early-stage folding in proteins (in silico) sequence-to-structure relation早期在蛋白质折叠(在网上)sequence-to-structure关系.pdfVIP

Journal of Biomedicine and Biotechnology • 2005:2 (2005) 65–79 • DOI: 10.1155/JBB.2005.65 RESEARCH ARTICLE Early-Stage Folding in Proteins (In Silico) Sequence-to-Structure Relation Michał Brylinski,1, 2 Leszek Konieczny,3 Patryk Czerwonko,1 Wiktor Jurkowski,1, 2 and Irena Roterman1 1Department of Bioinformatics and Telemedicine, Medical Faculty, Jagiellonian University, Kopernika 17, 31-501 Cracow, Poland 2 Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland 3 Institute of Biochemistry, Medical Faculty, Jagiellonian University, Kopernika 7, 31-501 Cracow, Poland Received 16 September 2004; revised 3 January 2005; accepted 5 January 2005 A sequence-to-structure library has been created based on the complete PDB database. The tetrapeptide was selected as a unit representing a well-defined structural motif. Seven structural forms were introduced for structure classification. The early-stage folding conformations were used as the objects for structure analysis and classification. The degree of determinability was estimated for the sequence-to-structure and structure-to-sequence relations. Probability calculus and informational entropy were applied for quantitative estimation of the mutual relation between them. The structural motifs representing different forms of loops and bends were found to favor particular sequences in structure-to-sequence analysis. INTRODUCTION ical principles [8] or statistics [9, 10, 11, 12]. Nearest- Prediction of three-dimensional protein structures re- neighbor methods use a database of proteins with known mains a major challenge to modern molecul