Changes In Conformational Properties Research Articles

Oxidation driven surface hydrophobicity in human seminal plasma results in protein structural changes

Oxidative stress induced changes in conformational properties of proteins are potential causes of functional impairment in protein system. This phenomenon becomes an important study area when the affected proteins present a role in disease aetiology. The current study was aimed at studying seminal plasma protein conformation changes under higher Reactive oxygen species levels. A total of 100 semen samples (control: n = 50 and infertile n = 50) were used after routine semen parameter analysis. Samples were analysed for their total protein content, ROS levels, total antioxidant capacity and polyacrylamide gel electrophoresis was performed under native conditions. A protein band of molecular weight less than 14 KDa was seen differentially in infertile sample presented with higher ROS levels(>72.6 μg formazan/107 sperm cells). MALDI analysis identified the protein to be Tumor Necrosis Factor alpha super family 18 (TNFα-18) ligand. Further analysis of biophysical properties of the protein showed a significant increase in surface hydrophobicity. Binding of seminal plasma TNFα-18 with ANS dye resulted in an increased fluorescence and broadening of emission curves in infertile samples. Changes in structural properties of TNFα-18ligand prevented it from forming stable oligomeric structures which are essential for effective functioning of the protein.

Highly Heat-Resistant Materials for Microelectronics: Hydrodynamic, Optical, and Conformational Properties of Fluorine Containing Poly(Amido-ortho-Hydroxy Amide)

The polycondensation of the mixture of diamines 5,5-methylene bis(2-aminophenol) and 4,4-(hexafluoroisopropylidene)dianiline (molar ratio 0.8:0.2) with isophthaloyl dichloride was used to synthesize poly(amido-o-hydroxy amide) (POA-F) - new heat resistant binder of the composites for microelectronics. The copolymer was fractionated, its hydrodynamic, optical, and conformational properties were researched, and molecular masses (ММ) of the fractions were defined. The polydispersity index was estimated. Based on experimental data, calculation of the size of a segment of Kuhn characterizing degree of an intramolecular orientation order and value of coefficients of the equation of Mark-Kuhn-Hauvink for viscometric and diffusion data were performed. It was demonstrated that introducing 20 mol % of the monomer with -CF3-groups does not lead to any changes in conformational properties of the macromolecules and does not change the degree of intramolecular orientational order (the Kuhn segment length). Optical characteristics of POA-F solutions are virtually similar to the corresponding values for POA prepared with the use of single amine-containing component-5,5-methylene bis(2-aminophenol). The received MM distribution for POA-F (prepolymer) provided the solubility of its films in alkaline solutions. The heat resistance (τ5 and τ10-temperatures corresponding to 5% and of 10% PBO-F mass loss of a polymer) of the powders and the films of PBO, PBO-F were determined. The electrophysical parameters-dielectric permittivity (e) and dielectric loss tangent (tan δ) of the PBO-F films decreased down to 3.30 and 0.017, in comparison 3.40 and 0.025 for PBO respectively.

DIRECT-ID: An automated method to identify and quantify conformational variations--application to β2 -adrenergic GPCR.

The conformational dynamics of a macromolecule can be modulated by a number of factors, including changes in environment, ligand binding, and interactions with other macromolecules, among others. We present a method that quantifies the differences in macromolecular conformational dynamics and automatically extracts the structural features responsible for these changes. Given a set of molecular dynamics (MD) simulations of a macromolecule, the norms of the differences in covariance matrices are calculated for each pair of trajectories. A matrix of these norms thus quantifies the differences in conformational dynamics across the set of simulations. For each pair of trajectories, covariance difference matrices are parsed to extract structural elements that undergo changes in conformational properties. As a demonstration of its applicability to biomacromolecular systems, the method, referred to as DIRECT-ID, was used to identify relevant ligand-modulated structural variations in the β2 -adrenergic (β2 AR) G-protein coupled receptor. Micro-second MD simulations of the β2 AR in an explicit lipid bilayer were run in the apo state and complexed with the ligands: BI-167107 (agonist), epinephrine (agonist), salbutamol (long-acting partial agonist), or carazolol (inverse agonist). Each ligand modulated the conformational dynamics of β2 AR differently and DIRECT-ID analysis of the inverse-agonist vs. agonist-modulated β2 AR identified residues known through previous studies to selectively propagate deactivation/activation information, along with some previously unidentified ligand-specific microswitches across the GPCR. This study demonstrates the utility of DIRECT-ID to rapidly extract functionally relevant conformational dynamics information from extended MD simulations of large and complex macromolecular systems.

