Distinct mode of membrane interaction and disintegration by diverse class of antimicrobial peptides
Tài liệu tham khảo
JJBJOCP, 1984, Use and abuse of antibiotics, 18, 469
Chandel, 2013, The good and the bad of antibiotics, 5
Llor, 2014, Antimicrobial resistance: risk associated with antibiotic overuse and initiatives to reduce the problem, 5, 229
Naafs, 2018, The antimicrobial peptides: ready for clinical trials, Biomed J Sci & Tech Res, 7, 6038
Mahlapuu, 2016, Antimicrobial peptides: an emerging category of therapeutic agents, Front. Cell. Infect. Microbiol., 6, 194, 10.3389/fcimb.2016.00194
Krizsan, 2015, Short proline-rich antimicrobial peptides inhibit either the bacterial 70S ribosome or the assembly of its large 50S subunit, 16, 2304
de Kruijff, 2008, Leukotrienes, acids EFLipid II: a central component in bacterial cell wall synthesis and a target for antibiotics, 79, 117
Subbalakshmi, 1998, Mechanism of antimicrobial action of indolicidin, 160, 91
Brogden, 2005, Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria?, Nat. Rev. Microbiol., 3, 238, 10.1038/nrmicro1098
Otvos, 2005, Antibacterial peptides and proteins with multiple cellular targets, 11, 697
Mwangi, 2019, Antimicrobial peptides: new hope in the war against multidrug resistance, 40, 488
Vandamme, 2012, A comprehensive summary of LL-37, the factotum human cathelicidin peptide, 280, 22
Selsted, 1984, Purification and antibacterial activity of antimicrobial peptides of rabbit granulocytes, Immunity, 45, 150, 10.1128/iai.45.1.150-154.1984
AJJOLB, 2000, Leukocyte antimicrobial peptides: multifunctional effector molecules of innate immunity, 68, 785
Sani, 2016, How membrane-active peptides get into lipid membranes, 49, 1130
Ludtke, 1995, Membrane thinning caused by magainin 2, 34, 16764
Dean, 2010, A carpet-based mechanism for direct antimicrobial peptide activity against vaccinia virus membranes, 31, 1966
Ciobanasu, 2015, NKCS, a mutant of the NK-2 peptide, causes severe distortions and perforations in bacterial, but not human model lipid membranes, Molecules, 20, 6941, 10.3390/molecules20046941
WCJAcb, 2010, Describing the mechanism of antimicrobial peptide action with the interfacial activity model, 5, 905
Vasudevan, 2008, Synthesis, structure, and activities of an oral mucosal α-defensin from rhesus macaque, J. Biol. Chem., 283, 35869, 10.1074/jbc.M806915200
Mui, 2003, Extrusion technique to generate liposomes of defined size, Methods Enzymol., 367, 3, 10.1016/S0076-6879(03)67001-1
Olson, 1979, Preparation of liposomes of defined size distribution by extrusion through polycarbonate membranes, Biochim. Biophys. Acta, Biomembr., 557, 9, 10.1016/0005-2736(79)90085-3
Bax, 1985, MLEV-17-based two-dimensional homonuclear magnetization transfer spectroscopy, Journal of Magnetic Resonance, 65, 355
Kumar, 1980, A two-dimensional nuclear overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules, Biochem. Biophys. Res. Commun., 95, 1, 10.1016/0006-291X(80)90695-6
Vranken, 2005, The CCPN data model for NMR spectroscopy: development of a software pipeline, Proteins: Struct., Funct., Bioinf., 59, 687, 10.1002/prot.20449
Wuthrich, 1986
Shen, 2013, Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks, J. Biomol. NMR, 56, 227, 10.1007/s10858-013-9741-y
Güntert, 2015, Combined automated NOE assignment and structure calculation with CYANA, J. Biomol. NMR, 62, 453, 10.1007/s10858-015-9924-9
Laskowski, 1996, AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR, J. Biomol. NMR, 8, 477, 10.1007/BF00228148
Schrodinger, 2010, 2015
Hazan, 2012, A method for high throughput determination of viable bacteria cell counts in 96-well plates, BMC Microbiol., 12, 259, 10.1186/1471-2180-12-259
Tai, 2014, Hydrophobic determinants of α-defensin bactericidal activity, Infection and immunity, 82, 2195, 10.1128/IAI.01414-13
2016
Muscariello, 2005, A critical overview of ESEM applications in the biological field, J. Cell. Physiol., 205, 328, 10.1002/jcp.20444
Ramírez-Camacho, 2008, Microscopia electrónica de barrido ambiental Para la detección de biopelículas en las amígdalas, Acta Otorrinolaringol. Esp., 59, 16, 10.1016/S0001-6519(08)73252-7
