Effects of protein-protein interactions on electron transfer: docking and electron transfer calculations for complexes between flavodoxin and c-type cytochromes

 Theoretical studies of protein-protein association and electron transfer were performed on the binary systems formed by Desulfovibrio vulgaris Hildenborough (D. v. H.) flavodoxin and D. v. H. cytochrome c ₅₅₃ and by flavodoxin and horse heart cytochrome c. Initial structures for the complexes were obtained by rigid-body docking and were refined by MD to allow for molecular flexibility. The structures thus obtained were analysed in terms of their relative stability through the calculation of excess energies. Electrostatic, van der Waals and solvation energy terms showed all to have significant contributions to the stability of complexes. In the best association solutions found for both cytochromes, these bind to different zones of flavodoxin. The binding site of flavodoxin observed for cytochrome c is in accordance with earlier works [27]. The various association modes found were characterised in terms of electron transfer using the Pathways model. For complexes between flavodoxin and horse heart cytochrome c, some correlation was observed between electron tunnelling coupling factors and conformation energy; the best conformation found for electron transfer corresponded also to the best one in terms of energy. For complexes between flavodoxin and cytochrome c ₅₅₃ this was not the case and a lower correlation was observed between electron tunnelling coupling factors and excess energies. These results are in accordance with the differences in the experimental dependence of electron transfer rates with ionic strength observed between these two cases. Received: 29 December 1998 / Accepted: 22 March 1999     

Direct kinetic evidence for folding via a highly compact, misfolded state.

The 2 S seed storage protein, sunflower albumin 8 (SFA-8), contains an unusually high proportion of hydrophobic residues including 16 methionines (some of which may form a surface hydrophobic patch) in a disulfide cross-linked, alpha-helical structure. Circular dichroism and fluorescence spectroscopy show that SFA-8 is highly stable to denaturation by heating or chaotropic agents, the latter resulting in a reversible two-state unfolding transition. The small m(U) (-4.7 M(-1) at 10 degrees C) and DeltaC(p) (-0.95 kcal mol(-1) K(-1)) values indicate that relatively little nonpolar surface of the protein is exposed during unfolding. Commensurate with the unusual distribution of hydrophobic residues, stopped-flow fluorescence data show that the folding pathway of SFA-8 is highly atypical, in that the initial product of the rapid collapse phase of folding is a compact nonnative state (or collection of nonnative states) that must unfold before acquiring the native conformation. The inhibited folding reaction of SFA-8, in which the misfolded state (m(M) = -0.95 M(-1) at 10 degrees C) is more compact than the transition state for folding (m(T) = -2.5 M(-1) at 10 degrees C), provides direct kinetic evidence for the transient misfolding of a protein.     

Preparation and properties of a phosphoenzyme from the phosphoglucomutase of Micrococcus lysodeikticus

1. Phosphoglucomutase from Micrococcus lysodeikticus was incubated with (14)C- and (32)P-labelled glucose 1,6-diphosphate and separated from the cofactor on a Sephadex column. (32)P-labelled phosphate (0.7mol/mol of enzyme) was associated with the enzyme, but no (14)C label was. 2. The (32)P-labelled enzyme exchanged its label with the substrates. When the labelled enzyme was incubated in Tris buffer, pH8.3, at 30 degrees C the proportion of exchangeable label slowly fell indicating a half-life of the phosphoenzyme of about 50h. 3. When HClO(4) was added to the labelled phosphoenzyme all of the label was precipitated with the protein and none was released as P(i). On alkaline hydrolysis P(i) was released at a rate comparable with the rate of hydrolysis of the phosphoenzyme from rabbit muscle. 4. We conclude that the phosphoenzyme from Micrococcus lysodeikticus yields a relatively stable, catalytically active phosphoenzyme when treated with cofactor, and that there is no evidence for the formation of an enzyme-glucose 1,6-diphosphate complex. The properties of the phosphoenzyme, which resemble those of rabbit muscle phosphoglucomutase, suggest that the phosphate may be bound to serine.     

