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Ribić R, Manček-Keber M, Chain F, Sinnaeve D, Martins JC, Jerala R, Tomić S, Fehér K. Targeted Delivery of Adamantylated Peptidoglycan Immunomodulators in Lipid Nanocarriers: NMR Shows That Cargo Fragments Are Available on the Surface. J Phys Chem B 2020; 124:4132-4145. [PMID: 32283934 DOI: 10.1021/acs.jpcb.0c00029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We present an in-depth investigation of the membrane interactions of peptidoglycan (PGN)-based immune adjuvants designed for lipid-based delivery systems using NMR spectroscopy. The derivatives contain a cargo peptidoglycan (PGN) dipeptide fragment and an adamantyl group, which serves as an anchor to the lipid bilayer. Furthermore, derivatives with a mannose group that can actively target cell surface receptors on immune cells are also studied. We showed that the targeting mannose group and the cargo PGN fragment are both available on the lipid bilayer surface, thereby enabling interactions with cognate receptors. We found that the nonmannosylated compounds are incorporated stronger into the lipid assemblies than the mannosylated ones, but the latter compounds penetrate deeper in the bilayer. This might be explained by stronger electrostatic interactions available for zwitterionic nonmannosylated derivatives as opposed to the compounds in which the charged N-terminus is capped by mannose groups. The higher incorporation efficiency of the nonmannosylated compounds correlated with a larger relative enhancement in immune stimulation activities upon lipid incorporation compared to that of the derivatives with the mannose group. The chirality of the adamantyl group also influenced the incorporation efficiency, which in turn correlated with membrane-associated conformations that affect possible intermolecular interactions with lipid molecules. These findings will help in improving the development of PGN-based immune adjuvants suitable for delivery in lipid nanoparticles.
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Affiliation(s)
- Rosana Ribić
- University Center Varaždin, University North, Jurja Križanića 31b, HR-42 000 Varaždin, Croatia.,Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Mateja Manček-Keber
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, P.O. Box 660, SI-1001 Ljubljana, Slovenia.,Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Fernando Chain
- Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre S4, Krijgslaan 281, 9000 Ghent, Belgium
| | - Davy Sinnaeve
- Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre S4, Krijgslaan 281, 9000 Ghent, Belgium.,Univ. Lille, Inserm, Institut Pasteur de Lille, CHU Lille, U1167 - Labex DISTALZ - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France.,CNRS, ERL9002 - Integrative Structural Biology, F-59000 Lille, France
| | - José C Martins
- Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre S4, Krijgslaan 281, 9000 Ghent, Belgium
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, P.O. Box 660, SI-1001 Ljubljana, Slovenia
| | - Srđanka Tomić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, HR-10 000 Zagreb, Croatia
| | - Krisztina Fehér
- Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre S4, Krijgslaan 281, 9000 Ghent, Belgium.,Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Molecular Recognition and Interaction Research Group, Hungarian Academy of Sciences, Egyetem tér 1, H-4032 Debrecen, Hungary
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2
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F Dudás E, Wacha A, Bóta A, Bodor A. Peptide-bicelle interaction: Following variations in size and morphology by a combined NMR-SAXS approach. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183095. [PMID: 31672542 DOI: 10.1016/j.bbamem.2019.183095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/25/2019] [Accepted: 10/16/2019] [Indexed: 10/25/2022]
Abstract
Changes in membrane properties occurring upon protein interaction are key questions in understanding membrane protein function. To report on the occurring size and shape variation we present here a combined NMR-SAXS method performed under physiological conditions using the same samples, enabling determination of a global parameter, the hydration radius (rH) and estimating the bicelle shape. We use zwitterionic (DMPC/DHPC) and negatively charged (DMPC/DHPC/DMPG) bicelles and investigate the interaction with model transmembrane and surface active peptides (KALP23 and melittin). 1H NMR measurements based mostly on the translational diffusion coefficient D determination are used to characterize cmc values of DHPC micelles under the investigated conditions, to describe DHPC distribution with exact determination of the q (long chain/short chain) lipid ratio, to estimate aggregation numbers and effective rH values. The scattering curve is used to fit a lenticular core-shell model enabling us to describe the bicelle shape in terms of ellipsoidal axis length parameters. For all studied systems formation of oblate ellipsoids is found. Even though the rG/rH ratio would be an elegant way to characterize shape variations, we show that changes occurring upon peptide-bicelle interaction in the "effective" size and in the measure on the anisometry - morphology - of the objects can be described by using rH and the simplistic ellipsoidal core-shell model. While the influence of the transmembrane KALP peptide is significant, effects upon addition of surface active melittin peptide seem negligible. This synergy of techniques under controlled conditions can provide information about bicellar shape modulation occurring during peptide-bicelle interactions.
