Gaussian process: an alternative approach for QSAM modeling of peptides

Different statistical modeling methods (SMMs) are used for nonlinear system classification and regression. On the basis of Bayesian probabilistic inference, Gaussian process (GP) is preliminarily used in the field of quantitative structure-activity relationship (QSAR) but has not yet been applied to quantitative sequence-activity model (QSAM) of biosystems. This paper proposes the application of GP as an alternative tool for the QSAM modeling of peptides. To investigate the modeling performance of GP, three classical peptide panels were used: Angiotensin-I converting enzyme inhibitory dipeptides, bradykinin-potentiating pentapeptides and cationic antimicrobial pentadecapeptides. On this basis, we made a comprehensive comparison between the GP and some widely used SMMs such as PLS, artificial neural network (ANN) and support vector machine (SVM), and gave the conclusions as follow: (1) for those of structurally complicated peptides, particularly the polypeptides, linear PLS was incapable of capturing all dependences hidden in the peptide systems, (2) even in assistance with the monitoring technique, ANN was inclined to be overtrained in the cases of insufficient number of peptide samples, (3) SVM and GP performed best for the three peptide panels. Moreover, since GP was able to correlate the linear and nonlinear-hybrid relationship, it was slightly superior to SVM at most peptide sets.     

Identification of polypeptide markers of barley yellow dwarf virus resistance and susceptibility genes in non-infected barley (Hordeum vulgare) plants

Summary Barley yellow dwarf (BYDV) is a group a closely related viruses which cause economic losses in a wide range of graminaceous species throughout the world. Barley plants can be protected from the effects of BYDV by the Yd2 resistance gene. Plants which contain the Yd2 gene also contain a constitutively expressed polypeptide which was not found in any plants without Yd2. Conversely, BYDV susceptible plants contain another constitutively expressed polypeptide which was not found in any of the BYDV-resistant lines examined. These two polypeptides appear to have the same molecular weight (as assessed by SDS-PAGE) and only slightly different iso-electric points. They also appear to contain an extensive range of similar antigenic determinants. Both polypeptides were found in F₁ hybrids made from resistant and susceptible plants. We suggest that these two polypeptides are the products of two allelic genes. Analysis of near-isogenic lines showed that the locus which controls the Yd2 resistance gene and the locus controlling the synthesis of the two polypeptides may be within ± 9 cM of each other. We have developed a Western blot technique which allows assessment of barley lines, 4-days after seed imbibition, for the presence of the Yd2 gene.     

Genome-wide identification and analysis of sulfatase and sulfatase modifying factor genes in Bemisia tabaci (Hemiptera: Aleyrodidae)

The invasive pest whitefly (Bemisia tabaci) is a complex species, of which Middle East-Minor Asia 1 (MEAM1) and Mediterranean (MED) are the two most damaging members. Previous research showed that cabbage is frequently infested with MEAM1 but seldomly with MED, and this difference in performance is associated with glucosinolate (GS) content. Some insects can modify GS using glucosinolate sulfatase (SULF), the activity of which is regulated by sulfatase modifying factor 1 (SUMF1); therefore, to increase our understanding of different performances of MEAM1 and MED on cabbage plants, we identified and compared nine putative SULFs and one SUMF in MEAM1 and MED. We found that the lengths of two genes, BtSulf2 and BtSulf4, differed between MEAM1 and MED. The messenger RNA levels of BtSulf4 increased more than 20-fold after MEAM1 and MED adults were exposed to GS, but BtSulf2 expression was only induced by GS in MEAM1. Knockdown of BtSulf2 and BtSulf4 in MEAM1 resulted in a substantial increase in the mortality of GS-treated adults but not in MED. These results indicate that differences in BtSulf2 and BtSulf4 sequences and/or expression may explain why MEAM1 performs better than MED on cabbage. Our results provide a basis for future functional research on SULF and SUMF in B. tabaci.     

