1
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Has C, Das SL. The Functionality of Membrane-Inserting Proteins and Peptides: Curvature Sensing, Generation, and Pore Formation. J Membr Biol 2023; 256:343-372. [PMID: 37650909 DOI: 10.1007/s00232-023-00289-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
Proteins and peptides with hydrophobic and amphiphilic segments are responsible for many biological functions. The sensing and generation of membrane curvature are the functions of several protein domains or motifs. While some specific membrane proteins play an essential role in controlling the curvature of distinct intracellular membranes, others participate in various cellular processes such as clathrin-mediated endocytosis, where several proteins sort themselves at the neck of the membrane bud. A few membrane-inserting proteins form nanopores that permeate selective ions and water to cross the membrane. In addition, many natural and synthetic small peptides and protein toxins disrupt the membrane by inducing nonspecific pores in the membrane. The pore formation causes cell death through the uncontrolled exchange between interior and exterior cellular contents. In this article, we discuss the insertion depth and orientation of protein/peptide helices, and their role as a sensor and inducer of membrane curvature as well as a pore former in the membrane. We anticipate that this extensive review will assist biophysicists to gain insight into curvature sensing, generation, and pore formation by membrane insertion.
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Affiliation(s)
- Chandra Has
- Department of Chemical Engineering, GSFC University, Vadodara, 391750, Gujarat, India.
| | - Sovan Lal Das
- Physical and Chemical Biology Laboratory and Department of Mechanical Engineering, Indian Institute of Technology, Palakkad, 678623, Kerala, India
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2
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Chen L, Zhang Q, Meng Y, Zhao T, Mu C, Fu C, Deng C, Feng J, Du S, Liu W, Geng G, Ma K, Cheng H, Liu Q, Luo Q, Zhang J, Du Z, Cao L, Wang H, Liu Y, Lin J, Chen G, Liu L, Lam SM, Shui G, Zhu Y, Chen Q. Saturated fatty acids increase LPI to reduce FUNDC1 dimerization and stability and mitochondrial function. EMBO Rep 2023; 24:e54731. [PMID: 36847607 PMCID: PMC10074135 DOI: 10.15252/embr.202254731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 01/19/2023] [Accepted: 02/02/2023] [Indexed: 03/01/2023] Open
Abstract
Ectopic lipid deposition and mitochondrial dysfunction are common etiologies of obesity and metabolic disorders. Excessive dietary uptake of saturated fatty acids (SFAs) causes mitochondrial dysfunction and metabolic disorders, while unsaturated fatty acids (UFAs) counterbalance these detrimental effects. It remains elusive how SFAs and UFAs differentially signal toward mitochondria for mitochondrial performance. We report here that saturated dietary fatty acids such as palmitic acid (PA), but not unsaturated oleic acid (OA), increase lysophosphatidylinositol (LPI) production to impact on the stability of the mitophagy receptor FUNDC1 and on mitochondrial quality. Mechanistically, PA shifts FUNDC1 from dimer to monomer via enhanced production of LPI. Monomeric FUNDC1 shows increased acetylation at K104 due to dissociation of HDAC3 and increased interaction with Tip60. Acetylated FUNDC1 can be further ubiquitinated by MARCH5 for proteasomal degradation. Conversely, OA antagonizes PA-induced accumulation of LPI, and FUNDC1 monomerization and degradation. A fructose-, palmitate-, and cholesterol-enriched (FPC) diet also affects FUNDC1 dimerization and promotes its degradation in a non-alcoholic steatohepatitis (NASH) mouse model. We thus uncover a signaling pathway that orchestrates lipid metabolism with mitochondrial quality.
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Affiliation(s)
- Linbo Chen
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Qianping Zhang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Yuanyuan Meng
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Tian Zhao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Chenglong Mu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Changying Fu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Caijuan Deng
- College of Pharmacy, Frontiers Science Center for Cell ResponsesNankai UniversityTianjinChina
| | - Jianyu Feng
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Siling Du
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Wei Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Guangfeng Geng
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Kaili Ma
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Hongcheng Cheng
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Qiangqiang Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Qian Luo
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Jiaojiao Zhang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Zhanqiang Du
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Lin Cao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Hui Wang
- Cancer InstituteXuzhou Medical UniversityXuzhouChina
| | - Yong Liu
- Cancer InstituteXuzhou Medical UniversityXuzhouChina
| | - Jianping Lin
- College of Pharmacy, Frontiers Science Center for Cell ResponsesNankai UniversityTianjinChina
| | - Guo Chen
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Lei Liu
- State Key Laboratory of Membrane Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- LipidAll Technologies Company LimitedChangzhouChina
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Yushan Zhu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Quan Chen
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
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3
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Díaz Vázquez G, Cui Q, Senes A. Thermodynamic analysis of the GAS right transmembrane motif supports energetic model of dimerization. Biophys J 2023; 122:143-155. [PMID: 36371634 PMCID: PMC9822795 DOI: 10.1016/j.bpj.2022.11.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/12/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022] Open
Abstract
The GASright motif, best known as the fold of the glycophorin A transmembrane dimer, is one of the most common dimerization motifs in membrane proteins, characterized by its hallmark GxxxG-like sequence motifs (GxxxG, AxxxG, GxxxS, and similar). Structurally, GASright displays a right-handed crossing angle and short interhelical distance. Contact between the helical backbones favors the formation of networks of weak hydrogen bonds between Cα-H carbon donors and carbonyl acceptors on opposing helices (Cα-H···O=C). To understand the factors that modulate the stability of GASright, we previously presented a computational and experimental structure-based analysis of 26 predicted dimers. We found that the contributions of van der Waals packing and Cα-H hydrogen bonding to stability, as inferred from the structural models, correlated well with relative dimerization propensities estimated experimentally with the in vivo assay TOXCAT. Here we test this model with a quantitative thermodynamic analysis. We used Förster resonance energy transfer (FRET) to determine the free energy of dimerization of a representative subset of seven of the 26 original TOXCAT dimers using FRET. To overcome the technical issue arising from limited sampling of the dimerization isotherm, we introduced a globally fitting strategy across a set of constructs comprising a wide range of stabilities. This strategy yielded precise thermodynamic data that show strikingly good agreement between the original propensities and ΔG° of association in detergent, suggesting that TOXCAT is a thermodynamically driven process. From the correlation between TOXCAT and thermodynamic stability, the predicted free energy for all the 26 GASright dimers was calculated. These energies correlate with the in silico ΔE scores of dimerization that were computed on the basis of their predicted structure. These findings corroborate our original model with quantitative thermodynamic evidence, strengthening the hypothesis that van der Waals and Cα-H hydrogen bond interactions are the key modulators of GASright stability.
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Affiliation(s)
- Gladys Díaz Vázquez
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, Massachusetts
| | - Alessandro Senes
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin.
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4
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Yano Y, Morise T, Matsuzaki K. Effects of Gly Residue and Cholesterol on the GXXXG-Mediated Parallel Association of Transmembrane Helices: A Single-Pair FRET Study. Chembiochem 2022; 23:e202200160. [PMID: 36229427 DOI: 10.1002/cbic.202200160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 10/12/2022] [Indexed: 01/25/2023]
Abstract
Small residue-mediated interhelical packing is ubiquitous in helical membrane proteins: however, the lipid dependence of its stability remains unclear. We previously demonstrated that the introduction of a GXXXG sequence in the middle of de novo-designed (AALALAA)3 helices (AALALAA AGLALGA AALALAA) facilitated their dimerization, which was abolished by cholesterol. Here single-pair FRET measurements revealed that a longer GXXXGXXXG segment (AALALAA A GLALGA AAGALAA) promoted helix dimerization in POPC/cholesterol bilayers, but not without cholesterol. The predicted dimer structures and degrees of helix packing suggested that helix dimers with small (∼10°) and large (∼55°) crossing angles were only stabilized in POPC and POPC/cholesterol membranes, respectively. A steric hindrance in the dimer interface and the large flexibility of helices prevented the formation of stable dimers. Therefore, amino acid sequences and lipid compositions distinctively constrain stable dimer structures in membranes.
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Affiliation(s)
- Yoshiaki Yano
- School of Pharmacy and Pharmaceutical Sciences, Mukogawa Woman's University, Nishinomiya, 663-8179, Japan
| | - Takayuki Morise
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
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5
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Hellmann N, Schneider D. Hydrophobic mismatch and sequence specificity compete when transmembrane helix-helix interactions are measured with the TOXCAT assay. Front Chem 2022; 10:1049310. [DOI: 10.3389/fchem.2022.1049310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/16/2022] [Indexed: 11/29/2022] Open
Abstract
Genetic assays capable of measuring the propensity of transmembrane helices to oligomerize within the cytoplasmic membrane of the bacterium E. coli are frequently used when sequence-specificity in transmembrane helix-helix interactions is investigated. In the present study, dimerization of the well-investigated wild-type and G83I-mutated transmembrane helix of the human glycophorin A protein was studied. Gradual prolongation of the transmembrane helix at the C-terminus with Leu residues lead to pronounced changes in the dimerization propensity when measured with the TOXCAT assay. Thus, besides sequence specificity, hydrophobic mismatch between the hydrophobic core of a studied transmembrane helix and the E. coli membrane can impact the oligomerization propensity of a transmembrane helix. This suggests that the results of genetic assays aiming at determining interactions of heterologous transmembrane helices within the E. coli membrane do not necessarily solely reflect sequence specificity in transmembrane helix-helix interactions, but might be additionally modulated by topological and structural effects caused by hydrophobic mismatch.
