The conformation of the anticodon loop of yeast tRNAPhe in solution and on ribosomes.

The Y-base of yeast tRNA^Phe was replaced by the fluorophores 1-aminoanthracene or proflavine to yield derivatives which are active in all of the reactions of peptide elongation on reticulocyte ribosomes. The relatively long lifetime, higher quantum yield, and environmental sensitivity of 1-aminoanthracene make it a particulary useful adjunct to the Y-base in studying conformational changes in the anticodon region. The absorption and emission spectra of 1-aminoanthracene in tRNA in solutions in which it is active in peptide synthesis indicate that the probe is in a hydrophobic environment, apparently provided by stacking with the adjacent bases in the anticodon loop. The proflavine derivative, tRNA, was employed in iodide quenching, D₂O enhancement, and fluorescence depolarization experiments. The results indicate that the fluorophore in partially but not completely protected from the solvent. Anisotropy studies indicate that in solutions approximating those which support peptide synthesis on ribosomes, the probes have significant but restricted flexibility within the anticodon loop. Considered with nmr data and Y-base fluorescence from crystals of tRNA, the results indicate that the solution and crystal structures of tRNA^Phe are very similar. In turn, fluorescene from modified tRNA^Phe bound to ribosomes is similar to that observed in solution. It is of special significance for future experiments involving nonradiative energy transfer that these probles adjacent to the anticodon retain independent flexibility when bound to ribosomes with poly(U). The tRNA^Phe itself appears to be held rigidly on the ribosomes. It is concluded that within the limits dictated by the position and sensitivity of the probes used in this study, the mechanism of tRNA^Phe binding to ribosomes and the movement of tRNA and mRNA during the translocation steps of peptide synthesis can be interpreted in terms of the well-defined crystal structure of tRNA^Phe.     

Bioactive peptides: Conformational study of a cystinyl cycloheptapeptide in its free and calcium complexed forms

The disulphide bridged heptapeptide has been synthesized by classical solution methods. An ion binding study showed the peptide's ability to complex calcium ions with definite stoichiometry. The solution conformation of the peptide in its free and calcium-complexed form has been investigated by CD and nmr. The model structure derived from nmr data has been energy minimized and the resulting structure investigated by molecular dynamics simulation in water. The structure of the equimolar peptide/Ca^2? complex in acetonitrile at room temperature shows the presence of two transannular hydrogen bonds, with the formation of two ring structures of the C₁₀ (type VIa) and C₁₄ type. One peptide unit (Pro-Pro) is cis, all others are trans. © 1993 John Wiley & Sons, Inc.     

Stereochemical constraints in peptide design: Analysis of the influence of a disulfide bridge and an α-aminoisobutyryl residue on the conformation of a hexapeptide

The competing effects of a disulfide bridge and an α-aminoisobutyryl residue (Aib) in determining the conformation of a hexapeptide have been investigated, by comparing the cyclic disulfide (1) and the acylic peptide Boc-Cys(SBzl)-Val-Aib-Ala-Leu-Cys(SBzl)-NHMe ( 2 ). Previously published nmr and crystallographic studies [R. Kishore, S. Raghothama, and P. Balaram (1987) Biopolymers, Vol. 26, pp. 873–891; I. L. Karle, R. Kishore, S. Raghothama, & P. Balaram, (1988) Journal of the American Chemical Society Vol. 110, pp. 1958–1963] have established an antiparallel β-hairpin structure for 1 with a central Aib-Ala β-turn. A comparison of nmr data for 1 and 2 in chloroform and dimethylsulfoxide reveals that the acyclic peptide is conformationally labile. Evidence for a 3₁₀-helical conformation in CDCl₃ is obtained from sensitivity of NH chemical shifts to temperature and solvent perturbation and low J_HNCαH values. Studies in solvent mixtures establish a conformational transition on going from CDCl₃ to (CD₃)₂SO. The changes in NH nmr parameters, together with the observation of several interresidue C H-N_{i + 1}H nuclear Overhauser effects support a conformation having a central β-turn with extended arms in (CD₃)₂SO. A single Aib residue appears to stabilize a helix in apolar solvents, for the acyclic hexapeptide, while the disulfide bridge serves to lock the β-hairpin conformation. © 1993 John Wiley & Sons, Inc.     

Solution structure and dynamics of a glycoinositol phospholipid (GIPL-6) from Leishmania major

By use of a combination of ¹H nuclear Overhauser effect measurements, restrained molecular dynamics simulations, and ¹³C spin–lattice relaxation time measurements, the solution behavior of the glycan moiety of a complex glycoinositol phospholipid termed G1PL-6, from the protozoan parasite Leishmania major has been determined. The glycan moiety of GIPL-6 has the following structure, which is characterized by the presence of an internal β-galactofuranose residue: The glycan does not adopt a single conformation in solution, due to significant torsional variations about the two phosphodiester linkages and certain glycosidic linking in the molecule. The present of the internal galactofuranose residue results in an average solution conformation of the oligosaccharide, which resembles a “hairpin,” with the galactofuranose residue at the apex. © 1994 John Wiley & Sons, Inc.     

