Magainin 2 and PGLa in Bacterial Membrane Mimics I: Peptide-Peptide and Lipid-Peptide Interactions

. 2019 Nov 19 ; 117 (10) : 1858-1869. [epub] 20191024

Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid31703802

Grantová podpora
I 1763 Austrian Science Fund FWF - Austria

Odkazy

PubMed 31703802
PubMed Central PMC7031808
DOI 10.1016/j.bpj.2019.10.022
PII: S0006-3495(19)30870-7
Knihovny.cz E-zdroje

We addressed the onset of synergistic activity of the two well-studied antimicrobial peptides magainin 2 (MG2a) and PGLa using lipid-only mimics of Gram-negative cytoplasmic membranes. Specifically, we coupled a joint analysis of small-angle x-ray and neutron scattering experiments on fully hydrated lipid vesicles in the presence of MG2a and L18W-PGLa to all-atom and coarse-grained molecular dynamics simulations. In agreement with previous studies, both peptides, as well as their equimolar mixture, were found to remain upon adsorption in a surface-aligned topology and to induce significant membrane perturbation, as evidenced by membrane thinning and hydrocarbon order parameter changes in the vicinity of the inserted peptide. These effects were particularly pronounced for the so-called synergistic mixture of 1:1 (mol/mol) L18W-PGLa/MG2a and cannot be accounted for by a linear combination of the membrane perturbations of two peptides individually. Our data are consistent with the formation of parallel heterodimers at concentrations below a synergistic increase of dye leakage from vesicles. Our simulations further show that the heterodimers interact via salt bridges and hydrophobic forces, which apparently makes them more stable than putatively formed antiparallel L18W-PGLa and MG2a homodimers. Moreover, dimerization of L18W-PGLa and MG2a leads to a relocation of the peptides within the lipid headgroup region as compared to the individual peptides. The early onset of dimerization of L18W-PGLa and MG2a at low peptide concentrations consequently appears to be key to their synergistic dye-releasing activity from lipid vesicles at high concentrations.

Zobrazit více v PubMed

Wimley W.C., Hristova K. Antimicrobial peptides: successes, challenges and unanswered questions. J. Membr. Biol. 2011;239:27–34. PubMed PMC

Lohner K. Membrane-active antimicrobial peptides as template structures for novel antibiotic agents. Curr. Top. Med. Chem. 2017;17:508–519. PubMed

Zasloff M. Antimicrobial peptides of multicellular organisms. Nature. 2002;415:389–395. PubMed

Bechinger B. The SMART model: soft membranes adapt and respond, also transiently, in the presence of antimicrobial peptides. J. Pept. Sci. 2015;21:346–355. PubMed

Leber R., Pachler M., Pabst G. Synergism of antimicrobial frog peptides couples to membrane intrinsic curvature strain. Biophys. J. 2018;114:1945–1954. PubMed PMC

Matsuzaki K., Mitani Y., Miyajima K. Mechanism of synergism between antimicrobial peptides magainin 2 and PGLa. Biochemistry. 1998;37:15144–15153. PubMed

Hara T., Mitani Y., Matsuzaki K. Heterodimer formation between the antimicrobial peptides magainin 2 and PGLa in lipid bilayers: a cross-linking study. Biochemistry. 2001;40:12395–12399. PubMed

Nishida M., Imura Y., Matsuzaki K. Interaction of a magainin-PGLa hybrid peptide with membranes: insight into the mechanism of synergism. Biochemistry. 2007;46:14284–14290. PubMed

Tremouilhac P., Strandberg E., Ulrich A.S. Synergistic transmembrane alignment of the antimicrobial heterodimer PGLa/magainin. J. Biol. Chem. 2006;281:32089–32094. PubMed

Salnikov E.S., Bechinger B. Lipid-controlled peptide topology and interactions in bilayers: structural insights into the synergistic enhancement of the antimicrobial activities of PGLa and magainin 2. Biophys. J. 2011;100:1473–1480. PubMed PMC

Strandberg E., Zerweck J., Ulrich A.S. Synergistic insertion of antimicrobial magainin-family peptides in membranes depends on the lipid spontaneous curvature. Biophys. J. 2013;104:L9–L11. PubMed PMC

