Folding Behavior of Polypeptides. A Monte Carlo Study of Simplified Models

Summary. A simple model of polypeptide chains was designed and studied. The chains were constructed on a flexible [310] lattice and consisted of united atoms located at the position of alpha carbons. Each united atom represented amino acid residues of two kinds: hydrophilic and hydrophobic. The sequence of the residues was assumed to be characteristic for α- and β-type of proteins. The force field used consisted of the long-range contact potential between polymer segments, the short range repulsion, and the local potential preferring conformational states characteristic for α-helices and β-strands. The Monte Carlo simulations of this model were carried out using the replica exchange technique coupled with the histogram method. The influence of temperature and the local potential on the size and internal structure of collapsed low temperature chains were studied. Thermodynamics of these systems consisting mainly of α and β secondary structures were determined. The properties of the coil-to-globule transition were presented and compared with other theoretical predictions and simulation results.     

Molecular mobility of a comb-shaped copolymethacrylate with chalcone chromophore-containing side groups

The molecular mobility of copolymethacrylate with chromophore-containing chalcone side chains is studied by broadband dielectric spectroscopy. Five regions of dipolar polarization relaxation are identified: namely, γ, β, β₁, α, and δ processes. It is shown that γ and β1 processes are related to the local mobility of methylene sequences and ester groups adjoining the backbone, while the α process is associated with the cooperative segmental mobility of the backbone. The β and δ processes are attributed to the mobility of chalcone groups: the local mobility in the glassy state (reorientation relative to the long axis of chromophores) and the cooperative mobility in the rubbery state (reorientation relative to the short axis of chromophores), respectively. The incorporation of 20% chalcone groups does not change the glass-transition temperature but enhances the cooperativity of the α process and intermolecular interactions.     

Identification of α- and β-hydroxy acid containing cyclodepsipeptides in natural peptide mixtures using negative ion mass spectrometry

Natural peptide libraries often contain cyclodepsipeptides containing α- or β-hydroxy residues. Extracts of fungal hyphae of Isaria yield a microheterogenous cyclodepsipeptide mixture in which two classes of molecules can be identified by mass spectral fragmentation of negative ions. In the case of isaridins, which contain an α-hydroxy residue and a β-amino acid residue, a characteristic product ion corresponding to a neutral loss of 72 Da is obtained. In addition, neutral loss of water followed by a 72 Da loss is also observed. Two distinct modes of fragmentation rationalize the observed product ion distribution. The neutral loss of 72 Da has also been obtained for a roseotoxin component, which is also an α-hydroxy residue containing cyclodepsipeptide. In the case of isariins, which contain a β-hydroxy acid residue, ring opening and subsequent loss of the terminal residue as an unsaturated ketene fragment, rationalizes the observed product ion formation. Fragmentation of negative ions provide characteristic neutral losses, which are diagnostic of the presence of α-hydroxy or β-hydroxy residues.     

Structural Characteristics of Xyloglucan – Congo Red Aggregates as Observed by Small Angle X-ray Scattering

Xyloglucan is a type of hemicellulose with a cellulose backbone containing (1→6)-α-xylose or (1→2)-β-galactoxylose as a side chain. It is soluble in water. Its aqueous solution forms a gel or gel-like precipitate by addition of Congo red. Xyloglucan gel structures with various concentrations of Congo red were observed by small angle X-ray scattering (SAXS) at the nano-level. SAXS results indicated that the xyloglucan chains interacted with Congo red, and that an increase of concentration of Congo red induced a characteristic cross-linking domain, which consisted of a flat structure containing stacked xyloglucan chain assemblies. The Congo red molecules are inserted between the xyloglucan chains.     

Kinetics and thermodynamics of liquid phase isomerization of α- and β-pinene over Pd/C catalyst

The kinetics and thermodynamics of the liquid phase isomerization of an α- and β-pinene mixture on a Pd/C catalyst were studied. The effects of pinene concentration, catalyst particle size, stirring rate, reaction temperature (293–423 K) and hydrogen pressure (0.5–11 bar) on the rate of α- and β-pinene isomerization were investigated. The reaction rate of the α-pinene isomerization has the first order with respect to the α-pinene concentration and 0.5 order with respect to the hydrogen pressure. The thermodynamic parameters of the isomerization (Gibbs energy, reaction enthalpy and reaction entropy) and the equilibrium ratio of pinenes under the conditions studied were determined. The general scheme of the reaction mechanism of α- and β-pinene isomerization over the Pd/C catalyst was proposed.     

