Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information

Background The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. Results In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively. Conclusion A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis.

tert-Butylaminium 2-carboxy-4,5-dichlorobenzoate

In the structure of the title anhydrous salt C4H12N+ C8H3Cl2O4-, the 4,5-dichlorophthalate monoanions have the common 'planar' conformation with the carboxyl groups close to coplanar with the benzene ring and with a short intramolecular carboxylic acid O-H...O hydrogen bond. A two-dimensional sheet structure is formed through aminium N-H...O(carboxyl) hydrogen-bonding associations.

Structural Systematics of the Anhydrous 1:1 Proton-Transfer Compounds of 3,5-Dinitrosalicylic Acid with Aniline and Monosubstituted Anilines

The crystal structures of the proton-transfer compounds of 3,5-dinitrosalicylic acid (DNSA) with a series of aniline-type Lewis bases [aniline, 2-hydroxyaniline, 2-methoxyaniline, 3-methoxyaniline, 4-fluoroaniline, 4-chloroaniline and 2-aminoaniline] have been determined and their hydrogen-bonding systems analysed. All are anhydrous 1:1 salts: [(C6H8N)+(C7H3N2O7)-], (1), [(C6H8NO)+(C7H3N2O7)-], (2), [(C7H10NO)+(C7H3N2O7)-], (3), [(C7H10NO)+(C7H3N2O7)-], (4), [(C6H7FN)+(C7H3N2O7)-], (5), [(C6H7ClN)+(C7H3N2O7)-], (6), and [(C6H9N2)+(C7H3N2O7)-], (7) respectively. Crystals of 1 and 6 are triclinic, space group P-1 while the remainder are monoclinic with space group either P21/n (2, 4, 5 and 7) or P21 (3). Unit cell dimensions and contents are: for 1, a = 7.2027(17), b = 7.5699(17), c = 12.9615(16) Å, α = 84.464(14), β = 86.387(15), γ = 75.580(14)o, Z = 2; for 2, a = 7.407(3), b = 6.987(3), c = 27.653(11) Å, β = 94.906(7)o, Z = 4; for 3, a = 8.2816(18), b = 23.151(6), c = 3.9338(10), β = 95.255(19)o, Z = 2; for 4, a = 11.209(2), b = 8.7858(19), c = 15.171(3) Å, β = 93.717(4)o, Z = 4; for 5, a = 26.377(3), b = 10.1602(12), c = 5.1384(10) Å, β = 91.996(13)o, Z = 4; for 6, a = 11.217(3), b = 14.156(5), c = 4.860(3) Å, α = 99.10(4), β = 96.99(4), γ = 76.35(2)o, Z = 2; for 7, a = 12.830(4), b = 8.145(3), c = 14.302(4) Å, β = 102.631(6)o, Z = 4. In all compounds at least one primary linear intermolecular N+-H…O(carboxyl) hydrogen-bonding interaction is present which, together with secondary hydrogen bonding results in the formation of mostly two-dimensional network structures, exceptions being with compounds 4 and 5 (one-dimensional) and compound 6 (three-dimensional). In only two cases [compounds 1 and 4], are weak cation-anion or cation-cation π-π interactions found while weak aromatic C-H…O interactions are insignificant. The study shows that all compounds fit the previously formulated classification scheme for primary and secondary interactive modes for proton-transfer compounds of 3,5-dinitrosalicylic acid but there are some unusual variants.

catena-Poly[[diaqualithium]-mu-[rac-cis-(2-carboxycyclohexane-1-carboxylato-kO1:O2]]

In the structure of the title compound, [C8H11LiO4(H2O)2]n the distorted tetrahadral LiO4 coordination sphere comprises two water molecules and two carboxyl O-donors from separate bridging cis-2-carboxycyclohexane-1-carboxylate monoanions [Li-O range, 1.887(4)-1.946(3)A], giving chain substructures which extend along (010). Water-water and water-carboxyl O-H...O hydrogen bonds stabilize these chain structures and provide inter-chain links, resulting in a two-dimensional layered structure extending across (011).

Bis(benzylaminium) 4,5-dichlorobenzene-1,2-dicarboxylate monohydrate

In the structure of the title salt 2C7H10N+.C8H2Cl2O4(2-) .H2O the two benzylaminium anions have different conformations, one being essentially planar the other having the side-chain rotated out of the benzene plane (minimum ring to side-chain C-C-C-N torsion angles = -3.6(6) and 50.1(5)\%, respectively). In the 4,5-dichlorophthalate dianion the carboxyl groups make ihedral angles of 23.0(2) and 76.5(2)\% with the benzene ring. Aminium N-H...O and water O-H...O hydrogen-bonding associations with carboxyl O-atom acceptors give a two-dimensional duplex sheet structure which extends along the (011) plane. Weak pi-pi interactions are also present between the benzene ring and one of the cation rings [minimum ring centroid separation = 3.749(3)Ang.

