Biomedical subjects
Publications and source records attributed to Jessica Shapiro.
Chlamydomonas flagella contain a molecular chaperone now identified as HSP70A, a major cytoplasmic isoform. HSP70A synthesis is upregulated by deflagellation, and its distribution in the flagellum overlaps with the IFT kinesin-II motor FLA10. HSP70A may chaperone flagellar proteins during transport, participating in the assembly and maintenance of the flagellum.
The FoldMiner web server (http://foldminer.stanford.edu/) provides remote access to methods for protein structure alignment and unsupervised motif discovery. FoldMiner is unique among such algorithms in that it improves both the motif definition and the sensitivity of a structural similarity search by combining the search and motif discovery methods and using information from each process to enhance the other. In a typical run, a query structure is aligned to all structures in one of several databases of single domain targets in order to identify its structural neighbors and to discover a motif that is the basis for the similarity among the query and statistically significant targets. This process is fully automated, but options for manual refinement of the results are available as well. The server uses the Chime plugin and customized controls to allow for visualization of the motif and of structural superpositions. In addition, we provide an interface to the LOCK 2 algorithm for rapid alignments of a query structure to smaller numbers of user-specified targets.
The theoretical concept of folding probability, p(fold), has proven to be a useful means to characterize the kinetics of protein folding. Here, we illustrate the practical importance of p(fold) and demonstrate how it can be determined theoretically. We derive a general analytical expression for p(fold) and show how it can be estimated from simulations for systems where the transition rates between the relevant microstates are not known. By analyzing the Ising model we are able to determine the scaling behavior of the numerical error in the p(fold) estimate as function of the number of analyzed Monte Carlo runs. We apply our method to a simple, newly developed protein folding model for the formation of alpha helices. It is demonstrated that our technique highly parallelizes the calculation of p(fold) and that it is orders of magnitude more efficient than conventional approaches.
We report an unsupervised structural motif discovery algorithm, FoldMiner, which is able to detect global and local motifs in a database of proteins without the need for multiple structure or sequence alignments and without relying on prior classification of proteins into families. Motifs, which are discovered from pairwise superpositions of a query structure to a database of targets, are described probabilistically in terms of the conservation of each secondary structure element's position and are used to improve detection of distant structural relationships. During each iteration of the algorithm, the motif is defined from the current set of homologs and is used both to recruit additional homologous structures and to discard false positives. FoldMiner thus achieves high specificity and sensitivity by distinguishing between homologous and nonhomologous structures by the regions of the query to which they align. We find that when two proteins of the same fold are aligned, highly conserved secondary structure elements in one protein tend to align to highly conserved elements in the second protein, suggesting that FoldMiner consistently identifies the same motif in members of a fold. Structural alignments are performed by an improved superposition algorithm, LOCK 2, which detects distant structural relationships by placing increased emphasis on the alignment of secondary structure elements. LOCK 2 obeys several properties essential in automated analysis of protein structure: It is symmetric, its alignments of secondary structure elements are transitive, its alignments of residues display a high degree of transitivity, and its scoring system is empirically found to behave as a metric.
The superfamily of ligand-gated ion channels (LGICs) has been implicated in anesthetic and alcohol responses. Mutations within glycine and GABA receptors have demonstrated that possible sites of anesthetic action exist within the transmembrane subunits of these receptors. The exact molecular arrangement of this transmembrane region remains at intermediate resolution with current experimental techniques. Homology modeling methods were therefore combined with experimental data to produce a more exact model of this region. A consensus from multiple bioinformatics techniques predicted the topology within the transmembrane domain of a glycine alpha one receptor (GlyRa1) to be alpha helical. This fold information was combined with sequence information using the SeqFold algorithm to search for modeling templates. Independently, the FoldMiner algorithm was used to search for templates that had structural folds similar to published coordinates of the homologous nAChR (1OED). Both SeqFold and Foldminer identified the same modeling template. The GlyRa1 sequence was aligned with this template using multiple scoring criteria. Refinement of the alignment closed gaps to produce agreement with labeling studies carried out on the homologous receptors of the superfamily. Structural assignment and refinement was achieved using Modeler. The final structure demonstrated a cavity within the core of a four-helix bundle. Residues known to be involved in modulating anesthetic potency converge on and line this cavity. This suggests that the binding sites for volatile anesthetics in the LGICs are the cavities formed within the core of transmembrane four-helix bundles.