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Related Concept Videos

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

BuildBeta--a system for automatically constructing beta sheets.

Nelson Max1, Chengcheng Hu, Oliver Kreylos

  • 1Department of Computer Science, University of California, Davis, California 95616, USA.

Proteins
|September 22, 2009
PubMed
Summary
This summary is machine-generated.

This study presents a novel method for predicting protein structures, particularly those with beta-sheets, by sampling conformational space. The approach accurately models complex beta-sheet arrangements, aiding in ab initio protein structure prediction.

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Accurate protein structure prediction is crucial for understanding biological function.
  • Proteins with beta-sheets present significant challenges for ab initio structure prediction due to complex long-range strand pairings.

Purpose of the Study:

  • To develop a robust method for thoroughly sampling protein conformational space.
  • To specifically address the challenges in predicting structures of proteins containing beta-sheets.

Main Methods:

  • Utilizes basic packing principles, inverse kinematics (IK), and beta-pairing scores.
  • Employs IK algorithms to manipulate alpha-helices and beta-strands as rigid bodies.
  • Systematically generates all possible beta-sheet arrangements, including correctly packed ones.

Main Results:

  • The method successfully models proteins with diverse beta-sheet topologies and sizes.
  • Generated structures achieve root-mean-square deviation (RMSD) of 4-6 Å compared to native structures.
  • Accuracy may be affected by long loops or complex alpha-helical regions.

Conclusions:

  • The developed method offers a reliable approach for ab initio protein structure prediction, especially for beta-sheet rich proteins.
  • This technique enhances the ability to model complex protein structures computationally.