The chemistry of acid catalyzed delignification of sugarcane bagasse in the ionic liquid trihexyl tetradecyl phosphonium chloride

This article reports on the cleavage of lignin ß-aryl ether bonds in sugarcane bagasse by the ionic liquid (IL) trihexyl tetradecyl phosphonium chloride [P66614] Cl, in the presence of catalytic amounts of mineral acid fca. 0.4%). The deligniflcation process of bagasse was studied over a range of temperatures (120°C to 150°C) by monitoring the production of ß-ketones (indicative of cleavage of ß-aryl ethers) using FTIR spectroscopy and by compositional analysis of the undissolved fractions. Maximum deligniflcation was obtained at 150°C, with 52% of lignin removed from the original lignin content of bagasse. No deligniflcation was observed in the absence of acid, which suggests that the reaction is acid catalyzed with the IL solubilizing the lignin fragments. The rate of deligniflcation was significantly higher at 150°C, suggesting that crossing the glass transition temperature of lignin effects greater freedom of rotation about the propanoid carbon-carbon bonds and leads to increased cleavage of ß-aryl ethers. An attempt has been made to propose a probable mechanism of deligniflcation of bagasse with the phosphonuim IL. © Taylor & Francis Group, LLC.

Zoledronic acid preserves bone structure and increases survival but does not limit tumour incidence in a prostate cancer bone metastasis model

Background The bisphosphonate, zoledronic acid (ZOL), can inhibit osteoclasts leading to decreased osteoclastogenesis and osteoclast activity in bone. Here, we used a mixed osteolytic/osteoblastic murine model of bone-metastatic prostate cancer, RM1(BM), to determine how inhibiting osteolysis with ZOL affects the ability of these cells to establish metastases in bone, the integrity of the tumour-bearing bones and the survival of the tumour-bearing mice. Methods The model involves intracardiac injection for arterial dissemination of the RM1(BM) cells in C57BL/6 mice. ZOL treatment was given via subcutaneous injections on days 0, 4, 8 and 12, at 20 and 100 µg/kg doses. Bone integrity was assessed by micro-computed tomography and histology with comparison to untreated mice. The osteoclast and osteoblast activity was determined by measuring serum tartrate-resistant acid phosphatase 5b (TRAP 5b) and osteocalcin, respectively. Mice were euthanased according to predetermined criteria and survival was assessed using Kaplan Meier plots. Findings Micro-CT and histological analysis showed that treatment of mice with ZOL from the day of intracardiac injection of RM1(BM) cells inhibited tumour-induced bone lysis, maintained bone volume and reduced the calcification of tumour-induced endochondral osteoid material. ZOL treatment also led to a decreased serum osteocalcin and TRAP 5b levels. Additionally, treated mice showed increased survival compared to vehicle treated controls. However, ZOL treatment did not inhibit the cells ability to metastasise to bone as the number of bone-metastases was similar in both treated and untreated mice. Conclusions ZOL treatment provided significant benefits for maintaining the integrity of tumour-bearing bones and increased the survival of tumour bearing mice, though it did not prevent establishment of bone-metastases in this model. From the mechanistic view, these observations confirm that tumour-induced bone lysis is not a requirement for establishment of these bone tumours.

Two-dimensional coordination polymers in rubidium and caesium complexes with orthanilic acid

The crystal structures of the rubidium and caesium complexes with 2-aminobenzenesulfonic acid (orthanilic acid), [Rb4(C6H6NO3S)4(H2O)]n (1) and [Cs(C6H6NO3S)]n (2) and have been determined at 200 K. Complex 1 has a repeating unit comprising four independent and different Rb coordination centres, (RbO8), (RbO7), (RbN2O4) and (RbO10), each having irregular stereochemistry and involving a number of bidentate chelate sulfonate-O,O’-metal and bridging interactions, giving a two-dimensional polymeric layered structure. Anhydrous complex 2 is also polymeric with the irregular (CsO7) coordination polyhedron comprising six sulfonate oxygen donors from three separate bidentate chelate sulfonate ligands and one monodentate bridging sulfonate oxygen, giving a two-dimensional layered structure.

