Of bits and bugs

Pur-α is a nucleic acid-binding protein involved in cell cycle control, transcription, and neuronal function. Initially no prediction of the three-dimensional structure of Pur-α was possible. However, recently we solved the X-ray structure of Pur-α from the fruitfly Drosophila melanogaster and showed that it contains a so-called PUR domain. Here we explain how we exploited bioinformatics tools in combination with X-ray structure determination of a bacterial homolog to obtain diffracting crystals and the high-resolution structure of Drosophila Pur-α. First, we used sensitive methods for remote-homology detection to find three repetitive regions in Pur-α. We realized that our lack of understanding how these repeats interact to form a globular domain was a major problem for crystallization and structure determination. With our information on the repeat motifs we then identified a distant bacterial homolog that contains only one repeat. We determined the bacterial crystal structure and found that two of the repeats interact to form a globular domain. Based on this bacterial structure, we calculated a computational model of the eukaryotic protein. The model allowed us to design a crystallizable fragment and to determine the structure of Drosophila Pur-α. Key for success was the fact that single repeats of the bacterial protein self-assembled into a globular domain, instructing us on the number and boundaries of repeats to be included for crystallization trials with the eukaryotic protein. This study demonstrates that the simpler structural domain arrangement of a distant prokaryotic protein can guide the design of eukaryotic crystallization constructs. Since many eukaryotic proteins contain multiple repeats or repeating domains, this approach might be instructive for structural studies of a range of proteins

siRNA basierter Screen zur Identifikation neuer Imatinib-Resistenzmechanismen bei chronischer myeloischer Leukämie

Resistenz gegenüber IM stellt ein klinisches relevantes und in den zugrunde liegenden Mechanismen bislang nur teilweise verstandenes Problem dar. Um mögliche Ursachen für eine Resistenzentwicklung zu finden, bedienten wir uns eines shRNA basierten Screen mit der von Brummelkamp et al. 2002 etablierten NKI-Library. K562-wt wurden mit der Library und Kontroll-Vektoren transfiziert und mit 750 nM IM drei Wochen inkubiert. Es konnten insgesamt vier Gene isoliert werden: Tanscriptional regulating factor 1 (TRERF1), ein Transkriptionsfaktor, der primär im Zusammenhang mit Steroidhormonsynthese und Tamoxifenresistenz bei Mamm- akarzinom beschrieben ist. BCL2-like Protein 11 (Bim, Bcl-2 interacting mediator of cell death), ein Protein der Bcl-2 Familie, welches Apoptose regelt und als Resistenzmechanismus gegenüber IM beschrieben ist. Seizure-Related 6 Homolog (Mouse)-Like 2 (SEZ6L2) ist ein Oberflächenprotein, dessen Gen auf dem Chromosom 16p11.2 lokalisiert ist und von welchem angenommen wird, dass es Kandidatengene für Erkrankungen des autistischen Formenkreises (autism spectrum disorders [ASD]) beinhaltet. Homo sapiens Enhancer of Zeste Homolog 1 (Drosophila) (EZH1) ist ein Gen der Polycomp Gruppe (PcG). Proteine dieser Gruppe sind an der epigenetischen Regulation in der Embryonalentwicklung durch Methylierung des Histon H3 am Lysin-Rest 27 (H3K27) beteiligt

Solvent content of protein crystals from diffraction intensities by Independent Component Analysis

An analysis of the protein content of several crystal forms of proteins has been performed. We apply a new numerical technique, the Independent Component Analysis (ICA), to determine the volume fraction of the asymmetric unit occupied by the protein. This technique requires only the crystallographic data of structure factors as input.Comment: 9 pages, 2 figures, 1 tabl

A Bacterial Homolog of a Eukaryotic Inositol Phosphate Signaling Enzyme Mediates Cross-kingdom Dialog in the Mammalian Gut

