stabilizing it. Caveolin interacts, both directly and indirectly, with a large number of signaling molecules, and presides over the endocytosis of molecular cargo by caveolae. However, many of the key biophysical aspects of the caveolin protein, its structure, topology, and oligomeric behavior, are just beginning to come to light. Herein is an up-to-date summary and critique of the progress that has been made in understanding caveolin on a molecular and atomic level.
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Affiliation(s)
- Kyle T Root
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA
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30
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Wu EL, Cheng X, Jo S, Rui H, Song KC, Dávila-Contreras EM, Qi Y, Lee J, Monje-Galvan V, Venable RM, Klauda JB, Im W. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J Comput Chem 2014; 35:1997-2004. [PMID: 25130509 DOI: 10.1002/jcc.23702] [Citation(s) in RCA: 1619] [Impact Index Per Article: 161.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/16/2014] [Accepted: 07/18/2014] [Indexed: 01/12/2023]
Abstract
CHARMM-GUI Membrane Builder, http://www.charmm-gui.org/input/membrane, is a web-based user interface designed to interactively build all-atom protein/membrane or membrane-only systems for molecular dynamics simulations through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types, such as phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance-based algorithm for faster initial ion displacement, (5) CHARMM inputs for P21 image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: CL lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM-GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments.
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Affiliation(s)
- Emilia L Wu
- Department of Molecular Biosciences and Center for Bioinformatics, University of Kansas, Lawrence, Kansas, 66047
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Kim JH, Peng D, Schlebach JP, Hadziselimovic A, Sanders CR. Modest effects of lipid modifications on the structure of caveolin-3. Biochemistry 2014; 53:4320-2. [PMID: 24960539 PMCID: PMC4100780 DOI: 10.1021/bi5005238] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
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Caveolin-3
(Cav3) is an unconventional membrane protein that serves
as a critical scaffolding hub in caveolae and is genetically linked
to various muscle disorders. In this work, we report the expression,
purification, and characterization of full-length human Cav3. To mimic
the palmitoylation of endogenous Cav3, we developed a generally applicable
approach to covalently attached thioalkyl chains at natively modified
cysteine residues. Nuclear magnetic resonance measurements indicate
that lipidation exerts only a modest and local effect on the Cav3
structure, with little impact on the structures of the N-terminal
domain, the scaffolding domain, and the extreme C-terminus.
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Affiliation(s)
- Ji-Hun Kim
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine , Nashville, Tennessee 37232, United States
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