Mechanism of the binding of 2-(4'-hydroxyphenylazo)benzoic acid to bovine serum albumin

The mechanism of the binding of 2-(4'-hydroxyphenylazo)benzoic acid (HABA) to bovine serum albumin was studied by relaxation methods as well as the binding isotherm using gel chromatography. A single relaxation was observed over a wide range of HABA concentration except at the extremes of high concentration where another slow process was observed. The concentration dependence of the reciprocal relaxation time of the fast process decreased monotonically with increase in concentration of HABA at constant polymer concentration. The data were analyzed on the basis of Brown's domain structure model and were found to be consistent with a sequential binding mechanism. The azohydrazon tautomerism of HABA was identified with the intramolecular step of the complex. The activation parameters of the step, determined from the temperature dependence of the relaxation time of the fast process, showed that this step is rate limited by an enthalpy barrier in both forward and backward directions. Comparison of the activation parameters with those of other serum albumin-ligand systems suggests that there is an enthalpy-entropy compensation in the activation process of the intramolecular step with the compensation temperature at about 270 K; the enthalpy-entropy compensation is thought to be related to the hydrophobic nature of the ligand.     

Foraminifera may structure meiobenthic communities

The cosmopolitan benthic foraminiferan, Ammonia beccarii, is a fervent microfloral predator which often forms densely-populated 2–4 cm² aggregates in the field. Sediments within aggregate patches become extensively pelletized, mucus bound and depleted in microfloral food. On a West German Wattenmeer mudflat, copepodite and naupliar densities of a predominant harpacticoid copepod, Amphiascoides limicola, were significantly depressed in sediments containing>100 A. beccarii·3 cm^-2 suggesting a possible foraminiferal: copepod amensalism. Therefore, I cultured A. beccarii and A. limicola separately in sediment microcosms and then tested if A. limicola's seemingly negative reaction to sediments containing A. beccarii occurs under controlled conditions, how various life stages of A. limicola are affected, and what the repulsive mechanisms of A. beccarii may be. In natural field sediments seeded with a latin-square dispersion of sterile sediment patches containing 0 or 100 A. beccarii, mean A. limicola naupliar and copepodite densities were 2 to 6 times lower in Ammonia-rich patches than Ammonia-poor patches (i.e. patches containing <100 A. beccarii·3 cm^-2). Choice experiments directly testing potential A. beccarii inhibitory mechanisms were conducted with A. limicola copepodites: Cubic microcosms containing a latin-square patch dispersion of (1) sterile sediments (SS) seeded with 100 A. beccarii (low microflora), (2) SS bound with sterile mucus (0.0001%) (low microflora), (3) SS seeded with pelletized sediments (high microflora), and (4) SS seeded with mucus and pellets (high microflora), showed that copepodites colonized 12 & 3, but 1 & 4 were not significantly different. Mucus addition by itself, in the absence of pelletization and microflora, strongly facilitated colonization—as did addition of microfloral-rich pelletized sediments. Pelletization and mucousbinding combined, but with low microflora, were least attractive to A. limicola. Pelletization and mucous-binding combined, but with high microflora, were more attractive to A. limicola than its complement, but not significantly so. Thus A. beccarii's inhibition of A. limicola is probably not caused by sediment pelletization and simple mucous exudates but by local microfloral depletion within aggregate foraminiferal patches.Contribution No 774 of the Belle W. Baruch Institute for Marine Biology and Coastal Research     

Dispersion population models discrete in time and continuous in space

We analyze a discrete-time model of populations that grow and disperse in separate phases. The growth phase is a nonlinear process that allows for the effects of local crowding. The dispersion phase is a linear process that distributes the population throughout its spatial habitat. Our study quantifies the issues of survival and extinction, the existence and stability of nontrivial steady states, and the comparison of various dispersion strategies. Our results show that all of these issues are tied to the global nature of various model parameters. The extreme strategies of staying-in place and going-everywhere-uniformly are compared numerically to diffusion strategies in various contexts. We approach the mathematical analysis of our model from a functional analysis and an operator theory point of view. We use recent results from the theory of positive operators in Banach lattices.     

