Fibre X-ray and conformational study of the binding of metal ions on DNA

Results obtained from X-ray diffraction as well as from conformational analysis of Ag-DNA fibres are presented. For small percentages of Ag+ bound and high humidity, the B-DNA form is maintained. As the percentage of Ag+ is increased, the helical parameters of the B-DNA are modified. These modifications are directly related to the percentage of G-C bases. The periodicity of the DNA fibres are perturbed as Ag+ is mainly bound to G-C pairs and, thus, only the equatorial diffracted intensities can be compared to values calculated from molecular models. It is shown, by this way, that the first binding site is located on N7 of G. A second site is situated between N3 and N1 of the G-C pair, at the place of a hydrogen bond. A molecular model of the Ag-DNA complex is proposed and shown to be in agreement with experimental data. Results obtained allow to get some information on the binding of other ions such as Cu2+ and Hg2+ which give very little modification of the fibre X-ray patterns.     

A histoenzymatic study of rat intrafusal muscle fibres.

The histochemical activities of myofibrillar adenosine triphosphatase (ATPase), succinic dehydrogenase (SDH) and alpha glycerophosphate dehydrogenase (alpha-GPD) were studied in intrafusal muscle fibres of rat fast and slow muscles. The ATPase reaction was carried out after the three standard acid preincubations. The cold K2-EDTA preincubated ATPase reaction product was similar to that seen following the regular or alkali-preincubated ATPase reaction, except that the intermediate bag fibres exhibited much higher activity after cold K2-EDTA preincubation. Following either acetic acid solution or cold and room temperature K2-EDTA-preincubation, followed by the ATPase reaction, chain fibres of the fast muscles vastus lateralis and extensor digitorum longus exhibited a very low amount of reaction product as compared with those of the slow soleus. Veronal acetate and K2-EDTA preincubations (and equally preincubation in acetic acid solution) resulted in acid stable ATPase activity along the entire length of the typical bag fibres but only in the polar regions of the intermediate bag fibres. On the basis of differing alpha-GPD reaction, two sub populations of nuclear chain fibres were discovered in one spindle. It is a matter of conjecture, to what extent the histochemical differences of intrafusal fibres from fast and slow muscles reflects functional distinctions in the response to stretch of muscle spindles from fast and slow muscles.     

Histochemical differentiation of extrafusal muscle fibres of the anterior latissimus dorsi in the chick

Histochemical differentiation of the chick anterior latissimus dorsi (ALD) muscle was studied during embryonic development and after hatching. The two types of adult ALD tonic fibres (alpha' and beta') differentiate from a pool of acid and alkali-stable myofibrillar ATPase fibres. Intermediate stages of the transformation from beta' to alpha' were observed. At all developmental stages studied, a low percentage of formalin-resistant, alkali-stable and acid-labile ATPase fibres were observed. Such fibres have the histochemical properties of the alpha R or fast oxidative-glycolytic fibres and are assumed to be focally innervated.     

Histochemical heterogeneity of intrafusal muscle fibres in slow and fast skeletal muscles of the rat

Summary Intrafusal muscle fibres of the slow soleus (Sol) and fast vastus lateralis (VL) muscles of the rat were studied histochemically. Serial transverse sections were incubated for the localization of succinate dehydrogenase (SDH), alpha glycerophosphate dehydrogenase (GPD) and adenosine triphosphatase (ATPase). The latter was examined further after preincubation in acidic solution held at either low or room temperature (R_T). The bag₂ intrafusal fibres in both muscles displayed high regular and acid stable ATPase, but low SDH and GPD activities. Bag₁ intrafusal fibres showed low to moderate regular ATPase, a regional heterogeneity after R_T acid preincubation (low activity in juxtaequatorial and high in polar zones), moderate SDH, but low GPD reactions. In both muscles the chain fibres usually exhibited high ATPase for both regular and cold acid preincubated reactions, but usually low activity after R_T acid preincubation; they had high SDH but variable GPD activities. In Sol muscle, however, approximately 25% of spindles contained chain fibres that showed high acid-stable ATPase reaction after both cold and R_T acid preincubation. In contrast, chain fibres in some VL spindles had a characteristically low ATPase reaction even after cold acid preincubation. This study, therefore, has delineated the existence of an inherent heterogeneity among chain fibres (with respect to their histochemical reactions) in muscle spindles located within slow and fast muscles and also between those found within populations of either Sol or VL muscle spindles.     

