A method for determining overall protein fold from NMR distance restraints

Summary We describe a simple method for determining the overall fold of a polypeptide chain from NOE-derived distance restraints. The method uses a reduced representation consisting of two particles per residue, and a force field containing pseudo-bond and pseudo-angle terms, an electrostatic term, but no van der Waals or hard shell repulsive terms. The method is fast and robust, requiring relatively few distance restraints to approximate the correct fold, and the correct mirror image is readily determined. The method is easily implemented using commercially available molecular modeling software.     

Prospective theoretical and experimental study towards electrochemically grafted poly(N-vinyl-2-pyrrolidone) films on metallic surfaces

Quantum chemistry calculations of equilibrium geometry, atomic charges, dipole moment, and frontier orbital energies are carried out on model N-vinyl-2-pyrrolidone, its radical anion and cation, and three protonated derivatives. Attempts to obtain poly(N-vinyl-2-pyrrolidone) films grafted on nickel and platinum electrodes, respectively by cathodic and anodic polarizations, are reported. A thin, covering and insulating film is obtained on the Pt anode, as indicated by surface characterizations carried out with UPS and IRRAS spectroscopies. The fact that the film remains adherent to the metallic surface in spite of a permanent contact with an acetonitrile solution in which poly(N-vinyl-2-pyrrolidone) is soluble suggests that chemisorption has indeed been achieved.     

Solution-state structure by NMR of zinc-substituted rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus.

The three-dimensional solution-state structure is reported for the zinc-substituted form of rubredoxin (Rd) from the marine hyperthermophilic archaebacterium Pyrococcus furiosus, an organism that grows optimally at 100 degrees C. Structures were generated with DSPACE by a hybrid distance geometry (DG)-based simulated annealing (SA) approach that employed 403 nuclear Overhauser effect (NOE)-derived interproton distance restraints, including 67 interresidue, 124 sequential (i-j = 1), 75 medium-range (i-j = 2-5), and 137 long-range (i-j > 5) restraints. All lower interproton distance bounds were set at the sum of the van Der Waals radii (1.8 A), and upper bounds of 2.7 A, 3.3 A, and 5.0 A were employed to represent qualitatively observed strong, medium, and weak NOE cross peak intensities, respectively. Twenty-three backbone-backbone, six backbone-sulfur (Cys), two backbone-side chain, and two side chain-side chain hydrogen bond restraints were include for structure refinement, yielding a total of 436 nonbonded restraints, which averages to > 16 restraints per residue. A total of 10 structures generated from random atom positions and 30 structures generated by molecular replacement using the backbone coordinates of Clostridium pasteurianum Rd converged to a common conformation, with the average penalty (= sum of the square of the distance bounds violations; +/- standard deviation) of 0.024 +/- 0.003 A2 and a maximum total penalty of 0.035 A2. Superposition of the backbone atoms (C, C alpha, N) of residues A1-L51 for all 40 structures afforded an average pairwise root mean square (rms) deviation value (+/- SD) of 0.42 +/- 0.07 A. Superposition of all heavy atoms for residues A1-L51, including those of structurally undefined external side chains, afforded an average pairwise rms deviation of 0.72 +/- 0.08 A. Qualitative comparison of back-calculated and experimental two-dimensional NOESY spectra indicate that the DG/SA structures are consistent with the experimental spectra. The global folding of P. furiosus Zn(Rd) is remarkably similar to the folding observed by X-ray crystallography for native Rd from the mesophilic organism C. pasteurianum, with the average rms deviation value for backbone atoms of residues A1-L51 of P. furiosus Zn(Rd) superposed with respect to residues K2-V52 of C. pasteurianum Rd of 0.77 +/- 0.06 A. The conformations of aromatic residues that compose the hydrophobic cores of the two proteins are also similar. However, P. furiosus Rd contains several unique structural elements, including at least four additional hydrogen bonds and three potential electrostatic interactions.(ABSTRACT TRUNCATED AT 400 WORDS)     

Computed tomography and automated image analysis of prehistoric femora

Non-invasive characterization of limb bone cross-sectional geometry would be useful for biomechanical analyses of skeletal collections. Computed tomography (CT) is potentially the method of choice. Additionally, CT images are suitable for automated analysis. CT is here shown to be both accurate and precise in the analysis of cross-sectional geometry of prehistoric femora. Beam hardening artifacts can be reduced by using a water bath. As the availability of CT for research increases, both bone density and geometry could be determined simultaneously with this method.     

