Genome Comparsions to Monitor Molecular Evolution.
In: Microbial Evolution and Infection. (Goebel, U.B., Ruf, B.R.)
pp.80-92. BID: 8.
Publisher: Einhorn-Presse Verlag Reinbek
Analyzing the interplay between secondary and tertiary structure predictions in folding simulations with a genetic algorithm.
Dandekar T, Du F
1999; 5: 78-89. PID: 341.
Pathway alignment: application to the comparative analysis of glycolytic enzymes.
1999 Oct 1; 343 Pt 1: 115-24. PubMed: 10493919.
Abstract + PDF
Comparative analysis of metabolic pathways in different genomes yields important information on their evolution, on pharmacological targets and on biotechnological applications. In this study on glycolysis, three alternative ways of comparing biochemical pathways are combined: (1) analysis and comparison of biochemical data, (2) pathway analysis based on the concept of elementary modes, and (3) a comparative genome analysis of 17 completely sequenced genomes. The analysis reveals a surprising plasticity of the glycolytic pathway. Isoenzymes in different species are identified and compared; deviations from the textbook standard are detailed. Several potential pharmacological targets and by-passes (such as the Entner-Doudoroff pathway) to glycolysis are examined and compared in the different species. Archaean, bacterial and parasite specific adaptations are identified and described.
Variation and evolution of the citric-acid cycle: a genomic perspective.
Abstract + PDF
The presence of genes encoding enzymes involved in the citric-acid cycle has been studied in 19 completely sequenced genomes. In the majority of species, the cycle appears to be incomplete or absent. Several distinct, incomplete cycles reflect adaptations to different environments. Their distribution over the phylogenetic tree hints at precursors in the evolution of the citric-acid cycle.
Microinjected glutathione reductase crystals as indicators of the redox status in living cells.
Keese MA, Saffrich R, Dandekar T, Becker K, Schirmer RH
1999 Mar 26; 447(2-3): 135-8. PubMed: 10214933.
The flavoenzyme glutathione reductase catalyses electron transfer reactions between two major intracellular redox buffers, namely the NADPH/NADP+ couple and the 2 glutathione/glutathione disulfide couple. On this account, microcrystals of the enzyme were tested as redox probes of intracellular compartments. For introducing protein crystals into human fibroblasts, different methods (microinjection, particle bombardment and optical tweezers) were explored and compared. When glutathione reductase crystals are present in a cytosolic environment, the transition of the yellow Eox form to the orange-red 2-electron reduced charge transfer form, EH2, is observed. Taking into account the midpoint potential of the Eox/EH2 couple, the redox potential of the cytosol was found to be < -270 mV at pH 7.4 and 37 degrees C. As a general conclusion, competent proteins in crystalline--that is signal-amplifying--form are promising probes for studying intracellular events.
Mice lacking bombesin receptor subtype-3 develop metabolic defects and obesity (Condensation and commentary).
Kelly L, Sharma K, Dandekar T
1999; 12: 223-228. PID: 342.
Improving genetic algorithms for protein folding simulations by systematic crossover.
König R, Dandekar T
To improve protein folding simulations, we investigated a new search strategy in combination with the simple genetic algorithm on a two-dimensional lattice model. This search strategy, we called systematic crossover, couples the best individuals, tests every possible crossover point, and takes the two best individuals for the next generation. We compared the standard genetic algorithm with and without this new implementation for various chain lengths and showed that this strategy finds local minima with better energy values and is significantly faster in identifying the global minimum than the standard genetic algorithm.
Refined genetic algorithm simulations to model proteins.
König R, Dandekar T
1999; 5: 317-324. PID: 343.
Fine mapping of the antigen-antibody interaction of scFv215, a recombinant antibody inhibiting RNA polymerase II from Drosophila melanogaster.