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6
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Yano Y. Effects of Membrane Cholesterol on Stability of Transmembrane Helix Associations. Chem Pharm Bull (Tokyo) 2022; 70:514-518. [DOI: 10.1248/cpb.c22-00144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yoshiaki Yano
- School of Pharmacy and Pharmaceutical Sciences, Mukogawa Woman’s University
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7
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Alavizargar A, Elting A, Wedlich-Söldner R, Heuer A. Lipid-Mediated Association of the Slg1 Transmembrane Domains in Yeast Plasma Membranes. J Phys Chem B 2022; 126:3240-3256. [PMID: 35446028 DOI: 10.1021/acs.jpcb.2c00192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Clustering of transmembrane proteins underlies a multitude of fundamental biological processes at the plasma membrane (PM) such as receptor activation, lateral domain formation, and mechanotransduction. The self-association of the respective transmembrane domains (TMDs) has also been suggested to be responsible for the micron-scaled patterns seen for integral membrane proteins in the budding yeast PM. However, the underlying interplay between the local lipid composition and the TMD identity is still not mechanistically understood. In this work, we combined coarse-grained molecular dynamics simulations of simplified bilayer systems with high-resolution live-cell microscopy to analyze the distribution of a representative helical yeast TMD from the PM sensor Slg1 within different lipid environments. In our simulations, we specifically evaluated the effects of acyl chain saturation and anionic lipid head groups on the association of two TMDs. We found that weak lipid-protein interactions significantly affect the configuration of TMD dimers and the free energy of association. Increased amounts of unsaturated phospholipids (PLs) strongly reduced the helix-helix interaction, while the presence of anionic phosphatidylserine (PS) hardly affected the dimer formation. We could experimentally confirm this surprising lack of effect of PS using the network factor, a mesoscopic measure of PM pattern formation in yeast cells. Simulations also showed that the formation of TMD dimers in turn increased the order parameter of the surrounding lipids and induced long-range perturbations in lipid organization. In summary, our results shed new light on the mechanisms of lipid-mediated dimerization of TMDs in complex lipid mixtures.
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Affiliation(s)
- Azadeh Alavizargar
- Institute of Physical Chemistry, University of Muenster, Corrensstr. 28/30, 48149 Muenster, Germany
| | - Annegret Elting
- Institute of Cell Dynamics and Imaging, University of Muenster, Von-Esmarch-Str. 56, 48149 Muenster, Germany
| | - Roland Wedlich-Söldner
- Institute of Cell Dynamics and Imaging, University of Muenster, Von-Esmarch-Str. 56, 48149 Muenster, Germany
| | - Andreas Heuer
- Institute of Physical Chemistry, University of Muenster, Corrensstr. 28/30, 48149 Muenster, Germany
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8
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Sofińska K, Lupa D, Chachaj-Brekiesz A, Czaja M, Kobierski J, Seweryn S, Skirlińska-Nosek K, Szymonski M, Wilkosz N, Wnętrzak A, Lipiec E. Revealing local molecular distribution, orientation, phase separation, and formation of domains in artificial lipid layers: Towards comprehensive characterization of biological membranes. Adv Colloid Interface Sci 2022; 301:102614. [PMID: 35190313 DOI: 10.1016/j.cis.2022.102614] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 01/01/2023]
Abstract
Lipids, together with molecules such as DNA and proteins, are one of the most relevant systems responsible for the existence of life. Selected lipids are able to assembly into various organized structures, such as lipid membranes. The unique properties of lipid membranes determine their complex functions, not only to separate biological environments, but also to participate in regulatory functions, absorption of nutrients, cell-cell communication, endocytosis, cell signaling, and many others. Despite numerous scientific efforts, still little is known about the reason underlying the variability within lipid membranes, and its biochemical significance. In this review, we discuss the structural complexity of lipid membranes, as well as the importance to simplify studied systems in order to understand phenomena occurring in natural, complex membranes. Such systems require a model interface to be analyzed. Therefore, here we focused on analytical studies of artificial systems at various interfaces. The molecular structure of lipid membranes, specifically the nanometric thickens of molecular bilayer, limits in a major extent the choice of highly sensitive methods suitable to study such structures. Therefore, we focused on methods that combine high sensitivity, and/or chemical selectivity, and/or nanometric spatial resolution, such as atomic force microscopy, nanospectroscopy (tip-enhanced Raman spectroscopy, infrared nanospectroscopy), phase modulation infrared reflection-absorption spectroscopy, sum-frequency generation spectroscopy. We summarized experimental and theoretical approaches providing information about molecular structure and composition, lipid spatial distribution (phase separation), organization (domain shape, molecular orientation) of lipid membranes, and real-time visualization of the influence of various molecules (proteins, drugs) on their integrity. An integral part of this review discusses the latest achievements in the field of lipid layer-based biosensors.
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9
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Gaffney KA, Guo R, Bridges MD, Muhammednazaar S, Chen D, Kim M, Yang Z, Schilmiller AL, Faruk NF, Peng X, Jones AD, Kim KH, Sun L, Hubbell WL, Sosnick TR, Hong H. Lipid bilayer induces contraction of the denatured state ensemble of a helical-bundle membrane protein. Proc Natl Acad Sci U S A 2022; 119:e2109169119. [PMID: 34969836 PMCID: PMC8740594 DOI: 10.1073/pnas.2109169119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 12/19/2022] Open
Abstract
Defining the denatured state ensemble (DSE) and disordered proteins is essential to understanding folding, chaperone action, degradation, and translocation. As compared with water-soluble proteins, the DSE of membrane proteins is much less characterized. Here, we measure the DSE of the helical membrane protein GlpG of Escherichia coli (E. coli) in native-like lipid bilayers. The DSE was obtained using our steric trapping method, which couples denaturation of doubly biotinylated GlpG to binding of two streptavidin molecules. The helices and loops are probed using limited proteolysis and mass spectrometry, while the dimensions are determined using our paramagnetic biotin derivative and double electron-electron resonance spectroscopy. These data, along with our Upside simulations, identify the DSE as being highly dynamic, involving the topology changes and unfolding of some of the transmembrane (TM) helices. The DSE is expanded relative to the native state but only to 15 to 75% of the fully expanded condition. The degree of expansion depends on the local protein packing and the lipid composition. E. coli's lipid bilayer promotes the association of TM helices in the DSE and, probably in general, facilitates interhelical interactions. This tendency may be the outcome of a general lipophobic effect of proteins within the cell membranes.
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Affiliation(s)
- Kristen A Gaffney
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Ruiqiong Guo
- Department of Chemistry, Michigan State University, East Lansing, MI 48824
| | - Michael D Bridges
- Jules Stein Eye Institute, University of California, Los Angeles, CA 90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | | | - Daoyang Chen
- Department of Chemistry, Michigan State University, East Lansing, MI 48824
| | - Miyeon Kim
- Department of Chemistry, Michigan State University, East Lansing, MI 48824
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108
| | - Anthony L Schilmiller
- Research Technology Support Facility Mass Spectrometry and Metabolomics Core, Michigan State University, East Lansing, MI 48824
| | - Nabil F Faruk
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60637
| | - Xiangda Peng
- Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, IL 60637
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
- Research Technology Support Facility Mass Spectrometry and Metabolomics Core, Michigan State University, East Lansing, MI 48824
| | - Kelly H Kim
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, MI 48824
| | - Wayne L Hubbell
- Jules Stein Eye Institute, University of California, Los Angeles, CA 90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Tobin R Sosnick
- Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, IL 60637;
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
| | - Heedeok Hong
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824;
- Department of Chemistry, Michigan State University, East Lansing, MI 48824
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10
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Kratochvil HT, Newberry RW, Mensa B, Mravic M, DeGrado WF. Spiers Memorial Lecture: Analysis and de novo design of membrane-interactive peptides. Faraday Discuss 2021; 232:9-48. [PMID: 34693965 PMCID: PMC8979563 DOI: 10.1039/d1fd00061f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Membrane-peptide interactions play critical roles in many cellular and organismic functions, including protection from infection, remodeling of membranes, signaling, and ion transport. Peptides interact with membranes in a variety of ways: some associate with membrane surfaces in either intrinsically disordered conformations or well-defined secondary structures. Peptides with sufficient hydrophobicity can also insert vertically as transmembrane monomers, and many associate further into membrane-spanning helical bundles. Indeed, some peptides progress through each of these stages in the process of forming oligomeric bundles. In each case, the structure of the peptide and the membrane represent a delicate balance between peptide-membrane and peptide-peptide interactions. We will review this literature from the perspective of several biologically important systems, including antimicrobial peptides and their mimics, α-synuclein, receptor tyrosine kinases, and ion channels. We also discuss the use of de novo design to construct models to test our understanding of the underlying principles and to provide useful leads for pharmaceutical intervention of diseases.
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Affiliation(s)
- Huong T Kratochvil
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Robert W Newberry
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Bruk Mensa
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Marco Mravic
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
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11
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Tom AM, Kim WK, Hyeon C. Polymer brush-induced depletion interactions and clustering of membrane proteins. J Chem Phys 2021; 154:214901. [PMID: 34240971 DOI: 10.1063/5.0048554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We investigate the effect of mobile polymer brushes on proteins embedded in biological membranes by employing both Asakura-Oosawa type of theoretical model and coarse-grained molecular dynamics simulations. The brush polymer-induced depletion attraction between proteins changes non-monotonically with the size of brush. The depletion interaction, which is determined by the ratio of the protein size to the grafting distance between brush polymers, increases linearly with the brush size as long as the polymer brush height is shorter than the protein size. When the brush height exceeds the protein size, however, the depletion attraction among proteins is slightly reduced. We also explore the possibility of the brush polymer-induced assembly of a large protein cluster, which can be related to one of many molecular mechanisms underlying recent experimental observations of integrin nanocluster formation and signaling.
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Affiliation(s)
- Anvy Moly Tom
- Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Won Kyu Kim
- Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 02455, South Korea
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12
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Nakano M, Hanashima S, Hara T, Kabayama K, Asahina Y, Hojo H, Komura N, Ando H, Nyholm TKM, Slotte JP, Murata M. FRET detects lateral interaction between transmembrane domain of EGF receptor and ganglioside GM3 in lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183623. [PMID: 33933428 DOI: 10.1016/j.bbamem.2021.183623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/03/2021] [Accepted: 04/05/2021] [Indexed: 12/16/2022]
Abstract
Ganglioside GM3 in the plasma membranes suppresses cell growth by preventing the autophosphorylation of the epidermal growth factor receptor (EGFR). Biological studies have suggested that GM3 interacts with the transmembrane segment of EGFR. Further biophysical experiments are particularly important for quantitative evaluation of the peptide-glycolipid interplay in bilayer membranes using a simple reconstituted system. To examine these interactions in this way, we synthesized the transmembrane segment of EGFR bearing a nitrobenzoxadiazole fluorophore (NBD-TM) at the N-terminus. The affinity between EGFR and GM3 was evaluated based on Förster resonance energy transfer (FRET) between NBD-TM and ATTO594-labeled GM3 in bilayers where their non-specific interaction due to lateral proximity was subtracted by using NBD-labeled phospholipid. This method for selectively detecting the specific lipid-peptide interactions in model lipid bilayers disclosed that the lateral interaction between GM3 and the transmembrane segment of EGFR plays a certain role in disturbing the formation of active EGFR dimers.
