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Akhmadeev B, Retyunskaya O, Islamova L, Fazleeva G, Kalinin A, Katsyuba S, Elistratova J, Sinyashin O, Mustafina A. Biomimetic nanoplatforms constructed from dialkylaminostyryl hetarene dyes and phospholipids exhibiting selective fluorescent response to specific proteins. Colloids Surf B Biointerfaces 2024; 241:114046. [PMID: 38908044 DOI: 10.1016/j.colsurfb.2024.114046] [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: 03/26/2024] [Revised: 05/30/2024] [Accepted: 06/15/2024] [Indexed: 06/24/2024]
Abstract
The present work explores the specificity of supramolecular assemblies comprising dialkylaminostyrylhetarene dye molecules incorporated into phosphatidylcholine (PC) or phosphatidylserine (PS) aggregates. In PS-based assemblies, the dyes demonstrate a concentration-dependent fluorescent response, distinguishing anionic proteins such as bovine serum albumin (BSA) and pepsin from lysozyme (LYZ) in aqueous solutions. Conversely, no significant response is observed when the dyes are incorporated into the well-organized bilayers of neutral PC. The fluorescent response arises from the binding of dyes to proteins, leading to the detachment of dye molecules from the assemblies, rather than from the binding of proteins to the assemblies, although the latter process is facilitated by electrostatic attraction. Thus, both the poor ordering of PS molecules and the interfacial arrangement of the dyes are prerequisites for the fluorescent response of dye-PS aggregates. The structure of the dyes significantly impacts the spectral features of dye-PS and dye-protein assemblies. An optimal dye structure has been identified for the recognition of BSA, with a limit of detection (LOD) of 10.8 nM.
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Affiliation(s)
- Bulat Akhmadeev
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov St. Kazan 420088, Russia; Kazan (Volga region) Federal University, Kremlyovskaya Str., 18, Kazan 420008, Russia.
| | - Olga Retyunskaya
- Kazan (Volga region) Federal University, Kremlyovskaya Str., 18, Kazan 420008, Russia
| | - Liliya Islamova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov St. Kazan 420088, Russia
| | - Guzyal Fazleeva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov St. Kazan 420088, Russia
| | - Alexey Kalinin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov St. Kazan 420088, Russia
| | - Sergey Katsyuba
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov St. Kazan 420088, Russia
| | - Julia Elistratova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov St. Kazan 420088, Russia
| | - Oleg Sinyashin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov St. Kazan 420088, Russia
| | - Asiya Mustafina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov St. Kazan 420088, Russia
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Malik S, Karmakar S, Debnath A. Quantifying dynamical heterogeneity length scales of interface water across model membrane phase transitions. J Chem Phys 2023; 158:091103. [PMID: 36889951 DOI: 10.1063/5.0137727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
All-atom molecular dynamics simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine lipid membranes reveal a drastic growth in the heterogeneity length scales of interface water (IW) across fluid to ripple to gel phase transitions. It acts as an alternate probe to capture the ripple size of the membrane and follows an activated dynamical scaling with the relaxation time scale solely within the gel phase. The results quantify the mostly unknown correlations between the spatiotemporal scales of the IW and membranes at various phases under physiological and supercooled conditions.
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Affiliation(s)
- Sheeba Malik
- Department of Chemistry, IIT Jodhpur, Jodhpur, Rajasthan, India
| | - Smarajit Karmakar
- Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, India
| | - Ananya Debnath
- Department of Chemistry, IIT Jodhpur, Jodhpur, Rajasthan, India
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3
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Page EF, Blake MJ, Foley GA, Calhoun TR. Monitoring membranes: The exploration of biological bilayers with second harmonic generation. CHEMICAL PHYSICS REVIEWS 2022; 3:041307. [PMID: 36536669 PMCID: PMC9756348 DOI: 10.1063/5.0120888] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/03/2022] [Indexed: 12/23/2022]
Abstract
Nature's seemingly controlled chaos in heterogeneous two-dimensional cell membranes stands in stark contrast to the precise, often homogeneous, environment in an experimentalist's flask or carefully designed material system. Yet cell membranes can play a direct role, or serve as inspiration, in all fields of biology, chemistry, physics, and engineering. Our understanding of these ubiquitous structures continues to evolve despite over a century of study largely driven by the application of new technologies. Here, we review the insight afforded by second harmonic generation (SHG), a nonlinear optical technique. From potential measurements to adsorption and diffusion on both model and living systems, SHG complements existing techniques while presenting a large exploratory space for new discoveries.
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Affiliation(s)
- Eleanor F. Page
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Marea J. Blake
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Grant A. Foley
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Tessa R. Calhoun
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
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Interaction of human phospholipid scramblase 1 with cholesterol via CRAC motif is essential for functional regulation and subcellular localization. Int J Biol Macromol 2022; 209:850-857. [PMID: 35439477 DOI: 10.1016/j.ijbiomac.2022.04.087] [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: 12/27/2021] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 11/21/2022]
Abstract
Human phospholipid scramblase 1 (hPLSCR1) possesses a putative cholesterol binding CRAC (cholesterol interaction/recognition amino acid consensus) motif at the C-terminal. The CRAC motif of hPLSCR1 interacts with cholesterol with an energy of interaction -64.39 KJ mol-1. Since palmitoylated hPLSCR1 localizes to the cholesterol-rich lipid rafts, the interaction between hPLSCR1 and raft cholesterol is highly likely. The present study investigated the hPLSCR1-cholesterol interaction in plasma membrane via putative CRAC motif. hPLSCR1 remains at cholesterol-rich lipid rafts as long as they interact. This interaction is inhibited by mutations in the CRAC motif or cholesterol depletion. Thus, CRAC mutants I300D hPLSCR1 and ΔCRAC hPLSCR1 diffused to the cytoplasm and nucleus. Cholesterol depletion by methyl-β-cyclodextrin (MβCD) dose-dependently reduced cell viability in A549 cells. However, cholesterol depletion released 1.74 ± 0.12 times Ca2+ to the cytosol in A549 cells. Similarly, cholesterol depletion increased intracellular Ca2+ release by 1.81 ± 0.13 and 4.11 ± 0.19 times in RAJI cells expressing hPLSCR1 and ΔCRAC hPLSCR1, respectively. Moreover, the expression of hPLSCR1 and ΔCRAC hPLSCR1 increased apoptosis in RAJI cells by 21 ± 1.5% and 53.50 ± 4.40%, respectively. It was further increased to 43 ± 2.5% and 71.4 ± 1.4% upon cholesterol depletion. The current work links hPLSCR1 expression with cholesterol depletion, intracellular Ca2+ release, and induction of apoptosis.
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In Vitro Application of Langmuir Monolayer Model: The interfacial Behavior of Myelin Basic Protein with a Plasma Membrane Model. J Membr Biol 2022; 255:71-78. [PMID: 35084527 DOI: 10.1007/s00232-022-00214-4] [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: 11/24/2021] [Accepted: 12/31/2021] [Indexed: 10/19/2022]
Abstract
The stability and compactness of myelin structure and brain homeostasis depend on MBP and glial cell plasma membrane interactions. In order to get more detailed mechanisms of this interaction, the MBP of different concentrations interacting with plasma membrane (POPC/POPE/POPS/Cholesterol (Chol)) model to form bionic membrane was studied by atomic force microscopy (AFM) and Langmuir monolayer technology. The surface pressure(π)-area(A) curve is analyzed by the elastic modulus ([Formula: see text]) and two-dimensional virial equation of state (2D-VES), and the second virial coefficient of the interaction between MBP and plasma membrane molecules was calculated. (i) According to two-dimensional virial equation, it could be analyzed that with the increase of MBP concentration in the subphase, the value of the second virial coefficient increases also, which indicates that MBP is absorbed into lipid membrane of the plasma membrane model at low surface pressure and that the interaction between the molecules is spatial repulsive force, and (ii) in the monolayers with MBP, resulting in an increasing mean molecular area and monolayer stability due to hydrophobic and electrostatic interactions between the positively charged MBP with hydrophobic residues and negatively charged POPS and neutral lipid (POPC, POPE). AFM surface topographic results correspond to the results of the curve analysis, indicating that MBP of different concentrations has significant influences on alignment and conformation of plasma membrane, which is of great medical value and biological significance to the application of interaction between MBP and myelin lipid membrane in treatment of central nervous diseases. Adsorption model of interaction between MBP and plasma membrane model.
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Orekhov PS, Bozdaganyan ME, Voskoboynikova N, Mulkidjanian AY, Karlova MG, Yudenko A, Remeeva A, Ryzhykau YL, Gushchin I, Gordeliy VI, Sokolova OS, Steinhoff HJ, Kirpichnikov MP, Shaitan KV. Mechanisms of Formation, Structure, and Dynamics of Lipoprotein Discs Stabilized by Amphiphilic Copolymers: A Comprehensive Review. NANOMATERIALS 2022; 12:nano12030361. [PMID: 35159706 PMCID: PMC8838559 DOI: 10.3390/nano12030361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 12/16/2022]
Abstract
Amphiphilic copolymers consisting of alternating hydrophilic and hydrophobic units account for a major recent methodical breakthrough in the investigations of membrane proteins. Styrene–maleic acid (SMA), diisobutylene–maleic acid (DIBMA), and related copolymers have been shown to extract membrane proteins directly from lipid membranes without the need for classical detergents. Within the particular experimental setup, they form disc-shaped nanoparticles with a narrow size distribution, which serve as a suitable platform for diverse kinds of spectroscopy and other biophysical techniques that require relatively small, homogeneous, water-soluble particles of separate membrane proteins in their native lipid environment. In recent years, copolymer-encased nanolipoparticles have been proven as suitable protein carriers for various structural biology applications, including cryo-electron microscopy (cryo-EM), small-angle scattering, and conventional and single-molecule X-ray diffraction experiments. Here, we review the current understanding of how such nanolipoparticles are formed and organized at the molecular level with an emphasis on their chemical diversity and factors affecting their size and solubilization efficiency.
