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    National Tsing Hua University Institutional Repository > 生命科學院  > 生命科學系 > 期刊論文 >  Effects of ligand binding on the dynamics of rice nonspecific lipid transfer protein 1: A model from molecular simulations


    Please use this identifier to cite or link to this item: http://nthur.lib.nthu.edu.tw/dspace/handle/987654321/48675


    Title: Effects of ligand binding on the dynamics of rice nonspecific lipid transfer protein 1: A model from molecular simulations
    Authors: Lai, Yen-Ting;Cheng, Chao-Sheng;Liu, Yu-Nan;Liu, Yaw-Jen;Lyu, Ping-Chiang
    教師: 呂平江
    Date: 2008
    Publisher: John Wiley & Sons
    Relation: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,John Wiley & Sons,Volume 72,Issue 4,SEP 2008,Pages 1189-1198
    Keywords: N-15 NMR RELAXATION
    CRYSTAL-STRUCTURE
    HYDROPHOBIC CAVITY
    Abstract: Plant nonspecific lipid transfer proteins (nsLTPs) are small, basic proteins constituted mainly of a-helices and stabilized by four conserved disulfide bridges. They are characterized by the presence of a tunnel-like hydrophobic cavity, capable of transferring various lipid molecules between lipid bilayers in vitro. In this study, molecular dynamics (MD) simulations were performed at room temperature to investigate the effects of lipid binding on the dynamic properties of rice nsLTP1. Rice nsLTP1, either in the free form or complexed with one or two lipids was subjected to MD simulations. The C-terminal loop was very flexible both before and after lipid binding, as revealed by calculating the root-mean-square fluctuation. After lipid binding, the flexibility of some residues that were not in direct contact with lipid molecules increased significantly, indicating an increase of entropy in the region distal front the binding site. Essential dynamics analysis revealed clear differences in motion between unliganded and liganded rice nsLTPIs. In the free form of rice nsLTPI, loopl exhibited the largest directional motion. This specific essential motion mode diminished after binding one or two lipid molecules. To verify the origin of the essential motion observed in the free form of rice nsLTPI, we performed multiple sequence alignments to probe the intrinsic motion encoded in the primary sequence. We found that the amino acid sequence of loop1 is highly conserved among plant nsLTP1s, thus revealing its functional importance during evolution. Furthermore, the sequence of loop1 is composed mainly of amino acids with short side chains. In this study, we show that MD simulations, together with essential dynamics analysis, can be used to determine structural and dynamic differences of rice nsLTPI upon lipid binding.
    URI: http://www.wiley.com/
    http://nthur.lib.nthu.edu.tw/dspace/handle/987654321/48675
    Appears in Collections:[生命科學系] 期刊論文

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