Exploration of structural features of monomeric helical peptides designed with a genetic algorithm

A genetic algorithm (GA)-based strategy to dissect the determinants of peptide folding into alpha-helix was developed. The structural information of helical peptides was obtained with respect to patterns of sequence variability. In many previously reported studies the intrinsic alpha-helical propensities of amino acids although sequence-dependent are apparently independent of the amino acid position. In this research, monomeric helical peptides selected from possible sequences produced by a GA-chemical synthesis were analyzed to identify possible influential structural features. These hexadeca-peptides were obtained after four successive generations. A total of 128 synthetic peptides were evaluated via circular dichroism (CD) measurements in aqueous solution, while the mean ellipticity at 222 nm confirmed the monomeric state of the peptides. The results presented here show that our GA-based strategy may be useful in the design of proteins with increased alpha-helix content.     

Long glucocorticoid-induced leucine zipper (L-GILZ) protein interacts with ras protein pathway and contributes to spermatogenesis control

Correct function of spermatogonia is critical for the maintenance of spermatogenesis throughout life, but the cellular pathways regulating undifferentiated spermatogonia proliferation, differentiation, and survival are only partially known. We show here that long glucocorticoid-induced leucine zipper (L-GILZ) is highly expressed in spermatogonia and primary spermatocytes and controls spermatogenesis. Gilz deficiency in knock-out (gilz KO) mice leads to a complete loss of germ cell lineage within first cycles of spermatogenesis, resulting in male sterility. Spermatogenesis failure is intrinsic to germ cells and is associated with increased proliferation and aberrant differentiation of undifferentiated spermatogonia and with hyperactivity of Ras signaling pathway as indicated by an increase of ERK and Akt phosphorylation. Spermatogonia differentiation does not proceed beyond the prophase of the first meiotic division due to massive apoptosis associated with accumulation of unrepaired chromosomal damage. These results identify L-GILZ as a novel important factor for undifferentiated spermatogonia function and spermatogenesis.     

A comparative study of the interaction of Bacillus amyloliquefaciens ribonuclease (barnase) and Bacillus intermedius ribonuclease (binase) with barstar by brownian dynamics simulation

A comparative study of the interaction of two RNases (binase and barnase) with the polypeptide inhibitor barstar was performed by Brownian dynamics simulation. It was demonstrated that this method adequately reproduced the dependence of the association rate on the pH of solution as well as the effect of mutations at individual amino acid residues on the inhibition of barnase by barstar. Two types of energy-favorable binase-barstar encounter complexes were found. In type I complex, the amino acid residues of the binase active center are involved in formation of the complex; in type II complex, the active center remains free. It is suggested that temporary binding of free barstar into type II complex competes with the inhibition reaction. Presumably, this explains the decrease in the rate of binase inhibition by barstar as compared with the analogous reaction of barnase.     

Synthesis and Structural Studies of a Pentapeptide Sequence of Elastin. Poly (Val-Gly-Gly-Leu-Gly)

Abstract

Poly (Val-Gly-Gly-Leu-Gly), a polypeptide mimicking the physico-chemical properties of the glycine-rich regions of elastin, has been synthesized and studied both in solution and in the aggregated state. By comparison, also the conformation of different “monomeric” units has been investigated. The polymer showed increased disorder with respect to the “monomers”, the molecular conformation being accounted for by a more or less random collection of isolated β-turns. Nevertheless, in the solid state the polymer is able to adopt supramolecular structures reminiscent of those found for elastin.     

The Drosophila homolog of human AF10/AF17 leukemia fusion genes (Dalf) encodes a zinc finger/leucine zipper nuclear protein required in the nervous system for maintaining EVE expression and normal growth

