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Related Experiment Videos

Protein folding: the endgame

M Levitt1, M Gerstein, E Huang

  • 1Department of Structural Biology, Stanford University School of Medicine, California 94305, USA.

Annual Review of Biochemistry
|January 1, 1997
PubMed
Summary
This summary is machine-generated.

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Protein folding

Area of Science:

  • Protein folding
  • Structural biology
  • Computational biology

Background:

  • The final stage of protein folding, known as the "endgame," involves organizing amino acid side-chains into a stable, tightly packed structure.
  • Protein interiors are packed more densely than their surfaces, the surrounding solvent, or even simple organic molecule crystals.
  • In vitro experiments confirm that proteins achieve close packing in solution, with side-chain intercalation being a crucial final folding step.

Purpose of the Study:

  • To review methods for measuring and predicting side-chain packing in proteins.
  • To discuss the challenges and recent advancements in predicting protein side-chain configurations.
  • To survey methods for predicting main-chain conformation, which is critical for accurate side-chain prediction.

Main Methods:

Related Experiment Videos

  • Analysis of protein crystal structures to quantify side-chain packing density.
  • Review of in vitro protein folding experiments demonstrating close packing in solution.
  • Survey of computational approaches for predicting side-chain configurations, including ab initio and knowledge-based methods.
  • Examination of methods for predicting main-chain conformation.

Main Results:

  • Protein interiors exhibit exceptionally tight packing, essential for stable folded structures.
  • Predicting side-chain packing is feasible, akin to solving a 3D jigsaw puzzle.
  • Significant progress has been made in computational methods for predicting side-chain configurations, despite combinatorial challenges.
  • Main-chain conformation prediction methods are less developed than side-chain prediction techniques.

Conclusions:

  • Tight side-chain packing is a fundamental characteristic of folded proteins.
  • Computational approaches are advancing the prediction of protein structures.
  • Accurate main-chain conformation prediction is crucial for improving side-chain packing predictions.