Nucleosome core protein: Asymmetric dissociation of the octamer

The octameric nucleosomal core-histone complex, (H2A)2-(H2B)2-(H3)2-(H4)2, isolated from rat liver, undergoes dissociation during gel exclusion chromatography as a result of dilution occurring in the columns. The elution pattern at pH 7.0 and 4°C showed a sharp leading peak containing all four histones but predominantly H3 and H4, and a trailing peak containing equal amounts of histones H2A and H2B. As column length was increased the area under the leading peak decreased and that under the trailing peak increased. In addition the relative positions of the two peaks varied with column length. From an analysis of the data on increase in elution volume of the leading peak in relation to column length an apparent molecular weight of 86 000 was calculated for the undissociated molecule. Its apparent molecular weight, histone composition and pattern of further dissociation in relation to column length suggest that this species is the hexamer, (H2A-H2B)-(H3)2-(H4)2. At pH 7.0 and 4°C the dissociation of the core complex appears to be as follows: (H2A)2-(H2B)2-(H3)2-(H4)2 → (H2A-H2B) + (H2A-H2B)-(H3)2-(H4)2 → 2(H2A-H2B) + (H3)2-(H4)2 This dissociation was accelerated by an increase in temperature or decrease in pH and was accompanied by marked conformational changes as judged by circular dichroism measurements.

X-ray and IR characterisation of Nasicon solid solution, Na1+xZr2SixP3−xO12

X-ray and IR studies on Nasicon solid solutions, Na1+xZr2SixP3−xO12, are carried out as a function of composition x. X-ray diffraction studies show that the unit cell volume increases as x increases and exhibits a maximum at x ≈ 2. On further increase in x the unit cell volume decreases. The infrared absorption peak positions and the splitting of these absorption peaks suggest a distortion of the PO4 and SiO4 tetrahedra. But the distortion is not large enough to change the local symmetry around the phosphorus or silicon ion from Td to C3v.

X-Ray Structure Of A Ternary Metal-Complex - Copper(Ii) Inosine 5'-Monophosphate Imidazole - Metal-Binding To The N(7) Atom Of The Nucleotide In A Mixed-Ligand System Containing An Aromatic Amine

A ternary metal-nucleotide complex, Na2[Cu(5’-IMP)2(im)o,8(H20)l,2(H20)2h]as~ 1be2e.n4 pHr2ep0a,r ed and its structure analyzed by X-ray diffraction (5’-IMP = inosine 5’-monophos hate; im = imidazole). The complex crystallizes in space group C222, with a = 8.733 (4) A, b = 23.213 (5) A, c = 21.489 (6) 1, and Z = 4. The structure was solved by the heavy-atom method and refined by full-matrix least-squares technique on the basis of 2008 observed reflections to a final R value of 0.087. Symmetry-related 5’-IMP anions coordinate in cis geometry through the N(7) atoms of the bases. The other cis positions of the coordination plane are statistically occupied by nitrogen atoms of disordered im groups and water oxygens with occupancies 0.4 and 0.6, respectively. Water oxygens in axial positions complete the octahedral coordination of Cu(I1). The complex is isostructural with C~S-[P~(S’-IMP),(NH~)~a] m”,o del proposed for Pt(I1) binding to DNA. The base binding observed in the present case is different from the typical ”phosphate only” binding shown from earlier studies on metal-nucleotide complexes containing various other ?r-aromatic amines.

Laser flash photolysis study of triplets of cyclobutanethiones

Five cyclobutanethiones with different chromophores at the 3-position were examined for triplet state behaviour in benzene using laser excitation into their low lying nπ*1 band systems. A weak transient absorption attributable to the triplet state is observed in all these cases. Results concerning triplet lifetimes, intersystem crossing yields (S1 → T1), self-quenching kinetics and kinetics of energy transfer to all-trans-1,6-diphenyl-1,3,5-hexatriene and oxygen and quenching by di-t-butyl nitroxide (DTBN) are presented. Intersystem crossing yields estimated with reference to p,p′-dimethoxythiobenzophenone are roughly unity in all five cases. Self-quenching rates are found to be less than diffusion limited and this is attributed to steric crowding at the α positions (dimethyl group). The rates of oxygen and DTBN quenching compare well with those reported for several other thiones in the literature. No transients other than the triplet were detected in the above cyclobutane-thiones.

Identification and analysis of extended strands and beta-sheets in globular proteins

A method to identify β-sheets in globular proteins from extended strands, using only α-carbon positions, has been developed. The strands that form β-sheets are picked up by means of simple distance criteria. The method has been tested by applying it to three proteins with accurately known secondary structures. It has also been applied to ten other proteins wherein only α-carbon coordinates are available, and the list of β-sheets obtained. The following points are worth noting: (i) The sheets identified by the algorithm are found to agree satisfactorily with the reported ones based on backbone hydrogen bonding, wherever this information is available. (ii) β-Strands that do not form parts of any sheet are a common feature of protein structures. (iii) Such isolated β-strands tend to be short. (iv) The conformation corresponding to the preferred right-handed twist of the sheet is overwhelmingly observed in both the sheet-forming and isolated β-strands.