On the Effects of Departure from Normality on the F-Ratios in a Nested Random Effect Model by Mixture of Normals

In this paper we consider the following nested random effect model where the α_i's, the β_ij's and the e_ijk are independent random variables. By assuming that these variables follow a mixture of two normal densities, we study the effects of departure from normality on the classical JT-tests for variance components. It is shown that the departure from normality has little effects on the type 1 error and the power function; this indicates that the classical F-tests are quite robust with respect to departure from normality.     

Quasielastic light scattering from solutions of filamentous viruses. I. Experimental

Intensity fluctuations of laser light scattered from filamentous viruses Pf1 [length L (Å) × diameter d (Å) = 20,000 × 90], M13 (9000 × 90), potato virus X (5150 × 130), and tobacco mosaic virus (3000 × 180) in sucrose density gradients were measured with a photon correlation spectrometer over a range of scattering angles from 15° to 120°. The experimental data can be approximated by two exponential decays, “slow” and “fast.” The slow decay rate constant t corresponds to the translational diffusion D of the virus, i.e., t = K²D, where K is the magnitude of the scattering vector. The amplitude of the slow component, i.e., translational diffusion, remains greater than that of the fast component, even at high KL. The fast decay rate constant t is also proportional to K² for viruses such as Pf1, M13, and even potato virus X. In the companion paper, we shall attribute the amplitude enhancement of the translational diffusion to the coupling of its anisotropy to the rotational diffusion modes. In order to explain the excessive decay rates in the fast component, we need to consider the bending mode of rodlike viruses, especially in the longer viruses such as M13 and Pf1, in addition to the usually expected rotational diffusion modes.     

Identification of D-galactose-(1 → 7)-3-deoxy-d-manno-2-octulo-pyranosonate as component of the inner core region of escherichia coli EH 100 lipopolysaccharide

The dissaccharide D-galactosyl-3-deoxy-D-manno-2-octulosonic acid (Gal-KDO) from lipopolysaccharides (LPS) of the inner core region of the rough mutant EH100 of E. coli 0100 was isolated after mild acid hydrolysis of LPS by means of dialysis, ion-exchange chromatography, gelfiltration and high-voltage paper electrophresis. By chemical analysis galactose and KDO were identified in a molar ratio of approximately 1 : 1. ¹³C-NMR and ¹H-NMR studies, methylation analysis and GLC of the acetylated R.( – )-2-butyl-galactoside identified the structure .     

An Unbalanced Mixed Model with Random Effects Having Unequal Variances

Consider the mixed model where x_ijk's are known constants, β_k are unknown parameters and a_i, e_ij are random variables independently and normally distributed with zero means and variances σd_i and σ² respectively, where it is assumed that the d_i's are known (d_i >0). This paper presents procedures for estimating the variance components σ, σ², for testing the hypothesis σ = 0, and for making transformations to random variables with uncorrelated errors and constant variances in order to estimate as well as to test hypothesis concerning the β_k's in the model.     

Das Gesetz der absoluten Geschwindigkeiten biologischer Prozesse

The dependency of the velocity of biological processes from the temperature is described by the “Law of absolute velocity of biological processes”, which has only the individual parameters energy of activation ΔE, and the universal constant C. The law holds for all biological processes and is expressed by the equation: where C is: .     

Theoretical conformational analysis of a μ-selective cyclic opioid peptide analog

The allowed conformations of the μ-receptor-selective cyclic opioid peptide analog were determined using a grid search through the entire conformational space. Energy minimization of the 13-membered ring structure lacking the exocyclic Tyr¹ residue and the Phe³ side chain using the molecular mechanics program Maximin resulted in only four low-energy conformations. These four ring structures served as templates for a further energy minimization study with the Tyr¹ residue and Phe³ side chain added to the molecule. The results indicated that the Tyr¹ and Phe³ side chains enjoy considerable orientational freedom, but nevertheless, only a limited number of low-energy side-chain configurations were found. The obtained low-energy conformers are discussed in relation to various proposed models of the bioactive conformation of enkephalins and morphiceptin.     