Sibling neurons in the embryonic central nervous system (CNS) of Drosophila can adopt distinct states as judged by gene expression and axon projection. In the NB4-2 lineage, two even-skipped (eve)-expressing sibling neuronal cells, RP2 and RP2sib, are formed in each hemineuromere. Throughout embryogenesis, only RP2, but not RP2sib, maintains eve expression. In this report, we describe a P-element induced mutation that alters the expression pattern of EVE in RP2 motoneurons in the Drosophila embryonic CNS. The mutation was mapped to a Drosophila homolog of human AF10/AF17 leukemia fusion genes (alf), and therefore named Dalf. Like its human counterparts, Dalf encodes a zinc finger/leucine zipper nuclear protein that is widely expressed in embryonic and larval tissues including neurons and glia. In Dalf mutant embryos, the RP2 motoneuron no longer maintains EVE expression. The effect of the Dalf mutation on EVE expression is RP2-specific and does not affect other characteristics of the RP2 motoneuron. In addition to the embryonic phenotype, Dalf mutant larvae are retarded in their growth and this defect can be rescued by the ectopic expression of a Dalf transgene under the control of a neuronal GAL4 driver. This indicates a requirement for Dalf function in the nervous system for maintaining gene expression and the facilitation of normal growth.     

Improved isotopic deuterium labeling at the diastereotopic methyl group of leucine: a synthetic route to (4S)- and (4R)-[5-2H1]leucine

Two isotopomers of deuterium-labeled leucine in the diastereotopic methyl group were synthesized from inexpensively available (R)- and (S)-citronellol in a more convenient way than by previous methods.     

Chemistry at the apical position of square-pyramidal copper(II) complexes: Synthesis, crystal structures, and magnetic properties of homopolynuclear complexes with azido bridges containing [Cu(AA)(BB)] moieties (AA = acetylacetonate; BB = 1,10-phenanthroline, bipy = 2,2′-bipyridine)

Three new homopolynuclear complexes with azido bridges have been obtained by using [Cu(AA)(BB)]⁺ building-blocks (AA = acetylacetonate; BB = 1,10-phenanthroline or 2,2′-bipyridine). The reaction between [Cu(acac)(phen)(H₂O)](ClO₄) and NaN₃ leads to a mixture of two compounds: a binuclear complex, [{Cu(acac)(phen)}₂(μ_1,3-N₃)](ClO₄) · 2H₂O (1), and a linear tetranuclear one, [{Cu(acac)(phen)(ClO₄)}₂{Cu(phen)(μ_1,1-N₃)₂}₂] (2). The reaction between [Cu(acac)(bipy)(H₂O)](ClO₄) and NaN₃ affords also a mixture of two compounds: [{Cu(acac)(bipy)}₂(μ_1,3-N₃)]₃(ClO₄)₃ · 3.75H₂O (3) and [Cu(acac)(bipy)(N₃)][Cu(acac)(bipy)(H₂O)](ClO₄) (4). The X-ray crystal structures of compounds 1-4 have been solved (for compound 4 the crystal structure was previously reported). In compounds 1 and 3, two {Cu(AA)(BB)} fragments are bridged by the azido anion in an end-to-end fashion. Two isomers, cis and trans with respect to azido bridge, were found in crystal 3. The structure of compound 2 consists of two Cu(II) central cations bridged by two μ_1,1-azido ligands, each of them being also connected to a {Cu(acac)(phen)} fragment through another μ_1,1-azido ligand. The cryomagnetic properties of the compounds 1 and 2 have been investigated and discussed. The magnetic behaviour of compound 1 shows the absence of any interactions between the metallic ions. In the tetranuclear complex 2, the magnetic interactions between the external and central copper(II) ions(J₁), and between the central metallic ions (J₂) were found ferromagnetic (J₁ = 0.36 cm⁻¹, J₂ = 7.20 cm⁻¹).     

First total syntheses of (Z)-15-methyl-10-hexadecenoic acid and the (Z)-13-methyl-8-tetradecenoic acid

The first total syntheses for the (Z)-15-methyl-10-hexadecenoic acid and the (Z)-13-methyl-8-tetradecenoic acid were accomplished in seven steps and in 31-32% overall yields. The (trimethylsilyl)acetylene was the key reagent in both syntheses. It is proposed that the best synthetic strategy towards monounsaturated iso methyl-branched fatty acids with double bonds close to the omega end of the acyl chain is first acetylide coupling of (trimethylsilyl)acetylene to a long-chain bifunctional bromoalkane followed by a second acetylide coupling to a short-chain iso bromoalkane, since higher yields are thus obtained. Spectral data is also presented for the first time for these two unusual fatty acids with potential as biomarkers and as topoisomerase I inhibitors.     

