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The poly-l-proline type II (PPII) helix in recent years has emerged clearly as a structural class not only of fibrillar proteins (in collagen, PPII is a dominant conformation) but also of the folded and unfolded proteins. Although much less abundant in folded proteins than the α-helix and β-structure, the left-handed, extended PPII helix represents the only(More)
Accumulation of amyloid-β (Aβ) in neurons accompanies Alzheimer's disease progression. In the cytoplasm Aβ influences activity of proteasomes, the multisubunit protein complexes that hydrolyze the majority of intracellular proteins. However, the manner in which Aβ affects the proteolytic activity of proteasomes has not been established. In this study the(More)
The main-chain conformations of 80 proteins were analysed to identify helical structures that commonly occur but do not fall into the known classes of alpha-helix, 3(10)-helix and beta-sheet. The analysis yielded 96 occurrences of four or more sequential residues forming the threefold left-handed poly-L-proline II (PPII) helix. This contradicts the(More)
Viral protein R (Vpr) of HIV-1 belongs to a class of so called 'accessory' proteins, originally thought to be dispensable for virus replication, at least in vitro. Indeed, viruses with mutated or deleted Vpr replicate well in transformed T cell lines. However, recently published results reveal several important functions performed by Vpr, which are critical(More)
We report an analysis of a novel sequence-structure database of mammalian proteins incorporating nucleotide sequences of the exon regions of their genes together with protein sequence and structural information. We find that synonymous codon families (i.e. coding the same residue) have non-random codon distribution frequencies between protein secondary(More)
This paper describes the outcome of a ''Workshop on Biological Macromolecular Structure Models'' held in November 2005 in which experimentalists and mod-elers discussed the best way to archive models of biological macromolecules. Background and Goals of the Workshop We have entered a new era in structural biology in which many methods will be used in(More)
Left-handed polyproline II (PPII) helices commonly occur in globular proteins in segments of 4-8 residues. This paper analyzes the structural conservation of PPII-helices in 3 protein families: serine proteinases, aspartic proteinases, and immunoglobulin constant domains. Calculations of the number of conserved segments based on structural alignment of(More)
Left-handed polyproline-II type helix is a regular conformation of polypeptide chain not only of fibrous, but also of folded and natively unfolded proteins and peptides. It is the only class of regular secondary structure substantially represented in non-fibrous proteins and peptides on a par with right-handed alpha-helix and beta-structure. In this study,(More)
A complete classification of types of the protein secondary structure is developed on the basis of computer analysis of the crystallographic structural data deposited in the protein Data Bank. The majority of amino acid residues fall into five conformation types. A conclusion is drawn that the number of sequence variants of torsion angles phi, psi in(More)
Zinc-induced oligomerization of amyloid-β peptide (Aβ) produces potentially pathogenic agents of Alzheimer's disease. Mutations and modifications in the metal binding domain 1-16 of Aβ peptide crucially affect its zinc-induced oligomerization by changing intermolecular zinc mediated interface. The 3D structure of this interface appearing in a range of Aβ(More)