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Affiliation(s)
- E F Dudás
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - A Wacha
- Institute for Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | - A Bóta
- Institute for Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | - A Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary.
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3
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Liebau J, Ye W, Mäler L. Characterization of fast-tumbling isotropic bicelles by PFG diffusion NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:395-404. [PMID: 26662467 DOI: 10.1002/mrc.4399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/12/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
Small isotropic bicelles are versatile membrane mimetics, which, in contrast to micelles, provide a lipid bilayer and are at the same time suitable for solution-state NMR studies. The lipid composition of the bilayer is flexible allowing for incorporation of various head groups and acyl chain types. In bicelles, lipids are solubilized by detergents, which are localized in the rim of the disk-shaped lipid bilayer. Bicelles have been characterized by a broad array of biophysical methods, pulsed-field gradient NMR (PFG NMR) being one of them. PFG NMR can readily be used to measure diffusion coefficients of macromolecules. It is thus employed to characterize bicelle size and morphology. Even more importantly, PFG NMR can be used to study the degree of protein association to membranes. Here, we present the advances that have been made in producing small, fast-tumbling isotropic bicelles from a variety of lipids and detergents, together with insights on the morphology of such mixtures gained from PFG NMR. Furthermore, we review approaches to study protein-membrane interaction by PFG NMR. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Jobst Liebau
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Weihua Ye
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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4
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Hicks RP. Antibacterial and anticancer activity of a series of novel peptides incorporating cyclic tetra-substituted Cα amino acids. Bioorg Med Chem 2016; 24:4056-4065. [DOI: 10.1016/j.bmc.2016.06.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/20/2016] [Accepted: 06/23/2016] [Indexed: 11/26/2022]
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5
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Fast-tumbling bicelles constructed from native Escherichia coli lipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2097-2105. [DOI: 10.1016/j.bbamem.2016.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 11/20/2022]
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6
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Clark TD, Bartolotti L, Hicks RP. The application of DOSY NMR and molecular dynamics simulations to explore the mechanism(s) of micelle binding of antimicrobial peptides containing unnatural amino acids. Biopolymers 2016; 99:548-61. [PMID: 23712491 DOI: 10.1002/bip.22215] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/14/2013] [Accepted: 01/25/2013] [Indexed: 11/11/2022]
Abstract
Anionic and zwitterionic micelles are often used as simple models for the lipids found in bacterial and mammalian cell membranes to investigate antimicrobial peptide-lipid interactions. In our laboratory we have employed a variety of 1D, 2D, and diffusion ordered (DOSY) NMR experiments to investigate the interactions of antimicrobial peptides containing unnatural amino acids with SDS and DPC micelles. Complete assignment of the proton spectra of these peptides is prohibited by the incorporation of a high percentage of unnatural amino acids which don't contain amide protons into the backbone. However preliminary assignment of the TOCSY spectra of compound 23 in the presence of both micelles indicated multiple conformers are present as a result of binding to these micelles. Chemical Shift Indexing agreed with previously collected CD spectra that indicated on binding to SDS micelles compound 23 adopts a mixture of α-helical structures and on binding to DPC micelles this peptide adopts a mixture of helical and β-turn/sheet like structures. DOSY NMR experiments also indicated that the total positive charge and the relative placement of that charge at the N-terminus or C-terminus are important in determining the mole fraction of the peptide that will bind to the different micelles. DOSY and (1) H-NMR experiments indicated that the length of Spacer #1 plays a major role in defining the binding conformation of these analogs with SDS micelles. Results obtained from molecular simulations studies of the binding of compounds 23 and 36 with SDS micelles were consistent with the observed NMR results.
