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Do guanidinium and tetrapropylammonium ions specifically interact with aromatic amino acid side chains? Proc Natl Acad Sci U S A 2017; 114:1003-1008. [PMID: 28096375 DOI: 10.1073/pnas.1618071114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Many ions are known to affect the activity, stability, and structural integrity of proteins. Although this effect can be generally attributed to ion-induced changes in forces that govern protein folding, delineating the underlying mechanism of action still remains challenging because it requires assessment of all relevant interactions, such as ion-protein, ion-water, and ion-ion interactions. Herein, we use two unnatural aromatic amino acids and several spectroscopic techniques to examine whether guanidinium chloride, one of the most commonly used protein denaturants, and tetrapropylammonium chloride can specifically interact with aromatic side chains. Our results show that tetrapropylammonium, but not guanidinium, can preferentially accumulate around aromatic residues and that tetrapropylammonium undergoes a transition at ∼1.3 M to form aggregates. We find that similar to ionic micelles, on one hand, such aggregates can disrupt native hydrophobic interactions, and on the other hand, they can promote α-helix formation in certain peptides.
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Kocourková L, Novotná P, Čujová S, Čeřovský V, Urbanová M, Setnička V. Conformational study of melectin and antapin antimicrobial peptides in model membrane environments. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 170:247-255. [PMID: 27450123 DOI: 10.1016/j.saa.2016.07.015] [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: 08/18/2015] [Accepted: 07/07/2016] [Indexed: 06/06/2023]
Abstract
Antimicrobial peptides have long been considered as promising compounds against drug-resistant pathogens. In this work, we studied the secondary structure of antimicrobial peptides melectin and antapin using electronic (ECD) and vibrational circular dichroism (VCD) spectroscopies that are sensitive to peptide secondary structures. The results from quantitative ECD spectral evaluation by Dichroweb and CDNN program and from the qualitative evaluation of the VCD spectra were compared. The antimicrobial activity of the selected peptides depends on their ability to adopt an amphipathic α-helical conformation on the surface of the bacterial membrane. Hence, solutions of different zwitterionic and negatively charged liposomes and micelles were used to mimic the eukaryotic and bacterial biological membranes. The results show a significant content of α-helical conformation in the solutions of negatively charged liposomes mimicking the bacterial membrane, thus correlating with the antimicrobial activity of the studied peptides. On the other hand in the solutions of zwitterionic liposomes used as models of the eukaryotic membranes, the fraction of α-helical conformation was lower, which corresponds with their moderate hemolytic activity.
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Affiliation(s)
- Lucie Kocourková
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Pavlína Novotná
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Sabína Čujová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Václav Čeřovský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Marie Urbanová
- Department of Physics and Measurements, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Vladimír Setnička
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic.
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53
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Rao BD, Shrivastava S, Chattopadhyay A. Hydrophobic Mismatch in Membranes: When the Tail Matters. SPRINGER SERIES IN BIOPHYSICS 2017. [DOI: 10.1007/978-3-319-66601-3_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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54
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García-Linares S, Rivera-de-Torre E, Palacios-Ortega J, Gavilanes JG, Martínez-del-Pozo Á. The Metamorphic Transformation of a Water-Soluble Monomeric Protein Into an Oligomeric Transmembrane Pore. ADVANCES IN BIOMEMBRANES AND LIPID SELF-ASSEMBLY 2017. [DOI: 10.1016/bs.abl.2017.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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55
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Thibado JK, Martfeld AN, Greathouse DV, Koeppe RE. Influence of High pH and Cholesterol on Single Arginine-Containing Transmembrane Peptide Helices. Biochemistry 2016; 55:6337-6343. [PMID: 27782382 PMCID: PMC5266483 DOI: 10.1021/acs.biochem.6b00896] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
An essential component
of mammalian cells, cholesterol exerts significant
influence on the physical properties of the cell membrane and in turn
its constituents, including membrane proteins. Although sparse, polar
amino acid residues are highly conserved in membrane proteins and
play pivotal roles in determining specific structural and functional
properties. To improve our understanding of particular polar residues
in the membrane environment, we have examined two specific “guest”
Arg residues within a well-defined and deuterium-labeled “host”
framework provided by the transmembrane helical peptide GWALP23 (acetyl-GGALWLALALALALALALWLAGA-amide).
Solid-state 2H nuclear magnetic resonance (NMR) spectra
from aligned bilayer membrane samples effectively report changes in
the host helix properties because of the incorporation of the guest
residues. The focus of this work is two-pronged. First, GWALP23-R14
was examined over a pH range of 2–13 in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) ester- or ether-linked
bilayer membranes. Our findings indicate that the Arg guanidinium
side chain remains charged over this entire range, in agreement with
numerous molecular dynamics simulations. Second, GWALP23-R12 and GWALP23-R14
peptides were characterized in DOPC bilayers with varying cholesterol
content. Our findings suggest that 10 or 20% cholesterol content has
minimal impact on the orientation of the R14 peptide. Although the
NMR signals are broader and weaker in the presence of 20% cholesterol,
the deuterium quadrupolar splittings for [2H]Ala residues
in GWALP23-R14 change very little. Conversely, cholesterol appears
to modulate the multistate behavior of GWALP23-R12 and to favor a
major interfacial state for the helix, bound at the bilayer surface.
These results indicate a conditional sensitivity of a complex multistate
transmembrane Arg-containing peptide helix to the presence of cholesterol.
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Affiliation(s)
- Jordana K Thibado
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
| | - Ashley N Martfeld
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
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56
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Ekblad B, Kyriakou PK, Oppegård C, Nissen-Meyer J, Kaznessis YN, Kristiansen PE. Structure-Function Analysis of the Two-Peptide Bacteriocin Plantaricin EF. Biochemistry 2016; 55:5106-16. [PMID: 27538436 PMCID: PMC5026404 DOI: 10.1021/acs.biochem.6b00588] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 08/16/2016] [Indexed: 11/30/2022]
Abstract
Plantaricin EF is a two-peptide bacteriocin that depends on the complementary action of two different peptides (PlnE and PlnF) to function. The structures of the individual peptides have previously been analyzed by nuclear magnetic resonance spectroscopy ( Fimland, N. et al. ( 2008 ) , Biochim. Biophys. Acta 1784 , 1711 - 1719 ), but the bacteriocin structure and how the two peptides interact have not been determined. All two-peptide bacteriocins identified so far contain GxxxG motifs. These motifs, together with GxxxG-like motifs, are known to mediate helix-helix interactions in membrane proteins. We have mutated all GxxxG and GxxxG-like motifs in PlnE and PlnF in order to determine if any of these motifs are important for antimicrobial activity and thus possibly for interactions between PlnE and PlnF. Moreover, the aromatic amino acids Tyr and Trp in PlnE and PlnF were substituted, and four fusion polypeptides were constructed in order to investigate the relative orientation of PlnE and PlnF in target cell membranes. The results obtained with the fusion polypeptides indicate that PlnE and PlnF interact in an antiparallel manner and that the C-terminus of PlnE and N-terminus of PlnF are on the outer part of target cell membranes and the N-terminus of PlnE and C-terminus of PlnF are on the inner part. The preference for an aromatic residue at position 6 in PlnE suggests a positioning of this residue in or near the membrane interface on the cells inside. Mutations in the GxxxG motifs indicate that the G5xxxG9 motif in PlnE and the S26xxxG30 motif in PlnF are involved in helix-helix interactions. Atomistic molecular dynamics simulation of a structural model consistent with the results confirmed the stability of the structure and its orientation in membranes. The simulation approved the anticipated interactions and revealed additional interactions that further increase the stability of the proposed structure.
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Affiliation(s)
- Bie Ekblad
- Department
of Biosciences, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, Norway
| | - Panagiota K. Kyriakou
- Department
of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Camilla Oppegård
- Department
of Biosciences, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, Norway
| | - Jon Nissen-Meyer
- Department
of Biosciences, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, Norway
| | - Yiannis N. Kaznessis
- Department
of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Per Eugen Kristiansen
- Department
of Biosciences, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, Norway
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57
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Pahlke DM, Diederichsen U. Synthesis and characterization of β-peptide helices as transmembrane domains in lipid model membranes. J Pept Sci 2016; 22:636-641. [PMID: 27578420 DOI: 10.1002/psc.2912] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 08/04/2016] [Accepted: 08/04/2016] [Indexed: 11/07/2022]
Abstract
Aggregation, orientation and dynamics of transmembrane helices are of relevance for protein function and transmembrane signaling. To explore the interactions of transmembrane helices and the interdependence of peptide structure and lipid composition of the membranes, β-peptides were explored as model transmembrane domains. Various hydrophobic β-peptide sequences were synthesized by solid phase peptide synthesis. Conformational analyses of β-peptide helices were performed in organic solvents (methanol and 2,2,2-trifluoroethanol) and in large unilamellar liposomes (dimyristoylphosphatidylcholine, dipalmitoylphosphatidylcholine and dioleoylphosphatidylcholine) indicating 12- and 14-helix conformations, depending on β3 -amino acid sequences. The intrinsic tryptophan fluorescence of β3 -homotryptophan units inserted in the center or near the end of the sequence was used to verify the membrane insertion of the β-peptides. A characteristic blue shift with peripheral β3 -homotryptophan compared with β-peptides with central tryptophan served as indication for a transmembrane orientation of the β-peptides within the lipid bilayer. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Denis M Pahlke
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
| | - Ulf Diederichsen
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077, Göttingen, Germany.