Liu Z, Song D, Kramer A, Martin AC, Dandekar T, Schneider-Mergener J, Bautz EK, Dübel S
A bacterially expressed single chain antibody (scFv215) directed against the largest subunit of drosophila RNA polymerase II was analysed. Structure and function of the antigen binding site in scFv215 were probed by chain shuffling and by site-specific mutagenesis. The entire variable region of either the heavy or light chain was replaced by an unrelated heavy or light chain. Both replacements resulted in a total loss of binding activity suggesting that the antigen binding site is contributed by both chains. The functional contributions of each complementarity determining region (CDR) were investigated by site specific mutagenesis of each CDR separately. Mutations in two of the CDRs, CDR1 of light chain and CDR2 of heavy chain, reduced the binding activity significantly. Each of the amino acids in these two CDRs was replaced individually by alanine (alanine walking). Seven amino acid substitutions in the two CDRs were found to reduce the binding activity by more than 50%. The data support a computer model of scFv215 which fits an epitope model based on a mutational analysis of the epitope suggesting an alpha-helical structure for the main contact area.
Pore-forming peptides of Entamoeba dispar. Similarity and divergence to amoebapores in structure, expression and activity.
Nickel R, Ott C, Dandekar T, Leippe M
Amoebapore, a 77-residue peptide with pore-forming activity from the human pathogen Entamoeba histolytica, is implicated in the killing of phagocytosed bacteria and in the cytolytic reaction of the amoeba against host cells. Previously, we structurally and functionally characterized three amoebapore isoforms in E. histolytica but recognized only one homolog in the closely related but non-pathogenic species Entamoeba dispar. Here, we identified two novel amoebapore homologs from E. dispar by molecular cloning. Despite strong resemblance of the primary structures of the homologs, molecular modeling predicts a species-specific variance between the peptide structures. Parallel isolation from trophozoite extracts of the two species revealed a lower amount of pore-forming peptides in E. dispar and substantially higher activity of the major isoform from E. histolytica towards natural membranes than that from E. dispar. Differences in abundance and activity of the lytic polypeptides may have an impact on the pathogenicity of amoebae.
Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering.
Rational metabolic engineering requires powerful theoretical methods such as pathway analysis, in which the topology of metabolic networks is considered. All metabolic capabilities in steady states are composed of elementary flux modes, which are minimal sets of enzymes that can each generate valid steady states. The modes of the fructose-2,6-bisphosphate cycle, the combined tricarboxylic-acid-glyoxylate-shunt system and tryptophan synthesis are used here for illustration. This approach can be used for many biotechnological applications such as increasing the yield of a product, channelling a product into desired pathways and in functional reconstruction from genomic data.
Quality-of-life assessment in the old using the WHOQOL 100: differences between patients with senile dementia and patients with cancer.
Struttmann T, Fabro M, Romieu G, de Roquefeuil G, Touchon J, Dandekar T, Ritchie K
INTRODUCTION: The measurement of quality of life is an increasingly important issue, particularly in regard to treatment of severe and chronic diseases. The aim of this pilot study was to assess potentially divergent profiles of quality of life in persons with two different pathologies: moderate dementia and cancer. METHOD: This pilot study was carried out in the neurology and cancer services of the medical school in Montpellier, France (Hôpital Gui de Chaulliac and CRLC Val d'Aurelle). The cumulative self-reporting test WHOQOL 100 (World Health Organization Quality of Life with 100 questions) was administered in 57 patients with either moderate senile dementia (27 cases with a Mini-Mental State Examination score >15; mean age of 73) or cancer (30 cases, mainly women with breast cancer; mean age of 53). The stability of responses was tested in a 2-week period. RESULTS: Results of the study showed clear and significant differences between the two groups in the domains of mobility and psychology. Further, eight questions and six facets with a significant difference in responses were found. Responses seemed more stable in the domains of autonomy, social relationship, and religion for the cancer group, and in autonomy and psychology for the dementia group. The age difference may be an important factor in the different quality of life measured but did not significantly influence responses to the test questions. CONCLUSION: The WHOQOL 100 seems a powerful instrument to assess quality of life in diseases such as cancer and moderate dementia. In this study, interesting differences in responses to the test questions between the two pathologic conditions were identified. Items that were unreliable on retesting are singled out. These results will be applied and reevaluated in the development of future, illness-specific and shorter versions of the WHOQOL 100.