Acid-induced denaturation of cellular retinol-binding proteins types I and II studied by electrospray mass spectrometry.

The acid-induced denaturation of cellular retinol-binding proteins types I and II (CRBP I and II), in the presence and in the absence of the ligand, was studied by electrospray ionization mass spectrometry (ESI-MS) in the pH range 6.9-2.4. To avoid artifacts generated by the ESI process, suitable interface parameters were selected. Different charge-state distributions were observed in the ESI-MS spectra, reflecting the pH-dependent equilibria among protein conformations in solution. In the absence of retinol, CRBP II appeared to be more resistant than CRBP I to acid denaturation. The bound ligand stabilized both carriers, with a markedly higher effect on CRBP I. Retinol release from the ligand-bound carriers and protein denaturation occurred concomitantly. This finding suggests that the lowering of pH, reported to occur in proximity to a biomembrane, might contribute to the conformational transitions required to promote dissociation of the otherwise very stable retinal-carrier complexes and thus permit targeted delivery of vitamin A to the enzymes involved in its metabolism.

Predicting amino acid residues responsible for enzyme specificity solely from protein sequences.

We describe a general, modular method for developing protocols to identify the amino acid residues that most likely define the division of a protein superfamily into two subsets. As one possibility, we use PROBE to gather superfamily members and perform an ungapped alignment. We then use a modified BLOSUM62 substitution matrix to determine the discriminating power of each column of aligned residues. The overall method is particularly useful for predicting amino acids responsible for substrate or binding specificity when no structures are available. We apply our method to three pairs of protein classes in three different superfamilies, and present our results, some of which have been experimentally verified. This approach may accelerate the elucidation of enzymic substrate specificity, which is critical for both mechanistic insights into biocatalysis and ultimate application.

Evolution of the lipocalin family as inferred from a protein sequence phylogeny.

The lipocalins constitute a family of proteins that have been found in eubacteria and a variety of eukaryotic cells, where they play diverse physiological roles. It is the primary goal of this review to examine the patterns of change followed by lipocalins through their complex history, in order to stimulate scientists in the field to experimentally contrast our phylogeny-derived hypotheses. We reexamine our previous work on lipocalin phylogeny and update the phylogenetic analysis of the family. Lipocalins separate into 14 monophyletic clades, some of which are grouped in well supported superclades. The lipocalin tree was rooted with the bacterial lipocalin genes under the assumption that they have evolved from a single common ancestor with the metazoan lipocalins, and not by horizontal transfer. The topology of the rooted tree and the species distribution of lipocalins suggest that the newly arising lipocalins show a higher rate of amino acid sequence divergence, a higher rate of gene duplication, and their internal pocket has evolved towards binding smaller hydrophobic ligands with more efficiency.

Novel classes of fatty acid and retinol binding protein from nematodes.

Parasitic nematodes have recently been found to produce proteins which represent two new classes of fatty acid and retinoid binding protein. The first is the nematode polyprotein allergens/antigens (NPAs) which, as their name suggests, are synthesised as large polyproteins which are subsequently cleaved at regularly spaced sites to form multiple copies of a fatty acid binding protein of approximately 14.5 kDa. Binding studies using molecular environment-sensitive fluorescent ligands have shown that the binding site is highly unusual, producing blue-shifting in fluorescence to an unprecedented degree, suggesting a remarkably non-polar environment and isolation from solvent water. Computer-based structural predictions and biophysical observations have identified the NPAs as highly helical proteins which might form a four helix bundle, so constitute a new class of lipid binding protein from animals. The second class, like the NPAs, binds both fatty acids and retinol, but with a higher affinity for the latter. These are also highly helical but are structurally distinct from the NPAs. The biological function of these new classes of protein are discussed in the context of both the metabolic requirements of the parasites and the possible role of the proteins in control of the immune and inflammatory environment of the tissue sites parasitised.

Cloning of chick cellular retinol-binding protein, type II and comparison to that of some mammals: expression of the gene at different developmental stages, and possible involvement of RXRs and PPAR.

We cloned chick cellular retinol-binding protein, type two (CRBP II) cDNA and compared it with those of some mammals. The deduced amino acid sequence showed that chick CRBP II was one amino acid greater in size than those of mammals, and the nucleotide sequence of chick CRBP II shared 72%-75% similarity with those of mammals. RNA blot hybridization analysis showed that CRBP II transcript of 0.7 kb was first detected in the duodenum of day-18 embryonic chick, and exhibited a rapid increase during 24 hr around the hatching. Northern blot hybridization also revealed that the transcripts of two types of retinoid X receptors (RXR alpha and RXR gamma) and peroxisome proliferator-activated receptor (PPAR) were expressed in the chick duodenum at hatching. The organ culture of day 16 embryonic chick duodenum showed that the addition of 9-cis retinoic acid in the medium caused a significant increase in CRBP II mRNA levels. In addition, arachidonic acid, from which putative ligands for PPAR were supposed to be generated, was accumulated around hatching in the duodenum. The results may suggest that the abrupt increase of the CRBP II gene expression in the chick duodenum around hatching may be related with RXRs and/or PPAR.

Vitamin A trafficking in Caco-2 cells stably transfected with cellular retinol binding proteins.

During intestinal vitamin A absorption, retinol is esterified by long-chain fatty acids and secreted in chylomicron particles. Stable transfectants of the human intestinal Caco-2 cell line overexpressing cellular retinol binding protein II (CRBP II) or coexpressing CRBP II and CRBP were established to study their role in intestinal vitamin A trafficking. Compared with control cell lines, retinol uptake increased up to twofold by overexpression of CRBP II and up to 2.9-fold by coexpression of CRBP and CRBP II. Retinyl ester synthesis was increased proportionate to the increase in retinol absorption in all cell lines. Retinyl ester secretion was directly correlated with retinyl ester synthesis in control and CRBP II-transfected cell lines. However, transfection with CRBP increased the proportion secreted. Expression of CRBP and CRBP II also affected the polarity of retinyl ester secretion by increasing the proportion secreted basolaterally. Thus these studies provide evidence that intestinal retinol uptake, retinyl ester synthesis, and retinyl ester secretion are correlated with levels of CRBP and CRBP II and that the effects of CRBP on retinyl ester secretion can be distinguished from those of CRBP II.

Structure and sequence relationships in the lipocalins and related proteins.

The lipocalins and fatty acid-binding proteins (FABPs) are two recently identified protein families that both function by binding small hydrophobic molecules. We have sought to clarify relationships within and between these two groups through an analysis of both structure and sequence. Within a similar overall folding pattern, we find large parts of the lipocalin and FABP structures to be quantitatively equivalent. The three largest structurally conserved regions within the lipocalin common core correspond to characteristic sequence motifs that we have used to determine the constitution of this family using an iterative sequence analysis procedure. This afforded a new interpretation of the family, which highlighted the difficulties of determining a comprehensive and coherent classification of the lipocalins. The first of the three conserved sequence motifs is also common to the FABPs and corresponds to a conserved structural element characteristic of both families. Similarities of structure and sequence within the two families suggests that they form part of a larger "structural superfamily"; we have christened this overall group the calycins to reflect the cup-shaped structure of its members.