The Drosophila homolog of human AF10/AF17 leukemia fusion genes (Dalf) encodes a zinc finger/leucine zipper nuclear protein required in the nervous system for maintaining EVE expression and normal growth

Sibling neurons in the embryonic central nervous system (CNS) of Drosophila can adopt distinct states as judged by gene expression and axon projection. In the NB4-2 lineage, two even-skipped (eve)-expressing sibling neuronal cells, RP2 and RP2sib, are formed in each hemineuromere. Throughout embryogenesis, only RP2, but not RP2sib, maintains eve expression. In this report, we describe a P-element induced mutation that alters the expression pattern of EVE in RP2 motoneurons in the Drosophila embryonic CNS. The mutation was mapped to a Drosophila homolog of human AF10/AF17 leukemia fusion genes (alf), and therefore named Dalf. Like its human counterparts, Dalf encodes a zinc finger/leucine zipper nuclear protein that is widely expressed in embryonic and larval tissues including neurons and glia. In Dalf mutant embryos, the RP2 motoneuron no longer maintains EVE expression. The effect of the Dalf mutation on EVE expression is RP2-specific and does not affect other characteristics of the RP2 motoneuron. In addition to the embryonic phenotype, Dalf mutant larvae are retarded in their growth and this defect can be rescued by the ectopic expression of a Dalf transgene under the control of a neuronal GAL4 driver. This indicates a requirement for Dalf function in the nervous system for maintaining gene expression and the facilitation of normal growth.     

The Central Portion of Factor H (Modules 10-15) Is Compact and Contains a Structurally Deviant CCP Module

The first eight and the last two of 20 complement control protein (CCP) modules within complement factor H (fH) encompass binding sites for C3b and polyanionic carbohydrates. These binding sites cooperate self-surface selectively to prevent C3b amplification, thus minimising complement-mediated damage to host. Intervening fH CCPs, apparently devoid of such recognition sites, are proposed to play a structural role. One suggestion is that the generally small CCPs 10-15, connected by longer-than-average linkers, act as a flexible tether between the two functional ends of fH; another is that the long linkers induce a 180° bend in the middle of fH. To test these hypotheses, we determined the NMR-derived structure of fH12-13 consisting of module 12, shown here to have an archetypal CCP structure, and module 13, which is uniquely short and features a laterally protruding helix-like insertion that contributes to a prominent electropositive patch. The unusually long fH12-13 linker is not flexible. It packs between the two CCPs that are not folded back on each other but form a shallow vee shape; analytical ultracentrifugation and X-ray scattering supported this finding. These two techniques additionally indicate that flanking modules (within fH11-14 and fH10-15) are at least as rigid and tilted relative to neighbours as are CCPs 12 and 13 with respect to one another. Tilts between successive modules are not unidirectional; their principal axes trace a zigzag path. In one of two arrangements for CCPs 10-15 that fit well with scattering data, CCP 14 is folded back onto CCP 13. In conclusion, fH10-15 forms neither a flexible tether nor a smooth bend. Rather, it is compact and has embedded within it a CCP module (CCP 13) that appears to be highly specialised given both its deviant structure and its striking surface charge distribution. A passive, purely structural role for this central portion of fH is unlikely.     

The use of a transport medium (L15M15) for bulk tissue storage and retention of viability

Twenty-five human or mouse tissue samples, some up to 8×4×2 cm, were immersed in a special transport medium (TM), L15M15, up to 7 days before being processed or placed in tissue culture. To test the efficacy of this medium, we concurrently placed pieces of the same tissues in a sterile phosphate buffered solution (PBS). We also tested the preservative capabilities of TM and PBS at room temperature and with refrigeration. Differences between TM and PBS are demonstrated, which are more pronounced using room temperature up to 4 days time. The tissues stored in TM show fewer degenerative or autolytic changes than the same tissue stored in PBS under identical conditions. Using regrigeration further enhanced the preservative qualities of TM up to 4 days, but not PBS. There were no obvious differences between tissues stored in TM and PBS with refrigeration after 7 days. We conclude that transport medium L15M15 is a useful medium for preserving tissue viability, especially large tissue samples, up to 4 days, especially if refrigerated.     

