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Glatzová D, Mavila H, Saija MC, Chum T, Cwiklik L, Brdička T, Cebecauer M. The role of prolines and glycine in the transmembrane domain of LAT. FEBS J 2021; 288:4039-4052. [PMID: 33458942 DOI: 10.1111/febs.15713] [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: 09/18/2020] [Revised: 12/15/2020] [Accepted: 01/13/2021] [Indexed: 12/30/2022]
Abstract
Linker for activation in T cells (LAT) is a critical regulator of T-cell development and function. It organises signalling events at the plasma membrane. However, the mechanism, which controls LAT localisation at the plasma membrane, is not fully understood. Here, we studied the impact of helix-breaking amino acids, two prolines and one glycine, in the transmembrane segment on localisation and function of LAT. Using in silico analysis, confocal and super-resolution imaging and flow cytometry, we demonstrate that central proline residue destabilises transmembrane helix by inducing a kink. The helical structure and dynamics are further regulated by glycine and another proline residue in the luminal part of LAT transmembrane domain. Replacement of these residues with aliphatic amino acids reduces LAT dependence on palmitoylation for sorting to the plasma membrane. However, surface expression of these mutants is not sufficient to recover function of nonpalmitoylated LAT in stimulated T cells. These data indicate that geometry and dynamics of LAT transmembrane segment regulate its localisation and function in immune cells.
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Affiliation(s)
- Daniela Glatzová
- Department of Biophysical Chemistry, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic.,Laboratory of Leukocyte Signaling, Institute of Molecule Genetics, Czech Academy of Sciences, Prague, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Harsha Mavila
- Department of Biophysical Chemistry, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Maria Chiara Saija
- Department of Computational Chemistry, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Chum
- Department of Biophysical Chemistry, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Lukasz Cwiklik
- Department of Computational Chemistry, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Brdička
- Laboratory of Leukocyte Signaling, Institute of Molecule Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Marek Cebecauer
- Department of Biophysical Chemistry, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
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2
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Radlow M, Czjzek M, Jeudy A, Dabin J, Delage L, Leblanc C, Hartung J. X-ray Diffraction and Density Functional Theory Provide Insight into Vanadate Binding to Homohexameric Bromoperoxidase II and the Mechanism of Bromide Oxidation. ACS Chem Biol 2018; 13:1243-1259. [PMID: 29665335 DOI: 10.1021/acschembio.8b00041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
X-ray diffraction of native bromoperoxidase II (EC 1.11.1.18) from the brown alga Ascophyllum nodosum reveals at a resolution of 2.26 Å details of orthovanadate binding and homohexameric protein organization. Three dimers interwoven in contact regions and tightened by hydrogen-bond-clamped guanidinium stacks along with regularly aligned water molecules form the basic structure of the enyzme. Intra- and intermolecular disulfide bridges further stabilize the enzyme preventing altogether the protein from denaturing up to a temperature of 90 °C, as evident from dynamic light scattering and the on-gel ortho-dianisidine assay. Every monomer binds one equivalent of orthovanadate in a cavity formed from side chains of three histidines, two arginines, one lysine, serine, and tryptophan. Protein binding occurs primarily through hydrogen bridges and superimposed by Coulomb attraction according to thermochemical model on density functional level of theory (B3LYP/6-311++G**). The strongest attractor is the arginine side chain mimic N-methylguanidinium, enhancing in positive cooperative manner hydrogen bridges toward weaker acceptors, such as residues from lysine and serine. Activating hydrogen peroxide occurs in the thermochemical model by side-on binding in orthovanadium peroxoic acid, oxidizing bromide with virtually no activation energy to hydrogen bonded hypobromous acid.
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Affiliation(s)
- Madlen Radlow
- Fachbereich Chemie, Organische Chemie, Technische Universität Kaiserslautern, Erwin-Schrödinger-Straße, D-67663 Kaiserslautern, Germany
| | - Mirjam Czjzek
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France
| | - Alexandra Jeudy
- Sorbonne Université, CNRS, FR 2424, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France
| | - Jerome Dabin
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France
| | - Ludovic Delage
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France
| | - Catherine Leblanc
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France
| | - Jens Hartung
- Fachbereich Chemie, Organische Chemie, Technische Universität Kaiserslautern, Erwin-Schrödinger-Straße, D-67663 Kaiserslautern, Germany
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3
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Steindorf D, Schneider D. In vivo selection of heterotypically interacting transmembrane helices: Complementary helix surfaces, rather than conserved interaction motifs, drive formation of transmembrane hetero-dimers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:245-256. [DOI: 10.1016/j.bbamem.2016.11.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/23/2016] [Accepted: 11/29/2016] [Indexed: 11/16/2022]
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Kyriakou PK, Ekblad B, Kristiansen PE, Kaznessis YN. Interactions of a class IIb bacteriocin with a model lipid bilayer, investigated through molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:824-35. [PMID: 26774214 DOI: 10.1016/j.bbamem.2016.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/06/2016] [Accepted: 01/12/2016] [Indexed: 01/15/2023]
Abstract
The emergence of antibiotic resistant microorganisms poses an alarming threat to global health. Antimicrobial peptides (AMPs) are considered a possible effective alternative to conventional antibiotic therapies. An understanding of the mechanism of action of AMPs is needed in order to better control and optimize their bactericidal activity. Plantaricin EF is a heterodimeric AMP, consisting of two peptides Plantaricin E (PlnE) and Plantaricin F (PlnF). We studied the behavior of these peptides on the surface of a model lipid bilayer. We identified the residues that facilitate peptide-peptide interactions. We also identified residues that mediate interactions of the dimer with the membrane. PlnE interacts with the membrane through amino acids at both its termini, while only the N terminus of PlnF approaches the membrane. By comparing the activity of single-site mutants of the two-peptide bacteriocin and the simulations of the bacteriocin on the surface of a model lipid bilayer, structure activity relationships are proposed. These studies allow us to generate hypotheses that relate biophysical interactions observed in simulations with the experimentally measured activity. We find that single-site amino acid substitutions result in markedly stronger antimicrobial activity when they strengthen the interactions between the two peptides, while, concomitantly, they weaken peptide-membrane association. This effect is more pronounced in the case of the PlnE mutant (G20A), which interacts the strongest with PlnF and the weakest with the membrane while displaying the highest activity.