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Affiliation(s)
- Tiffany D Clark
- Department of Chemistry, East Carolina University, Science and Technology Building, Greenville, NC 27858, USA
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Synthetic Antimicrobial Peptides Exhibit Two Different Binding Mechanisms to the Lipopolysaccharides Isolated from Pseudomonas aeruginosa and Klebsiella pneumoniae. INTERNATIONAL JOURNAL OF MEDICINAL CHEMISTRY 2014; 2014:809283. [PMID: 25610647 PMCID: PMC4295349 DOI: 10.1155/2014/809283] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/26/2014] [Accepted: 11/26/2014] [Indexed: 01/03/2023]
Abstract
Circular dichroism and 1H NMR were used to investigate the interactions of a
series of synthetic antimicrobial peptides (AMPs) with lipopolysaccharides (LPS) isolated from
Pseudomonas aeruginosa and Klebsiella pneumoniae. Previous CD studies with AMPs
containing only three Tic-Oic dipeptide units do not exhibit helical characteristics upon
interacting with small unilamellar vesicles (SUVs) consisting of LPS. Increasing the number of
Tic-Oic dipeptide units to six resulted in five analogues with CD spectra that exhibited helical
characteristics on binding to LPS SUVs. Spectroscopic and in vitro inhibitory data suggest that
there are two possible helical conformations resulting from two different AMP-LPS binding
mechanisms. Mechanism one involves a helical binding conformation where the AMP binds
LPS very strongly and is not efficiently transported across the LPS bilayer resulting in the loss of
inhibitory activity. Mechanism two involves a helical binding conformation where the AMP
binds LPS very loosely and is efficiently transported across the LPS bilayer resulting in an
increase in inhibitory activity. Mechanism three involves a nonhelical binding conformation
where the AMP binds LPS very loosely and is efficiently transported across the LPS bilayer
resulting in an increase in inhibitory activity.
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8
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Ye W, Lind J, Eriksson J, Mäler L. Characterization of the morphology of fast-tumbling bicelles with varying composition. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:5488-5496. [PMID: 24785902 DOI: 10.1021/la500231z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Small, fast-tumbling bicelles are frequently used in solution NMR studies of protein-lipid interactions. For this purpose it is critical to have information about the organization of the lipids within the bicelle structure. We have studied the morphology of small, fast-tumbling bicelles containing DMPC and DHPC as a function of temperature, lipid concentration, and the relative ratio (q value) of lipid (DMPC) to detergent (DHPC) amounts. Dynamic light scattering and cryo-transmission electron microscopy techniques were used to measure the size of the bicelles and to monitor the shape and dispersity of the particles in the samples. The stability and size of DMPC-containing bicelle mixtures were found to be highly dependent on temperature and the total lipid concentration for mixtures with q = 1 and q = 1.5. Stable DMPC/DHPC bicelles are only formed at low q values (0.5). Bicelle mixtures with q > 0.5 appear to be multidisperse containing more than one component, one with r(H) around 2.5 nm and one with r(H) of 6-8 nm. This is interpreted as a coexistence of small (possibly mixed micelles) bicelles and much larger bicelles. Incubating the sample at 37 °C increases the phase separation. Moreover, low total amphiphile concentrations and low q values lead to the formation of a temperature-independent morphology, interpreted as the formation of small particles in which the DHPC and DMPC are more mixed. On the basis of these results, we propose the existence of a critical bicelle concentration, a parameter that determines the existence of bilayered bicelles, which varies with q value. This polymorphism was not observed at any concentrations for q = 0.5 bicelles, for which a small but detectable temperature dependence was observed at high concentrations. The results demonstrate that q = 0.5 mixtures predominantly form "classical" bicelles, but that caution is needed when using fast-tumbling mixtures with q values higher than 0.5.