Jorgensen, 1983, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys., 79, 926, 10.1063/1.445869
Klauda, 2010, Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types, J. Phys. Chem. B, 114, 7830, 10.1021/jp101759q
Best, 2012, Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone ϕ, ψ and side-chain χ1 and χ2 dihedral angles, J. Chem. Theory Comput., 8, 3257, 10.1021/ct300400x
Hess, 2008, GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation, J. Chem. Theory Comput., 4, 435, 10.1021/ct700301q
Darden, 1993, Particle mesh ewald: an N· log (N) method for Ewald sums in large systems, J. Chem. Phys., 98, 10089, 10.1063/1.464397
Nosé, 1984, A unified formulation of the constant temperature molecular dynamics methods, J. Chem. Phys., 81, 511, 10.1063/1.447334
Parrinello, 1981, Polymorphic transitions in single crystals: a new molecular dynamics method, J. Appl. Phys., 52, 7182, 10.1063/1.328693
Allen, 2009, GridMAT-MD: a grid-based membrane analysis tool for use with molecular dynamics, J. Comput. Chem., 30, 1952, 10.1002/jcc.21172
Humphrey, 1996, VMD: visual molecular dynamics, J. Mol. Graph., 14, 33, 10.1016/0263-7855(96)00018-5
Agadi, 2018, Structural insight into the mechanism of action of antimicrobial peptide BMAP-28 (1–18) and its analogue mutBMAP18, J. Struct. Biol., 204, 435, 10.1016/j.jsb.2018.10.003
Wu, 2003, Engineering disulfide bridges to dissect antimicrobial and chemotactic activities of human β-defensin 3, 100, 8880
Sivanesam, 2016, Hairpin structure stability plays a role in the activity of two antimicrobial peptides, 590, 4480
Navas, 2005, Composition dependence of vesicle morphology and mixing properties in a bacterial model membrane system, Biochim. Biophys. Acta, Biomembr., 1716, 40, 10.1016/j.bbamem.2005.08.003
Lohner, 1999, 38, 16514
Powers, 2005, Solution structure and interaction of the antimicrobial polyphemusins with lipid membranes, 44, 15504
Saenz, 2006, Physical properties and surface activity of surfactant-like membranes containing the cationic and hydrophobic peptide KL4, FEBS J., 273, 2515, 10.1111/j.1742-4658.2006.05258.x
Biltonen, 1993, The use of differential scanning calorimetry as a tool to characterize liposome preparations, Chem. Phys. Lipids, 64, 129, 10.1016/0009-3084(93)90062-8
Drazenovic, 2015, Effect of lamellarity and size on calorimetric phase transitions in single component phosphatidylcholine vesicles, 1848, 532
Ahmed, 2009, Effect of high surface curvature on the main phase transition of supported phospholipid bilayers on SiO2 nanoparticles, 25, 3682
Brumm, 1996, 70, 1373
Qiu, 1993, Magnetically induced orientation of phosphatidylcholine membranes, Biochim. Biophys. Acta, Biomembr., 1147, 59, 10.1016/0005-2736(93)90316-R
Massiot, 2002, Modelling one-and two-dimensional solid-state NMR spectra, Magn. Reson. Chem., 40, 70, 10.1002/mrc.984
Drechsler, 2010, Solid-state NMR study of membrane interactions of the pore-forming cytolysin, equinatoxin II, Biochim. Biophys. Acta, Biomembr., 1798, 244, 10.1016/j.bbamem.2009.10.012
Dave, 2004, Investigating structural changes in the lipid bilayer upon insertion of the transmembrane domain of the membrane-bound protein phospholamban utilizing 31P and 2H solid-state NMR spectroscopy, Biophys. J., 86, 1564, 10.1016/S0006-3495(04)74224-1
Cullis, 1976, 31P NMR studies of unsonicated aqueous dispersions of neutral and acidic phospholipids. Effects of phase transitions, p2H and divalent cations on the motion in the phosphate region of the polar headgroup, Biochim. Biophys. Acta, Biomembr., 436, 523, 10.1016/0005-2736(76)90438-7
Burnell, 1980, Effects of tumbling and lateral diffusion on phosphatidylcholine model membrane 31P-NMR lineshapes, Biochim. Biophys. Acta, Biomembr., 603, 63, 10.1016/0005-2736(80)90391-0
Raghothama, 2010
Rosengren, 2006, Structural and functional characterization of the conserved salt bridge in mammalian paneth cell α-defensins SOLUTION STRUCTURES OF MOUSE CRYPTDIN-4 AND (E15D)-CRYPTDIN-4, J. Biol. Chem., 281, 28068, 10.1074/jbc.M604992200
Leontiadou, 2006, Antimicrobial peptides in action, J. Am. Chem. Soc., 128, 12156, 10.1021/ja062927q
