"Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence

• Published in: Journal of biosciences 2007-01, Vol.32 (1), p.51-70
• Main Authors: De Brevern, A G, Etchebest, C, Benros, C, Hazout, S
• Format: Article
• Language: English
• Subjects: 3-D graphics; Amino Acid Sequence; Bayes Theorem; Biochemistry, Molecular Biology; Computational Biology - methods; Databases, Protein; Escherichia coli Proteins - chemistry; Life Sciences; Molecular Sequence Data; Peptide Library; Protein Conformation; Proteins; Proteins - chemistry; Quantitative Methods; Sequence Analysis, Protein
• ISSN: 0250-5991; 0973-7138
• DOI: 10.1007/s12038-007-0006-3

The description of protein 3D structures can be performed through a library of 3D fragments, named a structural alphabet. Our structural alphabet is composed of 16 small protein fragments of 5 C alpha in length, called protein blocks (PBs). It allows an efficient approximation of the 3D protein structures and a correct prediction of the local structure. The 72 most frequent series of 5 consecutive PBs, called structural words (SWs)are able to cover more than 90% of the 3D structures. PBs are highly conditioned by the presence of a limited number of transitions between them. In this study, we propose a new method called "pinning strategy" that used this specific feature to predict long protein fragments. Its goal is to define highly probable successions of PBs. It starts from the most probable SW and is then extended with overlapping SWs. Starting from an initial prediction rate of 34.4%, the use of the SWs instead of the PBs allows a gain of 4.5%. The pinning strategy simply applied to the SWs increases the prediction accuracy to 39.9%. In a second step, the sequence-structure relationship is optimized, the prediction accuracy reaches 43.6%.