The polar co-ordinate model for pattern regulation in epimorphic fields: A critical appraisal

The polar co-ordinate model for pattern regulation in epimorphic fields, as first proposed by French, Bryant & Bryant (1976), belongs to a general class of models employing two co-ordinates for describing the field value distribution over a monolayer of cells.I first analyse the constraints imposed by the use of polar co-ordinates for biological modelling. These constraints entail: distinction of the actual and derived spaces for the field with their specific and characteristic mapping modes; representation of the field value or a measure of the morphogenetic activity at various positions in the actual space by two polar co-ordinates—the phase or angle and the radius—in the derived space; and attribution of a singular property to the origin in the derived space, which ought to be mapped onto a putative field centre in the actual space.Upon reformulating the polar co-ordinate model while adhering to these constraints, one realizes that the choice of the shortest route between two points in the derived space applies only to the angular, and not to the radial, co-ordinate. Hence the shortest route between two points cannot be conceived as a straight line connecting them.If we assume that cells have certain limits in resolving differences in the field value, the field will virtually fall into territories of distinctive field values, each of which might encompass more than one cell; cells that lie within a single territory should be mutually interchangeable for prospective developmental pathways which may themselves diversify. The central postulate of the model is that disparate field values brought in apposition will induce a field value intercalation through cell proliferation to restore an unbroken sequence of field values for the newly emerging array of territories. This is assumed universally for the angular component of the field value but it need not apply to the radial component.It follows that angular territories meeting at the field centre will produce a central discontinuity of the field value, leading to a perpetual angular intercalation unless some theoretical provision is made. This may be resolved by any ad hoc hypotheses but also by introducing the concept of degeneracy towards the field centre of the angular co-ordinate down to three distinctive values at the innermost level of radial territories. One can then deduce and generalize various empirically recognized behaviours of epimorphic fields. These include the shortest intercalation rule (which may be modified into the more generally applicable, minor-in-major rule), and the distal transformation and so-called complete circle rules (which may now be unified into the more feasible distalization rule proposed by Bryant, French & Bryant, 1981).The models are assessed against various experimental observations mainly for theoretical consistency. A series of experimental tests for various theoretical alternatives are suggested. This work has simply explored the internal logic of the polar co-ordinate model and no suggestion is made, at this stage, to distinguish different families of alternative models for epimorphic systems on experimental grounds.     

X-ray diffraction study of the molecular association in aqueous solutions of d-fructose, d-glucose,and sucrose

X-ray diffractograms of aqueous solutions of d-fructose, d-glucose, and sucrose, and of two amorphous “solid” forms of these carbohydrates are recorded in the angular range of O 2-16°. The formation, in these diffractograms, of one or two intensity maxima as the concentration is varied is interpreted in terms of modification of the molecular association. A model is proposed that takes account of the state of organization of the solutions of the three sugars as a function of the concentration. Sucrose shows an “anomaly”, as it is the only sugar to establish intramolecular bonds. The number of these intramolecular bonds also depends on the concentration.     

Angular Circulation Speed of Tablets in a Vibratory Tablet Coating Pan

In this work, a single tablet model and a discrete element method (DEM) computer simulation are developed to obtain the angular circulation speed of tablets in a vibratory tablet coating pan for range of vibration frequencies and amplitudes. The models identify three important dimensionless parameters that influence the speed of the tablets: the dimensionless amplitude ratio (a/R), the Froude number (aω ²/g), and the tablet–wall friction coefficient, where a is the peak vibration amplitude at the drum center, ω is the vibration angular frequency, R is the drum radius, and g is the acceleration due to gravity. The models predict that the angular circulation speed of tablets increases with an increase in each of these parameters. The rate of increase in the angular circulation speed is observed to decrease for larger values of a/R. The angular circulation speed reaches an asymptote beyond a tablet–wall friction coefficient value of about 0.4. Furthermore, it is found that the Froude number should be greater than one for the tablets to start circulating. The angular circulation speed increases as Froude number increases but then does not change significantly at larger values of the Froude number. Period doubling, where the motion of the bed is repeated every two cycles, occurs at a Froude number larger than five. The single tablet model, although much simpler than the DEM model, is able to predict the maximum circulation speed (the limiting case for a large value of tablet–wall friction coefficient) as well as the transition to period doubling.     

