Conformational Profile Assessment of Cathelicidin (LL-37) Using Molecular Dynamics Simulation

Abstract

Understanding biological function at molecular level involves studying the spontaneous folding patterns of peptides to unique and biologically-active three-dimensional structures. Peptides are highly flexible in nature and fold at fast rates hence require probing at nanosecond time scale. Bioactive conformational structures of folded peptides need to be well characterized before using them in computer-aided drug design. Molecular dynamics (MD) simulations provide detailed information on the fluctuations and their affect. Cathelicidins are a novel family of antimicrobial peptides (AMP) characterized by conserved pro-peptide sequences and a common N-terminal “cathelin” domain which have been identified in several mammalian species. Cathelicidins are cationic, frequently α-helical, amphipathic host defense peptides and provide the first-line of defense against infection by serving as “natural antibiotics”. Recent evidence has indicated that the sole human cathelicidin, LL-37 so called as it starts with two leucines, possesses a broad range of chemotactic and immunostimulatory/ modulatory effects. It has the ability to neutralize bacterial lipopolysaccharide (LPS) attributed to its C-terminal end and multiple roles influencing diverse processes such as cell proliferation and migration, wound healing apoptosis and angiogenesis. LL-37 also enhances the responsiveness of hematopoietic stem cells to homing factors primarily because of its SDF-1-specific priming effect. Thus, cathelicidin antimicrobial peptides qualify as prototypes of innovative drugs that may be used to treat infection and modulate the immune response. The present study attempts to get a deeper insight into the conformational features of cathelicidin focused at establishing structure-activity relationships and investigates the propensities of cathelicidin to adopt different conformations by using different computational protocols.