Helical Symmetry of Nucleic Acids: Obstacle or Help in Structure Solution?

• Published in: Methods in molecular biology (Clifton, N.J.) Vol. 1320; p. 259
• Main Authors: Urzhumtsev, Alexandre, Urzhumtseva, Ludmila, Baumann, Ulrich
• Format: Journal Article
• Language: English
• Published: United States 2016
• Subjects: Algorithms; Cluster Analysis; Computational Biology - methods; Crystallization; Crystallography, X-Ray; Fourier Analysis; Models, Molecular; Models, Statistical; Molecular Conformation; Nucleic Acid Conformation; Nucleic Acids - chemistry; RNA - chemistry; Solutions
• ISSN: 1940-6029
• DOI: 10.1007/978-1-4939-2763-0_16

Crystallographic molecular replacement method is the key tool to define an atomic structure of nucleic acids. Frequently nucleic acids are packed forming continuous helices in the crystal. This arrangement of individual molecules in "infinite" pseudo helical structures in crystal may be the reason why the molecular replacement fails to find a unique position of the search atomic model as the method requires. The Patterson function, calculated as a Fourier series with diffraction intensities, has auxiliary peaks for such a molecular packing. Those near the origin peak indicate the orientation of the helices. The coordinates of other peaks are related to the molecular position and the rotation angle between two such "infinite" helices. Thus, the peak analysis allows getting molecular position even without a search model. An intelligent selecting and averaging of the phase sets corresponding to multiple probable positions of the search model again result in a unique solution but in the form of a Fourier synthesis and not a model. This synthesis can be used then to build an atomic model as it is the case for usual phasing methods.