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58
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Mukai M, Glover KJ, Regen SL. Evidence for Surface Recognition by a Cholesterol-Recognition Peptide. Biophys J 2016; 110:2577-2580. [PMID: 27283494 DOI: 10.1016/j.bpj.2016.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 04/19/2016] [Accepted: 05/06/2016] [Indexed: 01/28/2023] Open
Abstract
Two cholesterol recognition/interaction amino-acid consensus peptides, N-acetyl-LWYIKC-amide, and N-acetyl-CLWYIK-amide, have been coupled to exchangeable mimics of Chol (cholesterol) and Phos (1,2-dipalmitoyl-sn-glycerol-3-phospho-(1'rac-glycerol)) via disulfide bond formation. Equilibration between Chol and Phos via thiolate-disulfide interchange reactions has revealed that both peptides favor Chol as a nearest-neighbor in liquid-disordered (ld) bilayers to the same extent. In contrast, no Chol- or Phos-recognition could be detected by these peptides in analogous liquid-ordered (lo) bilayers. Fluorescence measurements of the tryptophan moiety have shown that both peptides favor the membrane-water interface. Taken together, these results provide strong evidence that the recognition behavior of the LWYIK motif is, fundamentally, a surface phenomenon but that partial penetration into the bilayer is also necessary.
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Affiliation(s)
- Masaru Mukai
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania
| | | | - Steven L Regen
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania.
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59
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Rost U, Xu Y, Salditt T, Diederichsen U. Heavy-Atom Labeled Transmembrane β-Peptides: Synthesis, CD-Spectroscopy, and X-ray Diffraction Studies in Model Lipid Multilayer. Chemphyschem 2016; 17:2525-34. [DOI: 10.1002/cphc.201600289] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Ulrike Rost
- Institute for Organic and Biomolecular Chemistry; Georg-August-University Göttingen; Tammannstr. 2 37077 Göttingen Germany
| | - Yihui Xu
- Institute for X-ray Physics; Georg-August-University Göttingen; Friedrich-Hund-Platz 1 37077 Göttingen Germany
| | - Tim Salditt
- Institute for X-ray Physics; Georg-August-University Göttingen; Friedrich-Hund-Platz 1 37077 Göttingen Germany
| | - Ulf Diederichsen
- Institute for Organic and Biomolecular Chemistry; Georg-August-University Göttingen; Tammannstr. 2 37077 Göttingen Germany
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60
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Rost U, Steinem C, Diederichsen U. β-Glutamine-mediated self-association of transmembrane β-peptides within lipid bilayers. Chem Sci 2016; 7:5900-5907. [PMID: 30034732 PMCID: PMC6022121 DOI: 10.1039/c6sc01147k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 05/18/2016] [Indexed: 11/21/2022] Open
Abstract
The rational design and synthesis of novel transmembrane β-peptides forming stable secondary structures in a membrane environment are described. Their state of aggregation within the membrane is controlled by hydrogen bonds.
Transmembrane β-peptide helices and their association in lipid membranes are still widely unexplored. We designed and synthesized transmembrane β-peptides harboring different numbers of d-β3-glutamine residues (hGln) by solid phase peptide synthesis. By means of circular dichroism spectroscopic measurements, the secondary structure of the β-peptides reconstituted into unilamellar vesicles was determined to be similar to a right-handed 314-helix. Fluorescence spectroscopy using d-β3-tryptophan residues strongly suggested a transmembrane orientation. Two or three hGln served as recognition units between the helices to allow helix–helix assembly driven by hydrogen bond formation. The association state of the transmembrane β-peptides as a function of the number of hGln residues was investigated by fluorescence resonance energy transfer (FRET). Therefore, two fluorescence probes (NBD, TAMRA) were covalently attached to the side chains of the transmembrane β-peptide helices. The results clearly demonstrate that only β-peptides with hGln as recognition units assemble into oligomers, presumably trimers. Temperature dependent FRET experiments further show that the strength of the helix–helix association is a function of the number of hGln residues in the helix.
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Affiliation(s)
- U Rost
- Institute of Organic and Biomolecular Chemistry , Georg-August-University Goettingen , Tammannstr. 2 , 37077 Goettingen , Germany . ;
| | - C Steinem
- Institute of Organic and Biomolecular Chemistry , Georg-August-University Goettingen , Tammannstr. 2 , 37077 Goettingen , Germany . ;
| | - U Diederichsen
- Institute of Organic and Biomolecular Chemistry , Georg-August-University Goettingen , Tammannstr. 2 , 37077 Goettingen , Germany . ;
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61
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Windisch D, Ziegler C, Grage SL, Bürck J, Zeitler M, Gor'kov PL, Ulrich AS. Hydrophobic Mismatch Drives the Interaction of E5 with the Transmembrane Segment of PDGF Receptor. Biophys J 2016; 109:737-49. [PMID: 26287626 PMCID: PMC4547410 DOI: 10.1016/j.bpj.2015.07.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 07/13/2015] [Accepted: 07/14/2015] [Indexed: 02/05/2023] Open
Abstract
The oncogenic E5 protein from bovine papillomavirus is a short (44 amino acids long) integral membrane protein that forms homodimers. It activates platelet-derived growth factor receptor (PDGFR) β in a ligand-independent manner by transmembrane helix-helix interactions. The nature of this recognition event remains elusive, as numerous mutations are tolerated in the E5 transmembrane segment, with the exception of one hydrogen-bonding residue. Here, we examined the conformation, stability, and alignment of the E5 protein in fluid lipid membranes of substantially varying bilayer thickness, in both the absence and presence of the PDGFR transmembrane segment. Quantitative synchrotron radiation circular dichroism analysis revealed a very long transmembrane helix for E5 of ∼26 amino acids. Oriented circular dichroism and solid-state 15N-NMR showed that the alignment and stability of this unusually long segment depend critically on the membrane thickness. When reconstituted alone in exceptionally thick DNPC lipid bilayers, the E5 helix was found to be inserted almost upright. In moderately thick bilayers (DErPC and DEiPC), it started to tilt and became slightly deformed, and finally it became aggregated in conventional DOPC, POPC, and DMPC membranes due to hydrophobic mismatch. On the other hand, when E5 was co-reconstituted with the transmembrane segment of PDGFR, it was able to tolerate even the most pronounced mismatch and was stabilized by binding to the receptor, which has the same hydrophobic length. As E5 is known to activate PDGFR within the thin membranes of the Golgi compartment, we suggest that the intrinsic hydrophobic mismatch of these two interaction partners drives them together. They seem to recognize each other by forming a closely packed bundle of mutually aligned transmembrane helices, which is further stabilized by a specific pair of hydrogen-bonding residues.
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Affiliation(s)
- Dirk Windisch
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Colin Ziegler
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Stephan L Grage
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marcel Zeitler
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Peter L Gor'kov
- National High Magnetic Field Laboratory, Tallahassee, Florida
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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62
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Vestergaard M, Kraft JF, Vosegaard T, Thøgersen L, Schiøtt B. Bicelles and Other Membrane Mimics: Comparison of Structure, Properties, and Dynamics from MD Simulations. J Phys Chem B 2015; 119:15831-43. [PMID: 26610232 DOI: 10.1021/acs.jpcb.5b08463] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The increased interest in studying membrane proteins has led to the development of new membrane mimics such as bicelles and nanodiscs. However, only limited knowledge is available of how these membrane mimics are affected by embedded proteins and how well they mimic a lipid bilayer. Herein, we present molecular dynamics simulations to elucidate structural and dynamic properties of small bicelles and compare them to a large alignable bicelle, a small nanodisc, and a lipid bilayer. Properties such as lipid packing and properties related to embedding both an α-helical peptide and a transmembrane protein are investigated. The small bicelles are found to be very dynamic and mainly assume a prolate shape substantiating that small bicelles cannot be regarded as well-defined disclike structures. However, addition of a peptide results in an increased tendency to form disc-shaped bicelles. The small bicelles and the nanodiscs show increased peptide solvation and difference in peptide orientation compared to embedding in a bilayer. The large bicelle imitated a bilayer well with respect to both curvature and peptide solvation, although peripheral binding of short tailed lipids to the embedded proteins is observed, which could hinder ligand binding or multimer formation.
