Modeling, docking and dynamics simulations of a non-specific lipid transfer protein from Peganum harmala L

Abstract

Non-specific lipid transfer proteins (ns-LTPs), ubiquitously found in various types of plants, have been well-known to transfer amphiphilic lipids and promote the lipid exchange between mitochondria and microbody. In this study, an in silico analysis was proposed to study ns-LTP in Peganum harmala L., which may belong to ns-LTP1 family, aiming at constructing its three-dimensional structure. Moreover, we adopted MEGA to analyze ns-LTPs and other species phylogenetically, which brought out an initial sequence alignment of ns-LTPs. In addition, we used molecular docking and molecular dynamics simulations to further investigate the affinities and stabilities of ns-LTP with several ligands complexes. Taken together, our results about ns-LTPs and their ligand-binding activities can provide a better understanding of the lipid-protein interactions, indicating some future applications of ns-LTP-mediated transport.

Keywords: Ala; C; Cys; Docking; Glu; Leu; MD; MEGA; Molecular Evolutionary Genetics Analysis; Molecular dynamics simulations; NMR; Non-specific transfer protein; PHL-nsLTP; Peganum harmala L.; Peganum harmala L. non-specific lipid transfer protein; RMSD; RMSF; Ser; Structure; Thr; alanine; carbon; cysteine; glutamic acid; isoelectric point; leucine; molecular dynamics; non-specific lipid transfer protein; nsLTP; nuclear magnetic resonance; pI; root-mean-square deviation; root-mean-square fluctuation; serine; threonine.