1
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Pandey Y, Dondapati SK, Wüstenhagen D, Kubick S. Cell-Free Synthesis and Electrophysiological Analysis of Multipass Voltage-Gated Ion Channels Tethered in Microsomal Membranes. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:103-120. [PMID: 37640910 DOI: 10.1007/10_2023_228] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Cell-free protein synthesis (CFPS) has emerged as a powerful tool for the rapid synthesis and analysis of various structurally and functionally distinct proteins. These include 'difficult-to-express' membrane proteins such as large multipass ion channel receptors. Owing to their membrane localization, eukaryotic CFPS supplemented with endoplasmic reticulum (ER)-derived microsomal vesicles has proven to be an efficient system for the synthesis of functional membrane proteins. Here we demonstrate the applicability of the eukaryotic cell-free systems based on lysates from the mammalian Chinese Hamster Ovary (CHO) and insect Spodoptera frugiperda (Sf21) cells. We demonstrate the efficiency of the systems in the de novo cell-free synthesis of the human cardiac ion channels: ether-a-go-go potassium channel (hERG) KV11.1 and the voltage-gated sodium channel hNaV1.5.
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Affiliation(s)
- Yogesh Pandey
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institut für Biochemie und Biologie, University of Potsdam, Potsdam, OT Golm, Germany
| | - Srujan Kumar Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany.
| | - Doreen Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- Institute of Chemistry and Biochemistry-Biochemistry, Freie Universität Berlin, Berlin, Germany
- Faculty of Health Science, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
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2
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Kermani AA. A guide to membrane protein X‐ray crystallography. FEBS J 2020; 288:5788-5804. [DOI: 10.1111/febs.15676] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/17/2020] [Accepted: 12/14/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Ali A. Kermani
- Department of Molecular, Cellular, and Developmental Biology University of Michigan Ann Arbor MI USA
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3
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Van Truong T, Ghosh M, Wachtel E, Friedman N, Jung KH, Sheves M, Patchornik G. Promoting crystallization of intrinsic membrane proteins with conjugated micelles. Sci Rep 2020; 10:12199. [PMID: 32699228 PMCID: PMC7376161 DOI: 10.1038/s41598-020-68689-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/29/2020] [Indexed: 11/09/2022] Open
Abstract
A new technique for promoting nucleation and growth of membrane protein (MP) crystals from micellar environments is reported. It relies on the conjugation of micelles that sequester MPs in protein detergent complexes (PDCs). Conjugation via amphiphilic [metal:chelator] complexes presumably takes place at the micelle/water interface, thereby bringing the PDCs into proximity, promoting crystal nucleation and growth. We have successfully applied this approach to two light-driven proton pumps: bacteriorhodopsin (bR) and the recently discovered King Sejong 1-2 (KS1-2), using the amphiphilic 4,4'-dinonyl-2,2'-dipyridyl (Dinonyl) (0.7 mM) chelator in combination with Zn2+, Fe2+, or Ni2+ (0.1 mM). Crystal growth in the presence of the [metal-chelator] complexes leads to purple, hexagonal crystals (50-75 µm in size) of bR or pink, rectangular/square crystals (5-15 µm) of KS1-2. The effects of divalent cation identity and concentration, chelator structure and concentration, ionic strength and pH on crystal size, morphology and process kinetics, are described.
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Affiliation(s)
- Thien Van Truong
- Department of Chemical Sciences, Ariel University, 40700, Ariel, Israel
| | - Mihir Ghosh
- Faculty of Chemistry, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Ellen Wachtel
- Faculty of Chemistry, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Noga Friedman
- Faculty of Chemistry, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 121-742, South Korea
| | - Mordechai Sheves
- Faculty of Chemistry, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Guy Patchornik
- Department of Chemical Sciences, Ariel University, 40700, Ariel, Israel.
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4
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Dias Mirandela G, Tamburrino G, Ivanović MT, Strnad FM, Byron O, Rasmussen T, Hoskisson PA, Hub JS, Zachariae U, Gabel F, Javelle A. Merging In-Solution X-ray and Neutron Scattering Data Allows Fine Structural Analysis of Membrane-Protein Detergent Complexes. J Phys Chem Lett 2018; 9:3910-3914. [PMID: 29939747 DOI: 10.1021/acs.jpclett.8b01598] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In-solution small-angle X-ray and neutron scattering (SAXS/SANS) have become popular methods to characterize the structure of membrane proteins, solubilized by either detergents or nanodiscs. SANS studies of protein-detergent complexes usually require deuterium-labeled proteins or detergents, which in turn often lead to problems in their expression or purification. Here, we report an approach whose novelty is the combined analysis of SAXS and SANS data from an unlabeled membrane protein complex in solution in two complementary ways. First, an explicit atomic analysis, including both protein and detergent molecules, using the program WAXSiS, which has been adapted to predict SANS data. Second, the use of MONSA which allows one to discriminate between detergent head- and tail-groups in an ab initio approach. Our approach is readily applicable to any detergent-solubilized protein and provides more detailed structural information on protein-detergent complexes from unlabeled samples than SAXS or SANS alone.
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Affiliation(s)
- Gaëtan Dias Mirandela
- Strathclyde Institute of Pharmacy and Biomedical Sciences , University of Strathclyde , Glasgow , G4 0RE , United Kingdom
| | - Giulia Tamburrino
- Computational Biology, School of Life Sciences , University of Dundee , Dundee , DD1 5EH , United Kingdom
- Physics, School of Science and Engineering , University of Dundee , Dundee , DD1 4NH , United Kingdom
| | - Miloš T Ivanović
- Theoretical Physics , Saarland University , Campus E2 6 , 66123 Saarbrücken , Germany
| | - Felix M Strnad
- Institute for Microbiology and Genetics , University of Goettingen , Justus-von-Liebig-Weg 11 , 37077 Göttingen , Germany
| | - Olwyn Byron
- School of Life Sciences, College of Medical, Veterinary and Life Sciences , University of Glasgow , Glasgow , G12 8QQ , United Kingdom
| | - Tim Rasmussen
- School of Medical Sciences , University of Aberdeen , Foresterhill, Aberdeen AB25 2ZD , United Kingdom
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences , University of Strathclyde , Glasgow , G4 0RE , United Kingdom
| | - Jochen S Hub
- Theoretical Physics , Saarland University , Campus E2 6 , 66123 Saarbrücken , Germany
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences , University of Dundee , Dundee , DD1 5EH , United Kingdom
- Physics, School of Science and Engineering , University of Dundee , Dundee , DD1 4NH , United Kingdom
| | - Frank Gabel
- Institut Laue-Langevin , 71 Avenue des Martyrs 38042 Grenoble , France
- University of Grenoble Alpes, CEA, CNRS, IBS , 38000 Grenoble , France
| | - Arnaud Javelle
- Strathclyde Institute of Pharmacy and Biomedical Sciences , University of Strathclyde , Glasgow , G4 0RE , United Kingdom
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5
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Mohan Bangalore D, Tessmer I. Unique insight into protein-DNA interactions from single molecule atomic force microscopy. AIMS BIOPHYSICS 2018. [DOI: 10.3934/biophy.2018.3.194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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6
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Murínová S, Dercová K. Response mechanisms of bacterial degraders to environmental contaminants on the level of cell walls and cytoplasmic membrane. Int J Microbiol 2014; 2014:873081. [PMID: 25057269 PMCID: PMC4099092 DOI: 10.1155/2014/873081] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/12/2014] [Accepted: 05/27/2014] [Indexed: 11/18/2022] Open
Abstract
Bacterial strains living in the environment must cope with the toxic compounds originating from humans production. Surface bacterial structures, cell wall and cytoplasmic membrane, surround each bacterial cell and create selective barriers between the cell interior and the outside world. They are a first site of contact between the cell and toxic compounds. Organic pollutants are able to penetrate into cytoplasmic membrane and affect membrane physiological functions. Bacteria had to evolve adaptation mechanisms to counteract the damage originated from toxic contaminants and to prevent their accumulation in cell. This review deals with various adaptation mechanisms of bacterial cell concerning primarily the changes in cytoplasmic membrane and cell wall. Cell adaptation maintains the membrane fluidity status and ratio between bilayer/nonbilayer phospholipids as well as the efflux of toxic compounds, protein repair mechanisms, and degradation of contaminants. Low energy consumption of cell adaptation is required to provide other physiological functions. Bacteria able to survive in toxic environment could help us to clean contaminated areas when they are used in bioremediation technologies.
