Crystal structure of rat intestinal fatty-acid-binding protein. Refinement and analysis of the Escherichia coli-derived protein with bound palmitate

Rat intestinal fatty-acid-binding protein (I-FABP) is a small (15,124 Mr) cytoplasmic polypeptide that binds long-chain fatty acids in a non-covalent fashion. I-FABP is a member of a family of intracellular binding proteins that are thought to participate in the uptake, transport and/or metabolic targeting of hydrophobic ligands. The crystal structure of Escherichia coli-derived rat I-FABP with a single molecule of bound palmitate has been refined to 2 A resolution using a combination of least-squares methods, energy refinement and molecular dynamics. The combined methods resulted in a model with a crystallographic R-factor of 17.8% (7775 reflections, sigma greater than 2.0), root-mean-square bond length deviation of 0.009 A and root-mean-square bond angle deviation of 2.85 degrees. I-FABP contains ten antiparallel beta-strands organized into two approximately orthogonal, beta-sheets. The hydrocarbon tail of its single C16:0 ligand is present in a well-ordered, distinctively bent conformation. The carboxylate group of the fatty acid is located in the interior of I-FABP and forms a unique "quintet" of electrostatic interactions involving Arg106; Gln 115, and two solvent molecules. The hydrocarbon tail is bent with a slight left-handed helical twist from the carboxylate group to C-16. The bent methylene chain resides in a "cradle" formed by the side-chains of hydrophobic, mainly aromatic, amino acid residues. The refined molecular model of holo-I-FABP suggests several potential locations for entry and exiting of the fatty acid.     

The primary structure of fatty-acid-binding protein from nurse shark liver. Structural and evolutionary relationship to the mammalian fatty-acid-binding protein family.

The primary structure of a fatty-acid-binding protein (FABP) isolated from the liver of the nurse shark (Ginglymostoma cirratum) was determined by high-performance tandem mass spectrometry (employing multichannel array detection) and Edman degradation. Shark liver FABP consists of 132 amino acids with an acetylated N-terminal valine. The chemical molecular mass of the intact protein determined by electrospray ionization mass spectrometry (Mr = 15124 +/- 2.5) was in good agreement with that calculated from the amino acid sequence (Mr = 15121.3). The amino acid sequence of shark liver FABP displays significantly greater similarity to the FABP expressed in mammalian heart, peripheral nerve myelin and adipose tissue (61-53% sequence similarity) than to the FABP expressed in mammalian liver (22% similarity). Phylogenetic trees derived from the comparison of the shark liver FABP amino acid sequence with the members of the mammalian fatty-acid/retinoid-binding protein gene family indicate the initial divergence of an ancestral gene into two major subfamilies: one comprising the genes for mammalian liver FABP and gastrotropin, the other comprising the genes for mammalian cellular retinol-binding proteins I and II, cellular retinoic-acid-binding protein myelin P2 protein, adipocyte FABP, heart FABP and shark liver FABP, the latter having diverged from the ancestral gene that ultimately gave rise to the present day mammalian heart-FABP, adipocyte FABP and myelin P2 protein sequences. The sequence for intestinal FABP from the rat could be assigned to either subfamily, depending on the approach used for phylogenetic tree construction, but clearly diverged at a relatively early evolutionary time point. Indeed, sequences proximately ancestral or closely related to mammalian intestinal FABP, liver FABP, gastrotropin and the retinoid-binding group of proteins appear to have arisen prior to the divergence of shark liver FABP and should therefore also be present in elasmobranchs. The presence in shark liver of an FABP which differs substantially in primary structure from mammalian liver FABP, while being closely related to the FABP expressed in mammalian heart muscle, peripheral nerve myelin and adipocytes, opens a further dimension regarding the question of the existence of structure-dependent and tissue-specific specialization of FABP function in lipid metabolism.     

