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Chatzigoulas A, Cournia Z. DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design. Bioinformatics 2022; 38:5449-5451. [PMID: 36355565 PMCID: PMC9750117 DOI: 10.1093/bioinformatics/btac680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/20/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
SUMMARY The allosteric modulation of peripheral membrane proteins (PMPs) by targeting protein-membrane interactions with drug-like molecules represents a new promising therapeutic strategy for proteins currently considered undruggable. However, the accessibility of protein-membrane interfaces by small molecules has been so far unexplored, possibly due to the complexity of the interface, the limited protein-membrane structural information and the lack of computational workflows to study it. Herein, we present a pipeline for drugging protein-membrane interfaces using the DREAMM (Drugging pRotein mEmbrAne Machine learning Method) web server. DREAMM works in the back end with a fast and robust ensemble machine learning algorithm for identifying protein-membrane interfaces of PMPs. Additionally, DREAMM also identifies binding pockets in the vicinity of the predicted membrane-penetrating amino acids in protein conformational ensembles provided by the user or generated within DREAMM. AVAILABILITY AND IMPLEMENTATION DREAMM web server is accessible via https://dreamm.ni4os.eu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alexios Chatzigoulas
- Biomedical Research Foundation, Academy of Athens, Athens 11527, Greece,Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Athens 15784, Greece
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Chatzigoulas A, Cournia Z. Predicting protein–membrane interfaces of peripheral membrane proteins using ensemble machine learning. Brief Bioinform 2022; 23:6527274. [PMID: 35152294 PMCID: PMC8921665 DOI: 10.1093/bib/bbab518] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/23/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022] Open
Abstract
Abstract
Abnormal protein–membrane attachment is involved in deregulated cellular pathways and in disease. Therefore, the possibility to modulate protein–membrane interactions represents a new promising therapeutic strategy for peripheral membrane proteins that have been considered so far undruggable. A major obstacle in this drug design strategy is that the membrane-binding domains of peripheral membrane proteins are usually unknown. The development of fast and efficient algorithms predicting the protein–membrane interface would shed light into the accessibility of membrane–protein interfaces by drug-like molecules. Herein, we describe an ensemble machine learning methodology and algorithm for predicting membrane-penetrating amino acids. We utilize available experimental data from the literature for training 21 machine learning classifiers and meta-classifiers. Evaluation of the best ensemble classifier model accuracy yields a macro-averaged F1 score = 0.92 and a Matthews correlation coefficient = 0.84 for predicting correctly membrane-penetrating amino acids on unknown proteins of a validation set. The python code for predicting protein–membrane interfaces of peripheral membrane proteins is available at https://github.com/zoecournia/DREAMM.
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Affiliation(s)
- Alexios Chatzigoulas
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
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3
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Bays JL, DeMali KA. Vinculin in cell-cell and cell-matrix adhesions. Cell Mol Life Sci 2017; 74:2999-3009. [PMID: 28401269 PMCID: PMC5501900 DOI: 10.1007/s00018-017-2511-3] [Citation(s) in RCA: 273] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 02/07/2023]
Abstract
Vinculin was identified as a component of focal adhesions and adherens junctions nearly 40 years ago. Since that time, remarkable progress has been made in understanding its activation, regulation and function. Here we discuss the current understanding of the roles of vinculin in cell–cell and cell–matrix adhesions. Emphasis is placed on the how vinculin is recruited, activated and regulated. We also highlight the recent understanding of how vinculin responds to and transmits force at integrin- and cadherin-containing adhesion complexes to the cytoskeleton. Furthermore, we discuss roles of vinculin in binding to and rearranging the actin cytoskeleton.
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Affiliation(s)
- Jennifer L Bays
- Department of Biochemistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Kris A DeMali
- Department of Biochemistry, University of Iowa, Iowa City, IA, 52242, USA.
