Equilibrium folding and unfolding pathways for a model protein

The folding–unfolding process of reduced bovine pancreatic trypsin inhibitor was investigated with an idealized model employing approximate free energies. The protein is regarded to consist of only C^α and C^β atoms. The backbone dihedral angles are the only conformational variables and are permitted to take discrete values at every 10°. Intraresidue energies consist of two terms: an empirical part taken from the observed frequency distributions of (?,ψ) and an additional favorable energy assigned to the native conformation of each residue. Interresidue interactions are simplified by assuming that there is an attractive energy operative only between residue pairs in close contact in the native structure. A total of 230,000 molecular conformations, with no atomic overlaps, ranging from the native state to the denatured state, are randomly generated by changing the sampling bias. Each conformation is classified according to its conformational energy, F; a conformational entropy, S(F) is estimated for each value of F from the number of samples. The dependence of S(F) on energy reveals that the folding–unfolding transition for this idealized model is an “all-or-none” type; this is attributable to the specific long-range interactions. Interresidue contact probabilities, averaged over samples representing various stages of folding, serve to characterize folding intermediates. Most probable equilibrium pathways for the folding–unfolding transition are constructed by connecting conformationally similar intermediates. The specific details obtained for bovine pancreatic trypsin inhibitor are as follows: (1) Folding begins with the appearance of nativelike medium-range contacts at a β-turn and at the α-helix. (2) These grow to include the native pair of interacting β-strands. This state includes intact regular secondary conformations, as well as the interstrand sheet contacts, and corresponds to an activated state with the highest free energy on the pathway. (3) Additional native long-range contacts are completely formed either toward the amino terminus or toward the carboxyl terminus. (4) In a final step, the missing contacts appear. Although these folding pathways for this model are not consistent with experimental reports, it does indicate multiple folding pathways. The method is general and can be applied to any set of calculated conformational energies and furthermore permits investigation of gross folding features.     

Geographical distribution of Polycelis (Seidlia) auriculata in Japan

Polycelis (Seidlia) auriculata is endemic to mountain districts of Japan, from the central part of Honshû to the area of the Daisetsu Mts of Hokkaidô. In northern Japan, it sometimes occurs in cold-water biotopes of lowland areas. The progenitor of P. auriculata appears to have been the oldest immigrant into northern Japan among the Japanese Polycelis species, entering through a northern route as a preglacial faunal element. P. auriculata now shows a discontinious distribution in northern Japan. By virtue of its geographical and vertical distribution, ecological niche, variation in anatomy of the copulatory apparatus, and cytodemes, this species appears to be in the process of transformation.     

Conversion of Tyrosine Hydroxylase to Stable and Inactive Form by the End Products

We have reported previously that tyrosine hydroxylase in the crude extract from rat striatum exists in the inactive form showing almost no activity at the physiological pH and that the inactive form is produced by the action of the end products of the enzyme, such as dopamine. The incubation of the enzyme with the end products resulted in not only the inactivation but also a remarkable stabilization of the enzyme. Catechols possessing amino groups but no negatively charged groups on the side chains (catecholamine-type catechols) were effective at a concentration as low as 10(-7) M in both the inactivation and stabilization of the enzyme. In contrast, catechols not possessing positively or negatively charged side chains (3,4-dihydroxyphenylethyleneglycol-type catechols) were ineffective at a concentration of 10(-7) M but effective at a concentration of 10(-6) M for both the inactivation and stabilization. Catechols possessing negatively charged groups (3,4-dihydroxyphenylacetic acid-type catechols) were ineffective even at a concentration of 10(-6) M. Thus, the end products of tyrosine hydroxylase appear to serve to keep the enzyme inactive and stable. The reaction mechanism of the conversion of the enzyme from the active/labile form to the inactive/stable form by dopamine was also investigated.     

Differential Effects of Nitrate and Light on the Expression of Glutamine Synthetases and Ferredoxin-Dependent Glutamate Synthase in Maize

The effects of nitrate and light on the expression of genesfor glutamine synthetase (GS) isoproteins and ferredoxin-dependentglutamate synthase (Fd-GOGAT) were studied in different organsof maize seedlings by analyzing the levels of the respectivepolypeptides and mRNAs. In roots, the levels of plastidic GSand of a novel, root-specific GS molecule localized in the extraplastidiccompartment were increased markedly by nitrate, whereas Fd-GOGATand cytosolic GS remained at their initial levels. Ammonia wasnot effective in inducing the plastidic GS and Fd-GOGAT butit did induce the novel GS isoprotein. In leaves, cytosolicand plastidic GSs and Fd-GOGAT were present in both mesophyllcells (MC) and bundle sheath cells (BSC). Upon addition of nitrate,the level of plastidic GS increased preferentially in MC, andupon exposure of etiolated seedlings to light, the levels ofplastidic GS and Fd-GOGAT increased in BSC in a coordinatedmanner. The relationship between the expression of genes forGSs and Fd-GOGAT and the physiological role of the GS/GOGATcycle is discussed in terms of the characteristics of nitrogenmetabolism in roots, MC, and BSC. (Received August 11, 1992; Accepted September 21, 1992)     

cDNA Cloning of Indole-3-Acetic Acid-Regulated Genes: Aux22 and SAUR from Mung Bean (Vigna radiata) Hypocotyl Tissue