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Affiliation(s)
- Mikito Nakano
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
| | - Toshiaki Hara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan; ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Kazuya Kabayama
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yuya Asahina
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita 565-0871, Japan
| | - Hironobu Hojo
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita 565-0871, Japan
| | - Naoko Komura
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu 501-1193, Japan; Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Hiromune Ando
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu 501-1193, Japan; Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Thomas K M Nyholm
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - J Peter Slotte
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan; ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
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13
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Yano Y, Watanabe Y, Matsuzaki K. Thermodynamic and kinetic stabilities of transmembrane helix bundles as revealed by single-pair FRET analysis: Effects of the number of membrane-spanning segments and cholesterol. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183532. [PMID: 33316240 DOI: 10.1016/j.bbamem.2020.183532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/02/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022]
Abstract
The tertiary structures and conformational dynamics of transmembrane (TM) helical proteins are maintained by the interhelical interaction network in membranes, although it is complicated to analyze the underlying driving forces because the amino acid sequences can involve multiple and various types of interactions. To obtain insights into basal and common effects of the number of membrane-spanning segments and membrane cholesterol, we measured stabilities of helix bundles composed of simple TM helices (AALALAA)3 (1TM) and (AALALAA)3-G5-(AALALAA)3 (2TM). Association-dissociation dynamics for 1TM-1TM, 1TM-2TM, and 2TM-2TM pairs were monitored to compare stabilities of 2-, 3-, and 4-helical bundles, respectively, with single-pair fluorescence resonance energy transfer (sp-FRET) in liposome membranes. Both thermodynamic and kinetic stabilities of the helix bundles increased with a greater number of membrane-spanning segments in POPC. The presence of 30 mol% cholesterol strongly enhanced the formation of 1TM-1TM and 1TM-2TM bundles (~ - 9 kJ mol-1), whereas it only weakly stabilized the 2TM-2TM bundle (~ - 3 kJ mol-1). Fourier transform infrared-polarized attenuated total reflection (ATR-FTIR) spectroscopy revealed an ~30° tilt of the helix axis relative to bilayer normal for the 1TM-2TM pair in the presence of cholesterol, suggesting the formation of a tilted helix bundle to release high lateral pressure at the center of cholesterol-containing membranes. These results demonstrate that the number of membrane-spanning segments affects the stability and structure of the helix bundle, and their cholesterol-dependences. Such information is useful to understand the basics of folding and assembly of multispanning TM proteins.
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Affiliation(s)
- Yoshiaki Yano
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuta Watanabe
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
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14
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García-Murria MJ, Duart G, Grau B, Diaz-Beneitez E, Rodríguez D, Mingarro I, Martínez-Gil L. Viral Bcl2s' transmembrane domain interact with host Bcl2 proteins to control cellular apoptosis. Nat Commun 2020; 11:6056. [PMID: 33247105 PMCID: PMC7695858 DOI: 10.1038/s41467-020-19881-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 10/29/2020] [Indexed: 12/20/2022] Open
Abstract
Viral control of programmed cell death relies in part on the expression of viral analogs of the B-cell lymphoma 2 (Bcl2) protein known as viral Bcl2s (vBcl2s). vBcl2s control apoptosis by interacting with host pro- and anti-apoptotic members of the Bcl2 family. Here, we show that the carboxyl-terminal hydrophobic region of herpesviral and poxviral vBcl2s can operate as transmembrane domains (TMDs) and participate in their homo-oligomerization. Additionally, we show that the viral TMDs mediate interactions with cellular pro- and anti-apoptotic Bcl2 TMDs within the membrane. Furthermore, these intra-membrane interactions among viral and cellular proteins are necessary to control cell death upon an apoptotic stimulus. Therefore, their inhibition represents a new potential therapy against viral infections, which are characterized by short- and long-term deregulation of programmed cell death.
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Affiliation(s)
- Maria Jesús García-Murria
- Department of Biochemistry and Molecular Biology, Institut de Biotecnologia i Biomedicina, Universitat de València, 46100, Burjassot, Spain
| | - Gerard Duart
- Department of Biochemistry and Molecular Biology, Institut de Biotecnologia i Biomedicina, Universitat de València, 46100, Burjassot, Spain
| | - Brayan Grau
- Department of Biochemistry and Molecular Biology, Institut de Biotecnologia i Biomedicina, Universitat de València, 46100, Burjassot, Spain
| | - Elisabet Diaz-Beneitez
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049, Madrid, Spain
| | - Dolores Rodríguez
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049, Madrid, Spain
| | - Ismael Mingarro
- Department of Biochemistry and Molecular Biology, Institut de Biotecnologia i Biomedicina, Universitat de València, 46100, Burjassot, Spain
| | - Luis Martínez-Gil
- Department of Biochemistry and Molecular Biology, Institut de Biotecnologia i Biomedicina, Universitat de València, 46100, Burjassot, Spain.
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15
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Leveraging a gain-of-function allele of Caenorhabditis elegans paqr-1 to elucidate membrane homeostasis by PAQR proteins. PLoS Genet 2020; 16:e1008975. [PMID: 32750056 PMCID: PMC7428288 DOI: 10.1371/journal.pgen.1008975] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/14/2020] [Accepted: 07/01/2020] [Indexed: 12/12/2022] Open
Abstract
The C. elegans proteins PAQR-2 (a homolog of the human seven-transmembrane domain AdipoR1 and AdipoR2 proteins) and IGLR-2 (a homolog of the mammalian LRIG proteins characterized by a single transmembrane domain and the presence of immunoglobulin domains and leucine-rich repeats in their extracellular portion) form a complex that protects against plasma membrane rigidification by promoting the expression of fatty acid desaturases and the incorporation of polyunsaturated fatty acids into phospholipids, hence increasing membrane fluidity. In the present study, we leveraged a novel gain-of-function allele of PAQR-1, a PAQR-2 paralog, to carry out structure-function studies. We found that the transmembrane domains of PAQR-2 are responsible for its functional requirement for IGLR-2, that PAQR-1 does not require IGLR-2 but acts via the same pathway as PAQR-2, and that the divergent N-terminal cytoplasmic domains of the PAQR-1 and PAQR-2 proteins serve a regulatory function and may regulate access to the catalytic site of these proteins. We also show that overexpression of human AdipoR1 or AdipoR2 alone is sufficient to confer increased palmitic acid resistance in HEK293 cells, and thus act in a manner analogous to the PAQR-1 gain-of-function allele.
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16
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Lietha D, Izard T. Roles of Membrane Domains in Integrin-Mediated Cell Adhesion. Int J Mol Sci 2020; 21:ijms21155531. [PMID: 32752284 PMCID: PMC7432473 DOI: 10.3390/ijms21155531] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/29/2020] [Accepted: 07/31/2020] [Indexed: 12/13/2022] Open
Abstract
The composition and organization of the plasma membrane play important functional and regulatory roles in integrin signaling, which direct many physiological and pathological processes, such as development, wound healing, immunity, thrombosis, and cancer metastasis. Membranes are comprised of regions that are thick or thin owing to spontaneous partitioning of long-chain saturated lipids from short-chain polyunsaturated lipids into domains defined as ordered and liquid-disorder domains, respectively. Liquid-ordered domains are typically 100 nm in diameter and sometimes referred to as lipid rafts. We posit that integrin β senses membrane thickness and that mechanical force on the membrane regulates integrin activation through membrane thinning. This review examines what we know about the nature and mechanism of the interaction of integrins with the plasma membrane and its effects on regulating integrins and its binding partners.
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Affiliation(s)
- Daniel Lietha
- Cell Signaling and Adhesion Group, Structural and Chemical Biology, Margarita Salas Center for Biological Research (CIB-CSIC), E-28040 Madrid, Spain;
| | - Tina Izard
- Cell Adhesion Laboratory, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
- Correspondence:
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17
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Pannwitt S, Kaltbeitzel J, Ahlers P, Spitzer D, Hellmann N, Depoix F, Besenius P, Schneider D. Lipid Bilayer Interactions of Peptidic Supramolecular Polymers and Their Impact on Membrane Permeability and Stability. Biochemistry 2020; 59:1845-1853. [PMID: 32320213 DOI: 10.1021/acs.biochem.0c00114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The synthesis and physicochemical characterization of supramolecular polymers with tunable assembly profiles offer exciting opportunities, involving the development of new biomedical carriers. Because synthetic nanocarriers aim to transport substances across or toward cellular membranes, we evaluated the interactions of amphiphilic peptide-based supramolecular polymers with lipid bilayers. Here, we focused on nanorod-like supramolecular polymers, obtained from two C3-symmetric dendritic peptide amphiphiles with alternating Phe/His sequences, equipped with a peripheral tetraethylene glycol dendron (C3-PH) or charged ethylenediamine end groups (C3-PH+). Triggered by pH changes, these amphiphiles assemble reversibly. Our results show that the supramolecular polymers have an impact on the lipid order in model membranes. Changes in the lipid order were observed depending on the charge state of the amphiphilic building blocks, as well as the chemical composition and physical properties of the bilayer. Furthermore, we further performed cell viability assays with the C3-PH+ and C3-PH supramolecular polymers. For C3-PH, the cell viability and extent of proliferation were decreased and the membrane permeability was enhanced, indicating a strong interaction of the polymer with cellular membranes. The results have implications for the design of novel pH-switchable supramolecular drug carriers and delivery vehicles that can respond to an altered microenvironment of tumorous or inflamed tissue.
