Convergent evolution in structural elements of proteins investigated using cross profile analysis.

Background: Evolutionary relations of similar segments shared by different protein folds remain controversial, even though many examples of such segments have been found. To date, several methods such as those based on the results of structure comparisons, sequence-based classifications, and sequence-based profile-profile comparisons have been applied to identify such protein segments that possess local similarities in both sequence and structure across protein folds. However, to capture more precise sequence-structure relations, no method reported to date combines structure-based profiles, and sequence-based profiles based on evolutionary information.

Crystal structure of a ten-amino acid protein.

What is the smallest protein? This is actually not such a simple question to answer, because there is no established consensus among scientists as to the definition of a protein. We describe here a designed molecule consisting of only 10 amino acids. Despite its small size, its essential characteristics, revealed by its crystal structure, solution structure, thermal stability, free energy surface, and folding pathway network, are consistent with the properties of natural proteins.

ProSeg: a database of local structures of protein segments.

Integration of knowledge on the sequence-structure correlation of proteins provides a basis for the structural design of artificial novel proteins. As one of strategies, it is effective to consider a short segment, whose size is in between an amino acid and a domain, as a correlation unit for exploring the structure-to-sequence relationship. Here we report the development of a database called ProSeg, which consists of two sub-databases, Segment DB and Cluster DB.

Structural diversity of protein segments follows a power-law distribution.

The local structures of protein segments were classified and their distribution was analyzed to explore the structural diversity of proteins. Representative proteins were divided into short segments using a sliding L-residue window. Each set of local structures consisting of consecutive 1-31 amino acids was classified using a single-pass clustering method.

10 residue folded peptide designed by segment statistics.

We have designed a peptide termed chignolin, consisting of only 10 amino acid residues (GYDPETGTWG), on the basis of statistics derived from more than 10,000 protein segments. The peptide folds into a unique structure in water and shows a cooperative thermal transition, both of which may be hallmarks of a protein. Also, the experimentally determined beta-hairpin structure was very close to what we had targeted.