title: 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.
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, School of Life Sciences, Sichuan University, Chengdu 610064, China; School of Life Sciences, Guizhou Normal University, Guiyang 550001, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Shi
authors.forename: Zi-jie
authors.initials: ZJ
authors.lastname: Wang
authors.forename: Huai-long
authors.initials: HL
authors.lastname: Xu
authors.forename: Yang
authors.initials: Y
authors.lastname: Tian
authors.forename: Xin
authors.initials: X
authors.lastname: Li
authors.forename: Jin-ku
authors.initials: JK
authors.lastname: Bao
authors.forename: Su-rong
authors.initials: SR
authors.lastname: Sun
authors.forename: Bi-song
authors.initials: BS
authors.lastname: Yue
mesh_terms: D052179:Antigens, Plant / Q000737:chemistry* / Q000378:metabolism*; D002352:Carrier Proteins / Q000737:chemistry* / Q000378:metabolism*; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D032443:Peganum / Q000737:chemistry*; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D052179:Antigens, Plant; D002352:Carrier Proteins; D010940:Plant Proteins; C511920:lipid transfer proteins, plant
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