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Affiliation(s)
- Mikkel Vestergaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), and Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Johan F Kraft
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), and Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Thomas Vosegaard
- Danish Center for Ultrahigh-Field NMR Spectroscopy and Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University , Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Lea Thøgersen
- Center for Membrane Pumps in Cells and Disease (PUMPKIN), Bioinformatics Research Centre, Aarhus University , C.F. Møllers Alle 8, DK-8000 Aarhus C, Denmark
| | - Birgit Schiøtt
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), and Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus C, Denmark
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63
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Ulmschneider JP, Ulmschneider MB. Folding Simulations of the Transmembrane Helix of Virus Protein U in an Implicit Membrane Model. J Chem Theory Comput 2015; 3:2335-46. [PMID: 26636223 DOI: 10.1021/ct700103k] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vpu is an 81-amino-acid auxiliary membrane protein encoded by human immunodeficiency virus type 1 (HIV-1). One of its roles is to amplify viral release by self-assembling in homo-oligomers to form functional water-filled pores enabling the flux of ions across the membrane. Various NMR and CD studies have shown that the transmembrane domain of Vpu has a helical conformation. With a recently developed implicit membrane model and an efficient Monte Carlo (MC) algorithm using concerted backbone rotations, we simulate the folding of the transmembrane domain of Vpu at atomic resolution. The implicit membrane environment is based on the generalized Born theory and enables very long time scale events, such as folding to be observed using detailed all-atom representation of the protein. Such studies are currently computationally unfeasible with fully explicit lipid bilayer molecular dynamics simulations. The correct helical transmembrane structure of Vpu is predicted from extended conformations and remains stably inserted. Tilt and kink angles agree well with experimental estimates from NMR measurements. The experimentally observed change in tilt angle in membranes of varying hydrophobic width is accurately reproduced. The extensive simulation of a pentamer of the Vpu transmembrane domain in the implicit membrane gives results similar to the ones reported previously for fully explicit bilayer simulations.
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Affiliation(s)
- Jakob P Ulmschneider
- Department of Chemistry, University of Rome "La Sapienza", Rome, Italy, and Department of Biochemistry, University of Oxford, Oxford, U.K
| | - Martin B Ulmschneider
- Department of Chemistry, University of Rome "La Sapienza", Rome, Italy, and Department of Biochemistry, University of Oxford, Oxford, U.K
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64
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Nishizawa M, Nishizawa K. Potential of mean force analysis of the self-association of leucine-rich transmembrane α-helices: difference between atomistic and coarse-grained simulations. J Chem Phys 2015; 141:075101. [PMID: 25149815 DOI: 10.1063/1.4891932] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Interaction of transmembrane (TM) proteins is important in many biological processes. Large-scale computational studies using coarse-grained (CG) simulations are becoming popular. However, most CG model parameters have not fully been calibrated with respect to lateral interactions of TM peptide segments. Here, we compare the potential of mean forces (PMFs) of dimerization of TM helices obtained using a MARTINI CG model and an atomistic (AT) Berger lipids-OPLS/AA model (AT(OPLS)). For helical, tryptophan-flanked, leucine-rich peptides (WL15 and WALP15) embedded in a parallel configuration in an octane slab, the AT(OPLS) PMF profiles showed a shallow minimum (with a depth of approximately 3 kJ/mol; i.e., a weak tendency to dimerize). A similar analysis using the CHARMM36 all-atom model (AT(CHARMM)) showed comparable results. In contrast, the CG analysis generally showed steep PMF curves with depths of approximately 16-22 kJ/mol, suggesting a stronger tendency to dimerize compared to the AT model. This CG > AT discrepancy in the propensity for dimerization was also seen for dilauroylphosphatidylcholine (DLPC)-embedded peptides. For a WL15 (and WALP15)/DLPC bilayer system, AT(OPLS) PMF showed a repulsive mean force for a wide range of interhelical distances, in contrast to the attractive forces observed in the octane system. The change from the octane slab to the DLPC bilayer also mitigated the dimerization propensity in the CG system. The dimerization energies of CG (AALALAA)3 peptides in DLPC and dioleoylphosphatidylcholine bilayers were in good agreement with previous experimental data. The lipid headgroup, but not the length of the lipid tails, was a key causative factor contributing to the differences between octane and DLPC. Furthermore, the CG model, but not the AT model, showed high sensitivity to changes in amino acid residues located near the lipid-water interface and hydrophobic mismatch between the peptides and membrane. These findings may help interpret CG and AT simulation results on membrane proteins.
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Affiliation(s)
- Manami Nishizawa
- Teikyo University School of Medical Technology, Itabashi, Tokyo, Japan
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65
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Genheden S, Essex JW. A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes. J Chem Theory Comput 2015; 11:4749-59. [PMID: 26574264 DOI: 10.1021/acs.jctc.5b00469] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We present an efficient all-atom/coarse-grained hybrid model and apply it to membrane processes. This model is an extension of the all-atom/ELBA model applied previously to processes in water. Here, we improve the efficiency of the model by implementing a multiple-time step integrator that allows the atoms and the coarse-grained beads to be propagated at different timesteps. Furthermore, we fine-tune the interaction between the atoms and the coarse-grained beads by computing the potential of mean force of amino acid side chain analogs along the membrane normal and comparing to atomistic simulations. The model was independently validated on the calculation of small-molecule partition coefficients. Finally, we apply the model to membrane peptides. We studied the tilt angle of the Walp23 and Kalp23 helices in two different model membranes and the stability of the glycophorin A dimer. The model is efficient, accurate, and straightforward to use, as it does not require any extra interaction particles, layers of atomistic solvent molecules or tabulated potentials, thus offering a novel, simple approach to study membrane processes.
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Affiliation(s)
- Samuel Genheden
- School of Chemistry, University of Southampton, Highfield , SO17 1BJ, Southampton, United Kingdom
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Highfield , SO17 1BJ, Southampton, United Kingdom
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66
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Nash A, Notman R, Dixon AM. De novo design of transmembrane helix–helix interactions and measurement of stability in a biological membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1248-57. [DOI: 10.1016/j.bbamem.2015.02.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/29/2015] [Accepted: 02/18/2015] [Indexed: 01/03/2023]
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67
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Johnston AJ, Zhang YR, Busch S, Pardo LC, Imberti S, McLain SE. Amphipathic solvation of indole: implications for the role of tryptophan in membrane proteins. J Phys Chem B 2015; 119:5979-87. [PMID: 25893741 DOI: 10.1021/acs.jpcb.5b02476] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The microscopic structure of the tryptophan side chain, indole, in an amphiphilic environment has been investigated using a combination of neutron diffraction measurements and simulations in solution. The results show that indole is preferentially solvated by hydrogen bonding interactions between water and alcohol -OH groups rather than the interaction being dominated by indole-methyl interactions. This has implications for understanding how tryptophan interacts with the amphipathic membrane environment to anchor proteins into membranes, where the results here suggest that the benzene ring of tryptophan interacts directly with the interfacial water at the membrane surface rather than being buried into the hydrophobic regions of the membrane bilayer.
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Affiliation(s)
| | - Yapei Rosie Zhang
- ‡Department of Biochemistry, Princeton University, Princeton, New Jersey, United States
| | - Sebastian Busch
- ⊥German Engineering Materials Science Centre (GEMS), Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Geesthacht GmbH Lichtenbergstrasse 1, 85747 Garching bei München, Germany
| | - Luis Carlos Pardo
- §Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Barcelona, Catalonia, Spain
| | - Silvia Imberti
- ∥ISIS Facility, Rutherford Appleton Laboratory, Didcot, Chilton, U.K
| | - Sylvia E McLain
- †Department of Biochemistry, University of Oxford, Oxford, U.K
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68
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Arnarez C, Uusitalo JJ, Masman MF, Ingólfsson HI, de Jong DH, Melo MN, Periole X, de Vries AH, Marrink SJ. Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simulations with Implicit Solvent. J Chem Theory Comput 2014; 11:260-75. [DOI: 10.1021/ct500477k] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Clément Arnarez
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Jaakko J. Uusitalo
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Marcelo F. Masman
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Djurre H. de Jong
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Manuel N. Melo
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Xavier Periole
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Alex H. de Vries
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
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69
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Bodor A, Kövér KE, Mäler L. Membrane interactions in small fast-tumbling bicelles as studied by 31P NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:760-6. [PMID: 25497765 DOI: 10.1016/j.bbamem.2014.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/11/2014] [Accepted: 12/01/2014] [Indexed: 01/02/2023]
Abstract
Small fast-tumbling bicelles are ideal for studies of membrane interactions at molecular level; they allow analysis of lipid properties using solution-state NMR. In the present study we used 31P NMR relaxation to obtain detailed information on lipid head-group dynamics. We explored the effect of two topologically different membrane-interacting peptides on bicelles containing either dimyristoylphosphocholine (DMPC), or a mixture of DMPC and dimyristoylphosphoglycerol (DMPG), and dihexanoylphosphocholine (DHPC). KALP21 is a model transmembrane peptide, designed to span a DMPC bilayer and dynorphin B is a membrane surface active neuropeptide. KALP21 causes significant increase in bicelle size, as evidenced by both dynamic light scattering and 31P T2 relaxation measurements. The effect of dynorphin B on bicelle size is more modest, although significant effects on T2 relaxation are observed at higher temperatures. A comparison of 31P T1 values for the lipids with and without the peptides showed that dynorphin B has a greater effect on lipid head-group dynamics than KALP21, especially at elevated temperatures. From the field-dependence of T1 relaxation data, a correlation time describing the overall lipid motion was derived. Results indicate that the positively charged dynorphin B decreases the mobility of the lipid molecules--in particular for the negatively charged DMPG--while KALP21 has a more modest influence. Our results demonstrate that while a transmembrane peptide has severe effects on overall bilayer properties, the surface bound peptide has a more dramatic effect in reducing lipid head-group mobility. These observations may be of general importance for understanding peptide-membrane interactions.
