174 results on '"Overduin M"'
Search Results
2. Calibration and preparation of field measurements of oblique wave run-up and overtopping on dikes using laser scanners
- Author
-
Oosterlo, P. Hofland, B. van der Meer, J. W. Overduin, M. Steendam, G. J. and Oosterlo, P. Hofland, B. van der Meer, J. W. Overduin, M. Steendam, G. J.
- Abstract
Wave overtopping is typically measured in the field using overtopping tanks. In this paper, an alternative system is developed that uses two laser scanners. The system also measures wave run-up, as well as run-up depths and velocities, both during perpendicular and oblique waves on a dike in the field. The paper considers the first calibration tests with the system in the field, with perpendicular and oblique waves generated by the wave run-up simulator on a grass dike slope. Furthermore, simulations are performed with the numerical wave model SWASH, to gain more insight in the potential performance of the system during actual oblique wave attack during a storm. The run-up is determined from the measured elevation and reflection intensity, which agrees well with the visually observed run-up. Run-up depths and front velocities can be determined accurately as well. The (virtual) wave overtopping discharge can be calculated from the data, which agrees well with the most commonly used overtopping equations for perpendicularly incident waves. Finally, from the simulated run-up data of obliquely incident waves, it is concluded that an estimate can be obtained of the incident wave period and wave angle of incidence at the toe of the structure.
- Published
- 2021
- Full Text
- View/download PDF
3. Structure-function analyses of dual-BON domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation to the cell division site
- Author
-
Bryant, J.A., primary, Morris, F.C., additional, Knowles, T.J., additional, Maderbocus, R., additional, Heinz, E., additional, Boelter, G., additional, Alodaini, D., additional, Colyer, A., additional, Wotherspoon, P.J., additional, Staunton, K.A., additional, Jeeves, M., additional, Browning, D.F., additional, Sevastsyanovich, Y.R., additional, Wells, T.J., additional, Rossiter, A.E., additional, Bavro, V.N., additional, Sridhar, P., additional, Ward, D.G., additional, Chong, Z.S., additional, Goodall, E.C.A., additional, Icke, C., additional, Teo, A., additional, Chng, S.S., additional, Roper, D.I., additional, Lithgow, T., additional, Cunningham, A.F., additional, Banzhaf, M., additional, Overduin, M., additional, and Henderson, I.R., additional
- Published
- 2020
- Full Text
- View/download PDF
4. Structure-function analyses of dual-BON domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation
- Author
-
Bryant, J. A., primary, Morris, F. C., additional, Knowles, T. J., additional, Maderbocus, R., additional, Heinz, E., additional, Boelter, G., additional, Alodaini, D., additional, Colyer, A., additional, Wotherspoon, P. J., additional, Staunton, K. A., additional, Jeeves, M., additional, Browning, D. F., additional, Sevastsyanovich, Y. R., additional, Wells, T. J., additional, Rossiter, A. E., additional, Bavro, V. N., additional, Sridhar, P., additional, Ward, D. G., additional, Chong, Z-S., additional, Icke, C., additional, Teo, A., additional, Chng, S-S., additional, Roper, D. I., additional, Lithgow, T., additional, Cunningham, A. F., additional, Banzhaf, M., additional, Overduin, M., additional, and Henderson, I. R., additional
- Published
- 2020
- Full Text
- View/download PDF
5. A method for detergent-free isolation of membrane proteins in their local lipid environment
- Author
-
Lee, SC, Knowles, TJ, Postis, VLG, Jamshad, M, Parslow, RA, Lin, YP, Goldman, A, Sridhar, P, Overduin, M, Muench, SP, and Dafforn, TR
- Abstract
Despite the great importance of membrane proteins, structural and functional studies of these proteins present major challenges. A significant hurdle is the extraction of the functional protein from its natural lipid membrane. Traditionally achieved with detergents, purification procedures can be costly and time consuming. A critical flaw with detergent approaches is the removal of the protein from the native lipid environment required to maintain functionally stable protein. This protocol describes the preparation of styrene maleic acid (SMA) co-polymer to extract membrane proteins from prokaryotic and eukaryotic expression systems. Successful isolation of membrane proteins into SMA lipid particles (SMALPs) allows the proteins to remain with native lipid, surrounded by SMA. We detail procedures for obtaining 25 g of SMA (4 d); explain the preparation of protein-containing SMALPs using membranes isolated from Escherichia coli (2 d) and control protein-free SMALPS using E. coli polar lipid extract (1–2 h); investigate SMALP protein purity by SDS–PAGE analysis and estimate protein concentration (4 h); and detail biophysical methods such as circular dichroism (CD) spectroscopy and sedimentation velocity analytical ultracentrifugation (svAUC) to undertake initial structural studies to characterize SMALPs (~2 d). Together, these methods provide a practical tool kit for those wanting to use SMALPs to study membrane proteins.
- Published
- 2016
6. The solution structure of Skint-1, a critical determinant of dendritic epidermal gamma-delta T cell selection
- Author
-
Salim, M., primary, Knowles, T.J., additional, Hart, R., additional, Mohammed, F., additional, Woodward, M.J., additional, Willcox, C.R., additional, Overduin, M., additional, Hayday, A.C., additional, and Willcox, B.E., additional
- Published
- 2016
- Full Text
- View/download PDF
7. Afgrenzing en angst op de gesloten afdeling
- Author
-
Hummelen, J.W., Overduin, M., van der Helm, P., Kröger, U., Schaftenaar, P., van Vliet, J., and Effective Criminal Law
- Published
- 2013
8. Crystal structure of human envoplakin plakin repeat domain
- Author
-
Mohammed, F., primary, Al-Jassar, C., additional, White, S.A., additional, Fogl, C., additional, Jeeves, M., additional, Knowles, T.J., additional, Odinstova, E., additional, Rodriguez-Zamora, P., additional, Overduin, M., additional, and Chidgey, M., additional
- Published
- 2015
- Full Text
- View/download PDF
9. Detergent-free purification of ABC (ATP-binding-cassette) transporters
- Author
-
Gulati, S., Jamshad, M., Knowles, T.J., Morrison, K.A., Downing, R., Cant, N., Collins, R., Koenderink, J.B., Ford, R.C., Overduin, M., Kerr, I.D., Dafforn, T.R., Rothnie, A.J., Gulati, S., Jamshad, M., Knowles, T.J., Morrison, K.A., Downing, R., Cant, N., Collins, R., Koenderink, J.B., Ford, R.C., Overduin, M., Kerr, I.D., Dafforn, T.R., and Rothnie, A.J.