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Affiliation(s)
- Slavomíra Murínová
- Department of Biochemical Technology, Faculty of Chemical and Food Technology, Institute of Biotechnology and Food Science, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
- Water Research Institute, Nábrežie arm. gen. L. Svobodu 5, 812 49 Bratislava, Slovakia
| | - Katarína Dercová
- Department of Biochemical Technology, Faculty of Chemical and Food Technology, Institute of Biotechnology and Food Science, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
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7
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Kar P, Gopal SM, Cheng YM, Panahi A, Feig M. Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix-Helix Association. J Chem Theory Comput 2014; 10:3459-3472. [PMID: 25136271 PMCID: PMC4132866 DOI: 10.1021/ct500443v] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Indexed: 12/03/2022]
Abstract
![]()
An
extension of the recently developed PRIMO coarse-grained force
field to membrane environments, PRIMO-M, is described. The membrane
environment is modeled with the heterogeneous dielectric generalized
Born (HDGB) methodology that simply replaces the standard generalized
Born model in PRIMO without further parametrization. The resulting
model was validated by comparing amino acid insertion free energy
profiles and application in molecular dynamics simulations of membrane
proteins and membrane-interacting peptides. Membrane proteins with
148–661 amino acids show stable root-mean-squared-deviations
(RMSD) between 2 and 4 Å for most systems. Transmembrane helical
peptides maintain helical shape and exhibit tilt angles in good agreement
with experimental or other simulation data. The association of two
glycophorin A (GpA) helices was simulated using replica exchange molecular
dynamics simulations yielding the correct dimer structure with a crossing
angle in agreement with previous studies. Finally, conformational
sampling of the influenza fusion peptide also generates structures
in agreement with previous studies. Overall, these findings suggest
that PRIMO-M can be used to study membrane bound peptides and proteins
and validates the transferable nature of the PRIMO coarse-grained
force field.
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Affiliation(s)
- Parimal Kar
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Srinivasa Murthy Gopal
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Yi-Ming Cheng
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Afra Panahi
- Departments of Chemistry and Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Michael Feig
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States ; Department of Biochemistry and Molecular Biology and Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
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8
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Abstract
We have developed a simple method to synthesize 6-seleno-2'-deoxyguanosine (SedG) by selectively replacing the 6-oxygen atom with selenium. This selenium-atom-specific modification (SAM) alters the optical properties of the naturally occurring 2'-deoxyguanosine (dG). Unlike the native dG, the UVabsorption of SedG is significantly influenced by the pH of the aqueous solution. Moreover, SedG is fluorescent at the physiological pH and exhibits pH-dependent fluorescence in aqueous solutions. Furthermore, SedG has noticeable fluorescence in non-aqueous solutions, indicating its sensitivity to environmental changes. This is the first time a fluorescent nucleoside by single-atom alteration has been observed. Fluorescent nucleosides modified by a single atom have great potential as molecular probes with minimal perturbations to investigate nucleoside interactions with proteins, such as membrane-transporter proteins.
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Affiliation(s)
- Kaur Manindar
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Huang Zhen
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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9
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Patchornik G, Danino D, Kesselman E, Wachtel E, Friedman N, Sheves M. Purification of a membrane protein with conjugated engineered micelles. Bioconjug Chem 2013; 24:1270-5. [PMID: 23758098 DOI: 10.1021/bc400069w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A novel method for purifying membrane proteins is presented. The approach makes use of engineered micelles composed of a nonionic detergent, β-octylglucoside, and a hydrophobic metal chelator, bathophenanthroline. Via the chelators, the micelles are specifically conjugated, i.e., tethered, in the presence of Fe(2+) ions, thereby forming micellar aggregates which provide the environment for separation of lipid-soluble membrane proteins from water-soluble proteins. The micellar aggregates (here imaged by cryo-transmission electron microscopy) successfully purify the light driven proton pump, bacteriorhodopsin (bR), from E. coli lysate. Purification takes place within 15 min and can be performed both at room temperature and at 4 °C. More than 94% of the water-soluble macromolecules in the lysate are excluded, with recovery yields of the membrane protein ranging between 74% and 85%. Since this approach does not require precipitants, high concentrations of detergent to induce micellar aggregates, high temperature, or changes in pH, it is suggested that it may be applied to the purification of a wide variety of membrane proteins.
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Affiliation(s)
- Guy Patchornik
- Department of Biological Chemistry, Ariel University, 70400, Israel.
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10
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Johnson MC, Schmidt-Krey I. Two-dimensional crystallization by dialysis for structural studies of membrane proteins by the cryo-EM method electron crystallography. Methods Cell Biol 2013; 113:325-37. [PMID: 23317909 DOI: 10.1016/b978-0-12-407239-8.00015-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Two-dimensional (2D) crystals of integral membrane proteins, comprising ordered protein reconstituted into a synthetic lipid bilayer, can be induced to form from detergent solubilized and purified membrane protein sources via the addition of exogenous lipid and the subsequent removal of the solubilizing detergent. This is most commonly accomplished by dialysis of a small volume of ternary protein-detergent-lipid mixture against a large volume of buffer, and can be carried out using common, easily available materials. Following successful crystallization, electron crystallographic data obtained by electron cryo-microscopy (cryo-EM) of vitrified 2D crystals can be used to determine the structure of the lipid bilayer-embedded integral membrane protein.
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Affiliation(s)
- Matthew C Johnson
- Georgia Institute of Technology, School of Biology, Atlanta, GA, USA
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11
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Pfefferkorn CM, Jiang Z, Lee JC. Biophysics of α-synuclein membrane interactions. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1818:162-71. [PMID: 21819966 PMCID: PMC3249522 DOI: 10.1016/j.bbamem.2011.07.032] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 07/20/2011] [Accepted: 07/21/2011] [Indexed: 12/14/2022]
Abstract
Membrane proteins participate in nearly all cellular processes; however, because of experimental limitations, their characterization lags far behind that of soluble proteins. Peripheral membrane proteins are particularly challenging to study because of their inherent propensity to adopt multiple and/or transient conformations in solution and upon membrane association. In this review, we summarize useful biophysical techniques for the study of peripheral membrane proteins and their application in the characterization of the membrane interactions of the natively unfolded and Parkinson's disease (PD) related protein, α-synuclein (α-syn). We give particular focus to studies that have led to the current understanding of membrane-bound α-syn structure and the elucidation of specific membrane properties that affect α-syn-membrane binding. Finally, we discuss biophysical evidence supporting a key role for membranes and α-syn in PD pathogenesis. This article is part of a Special Issue entitled: Membrane protein structure and function.
