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Related Concept Videos

Riboswitches01:56

Riboswitches

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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
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Transcriptional Regulation: Riboswitches01:23

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Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
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Translational Regulation01:29

Translational Regulation

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Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
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Types of RNA01:23

Types of RNA

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Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
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Leaky Scanning02:28

Leaky Scanning

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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Related Experiment Video

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Nanomanipulation of Single RNA Molecules by Optical Tweezers
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Using reweighted pulling simulations to characterize conformational changes in riboswitches.

Francesco Di Palma1, Francesco Colizzi1, Giovanni Bussi1

  • 1Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.

Methods in Enzymology
|March 2, 2015
PubMed
Summary

This study uses steered molecular dynamics (MD) to quantify how ligand binding affects riboswitch stability. Researchers successfully measured the free energy of ligand-riboswitch interactions, validating experimental findings.

Keywords:
Enhanced samplingFree energyLigand-induced foldingReweightingRiboswitchSteered molecular dynamics

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Area of Science:

  • Molecular biology
  • Biophysics
  • Computational chemistry

Background:

  • Riboswitches are RNA molecules that regulate gene expression by sensing small molecules.
  • Ligand binding induces conformational changes in riboswitches, affecting gene expression.
  • Understanding these ligand-induced changes at atomic resolution is experimentally challenging.

Purpose of the Study:

  • To apply steered molecular dynamics (MD) to investigate ligand-dependent behavior in riboswitches.
  • To quantify the stability of the aptamer terminal helix in an adenine-sensing riboswitch upon ligand binding.
  • To demonstrate the utility of enhanced sampling techniques for studying riboswitch mechanisms.

Main Methods:

  • Utilized steered molecular dynamics (MD) simulations.
  • Employed enhanced sampling techniques to overcome time-scale limitations of standard MD.
  • Focused on the add adenine-sensing riboswitch system.
  • Provided detailed methodology and sample input files for steered MD.

Main Results:

  • Successfully quantified the ligand-dependent stability of the aptamer terminal helix.
  • Calculated the free energy associated with the stacking interaction between adenine and the terminal helix.
  • Achieved results consistent with experimental thermodynamic data.
  • Demonstrated that steered MD can provide quantitative insights with limited computational cost.

Conclusions:

  • Steered MD is an effective computational tool for characterizing ligand-dependent riboswitch dynamics.
  • Enhanced sampling techniques enable the study of biologically relevant timescales.
  • This approach offers a cost-effective method to obtain quantitative, experimentally verifiable data on riboswitch mechanisms.