- Abstract
Item does not contain fulltext, ABC (ATP-binding-cassette) transporters carry out many vital functions and are involved in numerous diseases, but study of the structure and function of these proteins is often hampered by their large size and membrane location. Membrane protein purification usually utilizes detergents to solubilize the protein from the membrane, effectively removing it from its native lipid environment. Subsequently, lipids have to be added back and detergent removed to reconstitute the protein into a lipid bilayer. In the present study, we present the application of a new methodology for the extraction and purification of ABC transporters without the use of detergent, instead, using a copolymer, SMA (polystyrene-co-maleic acid). SMA inserts into a bilayer and assembles into discrete particles, essentially solubilizing the membrane into small discs of bilayer encircled by a polymer, termed SMALPs (SMA lipid particles). We show that this polymer can extract several eukaryotic ABC transporters, P-glycoprotein (ABCB1), MRP1 (multidrug-resistance protein 1; ABCC1), MRP4 (ABCC4), ABCG2 and CFTR (cystic fibrosis transmembrane conductance regulator; ABCC7), from a range of different expression systems. The SMALP-encapsulated ABC transporters can be purified by affinity chromatography, and are able to bind ligands comparably with those in native membranes or detergent micelles. A greater degree of purity and enhanced stability is seen compared with detergent solubilization. The present study demonstrates that eukaryotic ABC transporters can be extracted and purified without ever being removed from their lipid bilayer environment, opening up a wide range of possibilities for the future study of their structure and function.
- Published
- 2014
10. Membrane Bilayer complex with Matrix Metalloproteinase-12 at its Alpha-face
- Author
-
Koppisetti, R.K., primary, Fulcher, Y.G., additional, Prior, S.H., additional, Lenoir, M., additional, Overduin, M., additional, and Van Doren, S.R., additional
- Published
- 2014
- Full Text
- View/download PDF
11. Membrane Bilayer complex with Matrix Metalloproteinase-12 at its Beta-face
- Author
-
Koppisetti, R.K., primary, Fulcher, Y.G., additional, Prior, S.H., additional, Lenoir, M., additional, Overduin, M., additional, and Van Doren, S.R., additional
- Published
- 2014
- Full Text
- View/download PDF
12. Solution structure of the human wild type FAPP1-PH domain
- Author
-
Lenoir, M., primary and Overduin, M., additional
- Published
- 2014
- Full Text
- View/download PDF
13. Op zoek naar een optimale supermarktindeling
- Author
-
Overduin, M. and Overduin, M.
- Abstract
Het doel van dit onderzoek is om meer informatie te verkrijgen over de preferenties van de consument op het gebied van supermarktindelingen en dan met name over welke productcategorie/productcategorieën er hierbij aan het begin van de supermarkt worden gepositioneerd.
- Published
- 2013
14. Secondary structure and H, C and N resonance assignments of Skint-1: a selecting ligand for a murine γδ T cell subset implicated in tumour suppression.
- Author
-
Salim, M., Willcox, C., Mohammed, F., Hayday, A., Overduin, M., Willcox, B., and Knowles, T.
- Abstract
A study describing the H, C and N backbone and side chain chemical shift assignments and secondary structure of Skint-1 a prototypic member of a family of mouse genes, of which Skint-1 is involved in the development of the dendritic epidermal T cell (DETC) subset of γδ T cells. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
15. Solution structure of the human AKAP13 PH domain and stabilizing DH helix
- Author
-
Lenoir, M., primary, Sugawara, M., additional, Ball, L., additional, and Overduin, M., additional
- Published
- 2011
- Full Text
- View/download PDF
16. Solution Structure of BamE, a component of the outer membrane protein assembly machinery in Escherichia coli
- Author
-
Knowles, T.J., primary, Sridhar, P., additional, Rajesh, S., additional, Manoli, E., additional, Henderson, I.R., additional, and Overduin, M., additional
- Published
- 2011
- Full Text
- View/download PDF
17. solution structure of FAPP1 PH domain
- Author
-
Lenoir, M., primary, Coskun, U., additional, James, J., additional, Simons, K., additional, and Overduin, M., additional
- Published
- 2009
- Full Text
- View/download PDF
18. Solution Structure of an Escherichia coli YaeT tandem POTRA domain
- Author
-
Knowles, T.J., primary, Jeeves, M., additional, Bobat, S., additional, Dancea, F., additional, Mcclelland, D.M., additional, Palmer, T., additional, Overduin, M., additional, and Henderson, I.R., additional
- Published
- 2008
- Full Text
- View/download PDF
19. Solution Structure of Sla1 Homology Domain 1
- Author
-
Overduin, M., primary and Mahadev, R.K., additional
- Published
- 2007
- Full Text
- View/download PDF
20. Structure of complement receptor (CR) 2 and CR2-C3d complexes
- Author
-
Hannan, J., primary, Young, K., additional, Szakonyi, G., additional, Overduin, M. J., additional, Perkins, S. J., additional, Chen, X., additional, and Holers, V. M., additional
- Published
- 2002
- Full Text
- View/download PDF
21. SOLUTION STRUCTURE OF THE EEA1 FYVE DOMAIN
- Author
-
Kutateladze, T., primary and Overduin, M., additional
- Published
- 2001
- Full Text
- View/download PDF
22. STRUCTURE OF THE SECOND EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15 IN COMPLEX WITH PTGSSSTNPFL
- Author
-
De Beer, T., primary, Hoofnagle, A.N., additional, Enmon, J.L., additional, Bowers, R.C., additional, Yamabhai, M., additional, Kay, B.K., additional, and Overduin, M., additional
- Published
- 2000
- Full Text
- View/download PDF
23. CR2/CD21 SCR1,2 domain ligand binding, physical properties and structural analysis
- Author
-
Guthridge, J., primary, Rakstang, J., additional, Young, K., additional, Hinshelwood, J., additional, Sarrias, M.R., additional, Moore, W., additional, Perkins, S.J., additional, Overduin, M., additional, Lambris, J.D., additional, Karp, D., additional, Hannan, J., additional, and Holers, V.M., additional
- Published
- 2000
- Full Text
- View/download PDF
24. STRUCTURE OF THE THIRD EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15
- Author
-
Enmon, J.L., primary, De Beer, T., additional, and Overduin, M., additional
- Published
- 2000
- Full Text
- View/download PDF
25. STRUCTURE OF THE SECOND EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15, NMR, 20 STRUCTURES
- Author
-
De Beer, T., primary, Carter, R.E., additional, Lobel-Rice, K.E., additional, Sorkin, A., additional, and Overduin, M., additional
- Published
- 1999
- Full Text
- View/download PDF
26. Structural basis of calcium-induced E-cadherin rigidification and dimerization
- Author
-
Nagar, B., primary, Overduin, M., additional, Ikura, M., additional, and Rini, J. M., additional
- Published
- 1996
- Full Text
- View/download PDF
27. THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE SRC HOMOLOGY 2 DOMAIN OF C-ABL
- Author
-
Overduin, M., primary, Rios, C.B., additional, Mayer, B.J., additional, Baltimore, D., additional, and Cowburn, D., additional
