Antimicrobial peptide interactions with bacterial cell membranes

References

• Aktas, M., Wessel, M., Hacker, S., Klüsener, S., Gleichenhagen, J., & Narberhaus, F. (2010). Phosphatidylcholine biosynthesis and its significance in bacteria interacting with eukaryotic cells. European Journal of Cell Biology, 89(12), 888–894. https://doi.org/10.1016/j.ejcb.2010.06.013
   PubMed Web of Science ®Google Scholar
• Allsopp, R., Pavlova, A., Cline, T., Salyapongse, A. M., Gillilan, R. E., Di, Y. P., Deslouches, B., Klauda, J. B., Gumbart, J. C., & Tristram-Nagle, S. (2022). Antimicrobial peptide mechanism studied by scattering-guided molecular dynamics simulation. The Journal of Physical Chemistry. B, 126(36), 6922–6935. https://doi.org/10.1021/acs.jpcb.2c03193
   PubMed Web of Science ®Google Scholar
• Bellm, L., Lehrer, R. I., & Ganz, T. (2000). Protegrins: New antibiotics of mammalian origin. Expert Opinion on Investigational Drugs, 9(8), 1731–1742. https://doi.org/10.1517/13543784.9.8.173
   PubMed Web of Science ®Google Scholar
• Bouchet, A. M., Frías, M., Lairion, F., Martini, F., Almaleck, H., Gordillo, G., & Disalvo, E. A. (2009). Structural and dynamical surface properties of phosphatidylethanolamine containing membranes. Biochimica et Biophysica Acta, 1788(5), 918–925. https://doi.org/10.1016/j.bbamem.2009.02.012
   PubMed Web of Science ®Google Scholar
• Caputo, G. A., Litvinov, R. I., Li, W., Bennett, J. S., DeGrado, W. F., & Yin, H. (2008). Computationally designed peptide inhibitors of protein − protein interactions in membranes. Biochemistry, 47(33), 8600–8606. https://doi.org/10.1021/bi800687h
   PubMed Web of Science ®Google Scholar
• Case, D. A., Aktulga, H. M., Belfon, K., Ben-Shalom, I., Brozell, S. R., Cerutti, D. S., Cheatham, T. E., III, Cruzeiro, V. W. D., Darden, T. A., & Duke, R. E. (2021). Amber 2021. University of California.
   Google Scholar
• Chapman, D., Urbina, J., & Keough, K. M. (1974). Biomembrane phase transitions: Studies of lipid-water systems using differential scanning calorimetry. The Journal of Biological Chemistry, 249(8), 2512–2521. https://doi.org/10.1016/S0021-9258(19)42760-9
   PubMed Web of Science ®Google Scholar
• Cole, A. M., Weis, P., & Diamond, G. (1997). Isolation and characterization of pleurocidin, an antimicrobial peptide in the skin secretions of winter flounder. The Journal of Biological Chemistry, 272(18), 12008–12013. https://doi.org/10.1074/jbc.272.18.12008
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log (N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• Deslouches, B., Islam, K., Craigo, J. K., Paranjape, S. M., Montelaro, R. C., & Mietzner, T. A. (2005). Activity of the de novo engineered antimicrobial peptide WLBU2 against Pseudomonas aeruginosa in human serum and whole blood: Implications for systemic applications. Antimicrobial Agents and Chemotherapy, 49(8), 3208–3216. https://doi.org/10.1128/AAC.49.8.3208-3216.2005
   PubMed Web of Science ®Google Scholar
• Dürr, U. H. N., Sudheendra, U. S., & Ramamoorthy, A. (2006). LL-37, the only human member of the cathelicidin family of antimicrobial peptides. Biochimica et Biophysica Acta, 1758(9), 1408–1425. https://doi.org/10.1016/j.bbamem.2006.03.030
   PubMed Web of Science ®Google Scholar
• Fahrner, R. L., Dieckmann, T., Harwig, S. S., Lehrer, R. I., Eisenberg, D., & Feigon, J. (1996). Solution structure of protegrin-1, a broad-spectrum antimicrobial peptide from porcine leukocytes. Chemistry & Biology, 3(7), 543–550. https://doi.org/10.1016/s1074-5521(96)90145-3
