Relations between enzymatic and association reactions in the development of bovine fibrin clot structure

Development of fibrin clot structure was examined at pH 7.0, Γ/2 0.15, and 29 °C as a function of thrombin and fibrinogen concentrations. Parameters for the release of Apeptides, to give $\text{?}{}_{\mathrm{<mtext>A</mtext>}}$ were evaluated. Characteristics of time dependencies of development of turbidity, 90 ° light scattering, network, and compactible network were established. Mean mass/length ratios of fibrin in developing and mature networks were determined. Relationships between results combined with an inferred dependence of lateral interaction on release of B-peptides are used to disclose a model in which a protofibril network is formed first and the intrinsic length of this network (i.e., length exclusive of overlap or loose ends) determines network length, thus mean mass/length ratio, at maturity. Statements regarding initial protofibril network are: (i) A dominant group of $\text{?}{}_{\mathrm{<mtext>A</mtext>}}$-protofibrils appears first. With decreasing rate of production of $\text{?}{}_{\mathrm{<mtext>A</mtext>}}$ their average length increases and number decreases. (ii) Slower release of B-peptides produces $\text{?}{}_{\mathrm{<mtext>AB</mtext>}}$ whose fraction $\text{θ}{}_{\mathrm{<mtext>AB</mtext>}}\text{=}\text{?}{}_{\mathrm{<mtext>AB</mtext>}}\text{(?}{}_{\mathrm{A}}\text{+?}{}_{\mathrm{AB}}$) determines the occurrence of protofibril regions capable of contributing to a lateral interaction sufficiently stable for the formation of network. (iii) When dominant protofibrils attain a minimum combination of average length, number concentration, and frequency of occurrence of capable regions, an initial protofibril network is rapidly generated. (iv) Capable regions near protofibril ends are preferentially involved in initial network formation. (v) The initial network mesh size is large compared to average concomitant free protofibril length. (vi) With B-peptide release dependent on prior A-peptide release, protofibrils in the initial network have the highest capable region frequency, and this is maintained as lateral interaction progresses. Then, fibrin which is free at initial network formation and fibrin which is produced subsequently interact mainly to increase the mean mass/length ratio of initial network elements.     

Mechanism of action of thrombin on fibrinogen. Reaction of the N-terminal CNBr fragment from the Aalpha chain of human fibrinogen with bovine thrombin

The 51-residue N-terminal cyanogen bromide fragment from the Aα chain of human fibrinogen was isolated, and the Michaelis-Menten constants, K_m and k_cat, for its hydrolysis by bovine thrombin were determined. The measured values of K_m and k_cat are 4.7 × 10^?5m and 4.8 × 10^?10m [(NIH U/liter) sec]^?1, respectively. Since these values are similar to those for fibrinogen, it appears that the N-terminal CNBr fragment contains all amino acid residues whose interactions with thrombin account for the high specificity of this enzyme for fibrinogen.     

A pulsed N.M.R study of D2O bound to 1,2 dipalmitoyl phosphatidylcholine

Spin lattice relaxation times in both the lab and rotating frame, have been measured for deuterons (²H) in a number of unsonicated dispersions of 1,2 dipalmitoyl phosphatidylcholine in D₂O over a range of resonant frequencies from 13 MHz to 1 MHz for temperatures from ?20°C to 65°C.The proton (¹H) spin lattice relaxation time for the lecithin was measured for resonant frequencies of 8.5 MHz, and 40 MHz over a similar range of temperatures.The results agree with broadline measurements by Salsbury et al. [1], and for the liquid crystal phase are consistent with an anisotropic tumbling model of the water molecules bound to the lecithin headgroup. This tumbling occurs with correlation times of ≤10^?10 sec and ≈ 10^?6 sec about axes parallel to and perpendicular to the bisector of the D-O-D angle within a D₂O molecule, hydrogen bonded to the negatively charged phosphate headgroup.     

Control of the general amino acid permease of Penicillium chrysogenum by transinhibition and turnover

When nitrogen-starved mycelium of Penicillium chrysogenum is incubated with relatively high concentrations of labeled hydrophobic amino acids, influx is followed by efflux of the corresponding labeled α-ketoacid. In spite of the efflux, further transport activity is suppressed. Cell-free extracts contain a transaminase that accepts all those amino acids exhibiting α-ketoacid efflux. Transaminase activity is constitutive but is induced to a 2- to 3-fold higher level during a 2-hr preincubation period with a hydrophobic amino acid. Cycloheximide prevents efflux and also the induction of the transaminase. Cycloheximide itself stimulates a partial decay in transport activity but mycelium preincubated with l-leucine and cycloheximide together retain a greater fraction of the original transport activity than mycelium preincubated with l-leucine alone. The results suggest that transport is regulated partially by transinhibition but a significant part of the substrate-induced decay of transport activity is caused by either (a) the degradation of a permease component (perhaps facilitated by transinhibition), or (b) the induction by the substrate of a regulator protein (perhaps the transaminase).The uptake of labeled substrates by nutrient sufficient mycelium correlates well with lipid solubility of the substrates. This suggests that the nonsaturable uptake observed in these mycelia results from free diffusion of the uncharged species.     