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Affiliation(s)
- Candace M. Pfefferkorn
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Zhiping Jiang
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Jennifer C. Lee
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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12
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Detecting CD20-Rituximab interaction forces using AFM single-molecule force spectroscopy. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11434-011-4789-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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13
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Wan CK, Han W, Wu YD. Parameterization of PACE Force Field for Membrane Environment and Simulation of Helical Peptides and Helix–Helix Association. J Chem Theory Comput 2011; 8:300-13. [DOI: 10.1021/ct2004275] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Cheuk-Kin Wan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Wei Han
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yun-Dong Wu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- School of Chemical Biology and Biotechnology, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- College of Chemistry, Peking University, Beijing, 100871, China
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14
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Underbakke ES, Zhu Y, Kiessling LL. Protein footprinting in a complex milieu: identifying the interaction surfaces of the chemotaxis adaptor protein CheW. J Mol Biol 2011; 409:483-95. [PMID: 21463637 PMCID: PMC3179904 DOI: 10.1016/j.jmb.2011.03.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 03/16/2011] [Accepted: 03/17/2011] [Indexed: 10/18/2022]
Abstract
Characterizing protein-protein interactions in a biologically relevant context is important for understanding the mechanisms of signal transduction. Most signal transduction systems are membrane associated and consist of large multiprotein complexes that undergo rapid reorganization--circumstances that present challenges to traditional structure determination methods. To study protein-protein interactions in a biologically relevant complex milieu, we employed a protein footprinting strategy based on isotope-coded affinity tag (ICAT) reagents. ICAT reagents are valuable tools for proteomics. Here, we show their utility in an alternative application--they are ideal for protein footprinting in complex backgrounds because the affinity tag moiety allows for enrichment of alkylated species prior to analysis. We employed a water-soluble ICAT reagent to monitor cysteine accessibility and thereby to identify residues involved in two different protein-protein interactions in the Escherichia coli chemotaxis signaling system. The chemotaxis system is an archetypal transmembrane signaling pathway in which a complex protein superstructure underlies sophisticated sensory performance. The formation of this superstructure depends on the adaptor protein CheW, which mediates a functionally important bridging interaction between transmembrane receptors and histidine kinase. ICAT footprinting was used to map the surfaces of CheW that interact with the large multidomain histidine kinase CheA, as well as with the transmembrane chemoreceptor Tsr in native E. coli membranes. By leveraging the affinity tag, we successfully identified CheW surfaces responsible for CheA-Tsr interaction. The proximity of the CheA and Tsr binding sites on CheW suggests the formation of a composite CheW-Tsr surface for the recruitment of the signaling kinase to the chemoreceptor complex.
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Affiliation(s)
- Eric S Underbakke
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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15
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Mijajlovic M, Biggs MJ, Djurdjevic DP. On potential energy models for EA-based ab initio protein structure prediction. EVOLUTIONARY COMPUTATION 2010; 18:255-275. [PMID: 20210597 DOI: 10.1162/evco.2010.18.2.18204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Ab initio protein structure prediction involves determination of the three-dimensional (3D) conformation of proteins on the basis of their amino acid sequence, a potential energy (PE) model that captures the physics of the interatomic interactions, and a method to search for and identify the global minimum in the PE (or free energy) surface such as an evolutionary algorithm (EA). Many PE models have been proposed over the past three decades and more. There is currently no understanding of how the behavior of an EA is affected by the PE model used. The study reported here shows that the EA behavior can be profoundly affected: the EA performance obtained when using the ECEPP PE model is significantly worse than that obtained when using the Amber, OPLS, and CVFF PE models, and the optimal EA control parameter values for the ECEPP model also differ significantly from those associated with the other models.
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Affiliation(s)
- Milan Mijajlovic
- Exobiology Branch, NASA Ames Research Center, Mail-Stop 239-4, Moffett Field, California 94035, USA
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16
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In Cubo Crystallization of Membrane Proteins. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/b978-0-12-381266-7.00009-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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17
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Zhao G, Johnson MC, Schnell JR, Kanaoka Y, Haase W, Irikura D, Lam BK, Schmidt-Krey I. Two-dimensional crystallization conditions of human leukotriene C4 synthase requiring adjustment of a particularly large combination of specific parameters. J Struct Biol 2009; 169:450-4. [PMID: 19903529 DOI: 10.1016/j.jsb.2009.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 11/03/2009] [Accepted: 11/05/2009] [Indexed: 11/29/2022]
Abstract
Human leukotriene C(4) synthase (LTC(4)S) forms highly ordered two-dimensional (2D) crystals under specific reconstitution conditions. It was found that control of a larger number of parameters than is usually observed for 2D crystallization of membrane proteins was necessary to induce crystal formation of LTC(4)S. Here, we describe the parameters that were optimized to yield large and well-ordered 2D crystals of LTC(4)S. Careful fractioning of eluates during the protein purification was essential for obtaining crystals. While the lipid-to-protein ratio was critical in obtaining order, four parameters were decisive in inducing growth of crystals that were up to several microns in size. To obtain a favorable diameter, salt, temperature, glycerol, and initial detergent concentration had to be controlled with great care. Interestingly, several crystal forms could be grown, namely the plane group symmetries of p2, p3, p312, and two different unit cell sizes of plane group symmetry p321.
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Affiliation(s)
- G Zhao
- Georgia Institute of Technology, School of Biology, School of Chemistry and Biochemistry, 310 Ferst Drive, Atlanta, GA 30332, USA
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18
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Abstract
At the cross-roads of nanoscience and microbiology, the nanoscale analysis of microbial cells using atomic force microscopy (AFM) is an exciting, rapidly evolving research field. Over the past decade, there has been tremendous progress in our use of AFM to observe membrane proteins and live cells at high resolution. Remarkable advances have also been made in applying force spectroscopy to manipulate single membrane proteins, to map surface properties and receptor sites on cells and to measure cellular interactions at the single-cell and single-molecule levels. In addition, recent developments in cantilever nanosensors have opened up new avenues for the label-free detection of microorganisms and bioanalytes.
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Affiliation(s)
- Yves F Dufrêne
- Unité de chimie des interfaces, Université catholique de Louvain, Croix du Sud 2/18, B-1348 Louvain-la-Neuve, Belgium.
