title: Structural analysis as an alternative to identify and determine mode of action of antimicrobial peptides: proposition of a kinetic model based on molecular dynamics studies.
abstract: Antimicrobial peptides (AMPs) constitute an important alternative in the search for new treatments against pathogens. We analyzed the sequence variability in cytokine and chemokine proteins to investigate whether these molecules contain a sequence useful in the development of new AMPs. Cluster analysis allowed the identification of tracts, grouped in five categories showing structure and sequence homology. The structure and function relationship among these groups, was analyzed using physicochemical parameters such as length, sequence, charge, hydrophobicity and helicity, which allowed the selection of a candidate that could constitute an AMP. This peptide comprises the C-terminal alpha-helix of chemokines CXCL4/PF-457-70. Far-UV CD spectroscopy showed that this molecule adopts a random conformation in aqueous solution and the addition of 2, 2, 2 trifluoroethanol (TFE) is required to induce a helical secondary structure. The CXCL4/PF-457-70 peptide was found to have antimicrobial activity and very limited hemolytic activity. The mechanism of action was analyzed using model kinetics and molecular dynamics. The kinetic model led to a reasonable assumption about a rate constant and regulatory step on its mechanism of action. Using molecular dynamics simulations, the structural properties the CXCL4/PF-457-70 have been examined in a membrane environment. Our results show that this peptide has a strong preference for binding to the lipid head groups, consequently, increasing the surface density and decreasing the lateral mobility of the lipids alters its functionality.
authors.affiliation: Departamento de Quimica de Biomacromoleculas, Instituto de Quimica, Universidad Nacional Autonoma de Mexico, Circuito Exterior, Ciudad Universitaria, Mexico D. F. 04360, Mexico.
authors.forename: Edson Edinho
authors.initials: EE
authors.lastname: Robles-Gomez
authors.forename: Mirelle Citlali
authors.initials: MC
authors.lastname: Flores-Villegas
authors.forename: Alicia
authors.initials: A
authors.lastname: Gonzalez-Manjarrez
authors.forename: Manuel
authors.initials: M
authors.lastname: Soriano-Garcia
mesh_terms: D000818:Animals; D023181:Antimicrobial Cationic Peptides / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology*; D002942:Circular Dichroism; D016000:Cluster Analysis; D030562:Databases, Protein; D004912:Erythrocytes / Q000187:drug effects; D004926:Escherichia coli / Q000187:drug effects; D005452:Fluoresceins / Q000378:metabolism; D006461:Hemolysis / Q000187:drug effects; D006801:Humans; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D010978:Platelet Factor 4 / Q000737:chemistry; D015202:Protein Engineering; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D012441:Saccharomyces cerevisiae / Q000187:drug effects; D020539:Sequence Analysis, Protein
chemical_list: D023181:Antimicrobial Cationic Peptides; D005452:Fluoresceins; D011994:Recombinant Proteins; D010978:Platelet Factor 4; C007740:fluorexon