Publications

The quinone acceptor A1 in photosystem I: Binding site, and comparison to Qa in Purple bacteria reaction centers.
A.Kamlowski, B.Altenberg-Greulich, AvdEst, S.G.Zech, R.Bittl, P.Fromme, W.Lubitz, D.Stehlik
J Phys Chem B (1998) 102, 8278-8287.: The nature of the binding site of the quinone acceptor A1 is studied by modellin using very heterogenous data (ESR data, low resolution Xray, and homology to other already solved molecules).
Molecular modelling and macromolecular visualisation of the position of the Phyllochinone Vitamine K1 in Photosystem I by the help of the program WHAT IF.
Brigitte Altenberg-Greulich, and GerritVriend
Protein Science (1999) 8, 46-46.
A 3-dimensional model building by homology of the HFE protein: molecular consequences and application to antibody development.
Francois-Yves Dupradeau, Brigitte Altenberg-Greulich, Renaud Warin, Vincent Fuentes, Jean-Pierre Monti, Jacques Rochette
Biochimica et Biophysica Acta(2000) 1481, 213-221.: Genetic hemochromatosis (GH) is a common inherited disease of iron metabolism affecting 2^5 in 1000 individuals of European origin. A candidate gene for GH, namely HFE has been recently characterized. Structural studies of the protein product of the HFE gene are of major interest for a better understanding of the molecular physiopathology in iron overload. We have built a 3-dimensional model of the HFE protein based on w40% homology of sequence identity with HLA-Aw68, another MHC class I molecule. This work presents the first 3-dimensional structure of HFE available in the public domain (http://swift.embl-heidelberg.de/service/francois or directly: http://www.cmbi.kun.nl/swift/service/francois). The 3-dimensional characteristics of the protein complexed with the L2- microglobulin are presented. The model has been used to predict immunogenic loops and to develop an antibody able to recognize a protein exhibiting the same molecular weight as HFE. Structural consequences of two common mutations are debated and evolutionary hypotheses are considered in the discussion of the particular biological activity of HFE. This study shows that a strategy based on homology modeling is sufficient to undertake biological investigations.
Where to attach dye molecules to a protein: lessons from the computer program WHAT IF
B.Altenberg-Greulich and G. Vriend
J.Molecular Structure(2001) Vol 598/1,pp 1-8: Genomic and proteomic projects are producing a flood of data that all require interpretation which often is best performed based on a three dimensional structure of the molecule(s) involved. These structures can be determined experimentally, or modelled by homology. Because of the complexity of the questions and the heterogeneity of the data, the software used for modelling proteins must become even more versatile. We describe several case studies in which the questions asked, the data, and the requirements on the software all are very different. It is shown how structural knowledge about a protein helps to determine the best place to bind a fluorescent dye. Such dyes are needed to determine protein-protein, protein-DNA interactions or intrinsic fluorescence microscopy. Further, using dyes you can trace molecules in the cell and thus get a handle on subcellular localisation. The first example (OCT-1) involves the search for free amino groups in a protein DNA complex. The second example (BPTI) is a case, in which the amino acid distribution shows that amino groups are spread all over the structure, so that the natural structure has to be modified to get an answer. The third example (HFE) involves a model built by homology. In this case the amino group distribution can also be predicted. All these studies were performed using the WHAT IF software package. This package is available including source code, documentation, etc. See http://www.cmbi.kun.nl/whatif/
Physicist's simple access to protein structures: the computer program WHAT IF
Brigitte Altenberg-Greulich, Stephan G.Zech, Dietmar Stehlik and Gert Vriend
Proceedings of SPIE(2001)Vol.4430,pp 709-714: The computer program WHAT IF and its application in two physical examples is described. For the DNA binding protein, OCT-1 (pou domain) the location of amino acids with amino group in the sidechain is shown. Such knowledge is required when this molecule has to be stained with a fluorescence dye, which chemically binds to the amino terminus as well as amino groups in the sidechain. The use of the program shows that most sidechain amino groups can be protected when DNA is bound to OCT-1, thus allowing selective staining of the amino terminal (probably non-functional)NH2 group. A protein stained using this knowledge can be utilized in fluorescence spectroscopic studies on functional aspects of OCT-1. In a second example computer knowledge about protein characteristics is used to complement experimental information from electron paramagnetic resonance experiments in Photosystem I, a photosynthetic membrane-bound complex converting solar energy in electric energy and finally into chemical energy. The key primary process is charge separation via light-induced electron transfer along a chain of electron acceptors. A quinone acceptor plays an essential role in all well characterized reaction centers. Important structural details of the quinone binding site within the Photosystem I protein framework can be predicted.
Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries.
Gemund C, Ramu C, Altenberg-Greulich B, Gibson TJ.
Nucleic Acids Res. (2001)Vol.29(6), pp1272-7: Expressed sequence tags (ESTs) are randomly sequenced cDNA clones. Currently, nearly 3 million human and 2 million mouse ESTs provide valuable resources that enable researchers to investigate the products of gene expression. The EST databases have proven to be useful tools for detecting homologous genes, for exon mapping, revealing differential splicing, etc. With the increasing availability of large amounts of poorly characterised eukaryotic (notably human) genomic sequence, ESTs have now become a vital tool for gene identification, sometimes yielding the only unambiguous evidence for the existence of a gene expression product. However, BLAST-based Web servers available to the general user have not kept pace with these developments and do not provide appropriate tools for querying EST databases with large highly spliced genes, often spanning 50 000-100 000 bases or more. Here we describe Gene2EST (http://woody.embl-heidelberg.de/gene2est/), a server that brings together a set of tools enabling efficient retrieval of ESTs matching large DNA queries and their subsequent analysis. RepeatMasker is used to mask dispersed repetitive sequences (such as Alu elements) in the query, BLAST2 for searching EST databases and Artemis for graphical display of the findings. Gene2EST combines these components into a Web resource targeted at the researcher who wishes to study one or a few genes to a high level of detail.
Ubiquitous Cancer Genes: Candidates for Protein-Chips ? Altenberg B., Gemuend C., Greulich K.O.: Proceedings of the ESF Workshop: Protein Arrays-Bridging the Gap between Physics and Biomedicine(2004)Vol 1, pp13-15
Genes of glycolysis are ubiquitously overexpressed in 24 cancer classes.
Altenberg,B. and Greulich,K.O.
Genomics (2004) Dec;84(6):1014-20. online in Science Direct since Sept. 27 2004: Using NIH's public database dbEST on expression of genes and ESTs, genes of the glycolysis pathway have been found to be overexpressed in a set of 24 cancers representing more than 70 % of human cancer cases worldwide. Genes can be classified as those which are almost ubiquitously overexpressed, particularly glyceraldehyde 3 phosphate dehydrogenase, enolase 1 and also pyruvate kinase and in genes which are overexpressed in only less than 50 % of the investigated cancers. Cancers can be classified as those with overexpression of the majority of glycolysis genes, particularly lymph node, prostate and brain cancer where essentially all glycolysis genes are overexpressed and those with only sporatic overexpression, particularly cancers of the cartilage or bone marrow. This classification may be useful when cancer therapies aiming at the Warburg effect are designed.