   PubMedGoogle Scholar
• Fernandez, D. I., Sani, M.-A., & Separovic, F. (2011). Interactions of the antimicrobial peptide maculatin 1.1 and analogues with phospholipid bilayers. Australian Journal of Chemistry, 64(6), 798–805. https://doi.org/10.1071/CH11062
   Web of Science ®Google Scholar
• Geiger, O., López-Lara, I. M., & Sohlenkamp, C. (2013). Phosphatidylcholine biosynthesis and function in bacteria. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, 1831(3), 503–513. https://doi.org/10.1016/j.bbalip.2012.08.009
   PubMed Web of Science ®Google Scholar
• Gesell, J., Zasloff, M., & Opella, S. J. (1997). Two-dimensional 1H NMR experiments show that the 23-residue magainin antibiotic peptide is an α-helix in dodecylphosphocholine micelles, sodium dodecylsulfate micelles, and trifluoroethanol/water solution. Journal of Biomolecular NMR, 9(2), 127–135. https://doi.org/10.1023/A:1018698002314
   PubMed Web of Science ®Google Scholar
• Gullingsrud, J., & Schulten, K. (2004). Lipid bilayer pressure profiles and mechanosensitive channel gating. Biophysical Journal, 86(6), 3496–3509. https://doi.org/10.1529/biophysj.103.034322
   PubMed Web of Science ®Google Scholar
• Hancock, R. E. W. (1997). Peptide antibiotics. Lancet (London, England), 349(9049), 418–422. https://doi.org/10.1016/S0140-6736(97)80051-7
   PubMed Web of Science ®Google Scholar
• Hancock, R. E. W., & Rozek, A. (2002). Role of membranes in the activities of antimicrobial cationic peptides. FEMS Microbiology Letters, 206(2), 143–149. https://doi.org/10.1111/j.1574-6968.2002.tb11000.x
   PubMed Web of Science ®Google Scholar
• Hancock, R. E. W., & Sahl, H.-G. (2006). Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies. Nature Biotechnology, 24(12), 1551–1557. https://doi.org/10.1038/nbt1267
   PubMed Web of Science ®Google Scholar
• Hartkamp, R., Moore, T. C., Iacovella, C. R., Thompson, M. A., Bulsara, P. A., Moore, D. J., & McCabe, C. (2018). Composition dependence of water permeation across multicomponent gel-phase bilayers. The Journal of Physical Chemistry. B, 122(12), 3113–3123. https://doi.org/10.1021/acs.jpcb.8b00747
   PubMed Web of Science ®Google Scholar
• Hof, W., Veerman, E. C., Helmerhorst, E. J., & Amerongen, A. V. N. (2001). Antimicrobial peptides: Properties and applicability. Biological Chemistry, 382(4), 597-619. https://doi.org/10.1515/BC.2001.072
   Web of Science ®Google Scholar
• Huang, H. W. (2009). Free energies of molecular bound states in lipid bilayers: Lethal concentrations of antimicrobial peptides. Biophysical Journal, 96(8), 3263–3272. https://doi.org/10.1016/j.bpj.2009.01.030
   PubMed Web of Science ®Google Scholar
• Huang, Y., Huang, J., & Chen, Y. (2010). Alpha-helical cationic antimicrobial peptides: Relationships of structure and function. Protein & Cell, 1(2), 143–152. https://doi.org/10.1007/s13238-010-0004-3
   PubMed Web of Science ®Google Scholar
• Jafari, M., Mehrnejad, F., & Doustdar, F. (2017). Insight into the interactions, residue snorkeling, and membrane disordering potency of a single antimicrobial peptide into different lipid bilayers. PloS One, 12(11), e0187216. https://doi.org/10.1371/journal.pone.0187216
   PubMed Web of Science ®Google Scholar