Influence of deamidation(s) in the 67-74 region of ribonuclease on its refolding

The influence of chemical mutation featuring the selective conversion of asparagine or glutamine to aspartic or glutamic acid, respectively, on the kinetics of refolding of reduced RNase has been studied. The monodeamidated derivatives of RNase A, viz. RNase Aa1a, Aa1b, and Aa1c having their deamidations in the region 67-74, were found to regain nearly their original enzymatic activity. However, a marked difference in the kinetics of refolding is seen, the order of regain of enzymic activity being RNase A greater than Aa1c congruent to Aa1a greater than Aa1b. The similarities in the distinct elution positions on Amberlite XE-64, gel electrophoretic mobilities, and u.v. spectra of reoxidized and native derivatives indicated that the native structures are formed. The slower rate of reappearance of enzymic activity in the case of the monodeamidated derivatives appears to result from altered interactions in the early stages of refolding. The roles of some amino acid residues of the 67-74 region in the pathway of refolding of RNase A are discussed.

Glass transition. A new approach based on cluster model of glasses

The structure of real glasses has been considered to be microheterogeneous, composed of clusters and connective tissue. Particles in the cluster are assumed to be highly correlated in positions. The tissue is considered to have a truly amorphous structure with its particles vibrating in highly anharmonic potentials. Glass transition is recognized as corresponding to the melting of clusters. A simple mathematical model has been developed which accounts for various known features associated with glass transition, such as range of glass transition temperature,T g, variation ofT g with pressure, etc. Expressions for configurational thermodynamic properties and transport properties of glass forming systems are derived from the model. The relevence and limitations of the model are also discussed.

Stochastic kinetics of ribosomes: Single motor properties and collective behavior

Syntheses of protein molecules in a cell are carried out by ribosomes.A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the polymerization of the corresponding protein. The forward movement, however, is characterized by an alternating sequence of translocation and pause. Using a quantitative model, which captures the mechanochemical cycle of an individual ribosome, we derive an exact analytical expression for the distribution of its dwell times at the successive positions on the mRNA track. Inverse of the average dwell time satisfies a Michaelis-Menten-type'' equation and is consistent with the general formula for the average velocity of a molecular motor with an unbranched mechanochemical cycle. Extending this formula appropriately, we also derive the exact force-velocity relation for a ribosome. Often many ribosomes each synthesizes a copy of the same protein. We extend the model of a single ribosome by incorporating steric exclusion of different individuals on the same track. We draw the phase diagram of this model of ribosome traffic in three-dimensional spaces spanned by experimentally controllable parameters. We suggest new experimental tests of our theoretical predictions.

Proline-containing β-turns in peptides and proteins: Analysis of structural data on globular proteins

Tetrapeptide sequences of the type Z-Pro-Y-X were obtained from the crystal structure data on 34 globular proteins, and used in an analysis of the positional preferences of the individual amino acid residues in the β-turn conformation. The effect of fixing proline as the second position residue in the tetrapeptide sequence was studied by comparing the data obtained on the positional preferences with the corresponding data obtained by Chou and Fasman using the Z-R-Y-X sequence, where no particular residue was fixed in any of the four positions. While, in general, several amino acid residues having relatively very high or very low preferences for specific positions were found to be common to both the Z-Pro-Y-X and Z-R-Y-X sequences, many significant differences were found between the two sets of data, which are to be attributed to specific interactions arising from the presence of the proline residue.

Electron spin resonance studies of d5 ions (Fe3+ and Mn2+) in lead oxide-lead halide glasses

Electron spin resonance (ESR) of d5 ions (Fe3+ and Mn2+) has been investigated in PbO---PbF2 and PbO---PbCl2 glasses in wide ranges of composition. ESR spectra of d5 ions in these glasses exhibit significant differences which we have attributed to at least three important causes: (i) The ionic potentials of Fe3+ and Mn2+ are different. Hence Fe3+ ions tend to acquire their own environment while Mn2+ ions take up substitutional (Pb2+ ion) positions. (ii) The sizes and nephelauxetic behaviours of O2- and F- ions are similar. Thus even when there is a mixed anionic coordination, the environment of Mn2+ ions is highly symmetrical in oxyfluoride glasses. The Mn2+ spectra in oxychloride glasses are considerably different. (iii) Increase in halide ion concentration increases the ionicity of lead-ligand bonding and favours a more symmetrical environment around dopant ions in halide-rich glasses. The features in ESR spectra have been interpreted in the light of known behaviour of d5 ions in glasses and also in the context of known structural features of PbO---PbX2 glasses. Dopant ions appear to cluster at high concentrations although isolated low-symmetry sites are still observed. Effects of crystallization and annealing upon ESR spectra have also been investigated.

