Solving novel RNA structures using only secondary structural fragments. Methods 2010 Oct;52(2):168-72
Date
06/15/2010Pubmed ID
20541014Pubmed Central ID
PMC2948636DOI
10.1016/j.ymeth.2010.06.011Scopus ID
2-s2.0-77957127425 (requires institutional sign-in at Scopus site) 21 CitationsAbstract
The crystallographic phase problem is the primary bottleneck encountered when attempting to solve macromolecular structures for which no close crystallographic structural homologues are known. Typically, isomorphous "heavy-atom" replacement and/or anomalous dispersion methods must be used in such cases to obtain experimentally-determined phases. Even three-dimensional NMR structures of the same macromolecule are often not sufficient to solve the crystallographic phase problem. RNA crystal structures present additional challenges due to greater difficulty in obtaining suitable heavy-atom derivatives. We present a unique approach to solve the phase problem for novel RNA crystal structures that has enjoyed a reasonable degree of success. This approach involves modeling only those portions of the RNA sequence whose structure can be predicted readily, i.e., the individual A-form helical regions and well-known stem-loop sub-structures. We have found that no prior knowledge of how the helices and other structural elements are arranged with respect to one another in three-dimensional space, or in some cases, even the sequence, is required to obtain a useable solution to the phase problem, using simultaneous molecular replacement of a set of generic helical RNA fragments.
Author List
Robertson MP, Chi YI, Scott WGAuthor
Young-In Chi PhD Assistant Professor in the Surgery department at Medical College of WisconsinMESH terms used to index this publication - Major topics in bold
AlgorithmsCrystallization
Crystallography, X-Ray
RNA
Software
