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Related Concept Videos

RNA Structure01:19

RNA Structure

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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.
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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.
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Protein Folding Quality Check in the RER01:29

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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...
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Protein Complex Assembly02:41

Protein Complex Assembly

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Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
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Nucleic Acid Structure01:25

Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Using 3dRPC for RNA-protein complex structure prediction.

Yangyu Huang1, Haotian Li1, Yi Xiao1

  • 1Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, 430074 China.

Biophysics Reports
|March 21, 2017
PubMed
Summary
This summary is machine-generated.

3dRPC predicts three-dimensional RNA-protein complex structures using computational docking and ranking. This method aids in understanding complex formations by evaluating predicted structures.

Keywords:
Computational predictionDockingRNA–protein complexScoring functionTertiary structure

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Area of Science:

  • Computational biology
  • Structural biology
  • Bioinformatics

Background:

  • RNA-protein complexes are crucial for cellular functions.
  • Predicting the 3D structure of these complexes is challenging.
  • Accurate structural models are needed for functional and mechanistic studies.

Purpose of the Study:

  • To describe the usage of 3dRPC, a computational method for 3D RNA-protein complex structure prediction.
  • To provide a detailed guide for researchers utilizing the 3dRPC tool.

Main Methods:

  • 3dRPC employs RPDOCK for generating potential complex structures.
  • RPDOCK is an FFT-based docking algorithm considering RNA-protein interaction features.
  • RPRANK, a knowledge-based potential using root mean square deviation, evaluates the generated structures.

Main Results:

  • The study details the step-by-step usage of the 3dRPC method.
  • The source code for 3dRPC is made publicly available.
  • The described method facilitates the prediction of RNA-protein complex structures.

Conclusions:

  • 3dRPC offers a computational approach for predicting RNA-protein complex structures.
  • The availability of the source code promotes accessibility and further development in the field.
  • This tool aids researchers in structural biology and bioinformatics.