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Structural Scaffold (structural + scaffold)
Selected AbstractsThe myeloid leukemia factor interacts with COP9 signalosome subunit 3 in Drosophila melanogasterFEBS JOURNAL, Issue 3 2008Wakana Sugano The human myeloid leukemia factor 1 (hMLF1) gene was first identified as an NPM,hMLF1 fusion gene produced by chromosomal translocation. In Drosophila, dMLF has been identified as a protein homologous to hMLF1 and hMLF2, which interacts with various factors involved in transcriptional regulation. However, the precise cellular function of dMLF remains unclear. To generate further insights, we first examined the behavior of dMLF protein using an antibody specific to dMLF. Immunostaining analyses showed that dMLF localizes in the nucleus in early embryos and cultured cells. Ectopic expression of dMLF in the developing eye imaginal disc using eyeless-GAL4 driver resulted in a small-eye phenotype and co-expression of cyclin E rescued the small-eye phenotype, suggesting the involvement of dMLF in cell-cycle regulation. We therefore analyzed the molecular mechanism of interactions between dMLF and a dMLF-interacting protein, dCSN3, a subunit of the COP9 signalosome, which regulates multiple signaling and cell-cycle pathways. Biochemical and genetic analyses revealed that dMLF interacts with dCSN3 in vivo and glutathione S -transferase pull-down assays revealed that the PCI domain of the dCSN3 protein is sufficient for this to occur, possibly functioning as a structural scaffold for assembly of the COP9 signalosome complex. From these data we propose the possibility that dMLF plays a negative role in assembly of the COP9 signalosome complex. [source] Halloween genes and nuclear receptors in ecdysteroid biosynthesis and signalling in the pea aphidINSECT MOLECULAR BIOLOGY, Issue 2010O. Christiaens Abstract The pea aphid (Acyrthosiphon pisum) is the first whole genome sequenced insect with a hemimetabolic development and an emerging model organism for studies in ecology, evolution and development. The insect steroid moulting hormone 20-hydroxyecdysone (20E) controls and coordinates development in insects, especially the moulting/metamorphosis process. We, therefore present here a comprehensive characterization of the Halloween genes phantom, disembodied, shadow, shade, spook and spookiest, coding for the P450 enzymes that control the biosynthesis of 20E. Regarding the presence of nuclear receptors in the pea aphid genome, we found 19 genes, representing all of the seven known subfamilies. The annotation and phylogenetic analysis revealed a strong conservation in the class of Insecta. But compared with other sequenced insect genomes, three orthologues are missing in the Acyrthosiphon genome, namely HR96, PNR-like and Knirps. We also cloned the EcR, Usp, E75 and HR3. Finally, 3D-modelling of the ligand-binding domain of Ap-EcR exhibited the typical canonical structural scaffold with 12 ,-helices associated with a short hairpin of two antiparallel ,-strands. Upon docking, 20E was located in the hormone-binding groove, supporting the hypothesis that EcR has a role in 20E signalling. [source] Chemical synthesis and biosynthesis of the cyclotide family of circular proteinsIUBMB LIFE, Issue 9 2006Sunithi Gunasekera Abstract Cyclotides are a recently discovered class of proteins that have a characteristic head-to-tail cyclized backbone stabilized by a knotted arrangement of three disulfide bonds. They are exceptionally resistant to chemical, enzymatic and thermal treatments because of their unique structural scaffold. Cyclotides have a range of bio-activities, including uterotonic, anti-HIV, anti-bacterial and cytotoxic activity but their insecticidal properties suggest that their natural physiological role is in plant defense. They are genetically encoded as linear precursors and subsequently processed to produce mature cyclic peptides but the mechanism by which this occurs remains unknown. Currently most cyclotides are obtained via direct extraction from plants in the Rubiaceae and Violaceae families. To facilitate the screening of cyclotides for structure-activity studies and to exploit them in drug design or agricultural applications a convenient route for the synthesis of cyclotides is vital. In this review the current chemical, recombinant and biosynthetic routes to the production of cyclotides are discussed. iubmb Life, 58: 515-524, 2006 [source] Stably folded de novo proteins from a designed combinatorial libraryPROTEIN SCIENCE, Issue 1 2003Yinan Wei Abstract Binary patterning of polar and nonpolar amino acids has been used as the key design feature for constructing large combinatorial libraries of de novo proteins. Each position in a binary patterned sequence is designed explicitly to be either polar or nonpolar; however, the precise identities of these amino acids are varied extensively. The combinatorial underpinnings of the "binary code" strategy preclude explicit design of particular side chains at specified positions. Therefore, packing interactions cannot be specified a priori. To assess whether the binary code strategy can nonetheless