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4
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Role of the Helix in Talin F3 Domain (F3 Helix) in Talin-Mediated Integrin Activation. Cell Biochem Biophys 2017; 75:79-86. [PMID: 28101696 DOI: 10.1007/s12013-017-0781-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 01/09/2017] [Indexed: 02/05/2023]
Abstract
Increases in ligand binding to cellular integrins (activation) play an important role in platelet and leukocyte function. Talin is necessary in vivo and sufficient in vitro for integrin αIIbβ3 activation. The precise mechanisms by which talin activates integrin are still being elucidated. In particular, talin undergoes conformational changes (around the F3 helix) and inserts the F3 helix into lipid bilayer; however, the connection between this lipid-inserting mechanism of talin and talin's capacity to activate integrin has never been explored before. In this work, we used rational mutagenesis, modeled cell systems, and structural modeling to study the potential role of membrane-induced talin conformational changes in talin-mediated integrin activation. Mutations of the residues critical for talin F3 helix to insert into membrane completely abolished talin-mediated integrin activation without affecting the binding of talin to integrins. Furthermore, mutations of the lipid-binding sequences in talin F3 helix significantly reduced the capacity of talin to activate integrin. Our results suggest that the F3 helix may contribute to talin-mediated integrin activation.
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5
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Goldmann WH. Role of vinculin in cellular mechanotransduction. Cell Biol Int 2016; 40:241-56. [DOI: 10.1002/cbin.10563] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 11/14/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Wolfgang H. Goldmann
- Department of Biophysics; Friedrich-Alexander-University of Erlangen-Nuremberg; Erlangen Germany
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6
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Liu N, Van Voorst JR, Johnston JB, Kuhn LA. CholMine: Determinants and Prediction of Cholesterol and Cholate Binding Across Nonhomologous Protein Structures. J Chem Inf Model 2015; 55:747-59. [PMID: 25760928 DOI: 10.1021/ci5006542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Identifying physiological ligands is necessary for annotating new protein structures, yet this presents a significant challenge to biologists and pharmaceutical chemists. Here we develop a predictor of cholesterol and cholate binding that works across diverse protein families, extending beyond sequence motif-based prediction. This approach combines SimSite3D site comparison with the detection of conserved interactions in cholesterol/cholate bound crystal structures to define three-dimensional interaction motifs. The resulting predictor identifies cholesterol sites with an ∼82% unbiased true positive rate in both membrane and soluble proteins, with a very low false positive rate relative to other predictors. The CholMine Web server can analyze users' structures, detect those likely to bind cholesterol/cholate, and predict the binding mode and key interactions. By deciphering the determinants of binding for these important steroids, CholMine may also aid in the design of selective inhibitors and detergents for targets such as G protein coupled receptors and bile acid receptors.
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Affiliation(s)
- Nan Liu
- †Department of Chemistry, ‡Department of Computer Science and Engineering, and §Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, United States
| | - Jeffrey R Van Voorst
- †Department of Chemistry, ‡Department of Computer Science and Engineering, and §Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, United States
| | - John B Johnston
- †Department of Chemistry, ‡Department of Computer Science and Engineering, and §Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, United States
| | - Leslie A Kuhn
- †Department of Chemistry, ‡Department of Computer Science and Engineering, and §Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, United States
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7
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Mahalingam R, Peng HP, Yang AS. Prediction of fatty acid-binding residues on protein surfaces with three-dimensional probability distributions of interacting atoms. Biophys Chem 2014; 192:10-9. [PMID: 24934883 DOI: 10.1016/j.bpc.2014.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/22/2014] [Accepted: 05/22/2014] [Indexed: 10/25/2022]
Abstract
Protein-fatty acid interaction is vital for many cellular processes and understanding this interaction is important for functional annotation as well as drug discovery. In this work, we present a method for predicting the fatty acid (FA)-binding residues by using three-dimensional probability density distributions of interacting atoms of FAs on protein surfaces which are derived from the known protein-FA complex structures. A machine learning algorithm was established to learn the characteristic patterns of the probability density maps specific to the FA-binding sites. The predictor was trained with five-fold cross validation on a non-redundant training set and then evaluated with an independent test set as well as on holo-apo pair's dataset. The results showed good accuracy in predicting the FA-binding residues. Further, the predictor developed in this study is implemented as an online server which is freely accessible at the following website, http://ismblab.genomics.sinica.edu.tw/.
