Pathogenic microbes resistant to common antibiotics are emerging as a serious threat to public health. Optimism in antimicrobial peptides (AMPs) as substitutes of conventional antibiotics has been triggered by knowledge of their quick and strong antimicrobial action, and the non-specific membrane-mediated mechanism of AMP-induced cell death. However, design of novel AMPs with attenuated host-cell toxicity has been impeded by a lack of fundamental molecular-scale knowledge of AMP-membrane interaction events. Experimental systems can be complemented by computer simulations to probe peptide-membrane systems to the spatial and temporal resolution required to develop this insight. In this thesis, we have used all-atom molecular dynamics simulations of AMPs in membrane mimics to determine which sequence and structure components of AMPs are responsible for activity and toxicity. Zwitterionic micelles of dodecylphosphocholine (DPC) and bilayers of the zwitterionic lipid dilauroylphosphatidylcholine (DLPC) were used to model mammalian membrane interfaces, while simulations were also implemented in anionic sodiumdodecylsulfate (SDS) micelles to evaluate the peptide structure in the presence of an anionic bacterial membrane interface mimic. To develop comprehensive hypotheses, simulations were implemented for the three common structural classes of AMPs: unstructured, a-helical and ß-sheet (1-11).

For different AMP structural types, different biophysical interactions determined the peptide-membrane interaction dynamics, the membrane-bound peptide structure and the equilibrium peptide orientation near the interface. For the tryptophan- and proline-rich AMP indolicidin, intra-peptide cation-p interactions stabilized the structure in the DPC micelle, while the absence of these interactions led to an ill-defined extended structure in the SDS micelle. Conversely, for helical peptides, the structure was stable in SDS. Only toxic peptides were equally helical in both zwitterionic interfaces and anionic interfaces. This effect of interfacial electrostatics was suggested for the first time. The protonated N-terminus of the ß-hairpin peptide protegrin-1 anchored it to the DLPC bilayer.

In all cases, simulations results were in excellent agreement with NMR, X-ray and CD-spectroscopy data, and successfully rationalized experimental measurements. Based on the simulations, new design rules for less toxic AMP analogues were suggested, while simultaneously providing delightful molecular insights into the biophysics of peptide-membrane interaction. This information can potentially expedite the design of new antimicrobials.

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2. H. Khandelia, Y. Kaznessis, “Molecular Dynamics Simulations of Helical Antimicrobial Peptides in SDS micelles: What do Point Mutations Achieve?”, Peptides, Vol. 26(11), p. 2037-49, 2005.

3. H. Khandelia, Y. Kaznessis, “Molecular Dynamics Simulations of the Helical Antimicrobial Peptide Ovispirin-1 in Zwitterionic Dodecylphoshocholine Micelles: Insights into Host-cell Toxicity.” Journal of Physical Chemistry B, Vol. 109(26), p. 12990-12996, 2005.

4. Langham, H. Khandelia, Y. Kaznessis, "How can protegrin-1 be both a potent antimicrobial and harmfully toxic?: Molecular dynamics simulations of a beta-sheet antimicrobial peptide in micelles" Biopolymers: Peptide Science, 84 (2): 219-231, 2006.

5. H. Khandelia, Y. Kaznessis, “Molecular Dynamics Investigation of the Influence of Anionic and Zwitterionic Interfaces on Antimicrobial Peptides' Structure: Implications on Peptide Toxicity and Activity”, Peptides, 2006, 27(6):1192-1200.

6. H. Khandelia, A. Langham, Y. Kaznessis, "Driving engineering of novel antimicrobial peptides from simulations of peptide-micelle interactions", BBA Biomembranes, 2006, in press, available online.

7. W. Wang, C. Mulakala, S.C. Ward, G. Jung, H. Luong, D. Pham , A.J. Waring, Y. Kaznessis, W. Lu, K.A. Bradley, R.I. Lehrer. "Retrocyclins kill bacilli and germinating spores of Bacillus anthracis and inactivate anthrax lethal toxin." Journal of Biological Chemistry, 2006, in press, available online

8. Langham, Y. Kaznessis, “Effects of mutations on the C-terminus of Protegrin-1: A molecular dynamics simulation study”, Molecular Simulation, Vol. 32(3-4): p. 193-201, 2006.

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