• Jang, H., Ma, B., Woolf, T. B., & Nussinov, R. (2006). Interaction of protegrin-1 with lipid bilayers: Membrane thinning effect. Biophysical Journal, 91(8), 2848–2859. https://doi.org/10.1529/biophysj.106.084046
   PubMed Web of Science ®Google Scholar
• Jenssen, H., Hamill, P., & Hancock, R. E. (2006). Peptide antimicrobial agents. Clinical Microbiology Reviews, 19(3), 491–511. https://doi.org/10.1128/cmr.00056-05
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
   Web of Science ®Google Scholar
• Joung, I. S, & Cheatham, T. E. I. I. I. (2008). Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. The Journal of Physical Chemistry. B, 112(30), 9020–9041. https://doi.org/10.1021/jp8001614
   PubMed Web of Science ®Google Scholar
• Kucerka, N., Tristram-Nagle, S., & Nagle, J. F. (2006). Structure of fully hydrated fluid phase lipid bilayers with monounsaturated chains. The Journal of Membrane Biology, 208(3), 193–202. https://doi.org/10.1007/s00232-005-7006-8
   Web of Science ®Google Scholar
• Lam, K. L. H., Wang, H., Siaw, T. A., Chapman, M. R., Waring, A. J., Kindt, J. T., & Lee, K. Y. C. (2012). Mechanism of structural transformations induced by antimicrobial peptides in lipid membranes. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1818(2), 194–204. https://doi.org/10.1016/j.bbamem.2011.11.002
   PubMed Web of Science ®Google Scholar
• Last, N. B., & Miranker, A. D. (2013). Common mechanism unites membrane poration by amyloid and antimicrobial peptides. Proceedings of the National Academy of Sciences of the United States of America, 110(16), 6382–6387. https://doi.org/10.1073/pnas.1219059110
   PubMed Web of Science ®Google Scholar
• Lee, T.-H., K. N., Hall, & Aguilar, M.-I. (2016). Antimicrobial peptide structure and mechanism of action: A focus on the role of membrane structure. Current Topics in Medicinal Chemistry, 16(1), 25–39. https://doi.org/10.2174/1568026615666150703121700
   PubMed Web of Science ®Google Scholar
• Lee, J., Jung, S. W., & Cho, A. E. (2016). Molecular insights into the adsorption mechanism of human β-defensin-3 on bacterial membranes. Langmuir: The ACS Journal of Surfaces and Colloids, 32(7), 1782–1790. https://doi.org/10.1021/acs.langmuir.5b04113
   PubMed Web of Science ®Google Scholar
• Leekumjorn, S., & Sum, A. K. (2008). Molecular dynamics study on the stabilization of dehydrated lipid bilayers with glucose and trehalose. The Journal of Physical Chemistry. B, 112(34), 10732–10740. https://doi.org/10.1021/jp8025489
   PubMed Web of Science ®Google Scholar
• Liang, Y., Zhang, X., Yuan, Y., Bao, Y., & Xiong, M. (2020). Role and modulation of the secondary structure of antimicrobial peptides to improve selectivity. Biomaterials Science, 8(24), 6858–6866. https://doi.org/10.1039/D0BM00801J
   PubMed Web of Science ®Google Scholar
• Lohner K., & Blondelle, S. E. (2005). Molecular mechanisms of membrane perturbation by antimicrobial peptides and the use of biophysical studies in the design of novel peptide antibiotics. Combinatorial Chemistry & High Throughput Screening, 8(3), 241–256. https://doi.org/10.2174/1386207053764576
   PubMed Web of Science ®Google Scholar
• Lomize, A. L., & Pogozheva, I. D. (2013). Solvation models and computational prediction of orientations of peptides and proteins in membranes. Membrane Proteins: Folding, Association, and Design, 1063, 125–142. https://doi.org/10.1007/978-1-62703-583-5_7
   Google Scholar
