Metal binding sites of a gamma-carboxyglutamic acid-rich fragment of bovine prothrombin.

The metal binding sites of a gamma-carboxyglutamic acid-rich fragment derived from bovine prothrombin were examined using paramagnetic lanthanide ions to evaluate the role of gamma-carboxyglutamic acid resideus in metal binding. A gamma-carboxyglutamic acid-rich peptide, fragment 12-44, was isolated from a tryptic digest of prothrombin. Using 153Gd(III), fragment 12-44 was found to contain one high affinity metal binding site (KD = 0.55 microM) and four to six lower affinity metal binding sites (KD approximately 4 to 8 microM). The S-carboxymethyl derivative of fragment 12-44, in which the disulfide bond in fragment 12-44 was reduced and alkylated, contained no high affinity metal binding site and four or five lower affinity sites (KD = 8 microM). The effects of paramagnetic lanthanide ions on fragment 12-44 and its S-carboxymethyl derivative were studied by natural abundance 13C NMR spectroscopy. The 13C NMR spectrum of fragment 12-44 was recorded at 67.88 MHz and the resonances were assigned by comparison to the chemical shift of carbon resonances of amino acids and peptides previously studied. The proximity between bound metal ions and carbon atoms in fragment 12-44 was estimated using Gd(III), based upon the strategy that the magnitude of the change in the transverse relaxation rate of resonances of carbon nuclei induced by bound metal ions is related in part to the interatomic distances between bound metal and carbon nuclei. Titration of fragment 12-44 with Gd(III) resulted in the selective broadening of the gamma-carboxyl carbon, C gamma, C beta, and C alpha resonances of gamma-carboxyglutamic acid, and the C epsilon of the arginines. S-Carboxymethyl fragment 12-44, which lacked the high affinity metal binding site, showed markedly decreased perturbation of the C epsilon of the arginine residues upon titration with Gd(III). These studies indicate that gamma-carboxyglutamic acid residues in prothrombin fragment 12-44 participate in metal liganding. A high affinity metal binding site in fragment 12-44 is in close proximity of Arg 16 and Arg 25 and is stabilized by the disulfide bond. On the basis of these data, a model of the metal binding sites is proposed in which the high affinity site is composed of two gamma-carboxyglutamic acid residues which participate in intramolecular metal-dependent bridging of two regions of the polypeptide chain. The lower affinity metal binding sites, formed by single or paired adjacent gamma-carboxyglutamic acid residues, then may participate in intermolecular metal-dependent protein . protein or protein . membrane complex formation.     

Recombinant hBMP4 incorporated with non-canonical amino acid for binding to hydroxyapatite

A novel growth factor containing non-canonical amino acids was designed and synthesized to enhance the binding to hydroxyapatite (HA). The designed protein was human bone morphogenetic protein 4 (hBMP4) incorporating diphosporylated serines (pSpS) that was found in salivary protein statherin and was reported to be responsible for binding to HA. Recombinant hBMP4 and a short peptide sequences containing pSpS were ligated by enzymatice reaction of sortase A, which exchanges the terminal amino acids of two polypeptides. Resulting hBMP4 containing pSpS (hBMP4-pSpS) bound HA more efficiently than hBMP-4 tagged with canonical serines (hBMP4-SS). The HA-bound hBMP-4-pSpS exhibited osteogenesis inducing activity to multipotential mesenchyme cells (C3H10T1/2) as evidenced by increased expression of osteogenic markers, which was not seen by hBMP4-SS. This novel protein with non-canonical serines will be applicable to bone regeneration materials in combination with HA.     

Information content of binding sites on nucleotide sequences

Repressors, polymerases, ribosomes and other macromolecules bind to specific nucleic acid sequences. They can find a binding site only if the sequence has a recognizable pattern. We define a measure of the information (R sequence) in the sequence patterns at binding sites. It allows one to investigate how information is distributed across the sites and to compare one site to another. One can also calculate the amount of information (R frequency) that would be required to locate the sites, given that they occur with some frequency in the genome. Several Escherichia coli binding sites were analyzed using these two independent empirical measurements. The two amounts of information are similar for most of the sites we analyzed. In contrast, bacteriophage T7 RNA polymerase binding sites contain about twice as much information as is necessary for recognition by the T7 polymerase, suggesting that a second protein may bind at T7 promoters. The extra information can be accounted for by a strong symmetry element found at the T7 promoters. This element may be an operator. If this model is correct, these promoters and operators do not share much information. The comparisons between R sequence and R frequency suggest that the information at binding sites is just sufficient for the sites to be distinguished from the rest of the genome.     