Pretreatment of sugarcane bagasse by acid-catalysed process in aqueous ionic liquid solutions

A biomass pretreatment process was developed using acidified ionic liquid (IL) solutions containing 10-30% water. Pretreatment of sugarcane bagasse at 130°C for 30min by aqueous 1-butyl-3-methylimidazolium chloride (BMIMCl) solution containing 1.2% HCl resulted in a glucan digestibility of 94-100% after 72h of enzymatic hydrolysis. HCl was found to be a more effective catalyst than H(2)SO(4) or FeCl(3). Increasing acid concentration (from 0.4% to 1.2%) and reaction temperature (from 90 to 130°C) increased glucan digestibility. The glucan digestibility of solid residue obtained with the acidified BMIMCl solution that was re-used for three times was >97%. The addition of water to ILs for pretreatment could significantly reduce IL solvent costs and allow for increased biomass loadings, making the pretreatment by ILs a more economic proposition.

A novel cyclization product from the polyphosphoric acid catalyzed addition of propanal to limonene

The polyphosphoric acid catalyzed addition of propanal to limonene yielded a novel bicyclic ether 2,2,6-trimethyl-4-ethyl-3-oxabicyclo[3.3.1]non-6-ene (I). The yield of (I) was significantly increased by carrying out the reaction under nitrogen rather than in air.

Human Kallikrein 4 signal peptide induces cytotoxic T cell responses in healthy donors and prostate cancer patients.

Immunotherapy is a promising new treatment for patients with advanced prostate and ovarian cancer, but its application is limited by the lack of suitable target antigens that are recognized by CD8+ cytotoxic T lymphocytes (CTL). Human kallikrein 4 (KLK4) is a member of the kallikrein family of serine proteases that is significantly overexpressed in malignant versus healthy prostate and ovarian tissue, making it an attractive target for immunotherapy. We identified a naturally processed, HLA-A*0201-restricted peptide epitope within the signal sequence region of KLK4 that induced CTL responses in vitro in most healthy donors and prostate cancer patients tested. These CTL lysed HLA-A*0201+ KLK4 + cell lines and KLK4 mRNA-transfected monocyte-derived dendritic cells. CTL specific for the HLA-A*0201-restricted KLK4 peptide were more readily expanded to a higher frequency in vitro compared to the known HLA-A*0201-restricted epitopes from prostate cancer antigens; prostate-specific antigen (PSA), prostate-specific membrane antigen (PSMA) and prostatic acid phosphatase (PAP). These data demonstrate that KLK4 is an immunogenic molecule capable of inducing CTL responses and identify it as an attractive target for prostate and ovarian cancer immunotherapy.

4-(4-Nitrobenzyl)pyridinium 3-carboxy-4-hydroxybenzenesulfonate

In the title salt, C12H11N2O2+·C7H5O6S-, the dihedral angle between the benzene and pyridine rings in the 4-(4-nitrobenzyl)pyridinium cation is 82.7 (2)°. Within the anion there is an intramolecular hydroxy-O-HO(carboxylic acid) bond. In the crystal, the cation forms a single N+-HOsulfonate hydrogen bond with the anion. These cation-anion pairs interact through duplex anion carboxylic acid O-HOsulfonate hydrogen bonds, giving a centrosymmetric cyclic association [graph set R22(16)]. The crystals studied were non-merohedrally twinned.

ESEM study of authigenic chlorite acid sensitivity in sandstone reservoirs

The effect of HCl on authigenic chlorite in three different sandstones has been examined uisng an Environmental Scanning Electron Microscope (ESEM), together with conventional analytical techniques. The ESEM enabled chlorites to be directly observed in situ at high magnifications during HCl treatment, and was particularly effective in allowing the same chlorite areas to be closely compared before and after acid treatment. Chlorites were reacted with 1M to 10M HCl at temperatures up to 80°C and for periods up to five months. After all treatments, chlorites show extensive leaching of iron, magnesium and aluminum, and their crystalline structure is destroyed. However, despite these major compositional and structural changes, chlorites show little or no visible evidence of acid attack, with precise morphological detail of individual plates preserved in all samples following acid treatments. Chlorite dissolution, sensu stricto, did not occur as a result of acidization of the host sandstones. Acid-treated chlorides are likely to exits in a structurally weakened state that may make them susceptible to physical disintegration during fluid flow. Accordingly, fines migration may be a significant engineering problem associated with the acidization of chlorite-bearing sandstones. © 1993.