• Lomize, M. A., Pogozheva, I. D., Joo, H., Mosberg, H. I., & Lomize, A. L. (2012). OPM database and PPM web server: Resources for positioning of proteins in membranes. Nucleic Acids Research, 40(Database issue), D370–D376. https://doi.org/10.1093/nar/gkr703
   PubMed Web of Science ®Google Scholar
• Loose, M., & Schwille, P. (2009). Biomimetic membrane systems to study cellular organization. Journal of Structural Biology, 168(1), 143–151. https://doi.org/10.1016/j.jsb.2009.03.016
   PubMed Web of Science ®Google Scholar
• Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/10.1021/acs.jctc.5b00255
   PubMed Web of Science ®Google Scholar
• Maloy, W. L., & Kari, U. P. (1995). Structure–activity studies on magainins and other host defense peptides. Biopolymers, 37(2), 105–122. https://doi.org/10.1002/bip.360370206
   PubMed Web of Science ®Google Scholar
• Manzini, M. C., Perez, K. R., Riske, K. A., Bozelli, J. C., Santos, T. L., da Silva, M. A., Saraiva, G. K. V., Politi, M. J., Valente, A. P., Almeida, F. C. L., Chaimovich, H., Rodrigues, M. A., Bemquerer, M. P., Schreier, S., & Cuccovia, I. M. (2014). Peptide: Lipid ratio and membrane surface charge determine the mechanism of action of the antimicrobial peptide BP100. Conformational and functional studies. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1838(7), 1985–1999. https://doi.org/10.1016/j.bbamem.2014.04.004
   PubMed Web of Science ®Google Scholar
• Marr, A. K., Gooderham, W. J., & Hancock, R. E. (2006). Antibacterial peptides for therapeutic use: Obstacles and realistic outlook. Current Opinion in Pharmacology, 6(5), 468–472. https://doi.org/10.1016/j.coph.2006.04.006
   PubMed Web of Science ®Google Scholar
• Mehrnejad, F., Naderi‐Manesh, H., & Ranjbar, B. (2007). The structural properties of magainin in water, TFE/water, and aqueous urea solutions: Molecular dynamics simulations. Proteins, 67(4), 931–940. https://doi.org/10.1002/prot.21293
   PubMed Web of Science ®Google Scholar
• Miller, B. R., I. I. I., McGee, T. D., Jr, Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA. py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. https://doi.org/10.1021/ct300418h
   PubMed Web of Science ®Google Scholar
• Murzyn, K., Róg, T., & Pasenkiewicz-Gierula, M. (2005). Phosphatidylethanolamine-phosphatidylglycerol bilayer as a model of the inner bacterial membrane. Biophysical Journal, 88(2), 1091–1103. https://doi.org/10.1529/biophysj.104.048835
   PubMed Web of Science ®Google Scholar
• Neu, H. C. (1992). The crisis in antibiotic resistance. Science (New York, N.Y.), 257(5073), 1064–1073. https://doi.org/10.1126/science.257.5073.1064
   PubMed Web of Science ®Google Scholar
• Nguyen, L. T., Haney, E. F., & Vogel, H. J. (2011). The expanding scope of antimicrobial peptide structures and their modes of action. Trends in Biotechnology, 29(9), 464–472. https://doi.org/10.1016/j.tibtech.2011.05.001
   PubMed Web of Science ®Google Scholar
• Pan, J., Marquardt, D., Heberle, F. A., Kučerka, N., & Katsaras, J. (2014). Revisiting the bilayer structures of fluid phase phosphatidylglycerol lipids: Accounting for exchangeable hydrogens. Biochimica et Biophysica Acta, 1838(11), 2966–2969. https://doi.org/10.1016/j.bbamem.2014.08.009
   PubMed Web of Science ®Google Scholar
• Papo, N., & Shai, Y. (2003). Can we predict biological activity of antimicrobial peptides from their interactions with model phospholipid membranes? Peptides, 24(11), 1693–1703. https://doi.org/10.1016/j.peptides.2003.09.013