produce well-folded de novo proteins, we constructed a second-generation library based upon a new structural scaffold designed to fold into 102-residue four-helix bundles. Characterization of five proteins chosen arbitrarily from this new library revealed that (1) all are ,-helical and quite stable; (2) four of the five contain an abundance of tertiary interactions indicative of well-ordered structures; and (3) one protein forms a well-folded structure with native-like features. The proteins from this new 102-residue library are substantially more stable and dramatically more native-like than those from an earlier binary patterned library of 74-residue sequences. These findings demonstrate that chain length is a crucial determinant of structural order in libraries of de novo four-helix bundles. Moreover, these results show that the binary code strategy,if applied to an appropriately designed structural scaffold,can generate large collections of stably folded and/or native-like proteins. [source] Inheriting a structural scaffold for Golgi biosynthesisBIOESSAYS, Issue 7 2002Stephen A. Jesch In animal cells, the Golgi complex undergoes reversible disassembly during mitosis. The disassembly/reassembly process has been intensively studied in order to understand the mechanisms that govern organelle assembly and inheritance during cell division. A long-standing controversy in the field has been whether formation of Golgi structure is template-mediated or self-organizes from components of the endoplasmic reticulum. A recent study1 however, has demonstrated that a subset of proteins that form a putative Golgi matrix can be inherited during cell division in the absence of membrane input from the endoplasmic reticulum. The outcome of this study suggests that a templating mechanism for the formation of Golgi structure may exist. This study has important implications for understanding mechanisms that govern Golgi biogenesis. BioEssays 24:584,587, 2002. © 2002 Wiley Periodicals, Inc. [source] Guest-dependent conformation of 18-crown-6 tetracarboxylic acid: Relation to chiral separation of racemic amino acidsCHIRALITY, Issue 7 2008Hiroomi Nagata Abstract (+)-18-Crown-6 tetracarboxylic acid (18C6H4) has been used as a chiral selector for various amines and amino acids. To further clarify the structural scaffold of 18C6H4 for chiral separation, single crystal X-ray analysis of its glycine+ (1), H3O+ (2), H5O (3), NH (4), and 2CH3NH (5) complexes was performed and the guest-dependent conformation of 18C6H4 was investigated. The crown ether ring of 18C6H4 in 3, 4, and 5 took a symmetrical C2 or C2 -like conformation, whereas that in 1 and 2 took an asymmetric C1 conformation, which is commonly observed in complexes with various optically active amino acids. The overall survey of the present and related complexes suggests that the molecular conformation of 18C6H4 is freely changeable within an allowable range, depending on the molecular shape and interaction mode with the cationic guest. On the basis of the present results, we propose the allowable conformational variation of 18C6H4 and a possible transition pathway from its primary conformation to the conformation suitable for chiral separation of racemic amines and amino acids. Chirality, 2008. © 2008 Wiley-Liss, Inc. [source] Organic dyes as small molecule protein,protein interaction inhibitors for the CD40,CD154 costimulatory interactionJOURNAL OF MOLECULAR RECOGNITION, Issue 1 2010Peter Buchwald Abstract It is becoming increasingly clear that small molecules can often act as effective protein,protein interaction (PPI) inhibitors, an area of increasing interest for its many possible therapeutic applications. We have identified several organic dyes and related small molecules that (i) concentration-dependently inhibit the important CD40,CD154 costimulatory interaction with activities in the low micromolar (µM) range, (ii) show selectivity toward this particular PPI, (iii) seem to bind on the surface of CD154, and (iv) concentration-dependently inhibit the CD154-induced B cell proliferation. They were identified through an iterative activity screening/structural similarity search procedure starting with suramin as lead, and the best smaller compounds, the main focus of the present work, achieved an almost 3-fold increase in ligand efficiency (,G0/nonhydrogen atom,=,0.8,kJ/NnHa) approaching the average of known promising small-molecule PPI inhibitors (,1.0,kJ/NnHa). Since CD154 is a member of the tumor necrosis factor (TNF) superfamily of cell surface interaction molecules, inhibitory activities on the TNF-R1,TNF- , interactions were also determined to test for specificity, and the compounds selected here all showed more than 30-fold selectivity toward the CD40,CD154 interaction. Because of their easy availability in various structural scaffolds and because of their good protein-binding ability, often explored for tissue-specific staining and other purposes, such organic dyes can provide a valuable addition to the chemical space searched to identify small molecule PPI inhibitors in general. Copyright © 2009 John Wiley & Sons, Ltd. [source] | |||||||||||||