Dynamics of ribonuclease A and ribonuclease S: Computational and experimental studies

RNase S is a complex consisting of two proteolytic fragments of RNase A: the S peptide (residues 1-20) and S protein (residues 21-124). RNase S and RNase A have very similar X-ray structures and enzymatic activities. previous experiments have shown increased rates of hydrogen exchange and greater sensitivity to tryptic cleavage for RNase S relative to RNase A. It has therefore been asserted that the RNase S complex is considerably more dynamically flexible than RNase A. In the present study we examine the differences in the dynamics of RNaseS and RNase A computationally, by MD simulations, and experimentally, using trypsin cleavage as a probe of dynamics. The fluctuations around the average solution structure during the simulation were analyzed by measuring the RMS deviation in coordinates. No significant differences between RNase S and RNase A dynamics were observed in the simulations. We were able to account for the apparent discrepancy between simulation and experiment by a simple model, According to this model, the experimentally observed differences in dynamics can be quantitatively explained by the small amounts of free S peptide and S protein that are present in equilibrium with the RNase S complex. Thus, folded RNase A and the RNase S complex have identical dynamic behavior, despite the presence of a break in polypeptide chain between residues 20 and 21 in the latter molecule. This is in contrast to what has been widely believed for over 30 years about this important fragment complementation system.

Thermodynamics of ligand (substrate end product) binding to endoxylanase from Chainia sp. (NCL-82-5-1): isothermal calorimetry and fluorescence titration studies

The binding of xylo-oligosaccharides to Chainia endoxylanase resulted in a decrease in fluorescence intensity of the enzyme with the formation of 1:1 complex. Equilibrium and thermodynamic parameters of ligand binding were determined by fluorescence titrations and titration calorimetry. The affinity of xylanase for the oligosaccharides increases in the order X-2 < X-3 < X-4 less than or equal to X-5. Contributions from the enthalpy towards the free energy change decreased with increasing chain length from X-2 to X-4, whereas an increase in entropy was observed, the change in enthalpy and entropy of binding being compensatory. The entropically driven binding process suggested that hydrophobic interactions as well as hydrogen bonds play a predominant role in ligand binding.

Simultaneous Electrodeposition of MnO2 and Mn(OH)(2) for Supercapacitor Studies

Among the various Mn compounds, both MnO2 and Mn(OH)2 are electrochemically active in supercapacitor studies. MnO2 and Mn(OH)2 are simultaneously deposited, through a one-pot method, on the anode and cathode, respectively, of a galvanostatic electrolysis cell consisting of aqueous Mn(NO3)2 electrolyte. MnO2 and Mn(OH)2 coated stainless steel (SS) electrodes are found to exhibit a capacitive behavior with a high specific capacitance. MnO2/SS and Mn(OH)2/SS electrodes are used as the negative and positive electrodes, respectively, in assembling nonsymmetrical capacitors and testing. The results indicate that both Mn-based electrodes prepared simultaneously in a single electrolysis possess interesting electrochemical properties for supercapacitor application.

Scheme of squares: Part I. Systems formalism for potentiostatic studies

The so-called “Scheme of Squares”, displaying an interconnectivity of heterogeneous electron transfer and homogeneous (e.g., proton transfer) reactions, is analysed. Explicit expressions for the various partial currents under potentiostatic conditions are given. The formalism is applicable to several electrode geometries and models (e.g., semi-infinite linear diffusion, rotating disk electrodes, spherical or cylindrical systems) and the analysis is exact. The steady-state (t→∞) expressions for the current are directly given in terms of constant matrices whereas the transients are obtained as Laplace transforms that need to be inverted by approximation of numerical methods. The methodology employs a systems approach which replaces a system of partial differential equations (governing the concentrations of the several electroactive species) by an equivalent set of difference equations obeyed by the various partial currents.

Evidence for peroxide and Cul+ species in La1.8Sro.2Cu04 from photo-emission studies

Employing photo-emission and Auger electron spectroscopy, it is shown that La, ,Sr&uO,contains 0:- -typespeciesandCu'+ ions, proportionsof these speciesincrease with decreasing temperature. These species may play an important role in the high-temperature superconductivity of this oxide.