Immunfluorescence study of neuropeptides in identified neurons of the rat auditory superior olivary complex

 The present study was conducted to investigate the distribution and immunohistochemical characteristics of ascending and descending projection neurons of the rat superior olivary complex (SOC), a group of interrelated brainstem nuclei. Ascending neurons were identified by injection of cholera toxin B subunit (CTB) into the central nucleus of the inferior colliculus (IC), descending neurons were labeled by application of Fluoro-Gold (FG) into the scala tympani of the cochlea, ipsilaterally to the IC injection. In accordance with the literature, we observed neurons innervating the IC located in the lateral superior olivary nucleus (LSO) and dorsal periolivary groups (DPO) on both sides, in the superior paraolivary nucleus (SPO) predominantly ipsilateral, as well as in the ipsilateral medial superior olivary nucleus (MSO) and the medial nucleus of the trapezoid body (MNTB). Cochlear projection neurons were found predominantly in the ipsilateral LSO as well as in the bilateral SPO, DPO, MSO and MNTB. In addition, a considerable population of neurons in the ipsilateral LSO and SPO were identified as being both ascending and descending. To further characterize these double-projecting neurons, brainstem sections were incubated in antisera directed against different neuroactive substances. The majority of ascending/descending cells in the LSO contained calcitonin gene-related peptide, but not substance P (SP), met-enkephalin (ENK) or tyrosine hydroxylase (TH). Some of these neurons apparently were contacted by ENK- or SP-immunoreactive fibers and terminals. In addition, we found TH-immunoreactive neurons in the lateral MNTB region. These neurons, which were labeled upon tracer injection into the cochlea (but not upon IC injection), probably belong to the C1 catecholaminergic cell group and may represent a division of the uncrossed olivocochlear bundle. The present results reveal the existence of a previously unknown subpopulation of SOC neurons that project to both the cochlea and the inferior colliculus. Their CGRP immunoreactivity and their uncrossed projection pattern provide evidence that they may belong to the cholinergic, putatively excitatory cell group. Received: 4 January 1999 / Accepted: 17 February 1999     

A phylogeny of the families of Scarabaeoidea (Coleoptera)

Abstract. A study, based on examination of thirteen scarabaeoid families, was made of 134 adult and larval characters from the following character suites: 105 adult characters of the antennae, eye, epipharynx, mandible, maxillae, labium, tentorium, trochantin, procoxae, mesocoxae, mesothoracic spiracles, hind wing articulation, hind wing base, hind wing venation, hind wing folding, abdominal sternites, abdominal spiracles, male genitalia, ovarioles and karyotype; twenty larval characters of the antennae, fronto-clypeal suture, stemmata, labial palpi, maxillae, mandibles, legs, stridulatory apparatus, spiracles and ecdysial process; and nine adult and larval biological characters. In order to assess the reliability of different characters in resolving scarabaeoid family relationships, six data sets were subjected to cladistic analysis: the total evidence character set (134 characters), restricted adult character set (thirty-two characters, not including those of the wings), wing character set (seventy-three characters), larval character set (twenty characters), biological character set (nine characters) and re-coded Howden (1982) character set (thirty-nine characters). The complete character set and wing character set both produced phylograms with all nodes resolved; the restricted adult data set, larval data set, Howden (1982) data set and biological data set produced phylograms with diminishing levels of node resolution. The reconstructed phylogeny, from the preferred phylogram of the total evidence character set, shows that the Scarabaeoidea comprises three major lineages; a glaresid, passalid and scarabaeid lineage. The glaresid lineage consists only of the Glaresidae. The passalid lineage comprises two major lines; a glaphyrid line (containing Glaphyridae, Passalidae, Lucanidae, Diphyllostomatidae, Trogidae, Bolboceratidae and Pleocomidae) and a geotrupid line (containing Geotrupidae, Ochodaeidae, Ceratocanthidae and Hybosoridae). The scarabaeid lineage contains those taxa traditionally included within the Scarabaeidae (Aphodiinae, Scarabaeinae, Orphninae, Melolonthinae, Acoma, Chasmatopterinae, Hopliinae, Oncerinae, Rutelinae, Dynastinae, Trichiinae, Cetoniinae and Valginae).     