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Affiliation(s)
- Panagiota K Kyriakou
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, United States
| | - Bie Ekblad
- Department of Biosciences, University of Oslo, Post box 1041 Blindern, 0316 Oslo, Norway
| | - Per Eugen Kristiansen
- Department of Biosciences, University of Oslo, Post box 1041 Blindern, 0316 Oslo, Norway
| | - Yiannis N Kaznessis
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, United States.
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Klein N, Neumann J, O'Neil JD, Schneider D. Folding and stability of the aquaglyceroporin GlpF: Implications for human aqua(glycero)porin diseases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:622-33. [PMID: 25462169 DOI: 10.1016/j.bbamem.2014.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/12/2014] [Accepted: 11/14/2014] [Indexed: 01/22/2023]
Abstract
Aquaporins are highly selective polytopic transmembrane channel proteins that facilitate the permeation of water across cellular membranes in a large diversity of organisms. Defects in aquaporin function are associated with common diseases, such as nephrogenic diabetes insipidus, congenital cataract and certain types of cancer. In general, aquaporins have a highly conserved structure; from prokaryotes to humans. The conserved structure, together with structural dynamics and the structural framework for substrate selectivity is discussed. The folding pathway of aquaporins has been a topic of several studies in recent years. These studies revealed that a conserved protein structure can be reached by following different folding pathways. Based on the available data, we suggest a complex folding pathway for aquaporins, starting from the insertion of individual helices up to the formation of the tetrameric aquaporin structure. The consequences of some known mutations in human aquaporin-encoding genes, which most likely affect the folding and stability of human aquaporins, are discussed.
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Affiliation(s)
- Noreen Klein
- Department of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Jennifer Neumann
- Department of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Joe D O'Neil
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Dirk Schneider
- Department of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany.
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Wilman HR, Ebejer JP, Shi J, Deane CM, Knapp B. Crowdsourcing Yields a New Standard for Kinks in Protein Helices. J Chem Inf Model 2014; 54:2585-93. [DOI: 10.1021/ci500403a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Henry R. Wilman
- Department
of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, U.K
| | - Jean-Paul Ebejer
- Department
of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, U.K
| | - Jiye Shi
- UCB Celltech, a branch of UCB Pharma S. A., 208 Bath Road, Slough SL1 3WE, U.K
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Charlotte M. Deane
- Department
of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, U.K
| | - Bernhard Knapp
- Department
of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, U.K
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Wilman HR, Shi J, Deane CM. Helix kinks are equally prevalent in soluble and membrane proteins. Proteins 2014; 82:1960-70. [PMID: 24638929 PMCID: PMC4285789 DOI: 10.1002/prot.24550] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 01/28/2023]
Abstract
Helix kinks are a common feature of α-helical membrane proteins, but are thought to be rare in soluble proteins. In this study we find that kinks are a feature of long α-helices in both soluble and membrane proteins, rather than just transmembrane α-helices. The apparent rarity of kinks in soluble proteins is due to the relative infrequency of long helices (≥20 residues) in these proteins. We compare length-matched sets of soluble and membrane helices, and find that the frequency of kinks, the role of Proline, the patterns of other amino acid around kinks (allowing for the expected differences in amino acid distributions between the two types of protein), and the effects of hydrogen bonds are the same for the two types of helices. In both types of protein, helices that contain Proline in the second and subsequent turns are very frequently kinked. However, there are a sizeable proportion of kinked helices that do not contain a Proline in either their sequence or sequence homolog. Moreover, we observe that in soluble proteins, kinked helices have a structural preference in that they typically point into the solvent.
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Affiliation(s)
- Henry R Wilman
- Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, United Kingdom
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Werner T, Church WB. Kink Characterization and Modeling in Transmembrane Protein Structures. J Chem Inf Model 2013; 53:2926-36. [DOI: 10.1021/ci400236s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tim Werner
- Group in
Biomolecular Structure
and Informatics, Faculty of Pharmacy, The University of Sydney, Sydney NSW 2006, Australia
| | - W. Bret Church
- Group in
Biomolecular Structure
and Informatics, Faculty of Pharmacy, The University of Sydney, Sydney NSW 2006, Australia
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10
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Weber M, Schneider D. Six amino acids define a minimal dimerization sequence and stabilize a transmembrane helix dimer by close packing and hydrogen bonding. FEBS Lett 2013; 587:1592-6. [DOI: 10.1016/j.febslet.2013.03.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 03/21/2013] [Accepted: 03/22/2013] [Indexed: 11/26/2022]
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Akdogan Y, Anbazhagan V, Hinderberger D, Schneider D. Heme Binding Constricts the Conformational Dynamics of the Cytochrome b559′ Heme Binding Cavity. Biochemistry 2012; 51:7149-56. [DOI: 10.1021/bi300489s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Yasar Akdogan
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz,
Germany
| | - Veerappan Anbazhagan
- Institut für Pharmazie
und Biochemie, Johannes Gutenberg-Universität Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - Dariush Hinderberger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz,
Germany
| | - Dirk Schneider
- Institut für Pharmazie
und Biochemie, Johannes Gutenberg-Universität Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
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