Automated 3D RNA structure prediction using the RNAComposer method for riboswitches.
Understanding the numerous functions of RNAs depends critically on the knowledge of their three-dimensional (3D) structure. In contrast to the protein field, a much smaller number of RNA 3D structures have been assessed using X-ray crystallography, NMR spectroscopy, and cryomicroscopy. This has led to a great demand to obtain the RNA 3D structures using prediction methods. The 3D structure prediction, especially of large RNAs, still remains a significant challenge and there is still a great demand for high-resolution structure prediction methods. In this chapter, we describe RNAComposer, a method and server for the automated prediction of RNA 3D structures based on the knowledge of secondary structure. Its applications are supported by other automated servers: RNA FRABASE and RNApdbee, developed to search and analyze secondary and 3D structures. Another method, RNAlyzer, offers new way to analyze and visualize quality of RNA 3D models. Scope and limitations of RNAComposer in application for an automated prediction of riboswitches' 3D structure will be presented and discussed. Analysis of the cyclic di-GMP-II riboswitch from Clostridium acetobutylicum (PDB ID 3Q3Z) as an example allows for 3D structure prediction of related riboswitches from Clostridium difficile 4, Bacillus halodurans 1, and Thermus aquaticus Y5.1 of yet unknown structures.
Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland.
K J
KJ
Purzycka
Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland.
M
M
Popenda
Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland; European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland.
M
M
Szachniuk
European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland.
M
M
Antczak
Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland; European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland.
P
P
Lukasiak
Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland; European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland.
J
J
Blazewicz
Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland; European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland. Electronic address: adamiakr@ibch.poznan.pl.
R W
RW
Adamiak
D001483:Base Sequence; D016360:Clostridioides difficile / Q000235:genetics; D046969:Clostridium acetobutylicum / Q000235:genetics; D006152:Cyclic GMP / Q000031:analogs & derivatives / Q000378:metabolism; D020407:Internet; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry; D012329:RNA, Bacterial / Q000737:chemistry*; D058928:Riboswitch; D012984:Software
D012329:RNA, Bacterial; D058928:Riboswitch; C062025:bis(3',5')-cyclic diguanylic acid; D012313:RNA; D006152:Cyclic GMP
3D structure; RNA; RNAComposer; Riboswitches; Structure prediction; c-di-GMP-II riboswitch