- Published
- 1994
- Full Text
- View/download PDF
28. Secondary structure of Src homology 2 domain of c-Abl by heteronuclear NMR spectroscopy in solution.
- Author
-
Overduin, M, primary, Mayer, B, additional, Rios, C B, additional, Baltimore, D, additional, and Cowburn, D, additional
- Published
- 1992
- Full Text
- View/download PDF
29. Three-dimensional solution structure of the src homology 2 domain of c-abl
- Author
-
Overduin, M, primary
- Published
- 1992
- Full Text
- View/download PDF
30. Small-Molecule Protein-Protein Interaction Inhibitor of Oncogenic Rho Signaling
- Author
-
Cynthia Gonano, Erica Reggi, Francesco Raimondi, Michael Overduin, Francesca Fanelli, Clare L. Box, Elisa Dreyer, Dario Diviani, Halima Osman, Lucia Ruggieri, Michele Seeber, Sabrina Cavin, Luca Bellucci, Cosmo D. del Vescovo, Marc Lenoir, Diviani, D., Raimondi, F., Del Vescovo, C. D., Dreyer, E., Reggi, E., Osman, H., Ruggieri, L., Gonano, C., Cavin, S., Box, C. L., Lenoir, M., Overduin, M., Bellucci, L., Seeber, M., and Fanelli, F.
- Subjects
0301 basic medicine ,Models, Molecular ,rho GTP-Binding Proteins ,RHOA ,Clinical Biochemistry ,A Kinase Anchor Proteins ,RhoGEF ,Biochemistry ,Protein–protein interaction ,Minor Histocompatibility Antigens ,Small Molecule Libraries ,comparative modeling ,03 medical and health sciences ,0302 clinical medicine ,Neoplasms ,Proto-Oncogene Proteins ,AKAP13 oncogene ,Drug Discovery ,Humans ,Molecular Biology ,Pharmacology ,Virtual screening ,biology ,Molecular Structure ,Drug Discovery3003 Pharmaceutical Science ,Mutagenesis ,Ras GTPases ,Alanine scanning ,virtual screening ,Molecular medicine ,Small molecule ,Phenotype ,3. Good health ,Cell biology ,030104 developmental biology ,030220 oncology & carcinogenesis ,biology.protein ,Molecular Medicine ,Ras GTPase ,RhoGEFs ,Protein Binding ,Signal Transduction - Abstract
Uncontrolled activation of Rho signaling by RhoGEFs, in particular AKAP13 (Lbc) and its close homologs, isimplicated in a number of human tumors with poor prognosis and resistance to therapy. Structure predictions and alanine scanning mutagenesis of Lbc identified a circumscribed hot region for RhoA recognition and activation. Virtual screening targeting that region led to the discovery of an inhibitor of Lbc-RhoA interaction inside cells. By interacting with the DH domain, the compound inhibits the catalytic activity of Lbc, halts cellular responses to activation of oncogenic Lbc pathways, and reverses a number of prostate cancer cell phenotypes such asproliferation, migration, and invasiveness. This study provides insights into the structural determinants of Lbc-RhoA recognition. This is a successful example of structure-based discovery of a small protein-protein interaction inhibitor able to halt oncogenic Rho signaling incancer cells with therapeutic implications.
- Published
- 2014
31. Growth differentiation factor 15 alleviates diastolic dysfunction in mice with experimental diabetic cardiomyopathy.
- Author
-
Chan JSF, Tabatabaei Dakhili SA, Lorenzana-Carrillo MA, Gopal K, Pulente SM, Greenwell AA, Yang K, Saed CT, Stenlund MJ, Ferrari SR, Mangra-Bala IA, Shafaati T, Bhat RK, Eaton F, Overduin M, Jørgensen SB, Steinberg GR, Mulvihill EE, Sutendra G, and Ussher JR
- Subjects
- Animals, Mice, Humans, Mice, Inbred C57BL, Male, Diastole drug effects, Diabetes Mellitus, Type 2 metabolism, Diabetes Mellitus, Type 2 complications, Inflammation pathology, Inflammation metabolism, Macrophages metabolism, Macrophages drug effects, THP-1 Cells, Obesity metabolism, Lipopolysaccharides pharmacology, Growth Differentiation Factor 15 metabolism, Diabetic Cardiomyopathies metabolism, Diabetic Cardiomyopathies pathology, Diabetic Cardiomyopathies drug therapy, Myocytes, Cardiac metabolism, Myocytes, Cardiac drug effects, Myocytes, Cardiac pathology
- Abstract
Growth differentiation factor 15 (GDF15) is a peptide with utility in obesity, as it decreases appetite and promotes weight loss. Because obesity increases the risk for type 2 diabetes (T2D) and cardiovascular disease, it is imperative to understand the cardiovascular actions of GDF15, especially since elevated GDF15 levels are an established biomarker for heart failure. As weight loss should be encouraged in the early stages of obesity-related prediabetes/T2D, where diabetic cardiomyopathy is often present, we assessed whether treatment with GDF15 influences its pathology. We observed that GDF15 treatment alleviates diastolic dysfunction in mice with T2D independent of weight loss. This cardioprotection was associated with a reduction in cardiac inflammation, which was likely mediated via indirect actions, as direct treatment of adult mouse cardiomyocytes and differentiated THP-1 human macrophages with GDF15 failed to alleviate lipopolysaccharide-induced inflammation. Therapeutic manipulation of GDF15 action may thus have utility for both obesity and diabetic cardiomyopathy., Competing Interests: Declaration of interests G.R.S. has received research funding through McMaster University from Esperion Therapeutics, Nestle, Merck, Cambrian Biosciences, Novo Nordisk, Poxel Pharmaceuticals, and Espervita Therapeutics; has received honoraria and/or consulting fees from AstraZeneca, Cambrian Biosciences, Eli-Lilly, Esperion Therapeutics, Fibrocor Therapeutics, Poxel Therapeutics, Novo Nordisk, and Merck; and is a founder and shareholder of Espervita Therapeutics. S.B.J. is an employee of Novo Nordisk A/S, a pharmaceutical company producing and selling medicine for the treatment of chronic diseases such as diabetes and obesity., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
