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Understanding the roles of Lys33 and Arg45 in the binding-site stability of LjLTP10, an LTP related to drought stress in Lotus japonicus

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Abstract

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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Acknowledgments

C. Parra-Palma acknowledges CONICYT for providing a doctoral scholarship. The Center of Bioinformatics and Molecular Simulations (CBSM) of the University of Talca provided the ICM program. We acknowledge the helpful comments and suggestions made by the two anonymous reviewers of this manuscript. FONDECYT initiation project #11090243 and CONICYT PAI/ACADEMIA #79140027 supported this work.

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Authors and Affiliations

  1. Escuela de Ingeniería en Bioinformática, Facultad de Ingeniería, Universidad de Talca, Casilla 747, Talca, Chile

    Felipe Valenzuela-Riffo

  2. Unidad de Recursos Genéticos, Instituto de Investigaciones Agropecuarias, INIA-Quilamapu, Chillán, Chile

    Gerardo Tapia

  3. Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Casilla 747, Talca, Chile

    Carolina Parra-Palma & Luis Morales-Quintana

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  1. Felipe Valenzuela-Riffo
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  2. Gerardo Tapia
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  4. Luis Morales-Quintana
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Correspondence to Gerardo Tapia or Luis Morales-Quintana.

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Valenzuela-Riffo, F., Tapia, G., Parra-Palma, C. et al. Understanding the roles of Lys33 and Arg45 in the binding-site stability of LjLTP10, an LTP related to drought stress in Lotus japonicus . J Mol Model 21, 270 (2015). https://doi.org/10.1007/s00894-015-2807-x

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