Showing papers in "Trends in Biochemical Sciences in 2008"

TL;DR: Although both self-assemble in response to stress-induced perturbations in translation, several recent reports reveal novel proteins and RNAs that are components of these structures but also perform other cellular functions.

TL;DR: It is the view that protein disorder can be classified into four mechanistic categories, covering a continuous spectrum of structural states from static to dynamic disorder and from segmental to full disorder, and that fuzziness will become integral to understanding the interactome.

TL;DR: Multiple levels of molecular interactions are suggested, each of which contribute specific functional features and together create a sophisticated signaling device in bacteria that mediate chemotaxis.

TL;DR: The effects of specific post-translational modifications of the C-terminal tail of the catalytic subunit indicate that a 'code' might regulate dynamic exchange of regulatory B-type subunits, thus affecting the specificity of PP2A.

TL;DR: An updated view of the structure, functions and regulation of the CSN is provided, rapidly emerging as a key player in the DNA-damage response, cell-cycle control and gene expression.

TL;DR: The modular structure of CCN proteins provides important insight into their structure–function relationships, and recent results suggest that some of their biological functions require cooperation between modules.

TL;DR: Examination of highly conserved AS events has led to new insights into the functions of AS-NMD and the role it can have in physiological circumstances.

TL;DR: It is becoming clear that the chemical nature of the substrates, the energetic requirements for transport and the subsequent translocation across the cytoplasmic membrane can differ from those of the well-studied systems for iron complexes and vitamin B12.

TL;DR: Recent breakthroughs in understanding of semaphorin signaling link integrin and semaphorein signaling pathways, identify novel ligand-receptor interactions and provide insight into the cellular and molecular bases of bifunctional and reverse signaling events.

TL;DR: The Hypoxia-inducible factor-1 (HIF-1) is the master regulator of the cellular response to hypoxia and its expression levels are tightly controlled through synthesis and degradation.

TL;DR: A comparison of how one ligand binds in the absence, versus the presence, of a second ligand can distinguish allosteric from non-allosteric protein changes, the importance of which is frequently overlooked.

TL;DR: Structural and functional data regarding this fascinating complex and its many co-factors illuminate its diverse biochemical properties and indicate mechanisms by which RNAs are targeted for either processing or degradation.

TL;DR: Conclusions regarding the immunobiology of these powerful immunomodulatory molecules must take into account their dichotomous properties and their physiological role and importance must be interpreted in the context of the complex in vivo microenvironments in which these proteins exist.

TL;DR: The results of in vitro cellular and biochemical studies have been complimented by recent in vivo studies using genetically modified mouse strains, helping to unravel the mechanism(s) of action and biological functions of the RecQ helicases.

TL;DR: This work has shown that partner choice is not random; instead, dimerization specificities, which are strongly linked to the evolution of the protein family, apply.

TL;DR: It is shown that the human STUbL, RNF4, is implicated in several diseases including cancer, highlighting the importance of characterizing the cellular functions of ST UbLs.

TL;DR: There seems that there are fundamental differences in the 3D structures used by different IRESs, although there are some common features in how they interact with ribosomes.

TL;DR: The analysis of protein-domain rearrangements has provided us with functional and evolutionary insights and has aided improved functional predictions and domain assignments to previously uncharacterised genes and proteins.

TL;DR: Increasing evidence indicates that distinct scaffold proteins assemble IKK, and potentially TBK1 and IKK-epsilon subcomplexes, in a stimulus-specific manner, which might be a mechanism to achieve specificity.

TL;DR: A regulatory network has emerged that controls the expression and activity of SIRT1, a mammalian class-III protein deacetylase, which is an important regulator of metabolism, senescence, cancer and, possibly, longevity and is connected with crucial stress-responsive signal-transduction pathways.

TL;DR: The G protein-coupled receptor (GPCR) family comprises the largest class of cell surface receptors found in metazoan proteomes and has long been proposed to have vital dual roles in cellular adhesion and signalling.

TL;DR: iPath can pinpoint the complementarity of the host-symbiont metabolic capacities by merging human genome data with two important gut commensals, and generate and annotate pathway maps using various external data.

TL;DR: Three years after its discovery, lysine-specific demethylase 1 remains at the forefront of chromatin research and structural studies highlight a specific binding site for the histone H3 N-terminal tail and a catalytic machinery that is closely related to that of other flavin-dependent amine oxidases.

TL;DR: The genomes of many bacterial species, including pathogens, encode a homologue of a major poly P synthetic enzyme, poly P kinase 1 (PPK1), and PPK1 exhibits potential as a novel target for chemotherapy.

TL;DR: It is proposed that specific MIPs represent an ancient and indispensable transport mechanism for metalloids, which suggests that they could be potential pharmacological targets.

TL;DR: The Janus kinase-signal transducer and activator of transcription pathway mediates signaling by cytokines, which control survival, proliferation and differentiation of several cell types, and recent discoveries suggest that mutated JAK proteins will be potent targets for anti-cancer therapy.

TL;DR: Surprisingly, recent studies indicate that constitutive dimerization and negative cooperativity are also ubiquitous properties of G-protein-coupled receptors (GPCRs), which show allosteric mechanisms similar to those described for the IR.

TL;DR: Modeling based on small Abeta oligomers containing extramembranous N-termini predicts channels with shapes and dimensions consistent with experimentally derived channel structures, which support the hypothesis that small AbETA oligomers can form ion channels.

TL;DR: Recent solution studies of the Salmonella typhimurium alpha2beta2 complex coupled with X-ray crystal-structure determinations of complexes with substrates, intermediates and substrate analogs have driven important breakthroughs concerning the identification of the linkages between the bi-enzyme complex structure, catalysis at the alpha- and beta-active sites, and the allosteric regulation of substrate channeling.

TL;DR: It is proposed that existing findings and methodology already enable us to detect active centres in cells and can be expanded to social networks and ecosystems, and members of these active centres are termed here as 'creative elements' of their respective networks.