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Analysis of Structural Stability of Chignolin
Yutaka Maruyama1, Ayori Mitsutake2
1Co-Design Team, FLAGSHIP 2020 Project , RIKEN Advanced Institute for Computational Science , Kobe 650-0047 , Japan.
The Journal of Physical Chemistry. B
|March 13, 2018
Summary
Investigating protein folding, this study reveals that while native and misfolded chignolin states have similar total energies, their stability arises from different interactions. Side-chain interactions stabilize native states, while main-chain hydrogen bonds dominate misfolded states.
Area of Science:
- Biochemistry
- Computational Biology
- Biophysics
Background:
- Protein folding is crucial for biological function.
- Understanding the stability of different protein conformations is key to deciphering folding mechanisms.
- Chignolin serves as a model miniprotein for studying folding pathways.
Purpose of the Study:
- To investigate the protein-folding mechanism by analyzing the stability of entire proteins.
- To determine the influence of main chains and side chains of individual amino acids on protein stability.
- To compare the energetic contributions of different states (native, misfolded, intermediate, unfolded) of chignolin.
Main Methods:
- Calculated solvation free-energy contributions of individual atoms using the three-dimensional reference interaction site model (3D-RISM) with atomic decomposition.
- Generated chignolin miniprotein structures using molecular dynamics simulations.
- Classified simulated structures into six types: native 1, native 2, misfolded 1, misfolded 2, intermediate, and unfolded states.
Main Results:
- Total energies of native (-171.1 kcal/mol) and misfolded (-171.2 kcal/mol) states were comparable and lower than intermediate (-158.5 kcal/mol) and unfolded (-148.1 kcal/mol) states.
- Native state stability is linked to side-chain interactions (e.g., Thr6-Thr8) facilitating π-turn formation.
- Misfolded states exhibit stronger main-chain hydrogen bonds compared to intermediate states.
Conclusions:
- Protein stability is determined by the specific contributions of various interactions, not just total energy.
- Distinct interaction patterns characterize native and misfolded protein states.
- The study provides insights into the subtle energetic differences governing protein folding pathways.
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