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Affiliation(s)
- Philipp S. Orekhov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- Institute of Personalized Medicine, Sechenov University, 119146 Moscow, Russia
- Correspondence: (P.S.O.); (K.V.S.)
| | - Marine E. Bozdaganyan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Natalia Voskoboynikova
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Armen Y. Mulkidjanian
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
- Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Maria G. Karlova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Yury L. Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Valentin I. Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Olga S. Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
| | - Heinz-Jürgen Steinhoff
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Mikhail P. Kirpichnikov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Konstantin V. Shaitan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Correspondence: (P.S.O.); (K.V.S.)
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Rathod J, Yen HC, Liang B, Tseng YY, Chen CS, Wu WS. YPIBP: A repository for phosphoinositide-binding proteins in yeast. Comput Struct Biotechnol J 2021; 19:3692-3707. [PMID: 34285772 PMCID: PMC8261538 DOI: 10.1016/j.csbj.2021.06.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/08/2021] [Accepted: 06/22/2021] [Indexed: 11/25/2022] Open
Abstract
Phosphoinositides (PIs) are a family of eight lipids consisting of phosphatidylinositol (PtdIns) and its seven phosphorylated forms. PIs have important regulatory functions in the cell including lipid signaling, protein transport, and membrane trafficking. Yeast has been recognized as a eukaryotic model system to study lipid-protein interactions. Hundreds of yeast PI-binding proteins have been identified, but this research knowledge remains scattered. Besides, the complete PI-binding spectrum and potential PI-binding domains have not been interlinked. No comprehensive databases are available to support the lipid-protein interaction research on phosphoinositides. Here we constructed the first knowledgebase of Yeast Phosphoinositide-Binding Proteins (YPIBP), a repository consisting of 679 PI-binding proteins collected from high-throughput proteome-array and lipid-array studies, QuickGO, and a rigorous literature mining. The YPIBP also contains protein domain information in categories of lipid-binding domains, lipid-related domains and other domains. The YPIBP provides search and browse modes along with two enrichment analyses (PI-binding enrichment analysis and domain enrichment analysis). An interactive visualization is given to summarize the PI-domain-protein interactome. Finally, three case studies were given to demonstrate the utility of YPIBP. The YPIBP knowledgebase consolidates the present knowledge and provides new insights of the PI-binding proteins by bringing comprehensive and in-depth interaction network of the PI-binding proteins. YPIBP is available at http://cosbi7.ee.ncku.edu.tw/YPIBP/.
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Key Words
- ANTH, AP180 N-terminal Homology
- BAR, Bin-Amphiphysin-Rvs
- CAFA, Critical Assessment of Functional Annotation
- CRAL-TRIO, cellular retinaldehyde-binding protein (CRALBP) and TRIO guanine exchange factor
- Cvt, Cytoplasm-to-vacuole targeting
- ENTH, Epsin N-terminal Homology
- FDR, False Discovery Rate
- FYVE, Fab 1 (yeast orthologue of PIKfyve), YOTB, Vac 1 (vesicle transport protein), and EEA1
- GO, Gene Ontology
- ITC, Isothermal Titration Calorimetry
- LBD, Lipid-Binding Domain
- LMPD, LIPID MAPS Proteome Database
- LMSD, LIPID MAPS Structure Database
- LRD, Lipid-Related Domain
- Lipid-binding domain
- OMIM, Online Mendelian Inheritance in Man
- OSBP, Oxysterol-Binding Protein
- PH, Pleckstrin Homology
- PI(3,4)P2, phosphatidylinositol-3,4-bisphosphate
- PI(3,4,5)P3, phosphatidylinositol-3,4,5-trisphosphate
- PI(3,5)P2, phosphatidylinositol-3,5-bisphosphate
- PI(4,5)P2, phosphatidylinositol-4,5-bisphosphate
- PI-binding protein
- PI3P, phosphatidylinositol-3-phosphate
- PI4P, phosphatidylinositol-4-phosphate
- PI5P, phosphatidylinositol-5-phosphate
- PIs, Phosphoinositides
- PMID, PubMed ID
- PX, Phox Homology
- Phosphatidylinositol (PtdIns)
- Phosphoinositides (PIs)
- PtdIns, Phosphatidylinositol
- QCM, Quartz Crystal Microbalance
- S. cerevisiae
- SNX, Sorting Nexin
- SPR, Surface Plasmon Resonance
- YPIBP, Yeast Phosphoinositide-Binding Proteins
- Yeast
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Affiliation(s)
- Jagat Rathod
- Department of Earth Sciences, College of Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Han-Chen Yen
- Department of Electrical Engineering, College of Electrical Engineering and Computer Science, National Cheng Kung University, Tainan 701, Taiwan
| | - Biqing Liang
- Department of Earth Sciences, College of Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Yan-Yuan Tseng
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, MI 48201, USA
| | - Chien-Sheng Chen
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Wei-Sheng Wu
- Department of Electrical Engineering, College of Electrical Engineering and Computer Science, National Cheng Kung University, Tainan 701, Taiwan
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Li Y, Liu D, Wang Y, Su W, Liu G, Dong W. The Importance of Glycans of Viral and Host Proteins in Enveloped Virus Infection. Front Immunol 2021; 12:638573. [PMID: 33995356 PMCID: PMC8116741 DOI: 10.3389/fimmu.2021.638573] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
Animal viruses are parasites of animal cells that have characteristics such as heredity and replication. Viruses can be divided into non-enveloped and enveloped viruses if a lipid bilayer membrane surrounds them or not. All the membrane proteins of enveloped viruses that function in attachment to target cells or membrane fusion are modified by glycosylation. Glycosylation is one of the most common post-translational modifications of proteins and plays an important role in many biological behaviors, such as protein folding and stabilization, virus attachment to target cell receptors and inhibition of antibody neutralization. Glycans of the host receptors can also regulate the attachment of the viruses and then influence the virus entry. With the development of glycosylation research technology, the research and development of novel virus vaccines and antiviral drugs based on glycan have received increasing attention. Here, we review the effects of host glycans and viral proteins on biological behaviors of viruses, and the opportunities for prevention and treatment of viral infectious diseases.
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Affiliation(s)
- Yuqing Li
- Department of Biochemistry and Molecular Biology, Institute of Glycobiology, Dalian Medical University, Dalian, China
| | - Dongqi Liu
- The Queen's University of Belfast Joint College, China Medical University, Shenyang, China
| | - Yating Wang
- Department of Biochemistry and Molecular Biology, Institute of Glycobiology, Dalian Medical University, Dalian, China
| | - Wenquan Su
- Dalian Medical University, Dalian, China
| | - Gang Liu
- Department of Biochemistry and Molecular Biology, Institute of Glycobiology, Dalian Medical University, Dalian, China
| | - Weijie Dong
- Department of Biochemistry and Molecular Biology, Institute of Glycobiology, Dalian Medical University, Dalian, China
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Rakib F, Al-Saad K, Ahmed T, Ullah E, Barreto GE, Md Ashraf G, Ali MHM. Biomolecular alterations in acute traumatic brain injury (TBI) using Fourier transform infrared (FTIR) imaging spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 248:119189. [PMID: 33277210 DOI: 10.1016/j.saa.2020.119189] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 10/27/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
Acute injury is one of the substantial stage post-traumatic brain injury (TBI) occurring at the moment of impact. Decreased metabolism, unregulated cerebral blood flow and direct tissue damage are triggered by acute injury. Understating the biochemical alterations associated with acute TBI is critical for brain plasticity and recovery. The objective of this study was to investigate the biochemical and molecular changes in hippocampus, corpus callosum and thalamus brain regions post-acute TBI in rats. Fourier Transform Infrared (FTIR) imaging spectroscopy were used to collect chemical images from control and 3 hrs post-TBI (Marmarou model was used for the TBI induction) rat brains and adjacent sections were treated by hematoxylin and eosin (H&E) staining to correlate with the disruption in tissue morphology and injured brain biochemistry. Our results revealed that the total lipid and total protein content decreased significantly in the hippocampus, corpus callosum and thalamus after brain injury. Reduction in lipid acyl chains (-CH2) associated with an increase in methyl (-CH3) and unsaturated lipids olefin = CH concentrations is observed. Furthermore, there is a decrease in the lipid order (disorder), which leads to an increase in acyl chain fluidity in injured rats. The results suggest acute TBI damages brain tissues mechanically rather than chemical alterations. This will help in assessing successful therapeutic strategy in order to mitigate tissue damage in acute TBI period.
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Affiliation(s)
- Fazle Rakib
- Department of Chemistry and Earth Sciences, Qatar University, Doha, Qatar
| | - Khalid Al-Saad
- Department of Chemistry and Earth Sciences, Qatar University, Doha, Qatar
| | - Tariq Ahmed
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Ehsan Ullah
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - George E Barreto
- Department of Biological Sciences, University of Limerick, Limerick, Ireland; Health Research Institute, University of Limerick, Limerick, Limerick, Ireland
| | - Ghulam Md Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Mohamed H M Ali
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar.
