Source of the ice-binding specificity of antifreeze protein type I

Antifreeze proteins (AFPs) are a group of structurally very diverse proteins with the unique capability of binding to the surface of seed ice crystals and inhibiting ice crystal growth. The AFPs bind with high affinity to specific planes of the ice crystal. Previously, this affinity of AFPs has been ascribed to the formation of multiple hydrogen bonds across the protein-ice interface, but more recently van der Waals interactions have been suggested to be the dominant energetic factors for the adsorption. To determine whether van der Waals interactions are also responsible for the binding specificities of AFPs, the protein-ice interaction of the helical AFP Type I from winter flounder (HPLC6) was studied using a Monte Carlo rigid body docking approach. HPLC6 binds in the [1102] direction of the [2021] plane, with the Thr-Ala-Asn surface comprising the protein's binding face. The binding of HPLC6 to this ice plane is highly preferred, but the protein is also found to bind favorably to the [1010] prism plane using a different protein surface comprised of Thr and Ala residues. The results show that van der Waals interactions, despite accounting for most of the intermolecular energy (>80%), are not sufficient to completely explain the AFP binding specificity.     

Arsenobetaine as the major arsenic compound in the muscle of two species of freshwater fish

The chemical form of arsenic contained in the muscle of certain freshwater fish was examined using cultured specimens of rainbow trout (Salmo gairdneri) and wild specimens of Japanese smelt (Hypomesus nipponensis). More than 95% of the total arsenic of both species was extracted with methanol and recovered in the water-soluble fraction. The major arsenic compound of both species was purified by cation-exchange chromatography on Dowex 50, gel filtration on Bio-Gel P-2 and HPLC on Asahipak GS-220H. Behavior in the above purification procedure and analyses of the purified compounds by HPLC–ICP and TLC confirmed that the major arsenic compound of both species was arsenobetaine. Arsenobetaine found in cultured rainbow trout seems to be derived from the commercial assorted feed containing arsenobetaine as the major arsenical. On the other hand, the result with wild Japanese smelt suggested that arsenobetaine is a naturally occurring compound in the freshwater environment.     

Molecular dynamics study of the solvation of an alpha-helical transmembrane peptide by DMSO

A 10-ns molecular dynamics study of the solvation of a hydrophobic transmembrane helical peptide in dimethyl sulfoxide (DMSO) is presented. The objective is to analyze how this aprotic polar solvent is able to solvate three groups of amino acid residues (i.e., polar, apolar, and charged) that are located in a stable helical region of a transmembrane peptide. The 25-residue peptide (sMTM7) used mimics the cytoplasmic proton hemichannel domain of the seventh transmembrane segment (TM7) from subunit a of H(+)-V-ATPase from Saccharomyces cerevisiae. The three-dimensional structure of peptide sMTM7 in DMSO has been previously solved by NMR spectroscopy. The radial and spatial distributions of the DMSO molecules surrounding the peptide as well as the number of hydrogen bonds between DMSO and the side chains of the amino acid residues involved are extracted from the molecular dynamics simulations. Analysis of the molecular dynamics trajectories shows that the amino acid side chains are fully embedded in DMSO. Polar and positively charged amino acid side chains have dipole-dipole interactions with the oxygen atom of DMSO and form hydrogen bonds. Apolar residues become solvated by DMSO through the formation of a hydrophobic pocket in which the methyl groups of DMSO are pointing toward the hydrophobic side chains of the residues involved. The dual solvation properties of DMSO cause it to be a good membrane-mimicking solvent for transmembrane peptides that do not unfold due to the presence of DMSO.     

HSAB principle and desulphuration reaction during ionic coordination polymerization of thiiranes [1]

Desulphuration of trimethylthiirane (TMT), catalyzed by anionic and cationic catalysts for thiirane polymerization, has been studied. The possibility of obtaining polymers having mono-, di- and trisulphide bonds during TMT polymerization by typical cationic catalysts has been shown. Some peculiarities of the desulphuration reaction during the polymerization of thiiranes by ionic catalysts have been found. Differences in their catalytic action, shown by the formation of different quantities of both disulphide SSbonds in polymer chain and alkene, are discussed from the point of view of HSAB principle and symbiotic effect of ligands at the counterion. It is shown that desulphuration reactions during the cationic and anionic polymerization of thiiranes have a similar electronic nature, consisting of increase of coordinative state and the activation of the acceptor orbital of the thiirane sulphur atom. The nucleophilic attack by thiirane (during cationic polymerization) or growing thiolate-ion (during anionic polymerization) on the electrophilic sulphur atom of thiiranium intermediates

respectively, is accompanied by concerted fragmentation of these intermediates, giving the alkene and disulphide fragment. Possible mechanisms have been suggested for thiirane desulphuration and SSbond formation in products of the ionic polymerization of thiiranes. HSAB principle proved to be very useful for discussion of experimental results and other aspects of thiirane polymerization.     