Crystallization and Melting of β-Nucleated Isotactic Polypropylene

Ca salts of suberic (Ca-Sub) and pimelic acid (Ca-Pim) were synthesized and used as β-nucleating agents in different grades of isotactic polypropylene (IPP). Propylene homo-, random- and block-copolymers containing these additives crystallize principally in pure β-modification as demonstrated in isothermal and non-isothermal crystallization experiments. Ca-Sub proved the most effective β-nucleating agent known, so far. It broadens the upper crystallization temperature range of pure β-IPP formation up to 140°C. The effect of the additives on the crystallization and melting characteristics of the polymers was studied. The degree of crystallinity of the β-modification was found to be markedly higher than that of α-IPP. High temperature melting peak broadening was first observed and discussed in literary results regarding the same phenomenon for α-IPP. This revised version was published online in August 2006 with corrections to the Cover Date.     

Size scaling behaviour in protein domains belonging to the all-α, all-β, α / β, and α?+?β folding classes

We studied the size scaling behaviour in an ensemble of 8,614 non-redundant protein domains belonging to the all-α, all-β, α / β, and α + β folding classes. We find that the most compact structural domains can be characterized by an effective exponent ν _eff  = 0.39 ± 0.01, which is larger than the value for “collapsed-polymers,” i.e., ν = 1/3. We also show that the global ν _eff -exponent is an average of the scaling regimes for short and long compact chains, where the values change from ν _eff ≈ 0.37 to ν _eff ≈ 0.45 at chain length of ca. 269. A transition from short-chain to long-chain scaling behaviour is found in all major folding classes, over a window of chain lengths between 216 and 269 residues. In addition, variations in scaling exponent with respect to folding class indicates that the smallest domains in the (all-β) and (α / β) families appear to be more compact structures than the smallest (all-α)- and (α + β)-domains.     

AFM imaging of interfacial morphologies in carbon-fiber reinforced isotactic polypropylene

 The morphology of high-modulus carbon-fiber (HM-CF) reinforced isotactic polypropylene (iPP) was investigated for the first time by atomic force microscopy (AFM) using chemically etched specimens. The images exhibited α-transcrystalline morphology for samples crystallized from quiescent melts, nucleated by HM-CF. In melts sheared by fiber pulling, αβ-cylindritic columnar morphology was observed in agreement with earlier thermo-optical studies. AFM images in the interfacial region of the β-cylindrites unveiled fine morphological details of α-row nuclei. Based on the observations, we concluded that in β-cylindrites, the lamellar growth in α-row nuclei occurs during epitaxial crystallization on bundles of extended iPP chains which form during shearing of the polymer matrix by fiber pull. Received: 25 June 1996 Accepted: 17 October 1996     

Properties of star-branched and linear chains in confined space: a computer simulation study

We studied the properties of simple models of linear and star-branched polymer chains confined in a slit. The polymer chains were built of united atoms and were restricted to a simple cubic lattice. Two macromolecular architectures of the chain linear and star-branched with three branches (of equal length) were studied. The excluded volume was the only potential introduced into the model and thus, the system was athermal. The chains were put between two parallel and impenetrable surfaces. Monte Carlo simulations with a sampling algorithm based on chain’s local changes of conformation were carried out. The differences and similarities in the global size and the structure and of linear and star-branched chains were shown and discussed.     

Thermal oxidative destruction of isomeric dipyrrolylmethanes

3,3′,4,4′-tetramethyl-5,5′-dicarboethoxydipyrrolylmethane-2,2′ and its α,β and β,β′ isomers were synthesized. The compounds were characterized by recording of their proton NMR spectra. The thermal oxidative destruction of the compounds was studied by thermogravimetry. The thermal stability of dipyrrolylmethanes was found to be primarily characterised by molecular isomerism for symmetrically substituted α,α′-and β,β′-dipyrrolylmethanes compared with α,β isomer.     

Correlation between lactosylation and denaturation of major whey proteins: an investigation by liquid chromatography–electrospray ionization mass spectrometry

The Maillard-reaction-induced lactosylation of the major whey proteins, α-lactalbumin (α-La) and β-lactoglobulins (β-Lg) A and B, occurring upon heating at 70, 80 and 90 °C for 1 to 5 h in the presence of lactose excess, was studied by HPLC coupled to electrospray ionization single and tandem mass spectrometry (HPLC-ESI-MS, MS/MS). The presence of significant amounts of mono and bi-lactosylated forms of the three proteins and their increase with heating temperature and time were assessed from MS data. Evidences for a concomitant, significant denaturation, involving partial tertiary structure unfolding, were also obtained in the case of β-lactoglobulins. A subsequent ESI-MS and MS/MS investigation on the tryptic digests of heated protein solutions exhibiting high percentages of mono and bi-lactosylated forms provided information on lactosylation sites. In particular, the latter were identified both on tryptic and on aspecific peptides, whose unusual relevance (compared to similar studies) was found to be due mainly to heat-induced protein degradation, occurring before protein digestion with trypsin. Among lactosylation sites identified only on tryptic peptides, i.e., those reasonably related to intact protein lactosylation, two lysines residues were found for α-La, both located in accessible regions of its tertiary structure. In the case of β-Lg, besides three sites common to variants A and B (leucine 1, lysines 70, and 75), lysine 69 was found to be lactosylated only in variant B. Its proximity to a critical region of β-Lg tertiary structure suggests that the difference between the two variants could be ascribed to a different evolution of their conformation upon heating.     