32. Recruitment of Ahsa1 to Hsp90 is regulated by a conserved peptide that inhibits ATPase stimulation.
- Author
-
Hussein SK, Bhat R, Overduin M, and LaPointe P
- Subjects
- Humans, Protein Binding, Conserved Sequence, Amino Acid Motifs, Animals, Peptides metabolism, Peptides pharmacology, Peptides chemistry, Amino Acid Sequence, Molecular Chaperones metabolism, Molecular Chaperones genetics, Adenosine Triphosphate metabolism, Saccharomyces cerevisiae metabolism, Saccharomyces cerevisiae genetics, Receptors, Glucocorticoid metabolism, HSP90 Heat-Shock Proteins metabolism, Adenosine Triphosphatases metabolism
- Abstract
Hsp90 is a molecular chaperone that acts on its clients through an ATP-dependent and conformationally dynamic functional cycle. The cochaperone Accelerator of Hsp90 ATPase, or Ahsa1, is the most potent stimulator of Hsp90 ATPase activity. Ahsa1 stimulates the rate of Hsp90 ATPase activity through a conserved motif, NxNNWHW. Metazoan Ahsa1, but not yeast, possesses an additional 20 amino acid peptide preceding the NxNNWHW motif that we have called the intrinsic chaperone domain (ICD). The ICD of Ahsa1 diminishes Hsp90 ATPase stimulation by interfering with the function of the NxNNWHW motif. Furthermore, the NxNNWHW modulates Hsp90's apparent affinity to Ahsa1 and ATP. Lastly, the ICD controls the regulated recruitment of Hsp90 in cells and its deletion results in the loss of interaction with Hsp90 and the glucocorticoid receptor. This work provides clues to how Ahsa1 conserved regions modulate Hsp90 kinetics and how they may be coupled to client folding status., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
33. Recognition and remodeling of endosomal zones by sorting nexins.
- Author
-
Overduin M and Bhat R
- Subjects
- Sorting Nexins metabolism, Protein Transport, Proteolipids metabolism, Carrier Proteins chemistry, Vesicular Transport Proteins metabolism
- Abstract
The proteolipid code determines how cytosolic proteins find and remodel membrane surfaces. Here, we investigate how this process works with sorting nexins Snx1 and Snx3. Both proteins form sorting machines by recognizing membrane zones enriched in phosphatidylinositol 3-phosphate (PI3P), phosphatidylserine (PS) and cholesterol. This co-localized combination forms a unique "lipid codon" or lipidon that we propose is responsible for endosomal targeting, as revealed by structures and interactions of their PX domain-based readers. We outline a membrane recognition and remodeling mechanism for Snx1 and Snx3 involving this code element alongside transmembrane pH gradients, dipole moment-guided docking and specific protein-protein interactions. This generates an initial membrane-protein assembly (memtein) that then recruits retromer and additional PX proteins to recruit cell surface receptors for sorting to the trans-Golgi network (TGN), lysosome and plasma membranes. Post-translational modification (PTM) networks appear to regulate how the sorting machines form and operate at each level. The commonalities and differences between these sorting nexins show how the proteolipid code orchestrates parallel flows of molecular information from ribosome emergence to organelle genesis, and illuminates a universally applicable model of the membrane., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Michael Overduin reports funding was provided by Natural Sciences and Engineering Research Council of Canada. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
34. Membranes are functionalized by a proteolipid code.
- Author
-
Kervin TA and Overduin M
- Subjects
- Membranes metabolism, Cell Membrane metabolism, Proteolipids metabolism, Carrier Proteins metabolism
- Abstract
Membranes are protein and lipid structures that surround cells and other biological compartments. We present a conceptual model wherein all membranes are organized into structural and functional zones. The assembly of zones such as receptor clusters, protein-coated pits, lamellipodia, cell junctions, and membrane fusion sites is explained to occur through a protein-lipid code. This challenges the theory that lipids sort proteins after forming stable membrane subregions independently of proteins., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
35. A conserved epitope in VAR2CSA is targeted by a cross-reactive antibody originating from Plasmodium vivax Duffy binding protein.
- Author
-
Iyamu U, Vinals DF, Tornyigah B, Arango E, Bhat R, Adra TR, Grewal S, Martin K, Maestre A, Overduin M, Hazes B, and Yanow SK
- Subjects
- Pregnancy, Mice, Female, Rats, Animals, Plasmodium vivax, Epitopes, Plasmodium falciparum chemistry, Antibodies, Protozoan, Antigens, Protozoan, Placenta, Chondroitin Sulfates metabolism, Erythrocytes, Protein Binding, Malaria, Falciparum metabolism, Malaria, Vivax
- Abstract
During Plasmodium falciparum infection in pregnancy, VAR2CSA is expressed on the surface of infected erythrocytes (IEs) and mediates their sequestration in the placenta. As a result, antibodies to VAR2CSA are largely restricted to women who were infected during pregnancy. However, we discovered that VAR2CSA antibodies can also be elicited by P. vivax Duffy binding protein (PvDBP). We proposed that infection with P. vivax in non-pregnant individuals can generate antibodies that cross-react with VAR2CSA. To better understand the specificity of these antibodies, we took advantage of a mouse monoclonal antibody (3D10) raised against PvDBP that cross-reacts with VAR2CSA and identified the epitopes targeted by this antibody. We screened two peptide arrays that span the ectodomain of VAR2CSA from the FCR3 and NF54 alleles. Based on the top epitope recognized by 3D10, we designed a 34-amino acid synthetic peptide, which we call CRP1, that maps to a highly conserved region in DBL3X. Specific lysine residues are critical for 3D10 recognition, and these same amino acids are within a previously defined chondroitin sulfate A (CSA) binding site in DBL3X. We showed by isothermal titration calorimetry that the CRP1 peptide can bind directly to CSA, and antibodies to CRP1 raised in rats significantly blocked the binding of IEs to CSA in vitro . In our Colombian cohorts of pregnant and non-pregnant individuals, at least 45% were seroreactive to CRP1. Antibody reactivities to CRP1 and the 3D10 natural epitope in PvDBP region II, subdomain 1 (SD1), were strongly correlated in both cohorts. These findings suggest that antibodies arising from PvDBP may cross-react with VAR2CSA through the epitope in CRP1 and that CRP1 could be a potential vaccine candidate to target a distinct CSA binding site in VAR2CSA., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Iyamu, Vinals, Tornyigah, Arango, Bhat, Adra, Grewal, Martin, Maestre, Overduin, Hazes and Yanow.)