Three-dimensional structure of fatty-acid-binding protein from bovine heart

The complex of fatty-acid-binding protein (FABP) from bovine heart (cFABP, pI4.9) with endogenous lipid was crystallized in the presence of ammonium sulfate as precipitant. The needle-shaped crystals belong to the monoclinic space group C2, with unit-cell constants a = 5.262(6) nm, b = 7.631(8) nm, c = 3.945(5) nm and beta = 94.47(9) degrees. A native data set to 0.35 nm resolution was collected using synchrotron radiation and film methods. An initial model for the three-dimensional structure of the protein was constructed based on the crystal structure of the related bovine P2 myelin protein [Jones, T.A., Bergfors, T., Sedzik, J. & Unge, T. (1988) EMBO J. 7, 1597-1604] to which the amino acid sequence of bovine cFABP was adapted. Energy minimizations were carried out under different conditions using both an all-atom and a united-atom force field. The optimized models were used to determine the crystal structure of cFABP by molecular-replacement techniques. The structure was refined by simulated annealing to R = 0.267. As the bound lipid is heterogeneous, it could not be located in the electron-density map and/or the attained resolution was not sufficient. Bovine cFABP is composed of ten antiparallel beta strands forming a beta barrel, and by two alpha helices. The structural features are similar to those of other members of the superfamily of hydrophobic molecule transporters.     

Studies on fatty-acid-binding proteins. The purification of rat liver fatty-acid-binding protein and the role of cysteine-69 in fatty acid binding.

1. A new, simple and high-yield procedure is described for the purification of hepatic fatty-acid-binding protein from rat liver using naphthylaminodecyl-agarose as an affinity column. 2. Cysteine-69 is shown to react slowly, but quantitatively, with 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB), indicating that the thiol group is free, but may be buried within the protein. 3. Fatty acids do not affect the DTNB reactivity of this cysteine residue; however, cysteine reactivity is enhanced in the presence of haem and oleoyl-CoA. 4. Fatty-acid-binding protein that has been modified with DTNB is still able to bind the fluorescent fatty acid 11-(dansylamino)undecanoic acid, indicating that cysteine-69 may be remote from the fatty-acid-binding site.     

Purification and characterization of fatty-acid-binding proteins from rat heart and liver

Fatty-acid-binding proteins were purified from delipidated cytosols of rat heart and liver by gel filtration and anion-exchange chromatography at pH 8.0 and by repeated gel filtration, respectively. Homogeneity of both proteins was demonstrated by a single band on polyacrylamide gels; each had a molecular weight of about 14 000. Liver fatty-acid-binding protein is more basic (pI, 8.1) than that of heart (pI, 7.0) and contains more basic amino acids. Examination of fatty acid binding by the binding proteins from heart and liver revealed the presence of a single class of fatty-acid-binding sites in both cases with an apparent dissociation constant for palmitate of about 1 microM. Liver fatty- acid-binding protein shows similar binding characteristics for palmitate, oleate and arachidonate. Palmitate bound to heart fatty- acid-binding protein was a good substrate for oxidation by rat heart mitochondria. The results show that the fatty-acid-binding proteins from rat heart and liver are closely related, but that they are distinct proteins.     

Sequence of rat intestinal vitamin D-dependent calcium-binding protein derived from a cDNA clone. Evolutionary implications

We have recently reported molecular cloning of the cDNA synthesized from rat duodenal mRNA-encoding intestinal calcium-binding protein (ICaBP), a vitamin D3-induced protein (Desplan, C., Thomasset, M., and Moukhtar, M. S. (1983) J. Biol. Chem. 258, 2762-2765). Nucleotide sequence analysis of the longest cDNA insert (375 base pairs) permitted the assignment of 207 nucleotides of the coding region and 104 nucleotides of the entire 3'-noncoding region of the mRNA. Although the derived amino acid sequence for rat ICaBP differed from the bovine and porcine sequences by 16 and 14 residues, respectively, all the residues of each calcium-binding site met the proposed requirements of the "EF hand" theory. In contrast, several differences found in the linker regions might explain the absence of cross-immunoreactivity between rat and porcine ICaBPs. Analysis of nucleotide sequence homologies between the coding and noncoding regions showed that the region coding for the two calcium-binding sites (I and II) was immediately followed in the noncoding region by a sequence very similar to the sequence coding for site I. This suggests that rat ICaBP mRNA contains the remains of an untranslated calcium-binding site III-like structure and that low Mr ICaBP could result in early termination of the translation of a larger molecule containing four sites.     

The interferon-inducible 15-kDa ubiquitin homolog conjugates to intracellular proteins.

