Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism
نویسندگان
چکیده
منابع مشابه
The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch
Riboswitch operation involves the complex interplay between the aptamer domain and the expression platform. During transcription, these two domains compete against each other for shared sequence. In this study, we explore the cooperative effects of ligand binding and Magnesium interactions in the SAM-I riboswitch in the context of aptamer collapse and anti-terminator formation. Overall, our stu...
متن کاملTranslational control and Rho-dependent transcription termination are intimately linked in riboswitch regulation
Riboswitches are regulatory elements that control gene expression by altering RNA structure upon the binding of specific metabolites. Although Bacillus subtilis riboswitches have been shown to control premature transcription termination, less is known about regulatory mechanisms employed by Escherichia coli riboswitches, which are predicted to regulate mostly at the level of translation initiat...
متن کاملThe Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch
Riboswitches sense cellular concentrations of small molecules and use this information to adjust synthesis rates of related metabolites. Riboswitches include an aptamer domain to detect the ligand and an expression platform to control gene expression. Previous structural studies of riboswitches largely focused on aptamers, truncating the expression domain to suppress conformational switching. T...
متن کاملAtomistic details of the ligand discrimination mechanism of S(MK)/SAM-III riboswitch.
SAM-III riboswitch, involved in regulating sulfur metabolic pathways in lactic acid bacteria, is capable of differentiating S-adenosyl-l-methionine (SAM) from its structurally similar analogue S-adenosyl-l-homocysteine (SAH). Atomic level understanding of the ligand recognition mechanism of riboswitches is essential for understanding their structure-function relationships in general. In the pre...
متن کاملMagnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch.
Experiments demonstrate that Mg(2+) is crucial for structure and function of RNA systems, yet the detailed molecular mechanism of Mg(2+) action on RNA is not well understood. We investigate the interplay between RNA and Mg(2+) at atomic resolution through ten 2-μs explicit solvent molecular dynamics simulations of the SAM-I riboswitch with varying ion concentrations. The structure, including th...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: RNA
سال: 2017
ISSN: 1355-8382,1469-9001
DOI: 10.1261/rna.061796.117