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Affiliation(s)
| | - Hung-Pin Peng
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.
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8
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Multiple membrane interactions and versatile vesicle deformations elicited by melittin. Toxins (Basel) 2013; 5:637-64. [PMID: 23594437 PMCID: PMC3705284 DOI: 10.3390/toxins5040637] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/02/2013] [Accepted: 04/10/2013] [Indexed: 01/11/2023] Open
Abstract
Melittin induces various reactions in membranes and has been widely studied as a model for membrane-interacting peptide; however, the mechanism whereby melittin elicits its effects remains unclear. Here, we observed melittin-induced changes in individual giant liposomes using direct real-time imaging by dark-field optical microscopy, and the mechanisms involved were correlated with results obtained using circular dichroism, cosedimentation, fluorescence quenching of tryptophan residues, and electron microscopy. Depending on the concentration of negatively charged phospholipids in the membrane and the molecular ratio between lipid and melittin, melittin induced the “increasing membrane area”, “phased shrinkage”, or “solubilization” of liposomes. In phased shrinkage, liposomes formed small particles on their surface and rapidly decreased in size. Under conditions in which the increasing membrane area, phased shrinkage, or solubilization were mainly observed, the secondary structure of melittin was primarily estimated as an α-helix, β-like, or disordered structure, respectively. When the increasing membrane area or phased shrinkage occurred, almost all melittin was bound to the membranes and reached more hydrophobic regions of the membranes than when solubilization occurred. These results indicate that the various effects of melittin result from its ability to adopt various structures and membrane-binding states depending on the conditions.
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9
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Keller RCA. New user-friendly approach to obtain an Eisenberg plot and its use as a practical tool in protein sequence analysis. Int J Mol Sci 2011; 12:5577-91. [PMID: 22016610 PMCID: PMC3189734 DOI: 10.3390/ijms12095577] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 08/22/2011] [Accepted: 08/22/2011] [Indexed: 12/26/2022] Open
Abstract
The Eisenberg plot or hydrophobic moment plot methodology is one of the most frequently used methods of bioinformatics. Bioinformatics is more and more recognized as a helpful tool in Life Sciences in general, and recent developments in approaches recognizing lipid binding regions in proteins are promising in this respect. In this study a bioinformatics approach specialized in identifying lipid binding helical regions in proteins was used to obtain an Eisenberg plot. The validity of the Heliquest generated hydrophobic moment plot was checked and exemplified. This study indicates that the Eisenberg plot methodology can be transferred to another hydrophobicity scale and renders a user-friendly approach which can be utilized in routine checks in protein–lipid interaction and in protein and peptide lipid binding characterization studies. A combined approach seems to be advantageous and results in a powerful tool in the search of helical lipid-binding regions in proteins and peptides. The strength and limitations of the Eisenberg plot approach itself are discussed as well. The presented approach not only leads to a better understanding of the nature of the protein–lipid interactions but also provides a user-friendly tool for the search of lipid-binding regions in proteins and peptides.