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Affiliation(s)
- Weihua Ye
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, The Arrhenius Laboratory, Stockholm University , SE-10691 Stockholm, Sweden
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9
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Sommer LAM, Janke JJ, Bennett WFD, Bürck J, Ulrich AS, Tieleman DP, Dames SA. Characterization of the Immersion Properties of the Peripheral Membrane Anchor of the FATC Domain of the Kinase “Target of Rapamycin” by NMR, Oriented CD Spectroscopy, and MD Simulations. J Phys Chem B 2014; 118:4817-31. [DOI: 10.1021/jp501533d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lisa A. M. Sommer
- Chair
of Biomolecular NMR Spectroscopy, Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - J. Joel Janke
- Department
of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - W. F. Drew Bennett
- Department
of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Jochen Bürck
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O.B.
3640, 76021 Karlsruhe, Germany
| | - Anne S. Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O.B.
3640, 76021 Karlsruhe, Germany
| | - D. Peter Tieleman
- Department
of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Sonja A. Dames
- Chair
of Biomolecular NMR Spectroscopy, Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
- Institute
of Structural Biology, Helmholtz Zentrum München, Ingolstädter
Landstrasse 1, 85764 Neuherberg, Germany
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10
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Ye W, Liebau J, Mäler L. New Membrane Mimetics with Galactolipids: Lipid Properties in Fast-Tumbling Bicelles. J Phys Chem B 2013; 117:1044-50. [DOI: 10.1021/jp311093p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Weihua Ye
- Department
of Biochemistry and Biophysics, The Arrhenius
Laboratory, Stockholm University, 106 91
Stockholm, Sweden
| | - Jobst Liebau
- Department
of Biochemistry and Biophysics, The Arrhenius
Laboratory, Stockholm University, 106 91
Stockholm, Sweden
| | - Lena Mäler
- Department
of Biochemistry and Biophysics, The Arrhenius
Laboratory, Stockholm University, 106 91
Stockholm, Sweden
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11
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Gayen A, Goswami SK, Mukhopadhyay C. NMR evidence of GM1-induced conformational change of Substance P using isotropic bicelles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:127-39. [DOI: 10.1016/j.bbamem.2010.09.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 08/24/2010] [Accepted: 09/22/2010] [Indexed: 01/30/2023]
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12
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Matsumori N, Murata M. 3D structures of membrane-associated small molecules as determined in isotropic bicelles. Nat Prod Rep 2010; 27:1480-92. [DOI: 10.1039/c0np00002g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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13
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Kim C, Baek SB, Kim DH, Lim SC, Lee HJ, Lee HC. Thermodynamics of partitioning of substance P in isotropic bicelles. J Pept Sci 2009; 15:353-8. [PMID: 19189270 DOI: 10.1002/psc.1121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The temperature dependence of the partition of a neuropeptide, substance P (SP), in isotropic (q = 0.5) bicelles was investigated by using pulsed field gradient NMR diffusion technique. The partition coefficient decreases as the temperature is increased from 295 to 325 K, indicating a favorable (negative) enthalpy change upon partitioning of the peptide. Thermodynamic analysis of the data shows that the partitioning of SP at 300 K is driven by the enthalpic term (DeltaH) with the value of - 4.03 kcal mol(-1), while it is opposed by the entropic term (-TDeltaS) by approximately 1.28 kcal mol(-1) with a small negative change in heat capacity (DeltaC(p)). The enthalpy-driven process for the partition of SP in bicelles is the same as in dodecylphosphocholine (DPC) micelles, however, the negative entropy change in bicelles of flat bilayer surface is in sharp contrast with the positive entropy change in DPC micelles of highly curved surface, indicating that the curvature of the membrane surface might play a significant role in the partitioning of peptides.
