Sequence similarity in structurally dissimilar proteins

Digitalitzat per Artypla

Prediction of a common structural scaffold for proteasome lid, COP9-signalosome and eIF3 complexes

BACKGROUND: The 'lid' subcomplex of the 26S proteasome and the COP9 signalosome (CSN complex) share a common architecture consisting of six subunits harbouring a so-called PCI domain (proteasome, CSN, eIF3) at their C-terminus, plus two subunits containing MPN domains (Mpr1/Pad1 N-terminal). The translation initiation complex eIF3 also contains PCI- and MPN-domain proteins, but seems to deviate from the 6+2 stoichiometry. Initially, the PCI domain was defined as the region of detectable sequence similarity between the components mentioned above. RESULTS: During an exhaustive bioinformatical analysis of proteasome components, we detected multiple instances of tetratrico-peptide repeats (TPR) in the N-terminal region of most PCI proteins, suggesting that their homology is not restricted to the PCI domain. We also detected a previously unrecognized PCI domain in the eIF3 component eIF3k, a protein whose 3D-structure has been determined recently. By using profile-guided alignment techniques, we show that the structural elements found in eIF3k are most likely conserved in all PCI proteins, resulting in a structural model for the canonical PCI domain. CONCLUSION: Our model predicts that the homology domain PCI is not a true domain in the structural sense but rather consists of two subdomains: a C-terminal 'winged helix' domain with a key role in PCI:PCI interaction, preceded by a helical repeat region. The TPR-like repeats detected in the N-terminal region of PCI proteins most likely form an uninterrupted extension of the repeats found within the PCI domain boundaries. This model allows an interpretation of several puzzling experimental results

Sce3, a suppressor of the Schizosaccharomyces pombe septation mutant cdc11, encodes a putative RNA-binding protein

In the fission yeast Schizosaccharomyces pombe, the cdc11 gene is required for the initiation of septum formation at the end of mitosis. The sce3 gene was cloned as a multi-copy suppressor of the heat-sensitive mutant cdc11-136. When over-expressed, it rescues all mutants of cdc11 and also a heat-sensitive allele of cdc14, but not the cdc14 null mutant. Deletion shows that sce3 is not essential for cell proliferation. It encodes a putative RNA-binding protein which shows homology to human eIF4B. Immunolocalisation indicates that Sce3p is located predominantly in the cytoplasm. Elevated expression of sce3 increases the steady-state level of cdc14 mRNA. Possible mechanisms of its action are discusse

The PROSITE database, its status in 1999

The PROSITE database (http://www.expasy.ch/sprot/prosite.html) consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of protein (if any) a new sequence belongs, or which known domain(s) it contain

On Entangled Multi-particle Systems in Bohmian Theory

Arguments are presented to show that in the case of entangled systems there are certain difficulties in implementing the usual Bohmian interpretation of the wave function in a straightforward manner. Specific examples are given.Comment: 7 page

The effect of high-pressure torsion on irradiation hardening of Eurofer-97

We investigate the effect of nano-structuring by high-pressure torsion (HPT) on the irradiation performance of Eurofer-97. Material was deformed to shear strains from 0 to ∼230, and then exposed to Fe3+ irradiation doses of 0.01 and 0.1 displacements-per-atom (dpa). Nanoindentation hardness increases monotonically with deformation, and with irradiation for the undeformed material. For both damage levels, less irradiation hardening is observed in severely deformed material. This effect is most prominent in the strain range ∼60 to ∼160, suggesting that nano-structuring may provide an approach for reducing irradiation hardening

MPN+, a putative catalytic motif found in a subset of MPN domain proteins from eukaryotes and prokaryotes, is critical for Rpn11 function

BACKGROUND: Three macromolecular assemblages, the lid complex of the proteasome, the COP9-Signalosome (CSN) and the eIF3 complex, all consist of multiple proteins harboring MPN and PCI domains. Up to now, no specific function for any of these proteins has been defined, nor has the importance of these motifs been elucidated. In particular Rpn11, a lid subunit, serves as the paradigm for MPN-containing proteins as it is highly conserved and important for proteasome function. RESULTS: We have identified a sequence motif, termed the MPN+ motif, which is highly conserved in a subset of MPN domain proteins such as Rpn11 and Csn5/Jab1, but is not present outside of this subfamily. The MPN+ motif consists of five polar residues that resemble the active site residues of hydrolytic enzyme classes, particularly that of metalloproteases. By using site-directed mutagenesis, we show that the MPN+ residues are important for the function of Rpn11, while a highly conserved Cys residue outside of the MPN+ motif is not essential. Single amino acid substitutions in MPN+ residues all show similar phenotypes, including slow growth, sensitivity to temperature and amino acid analogs, and general proteasome-dependent proteolysis defects. CONCLUSIONS: The MPN+ motif is abundant in certain MPN-domain proteins, including newly identified proteins of eukaryotes, bacteria and archaea thought to act outside of the traditional large PCI/MPN complexes. The putative catalytic nature of the MPN+ motif makes it a good candidate for a pivotal enzymatic function, possibly a proteasome-associated deubiquitinating activity and a CSN-associated Nedd8/Rub1-removing activity

Annealing of focused ion beam damage in gold microcrystals: an in situ Bragg coherent X-ray diffraction imaging study