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Affiliation(s)
- Stefanie Pannwitt
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Johann-Joachim Becherweg 30, 55128 Mainz, Germany
| | - Jonas Kaltbeitzel
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Johann-Joachim Becherweg 30, 55128 Mainz, Germany
| | - Patrick Ahlers
- Department of Chemistry, Organic Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Daniel Spitzer
- Department of Chemistry, Organic Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Nadja Hellmann
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Johann-Joachim Becherweg 30, 55128 Mainz, Germany
| | - Frank Depoix
- Institute of Molecular Physiology, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 9-11, 55128 Mainz, Germany
| | - Pol Besenius
- Department of Chemistry, Organic Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Johann-Joachim Becherweg 30, 55128 Mainz, Germany
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18
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Ballweg S, Sezgin E, Doktorova M, Covino R, Reinhard J, Wunnicke D, Hänelt I, Levental I, Hummer G, Ernst R. Regulation of lipid saturation without sensing membrane fluidity. Nat Commun 2020; 11:756. [PMID: 32029718 PMCID: PMC7005026 DOI: 10.1038/s41467-020-14528-1] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/14/2020] [Indexed: 12/22/2022] Open
Abstract
Cells maintain membrane fluidity by regulating lipid saturation, but the molecular mechanisms of this homeoviscous adaptation remain poorly understood. We have reconstituted the core machinery for regulating lipid saturation in baker’s yeast to study its molecular mechanism. By combining molecular dynamics simulations with experiments, we uncover a remarkable sensitivity of the transcriptional regulator Mga2 to the abundance, position, and configuration of double bonds in lipid acyl chains, and provide insights into the molecular rules of membrane adaptation. Our data challenge the prevailing hypothesis that membrane fluidity serves as the measured variable for regulating lipid saturation. Rather, we show that Mga2 senses the molecular lipid-packing density in a defined region of the membrane. Our findings suggest that membrane property sensors have evolved remarkable sensitivities to highly specific aspects of membrane structure and dynamics, thus paving the way toward the development of genetically encoded reporters for such properties in the future. Cells maintain membrane fluidity by regulating lipid saturation, but the molecular mechanisms of this homeoviscous adaptation remain poorly understood. Here authors reconstituted the core machinery for regulating lipid saturation in baker’s yeast to directly characterize its response to defined membrane environments and uncover its mode-of-action.
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Affiliation(s)
- Stephanie Ballweg
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Kirrberger Strasse 100, Building 61.4, 66421, Homburg, Germany.,PZMS, Center for Molecular Signaling (PZMS), Medical Faculty, Saarland University, 66421, Homburg, Germany
| | - Erdinc Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Milka Doktorova
- Department of Integrative Biology and Pharmacology, McGovern Medical School at the University of Texas Health Science Center, Houston, Texas, USA
| | - Roberto Covino
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438, Frankfurt, Germany
| | - John Reinhard
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Kirrberger Strasse 100, Building 61.4, 66421, Homburg, Germany.,PZMS, Center for Molecular Signaling (PZMS), Medical Faculty, Saarland University, 66421, Homburg, Germany
| | - Dorith Wunnicke
- Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Inga Hänelt
- Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Ilya Levental
- Department of Integrative Biology and Pharmacology, McGovern Medical School at the University of Texas Health Science Center, Houston, Texas, USA
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438, Frankfurt, Germany.,Institute of Biophysics, Goethe University Frankfurt, 60438, Frankfurt, Germany
| | - Robert Ernst
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Kirrberger Strasse 100, Building 61.4, 66421, Homburg, Germany. .,PZMS, Center for Molecular Signaling (PZMS), Medical Faculty, Saarland University, 66421, Homburg, Germany.
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19
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Westerfield JM, Barrera FN. Membrane receptor activation mechanisms and transmembrane peptide tools to elucidate them. J Biol Chem 2019; 295:1792-1814. [PMID: 31879273 DOI: 10.1074/jbc.rev119.009457] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Single-pass membrane receptors contain extracellular domains that respond to external stimuli and transmit information to intracellular domains through a single transmembrane (TM) α-helix. Because membrane receptors have various roles in homeostasis, signaling malfunctions of these receptors can cause disease. Despite their importance, there is still much to be understood mechanistically about how single-pass receptors are activated. In general, single-pass receptors respond to extracellular stimuli via alterations in their oligomeric state. The details of this process are still the focus of intense study, and several lines of evidence indicate that the TM domain (TMD) of the receptor plays a central role. We discuss three major mechanistic hypotheses for receptor activation: ligand-induced dimerization, ligand-induced rotation, and receptor clustering. Recent observations suggest that receptors can use a combination of these activation mechanisms and that technical limitations can bias interpretation. Short peptides derived from receptor TMDs, which can be identified by screening or rationally developed on the basis of the structure or sequence of their targets, have provided critical insights into receptor function. Here, we explore recent evidence that, depending on the target receptor, TMD peptides cannot only inhibit but also activate target receptors and can accommodate novel, bifunctional designs. Furthermore, we call for more sharing of negative results to inform the TMD peptide field, which is rapidly transforming into a suite of unique tools with the potential for future therapeutics.
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Affiliation(s)
- Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996.
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20
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Tseytin I, Mitrovic B, David N, Langenfeld K, Zarivach R, Diepold A, Sal-Man N. The Role of the Small Export Apparatus Protein, SctS, in the Activity of the Type III Secretion System. Front Microbiol 2019; 10:2551. [PMID: 31798543 PMCID: PMC6863770 DOI: 10.3389/fmicb.2019.02551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/22/2019] [Indexed: 12/15/2022] Open
Abstract
Many gram-negative pathogens utilize a protein complex, termed the type III secretion system (T3SS), to inject virulence factors from their cytoplasm directly into the host cell. An export apparatus that is formed by five putative integral membrane proteins (SctR/S/T/U/V), resides at the center of the T3SS complex. In this study, we characterized the smallest export apparatus protein, SctS, which contains two putative transmembrane domains (PTMD) that dynamically extract from the inner membrane and adopt a helix-turn-helix structure upon assembly of the T3SS. Replacement of each SctS PTMD with an alternative hydrophobic sequence resulted in abolishment of the T3SS activity, yet SctS self- and hetero-interactions as well as the overall assembly of the T3SS complex were unaffected. Our findings suggest that SctS PTMDs are not crucial for the interactions or the assembly of the T3SS base complex but rather that they are involved in adjusting the orientation of the export apparatus relative to additional T3SS sub-structures, such as the cytoplasmic- and the inner-membrane rings. This ensures the fittings between the dynamic and static components of the T3SS and supports the functionality of the T3SS complex.
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Affiliation(s)
- Irit Tseytin
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Bosko Mitrovic
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Nofar David
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Katja Langenfeld
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Raz Zarivach
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Andreas Diepold
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Neta Sal-Man
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
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21
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Rajagopal N, Irudayanathan FJ, Nangia S. Computational Nanoscopy of Tight Junctions at the Blood-Brain Barrier Interface. Int J Mol Sci 2019; 20:E5583. [PMID: 31717316 PMCID: PMC6888702 DOI: 10.3390/ijms20225583] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/16/2022] Open
Abstract
The selectivity of the blood-brain barrier (BBB) is primarily maintained by tight junctions (TJs), which act as gatekeepers of the paracellular space by blocking blood-borne toxins, drugs, and pathogens from entering the brain. The BBB presents a significant challenge in designing neurotherapeutics, so a comprehensive understanding of the TJ architecture can aid in the design of novel therapeutics. Unraveling the intricacies of TJs with conventional experimental techniques alone is challenging, but recently developed computational tools can provide a valuable molecular-level understanding of TJ architecture. We employed the computational methods toolkit to investigate claudin-5, a highly expressed TJ protein at the BBB interface. Our approach started with the prediction of claudin-5 structure, evaluation of stable dimer conformations and nanoscale assemblies, followed by the impact of lipid environments, and posttranslational modifications on these claudin-5 assemblies. These led to the study of TJ pores and barriers and finally understanding of ion and small molecule transport through the TJs. Some of these in silico, molecular-level findings, will need to be corroborated by future experiments. The resulting understanding can be advantageous towards the eventual goal of drug delivery across the BBB. This review provides key insights gleaned from a series of state-of-the-art nanoscale simulations (or computational nanoscopy studies) performed on the TJ architecture.
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Affiliation(s)
| | | | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA
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22
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Rajagopal N, Nangia S. Obtaining Protein Association Energy Landscape for Integral Membrane Proteins. J Chem Theory Comput 2019; 15:6444-6455. [DOI: 10.1021/acs.jctc.9b00626] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nandhini Rajagopal
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, New York 13244, United States
| | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, New York 13244, United States
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23
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Hydrophobic matching of HIV-1 Vpu transmembrane helix-helix interactions is optimized for subcellular location. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183022. [PMID: 31302078 DOI: 10.1016/j.bbamem.2019.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 06/06/2019] [Accepted: 07/09/2019] [Indexed: 11/21/2022]
Abstract
The HIV-1 accessory protein Vpu mediates the downregulation of several host cell proteins, an activity that is critical for viral replication in vivo. As the first step in directing cell-surface proteins to internal cellular compartments, and in many cases degradation, Vpu binds a subset of its target proteins through their transmembrane domains. Each of the known targets of Vpu are synthesized in the ER, and must traverse the different membrane environments found along the secretory pathway, thus it is important to consider how membrane composition might influence the interactions between Vpu and its targets. We have used Förster resonance energy transfer (FRET) to measure the oligomerization of Vpu with the transmembrane domains of target proteins in model membranes of varying lipid composition. Our data show that both lipid bilayer thickness and acyl chain order can significantly influence monomer-oligomer equilibria within the Vpu-target system. Changes in oligomerization levels were found to be non-specific with no single Vpu-target interaction being favored under any condition. Our analysis of the influence of the membrane environment on the strength of helix-helix interactions between Vpu and its targets in vitro suggests that the strength of Vpu-target interactions in vivo will be partially dependent on the membrane environment found in specific membrane compartments.
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24
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Pannwitt S, Stangl M, Schneider D. Lipid Binding Controls Dimerization of the Coat Protein p24 Transmembrane Helix. Biophys J 2019; 117:1554-1562. [PMID: 31627840 DOI: 10.1016/j.bpj.2019.09.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 09/05/2019] [Accepted: 09/09/2019] [Indexed: 10/25/2022] Open
Abstract
Coat protein (COP) I and COP II complexes are involved in the transport of proteins between the endoplasmic reticulum and the Golgi apparatus in eukaryotic cells. The formation of COP I/II complexes at membrane surfaces is an early step in vesicle formation and is mastered by p24, a type I transmembrane protein. Oligomerization of p24 monomers was suggested to be mediated and/or stabilized via interactions within the transmembrane domain, and the p24 transmembrane helix appears to selectively bind a single sphingomyelin C18:0 molecule. Furthermore, a potential cholesterol-binding sequence has also been predicted in the p24 transmembrane domain. Thus, sphingomyelin and/or cholesterol binding to the transmembrane domain might directly control the oligomeric state of p24 and, thus, COP vesicle formation. In this study, we show that sequence-specific dimerization of the p24 transmembrane helix is mediated by a LQ7 motif, with Gln187 being of special importance. Whereas cholesterol has no direct impact on p24 dimerization, binding of the sphingolipid can clearly control dimerization of p24 in rigid membrane regions. We suggest that specific binding of a sphingolipid to the p24 transmembrane helix affects p24 dimerization in membranes with increased cholesterol contents. A clearly defined p24 dimerization propensity likely is crucial for the p24 activity, which involves shuttling in between the endoplasmic reticulum and the Golgi membrane, in which cholesterol and SM C18:0 concentrations differ.