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19
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Tjong SC, Wu PL, Wang CM, Huang WN, Ho NL, Wu WG. Role of Glycosphingolipid Conformational Change in Membrane Pore Forming Activity of Cobra Cardiotoxin. Biochemistry 2007; 46:12111-23. [DOI: 10.1021/bi700871x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Siu-Cin Tjong
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, National Synchrotron Radiation Research Center, and Yuan Pei University, Hsinchu, Taiwan
| | - Po-Long Wu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, National Synchrotron Radiation Research Center, and Yuan Pei University, Hsinchu, Taiwan
| | - Chang-Mao Wang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, National Synchrotron Radiation Research Center, and Yuan Pei University, Hsinchu, Taiwan
| | - Wei-Ning Huang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, National Synchrotron Radiation Research Center, and Yuan Pei University, Hsinchu, Taiwan
| | - Nan-Lu Ho
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, National Synchrotron Radiation Research Center, and Yuan Pei University, Hsinchu, Taiwan
| | - Wen-guey Wu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, National Synchrotron Radiation Research Center, and Yuan Pei University, Hsinchu, Taiwan
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20
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Cruzeiro-Silva C, Gomes-Neto F, Tinoco LW, Cilli EM, Barros PVR, Lapido-Loureiro PA, Bisch PM, Almeida FCL, Valente AP. Structural biology of membrane-acting peptides: conformational plasticity of anticoccidial peptide PW2 probed by solution NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3182-92. [PMID: 17927950 DOI: 10.1016/j.bbamem.2007.08.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 08/22/2007] [Accepted: 08/24/2007] [Indexed: 10/22/2022]
Abstract
The bottleneck for the complete understanding of the structure-function relationship of flexible membrane-acting peptides is its dynamics. At the same time, not only the structure but also the dynamics are the key points for their mechanism of action. Our model is PW2, a TRP-rich, cationic peptide selected from phage display libraries that shows anticoccidial activity against Eimeria acervulina. In this manuscript we used a combination of several NMR techniques to tackle these difficulties. The structural features of the membrane-acting peptide PW2 was studied in several membrane mimetic environments: we compared the structural features of PW2 in SDS and DPC micelles, that were reported earlier, with the structure properties in different lipid vesicles and the peptide free in water. We were able to unify the structural information obtained in each of these systems. The structural constraints of the peptide free in water were fundamental for the understanding of plasticity necessary for the membrane interaction. Our data suggested that the WWR sequence is the region responsible for anchoring the peptide to the interfaces, and that this same region displays some degree of conformational order in solution. For PW2, we found that affinity is related to the aromatic region, by anchoring the peptide to the membrane, and specificity is related to the N- and C-termini, which are able to accommodate in the membrane due to its plasticity.
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Affiliation(s)
- C Cruzeiro-Silva
- Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
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21
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Djurdjevic DP, Biggs MJ. Ab initio protein fold prediction using evolutionary algorithms: influence of design and control parameters on performance. J Comput Chem 2007; 27:1177-95. [PMID: 16752367 DOI: 10.1002/jcc.20440] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
True ab initio prediction of protein 3D structure requires only the protein primary structure, a physicochemical free energy model, and a search method for identifying the free energy global minimum. Various characteristics of evolutionary algorithms (EAs) mean they are in principle well suited to the latter. Studies to date have been less than encouraging, however. This is because of the limited consideration given to EA design and control parameter issues. A comprehensive study of these issues was, therefore, undertaken for ab initio protein fold prediction using a full atomistic protein model. The performance and optimal control parameter settings of twelve EA designs where first established using a 15-residue polyalanine molecule-design aspects varied include the encoding alphabet, crossover operator, and replacement strategy. It can be concluded that real encoding and multipoint crossover are superior, while both generational and steady-state replacement strategies have merits. The scaling between the optimal control parameter settings and polyalanine size was also identified for both generational and steady-state designs based on real encoding and multipoint crossover. Application of the steady-state design to met-enkephalin indicated that these scalings are potentially transferable to real proteins. Comparison of the performance of the steady state design for met-enkephalin with other ab initio methods indicates that EAs can be competitive provided the correct design and control parameter values are used.
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Affiliation(s)
- Dusan P Djurdjevic
- Institute for Materials and Processes, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JL, United Kingdom
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22
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White MA, Clark KM, Grayhack EJ, Dumont ME. Characteristics affecting expression and solubilization of yeast membrane proteins. J Mol Biol 2007; 365:621-36. [PMID: 17078969 PMCID: PMC1839945 DOI: 10.1016/j.jmb.2006.10.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 09/27/2006] [Accepted: 10/03/2006] [Indexed: 11/26/2022]
Abstract
Biochemical and structural analysis of membrane proteins often critically depends on the ability to overexpress and solubilize them. To identify properties of eukaryotic membrane proteins that may be predictive of successful overexpression, we analyzed expression levels of the genomic complement of over 1000 predicted membrane proteins in a recently completed Saccharomyces cerevisiae protein expression library. We detected statistically significant positive and negative correlations between high membrane protein expression and protein properties such as size, overall hydrophobicity, number of transmembrane helices, and amino acid composition of transmembrane segments. Although expression levels of membrane and soluble proteins exhibited similar negative correlations with overall hydrophobicity, high-level membrane protein expression was positively correlated with the hydrophobicity of predicted transmembrane segments. To further characterize yeast membrane proteins as potential targets for structure determination, we tested the solubility of 122 of the highest expressed yeast membrane proteins in six commonly used detergents. Almost all the proteins tested could be solubilized using a small number of detergents. Solubility in some detergents depended on protein size, number of transmembrane segments, and hydrophobicity of predicted transmembrane segments. These results suggest that bioinformatic approaches may be capable of identifying membrane proteins that are most amenable to overexpression and detergent solubilization for structural and biochemical analyses. Bioinformatic approaches could also be used in the redesign of proteins that are not intrinsically well-adapted to such studies.
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Affiliation(s)
- Michael A. White
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642
| | - Kathleen M. Clark
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642
| | - Elizabeth J. Grayhack
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642
| | - Mark E. Dumont
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642
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23
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Perry JL, Dembla-Rajpal N, Hall LA, Pritchard JB. A three-dimensional model of human organic anion transporter 1: aromatic amino acids required for substrate transport. J Biol Chem 2006; 281:38071-9. [PMID: 17038320 PMCID: PMC1847411 DOI: 10.1074/jbc.m608834200] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Organic anion transporters (OATs) play a critical role in the handling of endogenous and exogenous organic anions by excretory and barrier tissues. Little is known about the OAT three-dimensional structure or substrate/protein interactions involved in transport. In this investigation, a theoretical three-dimensional model was generated for human OAT1 (hOAT1) based on fold recognition to the crystal structure of the glycerol 3-phosphate transporter (GlpT) from Escherichia coli. GlpT and hOAT1 share several sequence motifs as major facilitator superfamily members. The structural hOAT1 model shows that helices 5, 7, 8, 10, and 11 surround an electronegative putative active site ( approximately 830A(3)). The site opens to the cytoplasm and is surrounded by three residues not previously examined for function (Tyr(230) (domain 5) and Lys(431) and Phe(438) (domain 10)). Effects of these residues on p-aminohippurate (PAH) and cidofovir transport were assessed by point mutations in a Xenopus oocyte expression system. Membrane protein expression was severely limited for the Y230A mutant. For the K431A and F438A mutants, [(3)H]PAH uptake was less than 30% of wild-type hOAT1 uptake after protein expression correction. Reduced V(max) values for the F438A mutant confirmed lower protein expression. In addition, the F438A mutant exhibited an increased affinity for cidofovir but was not significantly different for PAH. Differences in handling of PAH and cidofovir were also observed for the Y230F mutant. Little uptake was determined for cidofovir, whereas PAH uptake was similar to wild-type hOAT1. Therefore, the hOAT1 structural model has identified two new residues, Tyr(230) and Phe(438), which are important for substrate/protein interactions.
