51
|
Slivka PF, Wong J, Caputo GA, Yin H. Peptide probes for protein transmembrane domains. ACS Chem Biol 2008; 3:402-11. [PMID: 18533658 DOI: 10.1021/cb800049w] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Much current interest in chemical biology focuses on the transmembrane domains of proteins, which have emerged as targets for the development of novel diagnostics and therapeutics. Integral membrane proteins are a group of important biomolecules that play pivotal roles in many cellular activities. Previous studies primarily focused on the extra- and/or intracellular domains of membrane proteins. However, the importance of transmembrane regions in the regulation of protein complexes is beginning to emerge. As such, a number of methods for designing and testing novel exogenous peptides that recognize transmembrane targets and modulate cellular functions have been developed. This Review outlines current methodologies for developing these transmembrane probes that may provide useful tools to study a variety of biological phenomena in the membrane.
Collapse
Affiliation(s)
- Peter F. Slivka
- Department of Chemistry and Biochemistry, 215 UCB, University of Colorado, Boulder, Colorado 80309-0215
| | - Johnny Wong
- Department of Chemistry and Biochemistry, 215 UCB, University of Colorado, Boulder, Colorado 80309-0215
| | - Gregory A. Caputo
- Department of Chemistry and Biochemistry, 201 Mullica Hill Road, Rowan University, Glassboro, New Jersey 08028-1701
| | - Hang Yin
- Department of Chemistry and Biochemistry, 215 UCB, University of Colorado, Boulder, Colorado 80309-0215
| |
Collapse
|
52
|
Suchanova B, Tuma R. Folding and assembly of large macromolecular complexes monitored by hydrogen-deuterium exchange and mass spectrometry. Microb Cell Fact 2008; 7:12. [PMID: 18394161 PMCID: PMC2365927 DOI: 10.1186/1475-2859-7-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Accepted: 04/04/2008] [Indexed: 11/26/2022] Open
Abstract
Recent advances in protein mass spectrometry (MS) have enabled determinations of hydrogen deuterium exchange (HDX) in large macromolecular complexes. HDX-MS became a valuable tool to follow protein folding, assembly and aggregation. The methodology has a wide range of applications in biotechnology ranging from quality control for over-expressed proteins and their complexes to screening of potential ligands and inhibitors. This review provides an introduction to protein folding and assembly followed by the principles of HDX and MS detection, and concludes with selected examples of applications that might be of interest to the biotechnology community.
Collapse
|
53
|
Henriques ST, Quintas A, Bagatolli LA, Homblé F, Castanho MARB. Energy-independent translocation of cell-penetrating peptides occurs without formation of pores. A biophysical study with pep-1. Mol Membr Biol 2007; 24:282-93. [PMID: 17520484 DOI: 10.1080/09687860601142936] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Pep-1 is a cell-penetrating peptide (CPP) with the ability to translocate across biological membranes and introduce active proteins inside cells. The uptake mechanism used by this CPP is, as yet, unknown in detail. Previous results show that such a mechanism is endocytosis-independent and suggests that physical-chemical interactions between the peptide and lipid bilayers govern the translocation mechanism. Formation of a transmembrane pore has been proposed but this issue has always remained controversial. In this work the secondary structure of pep-1 in the absence/presence of lipidic bilayers was determined by CD and ATR-FTIR spectroscopies and the occurrence of pore formation was evaluated through electrophysiological measurements with planar lipid membranes and by confocal microscopy using giant unilamellar vesicles. Despite pep-1 hydrophobic domain tendency for amphipathic alpha-helix conformation in the presence of lipidic bilayers, there was no evidence for membrane pores in the presence of pep-1. Furthermore, alterations in membrane permeability only occurred for high peptide/lipid ratios, which induced the complete membrane disintegration. Such observations indicate that electrostatic interactions are of first importance in the pep-1-membrane interactions and show that pores are not formed. A peptide-lipid structure is probably formed during peptide partition, which favours peptide translocation.
Collapse
Affiliation(s)
- Sónia Troeira Henriques
- Centro de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | | | | | | | | |
Collapse
|
54
|
Svensson FR, Lincoln P, Nordén B, Esbjörner EK. Retinoid Chromophores as Probes of Membrane Lipid Order. J Phys Chem B 2007; 111:10839-48. [PMID: 17711329 DOI: 10.1021/jp072890b] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
There is a great need for development of independent methods to study the structure and function of membrane-associated proteins and peptides. Polarized light spectroscopy (linear dichroism, LD) using shear-aligned lipid vesicles as model membranes has emerged as a promising tool for the characterization of the binding geometry of membrane-bound biomolecules. Here we explore the potential of retinoic acid, retinol, and retinal to function as probes of the macroscopic alignment of shear-deformed 100 nm liposomes. The retinoids display negative LD, proving their preferred alignment perpendicular to the membrane surface. The magnitude of the LD indicates the order retinoic acid > retinol > retinal regarding the degree of orientation in all tested lipid vesicle types. It is concluded that mainly nonspecific electrostatic interactions govern the apparent orientation of the retinoids within the bilayer. We propose a simple model for how the effective orientation may be related to the polarity of the end groups of the retinoid probes, their insertion depths, and their angular distribution of configurations around the membrane normal. Further, we provide evidence that the retinoids can sense subtle structural differences due to variations in membrane composition and we explore the pH sensitivity of retinoic acid, which manifests in variations in absorption maximum wavelength in membranes of varying surface charge. Based on LD measurements on cholesterol-containing liposomes, the influence of membrane constituents on bending rigidity and vesicle deformation is considered in relation to the macroscopic alignment, as well as to lipid chain order on the microscopic scale.