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10
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Bagheri Y, Ali AA, You M. Current Methods for Detecting Cell Membrane Transient Interactions. Front Chem 2020; 8:603259. [PMID: 33365301 PMCID: PMC7750205 DOI: 10.3389/fchem.2020.603259] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 10/16/2020] [Indexed: 12/28/2022] Open
Abstract
Short-lived cell membrane complexes play a key role in regulating cell signaling and communication. Many of these complexes are formed based on low-affinity and transient interactions among various lipids and proteins. New techniques have emerged to study these previously overlooked membrane transient interactions. Exciting functions of these transient interactions have been discovered in cellular events such as immune signaling, host-pathogen interactions, and diseases such as cancer. In this review, we have summarized current experimental methods that allow us to detect and analyze short-lived cell membrane protein-protein, lipid-protein, and lipid-lipid interactions. These methods can provide useful information about the strengths, kinetics, and/or spatial patterns of membrane transient interactions. However, each method also has its own limitations. We hope this review can be used as a guideline to help the audience to choose proper approaches for studying membrane transient interactions in different membrane trafficking and cell signaling events.
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Affiliation(s)
| | | | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States
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11
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Krajewska M, Dopierała K, Wydro P, Broniatowski M, Prochaska K. Interfacial complex of α-lactalbumin with oleic acid: effect of protein concentration and PM-IRRAS study. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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12
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Chanphai P, Bourassa P, Tajmir-Riahi HA. An Overview of the Loading Efficacy of Cationic Lipids with Milk Proteins: A Potential Application for Lipid Delivery. Curr Med Chem 2020; 27:4109-4117. [DOI: 10.2174/0929867325666180608122439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 03/29/2018] [Accepted: 03/29/2018] [Indexed: 11/22/2022]
Abstract
In this review, the loading efficacies of helper and Cationic Lipids Cholesterol
(CHOL), 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP), Dioctadecyl Dimethyl-
Ammonium Bromide (DDAB) and Dioleoyl Phosphatidylethanolamine (DOPE) with milk β-
lactoglobulin, α-casein and β-casein were compared in aqueous solution at physiological conditions.
Structural analysis showed that lipids bind milk proteins via hydrophilic, hydrophobic
and H-bonding contacts with DOTAP and DDAB forming more stable protein conjugates.
Loading efficacy was 30-50% and enhanced with cationic lipids. Lipid conjugation altered
protein conformation, causing a partial protein structural destabilization. Milk proteins are
capable of transporting lipids in vitro.
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Affiliation(s)
- Penprapa Chanphai
- Department de Chemistry-Biochemistry, University of Quebec a Trois-Rivieres, C.P. 500, Trois-Rivieres (Quebec) G9A 5H7, Canada
| | - Philippe Bourassa
- Department de Chemistry-Biochemistry, University of Quebec a Trois-Rivieres, C.P. 500, Trois-Rivieres (Quebec) G9A 5H7, Canada
| | - Heidar Ali Tajmir-Riahi
- Department de Chemistry-Biochemistry, University of Quebec a Trois-Rivieres, C.P. 500, Trois-Rivieres (Quebec) G9A 5H7, Canada
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13
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Barros M, Houlihan WJ, Paresi CJ, Brendel M, Rynearson KD, Lee CW, Prikhodko O, Cregger C, Chang G, Wagner SL, Gilchrist ML, Li YM. γ-Secretase Partitioning into Lipid Bilayers Remodels Membrane Microdomains after Direct Insertion. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:6569-6579. [PMID: 32432881 PMCID: PMC7887708 DOI: 10.1021/acs.langmuir.0c01178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
γ-Secretase is a multisubunit complex that catalyzes intramembranous cleavage of transmembrane proteins. The lipid environment forms membrane microdomains that serve as spatio-temporal platforms for proteins to function properly. Despite substantial advances in the regulation of γ-secretase, the effect of the local membrane lipid microenvironment on the regulation of γ-secretase is poorly understood. Here, we characterized and quantified the partitioning of γ-secretase and its substrates, the amyloid precursor protein (APP) and Notch, into lipid bilayers using solid-supported model membranes. Notch substrate is preferentially localized in the liquid-disordered (Ld) lipid domains, whereas APP and γ-secretase partition as single or higher complex in both phases but highly favor the ordered phase, especially after recruiting lipids from the ordered phase, indicating that the activity and specificity of γ-secretase against these two substrates are modulated by membrane lateral organization. Moreover, time-elapse measurements reveal that γ-secretase can recruit specific membrane components from the cholesterol-rich Lo phase and thus creates a favorable lipid environment for substrate recognition and therefore activity. This work offers insight into how γ-secretase and lipid modulate each other and control its activity and specificity.
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Affiliation(s)
- Marilia Barros
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
| | - William J Houlihan
- Department of Chemical Engineering and the Department of Biomedical Engineering, The City College of the City University of New York, New York, New York 10031, United States
| | - Chelsea J Paresi
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
- Pharmacology Graduate Program, Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10021, United States
| | - Matthew Brendel
- Molecular Cytology Core, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
| | - Kevin D Rynearson
- Department of Neurosciences, University of California, San Diego, California 92093, United States
| | | | - Olga Prikhodko
- Department of Neurosciences, University of California, San Diego, California 92093, United States
| | - Cristina Cregger
- Department of Neurosciences, University of California, San Diego, California 92093, United States
| | | | - Steven L Wagner
- Department of Neurosciences, University of California, San Diego, California 92093, United States
- Research Biologist, VA San Diego Healthcare System, La Jolla, California 92161, United States
| | - M Lane Gilchrist
- Department of Chemical Engineering and the Department of Biomedical Engineering, The City College of the City University of New York, New York, New York 10031, United States
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
- Pharmacology Graduate Program, Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10021, United States
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14
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Llorente García I, Marsh M. A biophysical perspective on receptor-mediated virus entry with a focus on HIV. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2020; 1862:183158. [PMID: 31863725 PMCID: PMC7156917 DOI: 10.1016/j.bbamem.2019.183158] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 12/14/2022]
Abstract
As part of their entry and infection strategy, viruses interact with specific receptor molecules expressed on the surface of target cells. The efficiency and kinetics of the virus-receptor interactions required for a virus to productively infect a cell is determined by the biophysical properties of the receptors, which are in turn influenced by the receptors' plasma membrane (PM) environments. Currently, little is known about the biophysical properties of these receptor molecules or their engagement during virus binding and entry. Here we review virus-receptor interactions focusing on the human immunodeficiency virus type 1 (HIV), the etiological agent of acquired immunodeficiency syndrome (AIDS), as a model system. HIV is one of the best characterised enveloped viruses, with the identity, roles and structure of the key molecules required for infection well established. We review current knowledge of receptor-mediated HIV entry, addressing the properties of the HIV cell-surface receptors, the techniques used to measure these properties, and the macromolecular interactions and events required for virus entry. We discuss some of the key biophysical principles underlying receptor-mediated virus entry and attempt to interpret the available data in the context of biophysical mechanisms. We also highlight crucial outstanding questions and consider how new tools might be applied to advance understanding of the biophysical properties of viral receptors and the dynamic events leading to virus entry.
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Affiliation(s)
| | - Mark Marsh
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
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15
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Urban P, Pritzl SD, Ober MF, Dirscherl CF, Pernpeintner C, Konrad DB, Frank JA, Trauner D, Nickel B, Lohmueller T. A Lipid Photoswitch Controls Fluidity in Supported Bilayer Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:2629-2634. [PMID: 32069411 DOI: 10.1021/acs.langmuir.9b02942] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Supported lipid bilayer (SLB) membranes are key elements to mimic membrane interfaces on a planar surface. Here, we demonstrate that azobenzene photolipids (azo-PC) form fluid, homogeneous SLBs. Diffusion properties of azo-PC within SLBs were probed by fluorescence microscopy and fluorescence recovery after photobleaching. At ambient conditions, we find that the trans-to-cis isomerization causes an increase of the diffusion constant by a factor of two. Simultaneous excitation with two wavelengths and variable intensities furthermore allows to adjust the diffusion constant D continuously. X-ray reflectometry and small-angle scattering measurements reveal that membrane photoisomerization results in a bilayer thickness reduction of ∼0.4 nm (or 10%). While thermally induced back-switching is not observed, we find that the trans bilayer fluidity is increasing with higher temperatures. This change in diffusion constant is accompanied by a red-shift in the absorption spectra. Based on these results, we suggest that the reduced diffusivity of trans-azo-PC is controlled by intermolecular interactions that also give rise to H-aggregate formation in bilayer membranes.