- Published
- 2023
- Full Text
- View/download PDF
36. Comprehensive classification of proteins based on structures that engage lipids by COMPOSEL.
- Author
-
Overduin M, Kervin TA, Klarenbach Z, Adra TRC, and Bhat RK
- Subjects
- Humans, Membrane Lipids, Artificial Intelligence, Models, Molecular, SARS-CoV-2 metabolism, Lipid Bilayers chemistry, Adaptor Proteins, Signal Transducing metabolism, Membrane Proteins chemistry, COVID-19
- Abstract
Structures can now be predicted for any protein using programs like AlphaFold and Rosetta, which rely on a foundation of experimentally determined structures of architecturally diverse proteins. The accuracy of such artificial intelligence and machine learning (AI/ML) approaches benefits from the specification of restraints which assist in navigating the universe of folds to converge on models most representative of a given protein's physiological structure. This is especially pertinent for membrane proteins, with structures and functions that depend on their presence in lipid bilayers. Structures of proteins in their membrane environments could conceivably be predicted from AI/ML approaches with user-specificized parameters that describe each element of the architecture of a membrane protein accompanied by its lipid environment. We propose the Classification Of Membrane Proteins based On Structures Engaging Lipids (COMPOSEL), which builds on existing nomenclature types for monotopic, bitopic, polytopic and peripheral membrane proteins as well as lipids. Functional and regulatory elements are also defined in the scripts, as shown with membrane fusing synaptotagmins, multidomain PDZD8 and Protrudin proteins that recognize phosphoinositide (PI) lipids, the intrinsically disordered MARCKS protein, caveolins, the β barrel assembly machine (BAM), an adhesion G-protein coupled receptor (aGPCR) and two lipid modifying enzymes - diacylglycerol kinase DGKε and fatty aldehyde dehydrogenase FALDH. This demonstrates how COMPOSEL communicates lipid interactivity as well as signaling mechanisms and binding of metabolites, drug molecules, polypeptides or nucleic acids to describe the operations of any protein. Moreover COMPOSEL can be scaled to express how genomes encode membrane structures and how our organs are infiltrated by pathogens such as SARS-CoV-2., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Michael Overduin reports financial support was provided by Natural Sciences and Engineering Research Council of Canada. Michael Overduin reports financial support was provided by Campus Alberta Innovates Program., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)
- Published
- 2023
- Full Text
- View/download PDF
37. SARS-CoV-2 Omicron Subvariants Balance Host Cell Membrane, Receptor, and Antibody Docking via an Overlapping Target Site.
- Author
-
Overduin M, Bhat RK, and Kervin TA
- Subjects
- Humans, Cryoelectron Microscopy, Lipid Bilayers, Antibodies, Cell Membrane, SARS-CoV-2, COVID-19
- Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging rapidly and offer surfaces that are optimized for recognition of host cell membranes while also evading antibodies arising from vaccinations and previous infections. Host cell infection is a multi-step process in which spike heads engage lipid bilayers and one or more angiotensin-converting enzyme 2 (ACE-2) receptors. Here, the membrane binding surfaces of Omicron subvariants are compared using cryo-electron microscopy (cEM) structures of spike trimers from BA.2, BA.2.12.1, BA.2.13, BA.2.75, BA.3, BA.4, and BA.5 viruses. Despite significant differences around mutated sites, they all maintain strong membrane binding propensities that first appeared in BA.1. Both their closed and open states retain elevated membrane docking capacities, although the presence of more closed than open states diminishes opportunities to bind receptors while enhancing membrane engagement. The electrostatic dipoles are generally conserved. However, the BA.2.75 spike dipole is compromised, and its ACE-2 affinity is increased, and BA.3 exhibits the opposite pattern. We propose that balancing the functional imperatives of a stable, readily cleavable spike that engages both lipid bilayers and receptors while avoiding host defenses underlies betacoronavirus evolution. This provides predictive criteria for rationalizing future pandemic waves and COVID-19 transmissibility while illuminating critical sites and strategies for simultaneously combating multiple variants.
- Published
- 2023
- Full Text
- View/download PDF
38. Discovery of allosteric SHP2 inhibitors through ensemble-based consensus molecular docking, endpoint and absolute binding free energy calculations.
- Author
-
Jama M, Ahmed M, Jutla A, Wiethan C, Kumar J, Moon TC, West F, Overduin M, and Barakat KH
- Subjects
- Humans, Female, Molecular Docking Simulation, Cell Proliferation, Cell Differentiation, Enzyme Inhibitors pharmacology, Breast Neoplasms
- Abstract
SHP2 (Src homology-2 domain-containing protein tyrosine phosphatase-2) is a cytoplasmic protein -tyrosine phosphatase encoded by the gene PTPN11. It plays a crucial role in regulating cell growth and differentiation. Specifically, SHP2 is an oncoprotein associated with developmental pathologies and several different cancer types, including gastric, leukemia and breast cancer and is of great therapeutic interest. Given these roles, current research efforts have focused on developing SHP2 inhibitors. Allosteric SHP2 inhibitors have been shown to be more selective and pharmacologically appealing compared to competitive catalytic inhibitors targeting SHP2. Nevertheless, there remains a need for novel allosteric inhibitor scaffolds targeting SHP2 to develop compounds with improved selectivity, cell permeability, and bioavailability. Towards this goal, this study applied various computational tools to screen over 6 million compounds against the allosteric site within SHP2. The top-ranked hits from our in-silico screening were validated using protein thermal shift and biolayer interferometry assays, revealing three potent compounds. Kinetic binding assays were employed to measure the binding affinities of the top-ranked compounds and demonstrated that they all bind to SHP2 with a nanomolar affinity. Hence the compounds and the computational workflow described herein provide an effective approach for identifying and designing a generation of improved allosteric inhibitors of SHP2., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2022 Elsevier Ltd. All rights reserved.)