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Affiliation(s)
- Stefanie Pannwitt
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Michael Stangl
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Dirk Schneider
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany.
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25
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Karabadzhak AG, Weerakkody D, Deacon J, Andreev OA, Reshetnyak YK, Engelman DM. Bilayer Thickness and Curvature Influence Binding and Insertion of a pHLIP Peptide. Biophys J 2019; 114:2107-2115. [PMID: 29742404 DOI: 10.1016/j.bpj.2018.03.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 01/30/2018] [Accepted: 03/05/2018] [Indexed: 11/15/2022] Open
Abstract
The physical properties of lipid bilayers, such as curvature and fluidity, can affect the interactions of polypeptides with membranes, influencing biological events. Additionally, given the growing interest in peptide-based therapeutics, understanding the influence of membrane properties on membrane-associated peptides has potential utility. pH low insertion peptides (pHLIPs) are a family of water-soluble peptides that can insert across cell membranes in a pH-dependent manner, enabling the use of pH to follow peptide-lipid interactions. Here we study pHLIP interactions with liposomes varying in size and composition, to determine the influence of several key membrane physical properties. We find that pHLIP binding to bilayer surfaces at neutral pH is governed by the ease of access to the membrane's hydrophobic core, which can be facilitated by membrane curvature, thickness, and the cholesterol content of the membrane. After surface binding, if the pH is lowered, the kinetics of pHLIP folding to form a helix and subsequent insertion across the membrane depends on the fluidity and energetic dynamics of the membrane. We showed that pHLIP is capable of forming a helix across lipid bilayers of different thicknesses at low pH. However, the kinetics of the slow phase of insertion corresponding to the translocation of C-terminal end of the peptide across lipid bilayer, vary approximately twofold, and correlate with bilayer thickness and fluidity. Although these influences are not large, local curvature variations in membranes of different fluidity could selectively influence surface binding in mixed cell populations.
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Affiliation(s)
- Alexander G Karabadzhak
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | | | - John Deacon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Oleg A Andreev
- Physics Department, University of Rhode Island, Kingston, Rhode Island
| | - Yana K Reshetnyak
- Physics Department, University of Rhode Island, Kingston, Rhode Island.
| | - Donald M Engelman
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.
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26
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Bennett MK, Wallington-Beddoe CT, Pitson SM. Sphingolipids and the unfolded protein response. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:1483-1494. [PMID: 31176037 DOI: 10.1016/j.bbalip.2019.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/29/2019] [Accepted: 06/01/2019] [Indexed: 12/17/2022]
Abstract
The unfolded protein response (UPR) is a response by the endoplasmic reticulum to stress, classically caused by any disruption to cell homeostasis that results in an accumulation in unfolded proteins. However, there is an increasing body of research demonstrating that the UPR can also be activated by changes in lipid homeostasis, including changes in sphingolipid metabolism. Sphingolipids are a family of bioactive lipids with important roles in both the formation and integrity of cellular membranes, and regulation of key cellular processes, including cell proliferation and apoptosis. Bi-directional interactions between sphingolipids and the UPR have now been observed in a range of diseases, including cancer, diabetes and liver disease. Determining how these two key cellular components influence each other could play an important role in deciphering the causes of these diseases and potentially reveal new therapeutic approaches.
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Affiliation(s)
- Melissa K Bennett
- Centre for Cancer Biology, University of South Australia and SA Pathology, UniSA CRI Building, North Tce, Adelaide, SA 5001, Australia
| | - Craig T Wallington-Beddoe
- Centre for Cancer Biology, University of South Australia and SA Pathology, UniSA CRI Building, North Tce, Adelaide, SA 5001, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5001, Australia; Flinders Medical Centre, Bedford Park, SA 5042, Australia; College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Stuart M Pitson
- Centre for Cancer Biology, University of South Australia and SA Pathology, UniSA CRI Building, North Tce, Adelaide, SA 5001, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5001, Australia; School of Biological Sciences, University of Adelaide, Adelaide, SA 5000, Australia.
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27
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Alves DS, Westerfield JM, Shi X, Nguyen VP, Stefanski KM, Booth KR, Kim S, Morrell-Falvey J, Wang BC, Abel SM, Smith AW, Barrera FN. A novel pH-dependent membrane peptide that binds to EphA2 and inhibits cell migration. eLife 2018; 7:36645. [PMID: 30222105 PMCID: PMC6192698 DOI: 10.7554/elife.36645] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/16/2018] [Indexed: 12/19/2022] Open
Abstract
Misregulation of the signaling axis formed by the receptor tyrosine kinase (RTK) EphA2 and its ligand, ephrinA1, causes aberrant cell-cell contacts that contribute to metastasis. Solid tumors are characterized by an acidic extracellular medium. We intend to take advantage of this tumor feature to design new molecules that specifically target tumors. We created a novel pH-dependent transmembrane peptide, TYPE7, by altering the sequence of the transmembrane domain of EphA2. TYPE7 is highly soluble and interacts with the surface of lipid membranes at neutral pH, while acidity triggers transmembrane insertion. TYPE7 binds to endogenous EphA2 and reduces Akt phosphorylation and cell migration as effectively as ephrinA1. Interestingly, we found large differences in juxtamembrane tyrosine phosphorylation and the extent of EphA2 clustering when comparing TYPE7 with activation by ephrinA1. This work shows that it is possible to design new pH-triggered membrane peptides to activate RTK and gain insights on its activation mechanism.
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Affiliation(s)
- Daiane S Alves
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
| | - Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
| | - Xiaojun Shi
- Department of Chemistry, University of Akron, Akron, United States.,Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, United States.,Pharmacology, Case Western Reserve University, Cleveland, United States.,Rammelkamp Center for Research, MetroHealth Medical Center, Cleveland, United States
| | - Vanessa P Nguyen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
| | - Katherine M Stefanski
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, United States
| | - Kristen R Booth
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
| | - Soyeon Kim
- Department of Chemistry, University of Akron, Akron, United States
| | - Jennifer Morrell-Falvey
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, United States
| | - Bing-Cheng Wang
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, United States.,Pharmacology, Case Western Reserve University, Cleveland, United States.,Rammelkamp Center for Research, MetroHealth Medical Center, Cleveland, United States
| | - Steven M Abel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, United States.,National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, United States
| | - Adam W Smith
- Department of Chemistry, University of Akron, Akron, United States
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
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28
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The Third Transmembrane Domain of EscR Is Critical for Function of the Enteropathogenic Escherichia coli Type III Secretion System. mSphere 2018; 3:3/4/e00162-18. [PMID: 30045964 PMCID: PMC6060343 DOI: 10.1128/msphere.00162-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Many Gram-negative bacterial pathogens that cause life-threatening diseases employ a type III secretion system (T3SS) for their virulence. The T3SS comprises several proteins that assemble into a syringe-like structure dedicated to the injection of bacterial virulence factors into the host cells. Although many T3SS proteins are transmembrane proteins, our knowledge of these proteins is limited mostly to their soluble domains. In this study, we found that the third transmembrane domain (TMD) of EscR, a central protein of the T3SS in enteropathogenic E. coli, contributes to protein self-oligomerization. Moreover, we demonstrated that a single aspartic acid residue, located at the core of this TMD, is critical for the activity of the full-length protein and the function of the entire T3SS, possibly due to its involvement in mediating TMD-TMD interactions. Our findings should encourage the mapping of the entire interactome of the T3SS components, including interactions mediated through their TMDs. Many Gram-negative bacterial pathogens utilize a specialized protein delivery system, called the type III secretion system (T3SS), to translocate effector proteins into the host cells. The translocated effectors are crucial for bacterial infection and survival. The base of the T3SS transverses both bacterial membranes and contains an export apparatus that comprises five membrane proteins. Here, we study the export apparatus of enteropathogenic Escherichia coli (EPEC) and characterize its central component, called the EscR protein. We found that the third transmembrane domain (TMD) of EscR mediates strong self-oligomerization in an isolated genetic reporter system. Replacing this TMD sequence with an alternative hydrophobic sequence within the full-length protein resulted in a complete loss of function of the T3SS, further suggesting that the EscR TMD3 sequence has another functional role in addition to its role as a membrane anchor. Moreover, we found that an aspartic acid residue, located at the core of EscR TMD3, is important for the oligomerization propensity of TMD3 and that a point mutation of this residue within the full-length protein abolishes the T3SS activity and the ability of the bacteria to translocate effectors into host cells. IMPORTANCE Many Gram-negative bacterial pathogens that cause life-threatening diseases employ a type III secretion system (T3SS) for their virulence. The T3SS comprises several proteins that assemble into a syringe-like structure dedicated to the injection of bacterial virulence factors into the host cells. Although many T3SS proteins are transmembrane proteins, our knowledge of these proteins is limited mostly to their soluble domains. In this study, we found that the third transmembrane domain (TMD) of EscR, a central protein of the T3SS in enteropathogenic E. coli, contributes to protein self-oligomerization. Moreover, we demonstrated that a single aspartic acid residue, located at the core of this TMD, is critical for the activity of the full-length protein and the function of the entire T3SS, possibly due to its involvement in mediating TMD-TMD interactions. Our findings should encourage the mapping of the entire interactome of the T3SS components, including interactions mediated through their TMDs.