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Affiliation(s)
- Patrick Urban
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians-Universität München, Königinstrasse 10, 80539 Munich, Germany
| | - Stefanie D Pritzl
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians-Universität München, Königinstrasse 10, 80539 Munich, Germany
| | - Martina F Ober
- Faculty of Physics and CeNS, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Christina F Dirscherl
- Faculty of Physics and CeNS, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Carla Pernpeintner
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians-Universität München, Königinstrasse 10, 80539 Munich, Germany
| | - David B Konrad
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 München, Germany
| | - James A Frank
- Vollum Institute, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Dirk Trauner
- Department of Chemistry, New York University, Silver Center, 100 Washington Square East, Room 712, New York, New York 10003, United States
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 München, Germany
| | - Bert Nickel
- Faculty of Physics and CeNS, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Theobald Lohmueller
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians-Universität München, Königinstrasse 10, 80539 Munich, Germany
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16
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Pérez-Isidoro R, Ruiz-Suárez JC. Thermal behavior of a lipid-protein membrane model and the effects produced by anesthetics and neurotransmitters. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183099. [PMID: 31697903 DOI: 10.1016/j.bbamem.2019.183099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/16/2019] [Accepted: 10/02/2019] [Indexed: 11/25/2022]
Abstract
Despite decades of intense research to understand the phenomenon of anesthesia and its membrane-related changes in neural transmission, where lipids and proteins have been proposed as primary targets of anesthetics, the involved action mechanisms remain unclear. Based on the overall agreement that anesthetics and neurotransmitters induce particular modifications in the plasma membrane of neurons, triggering specific responses and changes in their energetic states, we present here a thermal study to investigate membrane effects in a lipid-protein model made of 1,2-dimyristoyl-sn-glycero-3-phosphocholine and albumin from chicken egg white under the influence of neurotransmitters and anesthetics. First, we observe how ovalbumin, ovotransferrin, and lysozyme (main albumin constituents from chicken egg white) interact with the lipid membrane enhancing their lipophilic character while exposing their hydrophobic domains. This produces a lipid separation and a more ordered hybrid lipid-protein assembly. Second, we measured the thermotropic changes of this assembly induced by acetylcholine, γ-aminobutiric acid, tetracaine, and pentobarbital. Although the protein in our study is not a receptor, our results are striking, for they give evidence of the great importance of non-specific interactions in the anesthesia mechanism.
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Affiliation(s)
- Rosendo Pérez-Isidoro
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México. Cd. Universitaria, Ciudad de México 04510, Mexico
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17
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Li X, Smith AW. Quantifying Lipid Mobility and Peptide Binding for Gram-Negative and Gram-Positive Model Supported Lipid Bilayers. J Phys Chem B 2019; 123:10433-10440. [DOI: 10.1021/acs.jpcb.9b09709] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaosi Li
- Department of Chemistry, The University of Akron, 190 Buchtel Common, Akron, Ohio 44325-3601, United States
| | - Adam W. Smith
- Department of Chemistry, The University of Akron, 190 Buchtel Common, Akron, Ohio 44325-3601, United States
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18
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Lei Z, Runguang S, Changchun H, Huihui Y, Chengxi H. Thermodynamic Analysis of Myelin Basic Protein Adsorbed on Liquid Crystalline Dioleoylphosphatidylcholine Monolayer. SCANNING 2019; 2019:8175413. [PMID: 31819781 PMCID: PMC6885183 DOI: 10.1155/2019/8175413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/15/2019] [Accepted: 08/13/2019] [Indexed: 06/10/2023]
Abstract
To investigate the stability and dynamic characteristics of monolayer adsorbed on unsaturated lipid dioleoylphosphatidylcholine (DOPC) with varying concentrations of myelin basic protein (MBP), the system is studied by applying Langmuir technique and making atomic force microscope (AFM) observation, which is based on the mass conservation equation analysis method referred to in the thermodynamics theory. As indicated by surface pressure-mean molecular area (π - A) and surface pressure-adsorption time (π - T) isotherms, the physical properties of monolayer derived from the interaction of varying concentrations of MBP with liquid crystalline unsaturated lipid DOPC molecules were qualitatively studied. As revealed by surface morphology analysis with AFM, the micro region was expanded as the concentration of MBP in the subphase was on the increase, suggesting that hydrophobic interactions led to the MBP insertion, thus causing accumulation of the MBP on the surface of the monolayer. Experimental results have demonstrated that the partition coefficient of the interaction between MBP and unsaturated phospholipid DOPC and the molecular area of MBP adsorbed on the monolayer film was calculated using the mass conservation equation. In addition, not only does the varying concentration of MBP in the subphase exerts significant effects on the arrangement and conformation of DOPC monolayer, it also has certain guiding significance to exploring the structural changes to biofilm supramolecular aggregates as well as the pathogenesis and treatment of related diseases.
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Affiliation(s)
- Zhang Lei
- Department of Experimental Teaching Center for Optoelectronic Science and Information Engineering, Xi'an Aeronautical University, Xi'an, 710077 Shaanxi, China
| | - Sun Runguang
- Schools of Physics and Information Technology, Shaanxi Normal University, Xi'an, 710119 Shaanxi, China
| | - Hao Changchun
- Schools of Physics and Information Technology, Shaanxi Normal University, Xi'an, 710119 Shaanxi, China
| | - Yang Huihui
- Department of Experimental Teaching Center for Optoelectronic Science and Information Engineering, Xi'an Aeronautical University, Xi'an, 710077 Shaanxi, China
| | - Hu Chengxi
- Department of Experimental Teaching Center for Optoelectronic Science and Information Engineering, Xi'an Aeronautical University, Xi'an, 710077 Shaanxi, China
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19
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Liu Y, Vashisth H. Conformational dynamics and interfacial interactions of peptide-appended pillar[5]arene water channels in biomimetic membranes. Phys Chem Chem Phys 2019; 21:22711-22721. [PMID: 31454001 DOI: 10.1039/c9cp04408f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide appended pillar[5]arene (PAP) is an artificial water channel resembling biological water channel proteins, which has shown a significant potential for designing bioinspired water purification systems. Given that PAP channels need to be incorporated at a high density in membrane matrices, it is critical to examine the role of channel-channel and channel-membrane interactions in governing the structural and functional characteristics of channels. To resolve the atomic-scale details of these interactions, we have carried out atomistic molecular dynamics (MD) simulations of multiple PAP channels inserted in a lipid or a block-copolymer (BCP) membrane matrix. Classical MD simulations on a sub-microsecond timescale showed clustering of channels only in the lipid membrane, but enhanced sampling MD simulations showed thermodynamically-favorable dimerized states of channels in both lipid and BCP membranes. The dimerized configurations of channels, with an extensive buried surface area, were stabilized via interactions between the aromatic groups in the peptide arms of neighboring channels. The conformational metrics characterizing the orientational and structural changes in channels revealed a higher flexibility in the lipid membrane as opposed to the BCP membrane although hydrogen bonds between the channel and the membrane molecules were not a major contributor to the stability of channels in the BCP membrane. We also found that the channels undergo wetting/dewetting transitions in both lipid and BCP membranes with a marginally higher probability of undergoing a dewetting transition in the BCP membrane. Collectively, these results highlight the role of channel dynamics in governing channel-channel and channel-membrane interfacial interactions, and provide atomic-scale insights needed to design stable and functional biomimetic membranes for efficient separations.
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Affiliation(s)
- Yong Liu
- Department of Chemical Engineering, University of New Hampshire, 33 Academic Way, Durham, NH 03824, USA.
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20
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Yu Y, Li M, Yu Y. Tracking Single Molecules in Biomembranes: Is Seeing Always Believing? ACS NANO 2019; 13:10860-10868. [PMID: 31589406 PMCID: PMC7179047 DOI: 10.1021/acsnano.9b07445] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The spatial organization of molecules in cell membranes and their dynamic interactions play a central role in regulating cell functions. Single-particle tracking (SPT), a technique in which single molecules are imaged and tracked in real time, has led to breakthrough discoveries regarding these spatiotemporal complexities of cell membranes. There are, however, emerging concerns about factors that might produce misleading interpretations of SPT results. Here, we briefly review the application of SPT to understanding the nanoscale heterogeneities of plasma membranes, with a focus on the unique challenges, pitfalls, and limitations that confront the use of nanoparticles as imaging probes for tracking the dynamics of single molecules in cell membranes.
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21
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Nastou KC, Tsaousis GN, Iconomidou VA. PerMemDB: A database for eukaryotic peripheral membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183076. [PMID: 31629694 DOI: 10.1016/j.bbamem.2019.183076] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 12/11/2022]
Abstract
The majority of all proteins in cells interact with membranes either permanently or temporarily. Peripheral membrane proteins form transient complexes with membrane proteins and/or lipids, via non-covalent interactions and are of outmost importance, due to numerous cellular functions in which they participate. In an effort to collect data regarding this heterogeneous group of proteins we designed and constructed a database, called PerMemDB. PerMemDB is currently the most complete and comprehensive repository of data for eukaryotic peripheral membrane proteins deposited in UniProt or predicted with the use of MBPpred - a computational method that specializes in the detection of proteins that interact non-covalently with membrane lipids, via membrane binding domains. The first version of the database contains 231,770 peripheral membrane proteins from 1009 organisms. All entries have cross-references to other databases, literature references and annotation regarding their interactions with other proteins. Moreover, additional sequence annotation of the characteristic domains that allow these proteins to interact with membranes is available, due to the application of MBPpred. Through the web interface of PerMemDB, users can browse the contents of the database, submit advanced text searches and BLAST queries against the protein sequences deposited in PerMemDB. We expect this repository to serve as a source of information that will allow the scientific community to gain a deeper understanding of the evolution and function of peripheral membrane proteins via the enhancement of proteome-wide analyses. The database is available at: http://bioinformatics.biol.uoa.gr/db=permemdb.
