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RNA Structure

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 Structure

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 Structure

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...

Protein Folding Quality Check in the RER

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

Protein Folding

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

Protein Folding

Protein Folding

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Related Experiment Video

Updated: Jun 12, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

Published on: September 15, 2010

Computing the conformational entropy for RNA folds.

Liang Liu¹, Shi-Jie Chen

¹Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, USA.

The Journal of Chemical Physics

|June 25, 2010

Summary

This summary is machine-generated.

We developed a polymer physics method to calculate RNA conformational entropy for tertiary folds. This approach accurately models complex RNA structures and their folding landscapes.

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Last Updated: Jun 12, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

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Practical Aspects of Sample Preparation and Setup of 1H R1ρ Relaxation Dispersion Experiments of RNA

Practical Aspects of Sample Preparation and Setup of ¹H R_1ρ Relaxation Dispersion Experiments of RNA

Published on: July 9, 2021

Area of Science:

Polymer Physics
Computational Biology
Structural Biology

Background:

RNA tertiary structures are crucial for biological function.
Calculating conformational entropy for RNA folds is computationally challenging.
Existing methods struggle with excluded volume interactions in complex folds.

Purpose of the Study:

To develop a polymer physics-based method for computing conformational entropy in RNA tertiary folds.
To accurately model RNA conformations involving multiple helices and loops.
To enable the study of molten globule-like folds in RNA.

Main Methods:

Utilized a virtual bond conformational model for the nucleotide chain.
Decomposed complex RNA structures into three-body building blocks (loop with two helices).
Developed an accurate method for computing conformational entropy of these building blocks and assembling them.

Main Results:

The method accurately computes conformational entropy for RNA tertiary folds.
Successfully treated molten globule-like folds (partially unfolded tertiary structures).
Validated results against experimental data and exact computer enumerations.

Conclusions:

The developed method provides an accurate way to calculate RNA conformational entropy.
This work is a foundational step towards a comprehensive theory for RNA and protein folding free energy landscapes.
Enables more accurate predictions of RNA structure and function.