We have previously identified a 15-kDa interferon-induced protein that is recognized by affinity-purified rabbit polyclonal antibodies against ubiquitin (Haas, A. L., Ahrens, P., Bright, P. M., and Ankel, H. (1987) J. Biol. Chem. 262, 11315-11323). This ubiquitin cross-reactive protein (UCRP) possesses significant homology to a tandem diubiquitin sequence. Since the biological effects of ubiquitin arise from its covalent ligation to intracellular target proteins, we hypothesized that the multiple cellular responses to inteferon are mediated in part by an analogous conjugation pathway for UCRP. Rabbit polyclonal antibodies specific for UCRP were prepared against homogeneous recombinant protein. Affinity-purified anti-UCRP antibodies detected the induction of UCRP in interferon-beta-treated A549 cells and recognized a group of high molecular weight UCRP conjugates on immunoblots of sodium dodecyl sulfate-polyacrylamide gel electrophoresis-resolved cell extracts. Both free and conjugated UCRP are constitutively present at low levels in untreated cells, suggesting a role for UCRP ligation in normal cellular regulation, and significantly accumulate following interferon treatment. The temporal induction of free UCRP following interferon treatment preceded a delayed increase in UCRP conjugates. Treatment of A549 cells with type I interferons (alpha and beta) strongly induced the expression of free and conjugated UCRP, whereas the response to type II interferon (gamma) was significantly less. A survey of selected cultured cell lines showed differential induction of free versus conjugated UCRP pools in response to interferon. Interferon-beta treatment of A549, MG63, and U937 cells induced high levels of both free and conjugated UCRP, whereas only free UCRP levels increased in Daudi, Namalwa, and K562 cells. These results confirm that UCRP represents a functional ubiquitin homolog participating in a parallel pathway of post-translational ligation and provides a novel mechanism for the response of susceptible cells to the effects of interferon exposure.     

Binding of phosphatidylinositol-3,4,5-triphosphate to 45-kDa sec14-like protein from the rat olfactory epithelium in liposomes

The binding of phosphatidylinositol-3,4,5-triphosphate to a protein with molecular mass of 45 kDa from rat olfactory epithelium (p45) was investigated using a model membrane system. Liposomes containing a mixture of phospholipids (phosphatidylethanolamine, phosphatidylcholine, and phosphatidylinositol-3,4,5-triphosphate) were used in the study. The binding of the protein to liposomes caused by its interaction with phosphatidylinositol-3,4,5-triphosphate was confirmed by cosedimentation and immunoblotting with chemiluminescent detection using monoclonal antibodies to the native protein p45. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2006, vol. 32, no. 3; see also http://www.maik.ru.     

Binding of phosphatidylinositol-3,4,5-triphosphate to 45-kDa Sec14-like protein from the rat olfactory epithelium in liposomes

The binding of phosphatidylinositol-3,4,5-triphosphate to a protein with molecular mass of 45 kDa from rat olfactory epithelium (p45) was investigated using a model membrane system. Liposomes containing a mixture of phospholipids (phosphatidylethanolamine, phosphatidylcholine, and phosphatidylinositol-3,4,5-triphosphate) were used in the study. The binding of the protein to liposomes caused by its interaction with phosphatidylinositol-3,4,5-triphosphate was confirmed by cosedimentation and immunoblotting with chemiluminescent detection using monoclonal antibodies to the native protein p45.     

Characterization of a 67-kDa S6 protein kinase from rat liver.

Fractionation of rat liver cytosol on DEAE-cellulose resolved two S6 kinases eluting at 25 mM KCl (peak I) and 100 mM KCl (peak II). The apparent molecular weights of the peak I and peak II kinases are 26,300 and 67,000, respectively. The peak II kinase was further purified and characterized. Incubation of the kinase with [gamma-32P] ATP and Mg2+ resulted in the incorporation of 32P predominantly into a 67-kDa band. Optimal activity of the kinase was observed in the presence of 5 mM Mg2+ and in the pH range of 8.0-8.5. The Km for ATP and 40S subunit were 7.3 microM and 1.5 microM, respectively. The Mg(2+)-stimulated kinase activity was inhibited by various divalent metals, NaF, and polyamines. The properties of the peak II S6 kinase are very similar or identical to the previously described mitogen-activated S6 protein kinase and may represent the nonactivated form of this enzyme.     