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Affiliation(s)
- Katerina C Nastou
- Section of Cell Biology and Biophysics, Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece
| | - Georgios N Tsaousis
- Section of Cell Biology and Biophysics, Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece
| | - Vassiliki A Iconomidou
- Section of Cell Biology and Biophysics, Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece.
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22
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Shelby ML, He W, Dang AT, Kuhl TL, Coleman MA. Cell-Free Co-Translational Approaches for Producing Mammalian Receptors: Expanding the Cell-Free Expression Toolbox Using Nanolipoproteins. Front Pharmacol 2019; 10:744. [PMID: 31333463 PMCID: PMC6616253 DOI: 10.3389/fphar.2019.00744] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/07/2019] [Indexed: 12/28/2022] Open
Abstract
Membranes proteins make up more than 60% of current drug targets and account for approximately 30% or more of the cellular proteome. Access to this important class of proteins has been difficult due to their inherent insolubility and tendency to aggregate in aqueous solutions. Understanding membrane protein structure and function demands novel means of membrane protein production that preserve both their native conformational state as well as function. Over the last decade, cell-free expression systems have emerged as an important complement to cell-based expression of membrane proteins due to their simple and customizable experimental parameters. One approach to overcome the solubility and stability limitations of purified membrane proteins is to support them in stable, native-like states within nanolipoprotein particles (NLPs), aka nanodiscs. This has become common practice to facilitate biochemical and biophysical characterization of proteins of interest. NLP technology can be easily coupled with cell-free systems to achieve functional membrane protein production for this purpose. Our approach involves utilizing cell-free expression systems in the presence of NLPs or using co-translation techniques to perform one-pot expression and self-assembly of membrane protein/NLP complexes. We describe how cell-free reactions can be modified to render control over nanoparticle size and monodispersity in support of membrane protein production. These modifications have been exploited to facilitate co-expression of full-length functional membrane proteins such as G-protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). In particular, we summarize the state of the art in NLP-assisted cell-free coexpression of these important classes of membrane proteins as well as evaluate the advances in and prospects for this technology that will drive drug discovery against these targets. We conclude with a prospective on the use of NLPs to produce as well as deliver functional mammalian membrane-bound proteins for a range of applications.
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Affiliation(s)
- Megan L Shelby
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Wei He
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Amanda T Dang
- University of California at Davis, Davis, CA, United States
| | - Tonya L Kuhl
- University of California at Davis, Davis, CA, United States
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, Livermore, CA, United States.,University of California at Davis, Davis, CA, United States
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23
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Agarwal G, Smith AW, Jones B. Discoidin domain receptors: Micro insights into macro assemblies. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118496. [PMID: 31229648 DOI: 10.1016/j.bbamcr.2019.06.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 12/19/2022]
Abstract
Assembly of cell-surface receptors into specific oligomeric states and/or clusters before and after ligand binding is an important feature governing their biological function. Receptor oligomerization can be mediated by specific domains of the receptor, ligand binding, configurational changes or other interacting molecules. In this review we summarize our understanding of the oligomeric state of discoidin domain receptors (DDR1 and DDR2), which belong to the receptor tyrosine kinase family (RTK). DDRs form an interesting system from an oligomerization perspective as their ligand collagen(s) can also undergo supramolecular assembly to form fibrils. Even though DDR1 and DDR2 differ in the domains responsible to form ligand-free dimers they share similarities in binding to soluble, monomeric collagen. However, only DDR1b forms globular clusters in response to monomeric collagen and not DDR2. Interestingly, both DDR1 and DDR2 are assembled into linear clusters by the collagen fibril. Formation of these clusters is important for receptor phosphorylation and is mediated in part by other membrane components. We summarize how the oligomeric status of DDRs shares similarities with other members of the RTK family and with collagen receptors. Unraveling the multiple macro-molecular configurations adopted by this receptor-ligand pair can provide novel insights into the intricacies of cell-matrix interactions.
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Affiliation(s)
- Gunjan Agarwal
- Biomedical Engineering Department, The Ohio State University, Columbus, OH 43210, USA.
| | - Adam W Smith
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
| | - Blain Jones
- Biomedical Engineering Department, The Ohio State University, Columbus, OH 43210, USA
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24
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Nintemann SJ, Palmgren M, López-Marqués RL. Catch You on the Flip Side: A Critical Review of Flippase Mutant Phenotypes. TRENDS IN PLANT SCIENCE 2019; 24:468-478. [PMID: 30885637 DOI: 10.1016/j.tplants.2019.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/24/2019] [Accepted: 02/04/2019] [Indexed: 05/05/2023]
Abstract
Lipid flippases are integral membrane proteins that use ATP hydrolysis to power the generation of phospholipid asymmetry between the two leaflets of biological membranes, a process essential for cell survival. Although the first report of a plant lipid flippase was published in 2000, progress in the field has been slow, partially due to the high level of redundancy in this gene family. However, recently an increasing number of reports have examined the physiological function of lipid flippases, mainly in Arabidopsis thaliana. In this review we aim to summarize recent findings on the physiological relevance of lipid flippases in plant adaptation to a changing environment and caution against misinterpretation of pleiotropic effects in genetic studies of flippases.
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Affiliation(s)
- Sebastian J Nintemann
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Rosa Laura López-Marqués
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark; https://plen.ku.dk/english/research/transport_biology/blf/.
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25
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Bolla JR, Agasid MT, Mehmood S, Robinson CV. Membrane Protein-Lipid Interactions Probed Using Mass Spectrometry. Annu Rev Biochem 2019; 88:85-111. [PMID: 30901263 DOI: 10.1146/annurev-biochem-013118-111508] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Membrane proteins that exist in lipid bilayers are not isolated molecular entities. The lipid molecules that surround them play crucial roles in maintaining their full structural and functional integrity. Research directed at investigating these critical lipid-protein interactions is developing rapidly. Advancements in both instrumentation and software, as well as in key biophysical and biochemical techniques, are accelerating the field. In this review, we provide a brief outline of structural techniques used to probe protein-lipid interactions and focus on the molecular aspects of these interactions obtained from native mass spectrometry (native MS). We highlight examples in which lipids have been shown to modulate membrane protein structure and show how native MS has emerged as a complementary technique to X-ray crystallography and cryo-electron microscopy. We conclude with a short perspective on future developments that aim to better understand protein-lipid interactions in the native environment.
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Affiliation(s)
- Jani Reddy Bolla
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Mark T Agasid
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Shahid Mehmood
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
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26
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Shahane G, Ding W, Palaiokostas M, Orsi M. Physical properties of model biological lipid bilayers: insights from all-atom molecular dynamics simulations. J Mol Model 2019; 25:76. [PMID: 30806797 DOI: 10.1007/s00894-019-3964-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/07/2019] [Indexed: 02/04/2023]
Abstract
The physical properties of lipid bilayers are sensitive to the specific type and composition of the lipids that make up the many different types of cell membranes. Studying model bilayers of representative heterogeneous compositions can provide key insights into membrane functionality. In this work, we use atomistic molecular dynamics simulations to characterize key properties in a number of bilayer membranes of varying composition. We first examine basic properties, such as lipid area, volume, and bilayer thickness, of simple, homogeneous bilayers comprising several lipid types, which are prevalent in biological membranes. Such lipids are then used in simulations of heterogeneous systems representative of bacterial, mammalian, and cancer membranes. Our analysis is especially focused on depth-dependent, transmembrane profiles; in particular, we calculate lateral pressure and dipole potential profiles, two fundamental properties which play key roles in a large number of biological functions.
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Affiliation(s)
- Ganesh Shahane
- Institute of Bioengineering, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Wei Ding
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Michail Palaiokostas
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Mario Orsi
- Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.
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Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Membrane
lipids interact with proteins in a variety of ways, ranging
from providing a stable membrane environment for proteins to being
embedded in to detailed roles in complicated and well-regulated protein
functions. Experimental and computational advances are converging
in a rapidly expanding research area of lipid–protein interactions.
Experimentally, the database of high-resolution membrane protein structures
is growing, as are capabilities to identify the complex lipid composition
of different membranes, to probe the challenging time and length scales
of lipid–protein interactions, and to link lipid–protein
interactions to protein function in a variety of proteins. Computationally,
more accurate membrane models and more powerful computers now enable
a detailed look at lipid–protein interactions and increasing
overlap with experimental observations for validation and joint interpretation
of simulation and experiment. Here we review papers that use computational
approaches to study detailed lipid–protein interactions, together
with brief experimental and physiological contexts, aiming at comprehensive
coverage of simulation papers in the last five years. Overall, a complex
picture of lipid–protein interactions emerges, through a range
of mechanisms including modulation of the physical properties of the
lipid environment, detailed chemical interactions between lipids and
proteins, and key functional roles of very specific lipids binding
to well-defined binding sites on proteins. Computationally, despite
important limitations, molecular dynamics simulations with current
computer power and theoretical models are now in an excellent position
to answer detailed questions about lipid–protein interactions.