Collapse
Affiliation(s)
- Frida R Svensson
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
| | | | | | | |
Collapse
|
55
|
Parikh SJ, Chorover J. Infrared spectroscopy studies of cation effects on lipopolysaccharides in aqueous solution. Colloids Surf B Biointerfaces 2007; 55:241-50. [PMID: 17275267 DOI: 10.1016/j.colsurfb.2006.12.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Revised: 12/20/2006] [Accepted: 12/20/2006] [Indexed: 11/26/2022]
Abstract
The conformation of amphiphilic lipopolysaccharides (LPS) influences the behavior of free and cell-bound LPS in aqueous environments, including their adhesion to surfaces. Conformational changes in Pseudomonas aeruginosa serotype 10 LPS aggregates resulting from changes in solution pH (3, 6, and 9), ionic strength [I] 1, 10, and 100 mmol L(-1), and electrolyte composition (NaCl and CaCl(2)) were investigated via attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy. ATR-FTIR data indicate that LPS forms more stable aggregates in NaCl relative to CaCl(2) solutions. Time- and cation-dependent changes in ATR-FTIR data suggest that LPS aggregates are perturbed by Ca(2+) complexation at lipid A phosphoryl groups, which leads to reorientation of the lipid A at the surface of a ZnSe ATR internal reflection element (IRE). Polarized ATR-FTIR investigations reveal orientation of LPS dipoles approximately perpendicular to the IRE plane for both Na- and Ca-LPS. The results indicate that changes in solution chemistry strongly impact the conformation, intermolecular and interfacial behavior of LPS in aqueous systems.
Collapse
Affiliation(s)
- Sanjai J Parikh
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ 85721, USA
| | | |
Collapse
|
56
|
Arkin IT. Isotope-edited IR spectroscopy for the study of membrane proteins. Curr Opin Chem Biol 2006; 10:394-401. [PMID: 16935550 PMCID: PMC7185810 DOI: 10.1016/j.cbpa.2006.08.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Accepted: 08/15/2006] [Indexed: 11/25/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy has long been a powerful tool for structural analysis of membrane proteins. However, because of difficulties in resolving contributions from individual residues, most of the derived measurements tend to yield average properties for the system under study. Isotope editing, through its ability to resolve individual vibrations, establishes FTIR as a method that is capable of yielding accurate structural data on individual sites in a protein.
Collapse
Affiliation(s)
- Isaiah T Arkin
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University of Jerusalem, Edmund J Safra Campus, Givat-Ram, Jerusalem, Israel.
| |
Collapse
|
57
|
Li H, Li B, Song H, Breydo L, Baskakov IV, Wang LX. Chemoenzymatic synthesis of HIV-1 V3 glycopeptides carrying two N-glycans and effects of glycosylation on the peptide domain. J Org Chem 2006; 70:9990-6. [PMID: 16292832 DOI: 10.1021/jo051729z] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[structure: see text] A highly efficient chemoenzymatic synthesis of HIV-1 V3 domain glycopeptides carrying two N-linked core tri- and pentasaccharides was achieved. The synthesis consisted of two key steps: a solid-phase synthesis of the cyclic, 47-mer V3 domain peptide containing two GlcNAc residues and a novel endoglycosidase-catalyzed transglycosylation that simultaneously added two N-glycan moieties to the peptide precursor from the oligosaccharide oxazoline donor substrates. The availability of the synthetic glycopeptides allowed the probing of the effects of glycosylation on the HIV-1 V3 domain. It was demonstrated that glycosylation influenced the global conformations of the V3 domain and provided protection of the V3 domain against protease digestion.
