The effect of structural parameters and positive charge distance on the interaction free energy of antimicrobial peptides with membrane surface

References

• Agerberth, B., Gunne, H., Odeberg, J., Kogner, P., Boman, H. G., & Gudmundsson, G. H. (1995). FALL-39, a putative human peptide antibiotic, is cysteine-free and expressed in bone marrow and testis. Proceedings of the National Academy of Sciences USA, 92, 195–199.10.1073/pnas.92.1.195
   PubMed Web of Science ®Google Scholar
• Anézo, C., de Vries, A. H., Höltje, H. D., Tieleman, D. P., & Marrink, S. J. (2003). Methodological issues in lipid bilayer simulations. The Journal of Physical Chemistry B, 107, 9424–9433.10.1021/jp0348981
   Web of Science ®Google Scholar
• Bai, Y., Liu, S., Jiang, P., Zhou, L., Li, J., Tang, C., … Pervushin, K. (2009). Structure-dependent charge density as a determinant of antimicrobial activity of peptide analogues of defensin. Biochemistry, 48, 7229–7239.10.1021/bi900670d
   PubMed Web of Science ®Google Scholar
• Berendsen, H., Grigera, J., & Straatsma, T. (1987). The missing term in effective pair potentials. The Journal of Physical Chemistry, 91, 6269–6271.10.1021/j100308a038
   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, 10089–10092.10.1063/1.464397
   Web of Science ®Google Scholar
• Dathe, M., Nikolenko, H., Meyer, J., Beyermann, M., & Bienert, M. (2001). Optimization of the antimicrobial activity of magainin peptides by modification of charge. FEBS Letters, 501, 146–150.10.1016/S0014-5793(01)02648-5
   PubMed Web of Science ®Google Scholar
• Dathe, M., & Wieprecht, T. (1999). Structural features of helical antimicrobial peptides: Their potential to modulate activity on model membranes and biological cells. Biochimica et Biophysica Acta (BBA) – Biomembranes, 1462, 71–87.10.1016/S0005-2736(99)00201-1
   PubMed Web of Science ®Google Scholar
• Dempsey, C. E. (1990). The actions of melittin on membranes. Biochimica et Biophysica Acta (BBA) – Reviews on Biomembranes, 1031, 143–161.10.1016/0304-4157(90)90006-X
   PubMed Web of Science ®Google Scholar
• Dennison, S. R., Wallace, J., Harris, F., & Phoenix, D. A. (2005). Amphiphilic alpha-helical antimicrobial peptides and their structure/function relationships. Protein & Peptide Letters, 12, 31–39.10.2174/0929866053406084
   PubMed Web of Science ®Google Scholar
• Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103, 8577–8593.10.1063/1.470117
   Web of Science ®Google Scholar
• Ganz, T., & Lehrer, R. I. (1995). Defensins. Pharmacology & Therapeutics, 66, 191–205.10.1016/0163-7258(94)00076-F
   PubMed Web of Science ®Google Scholar
• Gautier, R., Douguet, D., Antonny, B., & Drin, G. (2008). HELIQUEST: A web server to screen sequences with specific alpha-helical properties. Bioinformatics, 24, 2101–2102.10.1093/bioinformatics/btn392
   PubMed Web of Science ®Google Scholar
• Gordon, J. C., Myers, J. B., Folta, T., Shoja, V., Heath, L. S., & Onufriev, A. (2005). H++: A server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Research, 33, W368–W371.10.1093/nar/gki464
   PubMed Web of Science ®Google Scholar
• Hancock, R. E. (1997). Peptide antibiotics. The Lancet, 349, 418–422.10.1016/S0140-6736(97)80051-7
   PubMed Web of Science ®Google Scholar
• Hancock, R. E., & Lehrer, R. (1998). Cationic peptides: A new source of antibiotics. Trends in Biotechnology, 16, 82–88.10.1016/S0167-7799(97)01156-6
   PubMed Web of Science ®Google Scholar
• Hancock, R. E., & Scott, M. G. (2000). The role of antimicrobial peptides in animal defenses. Proceedings of the National Academy of Sciences, 97, 8856–8861.10.1073/pnas.97.16.8856
   PubMed Web of Science ®Google Scholar
• Hénin, J., & Chipot, C. (2004). Overcoming free energy barriers using unconstrained molecular dynamics simulations. The Journal of Chemical Physics, 121, 2904–2914.10.1063/1.1773132
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18, 1463–1472.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Hessa, T., Kim, H., Bihlmaier, K., Lundin, C., Boekel, J., Andersson, H., … von Heijne, G. (2005). Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature, 433, 377–381.
   PubMed Web of Science ®Google Scholar
• Hoover, W. G. (1985). Canonical dynamics: Equilibrium phase-space distributions. Physical Review A, 31, 1695–1697.10.1103/PhysRevA.31.1695
   PubMed Web of Science ®Google Scholar
• Jang, W. S., Kim, H. K., Lee, K. Y., Kim, S. A., Han, Y. S., & Lee, I. H. (2006). Antifungal activity of synthetic peptide derived from halocidin, antimicrobial peptide from the tunicate, Halocynthia aurantium. FEBS Letters, 580, 1490–1496.10.1016/j.febslet.2006.01.041
   PubMed Web of Science ®Google Scholar
• Jiang, Z., Vasil, A. I., Hale, J. D., Hancock, R. E., Vasil, M. L., & Hodges, R. S. (2008). Effects of net charge and the number of positively charged residues on the biological activity of amphipathic ailpha-helical cationic antimicrobial peptides. Biopolymers, 90, 369–383.10.1002/bip.20911
   PubMed Web of Science ®Google Scholar
• Johansson, A. C. V., & Lindahl, E. (2008). Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations. Proteins, 70, 1332–1344.