Classification of bovine muscle fibres by different histochemical techniques

The classification of bovine muscle fibres is of particular interest for the food industry because meat tenderness depends in part on the proportion of the different types of fibres. It is, therefore, important to define reliable methods for classifying fibre types. There are several classification systems. One is based on contractile type alone, as revealed by myofibrillar ATPase activity or with antibodies against myosin heavy chain. Others take both contractile and metabolic types into account. In this study, the classifications of fibres obtained by these three systems were compared on the semitendinosus and longissimus thoracis muscles of 35 Charolais bulls. Only the use of antibodies allowed the identification of a proportion of hybrid fibres containing two isoforms of fast myosin heavy chain (2a and 2b). In addition, the combination of metabolic types showed that the metabolism of these hybrid fibres differed according to the muscle.     

A Quantitative Description of the Relationship between the Area of Rabbit Ventricular Action Potentials and the Pattern of Stimulation

Intracellular microelectrodes were used to record action potentials from fibres of the isolated rabbit right ventricle and the areas of the action potentials were measured. The action potential area was found to depend in a reproducible way on the preceding pattern of stimulation. A mathematical model reproducing all the observed changes in the action potential area was developed. In the model the action potential area is taken as a linear function of the product of two time and stimulation dependent variables, M and N. The behaviour of each variable between action potentials is described by the solution of a second order differential equation. During each action potential the variables are assumed to change discontinuously, the magnitudes of the discontinuous changes being given by a set of subsidiary equations. It was found that the behaviour of all the fibres tested was described by the same set of equations, each single fibre being characterized by a set of ten independent constants.     

The effect of thrombomodulin on the cleavage of fibrinogen and fibrinogen fragments by thrombin

Thrombomodulin acts as a linear competitive inhibitor of thrombin with respect to the substrate fibrinogen. In the present study the effect of thrombomodulin on the activity of thrombin with fragments of the A alpha and B beta chain of fibrinogen has been examined. The cleavage of fibrinopeptide A from the N-terminal disulphide knot, fragment 1-44 and fragment 1-51 of the A alpha chain was inhibited by thrombomodulin. The average value for the inhibition constant obtained with these substrates was 0.83 +/- 0.09 nM, which was in good agreement with the values obtained previously for the inhibition of thrombin by thrombomodulin with native fibrinogen as the substrate [Hofsteenge, J., Taguchi, H. & Stone, S. R. (1986) Biochem. J. 237, 243-251]. In contrast, the cleavage of fibrinopeptide A from fragment 1-23 and fragment 1-29 of the A alpha chain was not affected by thrombomodulin. Although the cleavage of the B beta chain in the intact fibrinogen molecule was inhibited by thrombomodulin [Hofsteenge, J., Taguchi, H. & Stone, S. R. (1986) Biochem. J. 237, 243-251], the release of fibrinopeptide B from the N-terminal disulphide knot and the N-terminal 118-residue fragment of the B beta chain was not inhibited by thrombomodulin. In addition, we determined the second-order rate constants of cleavage of these substrates using human thrombin. Fragments of the A alpha chain whose cleavage was inhibited by thrombomodulin were found to have values for kcat/Km that were within one order of magnitude of that for the native fibrinogen, whereas those for A alpha chain fragments whose cleavage was not inhibited by thrombomodulin were found to be more than two orders of magnitudes lower. From these results we conclude that only a relatively small portion of the A alpha chain of the fibrinogen molecule is responsible for the specific binding to thrombin that is affected by thrombomodulin. Moreover, residues 30-44 of the A alpha chain play an important role in this thrombin-fibrinogen interaction.     

A mutation in the small (alpha) subunit of glycyl-tRNA synthetase affects amino acid activation and subunit association parameters