Sequential substitution of 1,2-dichloro-ethene: a convenient stereoselective route to (9Z,11E)-, (10E,12Z)- and (10Z,12Z)-

Conjugated linoleic acid (CLA) isomers are present in human foods derived from milk or ruminant meat. To study their metabolism, (9Z,11E)-, (10E,12Z)- and (10Z,12Z)-[1-(14)C]-octadecadienoic acids with high radiochemical and isomeric purities (>98%) were prepared by stereoselective multi-step syntheses involving sequential substitution of 1,2-dichloro-ethene. In the case of the (9Z,11E) isomer, a first metal-catalyzed cross-coupling reaction between (E)-1,2-dichloro-ethene and 2-non-8-ynyloxy-tetrahydro-pyran, obtained from 7-bromo-heptan-1-ol, gave a conjugated chloroenyne. A second coupling reaction with hexylmagnesium bromide provided a heptadecenynyl derivative. Stereoselective reduction of the triple bond and bromination afforded (7E,9Z)-17-bromo-heptadeca-7,9-diene. Formation of the Grignard reagent and carbonation with 14CO(2) gave (9Z,11E)-[1-(14)C]-octadeca-9,11-dienoic acid (overall yield from 7-bromo-heptan-1-ol, 14.4%). (10E,12Z)- and (10Z,12Z)-[1-(14)C]-octadeca-10,12-dienoic acids were synthesized by the same methodology using 1-heptyne, 8-bromo-octan-1-ol and, respectively, (E)-1,2-dichloro-ethene and its (Z) isomer (overall yield from 8-bromo-octan-1-ol, 13.1% (10E,12Z); 17.2% (10Z,12Z)). Impurities (<2% if present) were identified as being (E,E) CLA isomers and were removed by RP-HPLC. Metabolism studies in animal are in progress.     

Assessing the acid-base and conformational properties of histidine residues in human prion protein (125-228) by means of pK(a) calculations and molecular dynamics simulations

A thorough study of the acid-base behavior of the four histidines and the other titratable residues of the structured domain of human prion protein (125-228) is presented. By using multi-tautomer electrostatic calculations, average titration curves have been built for all titratable residues, using the whole bundles of NMR structures determined at pH 4.5 and 7.0. According to our results, (1) only histidine residues are likely to be involved in the first steps of the pH-driven conformational transition of prion protein; (2) the pK(a)'s of His140 and His177 are approximately 7.0, whereas those of His155 and His187 are < 5.5. 10-ns long molecular dynamics simulations have been performed on five different models, corresponding to the most significant combinations of histidine protonation states. A critical comparison between the available NMR structures and our computational results (1) confirms that His155 and His187 are the residues whose protonation is involved in the conformational rearrangement of huPrP in mildly acidic condition, and (2) shows how their protonation leads to the destructuration of the C-terminal part of HB and to the loss of the last turn of HA that represent the crucial microscopic steps of the rearrangement.     

Stereoselectivity of (R)- and (S)-hexahydro-difenidol binding to neuroblastoma M1, cardiac M2, pancreatic M3, and striatum M4 muscarinic receptors

(R)-Hexahydro-difenidol has a higher affinity for M1 receptors in NB-OK 1 cells, pancreas M3 and striatum M4 receptors (pKi 7.9 to 8.3) than for cardiac M2 receptors (pKi 7.0). (S)-Hexahydro-difenidol, by contrast, is nonselective (pKi 5.8 to 6.1). Our goal in the present study was to evaluate the importance of the hydrophobic phenyl, and cyclohexyl rings of hexahydro-difenidol for the stereoselectivity and receptor selectivity of hexahydro-difenidol binding to the four muscarinic receptors. Our results indicated that replacement of the phenyl ring of hexahydro-difenidol by a cyclohexyl group (----dicyclidol) and of the cyclohexyl ring by a phenyl moiety (----difenidol) induced a large (4- to 80-fold) decrease in binding affinity for all muscarinic receptors. Difenidol had a significant preference for M1, M3, and M4 over M2 receptors; dicyclidol, by contrast, had a greater affinity for M1 and M4 than for M2 and M3 receptors. The binding free energy decrease due to replacement of the phenyl and the cyclohexyl groups of (R)-hexahydro-difenidol by, respectively, a cyclohexyl and a phenyl moiety was almost additive in the case of M4 (striatum) binding sites. In the case of the cardiac M2, pancreatic M3, or NB-OK 1 M1 receptors the respective binding free energies were not completely additive. These results suggest that the four (R)-hexahydro-difenidol "binding moieties" (phenyl, cyclohexyl, hydroxy, and protonated amino group) cannot simultaneously form optimal interactions with the M1, M2, and M3 muscarinic receptors.(ABSTRACT TRUNCATED AT 250 WORDS)     

Calculation of protein ionization equilibria with conformational sampling: pK(a) of a model leucine zipper, GCN4 and barnase.