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Affiliation(s)
- Andrea Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, H-1117 Budapest, Hungary.
| | - Katalin E Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm Sweden.
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70
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Figueira TN, Veiga AS, Castanho MA. The interaction of antibodies with lipid membranes unraveled by fluorescence methodologies. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.02.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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71
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Absorption and folding of melittin onto lipid bilayer membranes via unbiased atomic detail microsecond molecular dynamics simulation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2243-9. [DOI: 10.1016/j.bbamem.2014.04.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 03/31/2014] [Accepted: 04/15/2014] [Indexed: 11/22/2022]
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72
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Carballo-Pacheco M, Vancea I, Strodel B. Extension of the FACTS Implicit Solvation Model to Membranes. J Chem Theory Comput 2014; 10:3163-76. [DOI: 10.1021/ct500084y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Martín Carballo-Pacheco
- Forschungszentrum Jülich GmbH, Institute of Complex
Systems: Structural Biochemistry (ICS-6), 52425 Jülich, Germany
| | - Ioan Vancea
- Forschungszentrum Jülich GmbH, Institute of Complex
Systems: Structural Biochemistry (ICS-6), 52425 Jülich, Germany
| | - Birgit Strodel
- Forschungszentrum Jülich GmbH, Institute of Complex
Systems: Structural Biochemistry (ICS-6), 52425 Jülich, Germany
- Institute
of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätstrasse 1, 40225 Düsseldorf, Germany
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73
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Macháň R, Jurkiewicz P, Olżyńska A, Olšinová M, Cebecauer M, Marquette A, Bechinger B, Hof M. Peripheral and integral membrane binding of peptides characterized by time-dependent fluorescence shifts: focus on antimicrobial peptide LAH₄. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:6171-9. [PMID: 24807004 DOI: 10.1021/la5006314] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Positioning of peptides with respect to membranes is an important parameter for biological and biophysical studies using model systems. Our experiments using five different membrane peptides suggest that the time-dependent fluorescence shift (TDFS) of Laurdan can help when distinguishing between peripheral and integral membrane binding and can be a useful, novel tool for studying the impact of transmembrane peptides (TMP) on membrane organization under near-physiological conditions. This article focuses on LAH4, a model α-helical peptide with high antimicrobial and nucleic acid transfection efficiencies. The predominantly helical peptide has been shown to orient in supported model membranes parallel to the membrane surface at acidic and, in a transmembrane manner, at basic pH. Here we investigate its interaction with fully hydrated large unilamellar vesicles (LUVs) by TDFS and fluorescence correlation spectroscopy (FCS). TDFS shows that at acidic pH LAH4 does not influence the glycerol region while at basic pH it makes acyl groups at the glycerol level of the membrane less mobile. TDFS experiments with antimicrobial peptides alamethicin and magainin 2, which are known to assume transmembrane and peripheral orientations, respectively, prove that changes in acyl group mobility at the glycerol level correlate with the orientation of membrane-associated peptide molecules. Analogous experiments with the TMPs LW21 and LAT show similar effects on the mobility of those acyl groups as alamethicin and LAH4 at basic pH. FCS, on the same neutral lipid bilayer vesicles, shows that the peripheral binding mode of LAH4 is more efficient in bilayer permeation than the transmembrane mode. In both cases, the addition of LAH4 does not lead to vesicle disintegration. The influence of negatively charged lipids on the bilayer permeation is also addressed.
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Affiliation(s)
- Radek Macháň
- J. Heyrovský Institute of Physical Chemistry of ASCR, v.v.i., Dolejškova 3, Prague 8, CZ-18223, Czech Repulic
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74
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Sparks KA, Gleason NJ, Gist R, Langston R, Greathouse DV, Koeppe RE. Comparisons of interfacial Phe, Tyr, and Trp residues as determinants of orientation and dynamics for GWALP transmembrane peptides. Biochemistry 2014; 53:3637-45. [PMID: 24829070 PMCID: PMC4053069 DOI: 10.1021/bi500439x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Aromatic
amino acids often flank the transmembrane alpha helices
of integral membrane proteins. By favoring locations within the membrane–water
interface of the lipid bilayer, aromatic residues Trp, Tyr, and sometimes
Phe may serve as anchors to help stabilize a transmembrane orientation.
In this work, we compare the influence of interfacial Trp, Tyr, or
Phe residues upon the properties of tilted helical transmembrane peptides.
For such comparisons, it has been critical to start with no more than
one interfacial aromatic residue near each end of a transmembrane
helix, for example, that of GWALP23 (acetyl-GGALW5(LA)6LW19LAGA-[ethanol]amide). To this end, we have
employed 2H-labeled alanines and solid-state NMR spectroscopy
to investigate the consequences of moving or replacing W5 or W19 in
GWALP23 with selected Tyr, Phe, or Trp residues at the same or proximate
locations. We find that GWALP23 peptides having F5, Y5, or W5 exhibit
essentially the same average tilt and similar dynamics in bilayer
membranes of 1,2-dilauroylphosphatidylcholine (DLPC) or 1,2-dioleoylphosphatidylcholine
(DOPC). When double Tyr anchors are present, in Y4,5GWALP23
the NMR observables are markedly more subject to dynamic averaging
and at the same time are less responsive to the bilayer thickness.
Decreased dynamics are nevertheless observed when ring hydrogen bonding
is removed, such that F4,5GWALP23 exhibits a similar extent
of low dynamic averaging as GWALP23 itself. When F5 is the sole aromatic
group in the N-interfacial region, the dynamic averaging is (only)
slightly more extensive than with W5, Y5, or Y4 alone or with F4,5,
yet it is much less than that observed for Y4,5GWALP23.
Interestingly, moving Y5 to Y4 or W19 to W18, while retaining only
one hydrogen-bond-capable aromatic ring at each interface, maintains
the low level of dynamic averaging but alters the helix azimuthal
rotation. The rotation change is about 40° for Y4 regardless
of whether the host lipid bilayer is DLPC or DOPC. The rotational
change (Δρ) is more dramatic and more complex when W19
is moved to W18, as Δρ is about +90° in DLPC but
about −60° in DOPC. Possible reasons for this curious
lipid-dependent helix rotation could include not only the separation
distances between flanking aromatic or hydrophobic residues but also
the absolute location of the W19 indole ring. For the more usual cases,
when the helix azimuthal rotation shows little dependence on the host
bilayer identity, excepting W18GWALP23, the transmembrane
helices adapt to different lipids primarily by changing the magnitude
of their tilt. We conclude that, in the absence of other functional
groups, interfacial aromatic residues determine the preferred orientations
and dynamics of membrane-spanning peptides. The results furthermore
suggest possibilities for rotational and dynamic control of membrane
protein function.