A strategy was designed to isolate mutants of glycyl-tRNA synthetase that are altered at the amino acid binding site, including a class with altered amino acid specificity. For this purpose, the plasmid pBR322 was mutated so that the codon (AGC) of the active site Ser-68 in the beta-lactamase gene was changed to the glycine codon GGC to inactivate the encoded enzyme. Suppressors that increase the amount of beta-lactamase activity of the Gly-68 allele of beta-lactamase were isolated and some mapped to the gene encoding glycyl-tRNA synthetase (glyS). While in vitro misaminoacylation of tRNA(Gly) with serine was not detected for any of the mutants, glycyl-tRNA synthetase activity was altered. One severely affected glyS mutant (N302) was studied in more detail. For this mutant, a single Pro-61----Leu substitution in the alpha chain confers an elevation of the Km values for glycine (25-fold) and for ATP (45-fold) in the aminoacylation reaction, but only a minor perturbation of the Km for tRNA. There also was a severely reduced adenylate synthesis activity (greater than 100-fold). In addition, a nonlinear dependence between aminoacylation activity and enzyme concentration was observed which implies that the alpha chain Pro-61----Leu mutation has disrupted the functionally essential subunit interactions of the holoenzyme. The results of the preceding paper have shown that the alpha chain and parts of the beta chain are required for aminoacylation and adenylate synthesis activity. The results of this study suggest that the alpha chain specifically contributes to amino acid and to ATP binding in a way that is affected by proper subunit interactions.     

Expression of an alpha cardiac-like myosin heavy chain in muscle spindle fibres

In the present study we have investigated the reactivity of rat muscle to a specific monoclonal antibody directed against alpha cardiac myosin heavy chain. Serial cross sections of rat hindlimb muscles from the 17th day in utero to adulthood, and after neonatal denervation and de-efferentation, were studied by light microscope immunohistochemistry. Staining with anti-alpha myosin heavy chain was restricted to intrafusal bag fibres in all specimens studied. Nuclear bag2 fibres were moderately to strongly stained in the intracapsular portion and gradually lost their reactivity towards the ends, whereas nuclear bag1 fibres were stained for a short distance in each pole. Nuclear bag2 fibres displayed reactivity to anti-alpha myosin heavy chain from the 21st day of gestation, whereas nuclear bag1 fibres only acquired reactivity to anti-alpha myosin heavy chain three days after birth. After neonatal de-efferentation, the reactivity of nuclear bag2 fibres to anti-alpha myosin heavy chain was decreased and limited to a shorter portion of the fibre, whereas nuclear bag1 fibres were unreactive. We showed that a myosin heavy chain isoform hitherto unknown for skeletal muscle is specifically expressed in rat nuclear bag fibres. These findings add further complexity to the intricate pattern of isomyosin expression in intrafusal fibres. Furthermore, we show that motor innervation influences the expression of this isomyosin along the length of the fibres.     

Binding of staphylococcal cell surface polysaccharide to human fibrinogen

The interaction between the binding site of a polysaccharide (called compact colony forming active substance (CCFAS)), obtained from the cell surface of a strain of Staphylococcus, and human fibrinogen (HF) was investigated. The CCFAS was found to bind specifically to both the B beta and gamma chains of HF at pH 7.0 and 8.0, and the A alpha chain at pH 5.0. The binding of CCFAS with fibrinogen fragments obtained by digestion with plasmin were also investigated. Fragments with Mr of 55,000, 24,000, and 19,000 were the major bands precipitated by CCFAS at pH 7.0 and 8.0. Fragments with Mr of 85,000 and 75,000 bound to CCFAS at pH 5.0. Binding of CCFAS (7 micrograms) with fibrinogen could be inhibited by 1.2 micrograms of B beta chain and 1.5 micrograms gamma chain at alkaline pH or 6.2 micrograms of the A alpha chain at pH 5.0. CCFAS was, therefore, assumed to be specifically bonded with HF molecules, in the alkaline range at least, resulting in compact colony forming activity in serum soft agar and paracoagulation.     

Amino acid sequences of the aplpha and beta chains of adult hemoglobin of the tupai, Tupaia glis.

Globin prepared from hemoglobin of adult tupai (Tupaia glis) was separated into alpha and beta polypeptide chains by CM-cellulose column chromatography. The S-aminoethylated alpha polypeptide chain and S-carboxymethylated beta polypeptide chain were each digested with trypsin, and the sequences of all the peptides thus obtained were established. The ordering of these tryptic peptides in the alpha and beta polypeptide chains was deduced from the homology of their primary structures with that of human adult hemoglobin. In this way the primary structures of the alpha and beta polypeptide chains of tupai hemoglobin were established; 27 amino acids in the alpha polypeptide chain and 26 in the beta chain differ from those in human adult hemoglobin.     