Spectral and fluorescent properties of cross-conjugated polyene ketones with terminalN-methylpyrrole residues

The spectral and fluorescent properties of a number of cross-conjugated ketones with one or two terminalN-methylpyrrole residues and those of polyene bis-ω, ω′-dimethylamino ketones with methyl substituents in the polyene chain and of some related compounds were studied. The photophysical properties of cross-conjugated ketones with terminalN-methylpyrrole residues are similar to those of the corresponding polyene bis-ω, ω′-dimethylamino ketones studied in detail previously. In both series of compounds, the absorption and fluorescence spectra undergo a bathochromic shift following an increase in the length of the polyene chains or introduction of α,α′-trimethylene or α,α′-dimethylene bridges into these chains; the same trend is observed on passing from less polar solvents to more polar solvents (positive solvatochromism). Thermochromism (long-wavelength shift of the absorption spectra upon cooling the solutions) is observed in both series of compounds. The introduction of methyl substituents into the polyene chains of bis-ω,ω′-dimethylamino ketones results in a decrease in the fluorescence quantum yield. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1293–1298, July, 1999.     

The Structure of Star-Branched Chains in a Confined Space

Summary. We studied the properties of a simplified model of star-branched polymers confined in a slit formed by two parallel and impenetrable surfaces. The chains were built of identical united atoms (segments) whose positions were restricted to vertices of a simple cubic lattice. The polymer excluded volume and polymer segment-surface contact interactions were also introduced into the model. The properties of the model chains were determined by means of Monte Carlo simulations with a Metropolis-type sampling algorithm based on local changes of chain’s conformation. The structure of star-branched chains was investigated and the influence of the confinement and the temperature on the chain dimensions and structure was studied. It was shown that for chains in the adsorbing slits their sizes do not exhibit a universal behavior contrary to confined athermal polymers. The polymers in narrow slits at higher temperatures still exhibited features of a three-dimensional chain. It was also shown that chains in small slits and at low temperatures were fully adsorbed at one of the surfaces but could also switch the surface rapidly.     

Lamiaceae carbohydrates. V. structure of glucoarabinogalactan from <Emphasis Type="Italic">Scutellaria baicalensis</Emphasis>

Chemical and spectral methods were used to establish that polysaccharide WSPS-3 isolated from the aerial part of Scutellaria baicalensis Georgi (Lamiaceae) was an acetylated glucoarabinogalactan, the main chain of which consisted of α-(1→6)-bonded galactopyranose with side chains consisting of arabinopyranose and partially acetylated glucopyranose residues located on C-2 and C-3. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 454–456, September-October, 2008.     

Molecular dynamics in fluorinated side-chain maleimide copolymers as studied by broadband dielectric spectroscopy

A series of alternating maleimide (MI) copolymers with fluorinated side chains have been investigated using broadband dielectric spectroscopy. The side chains consist of fluoroalkane (–C _x F_2x+1, x=1, 7, 9) end groups connected to the main chain via methylene spacers. The experiments were carried out in a frequency range of 0.1 Hz to 10 MHz and at temperatures between 120 K and 500 K. The fluorinated MI copolymers show a fast sub-T _g (β) relaxation characterized by an Arrhenius-type temperature dependence with activation energy in the range of 30–37 kJ/mol. Two more processes (α and δ-like) are observed, corresponding to independent relaxations of the main chain and the fluoroalkane domains respectively. For shorter side chains, the δ-like process is not observed but instead another relaxation process, α _S , occurs at temperatures higher than either the α and δ-like processes. When compared with unfluorinated MI copolymers, the fluorinated MI copolymers show the δ-like process and a slower β-relaxation unlike their unfluorinated counterparts. A model to explain the molecular origin of the four processes is proposed, supplemented by differential scanning calorimetry and published WAXS/SAXS data.     