La Rocca, 1999, Simulation studies of the interaction of antimicrobial peptides and lipid bilayers, Biochim. Biophys. Acta, Biomembr., 1462, 185, 10.1016/S0005-2736(99)00206-0
Meher, 2019, Cholesterol modulates membrane properties and the interaction of gp41 fusion peptide to promote membrane fusion, J. Phys. Chem. B, 123, 7113, 10.1021/acs.jpcb.9b04577
Kamath, 2002, Membrane structure of the human immunodeficiency virus gp41 fusion domain by molecular dynamics simulation, Biophys. J., 83, 135, 10.1016/S0006-3495(02)75155-2
Ponmalar, 2019, Correlated protein conformational states and membrane dynamics during attack by pore-forming toxins, Proc. Natl. Acad. Sci., 116, 12839, 10.1073/pnas.1821897116
Jorgensen, 2015, Susceptibility test methods: dilution and disk diffusion methods, 1253
Jang, 2007, Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect, 7, 1
Cheng, 2016, Maximally asymmetric transbilayer distribution of anionic lipids alters the structure and interaction with lipids of an amyloidogenic protein dimer bound to the membrane surface, 196, 33
Fan, 2016, DRAMP: a comprehensive data repository of antimicrobial peptides, Sci. Rep., 6, 1
Wang, 2016, APD3: the antimicrobial peptide database as a tool for research and education, Nucleic acids research, 44, 10.1093/nar/gkv1278
Lu, 2005, Solid-state nuclear magnetic resonance relaxation studies of the interaction mechanism of antimicrobial peptides with phospholipid bilayer membranes, Biochemistry, 44, 10208, 10.1021/bi050730p
Fillion, 2015, Membrane interactions of synthetic peptides with antimicrobial potential: effect of electrostatic interactions and amphiphilicity, Probiotics Antimicrob. Proteins, 7, 66, 10.1007/s12602-014-9177-z
Chen, 2003, Evidence for membrane thinning effect as the mechanism for peptide-induced pore formation, Biophys. J., 84, 3751, 10.1016/S0006-3495(03)75103-0
Glaser, 1988, Reversible electrical breakdown of lipid bilayers: formation and evolution of pores, 940, 275
Fuertes, 2011, A lipocentric view of peptide-induced pores, 40, 399
Arouri, 2009, Peptide induced demixing in PG/PE lipid mixtures: a mechanism for the specificity of antimicrobial peptides towards bacterial membranes?, 1788, 650
Epand, 2009, Lipid segregation explains selective toxicity of a series of fragments derived from the human cathelicidin LL-37, Antimicrob. Agents Chemother., 53, 3705, 10.1128/AAC.00321-09
Doherty, 2006, Peptide–lipid interactions of the β-hairpin antimicrobial peptide tachyplesin and its linear derivatives from solid-state NMR, Biochim. Biophys. Acta, Biomembr., 1758, 1285, 10.1016/j.bbamem.2006.03.016
Briggs, 2015, Interaction between the NS4B amphipathic helix, AH2, and charged lipid headgroups alters membrane morphology and AH2 oligomeric state—Implications for the hepatitis C virus life cycle, Biochim. Biophys. Acta, Biomembr., 1848, 1671, 10.1016/j.bbamem.2015.04.015
Zeth, 2017, The human antimicrobial peptides dermcidin and LL-37 show novel distinct pathways in membrane interactions, Front. Chem., 5, 86, 10.3389/fchem.2017.00086
Risso, 2002, BMAP-28, an antibiotic peptide of innate immunity, induces cell death through opening of the mitochondrial permeability transition pore, Mol. Cell. Biol., 22, 1926, 10.1128/MCB.22.6.1926-1935.2002
Lee, 2011, Transmembrane pores formed by human antimicrobial peptide LL-37, Biophys. J., 100, 1688, 10.1016/j.bpj.2011.02.018
Lv, 2014, Antimicrobial properties and membrane-active mechanism of a potential α-helical antimicrobial derived from cathelicidin PMAP-36, PloS one, 9, 10.1371/journal.pone.0086364
Dathe, 1999, Structural features of helical antimicrobial peptides: their potential to modulate activity on model membranes and biological cells, 1462, 71
Balhara, 2013, Membrane selectivity and biophysical studies of the antimicrobial peptide GL13K, Biochim. Biophys. Acta, Biomembr., 1828, 2193, 10.1016/j.bbamem.2013.05.027
Cummings, 2007, Kinetics of cryptdin-4 translocation coupled with peptide-induced vesicle leakage, Biochemistry, 46, 11882, 10.1021/bi701110m
Zhang, 2010, The membrane-bound structure and topology of a human α-defensin indicate a dimer pore mechanism for membrane disruption, Biochemistry, 49, 9770, 10.1021/bi101512j