Investigation of albumin properties in patients with chronic renal failure

The aim of this study was the investigation of HSA properties and its structural changes after modification induced in vivo among patients with CRF who underwent haemodialysis. Application of different fluorescent dyes allowed the investigation of different regions of albumin molecule using ANS, bis-ANS, piren, piren maleimide and fluorescein isothiocyanate. As markers of oxidative modification, the total protein thiol, carbonyls, glycosylated plasma proteins and hydroperoxide were estimated in plasma. Additionally, this study investigated plasma viscosity and total antioxidant capacity (TAC) of the plasma. Results show that haemodialysis provoked significant changes in conformational properties of plasma albumin, which resulted in the loss of its biological functions. These findings suggest that oxidative stress and glycation of proteins in plasma are developed during haemodialysis. The results depict that one of the features of uraemia is the presence of signs of oxidative stress before haemodialysis. Nevertheless, oxidative stress and glycation of proteins in plasma are exacerbated during haemodialysis and are a complex process.

Structural Basis for the Interaction of the Myosin Light Chain Mlc1p with the Myosin V Myo2p IQ Motifs

Calmodulin, regulatory, and essential myosin light chain are evolutionary conserved proteins that, by binding to IQ motifs of target proteins, regulate essential intracellular processes among which are efficiency of secretory vesicles release at synapsis, intracellular signaling, and regulation of cell division. The yeast Saccharomyces cerevisiae calmodulin Cmd1 and the essential myosin light chain Mlc1p share the ability to interact with the class V myosin Myo2p and Myo4 and the class II myosin Myo1p. These myosins are required for vesicle, organelle, and mRNA transport, spindle orientation, and cytokinesis. We have used the budding yeast model system to study how calmodulin and essential myosin light chain selectively regulate class V myosin function. NMR structural analysis of uncomplexed Mlc1p and interaction studies with the first three IQ motifs of Myo2p show that the structural similarities between Mlc1p and the other members of the EF-hand superfamily of calmodulin-like proteins are mainly restricted to the C-lobe of these proteins. The N-lobe of Mlc1p presents a significantly compact and stable structure that is maintained both in the free and complexed states. The Mlc1p N-lobe interacts with the IQ motif in a manner that is regulated both by the IQ motifs sequence as well as by light chain structural features. These characteristic allows a distinctive interaction of Mlc1p with the first IQ motif of Myo2p when compared with calmodulin. This finding gives us a novel view of how calmodulin and essential light chain, through a differential binding to IQ1 of class V myosin motor, regulate this activity during vegetative growth and cytokinesis.

Glycosyltransferase activity can be modulated by small conformational changes of acceptor substrates.

A range of N-acetyllactosamine derivatives (compounds 4-7) that have restricted mobilities around their glycosidic linkages have been employed to determine how small changes in conformational properties of an oligosaccharide acceptor affect catalytic efficiencies of glycosylations by alpha-2,6- and alpha-2,3-sialyltransferases and alpha-1,3-fucosyltransferases IV and VI. Restriction of conformational mobility was achieved by introducing tethers of different length and chemical composition between the C-6 and C-2' hydroxyl of LacNAc. Compound 4 is a 2',6-anhydro derivative which is highly constrained and can adopt only two unusual conformations at the LacNAc glycosidic linkage. Compound 5 is modified by a methylene acetal tether and can exist in a larger range of conformations; however, the Phi dihedral angle is restricted to values smaller than 30 degrees, which are not entirely similar to minimum energy conformations of LacNAc. The ethylene-tethered 6 can attain conformations in the relatively large energy plateau of LacNAc that include syn conformations A and B, whereas compound 7, which is modified by a methylamide tether, can only reside in the B-conformer. 2',6-Dimethoxy derivative 2 was employed to determine the effect of alkylation of the C-6 and C-2' hydroxyls of 5 and 6 whereas 3 was used to reveal the effects of the C-6 amide and C-2' alkylation of 7. The apparent kinetic parameters of transfer to the conformationally constrained 4-7 and reference compounds 1-3 catalyzed by alpha-2,6- and alpha-2,3-sialyltransferases and alpha-1,3-fucosyltransferases IV and VI were determined, and the results correlated with their conformational properties. The data for 4-6 showed that each enzyme recognizes N-acetyllactosamine in a low minimum energy conformation. A small change in conformational properties such as in compound 5 resulted in a significant loss of catalytic activity. Larger conformational changes such as in compound 4 abolished all activity of the sialyltransferases whereas the fucosyltransferases showed some activity, albeit very low. The kinetic data for compounds 4 and 5 demonstrate clearly that different glycosyltransferases respond differently to conformational changes, and the fucosyltransferases lost less activity than the sialyltransferases. Correlating apparent kinetic parameters of conformationally constrained 6 and 7 and their reference compounds 2 and 3 further supports the fact that different enzymes respond differently and indicates that sialyltransferases and fucosyltransferases recognize N-acetyllactosamine in a different conformation. Collectively, the data presented here indicate that small conformational changes of an oligosaccharide acceptor induced by, for example, the protein structure can be employed to modulate the patterns of protein glycosylation.