- Published
- 2023
- Full Text
- View/download PDF
39. How Choice of Model Membrane Affects Protein-Glycosphingolipid Interactions: Insights from Native Mass Spectrometry.
- Author
-
Han L, Nguyen L, Schmidt EN, Esmaili M, Kitova EN, Overduin M, Macauley MS, and Klassen JS
- Subjects
- Cholera Toxin chemistry, Liposomes, Proteins chemistry, Spectrometry, Mass, Electrospray Ionization methods, G(M1) Ganglioside chemistry, Glycosphingolipids chemistry
- Abstract
Interactions between glycan-binding proteins (GBPs) and glycosphingolipids (GSLs) are involved in numerous physiological and pathophysiological processes. Many model membrane systems are available for studying GBP-GSL interactions, but a systematic investigation has not been carried out on how the nature of the model membrane affects binding. In this work, we use electrospray ionization mass spectrometry (ESI-MS), both direct and competitive assays, to measure the binding of cholera toxin B subunit homopentamer (CTB
5 ) to GM1 ganglioside in liposomes, bilayer islands [styrene maleic acid lipid particles (SMALPs), nanodiscs (NDs), and picodiscs (PDs)], and micelles. We find that direct ESI-MS analysis of CTB5 binding to GM1 is unreliable due to non-uniform response factors, incomplete extraction of bound GM1 in the gas phase, and nonspecific CTB5 -GM1 interactions. Conversely, indirect proxy ligand ESI-MS measurements show that the intrinsic (per binding site) association constants of CTB5 for PDs, NDs, and SMALPs are similar and comparable to the affinity of soluble GM1 pentasaccharide (GM1os ). The observed affinity decreases with increasing GM1 content due to molecular crowding stemming from GM1 clustering. Unlike the smaller model membranes, the observed affinity of CTB5 toward GM1 liposomes is ∼10-fold weaker than GM1os and relatively insensitive to the GM1 content. GM1 glycomicelles exhibit the lowest affinity, ∼35-fold weaker than GM1os . Together, the results highlight experimental design considerations for quantitative GBP-GSL binding studies involving multisubunit GBPs and factors to consider when comparing results obtained with different membrane systems. Notably, they suggest that bilayer islands with a low percentage of GSL, wherein clustering is minimized, are ideal for assessing intrinsic strength of GBP-GSL interactions in a membrane environment, while binding to liposomes, which is sub-optimal due to extensive clustering, may be more representative of authentic cellular environments.- Published
- 2022
- Full Text
- View/download PDF
40. Transmembrane Membrane Readers form a Novel Class of Proteins That Include Peripheral Phosphoinositide Recognition Domains and Viral Spikes.
- Author
-
Overduin M, Tran A, Eekels DM, Overduin F, and Kervin TA
- Abstract
Membrane proteins are broadly classified as transmembrane (TM) or peripheral, with functions that pertain to only a single bilayer at a given time. Here, we explicate a class of proteins that contain both transmembrane and peripheral domains, which we dub transmembrane membrane readers (TMMRs). Their transmembrane and peripheral elements anchor them to one bilayer and reversibly attach them to another section of bilayer, respectively, positioning them to tether and fuse membranes while recognizing signals such as phosphoinositides (PIs) and modifying lipid chemistries in proximity to their transmembrane domains. Here, we analyze full-length models from AlphaFold2 and Rosetta, as well as structures from nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, using the Membrane Optimal Docking Area (MODA) program to map their membrane-binding surfaces. Eukaryotic TMMRs include phospholipid-binding C1, C2, CRAL-TRIO, FYVE, GRAM, GTPase, MATH, PDZ, PH, PX, SMP, StART and WD domains within proteins including protrudin, sorting nexins and synaptotagmins. The spike proteins of SARS-CoV-2 as well as other viruses are also TMMRs, seeing as they are anchored into the viral membrane while mediating fusion with host cell membranes. As such, TMMRs have key roles in cell biology and membrane trafficking, and include drug targets for diseases such as COVID-19.
- Published
- 2022
- Full Text
- View/download PDF
41. Progressive membrane-binding mechanism of SARS-CoV-2 variant spike proteins.
- Author
-
Overduin M, Kervin TA, and Tran A
- Abstract
Membrane recognition by viral spike proteins is critical for infection. Here we show the host cell membrane-binding surfaces of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike variants Alpha, Beta, Gamma, Delta, Epsilon, Kappa, and Omicron as well as SARS-CoV-1 and pangolin and bat relatives. They show increases in membrane binding propensities over time, with all spike head mutations in variants, and particularly BA.1, impacting the protein's affinity to cell membranes. Comparison of hundreds of structures yields a progressive model of membrane docking in which spike protein trimers shift from initial perpendicular stances to increasingly tilted positions that draw viral particles alongside host cell membranes before optionally engaging angiotensin-converting enzyme 2 (ACE2) receptors. This culminates in the assembly of the symmetric fusion apparatus, with enhanced membrane interactions of variants explaining their unique cell fusion capacities and COVID-19 disease transmission rates., Competing Interests: The authors declare that they have no known competing financial interests that could have appeared to influence the work reported in this paper., (© 2022 The Authors.)
- Published
- 2022
- Full Text
- View/download PDF
42. Multifaceted membrane binding head of the SARS-CoV-2 spike protein.
- Author
-
Tran A, Kervin TA, and Overduin M
- Abstract
The SARS-CoV-2 spike protein presents a surface with enormous membrane binding potential to host tissues and organelles of infected cells. Its exposed trimeric head binds not only the angiotensin-converting enzyme 2 (ACE2), but also host phospholipids which are missing from all existing structures. Hence, the membrane interaction surfaces that mediate viral fusion, entry, assembly and egress remain unclear. Here the spike:membrane docking sites are identified based on membrane optimal docking area (MODA) analysis of 3D structures of spike proteins in closed and open conformations at endocytic and neutral pH levels as well as ligand complexes. This reveals multiple membrane binding sites in the closed spike head that together prefer convex membranes and are modulated by pH, fatty acids and post-translational modifications including glycosylation. The exposure of the various membrane interaction sites adjusts upon domain repositioning within the trimer, allowing formation of intermediate bilayer complexes that lead to the prefusion state while also enabling ACE2 receptor recognition. In contrast, all antibodies that target the spike head would block the membrane docking process that precedes ACE2 recognition. Together this illuminates the engagements of the spike protein with plasma, endocytic, ER or exocytic vesicle membranes that help to drive the cycle of viral infection, and offers novel sites for intervention., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
43. Implementation of Inertia Sensor and Machine Learning Technologies for Analyzing the Behavior of Individual Laying Hens.