Collapse
Affiliation(s)
- Hengguang Li
- Institute of Human Virology and Medical Biotechnology Center, University of Maryland Biotechnology Institute, University of Maryland, 725 W. Lombard Street, Baltimore, Maryland 21201, USA
| | | | | | | | | | | |
Collapse
|
58
|
Arrondo JLR, Coto X, Milicua JCG, Kveder M, Pifat G. Interaction of alcohols with serum LDL. Chem Phys Lipids 2006; 141:205-15. [PMID: 16620801 DOI: 10.1016/j.chemphyslip.2006.02.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2005] [Accepted: 02/20/2006] [Indexed: 11/17/2022]
Abstract
The interaction of low molecular weight alcohols with low density lipoprotein (LDL) has been studied using amide I band-fitting, thermal profiling and two-dimensional infrared correlation spectroscopy (2D-IR). At 0.3 M alcohol, no changes in secondary structure are observed. In the presence of 1 M alcohol, ethanol and propanol decreases protein denaturation temperature and produces changes in the amide I thermal profiles of protein components and in the lipid bands. The 2D-IR synchronous map corresponding to protein or lipid component at 20-37 degrees C suggests differences in the presence of propanol. The asynchronous map corresponding to the lipid component indicates changes in bandwidth, compatible with a more fluid environment. In the 37-80 degrees C temperature range the thermal profile is different in the presence of propanol, both for the lipid and protein components. The results presented show that when alcohols affect the protein component, the lipid spectrum also varies pointing to an effect on the lipid-protein interaction.
Collapse
|
59
|
Churbanova IY, Tronin A, Strzalka J, Gog T, Kuzmenko I, Johansson JS, Blasie JK. Monolayers of a model anesthetic-binding membrane protein: formation, characterization, and halothane-binding affinity. Biophys J 2006; 90:3255-66. [PMID: 16473900 PMCID: PMC1432115 DOI: 10.1529/biophysj.105.072348] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
hbAP0 is a model membrane protein designed to possess an anesthetic-binding cavity in its hydrophilic domain and a cation channel in its hydrophobic domain. Grazing incidence x-ray diffraction shows that hbAP0 forms four-helix bundles that are vectorially oriented within Langmuir monolayers at the air-water interface. Single monolayers of hbAP0 on alkylated solid substrates would provide an optimal system for detailed structural and dynamical studies of anesthetic-peptide interaction via x-ray and neutron scattering and polarized spectroscopic techniques. Langmuir-Blodgett and Langmuir-Schaeffer deposition and self-assembly techniques were used to form single monolayer films of the vectorially oriented peptide hbAP0 via both chemisorption and physisorption onto suitably alkylated solid substrates. The films were characterized by ultraviolet absorption, ellipsometry, circular dichroism, and polarized Fourier transform infrared spectroscopy. The alpha-helical secondary structure of the peptide was retained in the films. Under certain conditions, the average orientation of the helical axis was inclined relative to the plane of the substrate, approaching perpendicular in some cases. The halothane-binding affinity of the vectorially oriented hbAP0 peptide in the single monolayers, with the volatile anesthetic introduced into the moist vapor environment of the monolayer, was found to be similar to that for the detergent-solubilized peptide.
Collapse
Affiliation(s)
- Inna Y Churbanova
- Departments of Chemistry and Anesthesiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
| | | | | | | | | | | | | |
Collapse
|
60
|
Abstract
Here we report the design, synthesis and antibacterial activity of 20 lysine-peptoid hybrids. The hybrids are based on the peptoid lead structure [N-(1-naphthalenemethyl)glycyl]-[N-(4-methylbenzyl)glycyl]-[N-(1-naphthalenemethyl)glycyl]-N-(butyl)glycin amide (1) and contain between one and six lysine residues each. The compounds were tested for antibacterial activity against S. aureus ATCC 25923 and E. coli ATCC 25922. Furthermore, the hemolytic activity toward human erythrocytes was assessed. Several compounds with potent antibacterial activity and low hemolytic activity were identified.
Collapse
Affiliation(s)
- Trine S Ryge
- Department of Natural Sciences, Section of Bioorganic Chemistry, Royal Veterinary and Agricultural University, Copenhagen, Denmark
| | | |
Collapse
|
61
|
Chapter 1 Piercing Lipid Bilayers with Peptides. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/s1554-4516(06)05001-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
62
|
Castanho MARB, Fernandes MX. Lipid membrane-induced optimization for ligand-receptor docking: recent tools and insights for the "membrane catalysis" model. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2005; 35:92-103. [PMID: 16217647 DOI: 10.1007/s00249-005-0007-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Revised: 07/07/2005] [Accepted: 07/18/2005] [Indexed: 11/25/2022]
Abstract
Cells in living organisms are regulated by chemical and physical stimuli from their environment. Often, ligands interact with membrane receptors to trigger responses and Sargent and Schwyzer conceived a model to describe this process, "membrane catalysis". There is a notion that the physical organization of membranes can control the response of cells by speeding up reactions. We revisit the "membrane catalysis" model in the light of recent technical, methodological and theoretical advances and how they can be exploited to highlight the details of membrane mediated ligand-receptor interactions. We examine the possible effects that ligand concentration causes in the membrane catalysis and focus our attention in techniques used to determine the partition constant. The hypothetical diffusional advantage associated with membrane catalysis is discussed and the applicability of existing models is assessed. The role of in-depth location and orientation of ligands is explored emphasizing the contribution of new analysis methods and spectroscopic techniques. Results suggest that membranes can optimize the interaction between ligands and receptors through several different effects but the relative contribution of each must be carefully investigated. We certainly hope that the conjugation of the methodological and technical advances here reported will revive the interest in the membrane catalysis model.