Unassembled polypeptides of the plastidic ribosomes in heat-treated 70S-ribosome-deficient rye leaves

The polypeptides of the subunits of 70S ribosomes isolated from rye (Secale cereale L.) leaf chloroplasts were analyzed by two-dimensional polyacrylamide gel electrophoresis. The 50S subunit contained approx. 33 polypeptides in the range of relative molecular mass (M_r) 13000–36000, the 30S subunit contained approx. 25 polypeptides in the range of M_r 13000–40500. Antisera raised against the individual isolated ribosomal subunits detected approx. 17 polypeptides of the 50S and 10 polypeptides of the 30S subunit in the immunoblotting assay. By immunoblotting with these antisera the major antigenic ribosomal polypeptides (r-proteins) of the chloroplasts were clearly and specifically visualized also in separations of leaf extracts or soluble chloroplast supernatants. In extracts from rye leaves grown at 32° C, a temperature which is non-permissive for 70S-ribosome formation, or in supernatants from ribosome-deficient isolated plastids, six plastidic r-proteins were visualized by immunoblotting with the anti-50S-serum and two to four plastidic r-proteins were detected by immunoblotting with the anti-30S-serum, while other r-proteins that reacted with our antisera were missing. Those plastidic r-proteins that were present in 70S-ribosome-deficient leaves must represent individual unassembled ribosomal polypeptides that were synthesized on cytoplasmic 80S ribosomes. For the biogenesis of chloroplast ribosomes the mechanism of coordinate regulation appear to be less strict than those known for the biogenesis of bacterial ribosomes, thus allowing a marked accumulation of several unassembled ribosomal polypeptides of cytoplasmic origin.Abbreviations L polypeptide of large ribosomal subunit - M_r relative molecular mass - r-protein ribosomal polypeptide - S polypeptide of small ribosomal subunit - SDS sodium dodecyl sulfate     

应用死端排除法考虑分子对接中的侧链柔性

假设分子对接面的紧密堆积类似于蛋白质内部的紧密堆积,因此用于蛋白质内部的侧链构象预测方法,如死端排除法,可应用于分子对接面内的侧链构象预测。应用９个晶体结构对这一假设进行检验,结果表明假设基本正确。对２个蛋白酶与抑制剂的应用比较成功。９个配体中的７个有正确的均方根差的趋势。还发现受体结构的柔性较小,说明由于对接面的紧密堆积产生的侧链构象变化很小。根据这些结果,提出一个新的分子对接流程图,即在刚体对接后加入对接面中氨基酸残基的侧链构象预测。对一个蛋白酶与抑制剂的复合结构的应用表明对接中的正确解的信号与噪音比相对错误解增加了。     

应用死端排除法考虑分子对接中的侧链柔性

假设分子对接面的紧密堆积类似于蛋白质内部的紧密堆积,因此用于蛋白质内部的侧链构象预测方法,如死端排除法,可应用于分子对接面内的侧链构象预测。应用９个晶体结构对这一假设进行检验。结果表明假设基本正确。对２个蛋白酶和抑制剂的应用比较成功。９个配体中的７个有正确的均方根差的趋势。还发现受体结构的柔性较小,说明由于对接面的紧密堆积产生的侧链构象变化很小。根据这些结果,提出一个新的分子对接流程图,即在刚体对     

Tuning electronic structure and photophysical properties of [Ir(ppy)2(py)2]+ by substituents binding in pyridyl ligand: a computational study

Iridium (III) 2-phenylpyridine (ppy) complexes with two suitable monodentate L ligands [Ir(ppy)(2)(L)(2)](+) (ppy = 2-phenylpyridine, py = pyridine, L = 4-pyCN 1, 4-pyCHO 2, 4-pyCl 3, py 4, 4-pyNH(2) 5) were studied by density functional theory (DFT) and time-dependent DFT methods. The influences of ligands L on the electronic structure and photophysical properties were investigated in detail. The compositions and energy levels of the lowest unoccupied molecular orbital (LUMO) are changed more significantly than those of the highest occupied molecular (HOMO) by tuning L ligands. With the electronegativity decrease of L ligands 4-pyCN > 4-pyCHO > 4-pyCl > py > 4-pyNH(2), the LUMO distributing changes from py to ppy, and the absorptions have an obvious red shift. The calculated results showed that the transition character of the absorption and emission can be changed by adjusting the electronegativity of the L ligands. In addition, no solvent effect was observed in the absorptions and emissions.     

