Crystal structure of nonspecific lipid transfer protein fromSolanum melongena

Abstract

Lipids are considered to protect protein allergens from proteolysis and are generally seen to exist in a bound form. One of the well-known plant protein families with bound lipids is non-specific lipid transfer proteins (nsLTPs). Structure-function relationships in the case of the members of non-specific lipid transfer protein family are not clearly understood. As part of exploring the seed proteome, we have analyzed the proteome of a member of Solanaceae family, Solanum melongena (eggplant) and a non-specific lipid transfer protein from S. melongena, SM80.2 was purified, crystallized and the structure was determined at 1.87 Å resolution. Overall, the tertiary structure is a cluster of α-helices forming an internal hydrophobic cavity. Absence of conserved Tyr79, known to govern the plasticity of hydrophobic cavity, and formation of hydrogen bond between Asn79 and Asn36 further reduced the pocket size. Structural analysis of SM80.2 thus gives insight about a new hydrogen bond mediated mechanism followed in closure of the binding pocket. Extra electron densities observed at two different places on the protein surface and not in the cavity could provide interesting physiological relevance. In light of allergenic properties, probably overlapping of epitopic region and ligand binding on surface could be a main reason. This work shows first crystal structure of A-like nsLTP with a close binding pocket and extra density on the surface suggesting a plausible intermediate state during transfer.

Structural insights into the lipid transfer mechanism of a non‐specific lipid transfer protein

“…The disulfide pairing patterns in S. melongena nsLTP is similar to that of rice nsLTP‐I with Cys 4 ‐Cys 51 , Cys 14 ‐Cys 28 , Cys 29 ‐Cys 74 , and Cys 49 ‐Cys 88 , which is a characteristic type‐I disulfide pattern. The native nsLTP structure showed no bound ligand and represents apo‐state in contrast with previously reported native structure from S. melongena (SM80.2) with electron density on the surface resembling lipid moieties (Jain and Salunke, ). The Asn‐79 amine and carbonyl groups form hydrogen bonds with the carbonyl group of Ala‐39 and NH group of Val‐80, respectively.…”

“…The canonical hydrophobic cavity as lipid binding site was very well established among different nsLTPs. Although binding of lipid on the nsLTP surface was vaguely suggested (Jain and Salunke, ), we have systematically explored and identified two unusual lipid binding sites on the surface. Further, using MD simulations, we were able to demonstrate the mobility of surface‐bound lipid which eventually attained the cavity bound state.…”

“…The S. melongena seeds were washed, dried, and grounded into a fine powder. The nsLTP was extracted by ammonium sulfate fractionation followed by size exclusion chromatography as described previously (Jain and Salunke, ) with some modifications. Briefly, delipidification of grounded seeds was carried out thrice at room temperature by continuous stirring for 3 h, it was then left to settle, and the petroleum ether was discarded, and this procedure was repeated with fresh petroleum ether.…”

“…Structural analyses of proteins with naturally bound ligands purified from the native source often provide insights toward their physiological functions (Shikhi et al , ). Two surface‐bound features for which the electron density could be prominently defined were observed on the surface of the S. melongena nsLTP‐I structure and were modeled as lipids (Jain and Salunke, ). The nsLTPs are evidently multifunctional and are engaged in various physiological processes.…”

Spectrum of Allergens and Allergen Biology in India

“…Moreover, it is also not clear whether the etching symptoms are caused by the residual pesticides applied to eggplant during farming. Despite these findings, certain serological investigations identified certain allergens, including one lipid transfer protein from this vegetable [113], and were found to be concentrated in the peel and seeds.…”