The use of conformational ensembles provided by nuclear magnetic resonance (NMR) experiments or generated by molecular dynamics (MD) simulations has been regarded as a useful approach to account for protein motions in the context of pK(a) calculations, yet the idea has been tested occasionally. This is the first report of systematic comparison of pK(a) estimates computed from long multiple MD simulations and NMR ensembles. As model systems, a synthetic leucine zipper, the naturally occurring coiled coil GCN4, and barnase were used. A variety of conformational averaging and titration curve-averaging techniques, or combination thereof, was adopted and/or modified to investigate the effect of extensive global conformational sampling on the accuracy of pK(a) calculations. Clustering of coordinates is proposed as an approach to reduce the vast diversity of MD ensembles to a few structures representative of the average electrostatic properties of the system in solution. Remarkable improvement of the accuracy of pK(a) predictions was achieved by the use of multiple MD simulations. By using multiple trajectories the absolute error in pK(a) predictions for the model leucine zipper was reduced to as low as approximately 0.25 pK(a) units. The validity, advantages, and limitations of explicit conformational sampling by MD, compared with the use of an average structure and a high internal protein dielectric value as means to improve the accuracy of pK(a) calculations, are discussed.     

World Dissemination of the Cereal-Cyst Nematode (Heterodera avenae) and Its Potential as a Pathogen of Wheat

World distribution of the cereal-cyst nematode is herein reviewed. It is suggested that Heterodera avenae originated in Europe and has been widely disseminated, largely by the activities of Man but also by wind movement of cysts. So far, it may not have spread to some major wheat-growing regions of the New World, but a non-friable soil structure limits population level and disease. Yield loss could result from the introduction of new cultivars to developing countries where H . avenae has not been detected or where existing cultivars possess tolerance.     

Preparation and diastereomeric separation of an (S)- and (R)-1-(methoxycarbonyl)tridec-10-yl glucoside derivative,a precursor for a monosaccharide constituent of resin glycosides

The 6-O-mesyl derivative of phenyl 1-thio-beta-D-glucopyranoside was prepared from D-glucose as a synthetic equivalent of a 6-deoxy-hexosyl donor. Racemic methyl 11-hydroxytetradecanoate (methyl convolvulinolate) was synthesized by Grignard reaction of propylmagnesium bromide with 10-undecenal followed by hydroboration. Both intermediates were coupled by NIS-TfOH-promoted glycosidation to give a mixture of two diasteromeric glucopyranosides, which were separated on a preparative scale by medium pressure chromatography. One of the products was identified as having the natural (S)-configuration by comparison of its 1H NMR spectrum with an authentic sample prepared from the corresponding chiral hydroxyfatty acid.     

Flight and Oviposition Behavior of the Adult Maritime Ringlet (Coenonympha nipisiquit McDunnough) Females in Response to Microhabitat

Maritime ringlet butterflies (Coenonympha nipisiquit McDunnough), an endangered species in Canada, inhabit salt marshes, which consist of microhabitat mosaics with varied larval survival rate. These microhabitats may influence the movement and reproductive behaviors of females, which in turn may affect population dynamics. I recorded behaviors and locations of females every minute with a GPS rover and calculated their move lengths and turning angles. Move lengths did not change in response to microhabitats, although turning angles became larger near bodies of water with sparse vegetation. Females spent a longer time in one location and oviposited more often where the principal larval host, Spartina patens (Aiton) Muhl., is abundant, regardless of larval survival rate. Older females tended to initiate flight more readily than younger females and spent more time flying and nectaring. Younger females were more fecund and spent a longer time at one location. Because young females tend to be less mobile and more fecund, the majority of oviposition should take place near eclosion sites. However, some eggs will be laid away from microhabitats favorable to larval survival when older females become mobile and move out of their natal microhabitats. Because it seems to have little potential to colonize new habitat on its own, monitoring population dynamics and habitat quality will be crucial for the persistence and recovery of this rare species.