Isolation and Characterization of Mustard (Sinapis alba L.) Seed Storage Proteins

A total storage protein fraction was prepared from mustard (Sinapis alba L.) seeds via isolated protein bodies and characterized by sedimentation, immunological, and electrophoretic techniques. Mustard seed storage protein consists of three fractions (1) a “legumin-like” 13-S complex composed of two pairs of disulfide-linked polypeptides (16.5 + 28.5 kDa and 19.5 + 34 kDa, respectively) and two single polypeptides (18 kDa and 26 kDa), (2) a “vicilin-like” 9-S complex composed of two glycoproteins (64 kDa and 77 kDa), and (3) two small polypeptides (10 kDa and 11 kDa) which probably represent the 1.7-S complex found in other Cruciferae. In contrast to related species, no glycosylated polypeptide was found in the 13-S complex. Immunological relationships were found between the paired polypeptides of the 13-S complex but not between polypeptides of the 13-S complex and polypeptides of the 9-S complex. Pulse-chase labeling and in vitro translation of polysomal RNA from young embryos demonstrated that the polypeptides of the 13-S complex originate from high molecular mass precursors, except for the 18 kDa polypeptide which appears to be synthesized in its final size. The amino-acid composition of the major polypeptides of the mustard storage protein is given.     

Distinct second extracellular loop structures of the brain cannabinoid CB(1) receptor: implication in ligand binding and receptor function

The G-protein-coupled receptor (GPCR) second extracellular loop (E2) is known to play an important role in receptor structure and function. The brain cannabinoid (CB(1)) receptor is unique in that it lacks the interloop E2 disulfide linkage to the transmembrane (TM) helical bundle, a characteristic of many GPCRs. Recent mutation studies of the CB(1) receptor, however, suggest the presence of an alternative intraloop disulfide bond between two E2 Cys residues. Considering the oxidation state of these Cys residues, we determine the molecular structures of the 17-residue E2 in the dithiol form (E2(dithiol)) and in the disulfide form (E2(disulfide)) of the CB(1) receptor in a fully hydrated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer, using a combination of simulated annealing and molecular dynamics simulation approaches. We characterize the CB(1) receptor models with these two E2 forms, CB(1)(E2(dithiol)) and CB(1)(E2(disulfide)), by analyzing interaction energy, contact number, core crevice, and cross correlation. The results show that the distinct E2 structures interact differently with the TM helical bundle and uniquely modify the TM helical topology, suggesting that E2 of the CB(1) receptor plays a critical role in stabilizing receptor structure, regulating ligand binding, and ultimately modulating receptor activation. Further studies on the role of E2 of the CB(1) receptor are warranted, particularly comparisons of the ligand-bound form with the present ligand-free form.     

Copper(I) bromide complexes from 1,2-bis(diphenylphosphano) benzene and some heterocyclic thiones

The synthesis, characterization and solid state emission properties of a series of mixed-ligand copper(I)bromide complexes containing 1,2-bis(diphenylphosphano)benzene (dppbz) and some heterocyclic thiones (L) are reported. The complexes are readily synthesized by the addition of the appropriate thione to a CuBr-diphosphane adduct in acetonitrile/methanol or acetone solution. The molecular structures of [CuBr(dppbz)(py2SH)], [CuBr(dppbz)(pymtH)] and [CuBr(dppbz)(imdtH₂)] were established by single-crystal X-ray diffraction. Each of these structures features a tetrahedral copper(I) centre with two phosphorus atoms from the chelating diphos ligand, one bromine and the exocyclic sulfur atom of the heterocyclic thioamide unit. Slow decomposition of the mixed-ligand complexes via ligand dissociation occurs when their chloroform solutions are left to stand at room temperature for several weeks. On the basis of elemental analysis, NMR and IR spectra, the resulting coloured crystals are found to contain phosphane-free coordination polymers of composition [CuBr(L)]. At room temperature, some of the molecular complexes in the solid state exhibit strong emission assigned to a metal-ligand charge transfer of type Cu(I) → π*(PPh₂).     

Aleutian disease virus, a parvovirus, is proteolytically degraded during in vivo infection in mink.