Purification and characterization of a fatty-acid-binding protein from the gastric mucosa of rats. Possible identity with heart fatty-acid-binding protein and its parietal cell localization

Fatty acid-binding protein (FABP) was purified from rat gastric mucosa by successive Sephadex G-75 chromatography, DEAE-cellulose chromatography and HPLC on an RP-2 (Merck) reversed-phase column. The purified stomach FABP migrated as a single band corresponding to an apparent molecular mass of 15 kDa on SDS/PAGE. Stomach FABP appeared to be identical with rat heart FABP, as judged from its electrophoretic mobility, amino acid composition and tryptic peptide map. In addition, the amino acid sequences of two selected tryptic peptides coincided completely with the rat heart FABP sequence deduced from that of cDNA. Stomach FABP showed immunochemical identity with rat heart FABP when tested with an antiserum against rat heart FABP. Immunohistochemically, stomach FABP was specifically stained with anti-(rat heart FABP) serum in parietal cells of the gastric mucosa. The results suggested that the primary structure of stomach FABP is identical with that of rat heart FABP, and showed that stomach FABP is localized in parietal cells of the gastric mucosa.     

Molecular cloning of a cDNA for rat hepatic glutaminase. Sequence similarity to kidney-type glutaminase

Mammalian liver possesses a unique isozyme of phosphate-activated glutaminase which plays an important role in the regulation of glutamine catabolism. Antibodies to hepatic glutaminase were used to screen a lambda gt11 rat liver cDNA library. One cDNA to hepatic glutaminase was identified. Changes in the relative abundance of hepatic glutaminase mRNA were determined by hybridization to this cDNA. The mRNA is found only in liver; it is not present prior to birth but its abundance increases dramatically at birth. The abundance of the mRNA is increased approximately 4-fold in diabetes. The sequence of the cDNA was compared to that recently published for kidney (brain)-type glutaminase (Banner, C., Hwang, J.-J., Shapiro, R.A., Wenthold, R.J., Nakatani, Y., Lampel, K.A., Thomas, J.W., Huie, D., and Curthoys, N.P. (1988) Mol. Brain Res. 3, 247-254). When the predicted amino acid sequences were compared a region of 123 amino acids with greater than 80% identity was found. The presence of scattered amino acid substitutions within stretches of identical amino acids suggests that the glutaminase isozymes are encoded by separate genes. This is the first demonstration of any similarity between the two glutaminases at the molecular level.     

Study of structure of secretory 28 kDa protein from the rat olfactory epithelium

Clone lambda a26.1 isolated from rat olfactory epithelium contains a full-length 28-kDa protein cDNA (1414 b.p.). The reconstructed protein sequence comprises 223 aa with a calculated molecular mass of 24,630 Da. A substantial homology was revealed between the amino acid sequence of the 28-kDa protein and those of thiol-specific antioxidants (peroxiredoxines). The 28-kDa protein belongs to the 1 Cys-subfamily of peroxiredoxines and is the first member of peroxiredoxines identified in the olfactory epithelium.     

Primary structure of a pheromone-binding protein from Antheraea pernyi: homologies with other ligand-carrying proteins

Summary An antennal cDNA clone encoding the complete sequence (163 amino acids) of a pheromone-binding protein precursor from the male silk moth, Antheraea pernyi, was isolated using oligonucleotide probes. The cloned cDNA was expressed and the translation product detected by specific antibodies. The deduced protein sequence consists of a signal peptide of 21 amino acids and a mature binding protein of 142 amino acid residues. The predicted structure of this protein is homologous to binding-proteins from different insect species which have previously been identified, but shows no similarities to odorant-binding proteins from vertebrates, suggesting that soluble odorant-binding proteins in insects and vertebrates represent an evolutionary convergence.Abbreviations PBP pheromone-binding protein - OBP odorant-binding protein - cDNA complentary DNA - poly(A ⁺) RNA polyadenylated RNA - SSC 0.15 M sodium chloride+0.015 M sodium citrate - SDS-PAGE sodium dodecylsulfate polyacrylamide gelelectrophoresis     

A novel 45 kDa secretory protein from rat olfactory epithelium: primary structure and localisation.

cDNA clones encoding the 45 kDa protein were isolated from a rat olfactory epithelium cDNA library and their inserts were sequenced. The reconstructed protein sequence comprises 400 amino acids with a calculated molecular mass of 46,026 Da. A homology was revealed between the amino acid sequence of the 45 kDa protein and the proteins involved in the transfer of hydrophobic ligands. Using in situ hybridisation, the 45 kDa protein mRNA expression was detected in the layer of supportive cells of olfactory epithelium, apical region of trachea, surface layer of the ciliated bronchial epithelium in lung and in skin epidermis.     