   PubMed Web of Science ®Google Scholar
• Park, S., Jackman, J. A., & Cho, N.-J. (2019). Comparing the membrane-interaction profiles of two antiviral peptides: Insights into structure–function relationship. Langmuir: The ACS Journal of Surfaces and Colloids, 35(30), 9934–9943. https://doi.org/10.1021/acs.langmuir.9b01052
   PubMed Web of Science ®Google Scholar
• Ramamoorthy, A., Thennarasu, S., Tan, A., Gottipati, K., Sreekumar, S., Heyl, D. L., An, F. Y., & Shelburne, C. E. (2006). Deletion of all cysteines in tachyplesin I abolishes hemolytic activity and retains antimicrobial activity and lipopolysaccharide selective binding. Biochemistry, 45(20), 6529–6540. https://doi.org/10.1021/bi052629q
   PubMed Web of Science ®Google Scholar
• Rand, R.P., & Parsegian, V.A.(1989). Hydration forces between phospholipid bilayers. Biochimica et Biophysica Acta (BBA) - Reviews on Biomembranes, 988(3), 351–376. https://doi.org/10.1016/0304-4157(89)90010-5
   Google Scholar
• Rappolt, M., Hickel, A., Bringezu, F., & Lohner, K. (2003). Mechanism of the lamellar/inverse hexagonal phase transition examined by high resolution x-ray diffraction. Biophysical Journal, 84(5), 3111–3122. https://doi.org/10.1016/S0006-3495(03)70036-8
   PubMed Web of Science ®Google Scholar
• Resende, J. M., Moraes, C. M., Munhoz, V. H., Aisenbrey, C., Verly, R. M., Bertani, P., Cesar, A., Piló-Veloso, D., & Bechinger, B. (2009). Membrane structure and conformational changes of the antibiotic heterodimeric peptide distinctin by solid-state NMR spectroscopy. Proceedings of the National Academy of Sciences of the United States of America, 106(39), 16639–16644. https://doi.org/10.1073/pnas.0905069106
   PubMed Web of Science ®Google Scholar
• Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. (1997). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. https://doi.org/10.1016/0021-9991(77)90098-5
   Google Scholar
• Sindhikara, D. J., Kim, S., Voter, A. F., & Roitberg, A. E. (2009). Bad seeds sprout perilous dynamics: Stochastic thermostat induced trajectory synchronization in biomolecules. Journal of Chemical Theory and Computation, 5(6), 1624–1631. https://doi.org/10.1021/ct800573m
   PubMed Web of Science ®Google Scholar
• Skjevik, Å. A., Madej, B. D., Dickson, C. J., Lin, C., Teigen, K., Walker, R. C., & Gould, I. R. (2016). Simulation of lipid bilayer self-assembly using all-atom lipid force fields. Physical Chemistry Chemical Physics: PCCP, 18(15), 10573–10584. https://doi.org/10.1039/C5CP07379K
   PubMed Web of Science ®Google Scholar
• Sohlenkamp, C., López-Lara, I. M., & Geiger, O. (2003). Biosynthesis of phosphatidylcholine in bacteria. Progress in Lipid Research, 42(2), 115–162. https://doi.org/10.1016/S0163-7827(02)00050-4
   PubMed Web of Science ®Google Scholar
• Talandashti, R., Mahdiuni, H., Jafari, M., & Mehrnejad, F. (2019). Molecular basis for membrane selectivity of antimicrobial peptide pleurocidin in the presence of different eukaryotic and prokaryotic model membranes. Journal of Chemical Information and Modeling, 59(7), 3262–3276. https://doi.org/10.1021/acs.jcim.9b00245
   PubMed Web of Science ®Google Scholar