Zerweck J., Strandberg E., Ulrich A.S. Molecular mechanism of synergy between the antimicrobial peptides PGLa and magainin 2. Sci. Rep. 2017;7:13153. PubMed PMC

Harmouche N., Bechinger B. Lipid-mediated interactions between the antimicrobial peptides magainin 2 and PGLa in bilayers. Biophys. J. 2018;115:1033–1044. PubMed PMC

Kabelka I., Vácha R. Optimal hydrophobicity and reorientation of amphiphilic peptides translocating through membrane. Biophys. J. 2018;115:1045–1054. PubMed PMC

Kingsley P.B., Feigenson G.W. The synthesis of a perdeuterated phospholipid: 1,2-dimyristoyl-sn-glycero-3-phosphocholine-d72. Chem. Phys. Lipids. 1979;24:135–147.

Feoktystov A.V., Frielinghaus H., Brückel T. KWS-1 high-resolution small-angle neutron scattering instrument at JCNS: current state. J. Appl. Cryst. 2015;48:61–70.

Pencer J., Krueger S., Katsaras J. Method of separated form factors for polydisperse vesicles. J. Appl. Cryst. 2006;39:293–303.

Kucerka N., Nagle J.F., Katsaras J. Lipid bilayer structure determined by the simultaneous analysis of neutron and X-ray scattering data. Biophys. J. 2008;95:2356–2367. PubMed PMC

Heberle F.A., Pabst G. Complex biomembrane mimetics on the sub-nanometer scale. Biophys. Rev. 2017;9:353–373. PubMed PMC

Pan J., Tieleman D.P., Tristram-Nagle S. Alamethicin in lipid bilayers: combined use of X-ray scattering and MD simulations. Biochim. Biophys. Acta. 2009;1788:1387–1397. PubMed PMC

Dupuy F.G., Pagano I., Tristram-Nagle S. Selective interaction of colistin with lipid model membranes. Biophys. J. 2018;114:919–928. PubMed PMC

Khondker A., Alsop R.J., Rheinstädter M.C. Membrane cholesterol reduces polymyxin B nephrotoxicity in renal membrane analogs. Biophys. J. 2017;113:2016–2028. PubMed PMC

Nielsen J.E., Bjørnestad V.A., Lund R. Resolving the structural interactions between antimicrobial peptides and lipid membranes using small-angle scattering methods: the case of indolicidin. Soft Matter. 2018;14:8750–8763. PubMed

Kučerka N., van Oosten B., Katsaras J. Molecular structures of fluid phosphatidylethanolamine bilayers obtained from simulation-to-experiment comparisons and experimental scattering density profiles. J. Phys. Chem. B. 2015;119:1947–1956. PubMed

Pan J., Marquardt D., Katsaras J. Revisiting the bilayer structures of fluid phase phosphatidylglycerol lipids: accounting for exchangeable hydrogens. Biochim. Biophys. Acta. 2014;1838:2966–2969. PubMed

Heftberger P., Kollmitzer B., Pabst G. In situ determination of structure and fluctuations of coexisting fluid membrane domains. Biophys. J. 2015;108:854–862. PubMed PMC

Belička M., Weitzer A., Pabst G. High-resolution structure of coexisting nanoscopic and microscopic lipid domains. Soft Matter. 2017;13:1823–1833. PubMed

Narayanan T., Weerakkody D., Reshetnyak Y.K. pHLIP peptide interaction with a membrane monitored by SAXS. J. Phys. Chem. B. 2016;120:11484–11491. PubMed PMC

Wieprecht T., Apostolov O., Seelig J. Interaction of a mitochondrial presequence with lipid membranes: role of helix formation for membrane binding and perturbation. Biochemistry. 2000;39:15297–15305. PubMed

Nagle J.F., Tristram-Nagle S. Structure of lipid bilayers. Biochim. Biophys. Acta. 2000;1469:159–195. PubMed PMC

Storn R., Price K. Differential evolution – a simple and efficient heuristic for global optimization over continuous spaces. J. Glob. Optim. 1997;11:341–359.