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Affiliation(s)
- Chul Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
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14
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Kajiya K, Kumazawa S, Naito A, Nakayama T. Solid-state NMR analysis of the orientation and dynamics of epigallocatechin gallate, a green tea polyphenol, incorporated into lipid bilayers. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:174-177. [PMID: 18098154 DOI: 10.1002/mrc.2157] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Catechins are the principle polyphenolic compounds in green tea; the four major compounds identified are epicatechin (EC), epigallocatechin (EGC), epicatechin gallate (ECg) and epigallocatechin gallate (EGCg). Tea catechins tend to attach externally to their targets, such as viral envelopes, cell membranes, or the surface of low-density lipoproteins. In order to further our understanding of the molecular mobility of these compounds in cells, we examined the interaction of tea catechins with lipid membranes using solid-state NMR techniques. Our previous work indicated that the EGCg molecule is incorporated into lipid bilayers in a unique orientation. However, the detailed configuration, orientation, and dynamics of EGCg in lipid bilayers have not been well-characterized. Here, we investigated the orientation and dynamics of EGCg incorporated into multi-lamellar vesicles (MLVs) and bicelles using solid-state NMR spectroscopy.
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Affiliation(s)
- Katsuko Kajiya
- Department of Molecular Physiology, Yamaguchi University School of Medicine, 1-1-1 Minami-Kogushi, Ube 755-8505, Japan
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15
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Hicks RP, Bhonsle JB, Venugopal D, Koser BW, Magill AJ. De Novo Design of Selective Antibiotic Peptides by Incorporation of Unnatural Amino Acids. J Med Chem 2007; 50:3026-36. [PMID: 17547385 DOI: 10.1021/jm061489v] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The evolution of drug-resistant bacteria is one of the most critical problems facing modern medicine and requires the development of new drugs that exhibit their antibacterial activity via novel mechanisms of action. One potential source of new drugs could be the naturally occurring peptides that exhibit antimicrobial activity via membrane disruption. To develop antimicrobial peptides exhibiting increased potency and selectivity against Gram positive, Gram negative, and Mycobacterium bacteria coupled with reduced hemolytic activity, peptides containing unnatural amino acids have been designed, synthesized, and evaluated. These compounds were designed on the basis of the electrostatic surface potential maps derived from the NMR determined SDS and DPC micelle-bound conformations of (Ala8,13,18)magainin-2 amide. Unnatural amino acids were incorporated into the polypeptide backbone to control the structural and physicochemical properties of the peptides to introduce organism selectivity and potency. The methods and results of this investigation are described below.
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Affiliation(s)
- Rickey P Hicks
- Division of Experimental Therapeutics, Walter Reed Army Institute of Research 503 Robert Grant Avenue, Silver Spring, Maryland 20910, USA.