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Affiliation(s)
| | | | | | - John B. Pritchard
- To whom correspondence should be addressed: P. O. Box 12233, F1-03 Research Triangle Park, NC 27709. Tel.: 919-541-4054; Fax: 919-541-5737; E-mail:
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24
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Chugunov AO, Farce A, Chavatte P, Efremov RG. Differences in Binding Sites of Two Melatonin Receptors Help to Explain Their Selectivity to Some Melatonin Analogs: A Molecular Modeling Study. J Biomol Struct Dyn 2006; 24:91-107. [PMID: 16928133 DOI: 10.1080/07391102.2006.10507103] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Numerous diseases have been linked to the malfunction of G-protein coupled receptors (GPCRs). Their adequate treatment requires rational design of new high-affinity and high-selectivity drugs targeting these receptors. In this work, we report three-dimensional models of the human MT(1) and MT(2) melatonin receptors, members of the GPCR family. The models are based on the X-ray structure of bovine rhodopsin. The computational approach employs an original procedure for optimization of receptor-ligand structures. It includes rotation of one of the transmembrane alpha-helices around its axis with simultaneous assessment of quality of the resulting complexes according to a number of criteria we have developed for this purpose. The optimal geometry of the receptor-ligand binding is selected based on the analysis of complementarity of hydrophobic/hydrophilic properties between the ligand and its protein environment in the binding site. The elaborated "optimized" models are employed to explore the details of protein-ligand interactions for melatonin and a number of its analogs with known affinity to MT(1) and MT(2) receptors. The models permit rationalization of experimental data, including those that were not used in model building. The perspectives opened by the constructed models and by the optimization procedure in the design of new drugs are discussed.
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Affiliation(s)
- Anton O Chugunov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, GSP Moscow, 117997, Russia.
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25
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Lekka M, Laidler P, Labedź M, Kulik AJ, Lekki J, Zajac W, Stachura Z. Specific Detection of Glycans on a Plasma Membrane of Living Cells with Atomic Force Microscopy. ACTA ACUST UNITED AC 2006; 13:505-12. [PMID: 16720271 DOI: 10.1016/j.chembiol.2006.03.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Revised: 03/13/2006] [Accepted: 03/13/2006] [Indexed: 01/30/2023]
Abstract
Among the many alterations of cancer cells is the expression of different surface oligosaccharides. In this work, oligosaccharide expression in living cells (cancer and reference ones) was studied with atomic force microscopy by using lectins as probes. The unbinding force obtained for the same lectin type (concanavalin A or Sambucus nigra) suggested slightly dissimilar structures of binding sites of the same ligand type. For the lectin from Phaseolus vulgaris, a much larger unbinding force indicated a distinct structure of the binding site in cancer cells. The unbinding probability confirmed a higher content of both sialic acid and mannose-containing ligands in cancer and reference cells, respectively. These results demonstrate the potential of atomic force microscopy to directly probe the presence of molecules on a living cell surface, together with the quantitative description of their expression.
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Affiliation(s)
- Małgorzata Lekka
- The Henryk Niewodniczański Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Kraków, Poland.
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26
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Camp PJ, Duncan PD. Two-dimensional structure in a generic model of triangular proteins and protein trimers. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 73:046111. [PMID: 16711882 DOI: 10.1103/physreve.73.046111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2005] [Indexed: 05/09/2023]
Abstract
Motivated by the diversity and complexity of two-dimensional (2D) crystals formed by triangular proteins and protein trimers, we have investigated the structures and phase behavior of hard-disk trimers. In order to mimic specific binding interactions, each trimer possesses an "attractive" disk which can interact with similar disks on other trimers via an attractive square-well potential. At low density and low temperature, the fluid phase mainly consists of tetramers, pentamers, or hexamers. Hexamers provide the structural motif for a high-density, low-temperature periodic solid phase, but we also identify a metastable periodic structure based on a tetramer motif. At high density there is a transition between orientationally ordered and disordered solid phases. The connections between simulated structures and those of 2D protein crystals--as seen in electron microscopy--are briefly discussed.
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Affiliation(s)
- Philip J Camp
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom.
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27
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Kandasamy SK, Larson RG. Molecular dynamics simulations of model trans-membrane peptides in lipid bilayers: a systematic investigation of hydrophobic mismatch. Biophys J 2006; 90:2326-43. [PMID: 16428278 PMCID: PMC1403172 DOI: 10.1529/biophysj.105.073395] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrophobic mismatch, which is the difference between the hydrophobic length of trans-membrane segments of a protein and the hydrophobic width of the surrounding lipid bilayer, is known to play a role in membrane protein function. We have performed molecular dynamics simulations of trans-membrane KALP peptides (sequence: GKK(LA)nLKKA) in phospholipid bilayers to investigate hydrophobic mismatch alleviation mechanisms. By varying systematically the length of the peptide (KALP15, KALP19, KALP23, KALP27, and KALP31) and the lipid hydrophobic length (DLPC, DMPC, and DPPC), a wide range of mismatch conditions were studied. Simulations of durations of 50-200 ns show that under positive mismatch, the system alleviates the mismatch predominantly by tilting the peptide and to a smaller extent by increased lipid ordering in the immediate vicinity of the peptide. Under negative mismatch, alleviation takes place by a combination of local bilayer bending and the snorkeling of the lysine residues of the peptide. Simulations performed at a higher peptide/lipid molar ratio (1:25) reveal slower dynamics of both the peptide and lipid relative to those at a lower peptide/lipid ratio (1:128). The lysine residues have favorable interactions with specific oxygen atoms of the phospholipid headgroups, indicating the preferred localization of these residues at the lipid/water interface.
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Affiliation(s)
- Senthil K Kandasamy
- Chemical Engineering Department, University of Michigan, Ann Arbor, Michigan, USA
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28
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Chang CY, Liao HK, Juo CG, Chen SH, Chen YJ. Improved analysis of membrane protein by PVDF-aided, matrix-assisted laser desorption/ionization mass spectrometry. Anal Chim Acta 2006; 556:237-46. [PMID: 17723354 DOI: 10.1016/j.aca.2005.07.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Revised: 07/13/2005] [Accepted: 07/14/2005] [Indexed: 11/30/2022]
Abstract
Characterization of membrane proteins remains an analytical challenge because of difficulties associated with tedious isolation and purification. This study presents the utility of the polyvinylidene difluoride (PVDF) membrane for direct sub-proteome profiling and membrane protein characterization by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The hydrophobic adsorption of protein, particularly membrane proteins, on the PVDF surface enables efficient on-PVDF washing to remove high concentrations of detergents and salts, such as up to 5% sodium dodecyl sulfate (SDS). The enhanced spectrum quality for MALDI detection is particularly notable for high molecular weight proteins. By using on-PVDF washing prior to MALDI detection, we obtained protein profiles of the detergent-containing and detergent-insoluble membrane fractions from Methylococcus capsulatus (Bath). Similar improvements of signal-to-noise ratios were shown on the MALDI spectra for proteins electroblotted from SDS-polyacrylamide gel electrophoresis (SDS-PAGE) onto the PVDF membrane. We have applied this strategy to obtain intact molecular weights of the particulate methane monooxygenase (pMMO) composed of three intrinsic membrane-bound proteins, PmoA, PmoB, and PmoC. Together with peptide sequencing by tandem mass spectrometry, post-translational modifications including N-terminal acetylation of PmoA and PmoC and alternative C-terminal truncation of PmoB were identified. The above results show that PVDF-aided MALDI-MS can be an effective approach for profiling and characterization of membrane proteins.