The absolute configuration of phaseic and dihydrophaseic acids

A sample of phaseic acid methyl ester (5 mg, isolated from tomato plants fed (±)-abscisic acid, was reduced to a mixture of the epimeric dihydrophaseates which were separated by TLC. The more polar epimer was identical with the dihydrophaseate isolated from beans by Walton et al. [14]. Comparison of the NMR and IR spectra (H-bonding) of the two epimers shows the secondary hydroxyl of the less polar epimer is cis to the oxymethylene group, which is cis to the tertiary hydroxyl group. The absolute configuration of this centre is known so the absolute configuration of phaseic acid can be deduced. Phaseic acid is (−)-3-methyl-5{8[1(R), 5(R)-dimethyl-8(S)-hydroxy-3-oxo-6-oxabicyclo-(3,2,1)-octane]} 2-cis-4-trans-pentadienoic acid and both it and the reduction products exist in chair conformations. The more polar epimer isolated by Walton et al. is (−)-3-methyl-5{8[3(S,8(S)-dihydroxy-1(R,5(R)-dimethyl-6-oxabicyclo-(3,2,1)-octane]}2-cis-4-trans-pentadienoic acid. It is suggested that the less polar epimer should be referred to as epi-dihydrophaseic acid.     

Impact of transverse magnetic fields on dose response of a nanoDot OSLD in megavoltage photon beams

PurposeWe investigated the impact of transverse magnetic fields on the dose response of a nanoDot optically stimulated luminescence dosimetry (OSLD) in megavoltage photon beams.MethodsThe nanoDot OSLD response was calculated via Monte Carlo (MC) simulations. The responses R_Q and R_Q,B without and with the transverse magnetic fields of 0.35–3 T were analyzed as a function of depth at a 10 cm × 10 cm field for 4–18 MV photons in a solid water phantom. All responses were determined based on comparisons with the response under the reference conditions (depth of 10 cm and a 10 cm × 10 cm field) for 6 MV without the magnetic field. In addition, the influence of air-gaps on the nanoDot response in the magnetic field was estimated according to Burlin’s general cavity theory.ResultsThe R_Q as a function of depth for 4–18 MV ranged from 1.013 to 0.993, excepting the buildup region. The R_Q,B increased from 2.8% to 1.5% at 1.5 T and decreased from 3.0% to 1.1% at 3 T in comparison with R_Q as the photon energy increased. The depth dependence of R_Q,B was less than 1%, excepting the buildup region. The top air-gap and the bottom air- gap were responsible for the response reduction and the response increase, respectively.ConclusionsThe response R_Q,B varied depending on the magnetic field intensity, and the variation of R_Q,B reduced as the photon beam energy increased. The air-gaps affected the dose deposition in the magnetic fields.     

The use of liquid polyacrylamide in electrophoresis: III. Properties of liquid polyacrylamide in the presence of cellulose acetate

Solutions of uncross-linked liquid polyacrylamide (LPA) stabilized by cellulose acetate are shown to represent efficient molecular sieves for RNA and for sodium dodecyl sulfate-protein complexes. Endosmosis and evaporation have to be considered to obtain corrected estimates of mobilities of the macro-ions. The efficiency of molecular sieving is strongly influenced by the chain length of the single polymer molecules. This can be shown both in terms of the steepness of the relationship between logarithm of molecular weight and mobility and in the relationship between log (K_R) and log molecular weight. Comparable chain length effects are found in cross-linked polyacrylamide, suggesting a common mechanism of action of the two electrophoretic sieving media. The correlation of polymer viscosity and of the impedance towards migration of macro-ions, as demonstrated by LPA-electrophoresis, suggests the participation of hydrodynamic interactions in the molecular sieving process.     