Antigenic secreted proteins from Haemophilus paragallinarum. A 110-kDa putative RTX protein

Haemophilus paragallinarum is the causal agent of infectious coryza, an economically important disease for the poultry industry. This bacterium secreted proteins of 25-110 kDa during its growth in brain heart infusion, tryptic soy broth, or Luria-Bertani glucose phosphate media, all lacking serum. Some of these proteins were recognized by sera from chickens experimentally infected with H. paragallinarum. A 110-kDa protein was recognized by a serum pool from convalescent-phase pigs naturally infected with Actinobacillus pleuropneumoniae, and also by a rabbit polyclonal serum against Apx I as well as a rabbit serum against Mannheimia haemolytica leukotoxin, suggesting the presence of an RTX-like protein in H. paragallinarum. H. paragallinarum secreted proteins could be important immunogens in the control of infectious coryza.     

Primary structure of cAMP-gated channel from bovine olfactory epithelium

The complete amino-acid sequence of the bovine olfactory epithelium adenosine 3',5'cyclic monophosphate (cAMP)-gated channel has been determined by cloning and sequencing its cDNA. It exhibits a high degree of sequence homology with the cGMP-gated channel of rod photoreceptors, suggesting that cyclic nucleotide-gated channels fall into a new family of genetically related proteins.     

Crystallization, structure determination and least-squares refinement to 1.75 A resolution of the fatty-acid-binding protein isolated from Manduca sexta L.

The molecular structure of an insect fatty-acid-binding protein isolated from Manduca sexta L. has been determined and refined to a nominal resolution of 1.75 A. Crystals used in the investigation were grown from 1.6 M-ammonium sulfate solutions buffered at pH 4.5 with 50 mM-sodium succinate, and belonged to space group P2(1) with unit cell dimensions of a = 27.5 A, b = 71.0 A, c = 28.7 A and beta = 90.8 degrees. An electron density map, phased with four heavy-atom derivatives and calculated to 2.5 A resolution, allowed for complete tracing of the 131 amino acid residue polypeptide chain. Subsequent least-squares refinement of the model reduced the R-factor from 46.0% to 17.3% using all measured X-ray data from 30.0 A to 1.75 A. Approximately 92% of the amino acid residues fall into classical secondary structural elements including ten strands of anti-parallel beta-pleated sheet, two alpha-helices, one type I turn, three type II turns, four type II' turns and one type III turn. As in other fatty-acid-binding proteins, the overall molecular architecture of the insect molecule consists of ten strands of anti-parallel beta-pleated sheet forming two layers that are nearly orthogonal to one another. A helix-turn-helix motif at the N-terminal portion of the protein flanks one side of the up-and-down beta-barrel. The functional group of the fatty acid is within hydrogen-bonding distance of Gln39, Tyr129, Arg127 and a sulfate molecule, while the aliphatic portion of the ligand is surrounded by hydrophobic amino acid residues lining the beta-barrel. The binding of the carboxylic acid portion of the ligand is very similar to that observed in P2 myelin protein and the murine adipocyte lipid-binding protein, but the positioning of the hydrocarbon tail after approximately C6 is completely different.     

A 15-kDa interferon-induced protein is derived by COOH-terminal processing of a 17-kDa precursor

An interferon-induced 15-kDa protein is synthesized from a precursor of higher molecular weight; the precursor contains 165 amino acids (17 kDa), whereas the stable product (15 kDa) contains 156 amino acids. The stable 15-kDa form is derived from the precursor 17-kDa form by the removal of eight amino acids from the COOH terminus and the methionine from the NH2 terminus. The existence of the precursor 17-kDa protein can be demonstrated after brief periods of in vivo labeling with [35S]methionine and by translation of mRNA in vitro.