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Affiliation(s)
- Valentina Corradi
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Besian I Sejdiu
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Haydee Mesa-Galloso
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Haleh Abdizadeh
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands
| | - Sergei Yu Noskov
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - 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
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
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Li X, Shi X, Kaliszewski MJ, Smith AW. Fluorescence cross-correlation spectroscopy of lipid-peptide interactions on supported lipid bilayers. ADVANCES IN BIOMEMBRANES AND LIPID SELF-ASSEMBLY 2019. [DOI: 10.1016/bs.abl.2019.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Differential Scanning Calorimetry Analyses of Idebenone-Loaded Solid Lipid Nanoparticles Interactions with a Model of Bio-Membrane: A Comparison with In Vitro Skin Permeation Data. Pharmaceuticals (Basel) 2018; 11:ph11040138. [PMID: 30558360 PMCID: PMC6316718 DOI: 10.3390/ph11040138] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/07/2018] [Accepted: 12/14/2018] [Indexed: 11/26/2022] Open
Abstract
Differential scanning calorimetry (DSC) has emerged as a helpful technique both to characterize drug delivery systems and to study their interactions with bio-membranes. In this work, we compared idebenone (IDE)-loaded solid lipid nanoparticle (SLN) interactions with bio-membranes assessed by DSC with previous in vitro skin penetration data to evaluate the feasibility of predicting IDE skin penetration using DSC analyses. In vitro interactions experiments were performed using multi-lamellar liposomes as a model of bio-membrane. Enthalpy changes (ΔH) and transition temperature (Tm) were assessed during nine repeated DSC scans to evaluate IDE-loaded SLN–bio-membrane interactions over time. Analyzing ΔH and Tm values for each scan, we observed that the difference of ΔH and Tm values between the first and the last scan seemed to be related to SLN ability to locate IDE in the epidermis and in the stratum corneum, respectively. Therefore, the results of this study suggest the possibility of qualitatively predicting in vitro IDE skin penetration from IDE-loaded SLN utilizing the calorimetric parameters obtained from interaction experiments between the carriers under investigation and a model of bio-membrane.
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30
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Afanasyeva EF, Syryamina VN, De Zotti M, Formaggio F, Toniolo C, Dzuba SA. Peptide antibiotic trichogin in model membranes: Self-association and capture of fatty acids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1861:524-531. [PMID: 30550880 DOI: 10.1016/j.bbamem.2018.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 10/27/2022]
Abstract
The antimicrobial action of peptides in bacterial membranes is commonly related to their mode of self-assembling which results in pore formation. To optimize peptide antibiotic use for therapeutic purposes, a study on the concentration dependence of self-assembling process is thus desirable. In this work, we investigate this dependence for peptaibol trichogin GA IV (Tric) in the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) model membrane in the range of peptide concentrations between 0.5 and 3.3 mol%. Pulsed double electron-electron resonance (PELDOR) applied on spin-labeled peptide analogs highlights the onset of peptide dimerization above a critical peptide concentration value, namely ~ 2 mol%. Electron spin echo (ESE) envelope modulation (ESEEM) for D2O-hydrated bilayers shows that dimerization is accompanied by peptide re-orientation towards a trans-membrane disposition. For spin-labeled stearic acids (5-DSA) in POPC bilayers, the study of ESE decays and ESEEM in the presence of a deuterated peptide analog indicates that above the critical peptide concentration the 5-DSA molecules are attracted by peptide molecules, forming nanoclusters. As the 5-DSA molecules represent a model for the behavior of fatty acids participating in bacterial membrane homeostasis, such capturing action by Tric may represent an additional mechanism of its antibiotic activity.
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Affiliation(s)
- Ekaterina F Afanasyeva
- Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - Victoria N Syryamina
- Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - Marta De Zotti
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Fernando Formaggio
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Claudio Toniolo
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Sergei A Dzuba
- Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Novosibirsk 630090, Russian Federation.
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Nji E, Chatzikyriakidou Y, Landreh M, Drew D. An engineered thermal-shift screen reveals specific lipid preferences of eukaryotic and prokaryotic membrane proteins. Nat Commun 2018; 9:4253. [PMID: 30315156 PMCID: PMC6185904 DOI: 10.1038/s41467-018-06702-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 09/19/2018] [Indexed: 12/11/2022] Open
Abstract
Membrane bilayers are made up of a myriad of different lipids that regulate the functional activity, stability, and oligomerization of many membrane proteins. Despite their importance, screening the structural and functional impact of lipid–protein interactions to identify specific lipid requirements remains a major challenge. Here, we use the FSEC-TS assay to show cardiolipin-dependent stabilization of the dimeric sodium/proton antiporter NhaA, demonstrating its ability to detect specific protein-lipid interactions. Based on the principle of FSEC-TS, we then engineer a simple thermal-shift assay (GFP-TS), which facilitates the high-throughput screening of lipid- and ligand- interactions with membrane proteins. By comparing the thermostability of medically relevant eukaryotic membrane proteins and a selection of bacterial counterparts, we reveal that eukaryotic proteins appear to have evolved to be more dependent to the presence of specific lipids. Membrane bilayers are made up of a myriad of different lipids that affect membrane proteins, but identifying those specific lipid requirements remains a challenge. Here authors present an engineered thermal-shift screen which reveals specific lipid preferences of eukaryotic and prokaryotic membrane proteins.
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Affiliation(s)
- Emmanuel Nji
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Yurie Chatzikyriakidou
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Michael Landreh
- SciLifeLab and Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 65, Stockholm, Sweden
| | - David Drew
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden.
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32
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Siaw HMH, Raghunath G, Dyer RB. Peripheral Protein Unfolding Drives Membrane Bending. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8400-8407. [PMID: 29925237 PMCID: PMC6069603 DOI: 10.1021/acs.langmuir.8b01136] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Dynamic modulation of lipid membrane curvature can be achieved by a number of peripheral protein binding mechanisms such as hydrophobic insertion of amphipathic helices and membrane scaffolding. Recently, an alternative mechanism was proposed in which crowding of peripherally bound proteins induces membrane curvature through steric pressure generated by lateral collisions. This effect was enhanced using intrinsically disordered proteins that possess high hydrodynamic radii, prompting us to explore whether membrane bending can be triggered by the folding-unfolding transition of surface-bound proteins. We utilized histidine-tagged human serum albumin bound to Ni-NTA-DGS containing liposomes as our model system to test this hypothesis. We found that reduction of the disulfide bonds in the protein resulted in unfolding of HSA, which subsequently led to membrane tubule formation. The frequency of tubule formation was found to be significantly higher when the proteins were unfolded while being localized to a phase-separated domain as opposed to randomly distributed in fluid phase liposomes, indicating that the steric pressure generated from protein unfolding can drive membrane deformation. Our results are critical for the design of peripheral membrane protein-immobilization strategies and open new avenues for exploring mechanisms of membrane bending driven by conformational changes of peripheral membrane proteins.
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33
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Xu GQ, Hao CC, Zhang L, Chen S, Sun RG. Dynamic Behaviors and Morphology Change of Anionic Phospholipid DPPG Monolayer Caused by Bovine Serum Albumin at Air-Water Interface. CHINESE J CHEM PHYS 2017. [DOI: 10.1063/1674-0068/30/cjcp1703029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Guo-qing Xu
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
| | - Chang-chun Hao
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
| | - Lei Zhang
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
| | - Shi Chen
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
| | - Run-guang Sun
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
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34
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Heberle FA, Pabst G. Complex biomembrane mimetics on the sub-nanometer scale. Biophys Rev 2017; 9:353-373. [PMID: 28717925 PMCID: PMC5578918 DOI: 10.1007/s12551-017-0275-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/26/2017] [Indexed: 12/12/2022] Open
Abstract
Biomimetic lipid vesicles are indispensable tools for gaining insight into the biophysics of cell physiology on the molecular level. The level of complexity of these model systems has steadily increased, and now spans from domain-forming lipid mixtures to asymmetric lipid bilayers. Here, we review recent progress in the development and application of elastic neutron and X-ray scattering techniques for studying these systems in situ and under physiologically relevant conditions on the nanometer to sub-nanometer length scales. In particular, we focus on: (1) structural details of coexisting liquid-ordered and liquid-disordered domains, including their thickness and lipid packing mismatch as a function of a size transition from nanoscopic to macroscopic domains; (2) membrane-mediated protein partitioning into lipid domains; (3) the role of the aqueous medium in tuning interactions between membranes and domains; and (4) leaflet-specific structure in asymmetric bilayers and passive lipid flip-flop.
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Affiliation(s)
- Frederick A Heberle
- The Bredesen Center, University of Tennessee, Knoxville, TN, 37996, USA.,Joint Institute for Biological Sciences and Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Georg Pabst
- Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, University of Graz, 8010, Graz, Austria. .,BioTechMed-Graz, 8010, Graz, Austria.
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35
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Stevenson P, Tokmakoff A. Ultrafast Fluctuations of High Amplitude Electric Fields in Lipid Membranes. J Am Chem Soc 2017; 139:4743-4752. [DOI: 10.1021/jacs.6b12412] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Paul Stevenson
- Department
of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts
Ave., Cambridge, Massachusetts 02139, United States
- Department
of Chemistry, James Frank Institute, and The Institute
for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department
of Chemistry, James Frank Institute, and The Institute
for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
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36
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Singh P. Budding Yeast: An Ideal Backdrop for In vivo Lipid Biochemistry. Front Cell Dev Biol 2017; 4:156. [PMID: 28119915 PMCID: PMC5222803 DOI: 10.3389/fcell.2016.00156] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 12/27/2016] [Indexed: 12/29/2022] Open
Abstract
Biological membranes are non-covalent assembly of lipids and proteins. Lipids play critical role in determining membrane physical properties and regulate the function of membrane associated proteins. Budding yeast Saccharomyces cerevisiae offers an exceptional advantage to understand the lipid-protein interactions since lipid metabolism and homeostasis are relatively simple and well characterized as compared to other eukaryotes. In addition, a vast array of genetic and cell biological tools are available to determine and understand the role of a particular lipid in various lipid metabolic disorders. Budding yeast has been instrumental in delineating mechanisms related to lipid metabolism, trafficking and their localization in different subcellular compartments at various cell cycle stages. Further, availability of tools and enormous potential for the development of useful reagents and novel technologies to localize a particular lipid in different subcellular compartments in yeast makes it a formidable system to carry out lipid biology. Taken together, yeast provides an outstanding backdrop to characterize lipid metabolic changes under various physiological conditions.