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Affiliation(s)
- Kelsey A Sparks
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
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75
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Brice AR, Lazaridis T. Structure and dynamics of a fusion peptide helical hairpin on the membrane surface: comparison of molecular simulations and NMR. J Phys Chem B 2014; 118:4461-70. [PMID: 24712538 PMCID: PMC4010296 DOI: 10.1021/jp409412g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The conserved N-terminal residues of the HA2 subunit of influenza hemagglutinin (fusion peptide) are essential for membrane fusion and viral entry. Recent NMR studies showed that the 23-residue fusion peptide forms a helical hairpin that undergoes rocking motion relative to the membrane surface on a nanosecond time scale. To compare with NMR and to obtain a detailed molecular picture of the peptide-membrane interaction, we performed molecular dynamics simulations of the fusion peptide in explicit dimyristoylphosphatidylcholine and with the IMM1 implicit membrane model. To account for low and neutral pH conditions, simulations were performed with acidic groups (E11 and D19) protonated and unprotonated, respectively. The hairpin structure was stable in the simulations, with the N-terminal helix buried more deeply into the hydrophobic membrane interior than the C-terminal helix. Interactions between the tryptophans in the fusion peptide and phospholipid residues contribute to peptide orientation. Higher flexibility of the hairpin was observed in the implicit membrane simulations. Internal correlation functions of backbone N-H vectors were fit to the extended Lipari-Szabo model-free approach to obtain order parameters and correlation times. Good agreement with the NMR results was obtained for orientational fluctuations around the hairpin axis (rotation), but those around the perpendicular axis (tilting) were more limited in the simulations than inferred from the NMR experiments.
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Affiliation(s)
- Allyn R Brice
- Department of Chemistry, City College of New York , 160 Convent Avenue, New York, New York 10031, United States
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76
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Li XD, Li XF, Ye HQ, Deng CL, Ye Q, Shan C, Shang BD, Xu LL, Li SH, Cao SB, Yuan ZM, Shi PY, Qin CF, Zhang B. Recovery of a chemically synthesized Japanese encephalitis virus reveals two critical adaptive mutations in NS2B and NS4A. J Gen Virol 2013; 95:806-815. [PMID: 24362961 DOI: 10.1099/vir.0.061838-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A full-length genome infectious clone is a powerful tool for functional assays in virology. In this study, using a chemical synthesized complete genome of Japanese encephalitis virus (JEV) strain SA14 (GenBank accession no. U14163), we constructed a full-length genomic cDNA clone of JEV. The recovered virus from the cDNA clone replicated poorly in baby hamster kidney (BHK-21) cells and in suckling mice brain. Following serial passage in BHK-21 cells, adaptive mutations within the NS2B and NS4A proteins were recovered in the passaged viruses leading to viruses with a large-plaque phenotype. Mutagenesis analysis, using a genome-length RNA and a replicon of JEV, demonstrated that the adaptive mutations restored replication to different degrees, and the restoration efficiencies were in the order: NS2B-T102M<NS4A-R79K<NS2B-T102M+NS4A-R79K. An in vivo virulence assay in mice showed that the recombinant virus containing double mutations showed similar virulence to the WT SA14 (GenBank accession no. M55506). This study reports the first chemically synthesized JEV. A reverse genetics assay demonstrated that substitutions of NS2B-T102M and NS4A-R79K altered JEV replication.
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Affiliation(s)
- Xiao-Dan Li
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Xiao-Feng Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Han-Qing Ye
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Cheng-Lin Deng
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China.,Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Qing Ye
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Chao Shan
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Bao-Di Shang
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Lin-Lin Xu
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Shi-Hua Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Sheng-Bo Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Zhi-Ming Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China.,Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Pei-Yong Shi
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Cheng-Feng Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Bo Zhang
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China.,Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
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77
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Gleason NJ, Greathouse DV, Grant CV, Opella SJ, Koeppe RE. Single tryptophan and tyrosine comparisons in the N-terminal and C-terminal interface regions of transmembrane GWALP peptides. J Phys Chem B 2013; 117:13786-94. [PMID: 24111589 DOI: 10.1021/jp407542e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hydrophobic membrane-spanning helices often are flanked by interfacial aromatic or charged residues. In this paper, we compare the consequences of single Trp → Tyr substitutions at each interface for the properties of a defined transmembrane helix in the absence of charged residues. The choice of molecular framework is critical for these single-residue experiments because the presence of "too many" aromatic residues (more than one at either membrane-water interface) introduces excess dynamic averaging of solid state NMR observables. To this end, we compare the outcomes when changing W(5) or W(19), or both of them, to tyrosine in the well-characterized transmembrane peptide acetyl-GGALW(5)(LA)6LW(19)LAGA-amide ("GWALP23"). By means of solid-state (2)H and (15)N NMR experiments, we find that Y(19)GW(5)ALP23 displays similar magnitudes of peptide helix tilt as Y(5)GW(19)ALP23 and responds similarly to changes in bilayer thickness, from DLPC to DMPC to DOPC. The presence of Y(19) changes the azimuthal rotation angle ρ (about the helix axis) to a similar extent as Y(5), but in the opposite direction. When tyrosines are substituted for both tryptophans to yield GY(5,19)ALP23, the helix tilt angle is again of comparable magnitude, and furthermore, the preferred azimuthal rotation angle ρ is relatively unchanged from that of GW(5,19)ALP23. The extent of dynamic averaging increases marginally when Tyr replaces Trp. Yet, importantly, all members of the peptide family having single Tyr or Trp residues near each interface exhibit only moderate and not highly extensive dynamic averaging. The results provide important benchmarks for evaluating conformational and dynamic control of membrane protein function.
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Affiliation(s)
- Nicholas J Gleason
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
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78
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Finton KAK, Larimore K, Larman HB, Friend D, Correnti C, Rupert PB, Elledge SJ, Greenberg PD, Strong RK. Autoreactivity and exceptional CDR plasticity (but not unusual polyspecificity) hinder elicitation of the anti-HIV antibody 4E10. PLoS Pathog 2013; 9:e1003639. [PMID: 24086134 PMCID: PMC3784475 DOI: 10.1371/journal.ppat.1003639] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 08/04/2013] [Indexed: 01/19/2023] Open
Abstract
The broadly-neutralizing anti-HIV antibody 4E10 recognizes an epitope in the membrane-proximal external region of the HIV envelope protein gp41. Previous attempts to elicit 4E10 by vaccination with envelope-derived or reverse-engineered immunogens have failed. It was presumed that the ontogeny of 4E10-equivalent responses was blocked by inherent autoreactivity and exceptional polyreactivity. We generated 4E10 heavy-chain knock-in mice, which displayed significant B cell dysregulation, consistent with recognition of autoantigen/s by 4E10 and the presumption that tolerance mechanisms may hinder the elicitation of 4E10 or 4E10-equivalent responses. Previously proposed candidate 4E10 autoantigens include the mitochondrial lipid cardiolipin and a nuclear splicing factor, 3B3. However, using carefully-controlled assays, 4E10 bound only weakly to cardiolipin-containing liposomes, but also bound negatively-charged, non-cardiolipin-containing liposomes comparably poorly. 4E10/liposome binding was predominantly mediated by electrostatic interactions rather than presumed hydrophobic interactions. The crystal structure of 4E10 free of bound ligands showed a dramatic restructuring of the combining site, occluding the HIV epitope binding site and revealing profound flexibility, but creating an electropositive pocket consistent with non-specific binding of phospholipid headgroups. These results strongly suggested that antigens other than cardiolipin mediate 4E10 autoreactivity. Using a synthetic peptide library spanning the human proteome, we determined that 4E10 displays limited and focused, but unexceptional, polyspecificity. We also identified a novel autoepitope shared by three ER-resident inositol trisphosphate receptors, validated through binding studies and immunohistochemistry. Tissue staining with 4E10 demonstrated reactivity consistent with the type 1 inositol trisphosphate receptor as the most likely candidate autoantigen, but is inconsistent with splicing factor 3B3. These results demonstrate that 4E10 recognition of liposomes competes with MPER recognition and that HIV antigen and autoepitope recognition may be distinct enough to permit eliciting 4E10-like antibodies, evading autoimmunity through directed engineering. However, 4E10 combining site flexibility, exceptional for a highly-matured antibody, may preclude eliciting 4E10 by conventional immunization strategies.
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Affiliation(s)
- Kathryn A K Finton
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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79
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Sánchez-Muñoz OL, Strandberg E, Esteban-Martín E, Grage SL, Ulrich AS, Salgado J. Canonical azimuthal rotations and flanking residues constrain the orientation of transmembrane helices. Biophys J 2013; 104:1508-16. [PMID: 23561527 DOI: 10.1016/j.bpj.2013.02.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 01/31/2013] [Accepted: 02/20/2013] [Indexed: 12/22/2022] Open
Abstract
In biological membranes the alignment of embedded proteins provides crucial structural information. The transmembrane (TM) parts have well-defined secondary structures, in most cases α-helices and their orientation is given by a tilt angle and an azimuthal rotation angle around the main axis. The tilt angle is readily visualized and has been found to be functionally relevant. However, there exist no general concepts on the corresponding azimuthal rotation. Here, we show that TM helices prefer discrete rotation angles. They arise from a combination of intrinsic properties of the helix geometry plus the influence of the position and type of flanking residues at both ends of the hydrophobic core. The helical geometry gives rise to canonical azimuthal angles for which the side chains of residues from the two ends of the TM helix tend to have maximum or minimum immersion within the membrane. This affects the preferential position of residues that fall near hydrophobic/polar interfaces of the membrane, depending on their hydrophobicity and capacity to form specific anchoring interactions. On this basis, we can explain the orientation and dynamics of TM helices and make accurate predictions, which correspond well to the experimental values of several model peptides (including dimers), and TM segments of polytopic membrane proteins.
