Analysis of Structural Stability of Chignolin

Yutaka Maruyama, Ayori Mitsutake

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

We discuss the stability of an entire protein and the influence of main chains and side chains of individual amino acids to investigate the protein-folding mechanism. For this purpose, we calculated the solvation free-energy contribution of individual atoms using the three-dimensional reference interaction site model with the atomic decomposition method. We generated structures of chignolin miniprotein by a molecular dynamics simulation and classified them into six types: native 1, native 2, misfolded 1, misfolded 2, intermediate, and unfolded states. The total energies of the native (-171.1 kcal/mol) and misfolded (-171.2 kcal/mol) states were almost the same and lower than those of the intermediate (-158.5 kcal/mol) and unfolded (-148.1 kcal/mol) states; however, their components were different. In the native state, the side-chain interaction between Thr6 and Thr8 is important for the formation of π-turn. On the other hand, the hydrogen bonds between the atoms of the main chains in the misfolded state become stronger than those in the intermediate state.

Original languageEnglish
Pages (from-to)3801-3814
Number of pages14
JournalJournal of Physical Chemistry B
Volume122
Issue number14
DOIs
Publication statusPublished - 2018 Apr 12

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Protein Stability
Protein Folding
structural stability
Molecular Dynamics Simulation
Hydrogen
Protein folding
Amino Acids
Atoms
Solvation
Free energy
Molecular dynamics
Amino acids
Hydrogen bonds
proteins
Decomposition
Proteins
Computer simulation
folding
solvation
amino acids

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

Cite this

Analysis of Structural Stability of Chignolin. / Maruyama, Yutaka; Mitsutake, Ayori.

In: Journal of Physical Chemistry B, Vol. 122, No. 14, 12.04.2018, p. 3801-3814.

Research output: Contribution to journalArticle

Maruyama, Yutaka ; Mitsutake, Ayori. / Analysis of Structural Stability of Chignolin. In: Journal of Physical Chemistry B. 2018 ; Vol. 122, No. 14. pp. 3801-3814.
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