The Influence of Ecological Factors on Detecting Drumming Ruffed Grouse

Abstract: We surveyed drumming ruffed grouse (Bonasa umbellus) to estimate the probability of detecting an individual, and we used Bayesian model selection to assess the influence of factors that may affect detection probabilities of drumming grouse. We found the average probability of detecting a drumming ruffed grouse during a daily survey was 0.33. The probability of detecting a grouse was most strongly influenced by the temperature change during a survey (_{temp change} = 0.23, 95% probability interval [PI] = 0.13 ≤ ≤ 0.33) and its interaction with temperature at the start of the survey (_interaction = 0.01, 95% PI = 1.42 × 10⁻³ ≤ ≤ 0.03). Although the best model also included a main effect of temperature at the start of surveys, this variable did not strongly correlate with detection probabilities (_{start temp} = −0.03, 95% PI = −0.06 ≤ ≤ 9.80 × 10⁻⁵). Model assessment using data collected at other sites indicated that this best model performed adequately (i.e., positive correlation between observed and predicted values) but did not explain much of the variation in detection rates. Our results are useful for understanding the historical drumming index used to assess ruffed grouse populations and for designing auditory surveys for this important game bird.     

Crystallization and preliminary X-ray analysis of Escherichia coli methionyl–tRNA formyltransferase

Methionyl–tRNA formyltransferase from Escherichia coli, a monomer of 34kDa, was overexpressed from its cloned gene fmt (Guillon, J.M., Mechulam, Y., Schmitter, J.M., Blanquet, S., and Fayat, G., J. Bacteriol. 174:4294–4301, 1992) and crystallized using ammonium sulphate as precipitant. The crystals are trigonal and have unit cell parameters a = b = 151.0Å, c = 81.8Å. They belong to space group P3₂21 and diffract to 2.0Å resolution. The structure is being solved by multiple isomorphous replacement. © 1996 Wiley-Liss, Inc.     

Depolarized light scattering by amides and peptides

The Rayleigh ratios R_H have been measured for the depolarized scattering dilute solutions of N-ethylacetamide (EA), N-methylpropionamide (MP), and N-acetyl-pyrrolidine (AP) in P-dioxane, and dilute aqueous solutions of N-methylacetamide (MA), N,N-dimethylacetamide (DMA), EA, and MP. Squares of the optical anisot-ropies γ of the amides are obtained through extrapolation of these mesurements to infinite dilution. Values of γ² found for EA and MP in dioxane are in good agreement with calculations based principally on the previously evaluated polarizability tensor of the amide group in conjunction with C? C and C? H bond polarizabilities. The calculations also involve averaging over all conformations, each being weighted according to the estimated conformational energy. The mean-squared optical anisotropies (γ²) of the oligoglycines and oligoalanines are calculated by similarly averaging over all skeletal conformations. The anistropic polarizability tensor \documentclass{article}\pagestyle{empty}\begin{document}$ \hat \alpha $\end{document} for the prolyl structural unit is derived for γ² for AP. The much larger optical anisotropies exhibited by the amides when dissolved in water as compared with those observed in dixane are discussed.     

Homologous priming in chemotactic peptide-stimulated neutrophils

The kinetics and dose-dependence of activation of human neutrophils exposed to sequential additions of the chemotactic peptide n-formyl-methionyl-leucyl-phenylalanine (fMLP) have been investigated by multiwell microplate assays. Treatment of neutrophils with medium–high doses (from 10^?8 to 5 × 10^?7 M) of fMLP caused activation of superoxide anion (O) production, but prevented further activation by a subsequent addition of an optimal dose (from 10^?7 M to 5 × 10^?7 M) of fMLP. These findings represent an example of cell desensitization, or adaptation. However, neutrophils treated with low, sub-stimulatory doses (from 10^?10 to 5 × 10^?9 M) of the peptide and then treated with optimal doses of fMLP exhibited an O production that was two to three-fold higher than that induced by the same optimal doses on untreated cells. A similar phenomenon of homologous priming of the oxidative metabolism of neutrophil has not previously been described or characterized. Priming was maximal after about 30 min of incubation with fMLP, which differed from desensitization, which required only a few minutes. Homologous priming was not confined to O production, but was also observed with the release of the granule enzyme, lysozyme. Low doses of fMLP were also capable of triggering an increase of intracellular free Ca²⁺ and of fMLP membrane receptors, which are possible mechanisms responsible for priming.     

Critical oxygen tension increases during digestion in the perch Perca fluviatilis

Oxygen uptake () and critical oxygen tension (P_crit) were measured in resting perch Perca fluviatilis that were either fasting or digesting. Digestion caused to double (from 61 to 117 mg O₂ kg^?1h^?1) and was associated with a rise in P_crit (from 3·4 to 4·9 kPa), showing that the animal's digestive state must be considered when assessing the effect of hypoxia in natural conditions, and when defining optimal oxygen conditions in aquaculture.     