Aqueous chlorination and ozonation studies. I. Structure-toxicity correlations of phenolic compounds to Daphnia magna

A correlation showing the dependency of the observed biological activity (LC₅₀) of a series of phenols to the free energy related terms, π, F and R (field and resonance), which are specific for each compound, has been observed for the freshwater invertebrate, Daphnia magna. A series of 14 phenols was investigated and with F and R considered to be additive terms the following correlation was obtained. Log 1/c = 0.500 π + 0.453 F + 0.636 R + 3.731 r = 0.978 In those phenols containing chlorine it was noted the toxicity increased with increased chlorine content.     

Consideration of digitization precision when building local coordinate axes for a foot model

This study investigated whether points digitized for the purpose of embedding coordinate systems into the foot accurately represented the orientation of the bone described. Eight complete data sets were collected from 9 adult cadaver specimens. Palpable landmarks defined 5 segments to include the calcaneus, navicular, medial cuneiform, first metatarsal, and hallux. With use of the Flock of Birds electromagnetic motion tracking device, a single examiner digitized a minimum of 3 points for each segment. Coordinate definitions followed the right-hand rule, with left-sided data converted to right-sided equivalency. Local axes were created where X projected approximately forward, Y upward, and Z laterally. Matrix transformation computations calculated the angular precision in degrees between coordinates built from points digitized pre- and post-dissection of surface tissues covering bone. The condition of post-dissection was considered the criterion standard for comparison. Change about the X-axis represented the angular precision of the coordinate in the frontal anatomical plane; Y-axis in the transverse plane; Z-axis in the sagittal plane. The calcaneus and navicular coordinate axes changed by an average of <3° across conditions. Mean coordinate angulation of the cuneiform X, Y, Z axes changed by 6.0°, 4.6°, 11.9°, respectively. Change in coordinate angulation was largest for the X-axis at the first metatarsal (48.6°) and hallux (36.5°). A two-way repeated measures ANOVA found a significant interaction between the axis and segment (F=8.87, P=0.00). Tukey post-hoc comparisons indicated the change in coordinate angulation at the X-axis for the cuneiform, metatarsal, and hallux to be significantly different (P <0.05) from the calcaneus and navicular. The X-axis of the first metatarsal and hallux was different from all other axis-segment combinations except for the Z-axis of the cuneiform. Differences in locating landmarks reduced angular precision of the coordinate axes most in the smallest foot segments where points digitized were located close together. We can recommend the proposed landmarks for the calcaneus and navicular segments, but kinematics determined about the coordinate axes for the small sized medial cuneiform, and the long (X) axis for the first metatarsal and hallux have excessive error.     

Precision of sodium dodecyl sulfate-polyacrylamide-gel electrophoresis for the molecular weight estimation of a membrane glycoprotein: studies on bovine rhodopsin.

Criteria for assessing the precision and accuracy of methods for estimation of molecular weight for proteins using sodium dodecyl sulfate-polyacrylamide-gel electrophoresis have been applied to rhodopsin from bovine visual cell outer segment membranes. Various methods of preparing this hydrophobic protein for electrophoresis differ in their ability to solubilize and disaggregate polypeptide constituents of the outer segment membrane, with resultant variations in the pattern of protein bands and the apparent molecular weight of rhodopsin. Even with optimal solubilization and disaggregation, the behavior of rhodopsin relative to a series of standard proteins is such that the apparent molecular weight decreases systematically from 40,400 to 34,500 as the acrylamide concentration increases from 4 to 10%. As demonstrated by Ferguson plots of logR_f vs gel concentration and split gel experiments, this discrepancy is explained by the fact that the extrapolated R_f for zero gel concentration (Y₀) for rhodopsin is significantly lower than the Y₀'s for the soluble proteins used as molecular weight standards. In such cases, a possibly more reliable molecular weight estimate is obtained by plotting the retardation coefficient (K_R) vs molecular weight. This method yields a value of 29,500 ± 1000 for bovine rhodopsin if only the errors in measurement of R_f are considered and a quadratic relationship between K_R and molecular weight is used. Using weighted linear regression for K_R vs molecular weight, we obtain a molecular weight estimate of 32,700 ± 5000 when the uncertainty in the calibration curve is considered. Because of uncertainties regarding the detergent-binding properties of rhodopsin and the relationship of its Stokes radius to its molecular weight by comparison with the soluble protein standards, these values must be viewed with caution.     