Collapse
Affiliation(s)
- Miguel A R B Castanho
- Centro de Quìmica e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande Ed. C8, 1749-016 Lisboa, Portugal.
| | | |
Collapse
|
63
|
Hill JJ, Shalaev EY, Zografi G. Thermodynamic and dynamic factors involved in the stability of native protein structure in amorphous solids in relation to levels of hydration. J Pharm Sci 2005; 94:1636-67. [PMID: 15965985 DOI: 10.1002/jps.20333] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The internal, dynamical fluctuations of protein molecules exhibit many of the features typical of polymeric and bulk small molecule glass forming systems. The response of a protein's internal molecular mobility to temperature changes is similar to that of other amorphous systems, in that different types of motions freeze out at different temperatures, suggesting they exhibit the alpha-beta-modes of motion typical of polymeric glass formers. These modes of motion are attributed to the dynamic regimes that afford proteins the flexibility for function but that also develop into the large-scale collective motions that lead to unfolding. The protein dynamical transition, T(d), which has the same meaning as the T(g) value of other amorphous systems, is attributed to the temperature where protein activity is lost and the unfolding process is inhibited. This review describes how modulation of T(d) by hydration and lyoprotectants can determine the stability of protein molecules that have been processed as bulk, amorphous materials. It also examines the thermodynamic, dynamic, and molecular factors involved in stabilizing folded proteins, and the effects typical pharmaceutical processes can have on native protein structure in going from the solution state to the solid state.
Collapse
Affiliation(s)
- John J Hill
- ICOS Corporation, 22021 20th Avenue SE, Bothell, WA 98021, USA.
| | | | | |
Collapse
|
64
|
Stepanyugin AV, Samijlenko SP, Martynenko OI, Hovorun DM. ATR-IR spectroscopy as applied to nucleic acid films. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2005; 61:2267-9. [PMID: 15911421 DOI: 10.1016/j.saa.2004.09.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Revised: 09/20/2004] [Accepted: 09/21/2004] [Indexed: 05/02/2023]
Abstract
For the first time the ATR technique was applied to obtain IR absorption spectra of DNA and RNA dry films. There was worked out procedure of the nucleic acid removal from germanium plate, which obviously was a main obstacle to application of ATR-IR spectroscopy to nucleic acids. This technique of IR spectroscopy was applied to confirmation of RNA tropism of aurin tricarboxylic acid observed by molecular biological methods.
Collapse
Affiliation(s)
- Andriy V Stepanyugin
- Institute of Molecular Biology and Genetics, Ukrainian National Academy of Sciences, 150 vul. Zabolotnoho, 03143 Kyiv, Ukraine
| | | | | | | |
Collapse
|
65
|
Lee C, Bain CD. Raman spectra of planar supported lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1711:59-71. [PMID: 15904664 DOI: 10.1016/j.bbamem.2005.02.006] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Revised: 02/09/2005] [Accepted: 02/09/2005] [Indexed: 11/16/2022]
Abstract
Raman scattering has been used to obtain high quality vibrational spectra of planar supported lipid bilayers (pslb's) at the silica/water interface without the use of resonance or surface enhancement. A total internal reflection geometry was used both to increase the bilayer signal and to suppress the water background. Polarization control permits the determination of four components of the Raman tensor, of which three are independent for a uniaxial film. Spectra are reported of the phospholipids DMPC, DPPC, and POPC, in the C-H stretching region and the fingerprint region. The temperature-dependent polarized spectra of POPC show only small changes over the range 14-41 degrees C. The corresponding spectra of DMPC and DPPC bilayers show large thermal changes consistent with a decreasing tilt angle from the surface normal and increasing chain ordering at lower temperatures. The thermal behavior of DMPC pslb's is similar to that of vesicles of the same lipid in bulk suspension. In contrast to calorimetry, which shows a sharp phase transition (L alpha-L beta') with decreasing temperature, the changes in the Raman spectra occur over a temperature range of ca. 10 degrees C commencing at the calorimetric phase transition temperature.