The solution conformation of malformin A

Solution conformations of the cyclic pentapeptide plant-hormone malformin A, whose conformational freedom is constrained by an intramolecular disulfide bridge, are derived and presented here. The nmr and CD data of Ptak are used to place restrictions on the search for possible malformin A solution conformers of low energy. Only two distinct conformers were found to be consistent with Ptak's data. Both structures are characterized by an internally buried (solvent-shielded) D -Cys² amide proton, a seven-membered (1–3)hydrogen bond between (N–H) and (O?C), and a disulfide bridge conformation with a P chirality as manifested in the nmr study by the temperature independence of the amide proton chemical shifts for the D -Cys² and D -Leu⁴ residues and the negative sign of the long wavelength maximum in the CD spectrum, respectively. Inspection of space-filling molecular models of both structures indicates severe steric barriers to their rapid interconversion. Thus, it appears that only one of the two conformers may be present in solution. The difference in their calculated dipole moments (4.6 and 6.9D) suggests an experimental method for distinguishing between the two proposed solution structures.     

Transfer function matrix of the continuous cultivation system of Morchella crassipes in ammonia base waste sulfite liquor

A continuous stirred tank fermentor (CSTF) used for cultivation of the fungus Morchella crassipes in ammonia base waste sulfite liquor (NH₃-WSL) was considered as a multivariable linear system around its operating point. Pulse testing on the inputs (inlet jacket temperature, inlet pH, inlet substrate concentration) and their responses at the outputs (biomass, outlet temperature, outlet jacket temperature, outlet pH, outlet substrate concentration) were used for numerical determination of the transfer function matrix:      

Effects of temperature on microbial ethanol production. II. A thermodynamic interpretation of the temperature profile curve of ethanol production

An attempt is made to give a thermodynamic interpretation of the complete temperature profile curve of ethanol formation. Taking into consideration an enhancing competition between thermal activation and thermal deactivation of ethanol formation at increasing temperatures and supposing that the ethanol production is affected by a reversible and an irreversible term of thermal deactivation of a modified ARRHENIUS equation being current for the total biokinetic sphere may be derived: . The quantities ΔH and ΔH^D_2T are identical with the temperature functions of the change of entropy caused by reversible and irreversible deactivation of ethanol formation, respectively. Accordingly for the yeast strain Saccharomyces cerevisiae Sc 5 the calculated entropy coefficients of reversible and irreversible thermal deactivation of ethanol formation amount to C = (0.245± 0.013) kJ/mol · deg.² and C = (1.657 ± 0.046) kJ/mol · deg.².     

Polynucleotides. XI. Thermodynamics of (A) N -2(U) infinity from the dependence of T m N on oligomer length

The variation in the helix-coil transition temperature, T_m^N, with oligomer length, N, for the system ((I)) has been examined. The results for N = 4-13, measured in 0.2M Na+, have been analyzed in terms of the expression of Blake (1972): ((II)) where c_m is the free oligomer concentration at T_m^N, and V_r^f is the thermodynamic free volume available to a helical base-triplet residue. The correlation coefficient for the fit to expression (II) of data obtained over a 50° temperature range is 0.997 when ΔH_r = ?12.6 kcal/mole of base-triplets (independent of oligomer length (N ? 4) or temperature), the value previously obtained from both calorimetry of (A)_∞·2(U)_∞ and (A)₄ concentration dependence of T_m. It is found that V_r^f = 8.0 × 10^?4 1/mole (± 30%) or 1.33 ų per helical base-triplet, and is constant with temperature. A maximum value for V_r^f of 21.0 × 10^?4 1/M (± 1.3%), equivalent to 3.54 ų per helical basetriplet is obtained by the same treatment of the helix-coil transition data for the three-stranded helix formed by adenosine (N = 1) and 2(U)_∞ obtained by Davies and Davidson (1971).     

Confidence Estimation of an Unknown Component of the Vector of Regressor Variables in Multivariate Linear Regression

The model used in this paper is Y = Xβ, where with unknown x₀. Estimators of x₀ are derived by putting β_mx₀ =β_m+1 regarding β_m+1 as a new unknown parameter. Formally we use the model Y = X₁β₊ + e where β′₊ = (β₀, …β_m+1 and Then β_m+1/ β_m is a point estimator of x₀. Assuming normality for e and taking the random variable z=β_mx₀?β_m+1 we get a t-distributed variable and finally a confidence estimator of x₀. The formulas are applied in dose response relations in antibiotic assays refering to a standard. Now we can take into account not only the dependence on the dose/concentration but also on the position on the test agar plate where the test solution is filled in. As a consequence the confidence interval of the unknown dose/concentration x₀ becomes shorter and by it the statements more precise.