Molecular mechanism for dominance of a mutant allele of an ATP-dependent protease

We have demonstrated that the lon⁺ (capR⁺) ATP-hydrolysis-dependent protease is inhibited by the addition of an enzymatically inactive mutant form of the protein (capR9 protein). The enzymatic activity of the capR⁺-capR9 protein mixture is also more stable to heat than the capR⁺ protein alone indicating that hybrid molecules are formed. Independent measurements demonstrated that the lon⁺ ATP-hydrolysis-dependent protease is a tetramer of identical 94 × 10₃ molecular weight monomers. The pattern of defective subunit (capR9) inhibition indicates only tetramers containing three capR9 monomers and one capR⁺ monomer are inactive, i.e. two or more capR⁺ monomers are required for a tetramer to act as an ATP-hydrolysis-dependent protease. Two molecular mechanisms to explain the dominance of a mutant allele, termed anticomplementation, are considered.     

Plasma equilibrium in axisymmetric open divertor configurations

The equilibrium of a plasma with isotropic pressure in a periodic divertor configuration with a poloidal magnetic field is calculated. The issue of how the plasma equilibrium changes as the parameter β≡8πp/B ² increases is considered for a fairly representative class of pressure profiles p(ψ) (where ψ is the flux coordinate). It is shown that the plasma can be in equilibrium up to β values (in terms of the vacuum magnetic field at the divertor axis) on the order of unity.     

Genetic mapping of rust resistance genes in confection sunflower line HA-R6 and oilseed line RHA 397

Few widely effective resistance sources to sunflower rust, incited by Puccinia helianthi Schwein., have been identified in confection sunflower (Helianthus annuus L.). The USDA inbred line HA-R6 is one of the few confection sunflower lines resistant to rust. A previous allelism test indicated that rust resistance genes in HA-R6 and RHA 397, an oilseed-type restorer line, are either allelic or closely linked; however, neither have been characterized nor molecularly mapped. The objectives of this study are (1) to locate the rust resistance genes in HA-R6 and RHA 397 on a molecular map, (2) to develop closely linked molecular markers for rust resistance diagnostics, and (3) to determine the resistance spectrum of two lines when compared with other rust-resistant lines. Two populations of 140 F_2:3 families each from the crosses of HA 89, as susceptible parent, with HA-R6 and RHA 397 were inoculated with race 336 of P. helianthi in the greenhouse. The resistance genes (R-genes) in HA-R6 and RHA 397 were molecularly mapped to the lower end of linkage group 13, which encompasses a large R-gene cluster, and were designated as R _13a and R _13b, respectively. In the initial maps, SSR (simple sequence repeat) and InDel (insertion and deletion) markers revealed 2.8 and 8.2 cM flanking regions for R _13a and R _13b, respectively, linked with a common marker set of four co-segregating markers, ORS191, ORS316, ORS581, and ZVG61, in the distal side and one marker ORS464 in the proximal side. To identify new markers closer to the genes, sunflower RGC (resistance gene candidate) markers linked to the downy mildew R-gene Pl ₈ and located at the same region as R _13a and R _13b were selected to screen the two F₂ populations. The RGC markers RGC15/16 and a newly developed marker SUN14 designed from a BAC contig anchored by RGC251 further narrowed down the region flanking R _13a and R _13b to 1.1 and 0.1 cM, respectively. Both R _13a and R _13b are highly effective against all rust races tested so far. Our newly developed molecular markers will facilitate breeding efforts to pyramid the R ₁₃ genes with other rust R-genes and accelerate the development of rust-resistant sunflower hybrids in both confection and oilseed sunflowers.     