A favourable assessment of the O.P.T.--histamine reaction in the method of von Redlich and Glick

During the course of an investigation of the properties of triglyceride lipase in nerve endings of the central nervous system (1) there arose a need for rapid determinations of a lipase in a large number of membrane preparations. This communication reports a procedure for the determination of glyceride lipase in which fatty acid, formed from a radioactive substrate by the lipase, is separated from glycerides on DEAE-cellulose paper.     

Mutagenesis by 4-nitrobenzofurazans and furoxans.

15 nitrobenzofurazans and 10 nitrobenzofuroxans synthesized primarily for testing as potential anti-rheumatic drugs were also tested for mutagenicity in Salmonella typhimurium strains TA98 and TA100. The method used involved placing each compound in a "well" cut out of a plate of selective medium previously seeded with the appropriate tester strain, and then adding a rat liver microsome/cofactor mixture to one of the two wells on each plate. This method is considerably cheaper and more convenient than the conventional agar overlay technique, but in the present series of experiments failed to detect 4 compounds which could be detected by the overlay technique. Using a combination of the two techniques, 21 of the 25 compounds tested were found to be mutagenic. All 10 benzofuroxans and 9 of the 15 benzofurazans were detected as direct-acting mutagens with at least one of the two tester strains. Two of the benzofurazans gave positive results only in the presence of rat liver microsomes, and hence are pro-mutagens. One of the 4 benzofurazans which gave negative results for mutagenicity in these tests was found to be an efficient inhibitor of a neutral protease activity found in rheumatic synovial fluid, and may therefore have some potential as an anti-rheumatic drug.     

The ontogeny of social relationships with group companions among free-ranging infant rhesus monkeys II. Differentiation and attractiveness

Infants are frequently with their mothers when troop members initiate interaction with them. To what extent are the infants' companions attracted specifically to them rather than to the mother? A simple method is presented for approaching this question and for assessing the extent to which the relationships of 11 free-ranging rhesus (Macaca mulatta) infants on Cayo Santiago have acquired qualities independent of (differentiated from) those of the mother. Companions of all ages tend to be attracted specifically to infants between 1 and 14 weeks of age and not simply to their mothers. However, this tendency is less marked for sibling companions than for more distantly related companions. No differences are found between infants of high- and low-ranking mothers. Infantile attractiveness is not necessarily sustained when infants are 17 to 30 weeks of age. The degree to which relationships with infant companions and with older female companions have, differentiated by 17 to 30 weeks is negatively related to the companion's age. Infants show early and increasingly marked tendencies to develop differentiated relationships with one another; however, they show no signs of doing so with adult female companions by 30 weeks of age.     

Analyzing the joint effects of two antibodies and the design of molecularly engineered vaccines

A new analytical approach to determine how antibodies relate to each other in producing immunity is presented. One purpose of this analysis is to decide on the antigenic composition of vaccines. Regression analyses and single discrete analyses are shown to be inappropriate to this task. The proposed analyses makes multiple cut points on two pre-exposure antibody levels. At each resulting discrete classification, additive and multiplicative interaction parameters are calculated. Various models of joint antibody action are shown to produce two general patterns of interaction terms with this type of analysis. One pattern characterizes situations where each antibody, or something substituting for the action of each antibody, is always needed to eliminate all infections. This may be because the antigens to which the antibodies are directed are on separate microbes or because microbes can only be neutralized by the joint action of both antibodies. A second pattern characterizes situations where both antibodies act cooperatively but given high enough levels only one may be needed. This may be because the antibodies have the same molecular effect or because they act by separate means against the same organisms in an innoculum.     