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16
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Massad T, Jarvet J, Tanner R, Tomson K, Smirnova J, Palumaa P, Sugai M, Kohno T, Vanatalu K, Damberg P. Maximum entropy reconstruction of joint phi, psi-distribution with a coil-library prior: the backbone conformation of the peptide hormone motilin in aqueous solution from phi and psi-dependent J-couplings. JOURNAL OF BIOMOLECULAR NMR 2007; 38:107-23. [PMID: 17458509 DOI: 10.1007/s10858-007-9150-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Accepted: 02/13/2007] [Indexed: 05/15/2023]
Abstract
In this paper, we present a new method for structure determination of flexible "random-coil" peptides. A numerical method is described, where the experimentally measured 3J(H(alpha)Nalpha) and [3J(H(alpha)Nalpha+1 couplings, which depend on the phi and psi dihedral angles, are analyzed jointly with the information from a coil-library through a maximum entropy approach. The coil-library is the distribution of dihedral angles found outside the elements of the secondary structure in the high-resolution protein structures. The method results in residue specific joint phi,psi-distribution functions, which are in agreement with the experimental J-couplings and minimally committal to the information in the coil-library. The 22-residue human peptide hormone motilin, uniformly 15N-labeled was studied. The 3J(H(alpha)-N(i+1)) were measured from the E.COSY pattern in the sequential NOESY cross-peaks. By employing homodecoupling and an in-phase/anti-phase filter, sharp H(alpha)-resonances (about 5 Hz) were obtained enabling accurate determination of the coupling with minimal spectral overlap. Clear trends in the resulting phi,psi-distribution functions along the sequence are observed, with a nascent helical structure in the central part of the peptide and more extended conformations of the receptor binding N-terminus as the most prominent characteristics. From the phi,psi-distribution functions, the contribution from each residue to the thermodynamic entropy, i.e., the segmental entropies, are calculated and compared to segmental entropies estimated from 15N-relaxation data. Remarkable agreement between the relaxation and J-couplings based methods is found. Residues belonging to the nascent helix and the C-terminus show segmental entropies, of approximately -20 J K(-1) mol(-1) and -12 J K(-1) mol(-1), respectively, in both series. The agreement between the two estimates of the segmental entropy, the agreement with the observed J-couplings, the agreement with the CD experiments, and the assignment of population to sterically allowed conformations show that the phi,psi-distribution functions are indeed meaningful and useful descriptions of the conformational preferences for each residue in this flexible peptide.
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Affiliation(s)
- Tariq Massad
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius v. 12, 106 91, Stockholm, Sweden
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17
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Bárány-Wallje E, Andersson A, Gräslund A, Mäler L. Dynamics of transportan in bicelles is surface charge dependent. JOURNAL OF BIOMOLECULAR NMR 2006; 35:137-47. [PMID: 16705358 DOI: 10.1007/s10858-006-9008-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Accepted: 03/23/2006] [Indexed: 05/09/2023]
Abstract
In this study we investigated the dynamic behavior of the chimeric cell-penetrating peptide transportan in membrane-like environments using NMR. Backbone amide 15N spin relaxation was used to investigate the dynamics in two bicelles: neutral DMPC bicelles and partly negatively charged DMPG-containing bicelles. The structure of the peptide as judged from CD and chemical shifts is similar in the two cases. Both the overall motion as well as the local dynamics is, however, different in the two types of bicelles. The overall dynamics of the peptide is significantly slower in the partly negatively charged bicelle environment, as evidenced by longer global correlation times for all measured sites. The local motion, as judged from generalized order parameters, is for all sites in the peptide more restricted when bound to negatively charged bicelles than when bound to neutral bicelles (increase in S2 is on average 0.11 +/- 0.07). The slower dynamics of transportan in charged membrane model systems cause significant line broadening in the proton NMR spectrum, which in certain cases limits the observation of 1H signals for transportan when bound to the membrane. The effect of transportan on DMPC and DHPC motion in zwitterionic bicelles was also investigated, and the motion of both components in the bicelle was found to be affected.
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Affiliation(s)
- Elsa Bárány-Wallje
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories, Stockholm University, S-106 91, Stockholm, Sweden
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18
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Andersson A, Mäler L. Size and shape of fast-tumbling bicelles as determined by translational diffusion. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:2447-9. [PMID: 16519439 DOI: 10.1021/la053177l] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
In this study, the size and shape of an isotropic bicelle have been determined by measuring the translational diffusion as a function of the volume fraction of the lipids. A linear relation between the diffusion coefficients is obtained for both DMPC and DHPC in the bicelles. The slope of this linear function, which is strongly shape-dependent, is found to be different for the two molecules. This difference is direct evidence that the two molecules are not fully mixed in the bicelle. The shape- combined with the size-dependence of the diffusion coefficient allows us to calculate both the size and shape of the bicelle.