Evidence for active half-molecules of alpha 2-macroglobulin formed by dissociation in urea

Urea caused dissociation of alpha 2-macroglobulin (alpha 2M) into half-molecules (two disulfide-bonded subunits) as revealed by gel electrophoresis. The fraction of whole molecules remaining decreased with increasing urea concentration. Half-dissociation occurred at about 2.2 M. The ability of alpha 2M to inhibit trypsin also decreased with increasing urea concentration, but the activity-urea curve was shifted to the right as compared to the dissociation-urea curve. Thus, at 3 M urea, gel electrophoresis showed only 6.6% whole molecules, whereas the trypsin inhibitory activity was 95% of that in buffer with no urea, suggesting that half-molecules retain activity. In addition, complexes formed in urea with 125I-labeled trypsin were observed to migrate as half-molecules even though only 50% of such complexes were covalent. These results are surprising in light of the report by Gonias and Pizzo [Gonias, S., & Pizzo, S. (1983) Biochemistry 22, 536-546] that half-molecules formed by mild reduction are active; reduction is assumed to divide the molecule along an axis orthogonal to the break caused by urea. This suggests that active half-molecules can be formed by splitting either the covalent or noncovalent bonds that hold the subunits together. A model is proposed that can account for this possibility. It has the same dimensions and symmetry as a previous model of Feldman et al. [Feldman, S.R., Gonias, S.L., & Pizzo, S.V. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 5700-5704] and accounts in a similar way for previous functional studies of the protein.(ABSTRACT TRUNCATED AT 250 WORDS)     

Fibre X-Ray and Conformational Study of the Binding of Metal Ions on DNA

Abstract

Results obtained from X-ray diffraction as well as from conformational analysis of Ag-DNA fibres are presented. For small percentages of Ag⁺ bound and high humidity, the B-DNA form is maintained. As the percentage of Ag⁺ is increased, the helical parameters of the B-DNA are modified. These modifications are directly related to the percentage of G—C bases. The periodicity of the DNA fibres are perturbed as Ag⁺ is mainly bound to G—C pairs and, thus, only the equatorial diffracted intensities can be compared to values calculated from molecular models. It is shown, by this way, that the first binding site is located on N7 of G. A second site is situated between N3 and N1 of the G—C pair, at the place of a hydrogen bond. A molecular model of the Ag-DNA complex is proposed and shown to be in agreement with experimental data. Results obtained allow to get some information on the binding of other ions such as Cu²⁺ and Hg²⁺ which give very little modification of the fibre X-ray patterns.     

Prediction of the secondary and tertiary structure of plastocyanin.

The amino acid sequences of nine plastocyanins were examined using four published methods for the prediction of secondary structure in proteins. The results of the four methods were combined in such a way as to maximize agreement, and the position of alpha helices, beta sheets, and beta turns in plastocyanin was predicted. From this result and other information, such as the position of conserved residues and the requirements for coordination of copper, a preliminary model for the mainchain folding of the molecule was presented.     

A histoenzymatic study of rat intrafusal muscle fibres

Summary The histochemical activities of myofibrillar adenosine triphosphatase (ATPase), succinic dehydrogenase (SDH) and alpha glycerophosphate dehydrogenase (-GPD) were studied in intrafusal muscle fibres of rat fast and slow muscles. The ATPase reaction was carried out after the three standard acid preincubations. The cold K₂-EDTA preincubated ATPase reaction product was similar to that seen following the regular or alkalipreincubated ATPase reaction, except that the intermediate bag fibres exhibited much higher activity after cold K₂-EDTA preincubation. Following either acetic acid solution or cold and room temperature K₂-EDTA-preincubation, followed by the ATPase reaction, chain fibres of the fast muscles vastus lateralis and extensor digitorum longus exhibited a very low amount of reaction product as compared with those of the slow soleus. Veronal acetate and K₂-EDTA preincubations (and equally preincubation in acetic acid solution) resulted in acid stable ATPase activity along the entire length of the typical bag fibres but only in the polar regions of the intermediate bag fibres. On the basis of differing -GPD reaction, two sub populations of nuclear chain fibres were discovered in one spindle. It is a matter of conjecture, to what extent the histochemical differences of intrafusal fibres from fast and slow muscles reflects functional distinctions in the response to stretch of muscle spindles from fast and slow muscles.     