Dietary InsP6 can modulate eukaryotic cell proliferation and has complex nutritive consequences, but its metabolism in the mammalian gastrointestinal tract is poorly understood. Therefore, we performed phylogenetic analyses of the gastrointestinal microbiome in order to search for candidate InsP6 phosphatases. We determined that prominent gut bacteria express homologs of the mammalian InsP6 phosphatase (MINPP) and characterized the enzyme from Bacteroides thetaiotaomicron (BtMinpp). We show that BtMinpp has exceptionally high catalytic activity, which we rationalize on the basis of mutagenesis studies and by determining its crystal structure at 1.9 Å resolution. We demonstrate that BtMinpp is packaged inside outer membrane vesicles (OMVs) protecting the enzyme from degradation by gastrointestinal proteases. Moreover, we uncover an example of cross-kingdom cell-to-cell signaling, showing that the BtMinpp-OMVs interact with intestinal epithelial cells to promote intracellular Ca2+ signaling. Our characterization of BtMinpp offers several directions for understanding how the microbiome serves human gastrointestinal physiology

Learning effective amino acid interactions through iterative stochastic techniques

The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within coarse-grained models is the task of deducing effective interaction potentials between the amino acids. Over the years several techniques have been developed to extract potentials that are able to discriminate satisfactorily between the native and non-native folds of a pre-assigned protein sequence. In general, when these potentials are used in actual dynamical folding simulations, they lead to a drift of the native structure outside the quasi-native basin. In this study, we present and validate an approach to overcome this difficulty. By exploiting several numerical and analytical tools we set up a rigorous iterative scheme to extract potentials satisfying a pre-requisite of any viable potential: the stabilization of proteins within their native basin (less than 3-4 \AA$$ cRMS). The scheme is flexible and is demonstrated to be applicable to a variety of parametrizations of the energy function and provides, in each case, the optimal potentials.Comment: Revtex 17 pages, 10 eps figures. Proteins: Structure, Function and Genetics (in press

The linker domain of basal transcription factor TFIIB controls distinct recruitment and transcription stimulation functions

RNA polymerases (RNAPs) require basal transcription factors to assist them during transcription initiation. One of these factors, TFIIB, combines promoter recognition, recruitment of RNAP, promoter melting, start site selection and various post-initiation functions. The ability of 381 site-directed mutants in the TFIIB ‘linker domain’ to stimulate abortive transcription was systematically quantitated using promoter-independent dinucleotide extension assays. The results revealed two distinct clusters (mjTFIIB E78-R80 and mjTFIIB R90-G94, respectively) that were particularly sensitive to substitutions. In contrast, a short sequence (mjTFIIB A81-K89) between these two clusters tolerated radical single amino acid substitutions; short deletions in that region even caused a marked increase in the ability of TFIIB to stimulate abortive transcription (‘superstimulation’). The superstimulating activity did, however, not correlate with increased recruitment of the TFIIB/RNAP complex because substitutions in a particular residue (mjTFIIB K87) increased recruitment by more than 5-fold without affecting the rate of abortive transcript stimulation. Our work demonstrates that highly localized changes within the TFIIB linker have profound, yet surprisingly disconnected, effects on RNAP recruitment, TFIIB/RNAP complex stability and the rate of transcription initiation. The identification of superstimulating TFIIB variants reveals the existence of a previously unknown rate-limiting step acting on the earliest stages of gene expression

Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1.

Tight binding of Gdown1 represses RNA polymerase II (Pol II) function in a manner that is reversed by Mediator, but the structural basis of these processes is unclear. Although Gdown1 is intrinsically disordered, its Pol II interacting domains were localized and shown to occlude transcription factor IIF (TFIIF) and transcription factor IIB (TFIIB) binding by perfect positioning on their Pol II interaction sites. Robust binding of Gdown1 to Pol II is established by cooperative interactions of a strong Pol II binding region and two weaker binding modulatory regions, thus providing a mechanism both for tight Pol II binding and transcription inhibition and for its reversal. In support of a physiological function for Gdown1 in transcription repression, Gdown1 co-localizes with Pol II in transcriptionally silent nuclei of early Drosophila embryos but re-localizes to the cytoplasm during zygotic genome activation. Our study reveals a self-inactivation through Gdown1 binding as a unique mode of repression in Pol II function