Theoretical study of the binding site and mode of action for photosystem II herbicides

Several features of a proteinaceous binding site and a molecular mode of action are proposed for photosystem II (PS II) herbicides based upon a variety of experimental and theoretical evidence. Experimental studies have established that PS II herbicides bind non-covalently to a 32 kdalton protein in the PS II complex and inhibit electron transfer between the first quinone (Q) and the second quinone (B) on the reducing side of PS II. The herbicides each contain hydrophobic components as well as a flat polar component with a dipole moment in the range of 3–5 Debyes. The primary function of the hydrophobic components is to increase the lipid solubility of the entire herbicide molecule; the secondary function of the hydrophobic components is to fit the hydrophobic surface of the herbicide binding site. It is proposed that the flat polar component binds electrostatically at a highly polar protein site, probably a protein salt bridge or the terminus of a protein alpha helix. Further, it is proposed that the PS II herbicides shift the equilibrium Q^?Bz?QB^? to the left (i) by reducing the magnitude of an anion-stabilizing electric field across the B-binding site, or (ii) by inhibiting the conformational relaxation or protonation of the PS II protein in response to reduction of B to B^?, or (iii) by displacing the quinone head of B from its binding site. Ab initio molecular quantum mechanical calculations have been carried out to investigate the electrostatic interactions in specific herbicide-binding site models.     

(R)-Desmolactone Is a Sex Pheromone or Sex Attractant for the Endangered Valley Elderberry Longhorn Beetle Desmocerus californicus dimorphus and Several Congeners (Cerambycidae: Lepturinae)

We report here that (4R,9Z)-hexadec-9-en-4-olide [(R)-desmolactone] is a sex attractant or sex pheromone for multiple species and subspecies in the cerambycid genus Desmocerus. This compound was previously identified as a female-produced sex attractant pheromone of Desmocerus californicus californicus. Headspace volatiles from female Desmocerus aureipennis aureipennis contained (R)-desmolactone, and the antennae of adult males of two species responded strongly to synthetic (R)-desmolactone in coupled gas chromatography-electroantennogram analyses. In field bioassays in California, Oregon, and British Columbia, traps baited with synthetic (R)-desmolactone captured males of several Desmocerus species and subspecies. Only male beetles were captured, indicating that this compound acts as a sex-specific attractant, rather than as a signal for aggregation. In targeted field bioassays, males of the US federally threatened subspecies Desmocerus californicus dimorphus responded to the synthetic attractant in a dose dependent manner. Our results represent the first example of a “generic” sex pheromone used by multiple species in the subfamily Lepturinae, and demonstrate that pheromone-baited traps may be a sensitive and efficient method of monitoring the threatened species Desmocerus californicus dimorphus, commonly known as the valley elderberry longhorn beetle.     

Identification of macromolecules by quantitative polyacrylamide gel electrophoresis and isoelectric focusing: a comparison of three approaches.

Identification of macromolecules by zone electrophoresis has usually been based on differences in migration distances under a single set of electrophoretic conditions. Classically, it has taken the form of coelectrophoresis on gel slabs. In “quantitative” polyacrylamide gel electrophoresis (PAGE), separation conditions were standardized sufficiently to allow for identification of macromolecules between experiments on the basis of their relative electrophoretic mobilities, R_f ± σ_Rf. More reliably, molecular identity or distinguishability have been based on several R_f values at several gel concentrations (%T) and the linear relationship between log R_f and %T, the Ferguson plot. The slope (retardation coefficient K_R of this plot is desoriptive of molecular size while the γ-intercept (Y₀) is a measure of net charge. The joint 95% confidence envelopes for K_R and Y₀ may be used as criteria for identification of molecules. Distinction between two molecular species depends on the size and position of the two confidence envelopes or ellipses. By pooling estimates of residual varlance (scatter areund the regression line for the Ferguson plot) for several proteins, it is possible to reduce the size of the ellipses and improve the sensitivity of the method to distinguish elesely related species. The sensitivity of this method depends on the size and reprodueibility of the 95% confidence envelopes, and on the limitatiens in the number of electrophoretic fractionations that one is reasonably willing to invest. Any molecular identification problem therefore raises the implieit question whether to base distinction on migration distance, on R_f, or on the joint 95% confidence envelopes for K_R and Y₀ and related statistical (F test) eriteria. Further, in the event of inconsistent answers to the question of molecular distinguishability from the three approaches, we need rational criteria to select the “best” answer. These problems and some solutions are illustrated by the present study which was designed to determine whether the enzymatic digestion products of human growth hormone produced by subtilisin-B are or are not the same as those obtained by digestion with plasmin. It appears that the joint 95% confidence envelopes of K_R and Y₀ provide at this time the most discriminating criteria of distinction, indicating significant differences between nearly all the products of plasmin and subtilisin digestion of hGH. However, the lower resolution provided by the R_f criteria has the advantage that it allows one to group the products of the partial hydrolysis of hGH into “families” which may be associated with different ranges of specific bioactivities.     

