Frustration and hydrophobicity interplay in protein folding and protein evolution

A lattice model is used to study mutations and compacting effects on protein folding rates and folding temperature. In the context of protein evolution, we address the question regarding the best scenario for a polypeptide chain to fold: either a fast nonspecific collapse followed by a slow rearrangement to form the native structure or a specific collapse from the unfolded state with the simultaneous formation of the native state. This question is investigated for optimized sequences, whose native state has no frustrated contacts between monomers, and also for mutated sequences, whose native state has some degree of frustration. It is found that the best scenario for folding may depend on the amount of frustration of the native structure. The implication of this result on protein evolution is discussed. (c) 2006 American Institute of Physics.

Influence of ionic interactions on the photoinduced Birefringence of poly[1-[4-(3-carboxy-4 hydroxyphenylazo) benzene sulfonamido]-1 2-ethanediyl, sodium salt] films

Electrostatic interactions govern most properties of polyelectrolyte films, as in the photoinduced bire-fringence of azo-containing polymers. In this paper we report a systematic investigation of optical storage characteristics of cast and layer-by-layer (LbL) films of poly[1 -[4-(3-carboxy-4 hydroxypheny-lazo) benzene sulfonamido]-1,2-ethanediyl, sodium salt] (PAZO). Birefringence was photoinduced faster in PAZO cast films prepared at high pHs, with the characteristic writing times decreasing almost linearly with the pH in the range between 4 and 9. This was attributed to an increased free volume for the azochromophores with the enhanced electrostatic repulsion in PAZO charged to a greater extent. In contrast, in LbL films of PAZO alternated with poly(allylamine hydrochloride) (PAH), the electrostatic interactions between the oppositely charged polymers hampered photoisomerization and molecular rearrangement, thus leading to a slower writing kinetics for highly charged PAH or PAZO.

Clarifications on breakpoints in HSAX and BTAX by comparative mapping of F9, HPRT, and XIST in cattle

The coagulation factor IX gene (179), the hypoxanthine phosphoribosyl transferase 1 gene (HPRT1), and the X-inactive specific transcript gene (XIST) were physically assigned in cattle to analyze chromosomal breakpoints on BTAX recently identified by radiation hybrid (RH) mapping experiments. Whereas the FISH assignment of XIST indicates a similar location on the q-arm of the human and cattle X chromosomes, the locus of HPRT1 supported the assumption of a chromosome rearrangement between the distal half of the q-arm of HSAX and the p-arm of BTAX identified by RH mapping. F9 previously located on the Cl-arm of BTAX was assigned to the p-arm of BTAX using RH mapping and FISH. The suggested new position of F9 close to HPRT I supports the homology between HSAXq and BTAXp. The F9 locus corresponds with the gene order found in the homologous human chromosome segment. XIST was assigned on BTAXq23, HPRT1 and F9 were mapped to BTAXp22, and the verification of the location of F9 in a 5000 rad cattle-hamster whole genome radiation hybrid panel linked the gene to markers URB10 and HPRT1. Copyright (C) 2003 S. Karger AG, Basel.

CYTOGENETIC REPORT OF A MALE BREAST-CANCER

The cytogenetic findings on G-banding in an infiltrating ductal breast carcinoma in a 69-year-old man are reported. The main abnormalities observed were trisomy of chromosomes 8 and 9 and structural rearrangement in the long arm of chromosome 17 (add(17)(q25)). Our results confirm the trisomy of chromosome 8 in the characterization of the subtype of ductal breast carcinomas and demonstrate that chromosome 17, which is frequently involved in female breast cancers, is also responsible for the development or progression of primary breast cancers in males.

Kinetics of photoinduced birefringence in the guest-host system of poly(methyl methacrylate) doped with azobenzene-containing crown ethers

The kinetics of the buildup and decay of photoinduced birefringence was examined in a series of host-guest systems: azobenzene-containing crown ethers, differing in the size of the crowns, dissolved in a poly (methyl methacrylate) matrix. In all samples, the kinetics of the buildup of the birefringence was reasonably described by a sum of two exponential functions, the time constants being inversely proportional to the intensity of the pumping light and the magnitudes of the signals at the saturation level depending on the pumping light intensity and sample thickness. The dark decays were best described by the stretched exponential function, with the characteristic parameters (time constant and stretch coefficient) being practically independent of the type of crown ether. The time constants of the signal decay were orders of magnitude shorter than the respective constants of the dark isomerization of the azo crown ethers, thus indicating that the process controlling the decay was a relaxation of the polymer matrix and/or a rearrangement of the flexible parts of the crowns. (C) 2007 Wiley Periodicals, Inc.