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29
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Pawar AB, Sengupta D. Effect of Membrane Composition on Receptor Association: Implications of Cancer Lipidomics on ErbB Receptors. J Membr Biol 2018; 251:359-368. [DOI: 10.1007/s00232-018-0015-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/15/2018] [Indexed: 10/18/2022]
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30
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Megarajan S, Subramaniyan SB, Muthuswamy S, Anthony SP, Arunachalam J, Moon D, Veerappan A. Synthesis, supramolecular organization and thermotropic phase behaviour of N-acyltris(hydroxymethyl)aminomethane. RSC Adv 2018; 8:32823-32831. [PMID: 35547689 PMCID: PMC9086375 DOI: 10.1039/c8ra06479b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/18/2018] [Indexed: 02/01/2023] Open
Abstract
Herein, we reported the supramolecular organization of N-acyltris(hydroxymethyl)aminomethane (NATM) in the solid state as well as in aqueous solution. Single crystal X-ray diffraction revealed that NATM adopts a fully interdigitized structure. The thermodynamic parameters associated with thermotropic phase behaviour of NATM was determined by differential scanning calorimetry. The molecular packing and phase state of the NATM analyzed by laurdan and prodan fluorescence supports the formation of an interdigitized phase in aqueous solution. The potential application of the self-assembled NATM vesicles was demonstrated through entrapping model drug, Rhodamine B. Self assembly of N-acyltris(hydroxymethyl)aminomethane into interdigitized vesicles.![]()
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Affiliation(s)
- Sengan Megarajan
- School of Chemical and Biotechnology
- SASTRA Deemed University
- Thanjavur – 613401
- India
| | | | - Sureshan Muthuswamy
- School of Chemical and Biotechnology
- SASTRA Deemed University
- Thanjavur – 613401
- India
| | | | - Jothi Arunachalam
- School of Chemical and Biotechnology
- SASTRA Deemed University
- Thanjavur – 613401
- India
| | - Dohyun Moon
- Beamline Department
- Pohang Accelerator Laboratory
- Pohang
- Korea
| | - Anbazhagan Veerappan
- School of Chemical and Biotechnology
- SASTRA Deemed University
- Thanjavur – 613401
- India
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31
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FRET Analysis of the Promiscuous yet Specific Interactions of the HIV-1 Vpu Transmembrane Domain. Biophys J 2017; 113:1992-2003. [PMID: 29117523 DOI: 10.1016/j.bpj.2017.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 09/01/2017] [Accepted: 09/13/2017] [Indexed: 02/02/2023] Open
Abstract
The Vpu protein of HIV-1 functions to downregulate cell surface localization of host proteins involved in the innate immune response to viral infection. For several target proteins, including the NTB-A and PVR receptors and the host restriction factor tetherin, this antagonism is carried out via direct interactions between the transmembrane domains (TMDs) of Vpu and the target. The Vpu TMD also modulates homooligomerization of this protein, and the tetherin TMD forms homodimers. The mechanism through which a single transmembrane helix is able to recognize and interact with a wide range of select targets that do not share known interaction motifs is poorly understood. Here we use Förster resonance energy transfer to characterize the energetics of homo- and heterooligomer interactions between the Vpu TMD and several target proteins. Our data show that target TMDs compete for interaction with Vpu, and that formation of each heterooligomer has a similar dissociation constant (Kd) and free energy of association to the Vpu homooligomer. This leads to a model in which Vpu monomers, Vpu homooligomers, and Vpu-target heterooligomers coexist, and suggests that the conserved binding surface of Vpu TMD has been selected for weak binding to multiple targets.
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32
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Grau B, Javanainen M, García-Murria MJ, Kulig W, Vattulainen I, Mingarro I, Martínez-Gil L. The role of hydrophobic matching on transmembrane helix packing in cells. Cell Stress 2017; 1:90-106. [PMID: 31225439 PMCID: PMC6551820 DOI: 10.15698/cst2017.11.111] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Folding and packing of membrane proteins are highly influenced by the lipidic component of the membrane. Here, we explore how the hydrophobic mismatch (the difference between the hydrophobic span of a transmembrane protein region and the hydrophobic thickness of the lipid membrane around the protein) influences transmembrane helix packing in a cellular environment. Using a ToxRED assay in Escherichia coli and a Bimolecular Fluorescent Complementation approach in human-derived cells complemented by atomistic molecular dynamics simulations we analyzed the dimerization of Glycophorin A derived transmembrane segments. We concluded that, biological membranes can accommodate transmembrane homo-dimers with a wide range of hydrophobic lengths. Hydrophobic mismatch and its effects on dimerization are found to be considerably weaker than those previously observed in model membranes, or under in vitro conditions, indicating that biological membranes (particularly eukaryotic membranes) can adapt to structural deformations through compensatory mechanisms that emerge from their complex structure and composition to alleviate membrane stress. Results based on atomistic simulations support this view, as they revealed that Glycophorin A dimers remain stable, despite of poor hydrophobic match, using mechanisms based on dimer tilting or local membrane thickness perturbations. Furthermore, hetero-dimers with large length disparity between their monomers are also tolerated in cells, and the conclusions that one can draw are essentially similar to those found with homo-dimers. However, large differences between transmembrane helices length hinder the monomer/dimer equilibrium, confirming that, the hydrophobic mismatch has, nonetheless, biologically relevant effects on helix packing in vivo.
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Affiliation(s)
- Brayan Grau
- Departamento de Bioquímica y Biología Molecular, ERI BioTecMed, Universitat de València, E-46100 Burjassot, Spain
| | - Matti Javanainen
- Laboratory of Physics, Tampere University of Technology, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki, POB 64, FI-00014 Helsinki, Finland
| | - Maria Jesús García-Murria
- Departamento de Bioquímica y Biología Molecular, ERI BioTecMed, Universitat de València, E-46100 Burjassot, Spain
| | - Waldemar Kulig
- Laboratory of Physics, Tampere University of Technology, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki, POB 64, FI-00014 Helsinki, Finland
| | - Ilpo Vattulainen
- Laboratory of Physics, Tampere University of Technology, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki, POB 64, FI-00014 Helsinki, Finland.,MEMPHYS - Centre for Biomembrane Physics
| | - Ismael Mingarro
- Departamento de Bioquímica y Biología Molecular, ERI BioTecMed, Universitat de València, E-46100 Burjassot, Spain
| | - Luis Martínez-Gil
- Departamento de Bioquímica y Biología Molecular, ERI BioTecMed, Universitat de València, E-46100 Burjassot, Spain
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33
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Aoki T. A Comprehensive Review of Our Current Understanding of Red Blood Cell (RBC) Glycoproteins. MEMBRANES 2017; 7:membranes7040056. [PMID: 28961212 PMCID: PMC5746815 DOI: 10.3390/membranes7040056] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 09/20/2017] [Accepted: 09/24/2017] [Indexed: 12/11/2022]
Abstract
Human red blood cells (RBC), which are the cells most commonly used in the study of biological membranes, have some glycoproteins in their cell membrane. These membrane proteins are band 3 and glycophorins A-D, and some substoichiometric glycoproteins (e.g., CD44, CD47, Lu, Kell, Duffy). The oligosaccharide that band 3 contains has one N-linked oligosaccharide, and glycophorins possess mostly O-linked oligosaccharides. The end of the O-linked oligosaccharide is linked to sialic acid. In humans, this sialic acid is N-acetylneuraminic acid (NeuAc). Another sialic acid, N-glycolylneuraminic acid (NeuGc) is present in red blood cells of non-human origin. While the biological function of band 3 is well known as an anion exchanger, it has been suggested that the oligosaccharide of band 3 does not affect the anion transport function. Although band 3 has been studied in detail, the physiological functions of glycophorins remain unclear. This review mainly describes the sialo-oligosaccharide structures of band 3 and glycophorins, followed by a discussion of the physiological functions that have been reported in the literature to date. Moreover, other glycoproteins in red blood cell membranes of non-human origin are described, and the physiological function of glycophorin in carp red blood cell membranes is discussed with respect to its bacteriostatic activity.
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Affiliation(s)
- Takahiko Aoki
- Laboratory of Quality in Marine Products, Graduate School of Bioresources, Mie University, 1577 Kurima Machiya-cho, Mie, Tsu 514-8507, Japan.
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34
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Franz J, Bereau T, Pannwitt S, Anbazhagan V, Lehr A, Nubbemeyer U, Dietz U, Bonn M, Weidner T, Schneider D. Nitrated Fatty Acids Modulate the Physical Properties of Model Membranes and the Structure of Transmembrane Proteins. Chemistry 2017; 23:9690-9697. [DOI: 10.1002/chem.201702041] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Johannes Franz
- Institute for Pharmacy and BiochemistryJohannes Gutenberg University 55128 Mainz Germany
- Max Planck Institute for Polymer ResearchMolecular Spectroscopy Department 55128 Mainz Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer ResearchTheory group 55128 Mainz Germany
| | - Stefanie Pannwitt
- Institute for Pharmacy and BiochemistryJohannes Gutenberg University 55128 Mainz Germany
| | - Veerappan Anbazhagan
- Institute for Pharmacy and BiochemistryJohannes Gutenberg University 55128 Mainz Germany
- Current address: School of Chemical and BiotechnologySASTRA University Thanjavur 613401, Tamil Nadu India
| | - Alexander Lehr
- Institute for Organic ChemistryJohannes Gutenberg University 55128 Mainz Germany
| | - Udo Nubbemeyer
- Institute for Organic ChemistryJohannes Gutenberg University 55128 Mainz Germany
| | | | - Mischa Bonn
- Max Planck Institute for Polymer ResearchMolecular Spectroscopy Department 55128 Mainz Germany
| | - Tobias Weidner
- Max Planck Institute for Polymer ResearchMolecular Spectroscopy Department 55128 Mainz Germany
| | - Dirk Schneider
- Institute for Pharmacy and BiochemistryJohannes Gutenberg University 55128 Mainz Germany
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35
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Schneider D. Border controls: Lipids control proteins and proteins control lipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:507-508. [DOI: 10.1016/j.bbamem.2016.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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36
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Yano Y, Kondo K, Watanabe Y, Zhang TO, Ho JJ, Oishi S, Fujii N, Zanni MT, Matsuzaki K. GXXXG-Mediated Parallel and Antiparallel Dimerization of Transmembrane Helices and Its Inhibition by Cholesterol: Single-Pair FRET and 2D IR Studies. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yoshiaki Yano
- Graduate School of Pharmaceutical Sciences; Kyoto University; Kyoto 606-8501 Japan
| | - Kotaro Kondo
- Graduate School of Pharmaceutical Sciences; Kyoto University; Kyoto 606-8501 Japan
| | - Yuta Watanabe
- Graduate School of Pharmaceutical Sciences; Kyoto University; Kyoto 606-8501 Japan
| | - Tianqi O. Zhang
- Department of Chemistry; University of Wisconsin; Madison WI 53706 USA
| | - Jia-Jung Ho
- Department of Chemistry; University of Wisconsin; Madison WI 53706 USA
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences; Kyoto University; Kyoto 606-8501 Japan
| | - Nobutaka Fujii
- Graduate School of Pharmaceutical Sciences; Kyoto University; Kyoto 606-8501 Japan
| | - Martin T. Zanni
- Department of Chemistry; University of Wisconsin; Madison WI 53706 USA
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences; Kyoto University; Kyoto 606-8501 Japan
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37
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Yano Y, Furukawa N, Ono S, Takeda Y, Matsuzaki K. Selective amine labeling of cell surface proteins guided by coiled-coil assembly. Biopolymers 2017; 106:484-90. [PMID: 26285787 DOI: 10.1002/bip.22715] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/30/2015] [Accepted: 08/09/2015] [Indexed: 01/17/2023]
Abstract
Covalent labeling of target proteins in living cells is useful for both fluorescence live-cell imaging and the subsequent biochemical analyses of the proteins. Here, we report an efficient method for the amine labeling of membrane proteins on the cell surface, guided by a noncovalent coiled-coil interaction. A carboxyl sulfosuccinimidyl ester introduced at the C-terminus of the coiled-coil probe reacted with target proteins under mild labeling conditions ([probe] = 150 nM, pH 7.4, 25°C) for 20 min. Various fluorescent moieties with different hydrophobicities are available for covalent labeling with high signal/background labeling ratios. Using this method, oligomeric states of glycophorin A (GpA) were compared in mammalian CHO-K1 cells and sodium dodecyl sulfate (SDS) micelles. In the cell membranes, no significant self-association of GpA was detected, whereas SDS-PAGE suggested partial dimerization of the proteins. Membrane cholesterol was found to be an important factor that suppressed the dimerization of GpA. Thus, the covalent functionality enables direct comparison of the oligomeric state of membrane proteins under various conditions. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 484-490, 2016.
