Rate Of Bond Formation Research Articles

Slow fracture model based on strained silicate structures

Slow crack growth data, molecular-orbital calculations, and vibrational spectroscopy results are used to develop an atomistic model for environmentally controlled fracture of silica glass. The model is based on chemically active bond defects generated by the strain field of the crack tip. Molecular-orbital results suggest that bond angle deformations are most effective in increasing the chemical activity of the Si–O–Si bond. Vibrational spectra identify silica polymorphs containing highly strained bonding configurations. A comparison of strained bond reactivity with crack growth results shows that strained silica polymorphs can be used to model the crack tip chemical reactions controlling slow fracture. Based on model complexes, a two-dimensional fracture model involving kink site nucleation and motion is developed. The model shows that the stress intensity dependence of the crack growth rate is controlled by the energy required to form chemically active defects in the silica structure. The absolute rate of fracture depends on the combined rates of active bond formation and chemical attack at strain induced defects. Crack growth data suggest that for silica, strain activation occurs prior to the adsorption of environmental chemicals.

Decoding at the ribosomal A site. The effect of a defined codon-anticodon mismatch upon the behavior of bound aminoacyl transfer RNA.

Ribosomes from Escherichia coli were programmed by being allowed to bind a molecule of tRNAMetf or fMet-tRNAMetf and the hexanucleotide messenger AUGN1N2N3. The interaction of the ternary complex [EF-Tu X GTP X Phe-tRNAPhe] with the A site (containing the codon N1N2N3) was then studied by measuring the extent of (i) the binding of Phe-tRNAPhe to the ribosome, (ii) the hydrolysis of GTP, and (iii) the formation of the dipeptide fMet-Phe. By variation of N1,N2, and N3, a defined degree and position of mismatch could be obtained; the correct A-site codon UUU was compared with the incorrect codons CUU, UCU, GUU, and UUG. Each single-point alteration led to catalytic hydrolysis of GTP and to a strong reduction in the amounts of Phe-tRNAPhe binding and of dipeptide formation. The observations were explicable qualitatively by a hypothesis according to which the behavior of the bound aa-tRNA, after hydrolysis of GTP and before peptidyl transfer, is determined principally by the energy of binding of the aminoacyl-tRNA to the A site. This binding in turn was found to depend upon both the nature and the position of the mismatch. The results further suggest a steric interplay between the 3' (acceptor) end of the A-site tRNA and the second and third positions of the anticodon, so that a mismatch at one of these positions can impair directly the interaction between the aminoacylated 3' end and the ribosome and can thus reduce the rate of peptide bond formation and contribute to the overall fidelity of the elongation cycle.

Effect of hydroxyapatite impregnation on skeletal bonding of porous coated implants.

Skeletal fixation of permanent implants by new methods such as fixation by mechanical interlocking of bone with porous prosthetic coatings or chemical bonding with bioactive materials shows growing potential. This paper reports on the resulting skeletal fixation of a combined porous and bioactive material. Metal plugs with a porous metal fiber coating impregnated with hydroxyapatite were implanted for 2, 4, and 12 weeks and were compared to the parent porous, nonbioactive, metal fiber material. Statistical analysis of the interfacial failure shear stress, as obtained by mechanical testing, shows there is a marked influence of hydroxyapatite impregnation on the rate of bone ingrowth and the strength of the interfacial bond the few weeks following surgery. Microscopical examination reveals that the apparent stimulation of bone ingrowth into the surface pores of the implant is the reason for the increased rate of bond formation. The results are of particular clinical interest: with an increased rate of bone ingrowth, weight bearing might be allowed much earlier, thus reducing the recuperation period.

Comparison of rates of phosphotriester formation and sulphonation by coupling agents in oligodeoxyribonucleotide synthesis by the phosphotriester method

Rates of phosphotriester bond formation and amounts of sulphonation are compared for three popular coupling agents used in oligodeoxyribonucleotide synthesis by the phosphotriester approach.