On the Fourier refinement of protein structures

The situation normally encountered in the high-resolution refinement of protein structures is one in which the inaccurate positions of P out of a total of N atoms are known whereas those of the remaining atoms are unknown. Fourier maps with coefficients (FN -- F'P) × exp (i[alpha]'P) and (mFN -- nF'P) exp (i[alpha]'P), where FN is the observed structure factor and F'P and [alpha]'P are the magnitude and the phase angle of the calculated structure factor corresponding to the inaccurate atomic positions, are often used to correct the positions of the P atoms and to determine those of the Q unknown atoms. A general theoretical approach is presented to elucidate the effect of errors in the positions of the known atoms on the corrected positions of the known atoms and the positions of the unknown atoms derived from such maps. The theory also leads to the optimal choice of parameters used in the different syntheses. When the errors in the positions of the input atoms are systematic, their effects are not taken care of automatically by the syntheses.

Porphyrins with multiple crown ether voids: novel systems for cation complexation studies

Porphyrins appended with crown ether, benzo-15-crown-5, at the methine positions have been synthesized and characterized. The fully and partially substituted porphyrins and their metallo (Co, Cu, and Zn) derivatives describe one or more ether cavities in the periphery that are capable of recognizing spherical cations. The ability of these macrocycles to complex cations (Na+, K+, Mg2+, Ca2+, Ba2', and NH4+) is investigated by use of visible, 'H NMR, ESR, and emission spectral studies. The tetrasubstituted crown porphyrin (TCP) exhibits very high selectivity for K+. The cations (K', Ba2+, and NH4+) that require two crown ether cavities for complexation promote dimerization of the porphyrins. The ESR study of the cation-induced porphyrin dimers reveals axial symmetry with the porphyrin planes separated by -4.2 A. This distance increases from the fully substituted to partially substituted porphyrins. The cations (K', Ba2+, and NH4') quench efficiently the fluorescence of the free base porphyrins and their metallo derivatives. The quenching process is attributed to the steric geometry of the dimers.

An essential arginine residue at the substrate binding site of 4-hydroxyisophthalate hydroxylase.

4-Hydroxyisophthalate hydroxylase was inactivated by treatment with phenylglyoxal by a process obeying pseudo-first order kinetics indicating the presence of an essential arginine located presumably in the active site. Addition of saturating amounts of 4-hydroxyisophthalate during the treatment resulted in complete protection of the enzyme from the inactivation, but addition of NADPH was totally ineffective. Analysis of the effect of various substrate analogs on the protection of the enzyme showed that carboxyl and hydroxyl groups at para positions on the aromatic ring are essential for substrate binding to the active site. It was also observed that analogs which protect the enzyme against phenylglyoxal inactivation are themselves effective inhibitors of the enzyme activity.

Analysis and computation of the oil film thickness between the piston ring and cylinder liner of an internal combustion engine

A study of the essential features of piston rings in the cylinder liner of an internal combustion engine reveals that the lubrication problem posed by it is basically that of a slider bearing. According to steady-flow-hydrodynamics, viz. Image the oil film thickness becomes zero at the dead centre positions as the velocity, U = 0. In practice, however, such a phenomenon cannot be supported by consideration of the wear rates of pistion rings and cylinder liners. This can be explained by including the “squeeze” action term in the

Influence of Sm2O3 doping on formation and structure of SrBi2Nb2O9 nanocrystals in lithium borate glasses

New glasses of 16.66SrO–16.66[(1 − x)Bi2O3–xSm2O3]–16.66Nb2O5–50Li2B4O7 (0 ≤ x ≤ 0.5, in molar ratio), i.e., the pseudo-binary Sm2O3-doped SrBi2Nb2O9–Li2B4O7 glass system, giving the crystallization of Sm3+-doped SrBi2Nb2O9 nanocrystals are developed. It is found that the thermal stability of the glasses against the crystallization and the optical band gap energy increases with increasing Sm2O3 content. The formation of fluorite-type Sm3+-doped SrBi2Nb2O9 nanocrystals (diameters: 13–37 nm) with a cubic structure is confirmed in the crystallized (530 °C, 3 h) samples from X-ray powder diffraction analyses, Raman scattering spectrum measurements, and transmission electron microscope observations. The effect of Sm3+-doping on the microstructure, Raman scattering peak positions, and dielectric properties of composites comprising of fluorite-type SrBi2Nb2O9 nanocrystals and the Li2B4O7 glassy phase is clarified. It is found that fluorite-type SrBi2Nb2O9 nanocrystals transform to stable perovskite-type SrBi2Nb2O9 crystals with an orthorhombic structure by heat treatments at around 630 °C.