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Affiliation(s)
- Rob C A Keller
- Section Chemistry, Charlemagne College, Wilhelminastraat 13-15, 6524 AJ Nijmegen, The Netherlands; E-Mail: ; Tel.: +0031-243820460
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10
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Prediction of Lipid-Binding Sites Based on Support Vector Machine and Position Specific Scoring Matrix. Protein J 2010; 29:427-31. [DOI: 10.1007/s10930-010-9269-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Wirth VF, List F, Diez G, Goldmann WH. Vinculin's C-terminal region facilitates phospholipid membrane insertion. Biochem Biophys Res Commun 2010; 398:433-7. [PMID: 20599708 DOI: 10.1016/j.bbrc.2010.06.094] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Accepted: 06/23/2010] [Indexed: 01/13/2023]
Abstract
The focal adhesion protein vinculin has been implicated in associating with soluble and membranous phospholipids. Here, we investigated the intermolecular interactions of two vinculin tail domains with membrane phospholipids. Previous studies have shown that the tail's unstructured C-terminus affects the mechanical behavior of cells, but not the H3 region. The aim of this work was to establish whether the C-terminal or the H3 region either associate favorably with or anchor in lipid membranes. This work characterizes the energetics and dynamics of phospholipid interactions using differential scanning calorimetry (DSC) as well as circular dichroism (CD) spectroscopy. Biochemical data from tryptophan quenching and SDS-PAGE experiments support calorimetric and CD spectroscopic findings insofar that only vinculin's C-terminus inserts into lipid membranes. These in vitro results provide further insight into the mechanical behavior of vinculin tail regions in cells and contribute to the understanding of their structure and function.
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Affiliation(s)
- Volker F Wirth
- Center for Medical Physics and Technology, Biophysics Group, Friedrich-Alexander-University, Erlangen-Nuremberg, Erlangen, Germany
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12
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Correlation between the interaction of the vinculin tail domain with lipid membranes, its phosphorylation and cell mechanical behaviour. Cell Biol Int 2010; 34:339-42. [DOI: 10.1042/cbi20100085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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13
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Brzeska H, Guag J, Remmert K, Chacko S, Korn ED. An experimentally based computer search identifies unstructured membrane-binding sites in proteins: application to class I myosins, PAKS, and CARMIL. J Biol Chem 2010; 285:5738-47. [PMID: 20018884 PMCID: PMC2820801 DOI: 10.1074/jbc.m109.066910] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Revised: 12/01/2009] [Indexed: 11/06/2022] Open
Abstract
Programs exist for searching protein sequences for potential membrane-penetrating segments (hydrophobic regions) and for lipid-binding sites with highly defined tertiary structures, such as PH, FERM, C2, ENTH, and other domains. However, a rapidly growing number of membrane-associated proteins (including cytoskeletal proteins, kinases, GTP-binding proteins, and their effectors) bind lipids through less structured regions. Here, we describe the development and testing of a simple computer search program that identifies unstructured potential membrane-binding sites. Initially, we found that both basic and hydrophobic amino acids, irrespective of sequence, contribute to the binding to acidic phospholipid vesicles of synthetic peptides that correspond to the putative membrane-binding domains of Acanthamoeba class I myosins. Based on these results, we modified a hydrophobicity scale giving Arg- and Lys-positive, rather than negative, values. Using this basic and hydrophobic scale with a standard search algorithm, we successfully identified previously determined unstructured membrane-binding sites in all 16 proteins tested. Importantly, basic and hydrophobic searches identified previously unknown potential membrane-binding sites in class I myosins, PAKs and CARMIL (capping protein, Arp2/3, myosin I linker; a membrane-associated cytoskeletal scaffold protein), and synthetic peptides and protein domains containing these newly identified sites bound to acidic phospholipids in vitro.
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Affiliation(s)
- Hanna Brzeska
- Laboratory of Cell Biology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892, USA.
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14
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Alcaide P, Auerbach S, Luscinskas FW. Neutrophil recruitment under shear flow: it's all about endothelial cell rings and gaps. Microcirculation 2009; 16:43-57. [PMID: 18720226 DOI: 10.1080/10739680802273892] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Leukocyte recruitment to tissues and organs is an essential component of host defense. The molecular mechanisms controlling this process are complex and remain under active investigation. The combination of biochemical techniques and live cell imaging using in vivo and in vitro flow-model approaches have shed light on several aspects of neutrophil transmigration through the vascular endothelial lining of blood vessels. Here, we focus on the role of adhesion molecule signaling in endothelial cells and their downstream targets during the process of transendothelial migration at cell-cell borders (paracellular transmigration). An emerging model involves the leukocyte beta2 integrin engagement of endothelial cell ICAM-1, which triggers integrin-ICAM-1 clustering (rings) and stabilizes leukocyte adhesion at cell-cell junctions. This step recruits nonreceptor tyrosine kinases that phosphorylate key tyrosine residues in the cytoplasmic tail of VE-cadherin, which destabilizes its linkage to catenins and the actin cytoskeleton, triggering the transient opening of VE-cadherin homodimers to form a gap in the cell junction, through which the neutrophil transmigrates. Interestingly, the signaling events that lead to neutrophil transmigration occur independently of shear flow in vitro.
