PDBsum is a web server providing structural information on the entries in the Protein Data Bank (PDB). The analyses are primarily image-based and include protein secondary structure, protein-ligand and protein-DNA interactions, PROCHECK analyses of structural quality, and many others. The 3D structures can be viewed interactively in RasMol, PyMOL, and a JavaScript viewer called 3Dmol.js. Users can upload their own PDB files and obtain a set of password-protected PDBsum analyses for each. The server is freely accessible to all at: http://www.ebi.ac.uk/pdbsum.
Decades of intensive experimental studies of the recognition of DNA sequences by proteins have provided us with a view of a diverse and complicated world in which few to no features are shared between individual DNA-binding protein families. The originally conceived direct readout of DNA residue sequences by amino acid side chains offers very limited capacity for sequence recognition, while the effects of the dynamic properties of the interacting partners remain difficult to quantify and almost impossible to generalise. In this work we investigated the energetic characteristics of all DNA residue-amino acid side chain combinations in the conformations found at the interaction interface in a very large set of protein-DNA complexes by the means of empirical potential-based calculations. General specificity-defining criteria were derived and utilised to look beyond the binding motifs considered in previous studies. Linking energetic favourability to the observed geometrical preferences, our approach reveals several additional amino acid motifs which can distinguish between individual DNA bases. Our results remained valid in environments with various dielectric properties.
- MeSH
- adenin chemie metabolismus MeSH
- aminokyselinové motivy * MeSH
- aminokyseliny chemie metabolismus MeSH
- cytosin chemie metabolismus MeSH
- databáze proteinů MeSH
- DNA vazebné proteiny chemie genetika metabolismus MeSH
- DNA chemie genetika metabolismus MeSH
- guanin chemie metabolismus MeSH
- konformace nukleové kyseliny MeSH
- krystalografie rentgenová MeSH
- molekulární modely MeSH
- statistika jako téma metody MeSH
- terciární struktura proteinů MeSH
- termodynamika MeSH
- thymin chemie metabolismus MeSH
- vazba proteinů MeSH
- vazebná místa genetika MeSH
- výpočetní biologie metody MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: Enzyme active sites can be connected to the exterior environment by one or more channels passing through the protein. Despite our current knowledge of enzyme structure and function, surprisingly little is known about how often channels are present or about any structural features such channels may have in common. RESULTS: Here, we analyze the long channels (i.e. >15 Å) leading to the active sites of 4,306 enzyme structures. We find that over 64% of enzymes contain two or more long channels, their typical length being 28 Å. We show that amino acid compositions of the channel significantly differ both to the composition of the active site, surface and interior of the protein. CONCLUSIONS: The majority of enzymes have buried active sites accessible via a network of access channels. This indicates that enzymes tend to have buried active sites, with channels controlling access to, and egress from, them, and that suggests channels may play a key role in helping determine enzyme substrate.
- MeSH
- aminokyseliny chemie genetika MeSH
- enzymy chemie genetika MeSH
- iontové kanály fyziologie MeSH
- katalytická doména MeSH
- konformace proteinů MeSH
- lidé MeSH
- molekulární modely MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
PDBsum, http://www.ebi.ac.uk/pdbsum, is a website providing numerous pictorial analyses of each entry in the Protein Data Bank. It portrays the structural features of all proteins, DNA and ligands in the entry, as well as depicting the interactions between them. The latest features, described here, include annotation of human protein sequences with their naturally occurring amino acid variants, dynamic graphs showing the relationships between related protein domain architectures, analyses of ligand binding clusters across different experimental determinations of the same protein, analyses of tunnels in proteins and new search options.
- MeSH
- databáze proteinů * MeSH
- genetická variace MeSH
- internet MeSH
- konformace proteinů * MeSH
- lidé MeSH
- ligandy MeSH
- počítačová grafika MeSH
- proteiny chemie genetika MeSH
- racionální návrh léčiv MeSH
- shluková analýza MeSH
- terciární struktura proteinů MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
