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Related Concept Videos

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
Protein Folding01:22

Protein Folding

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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...
Protein Folding Quality Check in the RER01:29

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...

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Published on: July 25, 2013

A novel approach for large-scale polypeptide folding based on elastic networks using continuous optimization.

Sourav Rakshit1, G K Ananthasuresh

  • 1Mechanical Engineering, Indian Institute of Science, Bangalore 560012, India. srakshit@mecheng.iisc.ernet.in

Journal of Theoretical Biology
|October 17, 2009
PubMed
Summary

This study introduces an efficient computational method for polypeptide folding, significantly reducing simulation time on standard computers. The approach enhances accuracy and speed for protein structure prediction.

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Area of Science:

  • Computational Biology
  • Biophysics
  • Structural Biology

Background:

  • Accurate protein structure prediction is crucial for understanding biological function.
  • Simulating polypeptide folding from an unfolded state remains computationally intensive.
  • Existing methods often require significant computational resources.

Purpose of the Study:

  • To develop a computationally efficient method for large-scale polypeptide folding.
  • To reduce simulation time for protein folding on ordinary desktop computers.
  • To improve the accuracy of protein structure prediction.

Main Methods:

  • Utilized coarse-grained elastic networks and gradient-based continuous optimization.
  • Employed Miyazawa-Jernigan contact potentials for energy minimization.
  • Compared results with Protein Data Bank (PDB) structures and established software (MODELLER, GROMACS).

Main Results:

  • Achieved substantial reductions in computation time for simulating polypeptide folding.
  • Validated the method against native structures of de-novo, Ubiquitin, and Lysozyme proteins.
  • Successfully mapped the energy landscape for the de-novo protein Chignolin.

Conclusions:

  • The developed method offers a computationally efficient approach to polypeptide folding.
  • A modified elastic network model enhances both accuracy and simulation speed.
  • This technique holds promise for advancing protein structure prediction and analysis.