Analysis of disulphide linkages in bovine kappa-casein oligomers using two-dimensional electrophoresis

Disulphide bonds play an important role in protein structure and function. Bovine kappa-casein (kappa-csn), an important glycoprotein in milk, contains two cysteines that can form disulphide bonds. On 2-D gels run under nonreducing conditions the kappa-csn in milk presented a complex pattern of monomers and disulphide-linked oligomers. Trains of spots corresponding to monomers to hexamers were observed as a result of the participation of different glycoforms and phosphoforms in oligomer formation. The dimers and trimers ran as doublets on the gel and analysis of the disulphide-linked peptides released from them after in-gel tryptic digestion showed they were the result of different disulphide linkages. The linkages were confirmed by MSMS. When milks with electrophoretically distinct genetic variants of kappa-csn were mixed and run on 2-D gels, they retained their distinct patterns indicating that disulphide exchange reactions or disulphide 'scrambling' was not occurring during 2-D analysis. The patterns observed represent the native distribution of kappa-csn in milk at harvest. The role and significance of the disulphide bonding of kappa-csn are discussed.     

气相色谱-质谱联用鉴定基于水酶法制备的虹鳟鱼骨油组分

采用水酶法制备虹鳟鱼骨油,单因素分析法优化虹鳟鱼骨酶解的工艺条件,考察了料液比、pH值、酶解时间、酶解温度、加酶量5个因素对鱼油提取率的影响,采用气相色谱-质谱联用 (GC-MS) 技术对鱼骨油的脂肪酸组成和含量进行了分析鉴定.结果表明,在55℃、pH 7.5、酶解时间为3 h、料液比为1∶1、加酶量为2000 U/g的条件下,利用碱性蛋白酶提取的虹鳟鱼骨油中的油脂含量最高.GC-MS分析结果表明,虹鳟鱼骨油中主要成分是不饱和脂肪酸,含量为脂肪酸总量的80.4% (w/w),其中单不饱和脂肪酸和多不饱和脂肪酸分别约占不饱和脂肪酸的76.9%和23.1% (w/w), DHA和EPA的总量为3.4% (w/w).本研究优化了虹鳟鱼油的提取技术,对虹鳟鱼油的主要挥发性物质进行了分析鉴定,初步确定了其中对鱼油风味起主要贡献的物质,对鱼油产品的分析与鉴别具有参考价值.     

Stable isotope ratio analysis as a tool to discriminate between rainbow trout (O. mykiss) fed diets based on plant or fish-meal proteins

The use of stable isotope ratio analysis (SIRA) as a rapid analytical tool to characterize and discriminate farmed fish on the basis of the feedstuffs included in the diet formulation is discussed. Two isoproteic (44.8%) and isolipidic (19.6%) extruded diets were formulated: a fish-meal-based diet (FM diet), containing fish meal as the sole protein source; a plant-protein-based diet (PP diet), where pea protein concentrate and wheat gluten meal replaced 80% of fish meal protein. The diets were fed to eight groups of rainbow trout (initial body weight: 106.6g) for 103 days in two daily meals under controlled rearing conditions. Growth performance (final body weight: 318.5 g; specific growth rate: 1.06%) and feed-to-gain ratio (0.79) were not affected by the dietary treatment. The differences in isotopic values of the two diets were clearly reflected in the different carbon and nitrogen isotopic values in rainbow trout fillets. The delta(13)C and delta(15)N values of muscle of farmed rainbow trout showed differences between farmed fish fed a fish-protein-based diet (-20.47 +/- 0.34 and 12.38 +/- 0.57 for delta(13)C and delta(15)N, respectively) and those fed a plant-protein-based diet (-23.96 +/- 0.38 and 7.15 +/- 0.51 for delta(13)C and delta(15)N, respectively). The results suggest that SIRA provides a robust and verifiable analytical tool to discriminate between fish fed on a plant or a fish protein diet.     

Liquid chromatographic determination of benzocaine and N-acetylbenzocaine in the edible fillet tissue from rainbow trout.

