Circular dichroism of the parallel β helical proteins pectate lyase C and E

The pectate lyases, PelC and PelE, have an unusual folding motif, known as a parallel β-helix, in which the polypeptide chain is coiled into a larger helix composed of three parallel β-sheets connected by loops having variable lengths and conformations. Since the regular secondary structure consists almost entirely of parallel β-sheets these proteins provide a unique opportunity to study the effect of parallel β-helical structure on circular dichroism (CD). We report here the CD spectra of PelC and PelE in the presence and absence of Ca²⁺, derive the parallel β-helical components of the spectra, and compare these results with previous CD studies of parallel β-sheet structure. The shape and intensity of the parallel β-sheet spectrum is distinctive and may be useful in identifying other proteins that contain the parallel β-helical folding motif. © 1995 Wiley-Liss, Inc.     

Bahavioral fever in crayfish

Crayfish (Cambarus bartoni) were tested individually in an electronic shuttlebox thermoregulatory device which allowed them to control water temperature, and thereby their body temperature, by their movements.Crayfish which initially selected 22.1°C water increased their preferred temperature by 1.8°C following injection of killed bacteria (Aeromonas hydrophila) into the gill cavity.This behavioral fever appears similar to that of vertebrates, and may enhance host defense reactions against pathogens.     

Angiosperm classification and phylogeny: a criticism

This is a criticism of Dahlgren's recent classification of angiosperms (1980) and his basic diagram of angiosperm phylogeny. The first is shown to include unnatural orders and super-orders; the second is accordingly as questionable. Basic factors for phylogenetic taxonomy in the angiosperms are considered. Leptocauly leads to parallel evolution and specific multiplication. Nomenclatural artifices for taxonomic equivalence are exposed; the name 'pseudon' is suggested for a conjectural taxon.     

Angiosperm classification and phylogeny: a rectifying comment

A commentary is given on the criticism of Dahlgren's recent classification of angiosperms by Corner ( Botanical Journal of the Linnean Society, 82: 81–87 (1981)). In his dissatisfaction with the current, (almost) generally accepted nomenclatural concepts he has chosen to use my classification as a target. It is agreed that nomenclature is not 'fair' to plant groups playing the most important role in building up the biosphere, and that nomenclatural constructions do not reflect the consideration given to various parts of the plant. Corner does not seem to be familiar with the fact that his so-called 'pseudons' are common to all current systems of classification, nor that the termination '-florae' has been used by Thorne (1968) and in a number of publications since. This suffix does not imply that the botanists using it neglect vegetative characters, nor characters from fruits and seeds. Other misunderstandings are also pointed out. In no case has it been satisfactorily demonstrated by Corner that my orders or superorders are unnatural entities (even though a number of them most likely are).     

In vitro maintenance of differentiation marker synthesis by subpopulations of mouse thymocytes

Mouse thymocyte populations enriched in functionally incompetent, “immature” cells on the one hand, or in competent “mature” cells on the other hand, express different steady-state levels of certain surface antigens and marker enzymes. In the cases of the glycoproteins H-2 (K and D), Qa, and TL, and the DNA polymerase terminal deoxynucleotidyl transferase (TdT), these levels reflect different rates of de novo synthesis in the two populations. Thus each population appears to manifest a characteristic pattern of synthetic rates for the various products relative to total protein synthesis. To investigate the maintenance of these patterns, enriched pools of “immature” and “mature” thymocytes were incubated in vitro for 24 h, and the rates of product synthesis before and after culture were compared. H-2 synthesis, initially most rapid in the mature cells, continued to be made at the highest rate in this population. TdT synthesis, a characteristic activity of the immature cells, was not induced in the mature cells, but proceeded at an increased relative rate in the immature population. Therefore, the differences between the rates of H-2 and TdT synthesis were stable properties of the two thymocyte populations. Another marker of immature cells, TL, did not continue to be produced in parallel with TdT. Rather, its synthesis was selectively curtailed in relation to the continuing protein synthesis in the immature cultures. This non-coordinate regulation of TL and TdT production in immature thymocytes may be due to several mechanisms. These are discussed with regard to their implications for pathways of thymocyte maturation.     

Ontogeny of murine T lymphocytes: I. Maturation of thymocytes induced in vitro by tumor necrosis factor-positive serum (TNF+)

One question which is unresolved in developmental immunology is whether cortical thymocytes are the precursor cells which give rise to medullary thymocytes and peripheral T cells. Cortical thymocytes display a characteristic surface antigen phenotype (high TL and Thy-1, low H-2, no Qa-2, no Qa-3), are agglutinated by peanut agglutinin (PNA), and are unresponsive to concanavalin A (Con-A). The functionally more mature medullary thymocytes express a surface phenotype more closely resembling peripheral T cells (no TL, low Thy-1, high H-2, and some Qa-2), are not agglutinated by PNA, and are responsive to Con-A. An in vitro induction system has been devised in which mouse thymocytes undergo quantitative changes in surface antigens in less than 24 hr and increase their mitogen response to Con-A. The phenotypic changes are characterized by a decrease of TL and Thy-1 and an increase in H-2, Qa-2, and Qa-3. Studies in which thymocytes were fractionated on BSA gradients and by PNA agglutination demonstrate that the inducible cells have the properties of cortical thymocytes. Our data show that a subpopulation of cortical thymocytes can acquire phenotypic characteristics similar to medullary thymocytes and peripheral T cells.     

Enzymatic inactivation of human alpha-1-proteinase inhibitor by neutrophil myeloperoxidase.

Peanut agglutinin was acylated with a new heterobifunctional, cleavable photosensitive crosslinking reagent, N-[4-(p-azidophenylazo)benzoyl]-3-aminopropyl-N′-oxysuccinimide ester. The lectin derivative binds specifically and reversibly to neuraminidase-treated human erythrocyte ghosts and upon irradiation covalent attachment of over 35% of the bound lectin occurs. The affinity-crosslinked ghosts were solublized in deoxycholate, immunoprecipitated with anti-peanut agglutinin antiserum, and analyzed by sodium dodecylsulfate polyacrylamine gel electrophoresis. Bands containing both peanut agglutinin and membrane glycoproteins were detected with apparent molecular weights of 58 000, 85 000, 110 000 and 135 000. Upon subsequent cleavage with sodium dithionite, asialoglycophorin A (apparent M.W. 41 000 and 85 000) and a second glycoprotein (apparent M.W. 58 000 – 61 000) were tentatively identified as the receptors for peanut agglutinin in the intact membrane.     

Generalized Verlet Algorithm for Efficient Molecular Dynamics Simulations with Long-range Interactions

For the purpose of molecular dynamics simulations of large biopolymers we have developed a new method to accelerate the calculation of long-range pair interactions (e.g. Coulomb interaction). The algorithm introduces distance classes to schedule updates of non-bonding interactions and to avoid unnecessary computations of interactions between particles which are far apart. To minimize the error caused by the updating schedule, the Verlet integration scheme has been modified. The results of the method are compared to those of other approximation schemes as well as to results obtained by numerical integration without approximation. For simulation of a protein with 12 637 atoms our approximation scheme yields a reduction of computer time by a factor of seven. The approximation suggested can be implemented on sequential as well as on parallel computers. We describe an implementation on a (Transputer-based) MIMD machine with a systolic ring architecture.