Collapse
Affiliation(s)
- Chongsoo Lee
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | | |
Collapse
|
66
|
Manor J, Khattari Z, Salditt T, Arkin IT. Disorder influence on linear dichroism analyses of smectic phases. Biophys J 2005; 89:563-71. [PMID: 15834005 PMCID: PMC1366556 DOI: 10.1529/biophysj.104.058842] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Linear dichroism, the unequal absorption of parallel and perpendicular linear polarized light, is often used to determine the anisotropic ordering of rodlike polymers in a smectic phase, such as helices in a lipid bilayer. It is a measure of two properties of the sample: 1), orientation of the chromophore transition dipole moment (TDM) and 2), disorder. Since it is the orientation of the chromophore TDM that is needed for high resolution structural studies, it is imperative to either deconvolve sample disorder, or at a minimum, estimate its effect upon the calculated TDM orientation. Herein, a rigorous analysis of the effects of disorder is undertaken based on the recently developed Gaussian disorder model implemented in linear dichroism data. The calculation of both the rod tilt and rotational pitch angles as a function of the disorder and dichroism, yield the following conclusions: Disorders smaller than 5 degrees have a vanishingly small effect on the calculated polymer orientation, whereas values smaller than 10 degrees have a negligible effect on the calculated parameters. Disorders larger than 10 degrees have an appreciable effect on the calculated orientational parameters and as such must be estimated before any structural characterization. Finally the theory is tested on the HIV vpu transmembrane domain, employing experimental mosaicity measurements from x-ray reflectivity rocking scans and linear dichroism.
Collapse
Affiliation(s)
- Joshua Manor
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | | |
Collapse
|
67
|
Lin SY, Hsieh TF, Wei YS. pH- and thermal-dependent conformational transition of PGAIPG, a repeated hexapeptide sequence from tropoelastin. Peptides 2005; 26:543-9. [PMID: 15752567 DOI: 10.1016/j.peptides.2004.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2004] [Revised: 11/04/2004] [Accepted: 11/04/2004] [Indexed: 11/21/2022]
Abstract
The secondary structure of PGAIPG (Pro-Gly-Ala-IIe-Pro-Gly), a repeated hexapeptide of tropoelastin, in buffer solution of different pH was determined by using attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy. The thermal-dependent structural change of PGAIPG in aqueous solution or in solid state was also examined by thermal FTIR microspectroscopy. The conformation of PGAIPG in aqueous solution exhibited a pH-dependent structural characterization. A predominant peak at 1614 cm(-1) (aggregated beta-sheet) with a shoulder near 1560 cm(-1) (beta-sheet) appeared in pH 5.5-8.5 buffer solutions. A new broad shoulder at 1651 cm(-1) (random coil and/or alpha-helix) with 1614 cm(-1) was observed in the pH 4.5 buffer solution. However, the broad shoulder at 1651 cm(-1) was converted to a maximum peak at 1679 cm(-1) (beta-turn/antiparallel beta-sheet) when the pH shifted from 4.5 to 3.5, but the original pronounced peak at 1614 cm(-1) became a shoulder. Once the pH was lowered to 2.5, the IR spectrum of PGAIPG was dominated by major absorption at 1679 cm(-1) with a minor peak at 1552 cm(-1) (alpha-helix/random coil). The result indicates that the pH was a predominant factor to transform PGAIPG structure from aggregated beta-sheet (pH 8.5) to beta-turn/intermolecular antiparallel beta-sheet (pH 2.5). Moreover, a partial conformation of PGAIPG with minor alpha-helix/random coil structures was also explored in the lower pH buffer solution. There was no thermal-dependent structural change for solid-state PGAIPG. The thermal-induced formation of aggregated beta-sheet for PGAIPG in aqueous solution was found from 28 to 30 degrees C, however, which might be correlated with the formation of an opaque gel that turned from clear solution. The formation of aggregated beta-sheet structure for PGAIPG beyond 30 degrees C might be due to the intermolecular hydrogen bonded interaction between the hydrophobic PGAIPG fragments induced by coacervation.
Collapse
Affiliation(s)
- Shan-Yang Lin
- Biopharmaceutics Laboratory, Department of Medical Research and Education, Veterans General Hospital-Taipei, Shih-Pai, Taipei, Taiwan.
| | | | | |
Collapse
|
68
|
Vigano C, Manciu L, Ruysschaert JM. Structure, orientation, and conformational changes in transmembrane domains of multidrug transporters. Acc Chem Res 2005; 38:117-26. [PMID: 15709731 DOI: 10.1021/ar040021o] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Multidrug transporter proteins promote the active transmembrane efflux of noxious drugs, thereby decreasing their accumulation in the intracellular medium and reducing their therapeutic efficiency. Expression of such proteins drastically reduces the efficiency of chemotherapeutic treatments against cancer and various infectious diseases. To overcome major difficulties related to the crystallization of membrane proteins, other experimental approaches have been developed to gain information on the structural changes involved in drug transport. We examine here and illustrate with a few examples how infrared and fluorescence spectroscopy can provide new insights into the structure of the membrane domains of multidrug transporters in particular. Such domains contain the drug-binding site(s) and mediate the passage of substrates across the cell membrane.