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Affiliation(s)
- Pushpendra Singh
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of MedicineBaltimore, MD, USA; Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins UniversityBaltimore, MD, USA
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37
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Fosso-Tande J, Black C, G. Aller S, Lu L, D. Hills Jr R. Simulation of lipid-protein interactions with the CgProt force field. AIMS MOLECULAR SCIENCE 2017. [DOI: 10.3934/molsci.2017.3.352] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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38
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Affiliation(s)
- Benjamin J. Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Hoa Q. Do
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Collin G. Borcik
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Emily P. Hardy
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
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Abstract
Biological membranes allow life as we know it to exist. They form cells and enable separation between the inside and outside of an organism, controlling by means of their selective permeability which substances enter and leave. By allowing gradients of ions to be created across them, membranes also enable living organisms to generate energy. In addition, they control the flow of messages between cells by sending, receiving and processing information in the form of chemical and electrical signals. This essay summarizes the structure and function of membranes and the proteins within them, and describes their role in trafficking and transport, and their involvement in health and disease. Techniques for studying membranes are also discussed.
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40
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Frewein M, Kollmitzer B, Heftberger P, Pabst G. Lateral pressure-mediated protein partitioning into liquid-ordered/liquid-disordered domains. SOFT MATTER 2016; 12:3189-95. [PMID: 27003910 PMCID: PMC5462092 DOI: 10.1039/c6sm00042h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We have studied the contributions of stored elastic energies in liquid-ordered (Lo) and liquid-disordered (Ld) domains to transmembrane proteins using the lateral pressure concept. In particular we applied previously reported experimental data for the membrane thickness, intrinsic curvature and bending elasticities of coexisting Lo/Ld domains to calculate whether proteins of simple geometric shapes would preferentially diffuse into Lo or Ld domains and form oligomers of a certain size. For the studied lipid mixture we generally found that proteins with convex shapes prefer sorting to Ld phases and the formation of large clusters. Lo domains in turn would be enriched in monomers of concave shaped proteins. We further observed that proteins which are symmetric with respect to the bilayer center prefer symmetric Lo or Ld domains, while asymmetric proteins favor a location in domains with Lo/Ld asymmetry. In the latter case we additionally retrieved a strong dependence on protein directionality, thus providing a mechanism for transmembrane protein orientation.
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Affiliation(s)
- Moritz Frewein
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Humboldtstr. 50/III, A-8010 Graz, Austria.
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41
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Garcia-Fandiño R, Piñeiro Á, Trick JL, Sansom MSP. Lipid Bilayer Membrane Perturbation by Embedded Nanopores: A Simulation Study. ACS NANO 2016; 10:3693-3701. [PMID: 26943498 DOI: 10.1021/acsnano.6b00202] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A macromolecular nanopore inserted into a membrane may perturb the dynamic organization of the surrounding lipid bilayer. To better understand the nature of such perturbations, we have undertaken a systematic molecular dynamics simulation study of lipid bilayer structure and dynamics around three different classes of nanopore: a carbon nanotube, three related cyclic peptide nanotubes differing in the nature of their external surfaces, and a model of a β-barrel nanopore protein. Periodic spatial distributions of several lipid properties as a function of distance from the nanopore were observed. This was especially clear for the carbon nanotube system, for which the density of lipids, the bilayer thickness, the projection of lipid head-to-tail vectors onto the membrane plane, and lipid lateral diffusion coefficients exhibited undulatory behavior as a function of the distance from the surface of the channel. Overall, the differences in lipid behavior as a function of the nanopore structure reveal local adaptation of the bilayer structure and dynamics to different embedded nanopore structures. Both the local structure and dynamic behavior of lipids around membrane-embedded nanopores are sensitive to the geometry and nature of the outer surface of the macromolecule/molecular assembly forming the pore.
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Affiliation(s)
- Rebeca Garcia-Fandiño
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela , 15782 Santiago de Compostela, Spain
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Ángel Piñeiro
- Soft Matter & Molecular Biophysics Group, Department of Applied Physics, Faculty of Physics, University of Santiago de Compostela , 15782 Santiago de Compostela, Spain
| | - Jemma L Trick
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
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42
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Drabik D, Przybyło M, Sikorski A, Langner M. The Effect of a Fluorophore Photo-Physics on the Lipid Vesicle Diffusion Coefficient Studied by Fluorescence Correlation Spectroscopy. J Fluoresc 2016; 26:661-9. [PMID: 26695945 PMCID: PMC4773467 DOI: 10.1007/s10895-015-1752-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/14/2015] [Indexed: 11/28/2022]
Abstract
Fluorescence Correlation Spectroscopy (FCS) is a technique, which allows determination of the diffusion coefficient and concentration of fluorescent objects suspended in the solution. The measured parameter is the fluctuation of the fluorescence signal emitted by diffusing molecules. When 100 nm DOPC vesicles labeled with various fluorescent dyes (Fluorescein-PE, NBD-PE, Atto488 DOPE or βBodipy FL) were measured, different values of diffusion coefficients have been obtained. These diffusion coefficients were different from the expected values measured using the dynamic light scattering method (DLS). The FCS was initially developed for solutions containing small fluorescent molecules therefore the observed inconsistency may result from the nature of vesicle suspension itself. The duration of the fluorescence signal may depend on the following factors: the exposure time of the labeled object to the excitation beam, the photo-physical properties (e.g., stability) of a fluorophore, the theoretical model used for the calculations of the diffusion coefficient and optical properties of the vesicle suspension. The diffusion coefficients determined for differently labeled liposomes show that its dependence on vesicle size and quantity of fluorescent probed used for labeling was significant demonstrating that the fluorescence properties of the fluorophore itself (bleaching and/or blinking) were critical factors for a correct outcome of FCS experiment. The new, based on combined FCS and DLS measurements, method for the determination of the focal volume prove itself to be useful for the evaluation of a fluorescence dye with respect to its applicability for FCS experiment.
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Affiliation(s)
- Dominik Drabik
- Laboratory for Biophysics of Macromolecular Aggregates, Department of Biomedical Engineering, Wroclaw University of Technology, Pl. Grunwaldzki 13, 50-377, Wroclaw, Poland.
| | - Magda Przybyło
- Laboratory for Biophysics of Macromolecular Aggregates, Department of Biomedical Engineering, Wroclaw University of Technology, Pl. Grunwaldzki 13, 50-377, Wroclaw, Poland
- Lipid Systems sp. z. o. o. [Ltd], ul. Duńska 9, 54-066, Wrocław, Poland
| | - Aleksander Sikorski
- Laboratory of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, ul. Joliot-Curie 14a, Wrocław, Poland
| | - Marek Langner
- Laboratory for Biophysics of Macromolecular Aggregates, Department of Biomedical Engineering, Wroclaw University of Technology, Pl. Grunwaldzki 13, 50-377, Wroclaw, Poland
- Lipid Systems sp. z. o. o. [Ltd], ul. Duńska 9, 54-066, Wrocław, Poland
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43
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Postila PA, Vattulainen I, Róg T. Selective effect of cell membrane on synaptic neurotransmission. Sci Rep 2016; 6:19345. [PMID: 26782980 PMCID: PMC4725992 DOI: 10.1038/srep19345] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/07/2015] [Indexed: 12/25/2022] Open
Abstract
Atomistic molecular dynamics simulations were performed with 13 non-peptidic neurotransmitters (NTs) in three different membrane environments. The results provide compelling evidence that NTs are divided into membrane-binding and membrane-nonbinding molecules. NTs adhere to the postsynaptic membrane surface whenever the ligand-binding sites of their synaptic receptors are buried in the lipid bilayer. In contrast, NTs that have extracellular ligand-binding sites do not have a similar tendency to adhere to the membrane surface. This finding is a seemingly simple yet important addition to the paradigm of neurotransmission, essentially dividing it into membrane-independent and membrane-dependent mechanisms. Moreover, the simulations also indicate that the lipid composition especially in terms of charged lipids can affect the membrane partitioning of NTs. The revised paradigm, highlighting the importance of cell membrane and specific lipids for neurotransmission, should to be of interest to neuroscientists, drug industry and the general public alike.
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Affiliation(s)
- Pekka A. Postila
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
- Department of Chemistry and Biochemistry, University of California San Diego, 92093-0340 San Diego, CA, USA
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
- MEMPHYS– Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014, Helsinki, Finland
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
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44
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Saita E, Albanesi D, de Mendoza D. Sensing membrane thickness: Lessons learned from cold stress. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:837-846. [PMID: 26776056 DOI: 10.1016/j.bbalip.2016.01.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 10/22/2022]
Abstract
The lipid bilayer component of biological membranes is important for the distribution, organization, and function of bilayer spanning proteins. These physical barriers are subjected to bilayer perturbations. As a consequence, nature has evolved proteins that are able to sense changes in the bilayer properties and transform these lipid-mediated stimuli into intracellular signals. A structural feature that most signal-transducing membrane-embedded proteins have in common is one or more α-helices that traverse the lipid bilayer. Because of the interaction with the surrounding lipids, the organization of these transmembrane helices will be sensitive to membrane properties, like hydrophobic thickness. The helices may adapt to the lipids in different ways, which in turn can influence the structure and function of the intact membrane proteins. We review recent insights into the molecular basis of thermosensing via changes in membrane thickness and consider examples in which the hydrophobic matching can be demonstrated using reconstituted membrane systems. This article is part of a Special Issue entitled: The cellular lipid landscape edited by Tim P. Levine and Anant K. Menon.
