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Native and non-native interactions along protein folding and unfolding pathways
Emanuele Paci1, Michele Vendruscolo, Martin Karplus
1Oxford Centre for Molecular Sciences, Central Chemistry Laboratory, University of Oxford, Oxford United Kingdom.
Proteins
|April 12, 2002
Summary
Gō-type models accurately describe protein folding energy for native states. However, they introduce errors for non-native structures due to significant contributions from non-native contacts.
Area of Science:
- Computational biology
- Biophysics
- Protein dynamics
Background:
- Gō-type models simplify protein folding by using only native contact interactions.
- These models are increasingly used to simulate protein folding reactions.
Purpose of the Study:
- To evaluate the accuracy of Gō-type models by assessing the role of native and non-native interactions.
- To determine the validity of using only native contacts in protein folding energy functions.
Main Methods:
- Utilized a molecular mechanics energy function with an implicit solvation model.
- Employed a pairwise decomposable effective energy function (potential of mean force).
- Analyzed energy contributions from native and non-native contacts across various protein configurations.
Main Results:
- Native contact energy accurately describes the native state and many other configurations.
- Significant energy errors arise in non-native structures when only native contacts are considered.
- Non-native contacts contribute substantially, especially in molten globules and collapsed states during unfolding.
Conclusions:
- Gō-type models show limitations when non-native interactions are significant.
- The accuracy of Gō-type models depends on the cancellation of non-native contributions.
- Further considerations are needed for accurate protein folding simulations using Gō-type models.