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Affiliation(s)
- Chih-Yang Chang
- Institute of Chemistry, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan, ROC
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29
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Laurinmäki PA, Huiskonen JT, Bamford DH, Butcher SJ. Membrane Proteins Modulate the Bilayer Curvature in the Bacterial Virus Bam35. Structure 2005; 13:1819-28. [PMID: 16338410 DOI: 10.1016/j.str.2005.08.020] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2005] [Revised: 08/19/2005] [Accepted: 08/21/2005] [Indexed: 11/17/2022]
Abstract
Biological membranes control the flow of molecules into and out of cells, and they transmit information about the milieu. Structural studies of membrane-containing viruses provide one way to study these membranes in situ. Cryo-electron microscopy and image reconstruction of bacteriophage Bam35 to 7.3 A resolution revealed a membrane bilayer constrained within an icosahedrally symmetric pseudo T = 25 capsid. A total of 60 large transmembrane protein complexes affect the curvature and thickness of the membrane. Here, we describe these membrane parameters quantitatively. Furthermore, we show that Bam35 differs from bacteriophage PRD1 in these parameters, even though the two viruses share the same principles of capsid architecture. Most notably, each virus possesses a tape measure protein suggesting a general mechanism for capsid size determination in icosahedral viruses.
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Affiliation(s)
- Pasi Antero Laurinmäki
- Institute of Biotechnology and Department of Biological and Environmental Sciences, Viikki Biocenter, University of Helsinki, P.O. Box 65 (Viikinkaari 1), 00014 University of Helsinki, Finland
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30
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Maragakis P, Karplus M. Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase. J Mol Biol 2005; 352:807-22. [PMID: 16139299 DOI: 10.1016/j.jmb.2005.07.031] [Citation(s) in RCA: 251] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2005] [Revised: 06/06/2005] [Accepted: 07/12/2005] [Indexed: 10/25/2022]
Abstract
The plastic network model (PNM) is used to generate a conformational change pathway for Escherichia coli adenylate kinase based on two crystal structures, namely that of an open and a closed conformer. In this model, the energy basins corresponding to known conformers are connected at their lowest common energies. The results are used to evaluate and analyze the minimal energy pathways between these basins. The open to closed transition analysis provides an identification of hinges that is in agreement with the existing definitions based on the available X-ray structures. The elastic energy distribution and the C(alpha) pseudo-dihedral variation provide similar information on these hinges. The ensemble of the 45 published structures for this protein and closely related proteins is shown to always be within 3.0 A of the pathway, which corresponds to a conformational change between two end structures that differ by a C(alpha)-atom root-mean-squared deviation of 7.1A.
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Affiliation(s)
- Paul Maragakis
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge MA 02138, USA.
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31
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Raval MK, Biswal B, Biswal UC. The mystery of oxygen evolution: analysis of structure and function of photosystem II, the water-plastoquinone oxido-reductase. PHOTOSYNTHESIS RESEARCH 2005; 85:267-93. [PMID: 16170631 DOI: 10.1007/s11120-005-8163-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2004] [Accepted: 05/26/2005] [Indexed: 05/04/2023]
Abstract
Photosystem II (PS II) of thylakoid membrane of photosynthetic organisms has drawn attention of researchers over the years because it is the only system on Earth that provides us with oxygen that we breathe. In the recent past, structure of PS II has been the focus of research in plant science. The report of X-ray crystallographic structure of PS II complex by the research groups of James Barber and So Iwata in UK is a milestone in the area of research in photosynthesis. It follows the pioneering and elegant work from the laboratories of Horst Witt and W. Saenger in Germany, and J. Shen in Japan. It is time to analyze the historic events during the long journey made by the researchers to arrive at this point. This review makes an attempt to critically review the growth of the advancement of concepts and knowledge on the photosystem in the background of technological development. We conclude the review with perspectives on research and technology that should reveal the complete story of PS II of thylakoid in the future.
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Affiliation(s)
- M K Raval
- P.G. Department of Chemistry, Government College, Sundargarh, Orissa, India.
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32
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Farès C, Qian J, Davis JH. Magic angle spinning and static oriented sample NMR studies of the relaxation in the rotating frame of membrane peptides. J Chem Phys 2005. [DOI: 10.1063/1.1899645] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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33
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Liu F, Mizukami H, Sarnaik S, Ostafin A. Calcium-dependent human erythrocyte cytoskeleton stability analysis through atomic force microscopy. J Struct Biol 2005; 150:200-10. [PMID: 15866743 DOI: 10.1016/j.jsb.2005.02.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2004] [Revised: 01/23/2005] [Indexed: 11/21/2022]
Abstract
Erythrocytes affected by age and diseases such as sickle cell anemia, hypertension, diabetes, etc., exhibit abnormally high intracellular Ca2+ ion levels, and appear to have altered cytoskeleton properties. It has been proposed that extra binding of Ca2+ to membrane-associated calmodulin attenuates the spectrin-ankyrin-Band 3 tether of the cytoskeleton to the cytoplasmic membrane and might change the cytoskeleton structure. Due to the close apposition of the network, direct observation of such a structural change in vivo is restricted. In this study, atomic force microscopy and quantitative image analysis were applied to investigate the structural change of young healthy erythrocyte cytoskeletons upon extra Ca2+ binding to the cytoplasmic membrane in vitro. The results show that extra Ca2+ binding increased the cytoskeleton rigidity and prevented spectrin aggregation during sample preparation. The cytoskeleton morphology observed in Ca2+ -incubated healthy young cell were similar to the glutaraldehyde-fixed healthy young cells.
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Affiliation(s)
- Fei Liu
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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34
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Mukhopadhyay S, Kuhn RJ, Rossmann MG. A structural perspective of the flavivirus life cycle. Nat Rev Microbiol 2005; 3:13-22. [PMID: 15608696 DOI: 10.1038/nrmicro1067] [Citation(s) in RCA: 838] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dengue, Japanese encephalitis, West Nile and yellow fever belong to the Flavivirus genus, which is a member of the Flaviviridae family. They are human pathogens that cause large epidemics and tens of thousands of deaths annually in many parts of the world. The structural organization of these viruses and their associated structural proteins has provided insight into the molecular transitions that occur during the viral life cycle, such as assembly, budding, maturation and fusion. This review focuses mainly on structural studies of dengue virus.
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Affiliation(s)
- Suchetana Mukhopadhyay
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47907-2054, USA
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35
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Li H, Qian L, Chen Z, Thibault D, Liu G, Liu T, Thanassi DG. The Outer Membrane Usher Forms a Twin-pore Secretion Complex. J Mol Biol 2004; 344:1397-407. [PMID: 15561151 DOI: 10.1016/j.jmb.2004.10.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2004] [Revised: 09/24/2004] [Accepted: 10/06/2004] [Indexed: 10/26/2022]
Abstract
The PapC usher is an outer membrane protein required for assembly and secretion of P pili in uropathogenic Escherichia coli. P pilus biogenesis occurs by the chaperone/usher pathway, a terminal branch of the general secretory pathway. Periplasmic chaperone-subunit complexes target to the PapC usher for fiber assembly and secretion through the usher to the cell surface. The molecular details of pilus biogenesis at the usher, and protein secretion across the outer membrane in general, are unclear. We studied the structure and oligomeric state of PapC by gel filtration, dynamic light scattering, and electron microscopy and image analysis. Two-dimensional crystals of wild-type PapC and a C-terminal deletion mutant of PapC were produced by reconstituting detergent purified usher into E.coli lipids. PapC formed a dimer both in detergent solution and in the phospholipid bilayer. Cryo-electron microscopy revealed that the usher forms a twin-pore complex. Removal of the C-terminal domain did not change the basic shape of the PapC molecule, but altered the dimeric association of the usher, suggesting that the C terminus forms part of the dimerization interface. The overall molecular size (11 nm), pore size (2 nm), and twin-pore configuration of PapC resemble that of the Tom40 complex, a mitochondrial outer membrane protein translocase.