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Affiliation(s)
- August Andersson
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories, Stockholm University, S-106 91 Stockholm, Sweden
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Papadopoulos E, Oglecka K, Mäler L, Jarvet J, Wright PE, Dyson HJ, Gräslund A. NMR Solution Structure of the Peptide Fragment 1−30, Derived from Unprocessed Mouse Doppel Protein, in DHPC Micelles. Biochemistry 2005; 45:159-66. [PMID: 16388591 DOI: 10.1021/bi051313f] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The downstream prion-like Doppel (Dpl) protein is a homologue related to the prion protein (PrP). Dpl is expressed in the brains of mice that do not express PrP, and Dpl is known to be toxic to neurons. One mode of toxicity has been suggested to involve direct membrane interactions. PrP under certain conditions of cell trafficking retains an uncleaved signal peptide, which may also hold for the much less studied Dpl. For a peptide with a sequence derived from the N-terminal part (1-30) of mouse Dpl (mDpl(1-30)) CD spectroscopy shows about 40% alpha-helical structure in DHPC and SDS micelles. In aqueous solution it is mostly a random coil. The three-dimensional solution structure was determined by NMR for mDpl(1-30) associated with DHPC micelles. 2D 1H NMR spectra of the peptide in q = 0.25 DMPC/DHPC bicelles only showed signals from the unstructured termini, indicating that the structured part of the peptide resides within the lipid bilayer. Together with 2H2O exchange data in the DHPC micelle solvent, these results show an alpha-helix protected from solvent exchange between residues 7 and 19, and suggest that the alpha-helical segment can adopt a transmembrane localization also in a membrane. Leakage studies with entrapped calcein in large unilamellar phospholipid vesicles showed that the peptide is almost as membrane perturbing as melittin, known to form pores in membranes. The results suggest a possible channel formation mechanism for the unprocessed Dpl protein, which may be related to toxicity through direct cell membrane interaction and damage.
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Affiliation(s)
- Evangelos Papadopoulos
- Department of Biochemistry & Biophysics, The Arrhenius Laboratories, Stockholm University, SE-10691 Stockholm, Sweden
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Andersson A, Mäler L. Magnetic resonance investigations of lipid motion in isotropic bicelles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:7702-9. [PMID: 16089372 DOI: 10.1021/la0513003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The dynamics of DMPC in different isotropic bicelles have been investigated by NMR and EPR methods. The local dynamics were obtained by interpretation of 13C NMR relaxation measurements of DMPC in the bicelles, and these results were compared to EPR spectra of spin-labeled lipids. The overall size of the bicelles was investigated by PFG NMR translational diffusion measurements. The dynamics and relative sizes were compared among three different bicelles: [DMPC]/[DHPC] = 0.25, [DMPC]/[DHPC] = 0.5, and [DMPC]/[CHAPS] = 0.5. The local motion is found to depend much more strongly on the choice of the detergent, rather than the overall size of the bicelle. The results provide an explanation for differences in apparent dynamics for different peptides, which are bound to bicelles. This in turn determines under what conditions reasonable NMR spectra can be observed. A model is presented in which extensive local motion, in conjunction with the overall size, affects the spectral properties. An analytical expression for the size dependence of the bicelles, relating the radius of the bilayer region with physical properties of the detergent and the lipid, is also presented.