Collapse
Affiliation(s)
- Catherine Vigano
- Laboratory for Structure and Function of Biological Membranes, Structural Biology and Bioinformatics Center, Free University of Brussels, Brussels, Belgium
| | | | | |
Collapse
|
69
|
Iloro I, Chehín R, Goñi FM, Pajares MA, Arrondo JLR. Methionine adenosyltransferase alpha-helix structure unfolds at lower temperatures than beta-sheet: a 2D-IR study. Biophys J 2005; 86:3951-8. [PMID: 15189891 PMCID: PMC1304296 DOI: 10.1529/biophysj.103.028373] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two-dimensional infrared spectroscopy has been used to characterize rat liver methionine adenosyltransferase and the events taking place during its thermal unfolding. Secondary structure data have been obtained for the native recombinant enzyme by fitting the amide I band of infrared spectra. Thermal denaturation studies allow the identification of events associated with individual secondary-structure elements during temperature-induced unfolding. They are correlated to the changes observed in enzyme activity and intrinsic fluorescence. In all cases, thermal denaturation proved to be an irreversible process, with a T(m) of 47-51 degrees C. Thermal profiles and two-dimensional infrared spectroscopy show that unfolding starts with alpha-helical segments and turns, located in the outer part of the protein, whereas extended structure, associated with subunit contacts, unfolds at higher temperatures. The data indicate a good correlation between the denaturation profiles obtained from activity measurements, fluorescence spectroscopy, and the behavior of the infrared bands. A study of the sequence of events that takes place is discussed in light of the previous knowledge on methionine adenosyltransferase structure and oligomerization pathway.
Collapse
Affiliation(s)
- Ibon Iloro
- Unidad de Biofisica (Centro Mixto CSIC-UPV) and Departamento de Bioquimica, Universidad del Pais Vasco, Bilbao, Spain
| | | | | | | | | |
Collapse
|
70
|
Abstract
Anoplin is a decapeptide amide, GLLKRIKTLL-NH2 derived from the venom sac of the solitary spider wasp, Anoplius samariensis. It is active against Gram-positive and Gram-negative bacteria and is not hemolytic towards human erythrocytes. The present paper reports a structure-activity study of anoplin based on 37 analogues including an Ala-scan, C- and N-truncations, and single and multiple residue substitutions with various amino acids. The analogues were tested for antibacterial activity against both S. aureus ATCC 25923 and E. coli ATCC 25922, and several potent antibacterial analogues were identified. The cytotoxicity of the analogues against human erythrocytes was assessed in a hemolytic activity assay. The antibacterial activity and selectivity of the analogues against S. aureus and E. coli varied considerably, depending on the hydrophobicity and position of the various substituted amino acids. In certain cases the selectivity for Gram-positive and Gram-negative bacteria was either reversed or altogether eliminated. In addition, it was generally found that antibacterial activity coincided with hemolytic activity.
Collapse
Affiliation(s)
- Dan Ifrah
- Department of Chemistry, Royal Veterinary and Agricultural University, 1871 Frederiksberg C, Denmark.
| | | | | | | |
Collapse
|
71
|
Ryge TS, Doisy X, Ifrah D, Olsen JE, Hansen PR. New indolicidin analogues with potent antibacterial activity*. ACTA ACUST UNITED AC 2004; 64:171-85. [PMID: 15485555 DOI: 10.1111/j.1399-3011.2004.00177.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Indolicidin is a 13-residue antimicrobial peptide amide, ILPWKWPWWPWRR-NH2, isolated from the cytoplasmic granules of bovine neutrophils. Indolicidin is active against a wide range of microorganisms and has also been shown to be haemolytic and cytotoxic towards erythrocytes and human T lymphocytes. The aim of the present paper is two-fold. First, we examine the importance of tryptophan in the antibacterial activity of indolicidin. We prepared five peptide analogues with the format ILPXKXPXXPXRR-NH2 in which Trp-residues 4,6,8,9,11 were replaced in all positions with X = a single non-natural building block; N-substituted glycine residue or nonproteinogenic amino acid. The analogues were tested for antibacterial activity against both Staphylococcus aureus American type culture collection (ATCC) 25923 and Escherichia coli ATCC 25922. We found that tryptophan is not essential in the antibacterial activity of indolicidin, and even more active analogues were obtained by replacing tryptophan with non-natural aromatic amino acids. Using this knowledge, we then investigated a new principle for improving the antibacterial activity of small peptides. Our approach involves changing the hydrophobicity of the peptide by modifying the N-terminus with a hydrophobic non-natural building block. We prepared 22 analogues of indolicidin and [Phe(4,6,8,9,11)] indolicidin, 11 of each, carrying a hydrophobic non-natural building block attached to the N-terminus. Several active antibacterial analogues were identified. Finally, the cytotoxicity of the analogues against sheep erythrocytes was assessed in a haemolytic activity assay. The results presented here suggest that modified analogues of antibacterial peptides, containing non-natural building blocks, are promising lead structures for developing future therapeutics.