Differential winter mortality and seasonal selection in the polymorphic ladybird Adalia bipunctata (L) in the Netherlands

Seasonal selection acting on the melanic polymorphism in the two-spot ladybird Adalia bipunctata was investigated in The Netherlands. An increase in melanic frequency over the spring-summer reproductive period was quantified. The selective advantage gained by melanics averaged 9%, but significant heterogeneity occurred between populations. Adult hibernation behaviour is described. The beetles when outdoors show a highly clumped distribution both between and within trees. The distribution of the morph classes between aggregations is random. Survivorship in a hibernating cohort (initial n= 1898) on a grid of 70 lime trees near Utrecht was monitored by making three counts over the winter of 1981–1982. Intense selection favouring each melanic morph occurred during December and January. The relative fitness of non-melanics was 0.55 (melanics =1). The discovery of dead beetles in late January (about 5% of total losses) and the absence of spatially density-dependent mortality were consistent with a climatic stress rather than selective predation. The period of selection was associated with very cold temperatures averaging up to 4°C below normal and an overall mortality of nearly 75%. There was no change in morph frequency, near normal temperatures and a lower mortality from February to early April. Examination of groups of nearby trees in late January strongly suggested that similar differential mortality had occurred except on some willows. This difference was probably due to the more protected hibernation sites available on these trees. Samples of hibernating cohorts at three other sites showed no evidence of differential mortality. Laboratory experiments with hibernating beetles found no difference in survivorship or rate of weight loss between starved non-melanics and melanics in temperature regimes with and without periods of adult activity. It is concluded that the intense winter selection on the study limes is probably exceptional. Examination of changes in morph frequency through the annual cycle suggests that at some sites the selection favouring melanics during reproduction is counterbalanced by selection against melanics in late summer or early autumn. The results are discussed in relation to mathematical models of cyclical selection and to other field studies including that of Timoféeff-Ressovsky (1940), who found large decreases in melanic frequency during hibernation in Berlin.     

Sister chromatid differential staining and NOR activity of BrdU-resistant sublines

Summary Two 30 g/ml BrdU-resistant sublines and two 60 g/ml BrdU-resistant sublines are induced from a Chinese hamster cell line Wg3h (HGPRT^–) by one-step and two-step selections, respectively. By inoculating the cells into BrdU-free medium or by adding more BrdU into the culture medium for 26–27 h, it was found that the two BrdU-resistant sublines analysed have very clear sister chromatid differential (SCD) staining patterns. This indicates that some of the nuclear DNA of the BrdU-resistant cells incorporate with BrdU to reach a kinetic balance. Frequencies of sister chromatid exchange (SCE) of the resistant cells are twice to four times as high as those of the Wg3h cells, depending on which BrdU-resistant subline is analysed. The SCE frequencies of the resistant cells also increase with the BrdU concentration in the medium. Analysis of silver-stained nucleolar organizer regions (NORs) indicates that the NOR activity of three out of the four BrdU-resistant sublines is significantly suppressed, i.e., averages of the Ag-NOR number and number of the chromosomes bearing Ag-NORs per cell decrease significantly. The degree of suppression for different BrdU-resistant sublines may be quite different. The suppressed NOR activity of the resistant cells can gradually be restored when the cells are inoculated into BrdU-free medium, but the recovery speed is far lower than that of the Wg3h cells. The suppression of the NOR activity of the BrdU-resistant sublines should be due to BrdU toxicity.     

Numerical solution of a nonlinear advance-delay-differential equation from nerve conduction theory

A functional differential equation which is nonlinear and involves forward and backward deviating arguments is solved numerically. The equation models conduction in a myelinated nerve axon in which the myelin completely insulates the membrane, so that the potential change jumps from node to node. The equation is of first order with boundary values given at t=±. The problem is approximated via a difference scheme which solves the problem on a finite interval by utilizing an asymptotic representation at the endpoints, cubic interpolation and iterative techniques to approximate the delays, and a continuation method to start the procedure. The procedure is tested on a class of problems which are solvable analytically to access the scheme's accuracy and stability, then applied to the problem that models propagation in a myelinated axon. The solution's dependence on various model parameters of physical interest is studied. This is the first numerical study of myelinated nerve conduction in which the advance and delay terms are treated explicitly.Supported in part by NSF Grant MCS8301724 and by a Biomedical Research Support Grant 2SO7RR0706618 from NIH