Electron impact and chemical ionization mass spectral analyses of methyl esters species of free mycolic acid fraction from Rhodococcus lentifragmentus

The free mycolic acid fraction from Rhodococcus lentifragmentus was derivatized to methyl esters and further fractionated into saturated (F-0), monounsaturated (F-1) and diunsaturated (F-2) species using argentation-TLC. Methyl esters fractions F-0, F-1 and F-2, accounting for approximately 7.4%, 53.1% and 39.5%, respectively, were analyzed by electron impact (EI) and chemical ionization (CI) mass spectrometries. According to EI-MS, peaks observed for M(+)-18, that were prominent compared to those representing M(+)-32 and M(+)-(18 + 32), indicated that the carbon chain size ranged from C-36 to C-48. The pyrolytic cleavage of methyl mycolates (R(2)-CHOH-CH(R(1))-COOCH3), following the McLafferty rearrangement released fragment ions corresponding to, (a) the alpha-subunit, representing the fatty acid methyl ester (R(1)-CH2-COOCH3), methyl hexadecanoate, methyl tetradecanoate and methyl dodecanoate in decreasing order of relative intensity of peaks, and (b) the beta-subunit, representing the meroaldehyde moiety (R(2)-CHO). The saturated meroaldehyde species exhibited peaks representing meroaldehyde minus 18 mass units in which R(2) ranged from C19H39 to C31H63. The monunsaturated species exhibited peaks representing the meroaldehyde in which R(2) ranged from C19H37 to C31H61; peaks corresponding to meroaldehyde minus 18 mass units appeared only in the most abundant components, C29H57CHO, C27H53CHO, C25H49CHO and C31H61CHO, in a decreasing order of relative abundance. The diunsaturated species exhibited peaks essentially corresponding to meroaldehyde in which R(2) corresponded to C31H59 and C29H55; the latter displayed a relative intensity that was about one-half compared to that of the former. Fractions F-0, F-1 and F-2 showed a more intense pyrolytic fragmentation under CI-MS in contrast to results found under EI-MS. Therefore, peaks representing the alpha-subunit and the beta-subunit were more prominent than the ones representing the fragmentation of the hydrocarbon chain. Moreover, the beta-subunit of saturated species exhibited peaks corresponding to meroaldehyde plus hydrogen, and no dehydration of the beta-subunit occurred in this case. In turn, the beta-subunit of monounsaturated and diunsaturated species showed peaks representing both the meroaldehyde plus hydrogen and its dehydration product plus hydrogen. Thus, the presence of unsaturation in the meroaldehyde subunit of methyl mycolate facilitates appearance of dehydration fragment ions under chemical ionization procedure.

Differential cross sections for target excitation and positronium formation in positron-helium scattering

Positronium formation and target excitation in positron-helium scattering have been investigated using the close-coupling approximation with realistic wave functions for the positronium and helium atoms. The following eight states have been used in the close-coupling scheme: He(1s1s), He(1s2(1)s), He(1s2(1)p), He(1s3(1)s), He(1s3(1)p), Ps(1s), Ps(2s), and Ps(2p), where Ps stands for the positronium atom. Calculations are reported of differential cross sections for elastic scatering,, inelastic target excitation to He(1s2(1)s) and He(1s2(1)p) slates, and rearrangement transition to Ps(1s), Ps(2s), and Ps(2p) states for incident positron energies between 40 and 200 eV. The coincidence parameters for the transition to the He(1s2(1)p) state of helium are also reported and briefly discussed. [S1050-2947(98)05101-4].

Thermal analysis applied in the crystallization study of SrSnO3

SrSnO3 was synthesized by the polymeric precursor method with elimination of carbon in oxygen atmosphere at 250 A degrees C for 24 h. The powder precursors were characterized by TG/DTA and high temperature X-ray diffraction (HTXRD). After calcination at 500, 600 and 700 A degrees C for 2 h, samples were evaluated by X-ray diffraction (XRD), infrared spectroscopy (IR) and Rietveld refinement of the XRD patterns for samples calcined at 900, 1,000 and 1,100 A degrees C. During thermal treatment of the powder precursor ester combustion was followed by carbonate decomposition and perovskite crystallization. No phase transition was observed as usually presented in literature for SrSnO3 that had only a rearrangement of SnO6 polyhedra.