The ontogeny of social relationships with group companions among free-ranging infant rhesus monkeys I. Social networks and differentiation

Social networks of infant rhesus monkeys (Macaca mulatta) in a free-ranging, lineage-based group on Cayo Santiago are described by assessing the extent to which four measures of positive interaction between infants and finely-divided categories of companions are associated with (1) degree of relatedness through maternal lines; (2) sex of the companion; (3) age of the companion; and (4) dominance rank of the infant's lineage. The results suggest that the infant's social network mirrors that of its mother both in the first weeks of life and as late as 30 weeks of age. Infants have more positive social interaction with close kin than with distant kin or with unrelated individuals, and thus function as members of their lineage from the beginning. They associate more with female companions than with male companions, and more with younger immatures than with older immatures. Finally, infants in the top-ranking lineage spend more time with their own relatives than do infants in other lineages. The fact that these patterns change little as the infant gains independence from the mother supports suggestions that early maternal influence serves to pass on aspects of the mother's social network. It is suggested that the ontogeny of early social relationships resembles a process of differentiation.     

Conditions for the various types of co-operativity allowed by the adair,equation and their relation with the algebraic character of binding polynomials

A convenient way to obtain for any number, n, of sites, the functions of the constants of the Adair equation that decide the type of co-operativity of ligand binding to a non-dissociating protein is given and is illustrated by the examples n = 4 and n = 5. These functions are invariants of the binding polynomial and various of its derivatives.Although there are some simple sufficient conditions (inequalities relating successive Adair constants) for some co-operativity types, the full necessary and sufficient conditions even for uniform positive and negative co-operativity depend on very complicated functions of the constants for n > 4.However there are alternative ways of writing binding polynomials known as canonical forms. Up to at least n = 5, and probably beyond, the conditions that are complicated in terms of Adair constants are very simple in terms of the constants of canonical forms. For instance any fourth-degree polynomial can be written in the form p(x - α)⁴ + q(x - β)⁴ + 6μ (x - α)²(x - β)² although in three different ways. For one of these ways, the sign of μ distinguishes between mixed and uniform co-operativity. For any kind of mixed co-operativity μ > 0, while μ < 0 corresponds to uniform co-operativity. Advantages of the use of canonical forms are briefly commented on.     

Mössbauer studies on protoporphyrin IX iron(II) frozen solutions containing ligands that cause the iron to be in a five coordinate high spin iron(II) environment

Mössbauer parameters are presented for a number of protoporphyrin IX iron(II) complexes containing ligands that allow the iron to be in a five coordinate high spin iron(II) electronic environment. Such environments are characterised by large quadrupole splittings in the range 4.0 to 4.4 mm s^?1. These compounds have characteristic electronic spectra.The implications of catechol type ligands binding protoporphyrin IX iron II/III moieties are discussed.     

On the identity of the 640-nm component observed in chlorophyll b absorption spectra in vivo

Mathematical analysis of the results of mild acetone extraction of chloro-plast-fragment preparations from Ulva lactuca demonstrates that the 640-nm shoulder on the short-wave side of the red chlorophyll b absorption band is not due to this chlorophyll.

The analysis furthermore provides rather strong evidence that the 640-nm shoulder is correlated with an absorption band peaking around 682nm. It is suggested that the 640-nm component is due to the reaction center pigment of Photo-system II.     

Kinetics of photosynthetic membrane protein assembly in Rhodopseudomonas spheroides

Glycogen phosphorylase in cell-free extracts of Neurospora crassa is activated 10- to 15-fold by incubation with MgATP^2?. When the MgATP^2? is removed, the active form (a form) reverts to the inactive form (b form). The inactivation requires Mg²⁺ and is inhibited by NaF. The results confirm that Neurospora crassa glycogen phosphorylase exists in two interconvertible forms and strongly suggests that the interconversion is catalyzed by a kinase and phosphatase. The a form was partially purified. The enzyme has a molecular weight of 320,000. Uridine diphosphate glucose is a linear competitive inhibitor with respect to glucose-1-phosphate and a linear non-competitive inhibitor with respect to glycogen. Glucose-6-phosphate is a hyperbolic (partial) noncompetitive inhibitor with respect to all substrates in both directions. The b form of the enzyme in crude cell-free extracts is stimulated 2- to 3-fold by 5′-AMP. As the b form is purified, the 5′-AMP activation is diminished. The molecular weight of the partially purified “b” form was also 320,000.     

Protein symmetry and the co-operative ligand-binding behaviour predicted by allosteric Koshland models