- Author
-
Derakhshani SM, Overduin M, van Niekerk TGCM, and Groot Koerkamp PWG
- Abstract
Welfare-oriented regulations cause farmers worldwide to shift towards more welfare-friendly, e.g., loose housing systems such as aviaries with litter. In contrast to the traditional cage housing systems, good technical results can only be obtained if the behavior of hens is considered. With increasing flock sizes, the automation of behavioural assessment can be beneficial. This research aims to show a proof of principle of tools for analyzing laying-hen behaviors by using wearable inertia sensor technology and a machine learning model (ML). For this aim, the behaviors of hens were classified into three classes: static, semi-dynamic, and highly dynamic behavior. The activities of hens were continuously recorded on video and synchronized with the sensor signals. Two hens were equipped with sensors, one marked green and one blue, for five days to collect the data. The training data set indicated that the ML model can accurately classify the highly dynamic behaviors with a one-second time window; a four-second time window is accurate for static and semi-dynamic behaviors. The Bagged Trees model, with an overall accuracy of 89% was the best ML model with the F1-scores of 89%, 91%, and 87% for static, semi-dynamic, and highly dynamic behaviors. The Bagged Trees model also performed well in classifying the behaviors of the hen in the validation data set with an overall F1-score of 0.92 (uniform either % or decimals). This research illustrates that the combination of wearable inertia sensors and machine learning is a viable technique for analyzing the laying-hen behaviors and supporting farmers in the management of hens in loose housing systems.
- Published
- 2022
- Full Text
- View/download PDF
44. Effects of Specific Inhibitors for CaMK1D on a Primary Neuron Model for Alzheimer's Disease.
- Author
-
Grant P, Kumar J, Kar S, and Overduin M
- Subjects
- Alzheimer Disease metabolism, Alzheimer Disease pathology, Amyloid beta-Peptides antagonists & inhibitors, Amyloid beta-Peptides metabolism, Animals, Calcium-Calmodulin-Dependent Protein Kinase Type 1 metabolism, Cell Survival drug effects, Cells, Cultured, Mice, Mice, Inbred BALB C, Models, Molecular, Neurons metabolism, Neurons pathology, Protein Kinase Inhibitors chemistry, Alzheimer Disease drug therapy, Calcium-Calmodulin-Dependent Protein Kinase Type 1 antagonists & inhibitors, Disease Models, Animal, Neurons drug effects, Protein Kinase Inhibitors pharmacology
- Abstract
Alzheimer's disease (AD) is the most common cause of dementia worldwide. Despite extensive research and targeting of the main molecular components of the disease, beta-amyloid (Aβ) and tau, there are currently no treatments that alter the progression of the disease. Here, we examine the effects of two specific kinase inhibitors for calcium/calmodulin-dependent protein kinase type 1D (CaMK1D) on Aβ-mediated toxicity, using mouse primary cortical neurons. Tau hyperphosphorylation and cell death were used as AD indicators. These specific inhibitors were found to prevent Aβ induced tau hyperphosphorylation in culture, but were not able to protect cells from Aβ induced toxicity. While inhibitors were able to alter AD pathology in cell culture, they were insufficient to prevent cell death. With further research and development, these inhibitors could contribute to a multi-drug strategy to combat AD.
- Published
- 2021
- Full Text
- View/download PDF
45. Tetraspanin 6 is a regulator of carcinogenesis in colorectal cancer.
- Author
-
Andrijes R, Hejmadi RK, Pugh M, Rajesh S, Novitskaya V, Ibrahim M, Overduin M, Tselepis C, Middleton GW, Győrffy B, Beggs AD, and Berditchevski F
- Subjects
- Animals, Antineoplastic Agents, Immunological pharmacology, Apoptosis, Biomarkers, Tumor genetics, Cell Proliferation, Colorectal Neoplasms drug therapy, Colorectal Neoplasms metabolism, ErbB Receptors antagonists & inhibitors, ErbB Receptors genetics, ErbB Receptors metabolism, Humans, Mice, Mice, Inbred C57BL, Mice, Knockout, Prognosis, Survival Rate, Tetraspanins genetics, Tumor Cells, Cultured, Biomarkers, Tumor metabolism, Cetuximab pharmacology, Colorectal Neoplasms pathology, Gene Expression Regulation, Neoplastic, Tetraspanins metabolism, Tetraspanins physiology
- Abstract
Early stages of colorectal cancer (CRC) development are characterized by a complex rewiring of transcriptional networks resulting in changes in the expression of multiple genes. Here, we demonstrate that the deletion of a poorly studied tetraspanin protein Tspan6 in Apc
min/+ mice, a well-established model for premalignant CRC, resulted in increased incidence of adenoma formation and tumor size. We demonstrate that the effect of Tspan6 deletion results in the activation of EGF-dependent signaling pathways through increased production of the transmembrane form of TGF-α (tmTGF-α) associated with extracellular vesicles. This pathway is modulated by an adaptor protein syntenin-1, which physically links Tspan6 and tmTGF-α. In support of this, the expression of Tspan6 is frequently decreased or lost in CRC, and this correlates with poor survival. Furthermore, the analysis of samples from the epidermal growth factor receptor (EGFR)-targeting clinical trial (COIN trial) has shown that the expression of Tspan6 in CRC correlated with better patient responses to EGFR-targeted therapy involving Cetuximab. Importantly, Tspan6-positive patients with tumors in the proximal colon (right-sided) and those with KRAS mutations had a better response to Cetuximab than the patients that expressed low Tspan6 levels. These results identify Tspan6 as a regulator of CRC development and a potential predictive marker for EGFR-targeted therapies in CRC beyond RAS pathway mutations., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)- Published
- 2021
- Full Text
- View/download PDF
46. Structural biology of endogenous membrane protein assemblies in native nanodiscs.
- Author
-
Brown CJ, Trieber C, and Overduin M
- Subjects
- Biology, Cryoelectron Microscopy, Lipid Bilayers, Membrane Proteins, Nanostructures
- Abstract
The advent of amphiphilic copolymers enables integral membrane proteins to be solubilized into stable 10-30 nm native nanodiscs to resolve their multisubunit structures, post-translational modifications, endogenous lipid bilayers, and small molecule ligands. This breakthrough has positioned biological membrane:protein assemblies (memteins) as fundamental functional units of cellular membranes. Herein, we review copolymer design strategies and methods for the characterization of transmembrane proteins within native nanodiscs by cryo-electron microscopy (cryo-EM), transmission electron microscopy, nuclear magnetic resonance spectroscopy, electron paramagnetic resonance, X-ray diffraction, surface plasmon resonance, and mass spectrometry., Competing Interests: Conflict of interest statement MO is a director of the SMALP network and has awarded and filed patents on related polymers and methods., (Copyright © 2021 The Author(s). Published by Elsevier Ltd.. All rights reserved.)