Characterization of alinite cements through X-ray diffraction and mas 29Si NMR studies

Alinite cements have been synthesized using mining and steel plant wastes and pulverized fuel ash (fly ash) as raw materials and a clinkering temperature of 1150°C. The cements possess hydration characteristics comparable to those of portland cements. X-ray diffraction studies on these samples confirm the presence of alinite as the predominant phase. MAS 29Si NMR spectra have been used to distinguish alinite and alite cements. While both show resonances characteristic of Q° type silicate species, the portland cements exhibit three distinct peaks corresponding to three inequivalent SiO4 units present, while alinite shows a single sharp peak corresponding to the unique Si position.

Studies on tryptophan residues of Abrus agglutinin Stopped-flow kinetics of modification and fluorescence-quenching studies

The presence of two essential tryptophan residues/molecule was implicated in the binding site of Abrus agglutinin [Patanjali, Swamy, Anantharam, Khan & Surolia (1984) Biochem. J. 217, 773-781]. A detailed study of the stopped-flow kinetics of the oxidation of tryptophan residues revealed three classes of tryptophan residues in the native protein. A discrete reorganization of tryptophan residues into two phases was observed upon ligand binding. The heterogeneity of tryptophan exposure was substantiated by quenching studies with acrylamide, succinimide and Cs+. Our study revealed the microenvironment of tryptophan residues to be hydrophobic, and also the presence of acidic amino acid residues in the vicinity of surface-localized tryptophan residues.

Type II beta-turn conformation of pivaloyl-L-prolyl-alpha-aminoisobutyryl-N-methylamide: Theoretical, spectroscopic, and X-ray studies

Pivaloyl-L-Pro-Aib-N-methylamide has been shown to possess one intramolecular hydrogen bond in (CD3)2SO solution, by 1H-nmr methods, suggesting the existence of beta -turns, with Pro-Aib as the corner residues. Theoretical conformational analysis suggests that Type II beta-turn conformations are about 2 kcal mol-1 more stable than Type III structures. A crystallographic study has established the Type II beta-turn in the solid state. The molecule crystallizes in the space group P21 with a = 5.865 Å, b = 11.421 Å, c = 12.966 Å, beta = 97.55°, and Z = 2. The structure has been refined to a final R value of 0.061. The Type II -turn conformation is stabilized by an intramolecular 4 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are Pro = -57.8°, Pro = 139.3°, Aib = 61.4°, and Aib = 25.1°. The Type II beta-turn conformation for Pro-Aib in this peptide is compared with the Type III structures observed for the same segment in larger peptides.

Molecularly adsorbed oxygen on metals: electron spectroscopic studies

Oxygen is shown to adsorb molecularly on gold as well as on Ag and Pt. UV and X-ray photoelectron spectroscopy and Auger electron spectroscopy have been employed to investigate electron states of molecularly adsorbed oxygen.

beta.-Turn conformation of N-acetyl-L-prolylglycyl-L-phenylalanine. Crystal structure and solution studies

Pro-Gly segments in peptides and proteins are prone to adopt the 0-turn conformation. This paper reports experimental data for the presence of this conformation in a linear tripeptide N-acetyl-L-prolylglycyl-L-phenylalanineb oth in the solid state and in solution. X-ray diffraction data on the tripeptide crystal show that it exists in the type I1 0-turn conformation. CD and proton NMR data show that this conformation persists in trifluoroethanol and methanol solutions in equilibrium with the nonhydrogen-bonded structures. Isomerization around the acetyl-prolyl bond is seen to take place in dimethyl sulfoxide solutions of the tripeptide.

Quasi Crystalline A1-Mn Alloys: Pressure Induced Crystallization and Structural Studies

Irreversible, Pressure induced, quasicrystal-to-crystal transitions are observed for the first time in melt spun alloys at 4.9 GPa for Al 78 Mn22 and 9.3 GPa for Al86 Mn14 by monitoring the electrical resistivities of these alloys as a function of pressure. Electron diffraction and x-ray measurements are used to show that these quasicrystalline phases have icosohedral point group symmetry. The crystalline phases which appear at high pressures are identified as h.c.p. for Al78 Mn22 and orthorhombic for Al86 Mn14.