Focused ion beam (FIB) techniques are commonly used to machine, analyse and image materials at the micro- and nanoscale. However, FIB modifies the integrity of the sample by creating defects that cause lattice distortions. Methods have been developed to reduce FIB-induced strain; however, these protocols need to be evaluated for their effectiveness. Here, non-destructive Bragg coherent X-ray diffraction imaging is used to study the in situ annealing of FIB-milled gold microcrystals. Two non-collinear reflections are simultaneously measured for two different crystals during a single annealing cycle, demonstrating the ability to reliably track the location of multiple Bragg peaks during thermal annealing. The thermal lattice expansion of each crystal is used to calculate the local temperature. This is compared with thermocouple readings, which are shown to be substantially affected by thermal resistance. To evaluate the annealing process, each reflection is analysed by considering facet area evolution, cross-correlation maps of the displacement field and binarized morphology, and average strain plots. The crystal's strain and morphology evolve with increasing temperature, which is likely to be caused by the diffusion of gallium in gold below ∼280°C and the self-diffusion of gold above ∼280°C. The majority of FIB-induced strains are removed by 380–410°C, depending on which reflection is being considered. These observations highlight the importance of measuring multiple reflections to unambiguously interpret material behaviour

Deformation behaviour of ion-irradiated FeCr : A nanoindentation study

Understanding the mechanisms of plasticity in structural steels is essential for the operation of next-generation fusion reactors. This work on the deformation behaviour of FeCr, focusses on distinguishing the nucleation of dislocations to initiate plasticity, from their propagation through the material. Fe3Cr, Fe5Cr, and Fel OCr were irradiated with 20 MeV Fe3+ ions at room temperature to doses of 0.008 dpa and 0.08 dpa. Nanoindentation was then carried out with Berkovich and spherical indenter tips. Our results show that the nucleation of dislocations is mainly from pre-existing sources, which are not significantly affected by the presence of irradiation defects or Cr%. Yield strength, an indicator of dislocation mobility, increases with irradiation damage and Cr content, while work hardening capacity decreases mainly due to irradiation defects. The synergistic effects of Cr and irradiation damage in FeCr appear to be more important for the propagation of dislocations than for their nucleation.Peer reviewe

PII: S0968-0004(01)01835-7

Research Update We anticipate that further experimental investigation of the specific role of each of the five classes of Brix domain proteins in eukaryote model organisms, especially in yeast, will yield valuable new insights about ribosome synthesis and be key to our understanding of the ribosome biogenesis pathway. Acknowledgements We are grateful to E. Bogengruber, M. Breitenbach, F.M. Jantsch and G. Lepperdinger for supplying experimental data on sequence and function of Brix (AF319877) and yol077c before publication and for extensive discussion of the Brix sequence analysis results. This research was supported by Boehringer-Ingelheim International. Ubiquitin is a small protein, highly conserved among eukaryotes, that becomes covalently attached to both itself and a variety of cellular proteins 1,2 . The role of this ubiquitination is mostly to target proteins to the 26S proteasome degradation pathway 3 . In some cases, monoubiquitination (e.g. of histones) does not lead to degradation, but instead regulates other cellular processes such as chromatin remodeling 4 . Recently, several reports have described a role for monoubiquitination in a different pathway of protein degradation -the endocytosis and subsequent proteolysis of receptors and other transmembrane proteins by the vacuole or the lysosome 5,6 . According to the current model, the decisions about which protein is to be degraded at a specific time is made by the ubiquitination machinery, often in response to a prior event such as phosphorylation. Consequently, both the proteasome and the endocytosis machinery need a mechanism by which to faithfully recognize ubiquitinated proteins. The 26S proteasome comprises two main particles: the 20S core proteasome and the 19S regulatory complex. Subunit S5a (also known as Rpn10) of the 19S regulator binds polyubiquitin chains and has a preference for chains containing four or more ubiquitin monomers. The ubiquitin-interacting region has been mapped to two short, related motifs that are found in all members of the S5a family 7 . Using these regions, which comprise ~20 residues, as a starting point, we searched for other potential ubiquitin-binding sequences. Specifically, we used a combination of iterative database searches with generalized profiles, and Hidden Markov Models (profile-HMMs) 8 . Only sequences that matched a profile or an HMM derived from previously established family members, with error probabilities of p < 0.01, were used for subsequent iteration cycles. After eight cycles, the sequence motif 4 Migeon, J.C. et al. (1999) converged to a set of proteins shown in An observation of particular interest is the occurrence of UIMs in four classes of proteins involved in receptor endocytosisthe Eps15 subfamily of EH-domain proteins, the epsin subfamily of ENTH-domain proteins and two families of VHS-domain proteins, including the FYVE-finger proteins HRS and Vps27, and the SH3-domain proteins STAM and HBP. Eps15 is phosphorylated on Tyr850 by the ligandactivated epidermal growth factor (EGF) receptor and this phosphorylation is required for subsequent receptor endocytosis 10 . Furthermore, Eps15 binds to epsin, and both of these proteins interact with components of the endocytosis machinery, including clathrin and the AP-2 complex 11,12 . The fact that the phosphorylation site of Eps15 is immediately adjacent to a tandem UIM suggests that this motif might be involved in the regulated endocytosis of the EGF receptor. Liquid facets (lqf), an epsin from Drosophila melanogaster, was identified in a genetic screen as a dominant enhancer of the fat facets (faf) mutant eye phenotype 13 . This relationship links the gene encoding lqf with the ubiquitin system because faf is a deubiquitinating enzyme. An additional link between Eps15 and ubiquitin recognition is provided by the yeast protein Ede1p, the closest homolog of mammalian Eps15 (Ref. 14): in the yeast protein, the UIM is replaced by a UBA domain, a homology domain known to bind ubiquitin 15 . Proteins with an N-terminal VHS domain can be divided into three subtypes on the basis of their domain organization: (1) Vps27-HRS-like (type A); (2) STAM-HBP-like (type B); and (3) other proteins (type C) (se