Five cDNAs of auxin-regulated genes were isolated from mungbean (Vigna radiata) hypocotyl sections by differential hybridizationscreening. They were related to the soybean genes, Aux22 [Ainleyet al. (1988) J. Biol. Chem. 263: 10658] and SAUR [McClure etal. (1989) Plant Cell 1: 229]. Regulation of expression of thesegenes, examined by Northern blot analysis, appeared similarto that reported in soybean hypocotyls. (Received August 10, 1991; Accepted October 14, 1991)     

Some common properties of lectins from marine algae

Twelve kinds of lectins isolated from four species of marine algae, Boodlea coacta (Chlorophyta) and Hypnea japonica, Carpopeltis flabellata and Solieria robusta (Rhodophyta), were compared for their chemical and biological properties. These lectins were proteins or glycoproteins, similar to terrestrial plant lectins. However, unlike most terrestrial plant lectins, they had a small molecular size (4,200 to 25,000 daltons), were mostly monomeric, and had no affinity for monosaccharides. They strongly agglutinated trypsin-treated rabbit erythrocytes, and their activities commonly were inhibited by glycoproteins bearing N-glycans. From hemagglutination-inhibition tests with various glycoproteins and related compounds, it was found that B. coacta lectins recognize high-mannose N-glycans; H. japonica lectins complex N-glycans, and C. flabellata and S. robusta lectins recognize both types of N-glycans.     

Isolation of temperature-sensitive cell cycle mutants from mouse FM3A cells. Characterization of mutants with special reference to DNA replication

A large number of mutants that are temperature sensitive (ts) for growth have been isolated from mouse mammary carcinoma FM3A cells by an improved selection method consisting of cell synchronization and short exposures to restrictive temperature. The improved method increased the efficiency of isolating DNA ts mutants, which showed a rapid decrease in DNA-synthesizing ability after temperature shift-up. Sixteen mutants isolated by this and other methods were selected for this study. Flow microfluorometric analysis of these mutants cultured at a nonpermissive temperature (39 degrees C) for 16 h indicated that five clones were arrested in the G1 to S phase of the cell cycle, six clones were in the S to G2 phase, and two clones were arrested in the G2 phase. The remaining three clones exhibited 8C DNA content after incubation at 39 degrees C for 28 h, indicating defects in mitosis or cytokinesis. These mutants were classified into 11 complementation groups. All the mutants except for those arrested in the G2 phase and those exhibiting defects in mitosis or cytokinesis showed a rapid decrease in DNA synthesis after temperature shift-up without a decrease in RNA and protein synthesis. The polyomavirus DNA cell-free replication system, which consists of polyomavirus large tumor antigen and mouse cell extracts, was used for further characterization of these DNA ts mutants. Among these ts mutants, only the tsFT20 strain, which contains heat-labile DNA polymerase alpha, was unable to support the polyomavirus DNA replication. Analysis by DNA fiber autoradiography revealed that DNA chain elongation rates of these DNA ts mutants were not changed and that the initiation of DNA replication at the origin of replicons was impaired in the mutant cells.     

Global stability of stationary solutions to a nonlinear diffusion equation in phytoplankton dynamics

We consider a nonlinear diffusion equation proposed by Shigesada and Okubo which describes phytoplankton growth dynamics with a selfs-hading effect.We show that the following alternative holds: Either (i) the trivial stationary solution which vanishes everywhere is a unique stationary solution and is globally stable, or (ii) the trivial solution is unstable and there exists a unique positive stationary solution which is globally stable. A criterion for the existence of positive stationary solutions is stated in terms of three parameters included in the equation.     

A new electrophoretic method for the separation of disaccharides obtained by digestion of chondroitin sulfates and dermatan sulfate with chondroitinases

A new rapid and simple method has been developed for the separation of disaccharides obtained by chondroitinase digestion of chondroitin sulfates and dermatan sulfate using electrophoresis on cellulose acetate plates (Titan III cellulose acetate plates). Three disaccharides are completely separated by electrophoresis in barium acetate or calcium acetate in a short time, and less than 50 μg of glycosaminoglycan samples can be analyzed within 2 h.