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Affiliation(s)
- Huilin Li
- Biology Department, Brookhaven National Laboratory, 50 Bell Ave, Upton, NY 11973, USA
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36
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Harauz G, Ishiyama N, Hill CMD, Bates IR, Libich DS, Farès C. Myelin basic protein-diverse conformational states of an intrinsically unstructured protein and its roles in myelin assembly and multiple sclerosis. Micron 2004; 35:503-42. [PMID: 15219899 DOI: 10.1016/j.micron.2004.04.005] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The 18.5 kDa isoform of myelin basic protein (MBP) is a major component of the myelin sheath in the central nervous system of higher vertebrates, and a member of a larger family of proteins with a multiplicity of forms and post-translational modifications (PTMs). The 18.5 kDa protein is the exemplar of the family, being most abundant in adult myelin, and thus the most-studied. It is peripherally membrane-associated, but has generally been investigated in isolated form. MBP is an 'intrinsically unstructured' protein with a high proportion (approximately 75%) of random coil, but postulated to have core elements of beta-sheet and alpha-helix. We review here the properties of the MBP family, especially of the 18.5 kDa isoform, and discuss how its three-dimensional (3D) structure may be resolved by direct techniques available to us, viz., X-ray and electron crystallography, and solution and solid-state NMR spectrometry. In particular, we emphasise that creating an appropriate environment in which the protein can adopt a physiologically relevant fold is crucial to such endeavours. By solving the 3D structure of 18.5 kDa MBP and the effects of PTMs, we will attain a better understanding of myelin architecture, and of the molecular mechanisms that transpire in demyelinating diseases such as multiple sclerosis.
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Affiliation(s)
- George Harauz
- Department of Molecular Biology and Genetics, Biophysics Interdepartmental Group, University of Guelph, Room 230, Axelrod Building, 50 Stone Road East, Guelph, Ont., Canada N1G 2W1.
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37
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Abstract
YiiP is a 32.9-kDa metal transporter found in the plasma membrane of Escherichia coli (Chao, Y., and Fu, D. (2004) J. Biol. Chem. 279, 17173-17180). Here we report the determination of the YiiP oligomeric state in detergent-lipid micelles and in membranes. Molecular masses of YiiP solubilized with dodecyl-, undecyl-, decyl-, or nonyl-beta-d-maltoside were measured directly using size-exclusion chromatography coupled with laser light-scattering photometry, yielding a mass distribution of YiiP homo-oligomers within a narrow range (68.0-68.8 kDa) that equals the predicted mass of a YiiP dimer within experimental error. The detergent-lipid masses associated with YiiP in the mixed micelles were found to increase from 135.5 to 232.6 kDa, with an apparent correlation with the alkyl chain length of the maltoside detergents. Cross-linking the detergent-solubilized YiiP with 1-ethyl-3-[3-dimethylaminopropyl] carbodiimide hydrochloride (EDC) resulted in a dimeric cross-linked product in an EDC concentration-dependent manner. The oligomeric state of the purified YiiP in reconstituted membranes was determined by electron microscopic analysis of two-dimensional YiiP crystals in negative stain. A projection structure calculated from measurable optical diffractions to 25 A revealed a pseudo-2-fold symmetry within a molecular boundary of approximately 75 x 40 A, indicative of the presence of YiiP dimers in membranes. These data provide direct structural evidence for a dimeric association of YiiP both in detergent-lipid micelles and in the reconstituted lipid bilayer. The functional relevance of the dimeric association in YiiP is discussed.
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Affiliation(s)
- Yinan Wei
- Department of Biology, Brookhaven National Laboratory, Upton, New York 11973, USA
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38
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Ki JJ, Kawarasaki Y, Gam J, Harvey BR, Iverson BL, Georgiou G. A Periplasmic Fluorescent Reporter Protein and its Application in High-throughput Membrane Protein Topology Analysis. J Mol Biol 2004; 341:901-9. [PMID: 15328603 DOI: 10.1016/j.jmb.2004.05.078] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We have developed a periplasmic fluorescent reporter protein suitable for high-throughput membrane protein topology analysis in Escherichia coli. The reporter protein consists of a single chain (scFv) antibody fragment that binds to a fluorescent hapten conjugate with high affinity. Fusion of the scFv to membrane protein sites that are normally exposed in the periplasmic space tethers the scFv onto the inner membrane. Following permealization of the outer membrane to allow diffusion of the fluorescent hapten into the periplasm, binding to the anchored scFv renders the cells fluorescent. We show that cell fluorescence is an accurate and sensitive reporter of the location of residues within periplasmic loops. For topological analysis, a set of nested deletions in the membrane protein gene is employed to construct two libraries of gene fusions, one to the scFvand one to the cytoplasmic reporter green fluorescent protein (GFP). Fluorescent clones are isolated by flow cytometry and the sequence of the fusion junctions is determined to identify amino acid residues within periplasmic and cytoplasmic loops, respectively. We applied this methodology to the topology analysis of E. coli TatC protein for which previous studies had led to conflicting results. The ease of screening libraries of fusions by flow cytometry enabled the rapid identification of almost 90 highly fluorescent scFv and GFP fusions, which, in turn, allowed the fine mapping of TatC membrane topology.
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Affiliation(s)
- Jun Jeong Ki
- Department of Chemical Engineering, University of Texas, Austin 78712, USA
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39
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Lekka M, Laidler P, Dulińska J, Łabedź M, Pyka G. Probing molecular interaction between concanavalin A and mannose ligands by means of SFM. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2004; 33:644-50. [PMID: 15138737 DOI: 10.1007/s00249-004-0412-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2003] [Revised: 11/12/2003] [Accepted: 03/31/2004] [Indexed: 10/26/2022]
Abstract
Recently, the scanning force microscope (SFM) has been widely used for direct monitoring of specific interactions between biologically active molecules. Such studies have employed the SFM liquid-cell setup, which allows measurements to be made in the native environment with force resolution down to a tenth of a picoNewton. In this study, the ligand-receptor strength of monoclonal anti-human prostatic acid phosphatase and prostatic acid phosphatase, representing an antigen-antibody system with a single type of interaction, was determined. Then, the interaction force occurring between concanavalin A and the carbohydrate component of the glycoproteins arylsulfatase A and carboxypeptidase Y was measured. High mannose-type glycans were sought on the human prostate carcinoma cell surface. Application of an analysis based on the Poisson distribution of the number of bonds formed in all these measured systems allowed the strength of the molecular interaction to be calculated. The values of the force acting between two single molecules were 530+/-25, 790+/-32, and 940+/-39 pN between prostatic acid phosphatase and monoclonal anti-human prostatic acid phosphatase, between concanavalin A and arylsulfatase A, and between concanavalin A and carboxypeptidase Y, respectively. The value calculated from data collected for the force between concanavalin A and mannose-containing ligands present on the surface of human prostate carcinoma cells was smaller, 116+/-17 pN. The different values of the binding force between concanavalin A and mannose-containing ligands were attributed to the structural changes of the carbohydrate components.