Bacterial ribosomes with two ambiguity mutations: effects of translational fidelity, on the response to aminoglycosides and on the rate of protein synthesis.

A set of mutants affected in translational fidelity was constructed by transduction within an otherwise isogenic Escherichia coli B argF40 argR11 background. Alterations in ribosomal proteins S4, S5, S12 and L6 either as single mutations or in various combinations were compared for their effects on aminoglycoside phenotypes, on in vivo and in vitro misreading and on the rate of peptide bond formation. Results may be summarized as follows: (i) Strains carrying two ambiguity mutations on the ribosome without any restrictive mutation are viable. When together, they only weakly increase the level of mistranslation as judged by several in vivo and in vitro test systems. (ii) The combination of two ram mutations causes a very strong cooperative increase of streptomycin sensitivity, irrespective of whether the strains have a wild-type S12 or mutationally altered S12 proteins (of the drug-resistant or -dependent types) on their ribosomes; (iii) The S4 and S5 ram mutations do not alter the response of the ribosome to aminoglycosides of the 2-desoxystreptamine group which are structurally unrelated to streptomycin. This is interpreted in terms of an effect of these ram mutations on the streptomycin binding site but not on the site(s) of binding of the other aminoglycosides. (iv) The rate of polypeptide bond formation which was determined from the kinetics of beta-galactosidase induction is not significantly changed in strains bearing the ram and the strA (streptomycin-resistant) alleles. In contrast, the L6 and the strA (streptomycin-dependent) alleles strongly reduce the rate of polypeptide elongation which mechanistically might be connected with restriction of ambiguity (Nino, 1974) in these cases.

Catalytic effect of sulfhydryl oxidase on the formation of three-dimensional structure in chymotrypsinogen A

The effect of sulfhydryl oxidase on the rate of disulfide bond formation and polypeptide chain folding in reductively denatured chymotrypsinogen A has been investigated using an immobilized zymogen preparation and a cylindrical quartz flow-through fluorescence cell. Enzymatic oxidation of the 10 sulfhydryl groups in reduced chymotrypsinogen followed first order kinetics at pH 7.0 with an apparent first order rate constant governing sulfhydryl group disappearance of 4.2 × 10 −2 min −1. This provides a t 1 2 of 16.3 min for the sulfhydryl oxidase-catalyzed oxidation, whereas 165 min are required for nonenzymatic aerobic oxidation of one-half the sulfhydryl groups. Refolding of the reductively denatured polypeptide chains, monitored by changes in protein fluorescence, did not follow first order kinetics characteristic of a simple two-state mechanism, nor did the return of trypsin activatability. It appears that at least one intermediate must exist in such refolding, in both the uncatalyzed and sulfhydryl oxidase-catalyzed processes. Estimation of the rate constants governing refolding, assuming a single intermediate between the denatured and native states, provided values of 3 × 10 −2 min −1 and 7 × 10 −3 min −1 for uncatalyzed autoxidation and 4 × 10 −2 min −1 and 1.1 × 10 −2 min −1 for the sulfhydryl oxidase-catalyzed transition. Thus, enzymic catalysis of disulfide bond formation can lead to apparent catalysis of protein refolding as monitored both by fluorescence and by acquisition of biological function.

Models for the Specific Adhesion of Cells to Cells

A theoretical framework is proposed for the analysis of adhesion between cells or of cells to surfaces when the adhesion is mediated by reversible bonds between specific molecules such as antigen and antibody, lectin and carbohydrate, or enzyme and substrate. From a knowledge of the reaction rates for reactants in solution and of their diffusion constants both in solution and on membranes, it is possible to estimate reaction rates for membrane-bound reactants. Two models are developed for predicting the rate of bond formation between cells and are compared with experiments. The force required to separate two cells is shown to be greater than the expected electrical forces between cells, and of the same order of magnitude as the forces required to pull gangliosides and perhaps some integral membrane proteins out of the cell membrane.