Abraham M.J., Murtola T., Lindahl E. GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1–2:19–25.

Páll S., Abraham M.J., Lindahl E. Tackling exascale software challenges in molecular dynamics simulations with GROMACS. In: Laure E., Markidis S., editors. Solving Software Challenges for Exascale. Springer; 2015. pp. 3–27.

Lindorff-Larsen K., Piana S., Shaw D.E. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins. 2010;78:1950–1958. PubMed PMC

Sorin E.J., Pande V.S. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys. J. 2005;88:2472–2493. PubMed PMC

Jämbeck J.P., Lyubartsev A.P. Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids. J. Phys. Chem. B. 2012;116:3164–3179. PubMed PMC

Jämbeck J.P., Lyubartsev A.P. An extension and further validation of an all-atomistic force field for biological membranes. J. Chem. Theory Comput. 2012;8:2938–2948. PubMed

Nosé S. A unified formulation of the constant temperature molecular dynamics methods. J. Chem. Phys. 1984;81:511–519.

Nosé S. A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys. 1984;52:255–268.

Hoover W.G. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A Gen. Phys. 1985;31:1695–1697. PubMed

Parrinello M., Rahman A. Crystal structure and pair potentials: a molecular-dynamics study. Phys. Rev. Lett. 1980;45:1196–1199.

Parrinello M., Rahman A. Polymorphic transitions in single crystals: a new molecular dynamics method. J. Appl. Phys. 1981;52:7182–7190.

Essmann U., Perera L., Pedersen L.G. A smooth particle mesh Ewald method. J. Chem. Phys. 1995;103:8577–8593.

Allen M.P., Tildesley D.J. Oxford; 2017. Computer Simulation of Liquids, Second Edition: Oxford University Press.

Jo S., Kim T., Im W. CHARMM-GUI: a web-based graphical user interface for CHARMM. J. Comput. Chem. 2008;29:1859–1865. PubMed

Marrink S.J., Risselada H.J., de Vries A.H. The MARTINI force field: coarse grained model for biomolecular simulations. J. Phys. Chem. B. 2007;111:7812–7824. PubMed

Monticelli L., Kandasamy S.K., Marrink S.J. The MARTINI coarse-grained force field: extension to proteins. J. Chem. Theory Comput. 2008;4:819–834. PubMed

de Jong D.H., Singh G., Marrink S.J. Improved parameters for the Martini coarse-grained protein force field. J. Chem. Theory Comput. 2013;9:687–697. PubMed

Bussi G., Donadio D., Parrinello M. Canonical sampling through velocity rescaling. J. Chem. Phys. 2007;126:014101. PubMed

Lee J., Cheng X., Im W. CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. J. Chem. Theory Comput. 2016;12:405–413. PubMed PMC

Mihailescu M., Vaswani R.G., White S.H. Acyl-chain methyl distributions of liquid-ordered and -disordered membranes. Biophys. J. 2011;100:1455–1462. PubMed PMC

Han E., Lee H. Synergistic effects of magainin 2 and PGLa on their heterodimer formation, aggregation, and insertion into the bilayer. RSC Advances. 2015;5:2047–2055.

Javanainen M., Martinez-Seara H., Vattulainen I. Excessive aggregation of membrane proteins in the Martini model. PLoS One. 2017;12:e0187936. PubMed PMC

Ludtke S., He K., Huang H. Membrane thinning caused by magainin 2. Biochemistry. 1995;34:16764–16769. PubMed

Hristova K., Dempsey C.E., White S.H. Structure, location, and lipid perturbations of melittin at the membrane interface. Biophys. J. 2001;80:801–811. PubMed PMC

Ulmschneider J.P., Smith J.C., Strandberg E. Reorientation and dimerization of the membrane-bound antimicrobial peptide PGLa from microsecond all-atom MD simulations. Biophys. J. 2012;103:472–482. PubMed PMC

Cieplak P., Cornell W.d., Kollman P.A. Application of the multimolecule and multiconformational RESP methodology to biopolymers: charge derivation for DNA, RNA, and proteins. J. Comput. Chem. 1995;16:1357–1377.

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...