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80
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Bennett WD, Tieleman DP. Computer simulations of lipid membrane domains. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1765-76. [DOI: 10.1016/j.bbamem.2013.03.004] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 02/28/2013] [Accepted: 03/01/2013] [Indexed: 10/27/2022]
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81
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Mäler L. Solution NMR studies of cell-penetrating peptides in model membrane systems. Adv Drug Deliv Rev 2013; 65:1002-11. [PMID: 23137785 DOI: 10.1016/j.addr.2012.10.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 10/17/2012] [Accepted: 10/22/2012] [Indexed: 12/29/2022]
Abstract
Cell-penetrating peptides (CPPs) are a class of short, often cationic peptides that have the capability to translocate across cellular membranes, and although the translocation most likely involves several pathways, they interact directly with membranes, as well as with model bilayers. Most CPPs attain a three-dimensional structure when interacting with bilayers, while they are more or less unstructured in aqueous solution. To understand the relationship between structure and the effect that CPPs have on membranes it is of great importance to investigate CPPs at atomic resolution in a suitable membrane model. Moreover, the location in bilayers is likely to be correlated with the translocation mechanism. Solution-state NMR offers a unique possibility to investigate structure, dynamics and location of proteins and peptides in bilayers. This review focuses on solution NMR as a tool for investigating CPP-lipid interactions. Structural propensities and cell-penetrating capabilities can be derived from a combination of CPP solution structures and studies of the effect that the peptides have on bilayers and the localization in a bilayer.
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Affiliation(s)
- Lena Mäler
- Department of Biochemistry and Biophysics, The Arrhenius Laboratory, Stockholm University, Stockholm, Sweden.
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82
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Björnerås J, Gräslund A, Mäler L. Membrane Interaction of Disease-Related Dynorphin A Variants. Biochemistry 2013; 52:4157-67. [DOI: 10.1021/bi4004205] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Johannes Björnerås
- Department of Biochemistry
and Biophysics, The Arrhenius
Laboratory, Stockholm University, 10691
Stockholm, Sweden
| | - Astrid Gräslund
- Department of Biochemistry
and Biophysics, The Arrhenius
Laboratory, Stockholm University, 10691
Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry
and Biophysics, The Arrhenius
Laboratory, Stockholm University, 10691
Stockholm, Sweden
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83
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84
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Buried lysine, but not arginine, titrates and alters transmembrane helix tilt. Proc Natl Acad Sci U S A 2013; 110:1692-5. [PMID: 23319623 DOI: 10.1073/pnas.1215400110] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The ionization states of individual amino acid residues of membrane proteins are difficult to decipher or assign directly in the lipid-bilayer membrane environment. We address this issue for lysines and arginines in designed transmembrane helices. For lysines (but not arginines) at two locations within dioleoyl-phosphatidylcholine bilayer membranes, we measure pK(a) values below 7.0. We find that buried charged lysine, in fashion similar to arginine, will modulate helix orientation to maximize its own access to the aqueous interface or, if occluded by aromatic rings, may cause a transmembrane helix to exit the lipid bilayer. Interestingly, the influence of neutral lysine (vis-à-vis leucine) upon helix orientation also depends upon its aqueous access. Our results suggest that changes in the ionization states of particular residues will regulate membrane protein function and furthermore illustrate the subtle complexity of ionization behavior with respect to the detailed lipid and protein environment.
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85
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Yoo J, Cui Q. Three-dimensional stress field around a membrane protein: atomistic and coarse-grained simulation analysis of gramicidin A. Biophys J 2013; 104:117-27. [PMID: 23332064 PMCID: PMC3540266 DOI: 10.1016/j.bpj.2012.11.3812] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 10/29/2012] [Accepted: 11/21/2012] [Indexed: 01/25/2023] Open
Abstract
Using both atomistic and coarse-grained (CG) models, we compute the three-dimensional stress field around a gramicidin A (gA) dimer in lipid bilayers that feature different degrees of negative hydrophobic mismatch. The general trends in the computed stress field are similar at the atomistic and CG levels, supporting the use of the CG model for analyzing the mechanical features of protein/lipid/water interfaces. The calculations reveal that the stress field near the protein-lipid interface exhibits a layered structure with both significant repulsive and attractive regions, with the magnitude of the stress reaching 1000 bar in certain regions. Analysis of density profiles and stress field distributions helps highlight the Trp residues at the protein/membrane/water interface as mechanical anchors, suggesting that similar analysis is useful for identifying tension sensors in other membrane proteins, especially membrane proteins involved in mechanosensation. This work fosters a connection between microscopic and continuum mechanics models for proteins in complex environments and makes it possible to test the validity of assumptions commonly made in continuum mechanics models for membrane mediated processes. For example, using the calculated stress field, we estimate the free energy of membrane deformation induced by the hydrophobic mismatch, and the results for regions beyond the annular lipids are in general consistent with relevant experimental data and previous theoretical estimates using elasticity theory. On the other hand, the assumptions of homogeneous material properties for the membrane and a bilayer thickness at the protein/lipid interface being independent of lipid type (e.g., tail length) appear to be oversimplified, highlighting the importance of annular lipids of membrane proteins. Finally, the stress field analysis makes it clear that the effect of even rather severe hydrophobic mismatch propagates to only about two to three lipid layers, thus putting a limit on the range of cooperativity between membrane proteins in crowded cellular membranes.
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Affiliation(s)
- Jejoong Yoo
- Graduate Program in Biophysics, University of Wisconsin, Madison, Wisconsin
| | - Qiang Cui
- Graduate Program in Biophysics, University of Wisconsin, Madison, Wisconsin
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin
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86
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Grimm C, Meyer T, Czapla S, Nikolaus J, Scheidt HA, Vogel A, Herrmann A, Wessig P, Huster D, Müller P. Structure and Dynamics of Molecular Rods in Membranes: Application of a Spin-Labeled Rod. Chemistry 2013; 19:2703-10. [DOI: 10.1002/chem.201202500] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 11/19/2012] [Indexed: 11/07/2022]
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87
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Ijäs HK, Lönnfors M, Nyholm TKM. Sterol affinity for phospholipid bilayers is influenced by hydrophobic matching between lipids and transmembrane peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:932-7. [PMID: 23220446 DOI: 10.1016/j.bbamem.2012.11.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/29/2012] [Accepted: 11/30/2012] [Indexed: 01/04/2023]
Abstract
Lipid self-organization is believed to be essential for shaping the lateral structure of membranes, but it is becoming increasingly clear that also membrane proteins can be involved in the maintenance of membrane architecture. Cholesterol is thought to be important for the lateral organization of eukaryotic cell membranes and has also been implicated to take part in the sorting of cellular transmembrane proteins. Hence, a good starting point for studying the influence of lipid-protein interactions on membrane trafficking is to find out how transmembrane proteins influence the lateral sorting of cholesterol in phospholipid bilayers. By measuring equilibrium partitioning of the fluorescent cholesterol analog cholestatrienol between large unilamellar vesicles and methyl-β-cyclodextrin the effect of hydrophobic matching on the affinity of sterols for phospholipid bilayers was determined. Sterol partitioning was measured in 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers with and without WALP19, WALP23 or WALP27 peptides. The results showed that the affinity of the sterol for the bilayers was affected by hydrophobic matching. An increasing positive hydrophobic mismatch led to stronger sterol binding to the bilayers (except in extreme situations), and a large negative hydrophobic mismatch decreased the affinity of the sterol for the bilayer. In addition, peptide insertion into the phospholipid bilayers was observed to depend on hydrophobic matching. In conclusion, the results showed that hydrophobic matching can affect lipid-protein interactions in a way that may facilitate the formation of lateral domains in cell membranes. This could be of importance in membrane trafficking.
