1,919 research outputs found
RBR E3 ubiquitin ligases: new structures, new insights, new questions
The RBR (RING-BetweenRING-RING) or TRIAD [two RING fingers and a DRIL (double RING finger linked)] E3 ubiquitin ligases comprise a group of 12 complex multidomain enzymes. This unique family of E3 ligases includes parkin, whose dysfunction is linked to the pathogenesis of early-onset Parkinson's disease, and HOIP (HOIL-1-interacting protein) and HOIL-1 (haem-oxidized IRP2 ubiquitin ligase 1), members of the LUBAC (linear ubiquitin chain assembly complex). The RBR E3 ligases share common features with both the larger RING and HECT (homologous with E6-associated protein C-terminus) E3 ligase families, directly catalysing ubiquitin transfer from an intrinsic catalytic cysteine housed in the C-terminal domain, as well as recruiting thioester-bound E2 enzymes via a RING domain. Recent three-dimensional structures and biochemical findings of the RBRs have revealed novel protein domain folds not previously envisioned and some surprising modes of regulation that have raised many questions. This has required renaming two of the domains in the RBR E3 ligases to more accurately reflect their structures and functions: the C-terminal Rcat (required-for-catalysis) domain, essential for catalytic activity, and a central BRcat (benign-catalytic) domain that adopts the same fold as the Rcat, but lacks a catalytic cysteine residue and ubiquitination activity. The present review discusses how three-dimensional structures of RBR (RING1-BRcat-Rcat) E3 ligases have provided new insights into our understanding of the biochemical mechanisms of these important enzymes in ubiquitin biology.
INTRODUCTIO
Experimental evaluation of CTD package hydrodynamic behavior and recommendations for improved lowering techniques
This report is the last of a series of three reports on a comprehensive
study of CTD instrument lowering mechanics. The first
report, WHOI 79-81, "A Study of CTD Cables and Lowering Systems",
examines the causes and modes of lowering cable failures, both mechanical
and electrical, and makes recommendations to improve existing instrument
packages and lowering procedures. The second report, WHOI 81-76,
"Hydrodynamics of CTD Instrument Packages", is a theoretical study of
instrument package stability when cable lowered or free falling. The
model is used to predict the hydrodynamic response of CTD packages in
their present or improved configuration. This report, WHOI 83-21, is
more factual. It describes the tests performed on scale models and
actual CTD packages to actually observe and/or measure their hydrodynamic
behavior. Analytical results and experimental data obtained in this
study are used to draw recommendations for CTD package improvement and
future lowering procedures.Prepared for the Office of Naval Research under Contract
N00014-72-C-0019
Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation
The E3 ligase parkin ubiquitinates outer mitochondrial membrane
proteins during oxidative stress and is linked to early-onset
Parkinson’s disease. Parkin is autoinhibited but is activated by the
kinase PINK1 that phosphorylates ubiquitin leading to parkin
recruitment, and stimulates phosphorylation of parkin’s N-terminal
ubiquitin-like (pUbl) domain. How these events alter the
structure of parkin to allow recruitment of an E2~Ub conjugate
and enhanced ubiquitination is an unresolved question. We
present a model of an E2~Ub conjugate bound to the phosphoubiquitin-loaded
C-terminus of parkin, derived from NMR chemical
shift perturbation experiments. We show the UbcH7~Ub conjugate
binds in the open state whereby conjugated ubiquitin binds to the
RING1/IBR interface. Further, NMR and mass spectrometry experiments
indicate the RING0/RING2 interface is re-modelled,
remote from the E2 binding site, and this alters the reactivity of
the RING2(Rcat) catalytic cysteine, needed for ubiquitin transfer.
Our experiments provide evidence that parkin phosphorylation
and E2~Ub recruitment act synergistically to enhance a weak
interaction of the pUbl domain with the RING0 domain and rearrange
the location of the RING2(Rcat) domain to drive parkin
activity
Design analysis of levitation facility for space processing applications
Containerless processing facilities for the space laboratory and space shuttle are defined. Materials process examples representative of the most severe requirements for the facility in terms of electrical power, radio frequency equipment, and the use of an auxiliary electron beam heater were used to discuss matters having the greatest effect upon the space shuttle pallet payload interfaces and envelopes. Improved weight, volume, and efficiency estimates for the RF generating equipment were derived. Results are particularly significant because of the reduced requirements for heat rejection from electrical equipment, one of the principal envelope problems for shuttle pallet payloads. It is shown that although experiments on containerless melting of high temperature refractory materials make it desirable to consider the highest peak powers which can be made available on the pallet, total energy requirements are kept relatively low by the very fast processing times typical of containerless experiments and allows consideration of heat rejection capabilities lower than peak power demand if energy storage in system heat capacitances is considered. Batteries are considered to avoid a requirement for fuel cells capable of furnishing this brief peak power demand
Beyond a warming fingerprint: individualistic biogeographic responses to heterogeneous climate change in California.
Understanding recent biogeographic responses to climate change is fundamental for improving our predictions of likely future responses and guiding conservation planning at both local and global scales. Studies of observed biogeographic responses to 20th century climate change have principally examined effects related to ubiquitous increases in temperature - collectively termed a warming fingerprint. Although the importance of changes in other aspects of climate - particularly precipitation and water availability - is widely acknowledged from a theoretical standpoint and supported by paleontological evidence, we lack a practical understanding of how these changes interact with temperature to drive biogeographic responses. Further complicating matters, differences in life history and ecological attributes may lead species to respond differently to the same changes in climate. Here, we examine whether recent biogeographic patterns across California are consistent with a warming fingerprint. We describe how various components of climate have changed regionally in California during the 20th century and review empirical evidence of biogeographic responses to these changes, particularly elevational range shifts. Many responses to climate change do not appear to be consistent with a warming fingerprint, with downslope shifts in elevation being as common as upslope shifts across a number of taxa and many demographic and community responses being inconsistent with upslope shifts. We identify a number of potential direct and indirect mechanisms for these responses, including the influence of aspects of climate change other than temperature (e.g., the shifting seasonal balance of energy and water availability), differences in each taxon's sensitivity to climate change, trophic interactions, and land-use change. Finally, we highlight the need to move beyond a warming fingerprint in studies of biogeographic responses by considering a more multifaceted view of climate, emphasizing local-scale effects, and including a priori knowledge of relevant natural history for the taxa and regions under study
Generating natural language specifications from UML class diagrams
Early phases of software development are known to be problematic, difficult to manage and errors occurring during these phases are expensive to correct. Many systems have been developed to aid the transition from informal Natural Language requirements to semistructured or formal specifications. Furthermore, consistency checking is seen by many software engineers as the solution to reduce the number of errors occurring during the software development life cycle and allow early verification and validation of software systems. However, this is confined to the models developed during analysis and design and fails to include the early Natural Language requirements. This excludes proper user involvement and creates a gap between the original requirements and the updated and modified models and implementations of the system. To improve this process, we propose a system that generates Natural Language specifications from UML class diagrams. We first investigate the variation of the input language used in naming the components of a class diagram based on the study of a large number of examples from the literature and then develop rules for removing ambiguities in the subset of Natural Language used within UML. We use WordNet,a linguistic ontology, to disambiguate the lexical structures of the UML string names and generate semantically sound sentences. Our system is developed in Java and is tested on an independent though academic case study
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