Adsorption Of Methanol On The Surfaces Of Copper-Alloys - Ups And Eels Studies

Methanol adsorbs molecularly on the surfaces of Cu–Pd alloys at low temperatures and transforms to CH3O or CO on warming, depending upon the alloy composition. On oxygen presorbed Cu–Pd alloy surfaces, adsorption of methanol gives rise to H2O and H2CO. CH3OH adsorbed molecularly on the surfaces of Cu–Au alloys and CH3O is formed only at relatively high temperatures.

Bilirubin binding to polypeptides and chiral amines. Induced circular dichroism and fluorescence studies

Induced Cotton effects have been observed in the visible region on interaction of bilirubin with chiral mono- and diamines and poly-l-lysine. At alkaline pH distinct CD spectra are observed for bilirubin bound to the α-helical and β-sheet conformation of poly-l-lysine, which differ from that observed for the pigment bound to human serum albumin. The CD pattern observed on binding to N-acetyl-Lys-N1-methylamide in CH2Cl2 and dioxane is different from that observed in the presence of l-Ala-NH-(CH2)6-NH-l-Ala in dioxane. The latter case resembles the spectrum observed in the presence of human serum albumin. Binding to the helical polypeptide melittin and the antiparallel β-sheet peptide, gramicidin S, in aqueous solutions results in opposite signs of the bilirubin CD bands. The quenching of tryptophan fluorescence in melittin, in aqueous solution and enhancement of bilirubin fluorescence in dioxane on binding to gramicidin S have been used to monitor pigment-peptide interactions. The results suggest the utility of bilirubin as a conformational probe.

Interaction of rat testis protein, TP, with nucleic acids in vitro. Fluorescence quenching, UV absorption, and thermal denaturation studies

The nucleic acid binding properties of the testis protein, TP, were studied with the help of physical techniques, namely, fluorescence quenching, UV difference absorption spectroscopy, and thermal melting. Results of quenching of tyrosine fluorescence of TP upon its binding to double-stranded and denatured rat liver nucleosome core DNA and poly(rA) suggest that the tyrosine residues of TP interact/intercalate with the bases of these nucleic acids. From the fluorescence quenching data, obtained at 50 mM NaCl concentration, the apparent association constants for binding of TP to native and denatured DNA and poly(rA) were calculated to be 4.4 X 10(3) M-1, 2.86 X 10(4) M-1, and 8.5 X 10(4) M-1, respectively. UV difference absorption spectra upon TP binding to poly(rA) and rat liver core DNA showed a TP-induced hyperchromicity at 260 nm which is suggestive of local melting of poly(rA) and DNA. The results from thermal melting studies of binding of TP to calf thymus DNA at 1 mM NaCl as well as 50 mM NaCl showed that although at 1 mM NaCl TP brings about a slight stabilization of the DNA against thermal melting, a destabilization of the DNA was observed at 50 mM NaCl. From these results it is concluded that TP, having a higher affinity for single-stranded nucleic acids, destabilizes double- stranded DNA, thus behaving like a DNA-melting protein.

Ionophore-mediated transmembrane movement of divalent cations in small unilamellar liposomes: An evaluation of the chlortetracycline fluorescence technique and correlations with black lipid membrane studies

Conceptual advances in the field of membrane transport have, in the main, utilized artificial membranes, both planar and vesicular. Systems of biological interest,viz., cells and organelles, resemble vesicles in size and geometry. Methods are, therefore, required to extend the results obtained with planar membranes to liposome systems. In this report we present an analysis of a fluorescence technique, using the divalent cation probe chlortetracycline, in small, unilamellar vesicles, for the study of divalent cation fluxes. An ion carrier (X537 A) and a pore former (alamethicin) have been studied. The rate of rise of fluorescence signal and the transmembrane ion gradient have been related to transmembrane current and potential, respectively. A second power dependence of ion conduction-including the electrically silent portion thereof — on X537 A concentration, has been observed. An exponential dependence of ldquocurrentrdquo on ldquotransmembrane potentialrdquo in the case of alamethicin is also confirmed. Possible errors in the technique are discussed.