Spontaneous triploidy and NOR activity in Eigenmannia sp. (Pisces, Sternopygidae) from the Amazon basin

The occurrence of a natural triploid among diploid individuals of Eigenmannia sp from the Amazon basin is described. The diploid individuals had 2n=31 and 32 chromosomes, the difference in chromosome number being due to a Robertsonian rearrangement. The triploid individual presented 2n=46 and had two fused acrocentrics. NOR activity was present in the three homologues of triploid and a NOR polymorphism was detected in the triploid and diploids. © 1985 Dr W. Junk Publishers.

Pore size evolution during sintering of ceramic oxides

This paper reviews the influence of particle size distribution, agglomerates, rearrangement, sintering atmospheres and impurities on the pore evolution of some commonly studied oxides. These factors largely affect sintering mechanisms due to modifications of diffusion coefficients or evaporation-condensation. Very broad particle size distribution leads to grain growth and agglomerates densify first. Rearrangement of particles due to neck asymmetry mainly in the early stage of sintering is responsible for a high rate of densification in the first minutes of sintering by collapse of large pores. Sintering atmospheres play an important role in both densification and pore evolution. The chemical interaction of water molecules with several oxides like MgO, ZnO and SnO2 largely affects surface diffusion. As a consequence, there is an increase in the rates of pore growth and densification for MgO and ZnO and in the rate of pore growth for SnO2. Carbon dioxide does not affect the rate of sintering of MgO but greatly affects both rates of pore growth and densification of ZnO. Oxygen concentration in the atmosphere can especially affect semiconductor oxides but significantly affects the rate of pore growth of SnO2. Impurities like chlorine ions increase the rate of pore growth in MgO due to evaporation of HCl and Mg(OH)Cl, increasing the rate of densification and particle cuboidization. CuO promotes densification in SnO2, and is more effective in dry air. The rate of densification decrease and pore widening are promoted in argon. An inert atmosphere favors SnO2 evaporation due to reduction of CuO. © 1990.

Influence of polymerization on the synthesis of SrTiO3: Part II. Particle and agglomerate morphologies

Morphologies of SrTiO3 particles and agglomerates synthesized by the traditional Pechini route and by the polymer precipitation route were characterized by the nitrogen adsorption/desorption technique and by transmission electron microscopy (TEM). A cluster structure of nanometric particles forming large agglomerates which are broken during pressing followed by cluster rearrangement was observed. The mean particle size is larger for SrTiO3 obtained by the Pechini route and is related to the precursor thermal decomposition and particle growth during calcination. The particle growth is controlled by neck growth among particles and further motion of the particle boundary. © 1995.

Positron-helium scattering: Resonance and differential cross sections

We study positron-helium scattering using close coupling approximation (CCA) employing different combinations of the following basis functions: He(1s1s), He(1s2s), He(1s2p), Ps(1s). and Ps(2s), where Ps stands for the positronium atom. We observe a prominent S wave resonance of width 2 eV at about 30 eV, in excitation and rearrangement cross sections to He(1s2s), He(1s2p), Ps(1s) and Ps(2s) states. We also report results of differential cross sections for the excitation of helium and positronium formation.

Effect of atmosphere on the sintering and grain growth of tin oxide

High purity SnO 2 powder (>99.9%) was compacted in cylindrical pellets and sintered in atmospheres of dry argon, argon with water vapor, oxygen and CO 2 using 10 °C/min up to 1200 °C or isotherms in the range of 1000 to 1200 °C. Time, temperature and sintering atmosphere have large influence on grain growth and low influence on densification of this oxide. Surface diffusion is the dominant mechanism up to 1200 °C and evaporation-condensation is dominant above 1200 °C. The maximum linear shrinkage observed was about 2.0% and attributed to structural rearrangement of particles due to high capillary stresses developed with neighboring particles. © 1999 Trans Tech Publications.

Color evaporation induced rapidity gaps

We show that soft color rearrangement of final states can account for the appearance of rapidity gaps between jets. In the color evaporation model the probability to form a gap is simply determined by the color multiplicity of the final state. This model has no free parameters and reproduces all data obtained by the ZEUS, H1, DØ, and CDF Collaborations. ©1999 The American Physical Society.

Polarons, bipolarons, and crystallization in conducting polymers: An ESR study

Electron spin resonance (ESR) experiments give extremely important information concerning spin arrangements in conducting polymers. This is evidenced by the behavior of the ESR lines as a function of temperature and microwave power. Our ESR data of pressed pellets of ClO- 4 doped poly(3-methylthiophene) (P3MT) synthesized at 25 °C show the predominance of polarons. Instead, the sample prepared at 5 °C shows the predominance of bipolarons. Besides, for both types of samples, crystallization, observed from the ESR data, has shown a rearrangement of spin species.