Search PubMed⌕ Search

Biomedical subjects

A Lupas

Publications and source records attributed to A Lupas.

46 records · Page 3Linked to original sources
PubMed1994

Predicted secondary structure of the 20 S proteasome and model structure of the putative peptide channel.

Secondary structure prediction has made great progress in recent years due to the incorporation of evolutionary information, and may be close to a point where (in combination with biochemical and low-resolution structural data) it can guide the modelling of tertiary structure in cases where no model building is possible by homology. Towards this goal it is important to gather information on the performance of prediction methods in advance of the publication of new structures. In anticipation of the soon-to-be-released structure of the 20 S proteasome from Thermoplasma acidophilum, we have applied several widely used secondary structure prediction methods to proteasome sequences and have attempted to model the putative channel in the outer proteasome rings (alpha-rings) based on the obtained predictions.

Amino Acid Sequence↗
PubMed1994

Domain structure of the Acetogenium kivui surface layer revealed by electron crystallography and sequence analysis.

The three-dimensional structure of the Acetogenium kivui surface layer (S-layer) has been determined to a resolution of 1.7 nm by electron crystallographic techniques. Two independent reconstructions were made from layers negatively stained with uranyl acetate and Na-phosphotungstate. The S-layer has p6 symmetry with a center-to-center spacing of approximately 19 nm. Within the layer, six monomers combine to form a ring-shaped core surrounded by a fenestrated rim and six spokes that point towards the axis of threefold symmetry and provide lateral connectivity to other hexamers in the layer. The structure of the A. kivui S-layer protein is very similar to that of the Bacillus brevis middle wall protein, with which it shares an N-terminal domain of homology. This domain is found in several other extracellular proteins, including the S-layer proteins from Bacillus sphaericus and Thermus thermophilus, Omp alpha from Thermotoga maritima, an alkaline cellulase from Bacillus strain KSM-635, and xylanases from Clostridium thermocellum and Thermoanaerobacter saccharolyticum, and may serve to anchor these proteins to the peptidoglycan. To our knowledge, this is the first example of a domain conserved in several S-layer proteins.

Amino Acid Sequence↗
PubMed1993

Long charge-rich alpha-helices in systemic autoantigens.

Autoimmune diseases are characterized by the presence of antibodies and T-cells targeting restricted sets of host proteins. This phenomenon may be due in part to greater non-specific immunogenicity for these proteins compared to others which are not autoantigenic. We used computer-based methods to analyze the sequenced human autoantigens for distinctive patterns of potential immunologic importance. Sequences longer than 27 residues predicted by these methods to form coiled-coil alpha-helices with a probability greater than 0.9 were detected in 40 of 109 (36.7%) of the known human autoantigens. These include many predominantly systemic disease-specific autoantigens not previously known to contain this structure. In comparison, 8.7% of human proteins in the Swissprot data base, and 1.1% of the proteins in the Brookhaven data base were found to contain such segments. These predicted coiled-coil alpha-helices are distinguished from most globular protein helices by greater length, higher charge content, and a heptad repeat multivalency. Coiled-coil segments correlate in part with known autoantibody epitopes and may contribute to autoantigenic potential. Systemic autoantigens generally are either basic or contain extended, multivalent, charge-rich segments such as coiled-coils.

Algorithms↗
PubMed1993

Structural features of 26S and 20S proteasomes.

The 26S proteasome is the central protease of the ubiquitin-dependent pathway of protein degradation and has a highly conserved structure from slime molds to humans. The elongated molecule which has a molecular mass of approximately 2,000 kD is formed by a barrel-shaped 20S core complex and two polar 19S complexes. The 20S complex has C2 symmetry and is built by four seven-membered rings of which the outer rings are rotated by 26 degrees relative to the inner rings while the inner rings are in register. The 19S cap complex is asymmetric and therefore considerably less well understood on a structural level. From a comparison of the activity and regulation of the 26S and 20S particles, it can be deduced that the 20S particle contains the protease activity while the 19S complex is supposed to contain isopeptidase, oxidoreductase, ATPase and protein-unfolding activities. In this article we describe the structure of various proteasome complexes as determined by electron microscopy and discuss structural implications of their subunit sequences.

Adenosine Triphosphatases↗
PubMed1992

Folding and trimerization of clathrin subunits at the triskelion hub.