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Affiliation(s)
- Pilar Alcaide
- Center for Excellence in Vascular Biology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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15
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Brzeska H, Hwang KJ, Korn ED. Acanthamoeba myosin IC colocalizes with phosphatidylinositol 4,5-bisphosphate at the plasma membrane due to the high concentration of negative charge. J Biol Chem 2008; 283:32014-23. [PMID: 18772133 PMCID: PMC2581559 DOI: 10.1074/jbc.m804828200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Revised: 08/27/2008] [Indexed: 11/06/2022] Open
Abstract
The tail of Acanthamoeba myosin IC (AMIC) has a basic region (BR), which contains a putative pleckstrin homology (PH) domain, followed by two Gly/Pro/Ala (GPA)-rich regions separated by a Src homology 3 (SH3) domain. Cryoelectron microscopy had shown that the tail is folded back on itself at the junction of BR and GPA1, and nuclear magnetic resonance spectroscopy indicated that the SH3 domain may interact with the putative PH domain. The BR binds to acidic phospholipids, and the GPA region binds to F-actin. We now show that the folded tail does not affect the affinity of AMIC for acidic phospholipids. AMIC binds phosphatidylinositol 4,5-bisphosphate (PIP2) with high affinity (approximately 1 microm), but binding is not stereospecific. When normalized to net negative charge, AMIC binds with equal affinity to phosphatidylserine (PS) and PIP2. This and other data show that the putative PH domain of AMIC is not a typical PIP2-specific PH domain. We have identified a 13-residue sequence of basic-hydrophobic-basic amino acids within the putative PH domain that may be a major determinant of binding of AMIC to acidic phospholipids. Despite the lack of stereospecificity, AMIC binds 10 times more strongly to vesicles containing 5% PIP2 plus 25% PS than to vesicles containing only 25% PS, suggesting that AMIC may be targeted to PIP2-enriched regions of the plasma membrane. In agreement with this, AMIC colocalizes with PIP2 at dynamic, protrusive regions of the plasma membrane. We discuss the possibility that AMIC binding to PIP2 may initiate the formation of a multiprotein complex at the plasma membrane.
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Affiliation(s)
- Hanna Brzeska
- Laboratory of Cell Biology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892, USA.
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Diez G, List F, Smith J, Ziegler WH, Goldmann WH. Direct evidence of vinculin tail–lipid membrane interaction in beta-sheet conformation. Biochem Biophys Res Commun 2008; 373:69-73. [DOI: 10.1016/j.bbrc.2008.05.182] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Accepted: 05/29/2008] [Indexed: 11/26/2022]
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18
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Thermodynamic evidence of non-muscle myosin II–lipid-membrane interaction. Biochem Biophys Res Commun 2008; 366:500-5. [DOI: 10.1016/j.bbrc.2007.11.170] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Accepted: 11/29/2007] [Indexed: 11/19/2022]
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19
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Chapter Eight Cytoskeletal Proteins at the Lipid Membrane. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s1554-4516(07)06008-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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20
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Thelen K, Wolfram T, Maier B, Jährling S, Tinazli A, Piehler J, Spatz JP, Pollerberg GE. Cell adhesion molecule DM-GRASP presented as nanopatterns to neurons regulates attachment and neurite growth. SOFT MATTER 2007; 3:1486-1491. [PMID: 32900102 DOI: 10.1039/b707250c] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Adhesion and neurite formation of neurons and neuroblastoma cells critically depends on the lateral spacing of the cell adhesion molecule DM-GRASP offered as nanostructured substrate.