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Affiliation(s)
- H Kristian Ijäs
- Department of Bioscience, Åbo Akademi University, Tykistökatu 6A, Turku, Finland
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88
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Rankenberg JM, Vostrikov VV, Greathouse DV, Grant CV, Opella SJ, Koeppe RE. Properties of membrane-incorporated WALP peptides that are anchored on only one end. Biochemistry 2012; 51:10066-74. [PMID: 23171005 DOI: 10.1021/bi301394z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptides of the "WALP" family, acetyl-GWW(LA)(n)LWWA-[ethanol]amide, have proven to be opportune models for investigating lipid-peptide interactions. Because the average orientations and motional behavior of the N- and C-terminal Trp (W) residues differ, it is of interest to investigate how the positions of the tryptophans influence the properties of the membrane-incorporated peptides. To address this question, we synthesized acetyl-GGWW(LA)(n)-ethanolamide and acetyl-(AL)(n)WWG-ethanolamide, in which n = 4 or 8, which we designate as "N-anchored" and "C-anchored" peptides, respectively. Selected (2)H or (15)N labels were incorporated for solid-state nuclear magnetic resonance (NMR) spectroscopy. These peptides can be considered "half"-anchored WALP peptides, having only one pair of interfacial Trp residues near either the amino or the carboxyl terminus. The hydrophobic lengths of the (n = 8) peptides are similar to that of WALP23. These longer half-anchored WALP peptides incorporate into lipid bilayers as α-helices, as reflected in their circular dichroism spectra. Solid-state NMR experiments indicate that the longer peptide helices assume defined transmembrane orientations with small non-zero average tilt angles and moderate to high dynamic averaging in bilayer membranes of 1,2-dioleoylphosphatidylcholine, 1,2-dimyristoylphosphatidylcholine, and 1,2-dilauroylphosphatidylcholine. The intrinsically small apparent tilt angles suggest that interactions of aromatic residues with lipid headgroups may play an important role in determining the magnitude of the peptide tilt in the bilayer membrane. The shorter (n = 4) peptides, in stark contrast to the longer peptides, display NMR spectra that are characteristic of greatly reduced motional averaging, probably because of peptide aggregation in the bilayer environment, and CD spectra that are characteristic of β-structure.
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Affiliation(s)
- Johanna M Rankenberg
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
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89
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Haywood AF, Merner ND, Hodgkinson KA, Houston J, Syrris P, Booth V, Connors S, Pantazis A, Quarta G, Elliott P, McKenna W, Young TL. Recurrent missense mutations in TMEM43 (ARVD5) due to founder effects cause arrhythmogenic cardiomyopathies in the UK and Canada. Eur Heart J 2012; 34:1002-11. [DOI: 10.1093/eurheartj/ehs383] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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90
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Kasuya Y, Tsukamoto K, Yamada D, Matsumura K. Immobilization of a Single Intact Liposome onto a Peptide-modified Glass Microwell. CHEM LETT 2012. [DOI: 10.1246/cl.2012.1191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Yuzo Kasuya
- Faculty of Science and Engineering, Waseda University
- Graduate School of Engineering, Shibaura Institute of Technology
| | - Kei Tsukamoto
- Graduate School of Engineering, Shibaura Institute of Technology
| | - Daisuke Yamada
- Graduate School of Engineering, Shibaura Institute of Technology
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91
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de Jesus AJ, Allen TW. The role of tryptophan side chains in membrane protein anchoring and hydrophobic mismatch. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:864-76. [PMID: 22989724 DOI: 10.1016/j.bbamem.2012.09.009] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 12/27/2022]
Abstract
Tryptophan (Trp) is abundant in membrane proteins, preferentially residing near the lipid-water interface where it is thought to play a significant anchoring role. Using a total of 3 μs of molecular dynamics simulations for a library of hydrophobic WALP-like peptides, a long poly-Leu α-helix, and the methyl-indole analog, we explore the thermodynamics of the Trp movement in membranes that governs the stability and orientation of transmembrane protein segments. We examine the dominant hydrogen-bonding interactions between the Trp and lipid carbonyl and phosphate moieties, cation-π interactions to lipid choline moieties, and elucidate the contributions to the thermodynamics that serve to localize the Trp, by ~4 kcal/mol, near the membrane glycerol backbone region. We show a striking similarity between the free energy to move an isolated Trp side chain to that found from a wide range of WALP peptides, suggesting that the location of this side chain is nearly independent of the host transmembrane segment. Our calculations provide quantitative measures that explain Trp's role as a modulator of responses to hydrophobic mismatch, providing a deeper understanding of how lipid composition may control a range of membrane active peptides and proteins.
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92
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Lee JK, Park SC, Hahm KS, Park Y. Antimicrobial HPA3NT3 peptide analogs: placement of aromatic rings and positive charges are key determinants for cell selectivity and mechanism of action. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:443-54. [PMID: 22982494 DOI: 10.1016/j.bbamem.2012.09.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 12/26/2022]
Abstract
In an earlier study, we determined that HP(2-20) (residues 2-20 of parental HP derived from the N-terminus of the Helicobacter pylori ribosomal protein L1) and its analog, HPA3NT3, had potent antimicrobial effects. However, HPA3NT3 also showed undesirable cytotoxicity against HaCaT cells. In the present study, we designed peptide analogs including HPA3NT3-F1A (-F1A), HPA3NT3-F8A (-F8A), HPA3NT3-F1AF8A (-F1AF8A), HPA3NT3-A1 (-A1) and HPA3NT3-A2 (-A2) in an effort to investigate the effects of amino acid substitutions in reducing their hydrophobicity or increasing their cationicity, and any resulting effects on their selectivity in their interactions with human cells and pathogens, as well as their mechanism of antimicrobial action. With the exception of HPA3NT3-A1, all of these peptides showed potent antimicrobial activity. Moreover, substitution of Ala for Phe at positions 1 and/or 8 of the HPA3NT3 peptides (-F1A, -F8A and -F1AF8A) dramatically reduced their cytotoxicity. Thus the cytotoxicity of HPA3NT3 appears to be related to its Phe residues (positions 1 and 8), which strongly interact with sphingomyelin in the mammalian cell membrane. HPA3NT3 exerted its bactericidal effects through membrane permeabilization mediated by pore formation. In contrast, fluorescent dye leakage and nucleic acid gel retardation assays showed that -A2 acted by penetrating into the cytoplasm, where it bound to nucleic acids and inhibited protein synthesis. Notably, Staphylococcus aureus did not develop resistance to -A2 as it did with rifampin. These results suggest that the -A2 peptide could potentially serve as an effective antibiotic agent against multidrug-resistant bacterial strains.
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Affiliation(s)
- Jong-Kook Lee
- Research Center for Proteinaceous Materials (RCPM), Chosun University, Kwangju 501-759, Republic of Korea
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93
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Novotná P, Urbanová M. Vibrational circular dichroism study of polypeptide model–membrane systems. Anal Biochem 2012; 427:211-8. [DOI: 10.1016/j.ab.2012.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 03/25/2012] [Accepted: 03/26/2012] [Indexed: 12/01/2022]
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94
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Nagulapalli M, Parigi G, Yuan J, Gsponer J, Deraos G, Bamm VV, Harauz G, Matsoukas J, de Planque MRR, Gerothanassis IP, Babu MM, Luchinat C, Tzakos AG. Recognition pliability is coupled to structural heterogeneity: a calmodulin intrinsically disordered binding region complex. Structure 2012; 20:522-33. [PMID: 22405011 DOI: 10.1016/j.str.2012.01.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 12/01/2011] [Accepted: 01/03/2012] [Indexed: 11/18/2022]
Abstract
Protein interactions within regulatory networks should adapt in a spatiotemporal-dependent dynamic environment, in order to process and respond to diverse and versatile cellular signals. However, the principles governing recognition pliability in protein complexes are not well understood. We have investigated a region of the intrinsically disordered protein myelin basic protein (MBP(145-165)) that interacts with calmodulin, but that also promiscuously binds other biomolecules (membranes, modifying enzymes). To characterize this interaction, we implemented an NMR spectroscopic approach that calculates, for each conformation of the complex, the maximum occurrence based on recorded pseudocontact shifts and residual dipolar couplings. We found that the MBP(145-165)-calmodulin interaction is characterized by structural heterogeneity. Quantitative comparative analysis indicated that distinct conformational landscapes of structural heterogeneity are sampled for different calmodulin-target complexes. Such structural heterogeneity in protein complexes could potentially explain the way that transient and promiscuous protein interactions are optimized and tuned in complex regulatory networks.
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Affiliation(s)
- Malini Nagulapalli
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
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95
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Gofman Y, Haliloglu T, Ben-Tal N. The Transmembrane Helix Tilt May Be Determined by the Balance between Precession Entropy and Lipid Perturbation. J Chem Theory Comput 2012; 8:2896-2904. [PMID: 24932138 PMCID: PMC4053537 DOI: 10.1021/ct300128x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Indexed: 11/29/2022]
Abstract
Hydrophobic helical peptides interact with lipid bilayers
in various
modes, determined by the match between the length of the helix’s
hydrophobic core and the thickness of the hydrocarbon region of the
bilayer. For example, long helices may tilt with respect to the membrane
normal to bury their hydrophobic cores in the membrane, and the lipid
bilayer may stretch to match the helix length. Recent molecular dynamics
simulations and potential of mean force calculations have shown that
some TM helices whose lengths are equal to, or even shorter than,
the bilayer thickness may also tilt. The tilt is driven by a gain
in the helix precession entropy, which compensates for the free energy
penalty resulting from membrane deformation. Using this free energy
balance, we derived theoretically an equation of state, describing
the dependence of the tilt on the helix length and membrane thickness.