The orientations of reaction center transition moments in the chromatophore membrane of Rhodopseudomonas sphaeroides, based on new linear dichroism and photoselection measurements

Chromatophore membranes from Rhodopseudomonas sphaeroides were oriented by drying suspensions on the surfaces of glass slides. Polarized spectra of light-induced absorption changes were obtained between 500 and 1000 nm. As observed earlier, these spectra showed negative bands, reflecting photooxidation of the bacteriochlorophyll ‘special pair’ in the reaction centers, centered near 870, 810, 630 and 600 nm. These bands have been designated BY₁, BY₂, BX₁ and BX₂, respectively, corresponding to two Q_y transitions and two Q_x transitions of the dimeric special pair. We found the BY₁ and BX₁ transition moments to be parallel (within 20°) to the plane of the membrane, whereas the BX₂ moment makes an angle of 55–63° with the plane.Using the photoselection technique we found that the angle between the BY₁ and BX₁ transition moments is 30°, while that between BY₁ and BX₂ is 75°. The BX₁ and BX₂ moments were found to be orthogonal, consistent with the prediction of molecular exciton theory for a dimer.By combining these data, we have calculated the orientations of the transition moments of the bacteriochlorophyll dimer in spherical polar coordinates, with the pole of the coordinate system normal to the plane of the membrane. The orientations of the Q_y and Q_x transition moments of the two bacteriopheophytin molecules in the reaction center were also computed in this coordinate system by transforming the data reported by Clayton, C.N., Rafferty, R.K. and Vermeglio, A. ((1979) Biochim. Biophys. Acta 545, 58–68). We have derived the transformation equations for two polar coordinate systems: in one, the pole is an axis of symmetry as defined by the orientations of purified reaction centers in stretched gelatin films (Rafferty, C.N. and Clayton, R.K. (1979) Biochim. Biophys. Acta 545, 106–121). In the other, the pole is normal to the plane of the chromatophore membrane. These two polar axes are approximately orthogonal.     

Molecular weight estimation using sodium dodecyl sulfate-pore gradient electrophoresis

Pore gradient electrophoresis (PGE) in the presence of sodium dodecyl sulfate (SDS) provides a means for high resolution fractionation of multicomponent protein systems and permits estimation of molecular weights for macromolecules ranging from 10³ to 10⁶. We have evaluated the performance of several methods used to construct calibration curves for estimation of molecular weights using SDS-PGE. A linear relationship between the logarithm of molecular weight, log (M_r), and the logarithm of the relative mobility, log (R_l), can be obtained for a 30-fold range of molecular weights. However, this range of linearity depends on the choice of the concentration gradient, the degree of crosslinking of the gel, and on the nature of the underlying relationship between the retardation coefficient, K_R, and the molecular weight. An empirical relationship, first introduced by Lambin et al. (1976, Anal. Biochem.74, 567) between log (M_r) and the logarithm of the gel concentration at the position reached by the protein, log (%T), provides better linearity over a wider molecular weight range than does the use of log (R_l). We have compared these relatienships by experimental analysis of 10 standard proteins and by a theoretical analysis of an idealized model system. A computer program has been developed which provides appropriate statistical estimation of the molecular weight for an unknown protein, together with its standard error and 95% confidence limits. A new method has also been developed for analysis of nonlinear calibration curves in terms of molecular weight versus distance migrated, based on a theoretically justifiable, physical-chemical model. This model implies that either the relationship between log (M_r) and log (R_l) or the one between log (M_r) and log (%T) will become nonlinear as the range of molecular weight is extended. We suggest that the use of a nonlinear least-squares curve-fitting procedure provides an optimal method for molecular weight estimation when sufficient data are available. Based on these findings, a general strategy is presented for estimation of molecular weights by polyacrylamide gel electrophoresis.     

