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Related Concept Videos

Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

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 Folding01:22

Protein Folding

Overview
Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...

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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

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Published on: May 6, 2010

Abstract folding space analysis based on helices.

Jiabin Huang1, Rolf Backofen, Björn Voß

  • 1Genetics & Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg 79104, Germany.

RNA (New York, N.Y.)
|October 30, 2012
PubMed
Summary
This summary is machine-generated.

Understanding RNA structure is key to gene regulation. New methods like hishapes, RNAHeliCes, HiPath, and HiTed improve RNA folding analysis by abstracting complex folding spaces.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Non-coding RNAs (ncRNAs) play crucial roles in gene expression regulation.
  • Accurate RNA structure identification is essential for understanding ncRNA function.
  • Existing RNA structure prediction methods face limitations due to complex folding spaces and biological factors like base modifications and conformational switching.

Purpose of the Study:

  • To develop novel computational methods for more in-depth analysis of RNA folding spaces.
  • To address the limitations of existing RNA structure prediction algorithms, particularly concerning sequence length and computational complexity.
  • To introduce a new abstraction strategy for RNA folding analysis.

Main Methods:

  • Introduced a position-specific abstraction based on helices, termed helix index shapes (hishapes).
  • Implemented the hishape abstraction within a dynamic programming framework in the RNAHeliCes program.
  • Developed two hishape-based tools: HiPath for energy barrier estimation and HiTed for abstract structure comparison.

Main Results:

  • Demonstrated superior performance of the HiPath method for energy barrier estimation compared to existing approaches.
  • Showcased competitive accuracy of the HiTed method for abstract RNA structure comparison.
  • Successfully implemented and integrated these novel methods into the RNAHeliCes software package.

Conclusions:

  • The hishape abstraction strategy offers a promising approach to overcome the limitations of traditional RNA folding analysis.
  • RNAHeliCes, HiPath, and HiTed provide powerful and accurate tools for studying RNA structure and function.
  • These advancements facilitate a deeper understanding of RNA's role in biological processes, particularly in gene regulation.