Proton transfer reactions in aqueous solutions of pyridoxamine phosphate

UV-visible and ¹³C NMR measurements described in the literature and our ³¹P NMR measurements support the following mechanism of proton transfer reactions in aqueous solutions of pyridoxamine phosphate: Only the tautomeric equilibrium between neutral form, A _N, and zwitterion, A _Z, which is analogous to the tautomeric equilibrium of 3-hydroxypyridine in aqueous solution, is important, and that equilibrium does not change upon the dissociation of the second phosphate proton. With these simplifying assumption, we have simulated the relaxation spectrum of the proton transfer reactions of pyridoxamine phosphate in water using parameters from analogous reactions and compared it with our ultrasound and temperature jump measurements. We have found that the relaxation process measured by the temperature jump experiment is mainly caused by the overall reaction A _N=A _Z (or A _N ^- =A _Z ^- ) and the ultrasound absorption at the isoelectric point between pK₂ and pK₃ is mainly caused by the overall reaction .     

Computation of relaxation matrix elements from incomplete NOESY data sets

Summary The structural determination of biological molecules in solution by NMR relies on the determination of a set of interatomic distances obtained by measurement of intramolecular nuclear Overhauser effects (NOE). It is shown in this paper that it is possible to obtain the accurate relaxation rate (and hence the interatomic distance) from the direct measurement of a single NOE signal. The precise analysis of a NOESY peak evolution with respect to the mixing time allows the evaluation of the relaxation parameters for the pair of spins under consideration. This is done without any assumption on the relaxation of unmeasured spins, or on the movement of the molecule. The theoretical basis of this method is presented. In order to evaluate the proposed method, a simulated case on the protein BPTI is studied, which shows that the method performs very well even in the case of noisy data sets.     

Species dispersion profiles of anthropogenic grasslands in the Italian Eastern Pre-Alps

A method is proposed to analyse the dispersion profiles of species in classes of environmental variables, based on the decomposition of the expected frequencies in contingency tables with many interacting species. The method has been applied to data of dominant or very frequent graminoid species in grasslands of the Natisone Valley (Friuli, Italy). It allowed to make predictions by removing the random component of variation.Nomenclature follows: P. Zangheri (1976). Flora Italica, CEDAM, Padua.The authors were recipients of an Italian CNR grant (E. Feoli) and a Canadian NSERC grant (L. Orlóci) during tenure of this project. The results are in partial fulfillment of a commitment to the Centro Regionale per la Sperimentazione Agraria per il Friuli-Venezia Giulia.     

Increased straying by adult steelhead trout,Salmo gairdneri,following the 1980 eruption of Mount St. Helens

Synopsis This paper describes the magnitude and geographic dispersion of adult steelhead trout, Salmo gairdneri, diverted from Columbia River tributaries which were impacted by the 1980 volcanic eruption of Mount St. Helens. Compelling circumstantial evidence suggests that for 1–3 yr after the eruption, large numbers of adult steelhead migrating toward affected tributaries entered two non-affected tributaries flowing into the Columbia River upstream of natal streams. Streams downstream of affected tributaries did not appear to receive substantial numbers of displaced fish. I estimated that the percentage of non-natal steelhead migrating into the lower portions of the nearest upstream river increased from 16% pre-eruption to 45% post-eruption. Winter-run steelhead strays probably originated from both the Cowlitz and Toutle rivers, whereas summer-run strays originated predominantly from the Toutle River. Increased natural production in tributaries resulting from the infusion of large numbers of strays was of insufficient magnitude to be detected by the methods of this study.     

