Variability in phenylalanine side chain conformations facilitates broad substrate tolerance of fatty acid binding in cockroach milk proteins

Diploptera punctata, also known as the Pacific beetle cockroach, is a viviparous cockroach that gives birth to live offspring and secretes a highly concentrated mixture of glycosylated proteins as a source of nourishment for developing embryos. These proteins are lipocalins that bind to lipids and crystallize in the gut of the embryo. A structure of milk crystals harvested from the embryos showed that the milk-derived crystals were heterogeneous and made of three proteins (called Lili-Mips). We hypothesized that the isoforms of Lili-Mip would display different affinities for fatty acids due to the ability of the pocket to bind multiple acyl chain lengths. We previously reported the structures of Lili-Mip from crystals grown in vivo and recombinantly expressed Lili-Mip2. These structures are similar, and both bind to several fatty acids. This study explores the specificity and affinity of fatty acid binding to recombinantly expressed Lili-Mip 1, 2 & 3. We show that all isoforms can bind to different fatty acids with similar affinities. We also report the thermostability of Lili-Mip is pH dependent, where stability is highest at acidic pH and declines as the pH increases to physiological levels near 7.0. We show that thermostability is an inherent property of the protein, and glycosylation and ligand binding do not change it significantly. Measuring the pH in the embryo's gut lumen and gut cells suggests that the pH in the gut is acidic and the pH inside the gut cells is closer to neutral pH. In various crystal structures (reported here and previously by us), Phe-98 and Phe-100 occupy multiple conformations in the binding pocket. In our earlier work, we had shown that the loops at the entrance could adapt various conformations to change the size of the binding pocket. Here we show Phe-98 and Phe-100 can reorient to stabilize interactions at the bottom of the cavity-and change the volume of the cavity from 510 Å3 to 337 Å3. Together they facilitate the binding of fatty acids of different acyl chain lengths.

Sialic Acid Derivatives Inhibit SiaT Transporters and Delay Bacterial Growth

Antibiotic resistance is a major worldwide concern, and new drugs with mechanistically novel modes of action are urgently needed. Here, we report the structure-based drug design, synthesis, and evaluation in vitro and in cellular systems of sialic acid derivatives able to inhibit the bacterial sialic acid symporter SiaT. We designed and synthesized 21 sialic acid derivatives and screened their affinity for SiaT by a thermal shift assay and elucidated the inhibitory mechanism through binding thermodynamics, computational methods, and inhibitory kinetic studies. The most potent compounds, which have a 180-fold higher affinity compared to the natural substrate, were tested in bacterial growth assays and indicate bacterial growth delay in methicillin-resistant Staphylococcus aureus. This study represents the first example and a promising lead in developing sialic acid uptake inhibitors as novel antibacterial agents.

Structure of recombinantly expressed cockroach Lili-Mip protein in glycosylated and deglycosylated forms

BACKGROUND

The Pacific Beetle Cockroach is the only known viviparous cockroach. The pregnant females provide nutrition to the embryos by secreting milk proteins (Lili-Mips), which crystallize in vivo. The crystals that grow in the embryo are heterogeneous in their protein sequence. It is not apparent from the structure determined what role heterogeneity and glycosylation played in crystallization. Lili-Mips are very nutritious.

METHODS

Here, we report the cloning of synthesized Lili-Mip genes, their expression in Saccharomyces cerevisiae as secreted proteins, purification, crystallization, and the determination of a three-dimensional structure of one glycosylated and one deglycosylated form.

RESULTS

A 2.35 Å structure of the glycosylated form is bound to palmitoleic acid and has several Zn atom mediated interactions. A 1.45 Å structure of the deglycosylated protein revals a binding pocket that has both oleic and palmitoleic acid bound. Mass-spectrometry shows that oleic acid and palmitoleic acid are bound to the protein. Docking studies suggest that aliphatic chains of lengths 15, 16, and 18 carbons bind well in the pocket.

CONCLUSIONS

The recombinantly expressed and secreted protein is glycosylated, has a bound fatty acid, is homogenous in its protein sequences, and readily forms crystals. The deglycosylated protein also crystallizes readily, suggesting that the high crystallizability of this protein is independent of glycosylation.

GENERAL SIGNIFICANCE

Lili-Mips belong to the ubiquitous lipocalin family of proteins that bind to a large variety of ligands. While the residues lining the barrel are essential for the affinity of the ligand, our results show the role of side-chain orientations to ligand selectivity.