To this end, we conducted coarse-grained Monte Carlo simulations of
the interaction of helices of various lengths with lipid bilayers
of various thicknesses, reproducing and expanding the previous molecular
dynamics simulations. Insight from the simulations facilitated the
derivation of the theoretical model. The tilt angles calculated using
the theoretical model agree well with our simulations and with previous
calculations and measurements.
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Affiliation(s)
- Yana Gofman
- Helmholtz-Zentrum, 21502 Geesthacht, Germany ; The Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
| | - Turkan Haliloglu
- Chemical Engineering Department, Polymer Research Center, Life Sciences and Technologies Research Center, Bogazici University, 34342 Bebek-Istanbul, Turkey
| | - Nir Ben-Tal
- The Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
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96
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97
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Gleason NJ, Vostrikov VV, Greathouse DV, Grant CV, Opella SJ, Koeppe RE. Tyrosine replacing tryptophan as an anchor in GWALP peptides. Biochemistry 2012; 51:2044-53. [PMID: 22364236 DOI: 10.1021/bi201732e] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synthetic model peptides have proven useful for examining fundamental peptide-lipid interactions. A frequently employed peptide design consists of a hydrophobic core of Leu-Ala residues with polar or aromatic amino acids flanking each side at the interfacial positions, which serve to "anchor" a specific transmembrane orientation. For example, WALP family peptides (acetyl-GWW(LA)(n)LWWA-[ethanol]amide), anchored by four Trp residues, have received particular attention in both experimental and theoretical studies. A recent modification proved successful in reducing the number of Trp anchors to only one near each end of the peptide. The resulting GWALP23 (acetyl-GGALW(5)(LA)(6)LW(19)LAGA-[ethanol]amide) displays reduced dynamics and greater sensitivity to lipid-peptide hydrophobic mismatch than traditional WALP peptides. We have further modified GWALP23 to incorporate a single tyrosine, replacing W(5) with Y(5). The resulting peptide, Y(5)GWALP23 (acetyl-GGALY(5)(LA)(6)LW(19)LAGA-amide), has a single Trp residue that is sensitive to fluorescence experiments. By incorporating specific (2)H and (15)N labels in the core sequence of Y(5)GWALP23, we were able to use solid-state NMR spectroscopy to examine the peptide orientation in hydrated lipid bilayer membranes. The peptide orients well in membranes and gives well-defined (2)H quadrupolar splittings and (15)N/(1)H dipolar couplings throughout the core helical sequence between the aromatic residues. The substitution of Y(5) for W(5) has remarkably little influence on the tilt or dynamics of GWALP23 in bilayer membranes of the phospholipids DOPC, DMPC, or DLPC. A second analogue of the peptide with one Trp and two Tyr anchors, Y(4,5)GWALP23, is generally less responsive to the bilayer thickness and exhibits lower apparent tilt angles with evidence of more extensive dynamics. In general, the peptide behavior with multiple Tyr anchors appears to be quite similar to the situation when multiple Trp anchors are present, as in the original WALP series of model peptides.
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Affiliation(s)
- Nicholas J Gleason
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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98
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Strandberg E, Esteban-Martín S, Ulrich AS, Salgado J. Hydrophobic mismatch of mobile transmembrane helices: Merging theory and experiments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:1242-9. [PMID: 22326890 DOI: 10.1016/j.bbamem.2012.01.023] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 01/23/2012] [Accepted: 01/25/2012] [Indexed: 10/14/2022]
Abstract
Hydrophobic mismatch still represents a puzzle for transmembrane peptides, despite the apparent simplicity of this concept and its demonstrated validity in natural membranes. Using a wealth of available experimental ((2))H NMR data, we provide here a comprehensive explanation of the orientation and dynamics of model peptides in lipid bilayers, which shows how they can adapt to membranes of different thickness. The orientational adjustment of transmembrane α-helices can be understood as the result of a competition between the thermodynamically unfavorable lipid repacking associated with peptide tilting and the optimization of peptide/membrane hydrophobic coupling. In the positive mismatch regime (long-peptide/thin-membrane) the helices adapt mainly via changing their tilt angle, as expected from simple geometrical predictions. However, the adaptation mechanism varies with the peptide sequence in the flanking regions, suggesting additional effects that modulate hydrophobic coupling. These originate from re-adjustments of the peptide hydrophobic length and they depend on the hydrophobicity of the flanking region, the strength of interfacial anchoring, the structural flexibility of anchoring side-chains and the presence of alternative anchoring residues.
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Affiliation(s)
- Erik Strandberg
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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99
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Probing the lipid-protein interface using model transmembrane peptides with a covalently linked acyl chain. Biophys J 2012; 101:1959-67. [PMID: 22004750 DOI: 10.1016/j.bpj.2011.09.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 09/12/2011] [Accepted: 09/15/2011] [Indexed: 12/11/2022] Open
Abstract
The aim of this study was to gain insight into how interactions between proteins and lipids in membranes are sensed at the protein-lipid interface. As a probe to analyze this interface, we used deuterium-labeled acyl chains that were covalently linked to a model transmembrane peptide. First, a perdeuterated palmitoyl chain was coupled to the Trp-flanked peptide WALP23 (Ac-CGWW(LA)(8)LWWA-NH(2)), and the deuterium NMR spectrum was analyzed in di-C18:1-phosphatidylcholine (PC) bilayers. We found that the chain order of this peptide-linked chain is rather similar to that of a noncovalently coupled perdeuterated palmitoyl chain, except that it exhibits a slightly lower order. Similar results were obtained when site-specific deuterium labels were used and when the palmitoyl chain was attached to the more-hydrophobic model peptide WLP23 (Ac-CGWWL(17)WWA-NH(2)) or to the Lys-flanked peptide KALP23 (Ac-CGKK(LA)(8)LKKA-NH(2)). The experiments showed that the order of both the peptide-linked chains and the noncovalently coupled palmitoyl chains in the phospholipid bilayer increases in the order KALP23 < WALP23 < WLP23. Furthermore, changes in the bulk lipid bilayer thickness caused by varying the lipid composition from di-C14:1-PC to di-C18:1-PC or by including cholesterol were sensed rather similarly by the covalently coupled chain and the noncovalently coupled palmitoyl chains. The results indicate that the properties of lipids adjacent to transmembrane peptides mostly reflect the properties of the surrounding lipid bilayer, and hence that (at least for the single-span model peptides used in this study) annular lipids do not play a highly specific role in protein-lipid interactions.
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Papareddy P, Mörgelin M, Walse B, Schmidtchen A, Malmsten M. Antimicrobial activity of peptides derived from human ß-amyloid precursor protein. J Pept Sci 2012; 18:183-91. [PMID: 22249992 DOI: 10.1002/psc.1439] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 11/03/2011] [Accepted: 11/15/2011] [Indexed: 11/07/2022]
Abstract
Antimicrobial peptides are important effector molecules of the innate immune system. Here, we describe that peptides derived from the heparin-binding disulfide-constrained loop region of human ß-amyloid precursor protein are antimicrobial. The peptides investigated were linear and cyclic forms of NWCKRGRKQCKTHPH (NWC15) as well as the cyclic form comprising the C-terminal hydrophobic amino acid extension FVIPY (NWCKRGRKQCKTHPHFVIPY; NWC20c). Compared with the benchmark antimicrobial peptide LL-37, these peptides efficiently killed the Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa, the Gram-positive Staphylococcus aureus and Bacillus subtilis, and the fungi Candida albicans and Candida parapsilosis. Correspondingly, fluorescence and electron microscopy demonstrated that the peptides caused defects in bacterial membranes. Analogously, the peptides permeabilised negatively charged liposomes. Despite their bactericidal effect, the peptides displayed very limited hemolytic activities within the concentration range investigated and exerted very small membrane permeabilising effects on human epithelial cells. The efficiency of the peptides with respect to bacterial killing and liposome membrane leakage was in the order NWC20c > NWC15c > NWC15l, which also correlated to the adsorption density for these peptides at the model lipid membrane. Thus, whereas the cationic sequence is a minimum determinant for antimicrobial action, a constrained loop-structure as well as a hydrophobic extension further contributes to membrane permeabilising activity of this region of amyloid precursor protein.
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Affiliation(s)
- Praveen Papareddy
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, Biomedical Center, Tornavägen 10, SE-221 84, Lund, Sweden
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