We are analyzing https://link.springer.com/article/10.1007/s00894-015-2807-x.

Title:
Understanding the roles of Lys33 and Arg45 in the binding-site stability of LjLTP10, an LTP related to drought stress in Lotus japonicus | Journal of Molecular Modeling
Description:
In Lotus japonicus, as in most plants, long-chain fatty acids are important components of cuticular wax, one of the principal functions of which is to act as a barrier to water loss in response to drought stress. It is thought that lipid transfer proteins (LTPs) are involved in the process of cuticle formation. We previously described LjLTP10 as an LTP involved in cuticle formation during acclimation response to drought stress in L. japonicus. The structural model of LjLTP10 had two residues (K33 and R45) in the hydrophobic cavity, although the role of these residues was unclear. In the present work, we investigated the molecular mechanism involved in the transport of lipid precursors in L. japonicus and clarified the importance of the residues K33 and R45. First, in silico site-directed mutagenesis studies were carried out on the LjLTP10 structure. Structural analysis showed that LjLTP10 mutants possess similar structures but their hydrophobic cavities are somewhat different. Unfavorable energies for the interactions of the mutant proteins with different ligands were found by molecular docking and molecular dynamics simulations. We also examined the contributions of energetic parameters to the free energy of the protein–ligand complex using the MM-GBSA method. Results showed that the different complexes present similar, favorable van der Waals interactions, whereas electrostatic interactions were not favored in the mutant structures. Our study indicates that the residues K33 and R45 play a crucial role in maintaining the binding pocket structure required for lipid transport.
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Keywords {🔍}

article, google, scholar, lipid, cas, protein, transfer, plant, structure, molecular, proteins, nonspecific, mol, binding, japonicus, ljltp, drought, lotus, role, access, stress, tapia, lipidtransfer, biol, chem, privacy, cookies, content, journal, related, moralesquintana, involved, structural, dynamics, biochemistry, physiol, arabidopsis, talca, data, publish, research, search, modeling, stability, valenzuelariffo, parrapalma, plants, fatty, wax, residues,

Topics {✒️}

mm-gbsa method high-resolution x-ray crystallography article valenzuela-riffo month download article/chapter parra-palma acknowledges conicyt long-chain fatty acids specific lipid-transfer protein specific lipid-transfer protein luis morales-quintana molecular dynamics simulations fatty acid-binding proteins high-resolution crystal structure molecular dynamics simulation scalable molecular dynamics visual molecular dynamics lipid transfer protein author information authors plant cell physiology condensed phase simulations mackerell ad jr binding-site stability lipid transfer proteins lipid-transfer proteins lotus japonicus facultad de ingeniería phospholipid transfer protein lotus corniculatus leaves arabidopsis desperado/atwbc11 transporter vpaat1 protein related full article pdf nonspecific lipid binding privacy choices/manage cookies hydrophobic binding site bifunctional lipid-transfer european economic area protein–ligand complex morales-quintana molecular simulations amino acid sequence fungal plant pathogens parra-palma unliganded state reveals dunbrack rl jr check access instant access complexes present similar van gunsteren wf related subjects molecular modeling aims universidad de talca

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      description:In Lotus japonicus, as in most plants, long-chain fatty acids are important components of cuticular wax, one of the principal functions of which is to act as a barrier to water loss in response to drought stress. It is thought that lipid transfer proteins (LTPs) are involved in the process of cuticle formation. We previously described LjLTP10 as an LTP involved in cuticle formation during acclimation response to drought stress in L. japonicus. The structural model of LjLTP10 had two residues (K33 and R45) in the hydrophobic cavity, although the role of these residues was unclear. In the present work, we investigated the molecular mechanism involved in the transport of lipid precursors in L. japonicus and clarified the importance of the residues K33 and R45. First, in silico site-directed mutagenesis studies were carried out on the LjLTP10 structure. Structural analysis showed that LjLTP10 mutants possess similar structures but their hydrophobic cavities are somewhat different. Unfavorable energies for the interactions of the mutant proteins with different ligands were found by molecular docking and molecular dynamics simulations. We also examined the contributions of energetic parameters to the free energy of the protein–ligand complex using the MM-GBSA method. Results showed that the different complexes present similar, favorable van der Waals interactions, whereas electrostatic interactions were not favored in the mutant structures. Our study indicates that the residues K33 and R45 play a crucial role in maintaining the binding pocket structure required for lipid transport.
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