Literature DB >> 24607443

New molecular engineering approaches for crystallographic studies of large RNAs.

Jinwei Zhang1, Adrian R Ferré-D'Amaré2.   

Abstract

Crystallization of RNAs with complex three-dimensional architectures remains a formidable experimental challenge. We review a number of successful heuristics involving engineering of the target RNAs to facilitate crystal contact formation, such as those that enabled the crystallization and structure determination of the cognate tRNA complexes of RNase P holoenzyme and the Stem I domain of the T-box riboswitch. Recently, RNA-targeted antibody Fab fragments and Kink-turn binding proteins have joined the ranks of successful chaperones for RNA crystallization. Lastly, we review the use of structured RNAs to facilitate crystallization of RNA-binding proteins and other RNAs. Published by Elsevier Ltd.

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Year:  2014        PMID: 24607443      PMCID: PMC4127099          DOI: 10.1016/j.sbi.2014.02.001

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  71 in total

1.  Structure and folding of a rare, natural kink turn in RNA with an A*A pair at the 2b*2n position.

Authors:  Kersten T Schroeder; Peter Daldrop; Scott A McPhee; David M J Lilley
Journal:  RNA       Date:  2012-04-26       Impact factor: 4.942

2.  Structure of yeast phenylalanine tRNA at 3 A resolution.

Authors:  J D Robertus; J E Ladner; J T Finch; D Rhodes; R S Brown; B F Clark; A Klug
Journal:  Nature       Date:  1974-08-16       Impact factor: 49.962

3.  Three-dimensional tertiary structure of yeast phenylalanine transfer RNA.

Authors:  S H Kim; F L Suddath; G J Quigley; A McPherson; J L Sussman; A H Wang; N C Seeman; A Rich
Journal:  Science       Date:  1974-08-02       Impact factor: 47.728

4.  Structural domains of transfer RNA molecules.

Authors:  G J Quigley; A Rich
Journal:  Science       Date:  1976-11-19       Impact factor: 47.728

5.  YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops.

Authors:  Nathan J Baird; Jinwei Zhang; Tomoko Hamma; Adrian R Ferré-D'Amaré
Journal:  RNA       Date:  2012-02-21       Impact factor: 4.942

6.  Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches.

Authors:  Nathan J Baird; Adrian R Ferré-D'Amaré
Journal:  RNA       Date:  2012-12-17       Impact factor: 4.942

7.  Se-derivatized RNAs for X-ray crystallography.

Authors:  Lina Lin; Zhen Huang
Journal:  Methods Mol Biol       Date:  2012

Review 8.  Metabolite recognition principles and molecular mechanisms underlying riboswitch function.

Authors:  Alexander Serganov; Dinshaw J Patel
Journal:  Annu Rev Biophys       Date:  2012       Impact factor: 12.981

Review 9.  The structure and folding of kink turns in RNA.

Authors:  David M J Lilley
Journal:  Wiley Interdiscip Rev RNA       Date:  2012-09-13       Impact factor: 9.957

10.  The plasticity of a structural motif in RNA: structural polymorphism of a kink turn as a function of its environment.

Authors:  Peter Daldrop; David M J Lilley
Journal:  RNA       Date:  2013-01-16       Impact factor: 4.942

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  19 in total

1.  Fusion-protein-assisted protein crystallization.

Authors:  Bostjan Kobe; Thomas Ve; Simon J Williams
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2015-06-27       Impact factor: 1.056

2.  Improving RNA Crystal Diffraction Quality by Postcrystallization Treatment.

Authors:  Jinwei Zhang; Adrian R Ferré-D'Amaré
Journal:  Methods Mol Biol       Date:  2021

3.  Dramatic improvement of crystals of large RNAs by cation replacement and dehydration.

Authors:  Jinwei Zhang; Adrian R Ferré-D'Amaré
Journal:  Structure       Date:  2014-09-02       Impact factor: 5.006

4.  Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif.

Authors:  Kosuke Oshima; Xuzhu Gao; Seiichiro Hayashi; Toshifumi Ueda; Takashi Nakashima; Makoto Kimura
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2018-01-01       Impact factor: 1.056

5.  Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography.

Authors:  Deepak Koirala; Sandip A Shelke; Marcel Dupont; Stormy Ruiz; Saurja DasGupta; Lucas J Bailey; Steven A Benner; Joseph A Piccirilli
Journal:  Nucleic Acids Res       Date:  2018-03-16       Impact factor: 16.971

6.  Post-crystallization Improvement of RNA Crystal Diffraction Quality.

Authors:  Jinwei Zhang; Adrian R Ferré-D'Amaré
Journal:  Methods Mol Biol       Date:  2015

7.  In Crystallo Selection to Establish New RNA Crystal Contacts.

Authors:  Grant M Shoffner; Ruixuan Wang; Elaine Podell; Thomas R Cech; Feng Guo
Journal:  Structure       Date:  2018-06-14       Impact factor: 5.006

Review 8.  Structure and mechanism of the T-box riboswitches.

Authors:  Jinwei Zhang; Adrian R Ferré-D'Amaré
Journal:  Wiley Interdiscip Rev RNA       Date:  2015-05-08       Impact factor: 9.957

9.  Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution.

Authors:  Zhaoming Su; Kaiming Zhang; Kalli Kappel; Shanshan Li; Michael Z Palo; Grigore D Pintilie; Ramya Rangan; Bingnan Luo; Yuquan Wei; Rhiju Das; Wah Chiu
Journal:  Nature       Date:  2021-08-11       Impact factor: 49.962

10.  Post-crystallization Improvement of RNA Crystals by Synergistic Ion Exchange and Dehydration.

Authors:  Jinwei Zhang; Adrian R Ferré-D'Amaré
Journal:  Bio Protoc       Date:  2015-09-20
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