Carbon paste electrodes electrochemically modified with cyclodextrins

Cyclic voltammetry was used in order to obtain carbon paste electrodes (CPEs) modified with α- and β-cyclodextrins (CPE_α-CD, CPE_β-CD) in HClO₄ media as electrolyte. The modified CPEs were obtained by applying 30 potential cycles, thus forming on the substrate a film with electroactive characteristics; a rise in current for the anodic and cathodic peaks became apparent as the number of cycles increased. Such behaviour confirmed the CPE modification by the species mentioned. The CPE_α-CD and CPE_β-CD exhibited significant stability before various electrolytes. In order to evaluate the sort of modification attained on the CPEs, a study was conducted, varying the potential scan rate, that confirmed the CD's presence. The modified electrodes were used to determine Pb(II) ions in solution within the range from 1×10^–5 M up to 1×10^–3 M. The CPE_α-CD and CPE_β-CD electrochemical response was studied by means of anodic stripping voltammetry of the Pb(II) ions, thereby giving a linear relation between the current for the anodic peak as a function of Pb(II) concentration with r ²=0.996 for the CPE_β-CD and 0.992 for the CPE_α-CD. Electronic Publication     

Properties of grafted amphiphilic chains. A computer simulation study

The model of a heteropolymer film formed by polypeptide chains was used for theoretical considerations. The linear chains consisting of amino acid residues were approximated by alpha carbon chains. Each chain was constructed on a very flexible [310] lattice. The inter- and intramolecular interactions consisted of the long-range contact potential between residues. The chains were built of hydrophilic and hydrophobic residues. Chains were terminally attached to an impenetrable surface with lateral motions possible. The Monte Carlo simulations of this model were carried out by using the Metropolis algorithm. The influence of the grafting density, the sequence of the amino acid residues, and the temperature on the static properties of the formed layer were studied and discussed. It was shown that homopolymer chains collapsed at higher temperature than the heteropolymers. The size of the polymers forming brush was smaller for homopolymers than for heteropolymers. The structure of the resulting polymer film and of its external surface was determined. The block copolymers formed well defined hydrophobic and hydrophilic layers, while for the amphiphilic case the composition of the brush layers changed continuously at high temperature. It was observed that the latter effect vanished at the collapsed amphiphilic copolymer.     

Glycogen synthase kinase-3 inhibition by 3-anilino-4-phenylmaleimides: insights from 3D-QSAR and docking

Glycogen synthase kinase-3, a serine/threonine kinase, has been implicated in a wide variety of pathological conditions such as diabetes, Alzheimer’s disease, stroke, bipolar disorder, malaria and cancer. Herein we report 3D-QSAR analyses using CoMFA and CoMSIA and molecular docking studies on 3-anilino-4-phenylmaleimides as GSK-3α inhibitors, in order to better understand the mechanism of action and structure-activity relationship of these compounds. Comparison of the active site residues of GSK-3α and GSK-3β isoforms shows that all the key amino acids involved in polar interactions with the maleimides for the β isoform are the same in the α isoform, except that Asp133 in the β isoform is replaced by Glu196 in the α isoform. We prepared a homology model for GSK-3α, and showed that the change from Asp to Glu should not affect maleimide binding significantly. Docking studies revealed the binding poses of three subclasses of these ligands, namely anilino, N-methylanilino and indoline derivatives, within the active site of the β isoform, and helped to explain the difference in their inhibitory activity.     

Separation and detection of the α- and β-chains of hemoglobin of a single intact red blood cell using capillary electrophoresis/electrospray ionization time-of-flight mass spectrometry

A single intact red blood cell (erythrocyte) was injected into a capillary electrophoresis column, and following in-capillary lysing the α- and β-chains of the hemoglobin (∼450 amol) were separated and detected using capillary electrophoresis/electrospray ionization time-of-flight mass spectrometry. The mass spectra of the electropherogram peaks of the α and β chains showed identifiable peaks corresponding to multiply protonated and sodiated α- and β-chains of hemoglobin.     

Improved analytical procedure for determination of chlorinated pesticide residues in human serum using solid phase disc extraction (SPDE), single-step clean-up and gas chromatography

Summary An improved analytical methodology based on solid-phase disc extraction (SPDE) and a single-step clean-up on Florisil is proposed for a large number of organochlorine pesticide residues in serum. Extraction was performed following denaturation of proteins with formic acid after it was shown that it has no degradation effect on targeted analytes (α, β, γ-HCH isomers, HCB, DDT with its 5 analogues, endrin, aldrin, dieldrin, alachlor; heptachlor, heptachlorepaxide, α, β-endosulphan, endosulphansulphate, methoxychlor and mirex). Determination and quantification were by GC-ECD and GC-MS on two different, analytical capillary-columns using PCNB (pentachlonitrobenzene) and PCB 190 internal standards. Recoveries and limits of detection determined on pooled serum ranged 54–102% (for medium spiking level) and 10–50 pg ml⁻¹ serum respectively. Twenty-one individuals serum samples from the University Hospital of Antwerp were analysed and results were related to the ages of the donors. For compounds not detected by GC-MS, eventual coelution with PCBs in GC-ECD analysis was studied.