Daunomycin binding to deoxypolynucleotides with alternating sequences: complete thermodynamic profiles of heterogeneous binding sites

Complete thermodynamic binding profiles for the interaction of the anticancer drug, daunomycin with natural DNA and synthetic deoxypolynucleotides were described. Fluorescence titration method was used to estimate the equilibrium binding constants. Binding isotherms were found to be surprisingly complex in some cases, presumably because there were heterogeneous sites even in simple deoxypolynucleotides of repeating sequence. Some polynucleotides consisting of alternating sequence contain at least two different binding sites for daunomycin. The binding affinity of the primary binding sites of alternating and non-alternating sequences was found to differ by two orders of magnitude. An isothermal microtitration calorimeter was used to directly measure the binding enthalpy at 25 degrees C with a high sensitivity. The binding enthalpy of poly[d(A-T)] was found to be -5.5 Kcal/mol, which was much lower than any other polynucleotides, while the binding constant of the high affinity sites, was similar. In this report, the complete thermodynamic profiles of daunomycin binding to deoxypolynucleotides were reliably shown for the first time.     

Aggregation of hydroxyapatite crystals

A system to study the aggregation of hydroxyapatite crystals was developed. The effect of several factors (Ca²⁺ × P_i product, Ca²⁺ /P_i ratio, pH, and various substances) were tested. Pb²⁺, Zn²⁺, Mg²⁺ and methyleneblue had only small effects; citrate inhibited aggregation. Pyrophosphate was a strong inhibitor and the diphosphonates disodium ethane-1-hydroxy-1,1-diphosphonate and disodium duchloromethylene diphosphonate were even more potent. The monophosphonate pentanemonophosphonate had no effect. Potent inhibition also occurred with glycosaminoglycans: heparin > hyaluronic acid > dermatan sulfate > chondroitin 4-sulfate > chondroitin 6-sulfate. Urine also showed high inhibitory activity. The inhibition of heparin but not that of hyaluronic acid, PP_i or urine was abolished by egg white lysozyme. The effects described might be relevant in the normal mineralization process as well as in the mechanisms leading to pathological calcification, such as urinary stone formation.     

Enantioselective binding sites on bovine serum albumin to dansyl amino acids.

The enantioselective binding sites on bovine serum albumin were examined by HPLC using 19 racemic 5-N, N-dimethylamino-1-naphthalenesulfonyl derivatives of alpha-amino acids (dansyl amino acids) as chiral probes. On a bovine serum albumin bonded chiral stationary phase, seven L-forms eluted faster than their D-forms, while ten D-forms eluted before their L-forms. It was speculated that either two classes or two different binding sites exist on bovine serum albumin which can be distinguished by N-dansyl-L-proline and N-dansyl-D-norvaline. This was confirmed by fluorometric experiments where non-fluorescent 1-naphthalenesulfonyl derivatives were synthesized and competitive adsorption experiments were performed.     

Disaggregation of hydroxyapatite crystals

A system has been developed to measure quantitatively the disaggregation of hydroxyapatite crystals. Disaggregation was induced by pyrophosphate, ethane-1-hydroxy-1,1-diphosphonate, dichloromethylene diphosphonate, heparin and citrate. Hyaluronic acid stimulated aggregation at low concentrations and disaggregation at high concentrations. Lactate had no effect. The possible role might play in the resorption of calcified tissues in vivo is discussed.     

Disaggregation of hydroxyapatite crystals.

A system has been developed to measure quantitatively the disaggregation of hydroxyapatite crystals. Disaggregation was induced by pyrophosphate, ethane-1-hydroxy-1,1-diphosphonate, dichloromethylene diphosphonate, haparin and citrate. Hyaluronic acid stimulated aggregation at low concentrations and disaggregation at high concentrations. Lactate had no effect. The possible role disaggregation might play in the resorption of calcified tissues in vivo id discussed.     