Fibre composition and enzyme activities in five different muscles from the Svalbard reindeer

beta R fibres (type I) constitute less than 10% of the semimembranosus and longissimus dorsi muscles and about twice as much of the gluteobiceps and flexor hallucis. Except for longissimus dorsi, 50% or more consist of alpha W (type IIB) fibres--in semimembranous, as much as 70%. Despite the comparatively large content of alpha W fibres, both the oxidative capacity and the capacity to metabolize fatty acids is high. Furthermore, unexpectedly small differences in oxidative capacity between the three fibre types beta R, alpha R and alpha W (I, IIA and IIB) are revealed by histochemical staining. These results indicate a tendency to bring the three fibre types closer together as regards metabolic activities, as an adaptation to the relatively tranquil life of this animal. However, the large content of alpha W fibres does not accord well with this way of life, as they guarantee quick movements. The comparatively high oxidative capacity of the alpha W fibres in the Svalbard reindeer and the fact that during starvation it is primarily alpha W fibres that contribute to the energy supply by protein degradation may nevertheless account for their abundant occurrence.     

Backbone dynamics of SDF-1alpha determined by NMR: interpretation in the presence of monomer-dimer equilibrium

SDF-1alpha is a member of the chemokine family implicated in various reactions in the immune system. The interaction of SDF-1alpha with its receptor, CXCR4, is responsible for metastasis of a variety of cancers. SDF-1alpha is also known to play a role in HIV-1 pathogenesis. The structures of SDF-1alpha determined by NMR spectroscopy have been shown to be monomeric while X-ray structures are dimeric. Biochemical data and in vivo studies suggest that dimerization is likely to be important for the function of chemokines. We report here the dynamics of SDF-1alpha determined through measurement of main chain (15)N NMR relaxation data. The data were obtained at several concentrations of SDF-1alpha and used to determine a dimerization constant of approximately 5 mM for a monomer-dimer equilibrium. The dimerization constant was subsequently used to extrapolate values for the relaxation data corresponding to monomeric SDF-1alpha. The experimental relaxation data and the extrapolated data for monomeric SDF-1alpha were analyzed using the model free approach. The model free analysis indicated that SDF-1alpha is rigid on the nano- to picosecond timescale with flexible termini. Several residues involved in the dimer interface display slow micro- to millisecond timescale motions attributable to chemical exchange such as monomer-dimer equilibrium. NMR relaxation measurements are shown to be applicable for studying oligomerization processes such as the dimerization of SDF-1alpha.     

Click-evoked responses from the exposed intracranial portion of the eight nerve during vestibular nerve section: bipolar and monopolar recordings

We compare the click-evoked compound action potentials from the exposed intracranial portion of the eight nerve using bipolar and monopolar recording electrodes in patients undergoing vestibular nerve section. It is assumed that a bipolar recording electrode will only record propagated neural activity in the auditory nerve, whereas a monopolar recording electrode may in addition record electrical activity that is conducted passively to the recording site. The results of the present study confirm that the earliest detectable propagated neural activity in the intracranial portion of the auditory nerve occurs with a latency that is close to that of peak II of the brain-stem auditory evoked potentials, and the results also confirm that the late components in the click-evoked compound action potentials that have been demonstrated previously using the monopolar recording technique represent propagated neural activity in the auditory nerve. The results also indicate that the responses that are recorded by a bipolar recording electrode, when the small tips of which are placed on the eight nerve when it is relatively dry, represent only small populations of nerve fibers. Even when an attempt is made to align the two tips of a bipolar electrode with the course of the auditory nerve, this type of electrode may record from different populations of nerve fibers.     

A comparison of persistence-time estimation for discrete and continuous stochastic population models that include demographic and environmental variability

A discrete-time Markov chain model, a continuous-time Markov chain model, and a stochastic differential equation model are compared for a population experiencing demographic and environmental variability. It is assumed that the environment produces random changes in the per capita birth and death rates, which are independent from the inherent random (demographic) variations in the number of births and deaths for any time interval. An existence and uniqueness result is proved for the stochastic differential equation system. Similarities between the models are demonstrated analytically and computational results are provided to show that estimated persistence times for the three stochastic models are generally in good agreement when the models satisfy certain consistency conditions.     

Properties of membrane-bound sialyltransferase from rana temporaria liver]

It was demonstrated that microsomal membranes from frog liver contain at least two different sialyltransferases involved in the synthesis of alpha 2 leads to 3 and alpha 2 leads to 6 oligosaccharide isomers. Studies on acceptor specificity of the sialyltransferase system with respect to low molecular acceptors revealed its similarity to the mammalian sialyltransferase system. However, sharp distinctions were observed in sialylation of mammalian glycoproteins. It was assumed that that the disaccharide unit of the acceptor oligosaccharide chain is a structural element, which in necessary but not sufficient for glycoprotein recognition by sialyltransferases.