Automatic building of nucleic acids structures

Abstract

Molecular fragments are located in an electron density map by a phased rotation conformation and translation function, as implemented in the program NUT [1]. Two types of backbone fragments can be used. A rigid double helical fragment NAhelix of 90 atoms is used to locate stretches of regular A-RNA (DNA) structures. The position and orientation of the fragment can be refined. NAhelix is suitable for low-resolution structures. Typical RNA structure contains about 70% of the double-helical conformation. The second fragment is RNAbone (17 atoms), which represents mononucleotide of phosphate-sugar-phosphate type. The fragment is flexible and all backbone torsion angles can be varied during the search. For computation reasons the search is restricted by a table of allowed conformations. The most frequent conformations were determined by a conformation family generator [2] utilizing knowledge of sugar-phosphate-sugar conformation families [3]. TheRNAbone is suitable for intermediate resolution (2.0-3.0A). Individual fragments are connected into polynucleotide chains by a programHEL [4]. In the case of RNAbone also side-chains can be build. The PDB file is a result of connecting. The procedures were tested on RNA/DNA structures ranging form small nucleotide (1QYL) to ribosome (1FFK, 1J5E). About 65% to 100% of the structure can be built, depending on resolution, fragment used and phase quality.