Cloning and complete amino acid sequences of human and murine basement membrane protein BM-40 (SPARC, osteonectin)

Amino acid sequences of 285 and 286 residues, respectively, were deduced for mouse and human BM-40 from cDNA clones isolated from expression libraries. The sequences showed 92% identity and were also essentially identical to those of bone osteonectin and of the parietal endoderm protein SPARC. About 60% of the mouse BM-40 sequence was confirmed by Edman degradation. Two of the seven disulfide bonds were localized which apparently separate two distinct domains of mouse BM-40.     

Methanococcus jannaschii prolyl-cysteinyl-tRNA synthetase possesses overlapping amino acid binding sites

The protein translation apparatus of Methanococcus jannaschii possesses the unusual enzyme prolyl-cysteinyl-tRNA synthetase (ProCysRS), a single enzyme that attaches two different amino acids, proline and cysteine, to their cognate tRNA species. Measurement of the ATP-PP(i) exchange reaction revealed that amino acid activation, the first reaction step, differs for the two amino acids. While Pro-AMP can be formed in the absence of tRNA, Cys-AMP synthesis is tRNA-dependent. Studies with purified tRNAs indicate that tRNA(Cys) promotes cysteine activation. The k(cat) values of wild-type ProCysRS for tRNA prolylation (0.09 s(-1)) and cysteinylation (0.02 s(-1)) demonstrate that both aminoacyl-tRNAs are synthesized with comparable rates, the cysteinyl-tRNA synthetase activity being only 4.5-fold lower than prolyl-tRNA synthetase activity. Kinetic analysis of ProCysRS mutant enzymes, generated by site-directed mutagenesis, shows glutamate at position 103 to be critical for proline binding, and proline at position 100 to be involved in cysteine binding. The proximity in ProCysRS of amino acid residues affecting binding of either cysteine or proline strongly suggests that structural elements of the two amino acid binding sites overlap.     

Discovering amino acid patterns on binding sites in protein complexes

Discovering amino acid (AA) patterns on protein binding sites has recently become popular. We propose a method to discover the association relationship among AAs on binding sites. Such knowledge of binding sites is very helpful in predicting protein-protein interactions. In this paper, we focus on protein complexes which have protein-protein recognition. The association rule mining technique is used to discover geographically adjacent amino acids on a binding site of a protein complex. When mining, instead of treating all AAs of binding sites as a transaction, we geographically partition AAs of binding sites in a protein complex. AAs in a partition are treated as a transaction. For the partition process, AAs on a binding site are projected from three-dimensional to two-dimensional. And then, assisted with a circular grid, AAs on the binding site are placed into grid cells. A circular grid has ten rings: a central ring, the second ring with 6 sectors, the third ring with 12 sectors, and later rings are added to four sectors in order. As for the radius of each ring, we examined the complexes and found that 10Å is a suitable range, which can be set by the user. After placing these recognition complexes on the circular grid, we obtain mining records (i.e. transactions) from each sector. A sector is regarded as a record. Finally, we use the association rule to mine these records for frequent AA patterns. If the support of an AA pattern is larger than the predetermined minimum support (i.e. threshold), it is called a frequent pattern. With these discovered patterns, we offer the biologists a novel point of view, which will improve the prediction accuracy of protein-protein recognition. In our experiments, we produced the AA patterns by data mining. As a result, we found that arginine (arg) most frequently appears on the binding sites of two proteins in the recognition protein complexes, while cysteine (cys) appears the fewest. In addition, if we discriminate the shape of binding sites between concave and convex further, we discover that patterns {arg, glu, asp} and {arg, ser, asp} on the concave shape of binding sites in a protein more frequently (i.e. higher probability) make contact with {lys} or {arg} on the convex shape of binding sites in another protein. Thus, we can confidently achieve a rate of at least 78%. On the other hand {val, gly, lys} on the convex surface of binding sites in proteins is more frequently in contact with {asp} on the concave site of another protein, and the confidence achieved is over 81%. Applying data mining in biology can reveal more facts that may otherwise be ignored or not easily discovered by the naked eye. Furthermore, we can discover more relationships among AAs on binding sites by appropriately rotating these residues on binding sites from a three-dimension to two-dimension perspective. We designed a circular grid to deposit the data, which total to 463 records consisting of AAs. Then we used the association rules to mine these records for discovering relationships. The proposed method in this paper provides an insight into the characteristics of binding sites for recognition complexes.     