• Talandashti, R., Mehrnejad, F., Rostamipour, K., Doustdar, F., & Lavasanifar, A. (2021). Molecular insights into pore formation mechanism, membrane perturbation, and water permeation by the antimicrobial peptide Pleurocidin: A combined all-atom and coarse-grained molecular dynamics simulation study. The Journal of Physical Chemistry. B, 125(26), 7163–7176. https://doi.org/10.1021/acs.jpcb.1c01954
   PubMed Web of Science ®Google Scholar
• Uberuaga, B. P., Anghel, M., & Voter, A. F. (2004). Synchronization of trajectories in canonical molecular-dynamics simulations: Observation, explanation, and exploitation. The Journal of Chemical Physics, 120(14), 6363–6374. https://doi.org/10.1063/1.1667473
   PubMed Web of Science ®Google Scholar
• Venable, R. M., Brown, F. L., & Pastor, R. W. (2015). Mechanical properties of lipid bilayers from molecular dynamics simulation. Chemistry and Physics of Lipids, 2015192, 60–74. https://doi.org/10.1016/j.chemphyslip.2015.07.014
   Google Scholar
• Vermeer, L. S., De Groot, B. L., Réat, V., Milon, A., & Czaplicki, J. (2007). Acyl chain order parameter profiles in phospholipid bilayers: Computation from molecular dynamics simulations and comparison with 2 H NMR experiments. European Biophysics Journal: EBJ, 36(8), 919–931. https://doi.org/10.1007/s00249-007-0192-9
   PubMed Web of Science ®Google Scholar
• Wieprecht, T., Dathe, M., Krause, E., Beyermann, M., Maloy, W. L., MacDonald, D. L., & Bienert, M. (1997). Modulation of membrane activity of amphipathic, antibacterial peptides by slight modifications of the hydrophobic moment. FEBS Letters, 417(1), 135–140. https://doi.org/10.1016/S0014-5793(97)01266-0
   PubMed Web of Science ®Google Scholar
• Wimley, W. C. (2010). Describing the mechanism of antimicrobial peptide action with the interfacial activity model. ACS Chemical Biology, 5(10), 905–917. https://doi.org/10.1021/cb1001558
   PubMed Web of Science ®Google Scholar
• Wong-Ekkabut, J., Xu, Z., Triampo, W., Tang, I.-M., Tieleman, D. P., & Monticelli, L. (2007). Effect of lipid peroxidation on the properties of lipid bilayers: A molecular dynamics study. Biophysical Journal, 93(12), 4225–4236. https://doi.org/10.1529/biophysj.107.112565
   PubMed Web of Science ®Google Scholar
• Wu, E. L., Cheng, X., Jo, S., Rui, H., Song, K. C., Dávila-Contreras, E. M., Qi, Y., Lee, J., Monje-Galvan, V., Venable, R. M., Klauda, J. B., & Im, W. (2014). CHARMM‐GUI membrane builder toward realistic biological membrane simulations. Journal of Computational Chemistry, 35(27), 1997–2004. https://doi.org/10.1002/jcc.23702
   PubMed Web of Science ®Google Scholar
• Yoshida, K., Mukai, Y., Niidome, T., Takashi, C., Tokunaga, Y., Hatakeyama, T., & Aoyagi, H. (2001). Interaction of pleurocidin and its analogs with phospholipid membrane and their antibacterial activity. The Journal of Peptide Research: Official Journal of the American Peptide Society, 57(2), 119–126. https://doi.org/10.1034/j.1399-3011.2001.00802.x
   PubMedGoogle Scholar
• Zachowski, A. (1993). A. Phospholipids in animal eukaryotic membranes: Transverse asymmetry and movement. The Biochemical Journal, 294 (Pt 1)(Pt 1), 1–14. https://doi.org/10.1042/bj2940001
   PubMedGoogle Scholar
• Zhuang, X., Dávila-Contreras, E. M., Beaven, A. H., Im, W., & Klauda, J. B. (2016). An extensive simulation study of lipid bilayer properties with different head groups, acyl chain lengths, and chain saturations. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1858(12), 3093–3104. https://doi.org/10.1016/j.bbamem.2016.09.016
   PubMed Web of Science ®Google Scholar