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Computational study of ligand binding in lipid transfer proteins: Structures, interfaces, and free energies of protein‐lipid complexes
Author(s) -
Pacios Luis F.,
GómezCasado Cristina,
Tordesillas Leticia,
Palacín Arantxa,
SánchezMonge Rosa,
DíazPerales Araceli
Publication year - 2012
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.23012
Subject(s) - chemistry , solvation , ligand (biochemistry) , molecular dynamics , plant lipid transfer proteins , implicit solvation , poisson–boltzmann equation , molecular mechanics , computational chemistry , protein ligand , biophysics , chemical physics , molecule , receptor , biochemistry , ion , biology , organic chemistry , gene
Abstract Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed structural flexibility and nonspecificity of hydrophobic protein‐ligand interactions. We present here a computational study of protein‐ligand complexes formed between five nsLTPs and seven lipids bound in two different ways in every receptor protein. After optimizing geometries in molecular dynamics calculations, we computed Poisson‐Boltzmann electrostatic potentials, solvation energies, properties of the protein‐ligand interfaces, and estimates of binding free energies of the resulting complexes. Our results provide the first quantitative information on the ligand abilities of nsLTPs, shed new light into protein‐lipid interactions, and reveal new features which supplement commonly held assumptions on their lack of binding specificity. © 2012 Wiley Periodicals, Inc.