Datamining reveals a surprisingly simple relationship of biochemical-pathway gene expression among 24 phenotypically very different cancers B. Altenberg,C. Gemuend,S. Reissmann,A. Rapp and K.O.Greulich
European Journal of Cell Biology(2005),Volume 84, Suppl.1, P 28,S2-8: By data mining in NIH's dbEST database we found that only approx. 40 of the 19 000 so far annotated and named human genes are over expressed in a wide variety of different cancers. The finding that essentially all genes of glycolysis are overexpressed in cancer solves a recently emerged discussion on the importance and mechanism of the Warburg effect. It turned out that one might understand gene over expression in cancer pathway - wise, not gene - wise. This will significantly simplify the characterisation of over expression patterns in cancer, since instead of 20 - 25 000 genes only approx. 150 pathways will have to be considered. For all 5 pathways which were investigated so far (glycolysis, citric acid cycle, p53 signalling, rho cell motility signalling and cyclin and the cell cycle pathway a surprisingly simple relationship between 24 phenotypically very different cancers emerged: When in normal tissue the pathway reveals already high expression, it is down regulated or only slightly up regulated in cancer On the contrary, when a pathway is only moderately expressed in normal tissue, it is up regulated. Double logarithmic plots of amplification factors in cancer versus the cumulated expression of pathways in the corresponding cancer tissue yield straight lines, indicating a very simple relationship among all investigated cancers (Cervix, Kidney, Pancreas, Uterus, Stomach, Testis, Liver, Ovary, Lung, Prostate, Placenta, Nervous, Brain, Colon, Skin, Cartilage,
Ubiquitous cancer genes: Multipurpose molecules for protein micro-arrays
Brigitte Altenberg, Christine Gemuend,KarlOtto Greulich
PROTEOMICS(2006),Volume6, Issue1, P 67-71 Published Online: 30 Nov 2005: Multipurpose genes in the human genome which are over-expressed in a large variety of different cancers have been identified. Forty-two of the 19,016 human genes annotated to date (0.2%) are ubiquitously over-expressed in half or more of the 36 investigated human cancers. Of these genes, 15 are involved in protein biosynthesis and folding, six of them in glycolysis. A group of 13 solid tumours over-express almost all (39-42 of 42) ubiquitous cancer genes, suggesting a common mechanism underlying these cancers. Others, such as endocrine cancers, have only a few over-expressed ubiquitous cancer genes. The proteins for which these genes code or the corresponding antibodies are candidates for small protein microarrays aiming at maximum information with only a limited number of proteins. Since the over-expression pattern varies from cancer to cancer, distinction between different cancer classes is possible using one single set of protein or antibody molecules.
Expression levels of 63 p53-related genes add up to similar values in 24 different tissues and are unified in cancer
B. Altenberg, A. Rapp, E. Schmitt and K.O.Greulich
GENOMICS,Volume 90, Issue 6, December 2008, Pages 661-673 (Published Online: 24 Okt 2007): The expression patterns of 62 genes interacting with p53 have been investigated in 24 normal and cancerous tissues using NIH's dbEST library. The expression levels of individual genes, such as the TTP53 gene itself, but also other genes, vary up to 33-fold among the 24 different tissues and no consistent pattern can be recognized. However, when expression levels for all 63 genes are summed, these “cumulated levels” are surprisingly constant over the 24 investigated normal tissues. In cancers, the variation is further reduced. Essentially, the cumulated expression levels in cancer are independent of those in normal tissue. We furthermore constructed a linear statistical classifier, i.e., a weighted sum of gene expression levels, which robustly distinguishes normal from cancer tissue independent of the particular kind of tissue. Thus, despite very large differences for individual genes and considerable changes during carcinogenesis, the cumulated expressions have narrowly defined levels; One essential cause of human ageing is the accumulation of DNA damages during lifetime. Experimental studies require quantitative induction of damages and techniques to visualize the subsequent DNA repair. A new technique, the "immuno fluorescent comet assay", is used to directly visualize DNA damages in the microscope. Using DNA repair proteins fluorescently labeled with green fluorescent protein, it could be shown that the repair of the most dangerous DNA double strand breaks starts with the inaccurate "non homologous end joining" pathway and only after 1 - 1 minutes may switch to the more accurate "homologous recombination repair". One might suggest investigating whether centenarians use "homologous recombination repair" differently from those ageing at earlier years and speculate whether it is possible, for example by nutrition, to shift DNA repair to a better use of the error free pathway and thus promote healthy ageing. As a complementary technique optical tweezers, and particularly its variant "erythrocyte mediated force application", is used to simulate the effects of blood pressure on HUVEC cells representing the inner lining of human blood vessels. Stimulating one cell induces in the whole neighbourhood waves of calcium and nitric oxide, known to relax blood vessels. NIFEDIPINE and AMLODIPINE, both used as drugs in the therapy of high blood pressure, primarily a disease of the elderly, prolong the availability of nitric oxide. This partially explains their mode of action. In contrast, VERAPAMILE, also a blood pressure reducing drug, does not show this effect, indicating that obviously an alternative mechanism must be responsible for vessel relaxation.