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Affiliation(s)
- Yoshiaki Yano
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Nami Furukawa
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Satoshi Ono
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Yuki Takeda
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
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38
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Yano Y, Kondo K, Watanabe Y, Zhang TO, Ho JJ, Oishi S, Fujii N, Zanni MT, Matsuzaki K. GXXXG-Mediated Parallel and Antiparallel Dimerization of Transmembrane Helices and Its Inhibition by Cholesterol: Single-Pair FRET and 2D IR Studies. Angew Chem Int Ed Engl 2017; 56:1756-1759. [PMID: 28071848 DOI: 10.1002/anie.201609708] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/05/2016] [Indexed: 02/06/2023]
Abstract
Small-residue-mediated interhelical packings are ubiquitously found in helical membrane proteins, although their interaction dynamics and lipid dependence remain mostly uncharacterized. We used a single-pair FRET technique to examine the effect of a GXXXG motif on the association of de novo designed (AALALAA)3 helices in liposomes. Dimerization occurred with sub-second lifetimes, which was abolished by cholesterol. Utilizing the nearly instantaneous time-resolution of 2D IR spectroscopy, parallel and antiparallel helix associations were identified by vibrational couplings across helices at their interface. Taken together, the data illustrate that the GXXXG motif controls helix packing but still allows for a dynamic and lipid-regulated oligomeric state.
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Affiliation(s)
- Yoshiaki Yano
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Kotaro Kondo
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Yuta Watanabe
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Tianqi O Zhang
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Jia-Jung Ho
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Nobutaka Fujii
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
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39
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Bocharov EV, Mineev KS, Pavlov KV, Akimov SA, Kuznetsov AS, Efremov RG, Arseniev AS. Helix-helix interactions in membrane domains of bitopic proteins: Specificity and role of lipid environment. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:561-576. [PMID: 27884807 DOI: 10.1016/j.bbamem.2016.10.024] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/18/2016] [Accepted: 10/20/2016] [Indexed: 12/23/2022]
Abstract
Interaction between transmembrane helices often determines biological activity of membrane proteins. Bitopic proteins, a broad subclass of membrane proteins, form dimers containing two membrane-spanning helices. Some aspects of their structure-function relationship cannot be fully understood without considering the protein-lipid interaction, which can determine the protein conformational ensemble. Experimental and computer modeling data concerning transmembrane parts of bitopic proteins are reviewed in the present paper. They highlight the importance of lipid-protein interactions and resolve certain paradoxes in the behavior of such proteins. Besides, some properties of membrane organization provided a clue to understanding of allosteric interactions between distant parts of proteins. Interactions of these kinds appear to underlie a signaling mechanism, which could be widely employed in the functioning of many membrane proteins. Treatment of membrane proteins as parts of integrated fine-tuned proteolipid system promises new insights into biological function mechanisms and approaches to drug design. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.
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Affiliation(s)
- Eduard V Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation; National Research Centre "Kurchatov Institute", Akad. Kurchatova pl. 1, Moscow, 123182, Russian Federation.
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation
| | - Konstantin V Pavlov
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninskiy prospect 31/5, Moscow, 119071, Russian Federation
| | - Sergey A Akimov
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninskiy prospect 31/5, Moscow, 119071, Russian Federation; National University of Science and Technology "MISiS", Leninskiy prospect 4, Moscow, 119049, Russian Federation
| | - Andrey S Kuznetsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation
| | - Roman G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation; Higher School of Economics, Myasnitskaya ul. 20, Moscow, 101000, Russian Federation
| | - Alexander S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation.
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40
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Domański J, Hedger G, Best RB, Stansfeld PJ, Sansom MSP. Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association. J Phys Chem B 2016; 121:3364-3375. [PMID: 27807980 PMCID: PMC5402295 DOI: 10.1021/acs.jpcb.6b08445] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Potential of mean
force (PMF) calculations are used to characterize
the free energy landscape of protein–lipid and protein–protein
association within membranes. Coarse-grained simulations allow binding
free energies to be determined with reasonable statistical error.
This accuracy relies on defining a good collective variable to describe
the binding and unbinding transitions, and upon criteria for assessing
the convergence of the simulation toward representative equilibrium
sampling. As examples, we calculate protein–lipid binding PMFs
for ANT/cardiolipin and Kir2.2/PIP2, using umbrella sampling
on a distance coordinate. These highlight the importance of replica
exchange between windows for convergence. The use of two independent
sets of simulations, initiated from bound and unbound states, provide
strong evidence for simulation convergence. For a model protein–protein
interaction within a membrane, center-of-mass distance is shown to
be a poor collective variable for describing transmembrane helix–helix
dimerization. Instead, we employ an alternative intermolecular distance
matrix RMS (DRMS) coordinate to obtain
converged PMFs for the association of the glycophorin transmembrane
domain. While the coarse-grained force field gives a reasonable Kd for dimerization, the majority of the bound
population is revealed to be in a near-native conformation. Thus,
the combination of a refined reaction coordinate with improved sampling
reveals previously unnoticed complexities of the dimerization free
energy landscape. We propose the use of replica-exchange umbrella
sampling starting from different initial conditions as a robust approach
for calculation of the binding energies in membrane simulations.
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Affiliation(s)
- Jan Domański
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K.,Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - George Hedger
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
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41
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Khadria AS, Senes A. Fluorophores, environments, and quantification techniques in the analysis of transmembrane helix interaction using FRET. Biopolymers 2016; 104:247-64. [PMID: 25968159 DOI: 10.1002/bip.22667] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/15/2015] [Accepted: 05/04/2015] [Indexed: 12/31/2022]
Abstract
Förster resonance energy transfer (FRET) has been widely used as a spectroscopic tool in vitro to study the interactions between transmembrane (TM) helices in detergent and lipid environments. This technique has been instrumental to many studies that have greatly contributed to quantitative understanding of the physical principles that govern helix-helix interactions in the membrane. These studies have also improved our understanding of the biological role of oligomerization in membrane proteins. In this review, we focus on the combinations of fluorophores used, the membrane mimetic environments, and measurement techniques that have been applied to study model systems as well as biological oligomeric complexes in vitro. We highlight the different formalisms used to calculate FRET efficiency and the challenges associated with accurate quantification. The goal is to provide the reader with a comparative summary of the relevant literature for planning and designing FRET experiments aimed at measuring TM helix-helix associations.
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Affiliation(s)
- Ambalika S Khadria
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | - Alessandro Senes
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706
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42
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Bugge K, Lindorff-Larsen K, Kragelund BB. Understanding single-pass transmembrane receptor signaling from a structural viewpoint-what are we missing? FEBS J 2016; 283:4424-4451. [PMID: 27350538 DOI: 10.1111/febs.13793] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 06/10/2016] [Accepted: 06/27/2016] [Indexed: 11/30/2022]
Abstract
Single-pass transmembrane receptors are involved in essential processes of both physiological and pathological nature and represent more than 1300 proteins in the human genome. Despite the high biological relevance of these receptors, the mechanisms of the signal transductions they facilitate are incompletely understood. One major obstacle is the lack of structures of the transmembrane domains that connect the extracellular ligand-binding domains to the intracellular signaling platforms. Over a period of almost 20 years since the first structure was reported, only 21 of these receptors have become represented by a transmembrane domain structure. This scarceness stands in strong contrast to the significance of these transmembrane α-helices for receptor functionality. In this review, we explore the properties and qualities of the current set of structures, as well as the methodological difficulties associated with their characterization and the challenges left to be overcome. Without an increased and focused effort to bring this class of proteins on par with the remaining membrane protein field, a serious lag in their biological understanding looms. Design of pharmaceutical agents, prediction of mutational affects in relation to disease, and deciphering of functional mechanisms require high-resolution structural information, especially when dealing with a domain carrying so much functionality in so few residues.
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Affiliation(s)
- Katrine Bugge
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
| | - Birthe B Kragelund
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
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43
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Klein N, Hellmann N, Schneider D. Anionic Lipids Modulate the Activity of the Aquaglyceroporin GlpF. Biophys J 2016; 109:722-31. [PMID: 26287624 DOI: 10.1016/j.bpj.2015.06.063] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 06/11/2015] [Accepted: 06/15/2015] [Indexed: 01/30/2023] Open
Abstract
The structure and composition of a biological membrane can severely influence the activity of membrane-embedded proteins. Here, we show that the E. coli aquaglyceroporin GlpF has only little activity in lipid bilayers formed from native E. coli lipids. Thus, at first glance, GlpF appears to not be optimized for its natural membrane environment. In fact, we found that GlpF activity was severely affected by negatively charged lipids regardless of the exact chemical nature of the lipid headgroup, whereas GlpF was not sensitive to changes in the lateral membrane pressure. These observations illustrate a potential mechanism by which the activity of an α-helical membrane protein is modulated by the negative charge density around the protein.