Collapse
Affiliation(s)
- T S Ryge
- Department of Chemistry, Royal Veterinary and Agricultural University, Copenhagen 1871, Denmark
| | | | | | | | | |
Collapse
|
72
|
Pratap PR, Dediu O, Nienhaus GU. FTIR study of ATP-induced changes in Na+/K+-ATPase from duck supraorbital glands. Biophys J 2004; 85:3707-17. [PMID: 14645062 PMCID: PMC1303674 DOI: 10.1016/s0006-3495(03)74787-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The Na+/K+-ATPase uses energy from the hydrolysis of ATP to pump Na+ ions out of and K+ ions into the cell. ATP-induced conformational changes in the protein have been examined in the Na+/K+-ATPase isolated from duck supraorbital salt glands using Fourier transform infrared spectroscopy. Both standard transmission and attenuated total internal reflection sample geometries have been employed. Under transmission conditions, enzyme at 75 mg/ml was incubated with dimethoxybenzoin-caged ATP. ATP was released by flashing with a UV laser pulse at 355 nm, which resulted in a large change in the amide I band. The absorbance at 1659 cm(-1) decreased with a concomitant increase in the absorbance at 1620 cm(-1). These changes are consistent with a partial conversion of protein secondary structure from alpha-helix to beta-sheet. The changes were approximately 8% of the total absorbance, much larger than those seen with other P-type ATPases. Using attenuated total internal reflection Fourier transform infrared spectroscopy, the decrease in absorbance at approximately 1650 cm(-1) was titrated with ATP, and the titration midpoint K0.5 was determined under different ionic conditions. In the presence of metal ions (Na+, Na+ and K+, or Mg2+), K0.5 was on the order of a few microM. In the absence of these ions, K0.5 was an order of magnitude lower (0.1 microM), indicating a higher apparent affinity. This effect suggests that the equilibrium for the ATP-induced conformational changes is dependent on the presence of metal ions.
Collapse
Affiliation(s)
- Promod R Pratap
- Department of Physics and Astronomy, University of North Carolina at Greensboro, Greensboro, North Carolina 27402-6710, USA.
| | | | | |
Collapse
|
73
|
Abstract
Infrared spectroscopy has long been used to examine the average secondary structure and orientation of membrane proteins. With the recent utilization of site-specific isotope labeling (e.g., peptidic 1-(13)C = (18)O) it is now possible to examine localized properties, rather than global averages. The technique of site-specific infrared dichroism (SSID) capitalized on this fact, and derives site-specific orientational restraints for the labeled amino acids. These restraints can then be used to solve the backbone structure of simple alpha-helical bundles, emphasizing the capabilities of this approach. So far SSID has been carried out in attenuated total internal reflection optical mode, with all of the respective caveats of attenuated total internal reflection. In this report we extend SSID through the use of transmission infrared spectroscopy tilt series. We develop the corresponding theory and demonstrate that accurate site-specific orientational restraints can be derived from a simple transmission experiment.
Collapse
Affiliation(s)
- Eyal Arbely
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University, Givat-Ram, Jerusalem, Israel
| | | | | |
Collapse
|
74
|
Kosuri MR, Cone R, Li Q, Han SM, Bunker BC, Mayer TM. Adsorption kinetics of 1-alkanethiols on hydrogenated Ge(111). LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2004; 20:835-840. [PMID: 15773112 DOI: 10.1021/la035521p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We have investigated the liquid-phase self-assembly of 1-alkanethiols (HS(CH2)n-1CH3, n = 8, 16, and 18) on hydrogenated Ge(111), using attenuated total reflection Fourier transform infrared spectroscopy as well as water contact angle measurements. The infrared absorbance of C-H stretching modes of alkanethiolates on Ge, in conjunction with water contact angle measurements, demonstrates that the final packing density is a function of alkanethiol concentration in 2-propanol and its chain length. High concentration and long alkyl chain increase the steady-state surface coverage of alkanethiolates. A critical chain length exists between n = 8 and 16, above which the adsorption kinetics is comparable for all long alkyl chain 1-alkanethiols. The steady-state coverage of hexadecanethiolates, representing long-chain alkanethiolates, reaches a maximum at approximately 5.9 x 10(14) hexadecanethiolates/cm2 in 1 M solution. The characteristic time constant to reach a steady state also decreases with increasing chain length. This chain length dependence is attributed to the attractive chain-to-chain interaction in long-alkyl-chain self-assembled monolayers, which reduces the desorption-to-adsorption rate ratio (kd/ka). We also report the adsorption and desorption rate constants (ka and kd) of 1-hexadecanethiol on hydrogenated Ge(111) at room temperature. The alkanethiol adsorption is a two-step process following a first-order Langmuir isotherm: (1) fast adsorption with ka = 2.4 +/- 0.2 cm3/(mol s) and kd = (8.2 +/- 0.5) x 10(-6)(s-1); (2) slow adsorption with ka = 0.8 +/- 0.5 cm3/(mol s) and kd = (3 +/- 2) x 10(-6) s(-1).
