Structure and function of a novel type of ATP-dependent Clp protease.

The Clp protease is conserved among eubacteria and most eukaryotes, and uses ATP to drive protein substrate unfolding and translocation into a chamber of sequestered proteolytic active sites. The main constitutive Clp protease in photosynthetic organisms has evolved into a functionally essential and structurally intricate enzyme. The model Clp protease from the cyanobacterium Synechococcus consists of the HSP100 molecular chaperone ClpC and a mixed proteolytic core comprised of two distinct subunits, ClpP3 and ClpR. We have purified the ClpP3/R complex, the first for a Clp proteolytic core comprised of heterologous subunits. The ClpP3/R complex has unique functional and structural features, consisting of twin heptameric rings each with an identical ClpP3(3)ClpR(4) configuration. As predicted by its lack of an obvious catalytic triad, the ClpR subunit is shown to be proteolytically inactive. Interestingly, extensive modification to ClpR to restore proteolytic activity to this subunit showed that its presence in the core complex is not rate-limiting for the overall proteolytic activity of the ClpCP3/R protease. Altogether, the ClpP3/R complex shows remarkable similarities to the 20 S core of the proteasome, revealing a far greater degree of convergent evolution than previously thought between the development of the Clp protease in photosynthetic organisms and that of the eukaryotic 26 S proteasome.

Modeling AAA+ ring complexes from monomeric structures.

AAA+ proteins form large, ring-shaped complexes, which act as energy-dependent unfoldases of macromolecules. Many crystal structures of proteins in this superfamily have been determined, but mostly in monomeric or non-physiological oligomeric forms. The assembly of ring-shaped complexes from monomer coordinates is, therefore, of considerable interest. We have extracted structural features of complex formation relating to the distance of monomers from the central axis, their relative orientation and the molecular contacts at their interfaces from experimentally determined oligomers and have implemented a semi-automated modeling procedure based on RosettaDock into the iMolTalk server (http://protevo.eb.tuebingen.mpg.de/iMolTalk). As examples of this procedure, we present here models of Apaf-1, MalT and ClpB. We show that the recent EM-based model of the apoptosome is not compatible with the conserved structural features of AAA+ complexes and that the D1 and D2 rings of ClpB are most likely offset by one subunit, in agreement with the structure proposed for ClpA.

iMolTalk: an interactive, internet-based protein structure analysis server.

iMolTalk (http://i.moltalk.org) is a new and interactive web server for protein structure analysis. It addresses the need to identify and highlight biochemically important regions in protein structures. As input, the server requires only the four-digit Protein Data Bank (PDB) identifier, of an experimentally determined structure or a structure file in PDB format stemming e.g. from comparative modelling. iMolTalk offers a wide range of implemented tools (i) to extract general information from PDB files, such as generic header information or the sequence derived from three-dimensional co-ordinates; (ii) to map corresponding residues from sequence to structure; (iii) to search for contacts of residues (amino or nucleic acids) or heterogeneous groups to the protein, present cofactors and substrates; and (iv) to identify protein-protein interfaces between chains in a structure. The server provides results as user-friendly two-dimensional graphical representations and in textual format, ideal for further processing. At any time during the analysis, the user can choose, for the following step, from the set of implemented tools or submit his/her own script to the server to extend the functionality of iMolTalk.

The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants.

Missense mutation leading to single amino acid polymorphism (SAP) is the type of mutation most frequently related to human diseases. The Swiss-Prot protein knowledgebase records information on such mutations in various sections of a protein entry, namely in the "feature," "comment," and "reference" fields. To facilitate users in obtaining the most relevant information about each human SAP recorded in the knowledgebase, the Swiss-Prot Variant web pages were created to provide a summary of available sequence information, as well as additional structural information on each variant. In particular, the ModSNP database was set up to store information related to SAPs and to manage the modeling of SAPs onto protein structures via an automatic homology modeling pipeline. Currently, among the 16,566 human SAPs recorded in the Swiss-Prot knowledgebase (release 42.5, 21 November 2003), more than 25% have corresponding 3D-models. Of these variants, 47% are related to disease, 26% are polymorphisms, and 27% are not yet clearly classified. The ModSNP database is updated and the subsequent model construction pipeline is launched with each weekly Swiss-Prot release. Thus, the ModSNP database represents a valuable resource for the structural analysis of protein variation. The Swiss-Prot variant pages are accessible from the NiceProt view of a Swiss-Prot entry on the ExPASy server (www.expasy.org/), via a hyperlink created for the stable and unique identifier FTId of each human SAP.

MolTalk--a programming library for protein structures and structure analysis.

BACKGROUND: Two of the mostly unsolved but increasingly urgent problems for modern biologists are a) to quickly and easily analyse protein structures and b) to comprehensively mine the wealth of information, which is distributed along with the 3D co-ordinates by the Protein Data Bank (PDB). Tools which address this issue need to be highly flexible and powerful but at the same time must be freely available and easy to learn. RESULTS: We present MolTalk, an elaborate programming language, which consists of the programming library libmoltalk implemented in Objective-C and the Smalltalk-based interpreter MolTalk. MolTalk combines the advantages of an easy to learn and programmable procedural scripting with the flexibility and power of a full programming language. An overview of currently available applications of MolTalk is given and with PDBChainSaw one such application is described in more detail. PDBChainSaw is a MolTalk-based parser and information extraction utility of PDB files. Weekly updates of the PDB are synchronised with PDBChainSaw and are available for free download from the MolTalk project page http://www.moltalk.org following the link to PDBChainSaw. For each chain in a protein structure, PDBChainSaw extracts the sequence from its co-ordinates and provides additional information from the PDB-file header section, such as scientific organism, compound name, and EC code. CONCLUSION: MolTalk provides a rich set of methods to analyse and even modify experimentally determined or modelled protein structures. These methods vary in complexity and are thus suitable for beginners and advanced programmers alike. We envision MolTalk to be most valuable in the following applications:1) To analyse protein structures repetitively in large-scale, i.e. to benchmark protein structure prediction methods or to evaluate structural models. The quality of the resulting 3D-models can be assessed by e.g. calculating a Ramachandran-Sasisekharan plot.2) To quickly retrieve information for (a limited number of) macro-molecular structures, i.e. H-bonds, salt bridges, contacts between amino acids and ligands or at the interface between two chains.3) To programme more complex structural bioinformatics software and to implement demanding algorithms through its portability to Objective-C, e.g. iMolTalk.4) To be used as a front end to databases, e.g. PDBChainSaw.