A method was developed for determining benzocaine and N-acetylbenzocaine concentrations in fillet tissue of rainbow trout. The method involves extracting the analytes with acetonitrile, removing lipids or hydrophobic compounds from the extract with hexane, and providing additional clean-up with solid-phase extraction techniques. Analyte concentrations are determined using reversed-phase high-performance liquid chromatographic techniques with an isocratic mobile phase and UV detection. The accuracy (range, 92 to 121%), precision (R.S.D., < 14%), and sensitivity (method quantitation limit, < 24 ng/g) for each analyte indicate the usefulness of this method for studies characterizing the depletion of benzocaine residues from fish exposed to benzocaine.     

Effects of poloxamer on the gelation of silk sericin

Effects of the concentration of poloxamer 407, temperature, and the concentration of sericin on the gelation of silk sericin (SS) were studied. Gelation of SS was accelerated with an increase in poloxamer concentration and temperature. The sol‐gel transition of SS became irreversible with respect to the temperature in the presence of poloxamer, whereas the sol‐gel transition of SS itself was reversible. Infrared (IR) and circular dichroism (CD) spectra show that the conformational change of SS in the presence of poloxamer was accelerated from random coil to β‐structure. X‐ray diffraction and differential scanning calorimetry (DSC) show that the crystalline structure of poloxamer in the mixture was affected by the presence of SS and that its melting temperature was shifted to lower temperature with increasing SS content, indicating an interaction between poloxamer and SS through hydrogen and hydrophobic bondings.     

Properties of a water layer on hydrophilic and hydrophobic self-assembled monolayer surfaces: A molecular dynamics study

The microscopic behaviors of a water layer on different hydrophilic and hydrophobic surfaces of well ordered self-assembled monolayers (SAMs) are studied by molecular dynamics simulations. The SAMs consist of 18-carbon alkyl chains bound to a silicon(111) substrate, and the characteristic of its surface is tuned from hydrophobic to hydrophilic by using different terminal functional groups ( CH 3 , COOH). In the simulation, the properties of water membranes adjacent to the surfaces of SAMs were reported by comparing pure water in mobility, structure, and orientational ordering of water molecules. The results suggest that the mobility of water molecules adjacent to hydrophilic surface becomes weaker and the molecules have a better ordering. The distribution of hydrogen bonds indicates that the number of water-water hydrogen bonds per water molecule tends to be lower. However, the mobility of water molecules and distribution of hydrogen bonds of a water membrane in hydropho- bic system are nearly the same as those in pure water system. In addition, hydrogen bonds are mainly formed between the hydroxyl of the COOH group and water molecules in a hydrophilic system, which is helpful in understanding the structure of interfacial water.     

Photocatalytical reduction of disulphide bonds in peptides on Ag-loaded nano-TiO2 for subsequent derivatization and determination

We reported an alternative strategy to reduce disulphide bonds in peptides with Ag-nanoparticle loaded nano-TiO(2) (Ag/TiO(2)) under UV irradiation. The feasibility of this strategy was adequately demonstrated using the model peptides oxidized glutathione, vasopressin and insulin, which contain various disulphide bonds, as well as by its application to the determination of Cd-induced phytochelatins in Phaeodactylum tricornutum.     

Structural analysis of SNARE motifs from sea perch, Lateolabrax japonicus by computerized approaches

Three cDNA sequences encoding four SNARE (N-ethylmaleimide-sensitive fusion protein attachment protein receptors) motifs were cloned from sea perch, and the deduced peptide sequences were analyzed for structural prediction by using 14 different web servers and softwares. The “ionic layer” structure, the three dimensional extension and conformational characters of the SNARE 7S core complex by using bioinformatics approaches were compared respectively with those from mammalian X-ray crystallographic investigations. The result suggested that the formation and stabilization of fish SNARE core complex might be driven by hydrophobic association, hydrogen bond among R group of core amino acids and electrostatic attraction at molecular level. This revealed that the SNARE proteins interaction of the fish may share the same molecular mechanism with that of mammal, indicating the universality and solidity of SNARE core complex theory. This work is also an attempt to get the protein 3D structural information which appears to be similar to that obtained through X-ray crystallography, only by using computerized approaches.     

Structural study of the stability of the captopril drug regarding the formation of its captopril disulphide dimer

Captopril disulphide is obtained under hydrothermal conditions. The IR and Raman spectra data are in agreement with the X-ray diffraction results. The disappearance of the band at 2566 cm^–1 (ν(SH)) in both spectra of captopril disulphide is consistent with the formation of the S–S bond. The degradation of the captopril drug is investigated by Raman spectroscopy and the results indicate that after 6 weeks of air exposure, a band at 512 cm^–1, assigned as ν(SS), is observed, suggesting the formation of captopril disulphide. DFT calculations in the solid state are performed for captopril and captopril disulphide. The results indicate that captopril disulphide is approximately 30 kcal?mol^–1 more stable than captopril. The analysis of the total density of states (DOS) reveals that the captopril valence band contains a significant contribution from the S atom, whereas for captopril disulphide, the O atom is the most important for the valence band.     