The triskelion shape of the clathrin molecule enables it to form the polyhedral protein network that covers clathrin-coated pits and vesicles. Domains within the clathrin heavy chain that are responsible for maintaining triskelion shape and function were identified and localized. Sequences that mediate trimerization are distal to the carboxyl terminus and are adjacent to a domain that mediates both light chain binding and clathrin assembly. Structural modeling predicts that within this domain, the region of heavy chain-light chain interaction is a bundle of three or four alpha helices. These studies establish a low resolution model of clathrin subunit folding in the central portion (hub) of the triskelion, thus providing a basis for future mutagenesis experiments.

Clathrin↗
PubMed1992

Isolation and cloning of Omp alpha, a coiled-coil protein spanning the periplasmic space of the ancestral eubacterium Thermotoga maritima.

We have discovered a new oligomeric protein component associated with the outer membrane of the ancestral eubacterium Thermotoga maritima. In electron micrographs, the protein, Omp alpha, appears as a rod-shaped spacer that spans the periplasm, connecting the outer membrane to the inner cell body. Purification, biochemical characterization and sequencing of Omp alpha suggest that it is a homodimer composed of two subunits of 380 amino acids with a calculated M(r) of 43,000 and a pI of 4.54. The sequence of the omp alpha gene indicates a tripartite organization of the protein with a globular NH2-terminal domain of 64 residues followed by a putative coiled-coil segment of 300 residues and a COOH-terminal, membrane-spanning segment. The predicted length of the coiled-coil segment (45 nm) correlates closely with the spacing between the inner and outer membranes. Despite sequence similarity to a large number of coiled-coil proteins and high scores in a coiled-coil prediction algorithm, the sequence of the central rod-shaped domain of Omp alpha does not have the typical 3.5 periodicity of coiled-coil proteins but rather has a periodicity of 3.58 residues. Such a periodicity was also found in the central domain of staphylococcal M protein and beta-giardin and might be indicative of a subclass of fibrous proteins with packing interactions that are distinct from the ones seen in other two-stranded coiled-coils.

Amino Acid Sequence↗
PubMed1991

Predicting coiled coils from protein sequences.

The probability that a residue in a protein is part of a coiled-coil structure was assessed by comparison of its flanking sequences with sequences of known coiled-coil proteins. This method was used to delineate coiled-coil domains in otherwise globular proteins, such as the leucine zipper domains in transcriptional regulators, and to predict regions of discontinuity within coiled-coil structures, such as the hinge region in myosin. More than 200 proteins that probably have coiled-coil domains were identified in GenBank, including alpha- and beta-tubulins, flagellins, G protein beta subunits, some bacterial transfer RNA synthetases, and members of the heat shock protein (Hsp70) family.

Amino Acid Sequence↗
PubMed1989

Phosphorylation of an N-terminal regulatory domain activates the CheB methylesterase in bacterial chemotaxis.

Two types of reversible protein modification reactions have been identified in bacterial chemotaxis, methylation of membrane receptor-transducer proteins at glutamate side chains and phosphorylation of cytoplasmic signal transduction proteins at histidine and aspartate side chains. CheB is a bifunctional enzyme that is involved in both these modification processes. Its C-terminal domain is a methylesterase that catalyzes the hydrolysis of gamma-carboxyl glutamyl methyl esters in the cytoplasmic domain of chemoreceptor proteins. Its N-terminal domain is a phosphatase that catalyzes the hydrolysis of phospho-CheA, the central response regulator of bacterial chemotaxis. Phospho-CheB, produced as an intermediate in the phosphatase reaction, has dramatically increased methylesterase activity. The interplay between the methylesterase and phosphatase activities of CheB may provide a crucial link between adaptation and excitation in stimulus-response coupling.

Carboxylic Ester Hydrolases↗
PubMed1988

Two cellular components, PrlA and SecB, that recognize different sequence determinants are required for efficient protein export.

We exploited the conditional-lethal phenotype of secB null mutations to demonstrate that SecB function was required for PrlA-mediated suppression of signal sequence mutations. The results of these experiments provide information about the functions performed and the sequence determinants recognized by each of these components of the protein export machinery of Escherichia coli.

Bacterial Outer Membrane Proteins↗