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Affiliation(s)
- M Lekka
- The Henryk Niewodniczański Institute of Nuclear Physics, Radzikowskiego 152, 31-342 Cracow, Poland.
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40
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Abstract
The folding degree index (Estrada, Bioinformatics 2002;18:697-704) is extended to account for the contribution of amino acids to folding. First, the mathematical formalism for extending the folding degree index is presented. Then, the amino acid contributions to folding degree of several proteins are used to analyze its relation to secondary structure. The possibilities of using these contributions in helping or checking the assignation of secondary structure to amino acids are also introduced. The influence of external factors to the amino acids contribution to folding degree is studied through the temperature effect on ribonuclease A. Finally, the analysis of 3D protein similarity through the use of amino acid contributions to folding degree is studied by selecting a series of lysozymes. These results are compared to that obtained by sequence alignment (2D similarity) and 3D superposition of the structures, showing the uniqueness of the current approach.
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Affiliation(s)
- Ernesto Estrada
- Safety and Environmental Assurance Centre, Unilever, Colworth House, Sharnbrook, Beds, and RIAIDT, Edificio CACTUS, University of Santiago de Compostela, Spain.
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41
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Bennasroune A, Gardin A, Aunis D, Crémel G, Hubert P. Tyrosine kinase receptors as attractive targets of cancer therapy. Crit Rev Oncol Hematol 2004; 50:23-38. [PMID: 15094157 DOI: 10.1016/j.critrevonc.2003.08.004] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2003] [Indexed: 12/24/2022] Open
Abstract
Receptor tyrosine kinases (RTKs) are the main mediators of the signaling network that transmit extracellular signals into the cell, and control cellular differentiation and proliferation. Recent and rapid advances in our understanding of cellular signaling by receptor tyrosine kinases, in normal and malignant cells, have brought to light the potential of RTKs as selective anti-cancer targets. Their activity is normally tightly controlled and regulated. Overexpression of RTK proteins or functional alterations caused by mutations in the corresponding genes or abnormal stimulation by autocrine growth factor loops contribute to constitutive RTK signaling, resulting in dysregulated cell growth and cancer. The mechanisms of uncontrolled RTK signaling that leads to cancer has provided the rationale for anti-RTK drug development. Herceptin, Gleevec, and Iressa are the first examples of drugs which have successfully translated basic research on oncogenes into cancer therapeutics. RTKs can be viewed as multifunctional targets, and strategies towards the prevention and inhibition of RTK signaling include antibodies, antagonist ligands, small molecule inhibitors of protein kinase activity, and inhibitors of protein-protein interactions. Progresses in the field of rational drug design and computational chemistry will vastly benefit from the availability of increasing structural knowledge of both the kinase domains and the ligand-binding sites of these receptors.
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Affiliation(s)
- Amar Bennasroune
- INSERM Unit 575, 5 rue Blaise Pascal, 67084 Strasbourg Cedex, France
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42
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Lengqvist J, Svensson R, Evergren E, Morgenstern R, Griffiths WJ. Observation of an Intact Noncovalent Homotrimer of Detergent-solubilized Rat Microsomal Glutathione Transferase-1 by Electrospray Mass Spectrometry. J Biol Chem 2004; 279:13311-6. [PMID: 14726533 DOI: 10.1074/jbc.m310958200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microsomal glutathione transferase-1 (MGST1) is a membrane-bound enzyme involved in the detoxification of xenobiotics and the protection of cells against oxidative stress. The proposed active form of the enzyme is a noncovalently associated homotrimer that binds one substrate glutathione molecule/trimer. In this study, this complex has been directly observed by electrospray mass spectrometry analysis of active rat liver MGST1 reconstituted in a minimum amount of detergent. The measured mass of the homotrimer is 53 kDa, allowing for the mass of three MGST molecules in complex with one glutathione molecule. Collision-induced dissociation of the trimer complex resulted in the formation of monomer and homodimer ion species. Two distinct species of homodimer were observed, one unliganded and one identified as a homodimer.glutathione complex. Activation of the enzyme by N-ethylmaleimide through modification of Cys(49) (Svensson, R., Rinaldi, R., Swedmark, S., and Morgenstern, R. (2000) Biochemistry 39, 15144-15149) was monitored by the observation of an appropriate increase in mass in both the denatured monomeric and native trimeric forms of MGST1. Together, the data correspond well with the proposed functional organization of MGST1. These results also represent the first example of direct electrospray mass spectrometry analysis of a detergent-solubilized multimeric membrane protein complex in its native state.
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Affiliation(s)
- Johan Lengqvist
- Department of Medical Biochemistry and Biophysics, Lüdwig Institute for Cancer Research, Stockholm, Sweden
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43
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Abstract
Atomic force microscopy is being used ever more widely in biological imaging, because of its unique ability to provide structural information at the single molecule level and under near-physiological conditions. Detailed topographic images of potential drug targets, such as proteins and DNA, have been produced, and the folding of modular proteins has been studied using single-molecule force spectroscopy. Recently, atomic force microscopy has been used to examine ligand-protein and ligand-DNA interactions, and to begin to determine the architecture of multi-subunit proteins, including a member of the superfamily of ionotropic receptors. Atomic force microscopy is fast becoming a valuable addition to the pharmaceutical industry's toolkit.
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Affiliation(s)
- J Michael Edwardson
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, UK CB2 1PD
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44
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Zhang W, Chipman PR, Corver J, Johnson PR, Zhang Y, Mukhopadhyay S, Baker TS, Strauss JH, Rossmann MG, Kuhn RJ. Visualization of membrane protein domains by cryo-electron microscopy of dengue virus. Nat Struct Mol Biol 2003; 10:907-12. [PMID: 14528291 PMCID: PMC4148076 DOI: 10.1038/nsb990] [Citation(s) in RCA: 341] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2003] [Accepted: 07/30/2003] [Indexed: 12/22/2022]
Abstract
Improved technology for reconstructing cryo-electron microscopy (cryo-EM) images has now made it possible to determine secondary structural features of membrane proteins in enveloped viruses. The structure of mature dengue virus particles was determined to a resolution of 9.5 A by cryo-EM and image reconstruction techniques, establishing the secondary structural disposition of the 180 envelope (E) and 180 membrane (M) proteins in the lipid envelope. The alpha-helical 'stem' regions of the E molecules, as well as part of the N-terminal section of the M proteins, are buried in the outer leaflet of the viral membrane. The 'anchor' regions of E and the M proteins each form antiparallel E-E and M-M transmembrane alpha-helices, leaving their C termini on the exterior of the viral membrane, consistent with the predicted topology of the unprocessed polyprotein. This is one of only a few determinations of the disposition of transmembrane proteins in situ and shows that the nucleocapsid core and envelope proteins do not have a direct interaction in the mature virus.
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Affiliation(s)
- Wei Zhang
- Department of Biological Sciences, Lilly Hall, 915 W. State Street, Purdue University, West Lafayette, Indiana 47907, USA
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45
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Domene C, Bond PJ, Sansom MS. Membrane protein simulations: ion channels and bacterial outer membrane proteins. ADVANCES IN PROTEIN CHEMISTRY 2003; 66:159-93. [PMID: 14631819 DOI: 10.1016/s0065-3233(03)66005-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Carmen Domene
- Laboratory of Molecular Biophysics (LMB), Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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