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Related Experiment Videos

Discriminating compact nonnative structures from the native structure of globular proteins

Y Wang1, H Zhang, W Li

  • 1Department of Molecular Biology, Jilin University, Changchun, People's Republic of China.

Proceedings of the National Academy of Sciences of the United States of America
|January 31, 1995
PubMed
Summary

Developing accurate protein structure prediction models requires distinguishing native from nonnative protein structures. An atomic solvation model successfully differentiates native protein structures from 1200 near-native, compact alternatives.

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Area of Science:

  • Structural biology
  • Computational chemistry
  • Biophysics

Background:

  • Accurate prediction of native protein tertiary structure from primary sequence is crucial.
  • Potential energy models must discriminate nonnative structures, including compact, near-native ones.

Purpose of the Study:

  • To develop and test a robust method for generating near-native protein structures.
  • To evaluate the performance of empirical energy models in distinguishing native from nonnative protein conformations.

Main Methods:

  • Utilized molecular dynamics simulations to generate hundreds of compact, alternate protein structures near the native state.
  • Sampled conformational space around native structures for rigorous testing of protein folding models.
  • Tested eight empirical energy models using 1200 alternate structures from six small globular proteins.

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Main Results:

  • Seven of the eight tested empirical energy models failed to correctly identify all alternate structures as nonnative.
  • The proposed atomic solvation model successfully discriminated all 1200 near-native alternate structures from native structures.

Conclusions:

  • The atomic solvation model provides a reliable method for discriminating native from nonnative protein structures.
  • The generated near-native structures serve as a stringent benchmark for evaluating protein folding prediction models.