Using Constraints on Beta Partners to Reconstruct Mainly Beta Proteins

The knowledge of the spatial conformation of a protein can help the study of its function, but the number of resolved structures is still limited by the low throughput of the methods used. Structure prediction could bridge the sequence-structure gap, but no reliable and general methods have yet been proposed. An attempt to simplify the problem has been made by trying to predict the contact map of a protein instead of its atoms positions [1]. It has been demonstrated the protein structure can be reconstructed with sufficient precision even if the contact map contains error [2]. Unfortunately, the prediction of contact maps is still very unreliable and it is not clear whether the type of errors made by the predictor can be corrected by the reconstruction method. A low-detail representation of the protein conformation could extract the relevant information to train more efficient predictors. The coarse-grain contact map is defined using contacts between secondary structure segments. The prediction of this type of contacts has been tried [3], but no results exists about the feasibility of a reliable method that uses only this type of information to reconstruct the protein structure. In this work we concentrate on contacts defined by beta partners. The geometry and connectivity of beta strands imposes strong constraints on the overall structure of the protein, especially for those chains thar are formed mainly by residues in beta conformation. The reconstruction of the structure of this kind of proteins would be enhanced by the knowledge of the secondary structure and the indication of which strands are partners. We propose here an efficient procedure to find a structure that matches the aforementioned characteristics of a given protein in its native conformation.