Collapse
Affiliation(s)
- Madhava R Kosuri
- Department of Chemical and Nuclear Engineering, The University of New Mexico, Albuquerque, New Mexico 87131, USA
| | | | | | | | | | | |
Collapse
|
75
|
Tatulian SA. Attenuated Total Reflection Fourier Transform Infrared Spectroscopy: A Method of Choice for Studying Membrane Proteins and Lipids†. Biochemistry 2003; 42:11898-907. [PMID: 14556620 DOI: 10.1021/bi034235+] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Suren A Tatulian
- Biomolecular Science Center and Department of Molecular Biology and Microbiology, University of Central Florida, Orlando, Florida 32826, USA.
| |
Collapse
|
76
|
Azéma L, Lakhdar-Ghazal F, Sygusch J, Blonski C. Characterization of proton abstraction steps in enzymatic reactions by Fourier transform infrared spectroscopy. Anal Biochem 2003; 318:142-5. [PMID: 12782042 DOI: 10.1016/s0003-2697(03)00165-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- L Azéma
- Groupe de Chimie Organique Biologique, LSPCMIB UMR CNRS 5068, Université Paul Sabatier, Bât IIR1, 118 route de Narbonne, 31062 Toulouse Cedex 4, France
| | | | | | | |
Collapse
|
77
|
Pielesz A, Freeman H, Wesełucha-Birczyńska A, Wysocki M, Włochowicz A. Assessing secondary structure of a dyed wool fibre by means of FTIR and FTR spectroscopies. J Mol Struct 2003. [DOI: 10.1016/s0022-2860(03)00210-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
78
|
Kleiner O, Ramesh J, Huleihel M, Cohen B, Kantarovich K, Levi C, Polyak B, Marks RS, Mordehai J, Cohen Z, Mordechai S. A comparative study of gallstones from children and adults using FTIR spectroscopy and fluorescence microscopy. BMC Gastroenterol 2002; 2:3. [PMID: 11872150 PMCID: PMC65695 DOI: 10.1186/1471-230x-2-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2001] [Accepted: 02/11/2002] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Cholelithiasis is the gallstone disease (GSD) where stones are formed in the gallbladder. The main function of the gallbladder is to concentrate bile by the absorption of water and sodium. GSD has high prevalence among elderly adults. There are three major types of gallstones found in patients, White, Black and Brown. The major chemical component of white stones is cholesterol. Black and brown stones contain different proportions of cholesterol and bilirubin. The pathogenesis of gallstones is not clearly understood. Analysis of the chemical composition of gallstones using various spectroscopic techniques offers clues to the pathogenesis of gallstones. Recent years has seen an increasing trend in the number of cases involving children. The focus of this study is on the analysis of the chemical composition of gallstones from child and adult patients using spectroscopic methods. METHODS In this report, we present FTIR spectroscopic studies and fluorescence microscopic analysis of gallstones obtained from 67 adult and 21 child patients. The gallstones were removed during surgical operations at Soroka University Medical Center. RESULTS Our results show that black stones from adults and children are rich in bilirubin. Brown stones are composed of varying amounts of bilirubin and cholesterol. Green stones removed from an adult, which is rare, was found to be composed mainly of cholesterol. Our results also indicated that cholesterol and bilirubin could be the risk factors for gallstone formation in adults and children respectively. Fluorescence micrographs showed that the Ca-bilirubinate was present in all stones in different quantities and however, Cu-bilirubinate was present only in the mixed and black stones. CONCLUSIONS Analysis based on FTIR suggest that the composition of black and brown stones from both children and adults are similar. Various layers of the brown stone from adults differ by having varying quantities of cholesterol and calcium carbonate. Ring patterns observed mainly in the green stone using fluorescence microscopy have relevance to the mechanism of the stone formation. Our preliminary study suggests that bilirubin and cholesterol are the main risk factors of gallstone disease.
Collapse
Affiliation(s)
- Oleg Kleiner
- Department of Pediatric Surgery, Soroka University Medical Center, Ben Gurion University, Beer Sheva 84101 Israel
| | | | - Mahmoud Huleihel
- The Institute for Applied Biosciences, Ben Gurion University, Beer Sheva, 84105, Israel
| | - Beny Cohen
- Department of Chemistry, Ben Gurion University, Beer Sheva, 84105, Israel
| | - Keren Kantarovich
- Department of Physics, Ben Gurion University, Beer Sheva, 84105, Israel
| | - Chen Levi
- Department of Physics, Ben Gurion University, Beer Sheva, 84105, Israel
| | - Boris Polyak
- The Institute for Applied Biosciences, Ben Gurion University, Beer Sheva, 84105, Israel
| | - Robert S Marks
- The Institute for Applied Biosciences, Ben Gurion University, Beer Sheva, 84105, Israel
| | - Jacov Mordehai
- Department of Pediatric Surgery, Soroka University Medical Center, Ben Gurion University, Beer Sheva 84101 Israel
| | - Zahavi Cohen
- Department of Pediatric Surgery, Soroka University Medical Center, Ben Gurion University, Beer Sheva 84101 Israel
| | - Shaul Mordechai
- Department of Physics, Ben Gurion University, Beer Sheva, 84105, Israel
| |
Collapse
|