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Related Concept Videos

Protein Folding01:22

Protein Folding

Overview
Protein Folding01:22

Protein Folding

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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
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Molecular Chaperones and Protein Folding03:00

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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.
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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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Visualization and Quantification of Intermolecular RNA Base Pairing in in vitro RNA Clusters Using Split Broccoli RNA Reporters
10:52

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Improving strand pairing prediction through exploring folding cooperativity.

Jieun Jeong1, Piotr Berman, Teresa M Przytycka

  • 1Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA.

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|November 8, 2008
PubMed
Summary

Predicting beta-sheet topology relies on identifying hydrogen-bonded strand partners. Our new algorithm mimics protein folding pathways, improving accuracy in predicting these crucial interactions for beta-sheet structure.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Beta-sheet topology is determined by hydrogen-bonded strand pairing patterns.
  • Accurate prediction of strand partners is essential but challenging due to long-range interactions and general amino acid patterns.
  • Existing computational methods struggle with the complexity of specific contact recognition.

Purpose of the Study:

  • To develop a novel strand pairing algorithm for predicting beta-sheet topology.
  • To address the difficulties posed by long-range interactions and general amino acid sequence motifs.
  • To improve the accuracy of predicting hydrogen-bonded strand partners in beta-sheets.

Main Methods:

  • The new algorithm incorporates principles of protein folding pathways.
  • It ensures predicted hydrogen bonds meet global consistency constraints.
  • It models how forming one hydrogen bond influences probabilities of others.

Main Results:

  • The developed algorithm demonstrates improved performance over existing methods.
  • It effectively accounts for the dynamic nature of hydrogen bond formation during folding.
  • Performance was benchmarked against a global optimization approach using integer linear programming.

Conclusions:

  • The novel strand pairing algorithm offers enhanced accuracy in predicting beta-sheet topology.
  • Mimicking folding pathways provides a more effective strategy for identifying hydrogen-bonded strand partners.
  • This approach represents a significant advancement in computational protein structure prediction.