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Affiliation(s)
- Emilio Saita
- Laboratorio de Fisiología Microbiana, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario. Ocampo y Esmeralda, Predio CONICET Rosario, 2000 Rosario, Argentina
| | - Daniela Albanesi
- Laboratorio de Fisiología Microbiana, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario. Ocampo y Esmeralda, Predio CONICET Rosario, 2000 Rosario, Argentina
| | - Diego de Mendoza
- Laboratorio de Fisiología Microbiana, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario. Ocampo y Esmeralda, Predio CONICET Rosario, 2000 Rosario, Argentina.
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45
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Banerjee K. Dynamic memory of a single voltage-gated potassium ion channel: A stochastic nonequilibrium thermodynamic analysis. J Chem Phys 2015; 142:185101. [PMID: 25978913 DOI: 10.1063/1.4920937] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In this work, we have studied the stochastic response of a single voltage-gated potassium ion channel to a periodic external voltage that keeps the system out-of-equilibrium. The system exhibits memory, resulting from time-dependent driving, that is reflected in terms of dynamic hysteresis in the current-voltage characteristics. The hysteresis loop area has a maximum at some intermediate voltage frequency and disappears in the limits of low and high frequencies. However, the (average) dissipation at long-time limit increases and finally goes to saturation with rising frequency. This raises the question: how diminishing hysteresis can be associated with growing dissipation? To answer this, we have studied the nonequilibrium thermodynamics of the system and analyzed different thermodynamic functions which also exhibit hysteresis. Interestingly, by applying a temporal symmetry analysis in the high-frequency limit, we have analytically shown that hysteresis in some of the periodic responses of the system does not vanish. On the contrary, the rates of free energy and internal energy change of the system as well as the rate of dissipative work done on the system show growing hysteresis with frequency. Hence, although the current-voltage hysteresis disappears in the high-frequency limit, the memory of the ion channel is manifested through its specific nonequilibrium thermodynamic responses.
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Affiliation(s)
- Kinshuk Banerjee
- Department of Chemistry, University of Calcutta, 92 A.P.C. Road, Kolkata 700 009, India
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46
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Kumar S, Bhargava P, Sreekanth V, Bajaj A. Design, synthesis, and physico-chemical interactions of bile acid derived dimeric phospholipid amphiphiles with model membranes. J Colloid Interface Sci 2015; 448:398-406. [DOI: 10.1016/j.jcis.2015.01.069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 01/26/2015] [Accepted: 01/26/2015] [Indexed: 11/16/2022]
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47
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Battle AR, Ridone P, Bavi N, Nakayama Y, Nikolaev YA, Martinac B. Lipid-protein interactions: Lessons learned from stress. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1744-56. [PMID: 25922225 DOI: 10.1016/j.bbamem.2015.04.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/13/2015] [Accepted: 04/18/2015] [Indexed: 12/11/2022]
Abstract
Biological membranes are essential for normal function and regulation of cells, forming a physical barrier between extracellular and intracellular space and cellular compartments. These physical barriers are subject to mechanical stresses. As a consequence, nature has developed proteins that are able to transpose mechanical stimuli into meaningful intracellular signals. These proteins, termed Mechanosensitive (MS) proteins provide a variety of roles in response to these stimuli. In prokaryotes these proteins form transmembrane spanning channels that function as osmotically activated nanovalves to prevent cell lysis by hypoosmotic shock. In eukaryotes, the function of MS proteins is more diverse and includes physiological processes such as touch, pain and hearing. The transmembrane portion of these channels is influenced by the physical properties such as charge, shape, thickness and stiffness of the lipid bilayer surrounding it, as well as the bilayer pressure profile. In this review we provide an overview of the progress to date on advances in our understanding of the intimate biophysical and chemical interactions between the lipid bilayer and mechanosensitive membrane channels, focusing on current progress in both eukaryotic and prokaryotic systems. These advances are of importance due to the increasing evidence of the role the MS channels play in disease, such as xerocytosis, muscular dystrophy and cardiac hypertrophy. Moreover, insights gained from lipid-protein interactions of MS channels are likely relevant not only to this class of membrane proteins, but other bilayer embedded proteins as well. This article is part of a Special Issue entitled: Lipid-protein interactions.
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Affiliation(s)
- A R Battle
- Menzies Health Institute Queensland and School of Pharmacy, Griffith University, Gold Coast Campus, QLD 4222, Australia
| | - P Ridone
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - N Bavi
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, Australia
| | - Y Nakayama
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Y A Nikolaev
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW 2308, Australia
| | - B Martinac
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, Australia.
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48
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Sharma V, Ala-Vannesluoma P, Vattulainen I, Wikström M, Róg T. Role of subunit III and its lipids in the molecular mechanism of cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:690-7. [PMID: 25896562 DOI: 10.1016/j.bbabio.2015.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/07/2015] [Accepted: 04/12/2015] [Indexed: 12/31/2022]
Abstract
The terminal respiratory enzyme cytochrome c oxidase (CcO) reduces molecular oxygen to water, and pumps protons across the inner mitochondrial membrane, or the plasma membrane of bacteria. A two-subunit CcO harbors all the elements necessary for oxygen reduction and proton pumping. However, it rapidly undergoes turnover-induced irreversible damage, which is effectively prevented by the presence of subunit III and its tightly bound lipids. We have performed classical atomistic molecular dynamics (MD) simulations on a three-subunit CcO, which show the formation of water wires between the polar head groups of lipid molecules bound to subunit III and the proton uptake site Asp91 (Bos taurus enzyme numbering). Continuum electrostatic calculations suggest that these lipids directly influence the proton affinity of Asp91 by 1-2pK units. We surmise that lipids bound to subunit III influence the rate of proton uptake through the D-pathway, and therefore play a key role in preventing turnover-induced inactivation. Atomistic MD simulations show that subunit III is rapidly hydrated in the absence of internally bound lipids, which is likely to affect the rate of O2 diffusion into the active-site. The role of subunit III with its indigenous lipids in the molecular mechanism of CcO is discussed.
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Affiliation(s)
- Vivek Sharma
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland.
| | | | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland; MEMPHYS, Center for Biomembrane Physics, Department of Physics, University of Southern Denmark, Odense, Denmark
| | - Mårten Wikström
- Helsinki Bioenergetics Group, Programme for Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
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Morales-Cedillo F, González-Solís A, Gutiérrez-Angoa L, Cano-Ramírez DL, Gavilanes-Ruiz M. Plant lipid environment and membrane enzymes: the case of the plasma membrane H+-ATPase. PLANT CELL REPORTS 2015; 34:617-29. [PMID: 25577330 DOI: 10.1007/s00299-014-1735-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/18/2014] [Accepted: 12/29/2014] [Indexed: 05/06/2023]
Abstract
Several lipid classes constitute the universal matrix of the biological membranes. With their amphipathic nature, lipids not only build the continuous barrier that confers identity to every cell and organelle, but they are also active actors that modulate the activity of the proteins immersed in the lipid bilayer. The plasma membrane H(+)-ATPase, an enzyme from plant cells, is an excellent example of a transmembrane protein whose activity is influenced by the hydrophilic compartments at both sides of the membrane and by the hydrophobic domains of the lipid bilayer. As a result, an extensive documentation of the effect of numerous amphiphiles in the enzyme activity can be found. Detergents, membrane glycerolipids, and sterols can produce activation or inhibition of the enzyme activity. In some cases, these effects are associated with the lipids of the membrane bulk, but in others, a direct interaction of the lipid with the protein is involved. This review gives an account of reports related to the action of the membrane lipids on the H(+)-ATPase activity.
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Affiliation(s)
- Francisco Morales-Cedillo
- Dpto. de Bioquímica, Facultad de Química, Conj. E. Universidad Nacional Autónoma de México, UNAM. Cd. Universitaria, Coyoacán, 04510, Mexico, D.F., Mexico
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50
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Ghosh S, Ghosh C, Nandi S, Bhattacharyya K. Unfolding and refolding of a protein by cholesterol and cyclodextrin: a single molecule study. Phys Chem Chem Phys 2015; 17:8017-27. [DOI: 10.1039/c5cp00385g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cholesterol induced unfolding of a globular protein, human serum albumin (HSA), and β-cyclodextrin induced refolding of the unfolded protein is demonstrated in this study.
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Affiliation(s)
- Shirsendu Ghosh
- Department of Physical Chemistry
- Indian Association For The cultivation of Science
- Kolkata 700 032
- India
| | - Catherine Ghosh
- Department of Physical Chemistry
- Indian Association For The cultivation of Science
- Kolkata 700 032
- India
| | - Somen Nandi
- Department of Physical Chemistry
- Indian Association For The cultivation of Science
- Kolkata 700 032
- India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry
- Indian Association For The cultivation of Science
- Kolkata 700 032
- India
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