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PMID: 20637415 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

Free state conformational sampling of the SAM-I riboswitch aptamer domain.

Structure (London, England : 1993) ·Vol. 18 ·No. 7 ·2010-07-14 ·Pages 787-97

Stoddard CD, Montange RK, Hennelly SP, Rambo RP, Sanbonmatsu KY, Batey RT

Abstract

Riboswitches are highly structured elements residing in the 5' untranslated region of messenger RNAs that specifically bind cellular metabolites to alter gene expression. While there are many structures of ligand-bound riboswitches that reveal details of bimolecular recognition, their unliganded structures remain poorly characterized. Characterizing the molecular details of the unliganded state is crucial for understanding the riboswitch's mechanism of action because it is this state that actively interrogates the cellular environment and helps direct the regulatory outcome. To develop a detailed description of the ligand-free form of an S-adenosylmethionine binding riboswitch at the local and global levels, we have employed a series of biochemical, biophysical, and computational methods. Our data reveal that the ligand binding domain adopts an ensemble of states that minimizes the energy barrier between the free and bound states to establish an efficient decision making branchpoint in the regulatory process.

MeSH Terms
Aptamers, Nucleotide/chemistry,metabolism Binding Sites/genetics Crystallography Magnesium/metabolism Models, Molecular Nucleic Acid Conformation RNA, Messenger/chemistry S-Adenosylmethionine/metabolism Scattering, Small Angle
Chemicals
Aptamers, Nucleotide RNA, Messenger S-Adenosylmethionine Magnesium
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Stoddard Colby D
Department of Chemistry and Biochemistry, University of Colorado at Boulder, UCB 215, Boulder, CO 80309-0215, USA.
Montange Rebecca K
Hennelly Scott P
Rambo Robert P
Sanbonmatsu Karissa Y
Batey Robert T
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Article Info
Journal
Structure (London, England : 1993)
Abbr.
Structure
ISSN
1878-4186
DOI
10.1016/j.str.2010.04.006
Published
2010-07-14
Pages
787-97
Language
English
Region
United States
NLM ID
101087697
PMCID
PMC2917978
Subset
IM
Grants
NIGMS NIH HHS · RC1GM092031 · United States
NIGMS NIH HHS · GM083953 · United States
NIGMS NIH HHS · RC1 GM092031 · United States
NIGMS NIH HHS · R01 GM083953-03 · United States
NIGMS NIH HHS · R01 GM083953 · United States
Corrections
CommentIn
PMID: 20637410
External Links
PubMed source DOI: 10.1016/j.str.2010.04.006 PMC Full Text View journal details
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