Colon targeted drug delivery of branch-chained disulphide cross-linked polymers: design,synthesis, and characterisation studies

Drug delivery directly to the colon is a very useful approach for treating localised colonic diseases such as inflammatory bowel disease, ulcerative colitis, and Crohn’s disease. The use of disulphide cross-linked polymers in colon targeted drug delivery systems has received much attention because these polymers are redox sensitive, and the disulphide bonds are only cleaved by the low redox potential environment in the colon. The goal of this study was to synthesise tricarballylic acid-based trithiol monomers for polymerisation into branch-chained disulphide polymers. The monomer was synthesised via the amide coupling reaction between tricarballylic acid and (triphenylmethyl) thioethylamine using two synthesis steps. The disulphide cross-linked polymers which were synthesised using the air oxidation method were completely reduced after 1 h of reduction with different thiol concentrations detected for the different disulphide polymers. In simulated gastric and intestinal conditions, all polymers had low thiol concentrations compared to the thiol concentrations in the simulated colon condition with Bacteroides fragilis present. Degradation was more pronounced in polymers with loose polymeric networks, as biodegradability relies on the swelling ability of polymers in an aqueous environment. Polymer P15 which has the loosest polymeric networks showed highest degradation.     

Semisynthesis iii - the homoserine 12,105 analogue of hen egg-white lysozyme.

The homoserine ^12,105 analogue of Hen egg-white lysozyme has been prepared by two routes. In the first approach a large excess of cyanogen bromide was used to cleave the native enzyme at methionines 12 and 105, the tertiary structure being maintained by the presence of the four disulphide bonds. Formation of the two new amide bonds was achieved using the activation of the homoserine lactone residues generated at positions 12 and 105; the reaction being most efficient when anhydrous DMSO was used as the solvent. An alternative approach using limited (two-fold excess) cyanogen bromide digestion gave the same homoserine analogue without chain fragmentation. A purified sample of the analogue showed no enzymic activity.     

A innovative switchable polarity solvent,based on 1,8‐diazabicyclo‐[5.4.0]‐ undec‐7‐ene and decanol was prepared for enrichment of aluminum in biological sample prior to analysis by flame atomic absorption spectrometry

A novel switchable solvent (SS) extraction methodology has been used for the enrichment of aluminium (Al) in acid‐digested blood samples of patients with neurological disorders before proceeding to flame atomic absorption spectrometry. 1,8‐Diazabicyclo[5.4.0]undec‐7‐ene and decanol in combination made a SS which reversibly changes from hydrophobic (nonpolar) to hydrophilic (polar) according to switch‐on and switch‐off phenomena in aqueous medium by exposure to anti‐solvent trigger (CO₂). The SS polar micro‐emulsion was switched on by bubbling CO₂, and switched off by heating from 40 to 70°C with exposure to N₂ gas. The changes obtained in the structure and physical properties of the SS due to switching from lower polarity to higher polarity were investigated using Fourier transform infrared spectroscopic analysis. The SS was effectively analysed as an extractive medium for hydrophobic chelate of Al with 3,5,7,2,4‐pentahydroxyflavone (morin) and extracted in SS. Then hydrophobic enriched Al‐morin‐SS was treated with 1.0 M HNO₃ and CO₂ purging at various time intervals, switch to a miscible polar hydrophilic monophase state. The SS was easily recycled up to six times for further enrichment process. For the developed method, various parameters were optimized such as pH, volume of chelating reagent, CO₂ purging time and pressure, and rate of heating. Under favourable conditions, enhancement factor and limit of detection were observed as 25 and 0.47 μg l^?1, respectively, for 10 ml of samples/standards solution. The accuracy of the developed method was determined using certified reference material (SRM 3101a), with a standard addition procedure. The method was used for the pre‐concentration of Al in blood samples of patients with neurological disorders.     