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Affiliation(s)
- August Andersson
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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Soong R, Macdonald PM. Lateral diffusion of PEG-Lipid in magnetically aligned bicelles measured using stimulated echo pulsed field gradient 1H NMR. Biophys J 2004; 88:255-68. [PMID: 15475584 PMCID: PMC1305004 DOI: 10.1529/biophysj.104.043620] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lateral diffusion measurements of PEG-lipid incorporated into magnetically aligned bicelles are demonstrated using stimulated echo (STE) pulsed field gradient (PFG) proton (1H) nuclear magnetic resonance (NMR) spectroscopy. Bicelles were composed of dimyristoyl phosphatidylcholine (DMPC) plus dihexanoyl phosphatidylcholine (DHPC) (q = DMPC/DHPC molar ratio = 4.5) plus 1 mol % (relative to DMPC) dimyristoyl phosphatidylethanolamine-N-[methoxy(polyethylene glycol)-2000] (DMPE-PEG 2000) at 25 wt % lipid. 1H NMR STE spectra of perpendicular aligned bicelles contained only resonances assigned to residual HDO and to overlapping contributions from a DMPE-PEG 2000 ethoxy headgroup plus DHPC choline methyl protons. Decay of the latter's STE intensity in the STE PFG 1H NMR experiment (g(z) = 244 G cm(-1)) yielded a DMPE-PEG 2000 (1 mol %, 35 degrees C) lateral diffusion coefficient D = 1.35 x 10(-11) m2 s(-1). Hence, below the "mushroom-to-brush" transition, DMPE-PEG 2000 lateral diffusion is dictated by its DMPE hydrophobic anchor. D was independent of the diffusion time, indicating unrestricted lateral diffusion over root mean-square diffusion distances of microns, supporting the "perforated lamellae" model of bicelle structure under these conditions. Overall, the results demonstrate the feasibility of lateral diffusion measurements in magnetically aligned bicelles using the STE PFG NMR technique.
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Affiliation(s)
- Ronald Soong
- Department of Chemistry, University of Toronto, Ontario, Canada
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Bárány-Wallje E, Andersson A, Gräslund A, Mäler L. NMR solution structure and position of transportan in neutral phospholipid bicelles. FEBS Lett 2004; 567:265-9. [PMID: 15178334 DOI: 10.1016/j.febslet.2004.04.079] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2004] [Revised: 04/21/2004] [Accepted: 04/21/2004] [Indexed: 11/16/2022]
Abstract
Transportan is a chimeric cell-penetrating peptide constructed from the peptides galanin and mastoparan, which has the ability to internalize living cells carrying a hydrophilic load. In this study, we have determined the NMR solution structure and investigated the position of transportan in neutral bicelles. The structure revealed a well-defined alpha-helix in the C-terminal mastoparan part of the peptide and a weaker tendency to form an alpha-helix in the N-terminal domain. The position of the peptide in relation to the membrane, as studied by adding paramagnetic probes, shows that the peptide lies parallel to, and in the head-group region of the membrane surface. This result is supported by amide proton secondary chemical shifts.
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Affiliation(s)
- Elsa Bárány-Wallje
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories, Stockholm University, S-10691 Stockholm, Sweden
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Andersson A, Almqvist J, Hagn F, Mäler L. Diffusion and dynamics of penetratin in different membrane mimicking media. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2004; 1661:18-25. [PMID: 14967471 DOI: 10.1016/j.bbamem.2003.11.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2003] [Revised: 11/14/2003] [Accepted: 11/20/2003] [Indexed: 11/25/2022]
Abstract
The interaction between the cell-penetrating peptide (CPP) penetratin and different membrane mimetic environments has been investigated by two different NMR methods: 15N spin relaxation and translational diffusion. Diffusion coefficients were measured for penetratin in neutral and in negatively charged bicelles of different size, in sodium dodecyl sulfate micelles (SDS), and in aqueous solution. The diffusion coefficients were used to estimate the amount of free and bicelle/micelle-bound penetratin and the results revealed that penetratin binds almost fully to all studied membrane mimetics. 15N relaxation data for three sites in penetratin were interpreted with the model-free approach to obtain overall and local dynamics. Overall correlation times for penetratin were in agreement with findings for other peptides of similar size in the same solvents. Large differences in order parameters were observed for penetratin in the different membrane mimetics. Negatively charged surfaces were seen to restrict motional flexibility, while a more neutral membrane mimetic did not. This indicates that although the peptide binds to both bicelles and SDS micelles, the interaction between penetratin and the various membrane mimetics is different.
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Affiliation(s)
- August Andersson
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
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