Prediction of RNA binding sites in proteins from amino acid sequence

RNA-protein interactions are vitally important in a wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses. We have developed a computational tool for predicting which amino acids of an RNA binding protein participate in RNA-protein interactions, using only the protein sequence as input. RNABindR was developed using machine learning on a validated nonredundant data set of interfaces from known RNA-protein complexes in the Protein Data Bank. It generates a classifier that captures primary sequence signals sufficient for predicting which amino acids in a given protein are located in the RNA-protein interface. In leave-one-out cross-validation experiments, RNABindR identifies interface residues with >85% overall accuracy. It can be calibrated by the user to obtain either high specificity or high sensitivity for interface residues. RNABindR, implementing a Naive Bayes classifier, performs as well as a more complex neural network classifier (to our knowledge, the only previously published sequence-based method for RNA binding site prediction) and offers the advantages of speed, simplicity and interpretability of results. RNABindR predictions on the human telomerase protein hTERT are in good agreement with experimental data. The availability of computational tools for predicting which residues in an RNA binding protein are likely to contact RNA should facilitate design of experiments to directly test RNA binding function and contribute to our understanding of the diversity, mechanisms, and regulation of RNA-protein complexes in biological systems. (RNABindR is available as a Web tool from http://bindr.gdcb.iastate.edu.).     

High-performance liquid chromatography using novel square tile-shaped hydroxyapatite crystals as adsorbent

High-performance liquid chromatography using, as adsorbent, novel square tile-shaped hydroxyapatite crystals (with thicknesses of about 2 microns and diameters of 3-7 microns) has been developed. The chromatographic efficiencies of the novel hydroxyapatite packed columns are almost equal to those of the previously developed spherical hydroxyapatite packed columns; high chromatographic resolutions can be obtained by using extremely reduced column lengths of 0.5-3 cm. Since both the square and the spherical hydroxyapatite have roughly the same particle size of some micrometers, the chromatographic efficiency can be deduced to be determined mainly by the particle size rather than the particle shape.     

Biotransformation of fatty acid-rich tree oil hydrolysates to hydroxy fatty acid-rich hydrolysates by hydroxylases and their feasibility as biosurfactants

The fatty acid compositions of 10 types of tree oils were analyzed and Camellia japonica (CJ), Tetradium daniellii (TD), and Hovenia dulcis (HD) tree oils were selected to be oleic acid (OA)-, linoleic acid (LA)-, and α-linoleic acid (ALA)-rich tree oils, respectively. Recombinant Escherichia coli expressing 10-hydratase and 7,8-diol synthase converted 31.7 and 15.6 g/L unsaturated fatty acids (UFAs) in OA-rich oil hydrolysates to 21.7 g/L 10-monohydroxy fatty acid (monoHFA) and 13.3 g/L 7,8-diHFA, respectively. The cells expressing 13-hydratase, 13-lipoxygenase, 5,8-diol synthase, and 8,11-diol synthase converted 42.8, 28.5, 10.0, and 20.0 g/L UFAs in LA-rich oil hydrolysates to 28.2 g/L 13-monoHFA, 11.8 g/L 13-monoHFA, 7.2 g/L 5,8-diHFA, and 8.9 g/L 8,11-diHFA, respectively. The cells expressing 8,11-diol synthase converted containing 17.5 g/L UFAs in ALA-rich oil hydrolysate to 7.5 g/L 8,11-diHFA. The average emulsifying activities of diHFArich and monoHFA-rich tree oil hydrolysates were 13.9- and 4.3-fold higher than those of tree oil hydrolysates, respectively. Thus, HFA-rich tree oil hydrolysates derived from tree oils can be applied as biosurfactants, and the fatty acid-rich residue as by-product obtained from the tree refinery process may be recycled into biosurfactants.