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Affiliation(s)
- Karsten Thelen
- University of Heidelberg, Department of Developmental Neurobiology, Institute of Zoology, Im Neuenheimer Feld 232, 69120 Heidelberg, Germany
| | - Tobias Wolfram
- Max-Planck-Institute for Metals Research, Dept. New Materials and Biosystems, & University of Heidelberg, Dept. of Biophysical Chemistry, Heisenbergstrasse 3, 70569 Stuttgart, Germany and Institute for Molecular Biophysics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Bettina Maier
- University of Heidelberg, Department of Developmental Neurobiology, Institute of Zoology, Im Neuenheimer Feld 232, 69120 Heidelberg, Germany
| | - Steffen Jährling
- University of Heidelberg, Department of Developmental Neurobiology, Institute of Zoology, Im Neuenheimer Feld 232, 69120 Heidelberg, Germany
| | - Ahmed Tinazli
- Institute of Biochemistry, Biocenter N210, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Jacob Piehler
- Institute of Biochemistry, Biocenter N210, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Joachim P Spatz
- Max-Planck-Institute for Metals Research, Dept. New Materials and Biosystems, & University of Heidelberg, Dept. of Biophysical Chemistry, Heisenbergstrasse 3, 70569 Stuttgart, Germany
| | - G Elisabeth Pollerberg
- University of Heidelberg, Department of Developmental Neurobiology, Institute of Zoology, Im Neuenheimer Feld 232, 69120 Heidelberg, Germany
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Smith J, Diez G, Klemm AH, Schewkunow V, Goldmann WH. CapZ-lipid membrane interactions: a computer analysis. Theor Biol Med Model 2006; 3:30. [PMID: 16914033 PMCID: PMC1564000 DOI: 10.1186/1742-4682-3-30] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2006] [Accepted: 08/16/2006] [Indexed: 12/03/2022] Open
Abstract
Background CapZ is a calcium-insensitive and lipid-dependent actin filament capping protein, the main function of which is to regulate the assembly of the actin cytoskeleton. CapZ is associated with membranes in cells and it is generally assumed that this interaction is mediated by polyphosphoinositides (PPI) particularly PIP2, which has been characterized in vitro. Results We propose that non-PPI lipids also bind CapZ. Data from computer-aided sequence and structure analyses further suggest that CapZ could become partially buried in the lipid bilayer probably under mildly acidic conditions, in a manner that is not only dependent on the presence of PPIs. We show that lipid binding could involve a number of sites that are spread throughout the CapZ molecule i.e., alpha- and beta-subunits. However, a beta-subunit segment between residues 134–151 is most likely to be involved in interacting with and inserting into lipid membrane due to a slighly higher ratio of positively to negatively charged residues and also due to the presence of a small hydrophobic helix. Conclusion CapZ may therefore play an essential role in providing a stable membrane anchor for actin filaments.
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Affiliation(s)
- James Smith
- Friedrich-Alexander-University of Erlangen-Nuremberg Center for Medical Physics and Technology, Biophysics Group Henkestrasse 91, 91052 Erlangen, Germany
| | - Gerold Diez
- Friedrich-Alexander-University of Erlangen-Nuremberg Center for Medical Physics and Technology, Biophysics Group Henkestrasse 91, 91052 Erlangen, Germany
| | - Anna H Klemm
- Friedrich-Alexander-University of Erlangen-Nuremberg Center for Medical Physics and Technology, Biophysics Group Henkestrasse 91, 91052 Erlangen, Germany
| | - Vitali Schewkunow
- Friedrich-Alexander-University of Erlangen-Nuremberg Center for Medical Physics and Technology, Biophysics Group Henkestrasse 91, 91052 Erlangen, Germany
| | - Wolfgang H Goldmann
- Friedrich-Alexander-University of Erlangen-Nuremberg Center for Medical Physics and Technology, Biophysics Group Henkestrasse 91, 91052 Erlangen, Germany
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