Identification of ATP-sensitive Potassium Channel in Frog Ventricular Myocytes

Nuclear magnetic resonance (NMR) microimaging and proton relaxation times were used to monitor differences between the hydration state of the nucleus and cytoplasm in the Rana pipiens oocyte. Individual isolated ovarian oocytes were imaged in a drop of Ringer's solution with an in-plane resolution of 80 μm. Proton spin echo images of oocytes arrested in prophase I indicated a marked difference in contrast between nucleoplasm and cytoplasm with additional intensity gradations between the yolk platelet-rich region of the cytoplasm and regions with little yolk. Neither shortening τ_e (spin echo time) to 9 msec (from 18 msec) nor lengthening τ_r (spin recovery time) to 2 sec (from 0.5 sec) reduced the observed contrast between nucleus and cytoplasm. Water proton T₁ (spin-lattice) relaxation times of oocyte suspensions indicated three water compartments that corresponded to extracellular medium (T₁= 3.0 sec), cytoplasm (T₁= 0.8 sec) and nucleoplasm (T₁= 1.6 sec). The 1.6 sec compartment disappeared at the time of nuclear breakdown. Measurements of plasma and nuclear membrane potentials with KCl-filled glass microelectrodes demonstrated that the prophase I oocyte nucleus was about 25 mV inside positive relative to the extracellular medium. A model for the prophase-arrested oocyte is proposed in which a high concentration of large impermeant ions together with small counter ions set up a Donnan-type equilibrium that results in an increased distribution of water within the nucleus in comparison with the cytosol. This study indicates: (i) a slow exchange between two or more intracellular water compartments on the NMR time-scale, (ii) an increased rotational correlation time for water molecules in both the cytoplasmic and nuclear compartments compared to bulk water, and (iii) a higher water content (per unit dry mass) of the nucleus compared to the cytoplasm, and (iv) the existence of a large (about 75 mV positive) electropotential difference between the nuclear and cytoplasmic compartments. Received: 18 January 1996/Revised: 29 April 1996     

31P NMR Relaxation Does Not Affect the Quantitation of Changes in Phosphocreatine, Inorganic Phosphate, and ATP Measured In Vivo During Complete Ischemia in Swine Brain

Abstract: Ischemia-induced changes in ³¹P NMR relaxation were examined in 16 piglets. NMR spectra were acquired under control conditions and during complete cerebral ischemia induced via cardiac arrest. Changes in T ₁ were assessed directly in six animals during control conditions and after 30–45 min of complete ischemia when changes in brain P₁ levels had reached a plateau. The T ₁ for P₁ did not change, i.e., 2.3 ± 0.5 s during control conditions versus 2.4 ± 1.0 s during ischemia. To evaluate phosphocreatine and ATP, two types of spectra, with a long (25-s) or short (1-s) interpulse delay time, were collected during the first 10 min of ischemia (n = 10). Both types of spectra showed the same time course of changes in phosphocreatine and ATP levels, implying that the T ₁ relaxation times do not change during ischemia. There were no changes in the linewidths of phosphocreatine, ATP, or P₁ during ischemia, implying that the T *₂ values remain constant. Our results suggest that the ³¹P T ₁ and T *₂ for phosphocreatine, P_i, and ATP do not change during ischemia, and therefore changes in ³¹P NMR peak intensity accurately reflect changes in metabolite concentrations.     

Investigations of peptide hydration using NMR and molecular dynamics simulations: A study of effects of water on the conformation and dynamics of antamanide

Summary The influence of water binding on the conformational dynamics of the cyclic decapeptide antamanide dissolved in the model lipophilic environment chloroform is investigated by NMR relaxation measurements. The water-peptide complex has a lifetime of 35 s at 250 K, which is longer than typical lifetimes of water-peptide complexes reported in aqueous solution. In addition, there is a rapid intracomplex mobility that probably involves librational motions of the bound water or water molecules hopping between different binding sites. Water binding restricts the flexibility of antamanide. The experimental findings are compared with GROMOS molecular dynamics simulations of antamanide with up to eight bound water molecules. Within the simulation time of 600 ps, no water molecule leaves the complex. Additionally, the simulations show a reduced flexibility for the complex in comparison with uncomplexed antamanide. Thus, there is a qualitative agreement between the experimental NMR results and the computer simulations.