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Affiliation(s)
- Noreen Klein
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Nadja Hellmann
- Institut für Molekulare Biophysik, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Dirk Schneider
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany.
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44
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Nobre L, Wise D, Ron D, Volmer R. Modulation of Innate Immune Signalling by Lipid-Mediated MAVS Transmembrane Domain Oligomerization. PLoS One 2015; 10:e0136883. [PMID: 26317833 PMCID: PMC4552940 DOI: 10.1371/journal.pone.0136883] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/10/2015] [Indexed: 11/26/2022] Open
Abstract
RIG-I-like receptors detect viral RNA in infected cells and promote oligomerization of the outer mitochondrial membrane protein MAVS to induce innate immunity to viral infection through type I interferon production. Mitochondrial reactive oxygen species (mROS) have been shown to enhance anti-viral MAVS signalling, but the mechanisms have remained obscure. Using a biochemical oligomerization-reporter fused to the transmembrane domain of MAVS, we found that mROS inducers promoted lipid-dependent MAVS transmembrane domain oligomerization in the plane of the outer mitochondrial membrane. These events were mirrored by Sendai virus infection, which similarly induced lipid peroxidation and promoted lipid-dependent MAVS transmembrane domain oligomerization. Our observations point to a role for mROS-induced changes in lipid bilayer properties in modulating antiviral innate signalling by favouring the oligomerization of MAVS transmembrane domain in the outer-mitochondrial membrane.
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Affiliation(s)
- Luis Nobre
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust MRC Institute of Metabolic Science, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Daniel Wise
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust MRC Institute of Metabolic Science, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - David Ron
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust MRC Institute of Metabolic Science, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Romain Volmer
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust MRC Institute of Metabolic Science, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Université de Toulouse, INP, ENVT, UMR1225, IHAP, F-31076 Toulouse, France
- INRA, UMR1225, IHAP, F-31076 Toulouse, France
- * E-mail:
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45
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Kuznetsov AS, Polyansky AA, Fleck M, Volynsky PE, Efremov RG. Adaptable Lipid Matrix Promotes Protein–Protein Association in Membranes. J Chem Theory Comput 2015; 11:4415-26. [DOI: 10.1021/acs.jctc.5b00206] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Andrey S. Kuznetsov
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
| | - Anton A. Polyansky
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
- Department
of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna AT-1030, Austria
| | - Markus Fleck
- Department
of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna AT-1030, Austria
| | - Pavel E. Volynsky
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
| | - Roman G. Efremov
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
- Higher School of Economics, Myasnitskaya Str., 20, Moscow 101000, Russia
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46
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Dynamics of the Glycophorin A Dimer in Membranes of Native-Like Composition Uncovered by Coarse-Grained Molecular Dynamics Simulations. PLoS One 2015. [PMID: 26222139 PMCID: PMC4519189 DOI: 10.1371/journal.pone.0133999] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Membranes are central for cells as borders to the environment or intracellular organelle definition. They are composed of and harbor different molecules like various lipid species and sterols, and they are generally crowded with proteins. The membrane system is very dynamic and components show lateral, rotational and translational diffusion. The consequence of the latter is that phase separation can occur in membranes in vivo and in vitro. It was documented that molecular dynamics simulations of an idealized plasma membrane model result in formation of membrane areas where either saturated lipids and cholesterol (liquid-ordered character, Lo) or unsaturated lipids (liquid-disordered character, Ld) were enriched. Furthermore, current discussions favor the idea that proteins are sorted into the liquid-disordered phase of model membranes, but experimental support for the behavior of isolated proteins in native membranes is sparse. To gain insight into the protein behavior we built a model of the red blood cell membrane with integrated glycophorin A dimer. The sorting and the dynamics of the dimer were subsequently explored by coarse-grained molecular dynamics simulations. In addition, we inspected the impact of lipid head groups and the presence of cholesterol within the membrane on the dynamics of the dimer within the membrane. We observed that cholesterol is important for the formation of membrane areas with Lo and Ld character. Moreover, it is an important factor for the reproduction of the dynamic behavior of the protein found in its native environment. The protein dimer was exclusively sorted into the domain of Ld character in the model red blood cell plasma membrane. Therefore, we present structural information on the glycophorin A dimer distribution in the plasma membrane in the absence of other factors like e.g. lipid anchors in a coarse grain resolution.
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47
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Misiewicz J, Afonin S, Grage SL, van den Berg J, Strandberg E, Wadhwani P, Ulrich AS. Action of the multifunctional peptide BP100 on native biomembranes examined by solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2015; 61:287-98. [PMID: 25616492 DOI: 10.1007/s10858-015-9897-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/10/2015] [Indexed: 05/22/2023]
Abstract
Membrane composition is a key factor that regulates the destructive activity of antimicrobial peptides and the non-leaky permeation of cell penetrating peptides in vivo. Hence, the choice of model membrane is a crucial aspect in NMR studies and should reflect the biological situation as closely as possible. Here, we explore the structure and dynamics of the short multifunctional peptide BP100 using a multinuclear solid-state NMR approach. The membrane alignment and mobility of this 11 amino acid peptide was studied in various synthetic lipid bilayers with different net charge, fluidity, and thickness, as well as in native biomembranes harvested from prokaryotic and eukaryotic cells. (19)F-NMR provided the high sensitivity and lack of natural abundance background that are necessary to observe a labelled peptide even in protoplast membranes from Micrococcus luteus and in erythrocyte ghosts. Six selectively (19)F-labeled BP100 analogues gave remarkably similar spectra in all of the macroscopically oriented membrane systems, which were studied under quasi-native conditions of ambient temperature and full hydration. This similarity suggests that BP100 has the same surface-bound helical structure and high mobility in the different biomembranes and model membranes alike, independent of charge, thickness or cholesterol content of the system. (31)P-NMR spectra of the phospholipid components did not indicate any bilayer perturbation, so the formation of toroidal wormholes or micellarization can be excluded as a mechanism of its antimicrobial or cell penetrating action. However, (2)H-NMR analysis of the acyl chain order parameter profiles showed that BP100 leads to considerable membrane thinning and thereby local destabilization.
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Affiliation(s)
- Julia Misiewicz
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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48
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Wassenaar TA, Pluhackova K, Moussatova A, Sengupta D, Marrink SJ, Tieleman DP, Böckmann RA. High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach. J Chem Theory Comput 2015; 11:2278-91. [PMID: 26574426 DOI: 10.1021/ct5010092] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interactions between membrane proteins are of great biological significance and are consequently an important target for pharmacological intervention. Unfortunately, it is still difficult to obtain detailed views on such interactions, both experimentally, where the environment hampers atomic resolution investigation, and computationally, where the time and length scales are problematic. Coarse grain simulations have alleviated the later issue, but the slow movement through the bilayer, coupled to the long life times of nonoptimal dimers, still stands in the way of characterizing binding distributions. In this work, we present DAFT, a Docking Assay For Transmembrane components, developed to identify preferred binding orientations. The method builds on a program developed recently for generating custom membranes, called insane (INSert membrANE). The key feature of DAFT is the setup of starting structures, for which optimal periodic boundary conditions are devised. The purpose of DAFT is to perform a large number of simulations with different components, starting from unbiased noninteracting initial states, such that the simulations evolve collectively, in a manner reflecting the underlying energy landscape of interaction. The implementation and characteristic features of DAFT are explained, and the efficacy and relaxation properties of the method are explored for oligomerization of glycophorin A dimers, polyleucine dimers and trimers, MS1 trimers, and rhodopsin dimers. The results suggest that, for simple helices, such as GpA and polyleucine, in POPC/DOPC membranes series of 500 simulations of 500 ns each allow characterization of the helix dimer orientations and allow comparing associating and nonassociating components. However, the results also demonstrate that short simulations may suffer significantly from nonconvergence of the ensemble and that using too few simulations may obscure or distort features of the interaction distribution. For trimers, simulation times exceeding several microseconds appear needed, due to the increased complexity. Similarly, characterization of larger proteins, such as rhodopsin, takes longer time scales due to the slower diffusion and the increased complexity of binding interfaces. DAFT and its auxiliary programs have been made available from http://cgmartini.nl/ , together with a working example.
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Affiliation(s)
- Tsjerk A Wassenaar
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrasse 5, 91058 Erlangen, Germany
| | - Kristyna Pluhackova
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrasse 5, 91058 Erlangen, Germany
| | - Anastassiia Moussatova
- Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary , 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Durba Sengupta
- National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D Peter Tieleman
- Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary , 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrasse 5, 91058 Erlangen, Germany
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49
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Stangl M, Schneider D. Functional competition within a membrane: Lipid recognition vs. transmembrane helix oligomerization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1886-96. [PMID: 25791349 DOI: 10.1016/j.bbamem.2015.03.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/09/2015] [Accepted: 03/09/2015] [Indexed: 12/27/2022]
Abstract
Binding of specific lipids to large, polytopic membrane proteins is well described, and it is clear that such lipids are crucial for protein stability and activity. In contrast, binding of defined lipid species to individual transmembrane helices and regulation of transmembrane helix monomer-oligomer equilibria by binding of distinct lipids is a concept, which has emerged only lately. Lipids bind to single-span membrane proteins, both in the juxta-membrane region as well as in the hydrophobic membrane core. While some interactions counteract transmembrane helix oligomerization, in other cases lipid binding appears to enhance oligomerization. As reversible oligomerization is involved in activation of many membrane proteins, binding of defined lipids to single-span transmembrane proteins might be a mechanism to regulate and/or fine-tune the protein activity. But how could lipid binding trigger the activity of a protein? How can binding of a single lipid molecule to a transmembrane helix affect the structure of a transmembrane helix oligomer, and consequently its signaling state? These questions are discussed in the present article based on recent results obtained with simple, single-span transmembrane proteins. This article is part of a Special Issue entitled: Lipid-protein interactions.
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Affiliation(s)
- Michael Stangl
- Department of Pharmacy and Biochemistry, Johannes-Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - Dirk Schneider
- Department of Pharmacy and Biochemistry, Johannes-Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany.
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50
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Hong H. Role of Lipids in Folding, Misfolding and Function of Integral Membrane Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 855:1-31. [DOI: 10.1007/978-3-319-17344-3_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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