   PubMed Web of Science ®Google Scholar
• Johansson, A. C. V., & Lindahl, E. (2009). Protein contents in biological membranes can explain abnormal solvation of charged and polar residues. Proceedings of the National Academy of Sciences, 106, 15684–15689.10.1073/pnas.0905394106
   PubMed Web of Science ®Google Scholar
• Kumar, M., Chaturvedi, A. K., Kavishwar, A., Shukla, P. K., Kesarwani, A. P., & Kundu, B. (2005). Identification of a novel antifungal nonapeptide generated by combinatorial approach. International Journal of Antimicrobial Agents, 25, 313–320.10.1016/j.ijantimicag.2004.10.015
   PubMed Web of Science ®Google Scholar
• Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology, 157, 105–132.
   PubMed Web of Science ®Google Scholar
• Lohner, K., & Prenner, E. J. (1999). Differential scanning calorimetry and X-ray diffraction studies of the specificity of the interaction of antimicrobial peptides with membrane-mimetic systems. Biochimica et Biophysica Acta, 1462, 141–156.
   PubMed Web of Science ®Google Scholar
• Nosé, S., & Klein, M. (1983). Constant pressure molecular dynamics for molecular systems. Molecular Physics, 50, 1055–1076.10.1080/00268978300102851
   Web of Science ®Google Scholar
• Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52, 7182–7190.10.1063/1.328693
   Web of Science ®Google Scholar
• Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., … Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29, 845–85410.1093/bioinformatics/btt055
   PubMed Web of Science ®Google Scholar
• Radzicka, A., & Wolfenden, R. (1988). Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochemistry, 27, 1664–1670.
   Web of Science ®Google Scholar
• Rosenfeld, Y., Lev, N., & Shai, Y. (2010). Effect of the hydrophobicity to net positive charge ratio on antibacterial and anti-endotoxin activities of structurally similar antimicrobial peptides. Biochemistry, 49, 853–861.10.1021/bi900724x
   PubMed Web of Science ®Google Scholar
• Simmaco, M., Mignogna, G., & Barra, D. (1998). Antimicrobial peptides from amphibian skin: What do they tell us? Biopolymers, 47, 435–450.10.1002/(SICI)1097-0282(1998)47:6<>1.0.CO;2-W
   PubMed Web of Science ®Google Scholar
• Soltani, S., Keymanesh, K., & Sardari, S. (2007). In silico analysis of antifungal peptides. Expert Opinion on Drug Discovery, 2, 837–847.10.1517/edc.2007.2.issue-6
   PubMed Web of Science ®Google Scholar
• Soltani, S., Keymanesh, K., & Sardari, S. (2008). Evaluation of structural features of membrane acting antifungal peptides by artificial neural network. Journal of Biological Sciences, 8, 834–845.
   Google Scholar
• Song, L., Hobaugh, M. R., Shustak, C., Cheley, S., Bayley, H., & Gouaux, J. E. (1996). Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore. Science, 274, 1859–1865.10.1126/science.274.5294.1859
   PubMed Web of Science ®Google Scholar
• Tusnady, G. E., Dosztanyi, Z., & Simon, I. (2005). TMDET: Web server for detecting transmembrane regions of proteins by using their 3D coordinates. Bioinformatics, 21, 1276–1277.10.1093/bioinformatics/bti121
   PubMed Web of Science ®Google Scholar
• Ulmschneider, J. P., Andersson, M., & Ulmschneider, M. B. (2011). Determining peptide partitioning properties via computer simulation. The Journal of Membrane Biology, 239, 15–26.10.1007/s00232-010-9324-8
   PubMed Web of Science ®Google Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26, 1701–1718.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• van Gunsteren, W. F., Billeter, S., Eising, A., Hünenberger, P. H., Krüger, P., Mark, A. E., Tironi, I. G. (1996). Biomolecular simulation: The {GROMOS96} Manual and User Guide. Zurich, Switzerland.
   Google Scholar
• Wang, G., Li, X., & Wang, Z. (2009). APD2: The updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Research, 37, D933–D937.10.1093/nar/gkn823
   PubMed Web of Science ®Google Scholar
• Wimley, W. C., & White, S. H. (1996). Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nature Structural Biology, 3, 842–848.10.1038/nsb1096-842
   PubMedGoogle Scholar
• Woolley, S., Johnson, J., Smith, M. J., Crandall, K. A., & McClellan, D. A. (2003). TreeSAAP: Selection on amino acid properties using phylogenetic trees. Bioinformatics, 19, 671–672.
   PubMed Web of Science ®Google Scholar
• Yeaman, M. R., & Yount, N. Y. (2003). Mechanisms of antimicrobial peptide action and resistance. Pharmacological Reviews, 55, 27–55.
   PubMed Web of Science ®Google Scholar
• Zamyatnin, A. A. (1972). Protein volume in solution. Progress in Biophysics & Molecular Biology, 24, 107–123.
   PubMedGoogle Scholar