The role of neuronal death during the development of topographically ordered projections: a computational approach

At the time of synaptogenesis typically 50% of the neurons die. The biological role of this is still unclear, but there is evidence in the visual system that many neurons projecting to topographically inappropriate parts of their target are eliminated to improve the accuracy of the mapping. The signaling that determines neuronal survival involves electrical activity and trophic factors. Based on these observations, we have elaborated a computational model for the self-organization of a two-layered neural network. We observe changes in the topographical organization between the two layers. In layer 1, a traveling wave of electrical activity is used as input. Activity transmission to layer 2 can generate, according to a Hebbian rule, a retrograde death signal that is compensated by a trophic survival signal generated by the target cells. Approximately 50% of the neurons die, and we observe refinement in the topography between the two layers. In alternative versions of the model, we show that an equivalent reorganization can occur through Hebbian synaptic modification alone, but with less precision and efficiency. When the two mechanisms are combined, synaptic modification provides no further improvement over that produced by neuronal death alone. This computational study supports the hypothesis that neuronal death during development can play a role in the refinement of topographical projections in the nervous system. Received: 9 November 1998 / Accepted in revised form: 14 April 1999     

Cytomegalovirus (CMV) DNA Load Is an Independent Predictor of CMV Disease and Survival in Advanced AIDS

The impact of cytomegalovirus (CMV) on human immunodeficiency virus type 1 (HIV-1) disease progression has been controversial. In this study, we sought to determine if CMV viral load is independent of HIV-1 viral load in predicting CMV disease and survival. Our findings indicate that in patients with advanced AIDS, CMV DNA load is an independent marker of CMV disease and survival and is more predictive than HIV-1 RNA load. Moreover, patients who respond to preemptive therapy with oral ganciclovir, with resulting undetectable levels of CMV DNA, in their plasma, have a significantly lower risk of developing CMV disease and higher rates of survival, despite stable or increasing HIV-1 RNA loads. These data provide support for CMV as an independent risk factor for mortality in persons with advanced AIDS and further suggest that effective preemptive therapy for CMV can improve patient survival rates.     

Molecular Characterization of a Bovine Enteric Calicivirus: Relationship to the Norwalk-Like Viruses

Jena virus (JV) is a noncultivatable bovine enteric calicivirus associated with diarrhea in calves and was first described in Jena, Germany. The virus was serially passaged 11 times in colostrum-deprived newborn calves and caused diarrheal disease symptoms at each passage. The complete JV genome sequence was determined by using cDNA made from partially purified virus obtained from a single stool sample. JV has a positive-sense single-stranded RNA genome which is 7,338 nucleotides in length, excluding the poly(A) tail. JV genome organization is similar to that of the human Norwalk-like viruses (NLVs), with three separate open reading frames (ORFs) and a 24-nucleotide sequence motif located at the 5′ terminus of the genome and at the start of ORF 2. The polyprotein (ORF 1) consists of 1,680 amino acids and has the characteristic 2C helicase, 3C protease, and 3D RNA polymerase motifs also found in the NLVs. However, comparison of the N-terminal 100 amino acids of the JV polyprotein with those of the group 1 and group 2 NLVs showed a considerable divergence in sequence. The capsid protein (ORF 2) at 519 amino acids is smaller than that of all other caliciviruses. JV ORF 2 was translated in vitro to produce a 55-kDa protein that reacted with postinfection serum but not preinfection serum. Phylogenetic studies based on partial RNA polymerase sequences indicate that within the Caliciviridae JV is most closely related to the group 1 NLVs.