Explanation of Ionic Sequences in Various Phenomena. VI. The Formation and Destruction of Helices in Bovine Plasma Albumin in Neutral and Acidic Solutions

Abstract

The structure of bovine plasma albumin (BPA) was examined by optical rotatory dispersion studies at both low (pH 1.5 and 2.0) and high (pH 9.0) pH values in various aqueous salt solutions. The resulting cationic sequences were compared to those observed by Pedersen for values of the sedimentation constant. At pH 9.0 the destruction of the “helix” produces an acidic sequence. The relative pH position of the “helix” transition, the fact that addition of salt increases the apparent helical content of BPA, and the observed acidic-type of sequence rule out the possibility of (1)ionic bonds between carboxylate and ?-amino groups, (2) hydrophobic bonds, or (3) hydrogen bonds between peptide linkages as major contributing forces in the formation of the helix. The stability of the “helix” in BPA between pH 3.0 and 9.0 must therefore be due to hydrogen bonds between carboxylate ions and hydroxyl groups such as those of serine, threonine, and tyrosine. Repulsive forces between the positively charged groups on BPA strengthen these bonds by preventing the expanded form of BPA from collapsing. At pH 2.0 two types of sequences were observed: The s⁰ _{20, w}, [α]_D and a₀ values gave an acidic-type cationic sequence. The b₀ (helix content), λ_c and [λ]₂₃₃ values gave essentially a nonpolar sequence. The nonpolar or hydrophobic salting-out sequences show that the formation of hydrophobic bonds at pH 2.0 hinders the formation of the helix or folded structure. The acidic sequences show that hydrogen bonds between carboxylic acid groups stabilize both the apparent helix or helices and the intermolecular aggregation of the BPA molecules. From a comparison of the S⁰ ₂₀,w values and the helical content of BPA at pH 9.0 it is also concluded that the formation of these apparent helices or folded structures expands or stiffens the BPA molecule.     

Comparison between the behavior of different hydrophobic peptides allowing membrane anchoring of proteins

Membrane binding of proteins such as short chain dehydrogenase reductases or tail-anchored proteins relies on their N- and/or C-terminal hydrophobic transmembrane segment. In this review, we propose guidelines to characterize such hydrophobic peptide segments using spectroscopic and biophysical measurements. The secondary structure content of the C-terminal peptides of retinol dehydrogenase 8, RGS9-1 anchor protein, lecithin retinol acyl transferase, and of the N-terminal peptide of retinol dehydrogenase 11 has been deduced by prediction tools from their primary sequence as well as by using infrared or circular dichroism analyses. Depending on the solvent and the solubilization method, significant structural differences were observed, often involving α-helices. The helical structure of these peptides was found to be consistent with their presumed membrane binding. Langmuir monolayers have been used as membrane models to study lipid–peptide interactions. The values of maximum insertion pressure obtained for all peptides using a monolayer of 1,2-dioleoyl-sn-glycero-3-phospho-ethanolamine (DOPE) are larger than the estimated lateral pressure of membranes, thus suggesting that they bind membranes. Polarization modulation infrared reflection absorption spectroscopy has been used to determine the structure and orientation of these peptides in the absence and in the presence of a DOPE monolayer. This lipid induced an increase or a decrease in the organization of the peptide secondary structure. Further measurements are necessary using other lipids to better understand the membrane interactions of these peptides.     

Controlled release matrix tablet formulation using synthesized N-acyl Thiolated Chitosan derivatives

Chitosan derivative was successively synthesized by initial preparation of acyl thiourea reagent using ammonium thiocyanate and making it to react with at primary amino groups of chitosan and then reduced to yield Thiolated Chitosan. Due to the formation of disulphide bonds with mFucus glycoproteins, mucoadhesiveness is augmented. The thiol groups were then quantified using Ellman’s reagent. The derivatives inherit good swelling property in neutral and alkaline media. The different derivatives containing thiol groups were formulated into tablets using reference drug for evaluation. The Thiolated Chitosan display in situ gelling features due to the pH-dependent (alkaline pH) formation of inter-molecular disulphide bonds which makes the application of Thiolated Chitosan on intestinal mucosa and can guarantee prolonged controlled release of embedded therapeutic ingredients.     

Effect of antifreeze proteins on the nucleation, growth, and the memory effect during tetrahydrofuran clathrate hydrate formation

The inhibition activities of two antifreeze proteins (AFPs) on the formation of tetrahydrofuran (THF) clathrate hydrate have been tested. AFPs from fish (wfAFP) and insect (CfAFP) changed the morphology of growing THF hydrate crystals. Also, both AFPs showed higher activities in inhibiting the formation THF hydrate than a commercial kinetic inhibitor, poly(vinylpyrrolidone) (PVP). Strikingly, both AFPs also showed the ability to eliminate the "memory effect" in which the crystallization of hydrate occurs more quickly after the initial formation. This is the first report of molecules that can inhibit the memory effect. Since the homogeneous nucleation temperature for THF hydrate was measured to be 237 K, close to that observed for ice itself, the action of kinetic inhibitors must involve heterogeneous nucleation. On the basis of our results, we postulate a mechanism for heterogeneous nucleation, the memory effect and its elimination by antifreeze proteins.