- Published
- 2021
- Full Text
- View/download PDF
47. Phosphoinositide Recognition Sites Are Blocked by Metabolite Attachment.
- Author
-
Kervin TA, Wiseman BC, and Overduin M
- Abstract
Membrane readers take part in trafficking and signaling processes by localizing proteins to organelle surfaces and transducing molecular information. They accomplish this by engaging phosphoinositides (PIs), a class of lipid molecules which are found in different proportions in various cellular membranes. The prototypes are the PX domains, which exhibit a range of specificities for PIs. Our meta-analysis indicates that recognition of membranes by PX domains is specifically controlled by modification of lysine and arginine residues including acetylation, hydroxyisobutyrylation, glycation, malonylation, methylation and succinylation of sidechains that normally bind headgroups of phospholipids including organelle-specific PI signals. Such metabolite-modulated residues in lipid binding elements are named MET-stops here to highlight their roles as erasers of membrane reader functions. These modifications are concentrated in the membrane binding sites of half of all 49 PX domains in the human proteome and correlate with phosphoregulatory sites, as mapped using the Membrane Optimal Docking Area (MODA) algorithm. As these motifs are mutated and modified in various cancers and the responsible enzymes serve as potential drug targets, the discovery of MET-stops as a widespread inhibitory mechanism may aid in the development of diagnostics and therapeutics aimed at the readers, writers and erasers of the PI code., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Kervin, Wiseman and Overduin.)
- Published
- 2021
- Full Text
- View/download PDF
48. The phosphoinositide code is read by a plethora of protein domains.
- Author
-
Overduin M and Kervin TA
- Subjects
- Binding Sites, Humans, Protein Binding, Protein Domains, Phosphatidylinositols, Proteins
- Abstract
Introduction: The proteins that decipher nucleic acid- and protein-based information are well known, however, those that read membrane-encoded information remain understudied. Here, we report 70 different human, microbial and viral protein folds that recognize phosphoinositides (PIs), comprising the readers of a vast membrane code., Areas Covered: Membrane recognition is best understood for FYVE, PH and PX domains, which exemplify hundreds of PI code readers. Comparable lipid interaction mechanisms may be mediated by kinases, adjacent C1 and C2 domains, trafficking arrestins, GAT and VHS modules, membrane-perturbing annexins, BAR, CHMP, ENTH, HEAT, syntaxin and Tubby helical bundles, multipurpose FERM, EH, MATH, PHD, PDZ, PROPPIN, PTB and SH2 domains, as well as systems that regulate receptors, GTPases and actin filaments, transfer lipids, and assemble bacterial and viral particles., Expert Opinion: The elucidation of how membranes are recognized has extended the genetic code to the PI code. Novel discoveries include PIP-stop and MET-stop residues to which phosphates and metabolites are attached to block phosphatidylinositol phosphate (PIP) recognition, memteins as functional membrane protein apparatuses and lipidons as lipid 'codons' recognized by membrane readers. At least 5% of the human proteome senses such membrane signals and allows eukaryotic organelles and pathogens to operate and replicate.
- Published
- 2021
- Full Text
- View/download PDF
49. Structures and Dynamics of Native-State Transmembrane Protein Targets and Bound Lipids.
- Author
-
Overduin M, Trieber C, Prosser RS, Picard LP, and Sheff JG
- Abstract
Membrane proteins work within asymmetric bilayers of lipid molecules that are critical for their biological structures, dynamics and interactions. These properties are lost when detergents dislodge lipids, ligands and subunits, but are maintained in native nanodiscs formed using styrene maleic acid (SMA) and diisobutylene maleic acid (DIBMA) copolymers. These amphipathic polymers allow extraction of multicomponent complexes of post-translationally modified membrane-bound proteins directly from organ homogenates or membranes from diverse types of cells and organelles. Here, we review the structures and mechanisms of transmembrane targets and their interactions with lipids including phosphoinositides (PIs), as resolved using nanodisc systems and methods including cryo-electron microscopy (cryo-EM) and X-ray diffraction (XRD). We focus on therapeutic targets including several G protein-coupled receptors (GPCRs), as well as ion channels and transporters that are driving the development of next-generation native nanodiscs. The design of new synthetic polymers and complementary biophysical tools bodes well for the future of drug discovery and structural biology of native membrane:protein assemblies (memteins).
- Published
- 2021
- Full Text
- View/download PDF
50. Regulation of the Phosphoinositide Code by Phosphorylation of Membrane Readers.
- Author
-
Kervin TA and Overduin M
- Subjects
- Evolution, Molecular, Humans, Models, Molecular, Phosphorylation, Protein Binding, Saccharomyces cerevisiae, Phosphatidylinositol Phosphates metabolism, Saccharomyces cerevisiae Proteins metabolism
- Abstract
The genetic code that dictates how nucleic acids are translated into proteins is well known, however, the code through which proteins recognize membranes remains mysterious. In eukaryotes, this code is mediated by hundreds of membrane readers that recognize unique phosphatidylinositol phosphates (PIPs), which demark organelles to initiate localized trafficking and signaling events. The only superfamily which specifically detects all seven PIPs are the Phox homology (PX) domains. Here, we reveal that throughout evolution, these readers are universally regulated by the phosphorylation of their PIP binding surfaces based on our analysis of existing and modelled protein structures and phosphoproteomic databases. These PIP-stops control the selective targeting of proteins to organelles and are shown to be key determinants of high-fidelity PIP recognition. The protein kinases responsible include prominent cancer targets, underscoring the critical role of regulated membrane readership.
- Published
- 2021
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.