Antibacterial peptide

The well-defined helical structure associated with appropriately substituted peptoid oligomers (Section 1.6) can be employed to fashion compounds that closely mimic the stracture and function of certain bioactive peptides. There are many examples of small helical peptides (<100 residues) whose mimicry by non-natural ohgomers could potentially yield valuable therapeutic and bioactive compounds. This section describes peptoids that have been rationaUy designed as mimics of antibacterial peptides, lung surfactant proteins, and coUagen proteins. Mimics of HIV-Tat protein, although relevant to this discussion, were described previously in this chapter (Sections 1.3.2 and 1.4.1). 

The magaiitins are a class of hnear, cationic, faciaUy amphipathic and hehcal antibacterial peptides derived from frog skin [51]. The magaiitins exhibit highly selective and potent antimicrobial activity against a broad spectrum of organisms [52, 53]. As these peptides are faciaUy amphipathic, the magainins have a cationic heli-... 

H Bacteria -Streptomyces bottropenis Bottromycin A2 - antibacterial peptide 97, 98... 

Thermodynamics of Proteins Calculating the Entropy of a Helix-Coil Transition in a Small Antibacterial Peptide using Statistical Mechanics (J. Mol. Bio. 1999, 294, 785-794. "Thermodynamics of the a-Helix-Coil Transition of Amphipathic Peptides in a Membrane Environment Implications for the Peptide-Membrane Binding Equilibrium")... 

Schnapp, D., Schnapp, D., Kemp, G. D., and Smith, V. J. (1996). Purification and characterization of a proline-rich antibacterial peptide, with sequence similarity to bactenecin 7, from the haemocytes of the shore crab, Carcinus maenas. Eur. J. Biochem. 240,532-539. 

Molecular components Antibacterial peptides (defensins, complement, acute-phase proteins) Immunoglobulins... 

CONTENTS Preface, C. Allen Bush. Thermodynamic Solvent Isotope Effects and Molecular Hydrophobicity, Terrence G. Oas and Eric J. Toone. Membrane Interactions of Hemolytic and Antibacterial Peptides, Karl Lohner and Richard M. Epand. Spin-Labeled Metabolite Analogs as Probes of Enzyme Structure, Chakravarthy Narasimhan and Henry M. Miziorko. Current Perspectives on the Mechanism of Catalysis by the Enzyme Enolase, John M. Brewer and Lukasz Leb-ioda. Protein-DNA Interactions The Papillomavirus E2 Proteins as a Model System, Rashmi S. Hedge. NMR-Based Structure Determination for Unlabeled RNA and DNA, Philip N. Borer, Lucia Pappalardo, Deborah J. Kenwood, and Istvan Pelczer. Evolution of Mononuclear to Binuclear CuA An EPR Study, William E. Antholine. Index. 

Guyomard A, De E, Jouenne T et al. (2008) Incorporation of a hydrophobic antibacterial peptide into amphiphilic polyelectrolyte multilayers a bioinspired approach to prepare biocidal thin coatings. Adv Funct Mater 18 758-765... 

Otvos, L., Jr., Cudic, M., Chua, B.Y., Deliyannis, G., and Jackson, D.C. (2004) An insect antibacterial peptide-based drug delivery system. Mol. Pharmaceut. 1, 220-232. 

Cudic, M., Lockatell, C.V., Johnson, D.E., and Otvos, L., Jr. (2003) In vitro and in vivo activity of antibacterial peptide analogs against uropathogens. Peptides 24, 807-820. 

Otvos, L., Jr. (2005) Antibacterial peptides and proteins with multiple cellular targets. J. Pept. Sci. 11, 697-706. 

Lamberty, M., Zachary, D., Lanot, R., et al. (2001) Insect immunity. Constitutive expression of a cysteine-rich antifungal and a linear antibacterial peptide in a termite insect. J. Biol. Chem. 276(6), 4085 1092. 

Key Words Antibacterial peptide collision-induced dissociation (CID) electrospray ionization (ESI) matrix-assisted laser desorption/ionization (MALDI) peptide derivati-zation. 

Fig. 1. MALDI-TOF mass spectrum of an antibacterial peptide isolated from dog Canis familiaris using the CHCA matrix. The dominant signals at m/z 4190.38 and 2095.68 correspond to the [M+H]+ and [M+2H]2+ ions of the same peptide. The doubly charged ion, which is usually not obtained for peptides in MALDI-MS, is probably detected due to the high content of basic lysine and arginine residues.

Fig. 2. Manually acquired nanoESI-QqTOFMS/MS spectrum of the doubly charged peptide ion at m/z 590.81 of a tryptic digest of antibacterial peptide with mass 4189.38 (see Fig. 1). The peptide sequence ISGLIEETR was deduced from the singly and doubly charged y-ions starting at m/z 175.13 corresponding to a C-terminal arginine.

Key Words Screening high-throughput SPOT synthesis cellulose luminescence Pseudomonas aeruginosa, QSAR antimicrobial antibacterial peptide machine learning artificial neural networks. 

There are two separate but interrelated aspects to QSAR modeling of antibacterial peptides the choice of QSAR descriptors and the choice of numerical analysis techniques used to relate these values to antibacterial activity. A simple example of a QSAR descriptor is the total charge of a peptide. A large number of QSAR descriptors is available for small compounds in the literature and from commercial software products that may be considered. A smaller subset is used in QSAR studies of antibacterial peptides and may be separated into two categories descriptors based on empirical values and calculated descriptors. An example of an empirical value is HPLC retention time, which is a surrogate measure of solubility or hydrophilicity/hydrophobicity. An example of a calculated descriptor is total peptide charge at pH 7. 

These results show that the new availability of high-quantity and -quality antibacterial peptide data allows more rigorous treatment and evaluation using machine learning techniques. In addition, the diversity of peptide sequences is dramatically improved—no longer is it necessary to start with a prototype... 

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