A Nanosensor for TNT Detection Based on Molecularly Imprinted Polymers and Surface Enhanced Raman Scattering

We report on a new sensor strategy that integrates molecularly imprinted polymers (MIPs) with surface enhanced Raman scattering (SERS). The sensor was developed to detect the explosive, 2,4,6-trinitrotoluene (TNT). Micron thick films of sol gel-derived xerogels were deposited on a SERS-active surface as the sensing layer. Xerogels were molecularly imprinted for TNT using non-covalent interactions with the polymer matrix. Binding of the TNT within the polymer matrix results in unique SERS bands, which allow for detection and identification of the molecule in the MIP. This MIP-SERS sensor exhibits an apparent dissociation constant of (2.3 ± 0.3) × 10−5 M for TNT and a 3 μM detection limit. The response to TNT is reversible and the sensor is stable for at least 6 months. Key challenges, including developing a MIP formulation that is stable and integrated with the SERS substrate, and ensuring the MIP does not mask the spectral features of the target analyte through SERS polymer background, were successfully met. The results also suggest the MIP-SERS protocol can be extended to other target analytes of interest

Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage

RNA polymerase (Pol) I contains a 10-subunit catalytic core that is related to the core of Pol II and includes subunit A12.2. In addition, Pol I contains the heterodimeric subcomplexes A14/43 and A49/34.5, which are related to the Pol II subcomplex Rpb4/7 and the Pol II initiation factor TFIIF, respectively. Here we used lysine-lysine crosslinking, mass spectrometry (MS) and modeling based on five crystal structures, to extend the previous homology model of the Pol I core, to confirm the location of A14/43 and to position A12.2 and A49/34.5 on the core. In the resulting model of Pol I, the C-terminal ribbon (C-ribbon) domain of A12.2 reaches the active site via the polymerase pore, like the C-ribbon of the Pol II cleavage factor TFIIS, explaining why the intrinsic RNA cleavage activity of Pol I is strong, in contrast to the weak cleavage activity of Pol II. The A49/34.5 dimerization module resides on the polymerase lobe, like TFIIF, whereas the A49 tWH domain resides above the cleft, resembling parts of TFIIE. This indicates that Pol I and also Pol III are distantly related to a Pol II–TFIIS–TFIIF–TFIIE complex

Junctional adhesion molecule C mediates leukocyte adhesion to rheumatoid arthritis synovium

Objective Leukocyte infiltration into the rheumatoid arthritis (RA) synovium is a multistep process in which leukocytes leave the bloodstream and invade the synovial tissue (ST). Leukocyte transendothelial migration and adhesion to RA ST requires adhesion molecules on the surface of endothelial cells and RA ST fibroblasts. This study was undertaken to investigate the role of junctional adhesion molecule C (JAM-C) in mediating leukocyte recruitment and retention in the RA joint. Methods Immunohistologic analysis was performed on RA, osteoarthritis (OA), and normal ST samples to quantify JAM-C expression. Fibroblast JAM-C expression was also analyzed using Western blotting, cell surface enzyme-linked immunosorbent assay, and immunofluorescence. To determine the role of JAM-C in leukocyte retention in the RA synovium, in vitro and in situ adhesion assays and RA ST fibroblast transmigration assays were performed. Results JAM-C was highly expressed by RA ST lining cells, and its expression was increased in OA ST and RA ST endothelial cells compared with normal ST endothelial cells. JAM-C was also expressed on the surface of OA ST and RA ST fibroblasts. Furthermore, we demonstrated that myeloid U937 cell adhesion to both OA ST and RA ST fibroblasts and to RA ST was dependent on JAM-C. U937 cell migration through an RA ST fibroblast monolayer was enhanced in the presence of neutralizing antibodies against JAM-C. Conclusion Our results highlight the novel role of JAM-C in recruiting and retaining leukocytes in the RA synovium and suggest that targeting JAM-C may be important in combating inflammatory diseases such as RA.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/61229/1/23867_ftp.pd