Hydrodynamic and Conformational Properties of Aromatic Polyesters Containing Flexible Polyoxyethylene Fragments

Conformational properties of molecules of the thermotropic aromatic polyesters containing mesogenic and flexible very long oxyethylene fragments are discussed on the basis of molecular hydrodynamic investigations. Changes in Conformational properties and equilibrium flexibility of molecules, caused by changes in the way of biphenylene fragments insertion into the chain are analyzed. Intramolecular orientational mobility of mesogenic fragments is characterized by a dimentionless parameter δ/A.

Intramolecular hydrogen bonding and molecular conformations of nucleosides: uridine derivatives

The effect of intramolecular hydrogen bonding on the molecular conformations of uridine derivatives in solution was investigated by i.r., c.d., and n.m.r. spectroscopy. The 220 MHz 1H n.m.r. spectra of three uridine derivatives in CDCl3 solutions [3-methyl-5′-O-methyl-2′,3′-O-isopropylideneuridine (1), 3-methyl-2′,3′-O-isopropylideneuridine (2), 3,6-dimethyl-2′,3′-O-isopropylideneuridine (3)] were analysed in terms of the conformational properties of the O(5′)–C(5′) and C(5′)–C(4′) bonds, and the sugar ring conformation. The presence of the hydrogen bond in compounds (2) and (3) was confirmed directly by i.r. measurements whereas 5′-O-methylation precludes such hydrogen bond formation between the exocyclic CH2OH group and the base ring 2-carbonyl group in compound (1). The presence of the hydrogen bond was confirmed indirectly by c.d. measurements which showed that the base ring adopts the syn-conformation which is necessary for such hydrogen bond formation whereas the base ring of the 5′-O-methyl compound adopts a predominant anti-conformation. Changes in conformational properties of compound (2) in different solvents monitored by c.d. and n.m.r. measurements support the conformational model that hydrogen bond formation between the exocyclic CH2OH group and the pyrimidine ring 2-carbonyl group necessitates the base ring being in the syn-conformation and the O(5′)–C(5′) and C(5′)–C(4′) bonds adopting specific gauche-conformers. Hydrogen bond formation also promotes the sugar ring S [ca. C(2′)-endo] conformation though not as markedly as for an analogous purine derivative.

Study of kinetic regularities and mechanism of methyl methacrylate radical polymerization in the presence of orthophosphoric acid

AbstractPhotoinitiated homophase polymerization of methyl methacrylate (MMA) at 25°C in the presence of a complexing agent, orthophosphoric acid (H3PO4), was studied. It was found that in addition to the increase in initial polymerization rates and molecular weights of PMMA the system MMA/H3PO4 reveals postpolymerization that does not retard with time and is accompanied by an increase on average molecular weight. Macroradicals, lifetimes of which grow considerably in the presence of the complexing agent, are shown to be responsible for the termination‐free postpolymerization in this system by the living chain mechanism. The effect of various factors on the kinetics of postillumination polymerization was studied. A drastic decrease in the rate of bimolecular termination of poly(methyl methacrylate) radicals was shown to be related to the change in conformational properties and to the association of propagation chains via complexing with H3PO4. The mechanism of polymerization in this system was discussed.