Orientation and Dynamics of Peptides in Membranes Calculated from H-NMR Data

Solid-state ²H-NMR is routinely used to determine the alignment of membrane-bound peptides. Here we demonstrate that it can also provide a quantitative measure of the fluctuations around the distinct molecular axes. Using several dynamic models with increasing complexity, we reanalyzed published ²H-NMR data on two representative α-helical peptides: 1), the amphiphilic antimicrobial peptide PGLa, which permeabilizes membranes by going from a monomeric surface-bound to a dimeric tilted state and finally inserting as an oligomeric pore; and 2), the hydrophobic WALP23, which is a typical transmembrane segment, although previous analysis had yielded helix tilt angles much smaller than expected from hydrophobic mismatch and molecular dynamics simulations. Their ²H-NMR data were deconvoluted in terms of the two main helix orientation angles (representing the time-averaged peptide tilt and azimuthal rotation), as well as the amplitudes of fluctuation about the corresponding molecular axes (providing the dynamic picture). The mobility of PGLa is found to be moderate and to correlate well with the respective oligomeric states. WALP23 fluctuates more vigorously, now in better agreement with the molecular dynamics simulations and mismatch predictions. The analysis demonstrates that when ²H-NMR data are fitted to extract peptide orientation angles, an explicit representation of the peptide rigid-body angular fluctuations should be included.     

A simple and accurate method for quantification of magnetosomes in magnetotactic bacteria by common spectrophotometer

A simple apparatus for measuring the magnetism of magnetotactic bacteria was developed with a common laboratory spectrophotometer, which was based on measuring the change in light scattering resulting from cell alignment in a magnetic field. A multiple coils were built around the cuvette holder of the spectrophotometer to compensate geomagnetic field and to generate two mutually perpendicular magnetic fields. In addition, we defined a novel magnetism parameter, R_mag, by modifying the definition of C_mag to a normalized parameter with the culture absorbance obtained without application of magnetic field. The number of magnetosomes in each cell was determined by transmission electron microscopy to assess the relationship between the two magnetism parameters and the distribution of magnetosomes in the cells. We found that both R_mag and C_mag were linearly correlated rather with the percentage of magnetosome-containing bacteria than with the average magnetosome numbers, and R_mag exhibited a better linearity than C_mag with respect to the percentage of magnetosome-containing bacteria.     

The dynamic structure of thrombin in solution

The backbone dynamics of human α-thrombin inhibited at the active site serine were analyzed using R₁, R₂, and heteronuclear NOE experiments, variable temperature TROSY 2D [¹H-¹⁵N] correlation spectra, and R_ex measurements. The N-terminus of the heavy chain, which is formed upon zymogen activation and inserts into the protein core, is highly ordered, as is much of the double beta-barrel core. Some of the surface loops, by contrast, remain very dynamic with order parameters as low as 0.5 indicating significant motions on the ps-ns timescale. Regions of the protein that were thought to be dynamic in the zymogen and to become rigid upon activation, in particular the γ-loop, the 180s loop, and the Na⁺ binding site have order parameters below 0.8. Significant R_ex was observed in most of the γ-loop, in regions proximal to the light chain, and in the β-sheet core. Accelerated molecular dynamics simulations yielded a molecular ensemble consistent with measured residual dipolar couplings that revealed dynamic motions up to milliseconds. Several regions, including the light chain and two proximal loops, did not appear highly dynamic on the ps-ns timescale, but had significant motions on slower timescales.