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Related Concept Videos

Initiation of Translation02:33

Initiation of Translation

Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
RNA Structure01:19

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...

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Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs
10:37

Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs

Published on: May 10, 2018

Induced fit for mRNA/TIS11d complex.

Fang Qin1, Yue Chen, Yi-Xue Li

  • 1College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China.

The Journal of Chemical Physics
|September 26, 2009
PubMed
Summary
This summary is machine-generated.

The TIS11d tandem zinc finger domain folds upon binding to zinc and mRNA, regulating mRNA turnover. Molecular dynamics simulations revealed the mechanism of this binding-induced folding, aligning with NMR experiments.

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Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs
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Published on: February 12, 2022

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • The TIS11d tandem zinc finger (TZF) domain binds AU-rich elements in mRNA.
  • This interaction regulates mRNA turnover by influencing degradation pathways.
  • The TIS11d(TZF) domain transitions from a disordered to a folded state upon binding to zinc and mRNA, as observed by NMR.

Purpose of the Study:

  • To elucidate the mechanism of binding-induced folding in the mRNA-TIS11d(TZF) complex.
  • To investigate the interdependence of ligand binding and protein folding.
  • To validate computational methods for studying protein-ligand interactions.

Main Methods:

  • Explicit-solvent molecular dynamics (MD) simulations were employed.
  • Simulations were performed for both apo-TIS11d(TZF) and the mRNA-TIS11d(TZF) complex.
  • Results were compared with experimental Nuclear Magnetic Resonance (NMR) data.

Main Results:

  • MD simulations captured the transition of TIS11d(TZF) from a disordered to a folded state upon binding to mRNA and zinc.
  • The simulations provided insights into the dynamic interplay between binding and folding.
  • The computational findings were in qualitative agreement with NMR experimental data.

Conclusions:

  • The study reveals the mechanism of binding-induced folding of the TIS11d(TZF) domain.
  • Molecular dynamics simulations are a valuable tool for studying protein folding upon ligand binding.
  • This approach can be extended to investigate other protein-ligand systems.