The polypeptides of the highly virulent mink-passaged Utah I and the nonvirulent cell culture-adapted ADV-G strain of Aleutian disease virus (ADV) were compared. When CRFK cells infected with either Utah I or ADV-G were analyzed by immunoprecipitation, both viruses induced proteins with molecular weights characteristic of the ADV-G 85,000 ( 85k )- and 75k-dalton structural proteins (p85 and p75) as well as the 71k -dalton nonvirion protein p71 . However, when Utah I, Pullman ADV, and DK ADV (a Danish isolate of ADV) were purified from infected mink, only polypeptides with molecular weights between 27k and 30k could be identified. In addition, trypsin treatment of ADV-G degraded p85 and p75 to smaller antigenic proteins with molecular weights of 24k and 27k, similar to those found for the virulent in vivo viruses. The effect of proteolytic treatment of ADV was then studied in detail. Purification of Utah I ADV from mink organs in the presence of protease inhibitor did not prevent the appearance of the low-molecular-weight proteins and ADV-G proteins were not degraded upon purification from a homogenate of normal mink organs, suggesting that artifactual proteolysis was not occurring. When a serum pool from terminally diseased mink was analyzed by radioimmunoassay for antibody reactivity against trypsinized and nontrypsinized ADV-G, five times higher reactivity was found for the trypsinized ADV-G than for the nontrypsinized ADV-G, an effect which could not be elicited by chymotrypsin or V8 protease treatment, implying that in vivo-produced ADV was being modulated in vivo by trypsin or a trypsin-like enzyme. Trypsinization was shown not to cause a change in ADV virion density, but to decrease the in vitro infectivity of ADV-G for CRFK cells. These studies suggested that during infection of mink ADV proteins are degraded to highly antigenic smaller polypeptides.     

Binding behavior of aliphatic oligopeptides by bridged and metallobridged bis(beta-cyclodextrin)s bearing an oxamido bis(2-benzoic) carboxyl linker

beta-Cyclodextrin dimers bearing an oxamido bis(2-benzoic) carboxyl linker (1) or its metal complexes (2 and 3) were newly synthesized, and their inclusion complexation behavior with a series of representative aliphatic oligopeptides, i.e., Leu-Gly, Gly-Leu, Gly-Pro, Glu-Glu, Gly-Gly, Gly-Gly-Gly, and Glu(Cys-Gly), was elucidated by means of UV/vis, circular dichroism, fluorescence, and 2D NMR spectroscopy in Tris-HCl buffer solution (pH 7.4) at 25 degrees C. The results obtained indicated that metallobridged bis(beta-cyclodextrin)s 2 or 3 could significantly enhance the original molecular binding abilities of parent bis(beta-cyclodextrin) 1 toward model substrates through the cooperative binding of two cyclodextrin moieties and the additional chelation effect supplied by the coordinated metal centers. It is interesting that hosts 2 and 3 displayed an entirely different fluorescence behavior upon complexation with guest oligopeptides. Among the guest peptides examined, 3 showed the highest complex formation constant of 68 200 M(-)(1) for Glu-Glu, up to 510-fold as compared with 1 (135 M(-)(1)), while 1 gave excellent molecular selectivity for Glu(Cys-Gly)/Glu-Glu pair, up to 51-fold. The molecular binding ability and selectivity were discussed from the viewpoints of the induced-fit and multiple recognition mechanism between host and guest.     

Molecular basis of the globoside-deficient P(k) blood group phenotype. Identification of four inactivating mutations in the UDP-N-acetylgalactosamine: globotriaosylceramide 3-beta-N-acetylgalactosaminyltransferase gene

The biochemistry and molecular genetics underlying the related carbohydrate blood group antigens P, P(k), and LKE in the GLOB collection and P1 in the P blood group system are complex and not fully understood. Individuals with the rare but clinically important erythrocyte phenotypes P(1)(k) and P(2)(k) lack the capability to synthesize P antigen identified as globoside, the cellular receptor for Parvo-B19 virus and some P-fimbriated Escherichia coli. As in the ABO system, naturally occurring antibodies, anti-P of the IgM and IgG class with hemolytic and cytotoxic capacity, are formed. To define the molecular basis of the P(k) phenotype we analyzed the full coding region of a candidate gene reported in 1998 as a member of the 3-beta-galactosyltransferase family but later shown to possess UDP-N-acetylgalactosamine:globotriaosylceramide 3-beta-N-acetylgalactosaminyltransferase or globoside synthase activity. Homozygosity for different nonsense mutations (C(202) --> T and 538insA) resulting in premature stop codons was found in blood samples from two individuals of the P(2)(k) phenotype. Two individuals with P(1)(k) and P(2)(k) phenotypes were homozygous for missense mutations causing amino acid substitutions (E266A or G271R) in a highly conserved region of the enzymatically active carboxyl-terminal domain in the transferase. We conclude that crucial mutations in the globoside synthase gene cause the P(k) phenotype.