Racemization studies of amino acid derivatives. 6. Rates of racemization and peptide bond formation of glutamic and aspartic acid active esters

Racemization studies of amino acid derivatives. 6. Rates of racemization and peptide bond formation of glutamic and aspartic acid active esters

Racemization of amino acid derivatives. Rate of racemization and peptide bond formation of cysteine active esters.

Racemization of amino acid derivatives. Rate of racemization and peptide bond formation of cysteine active esters.

The Differential Inactivation of Histidinol Dehydrogenase from Salmonella typhimurium by Sulfhydryl Reagents

Abstract Treatment of histidinol dehydrogenase with either p-chloromercuribenzoate (CMB) or N-(4-dimethylamino-3,5-dinitrophenyl)maleimide (DDPM), but not with N-ethylmaleimide or iodoacetic acid, produces an enzyme form which is differentially inactivated with respect to the oxidation of its two substrates, histidinol and histidinal. The binding of 2 eq of DDPM reduces activity with histidinol and histidinal as substrate to 25 and 42% of their respective initial values. Binding of 4 eq of CMB reduces activity with histidinol as the substrate to 25% of its initial value although activity measured with histidinal is not decreased. Enzymatic activity measured with histidinol as the substrate decreases as a linear function of the concentration of CMB or DDPM added, but neither reagent can totally inactivate the enzyme. During the binding of 4 eq of mercuribenzoate the rate of mercaptide bond formation appears to be proportional to the rate of inactivation measured with histidinol as the substrate. We conclude that the addition of CMB produces a uniform differential inactivation of all enzyme molecules rather than the complete inactivation of a portion of the molecules. Apparent Km values for histidinol and histidinal do not change upon differential inactivation. However, LineweaverBurk plots of velocity with respect to DPN concentration with either substrate in excess, while linear with the native enzyme, are concave downward for differentially inactivated enzyme. These effects may be due to (a) the presence of nonidentical active sites; (b) negative cooperativity between multiple active sites; or (c) an alteration in the normal reaction mechanism.

Transition phenomena and solid‐state structure in glassy polymers

AbstractThe primary and secondary transitions observed in solid polymers have generally been interpreted in terms of the concept of “molecular motions.” A different interpretation is presented here in which these transitions are explained in terms of the thermal breakdown of different types of intermolecular secondary bonding in the solid state. It is assumed that the association‐dissociation equilibria involved are governed by normal thermodynamic considerations. The time‐temperature (or frequency‐temperature) dependence of such transitions can be associated with the “transport rate” (bond formation and breakdown rate) of the dynamic equilibrium involved. The glass transition behavior of polyacrylonitrile and poly(methyl methacrylate) are discussed in terms of the breakdown of dipole‐dipole bonding between chains, and it would appear that, the breakdown of hydrogen‐bonding and van der Waals bonding are involved in the transitions of nylon and polyethylene, respectively. From this point of view, a glass transition is regarded as having considerable similarity to a melting point, and this consequently provides a theoretical justification for the empirically observed correlation between the principal glass transition and the melting point for a wide variety of polymers.

Changes in the ribosome distribution during incubation of rabbit reticulocytes in vitro

Intact reticulocytes incubated in vitro synthesize hemoglobin at a linear rate for 1 h at 30°. During the first 30 min about one-third of the 80-S ribosomes are transferred into the polysome fraction, leading to an increase in the concentration and size of polysomes. Protein synthesis is accompanied by polysome breakdown, and by 1 h this is the dominant event. These changes in the ribosome distribution appear to be the result of changes in the initiation process (attachment of ribosomes to polysomes) rather than changes in the rates of peptide bond formation or release of completed polypeptide chains from ribosomes. The rate-limiting step in protein synthesis was located by: (a) determining the synthetic time for the β-chain of hemoglobin within two different time intervals during the incubation, and (b) investigating the kinetics of hemoglobin synthesis under conditions where amino acids were limiting.

The Influence of Dicyclohexylcarbodiimide Concentration on the Rate of Phospho Diester Bond Formation

The Influence of Dicyclohexylcarbodiimide Concentration on the Rate of Phospho Diester Bond Formation