beta-propeller domains composed of WD repeats are highly ubiquitous and typically used as multi-site docking platforms to coordinate and integrate the activities of groups of proteins. Here, we have used extensive homology modelling of the WD40-repeat family of seven-bladed beta-propellers coupled with subsequent structural classification and clustering of these models to define subfamilies of ...

On the basis of structural homology calculations, we previously showed that lecithin:cholesterol acyltransferase (LCAT), like lipases, belongs to the alpha/beta hydrolase fold family. As there is higher sequence conservation in the N-terminal region of LCAT, we investigated the contribution of the N- and C-terminal conserved basic residues to the catalytic activity of this enzyme. Most basic, a...

MOTIVATION Structural genomics eventually aims at determining structures for all proteins. However, in the beginning experimentalists are likely to focus on globular proteins to achieve a rapid basic coverage of protein sequence space. How many proteins will structural genomics have to target? How many proteins will be excluded since we already have structural information for these or since the...

The attachment protein G of respiratory syncytial virus (RSV) has a modular architecture. The ectodomain of the protein comprises a small folded conserved region which is bounded by two mucin-like regions. In this study, a sequence and structural homology is described between this central conserved region of RSV-G and the fourth subdomain of the 55-kDa tumor necrosis factor receptor (TNFr). The...

We have compared the sequences of the putative polypeptides of the human pathogenic B19 parvovirus with protein sequences in the National Bethesda Research Foundation Library, and have discovered a significant homology between a B19 parvovirus non-structural (NS) protein and the T antigens of polyomaviruses and simian virus 40 (SV40) and the putative E1 proteins of papillomaviruses. The region ...

The murine 17th chromosome contains two regions of particular interest to biologists , the Tit complex and the major histocompatibility complex (MHC). 1 The T/t complex controls a number of loci that have important functions in embryonic development (1); the MHC encodes gene products that are involved in cellular interactions critical for immune function (2). A third region, Tla, located telome...

Blood coagulation is a cascade of complex enzymatic reactions which involves specific proteins and cellular components to interact and prevent blood loss. The coagulation process begins by either "Tissue Dependent Pathway" (also known as extrinsic pathway) or by "contact activation pathway" (also known as intrinsic pathway). TFPI is an endogenous multivalent Kunitz type protease inhibitor which...

Computer alignments have been said to be more objective and repeatable than manual alignments. Here we suggest that computer alignment methods, particularly those using a program called POY, suffer from a series of practical problems, and philosophical inconsistencies. Subjective decisions are still a part of POY analyses, but are less transparent. We point out the problems POY has with ancestr...

BACKGROUND Cysteine rich protein families are notoriously difficult to align due to low sequence identity and frequent insertions and deletions. RESULTS Here we present an alignment method that ensures homologous cysteines align by assigning a unique 10 amino acid barcode to those identified as structurally homologous by the DALI webserver. The free inter-cysteine regions of the barcoded sequ...

UNLABELLED Homology modeling and structural analysis of human P-glycoprotein (hP-gp) were performed with a software package the Molecular Operating Environment (MOE). A mouse P-gp (mP-gp; PDB code: 3G5U) was selected as a template for the 3D structure modeling of hP-gp. The modeled hP-gp showed significant 3D similarities at the drug biding site (DBS) to the mP-gp structure. The contact energy ...