It is shown that the nearest-neighbour interaction two-conformation allosteric models of Koshland, Nemethy & Filmer (1966) predict binding curves with a centre of symmetry when the protein is also symmetrical and induced-fit is assumed. When nonexclusive binding to both conformations is assumed, the models predict that the family of homotropic binding curves obtained by varying the heterotropic ligand has a centre of symmetry. It is argued that the symmetry or asymmetry of binding curves is the main experimentally verifiable prediction of allosteric models insofar as they are models of interaction between protein subunits.Symmetry in a binding curve greatly simplifies the analysis of cooperative behaviour. The co-operative features possible with a symmetric binding curve for a four-site protein are analysed. The sign of co-operativity may either be uniform or change twice as saturation increases; the conditions for the various possibilities are given. For example, in terms of the intrinsic binding constants per site A^∥₁, A2, etc. the necessary and sufficient condition for positive macroscopic co-operativity over the whole symmetric binding curve is A^∥₁≤ A2, A ^∥₁ ≤ A3 which should be contrasted with the obvious A^∥₁ ≤ Al, AZ ≤A^∥₃ (positive microscopic co-operativity) which is only a sufficient but not a necessary condition. A symmetric curve may have one or three, but no more, extrema of the “Hill coefficient” h. For three extrema a change of sign of microscopic (but not necessarily macroscopic) co-operativity is necessary but not sufficient. In the case where there are off-centre maxima of h, then h < 2 everywhere on the curve.The Koshland models predict qualitative and quantitative restrictions on the forms of binding curves additional to that of symmetry. In tetrameric induced fit models, negative co-operativity in the mid-region of the curve and positive co-operativity in the outside regions is possible, but not the opposite, and three extrema of h are possible with uniform positive but not with uniform negative co-operativity.Thus by recognising the importance of symmetry it has been possible to describe and categorise all the co-operativity behaviour possible with the most plausible Koshland tetrameric models. Several experimental examples of probable non-exclusive binding to proteins and enzymes are discussed, and it is shown how the symmetry point of view illuminates their interpretation.     

Structural aspects of thrombin specificity.

Computer-assisted comparisons were made of the X-ray coordinates of all homologous atoms in the serine protease derivatives tosyl chymotrypsin Aα, tosyl elastase, and diisopropylphosphoryl trypsin. The results provided further quantitative support for the belief that sequence homology in proteins results in close similarity of conformation. On this basis, inferences were drawn about the three-dimensional structure of the serine protease thrombin, for which atomic coordinates have not yet been determined experimentally. Further, it was concluded that the unique specificity of thrombin, i.e., its selective cleavage of certain ArgGly bonds in fibrinogen, is unlikely to be due to the insertions in the amino acid sequence of thrombin or to differences in sequence in the region of the active site and binding pocket. It is possible, however, that the elongated A chain appended to thrombin may be a source of this specificity.     

Limiting nutrient patchiness and its rôle in phytoplankton ecology

Limiting nutrient patchiness is examined as a factor affecting the community structure and species succession of natural phytoplankton communities held in ammonia limited continuous culture at a dilution rate of 0.3 day^?1. It was found that under a homogeneous distribution of the limiting nutrient members of genus Chaetoceros dominated and when ammonia was added daily (patchy distribution), Skeletonema dominated. Intermediate patchiness gave rise to an assemblage dominated by both Chaetoceros and Skeletonema. The nutrient uptake ability of each assemblage was determined three weeks after experiment initiation. Each assemblage was best able to optimize uptake of ammonia under its particular patchy nutrient regime. Optimization of a patchy environment took place by an increased maximal uptake rate (V_max) while optimization of a homogeneous environment appeared to take place by increased substrate affinity (i.e., low K_s).This study demonstrates that limiting nutrient patchiness can alter the relative abundance of populations within a community based on each population's ability to exploit the limiting resource under a particular degree of patchiness. We also show that coexistence of two populations might be expected due to the patchiness of a single limiting nutrient. The importance of patchiness in relation to other factors which determine community structure is discussed.     

Human thrombin: Partial primary structure

Human thrombin, prepared from an extrinsically activated prothrombin, was finally chromatographed on an affinity column of p-chlorobenzylamido-?-aminocaproyl agarose. After reduction and s-pyridylethylation, the A and B chains were separated. The A chain contains 36 residues and no carbohydrate and has a formula weight of 4093. Its sequence corresponds to 14–49 of the bovine A chain sequence with nine replacements. Human B chain contains 264 residues. The carbohydrate content is 3.5% neutral sugar, 2.6% glucosamine, and 1.5% sialic acid. High-speed sedimentation equilibrium in guanidine gave a minimum molecular weight of 33,500. Sequenator analysis yielded the first 50 amino-terminal residues and established the positions of three of the cyanogen bromide fragments. A fourth fragment lacked homoserine and was placed at the carboxyl-terminus. The four remaining fragments, comprising half of the B chain, were tentatively assigned positions by assuming homology with bovine thrombin and with pancreatic serine proteases. Within the B chain, the active site histidine and serine were both in highly conservative regions, and an Arg-Tyr bond has been identified as a biological degradation site. Sixty-nine percent of the primary structure of human thrombin was identified by sequenator analysis. In comparing this sequence with that reported for the bovine molecule, 26 replacements are present.