TY - JOUR
T1 - Analysis of Structural Stability of Chignolin
AU - Maruyama, Yutaka
AU - Mitsutake, Ayori
N1 - Funding Information:
This work was supported by JST PRESTO (JPMJPR13LB). This research is partially supported by the Initiative on Promotion of Supercomputing for Young or Women Researchers, Supercomputing Division, Information Technology Center, The University of Tokyo. Numerical calculations were performed in part using HA-PACS at the Center for Computational Sciences (CCS), University of Tsukuba. Molecular graphics for Figures 3 and 5 were performed with the UCSF Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311).56 Figure 4 was drawn using VMD software support. VMD is developed with NIH support by the Theoretical and Computational Biophysics group at the Beckman Institute, University of Illinois, at Urbana-Champaign.52
Funding Information:
This work was supported by JST PRESTO (JPMJPR13LB). This research is partially supported by the Initiative on Promotion of Supercomputing for Young or Women Researchers, Supercomputing Division, Information Technology Center, The University of Tokyo. Numerical calculations were performed in part using HA-PACS at the Center for Computational Sciences (CCS), University of Tsukuba. Molecular graphics for Figures 3 and 5 were performed with the UCSF Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311).(56) Figure 4 was drawn using VMD software support. VMD is developed with NIH support by the Theoretical and Computational Biophysics group at the Beckman Institute, University of Illinois at Urbana-Champaign.
Publisher Copyright:
© 2018 American Chemical Society.
PY - 2018/4/12
Y1 - 2018/4/12
N2 - 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.
AB - 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.
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U2 - 10.1021/acs.jpcb.8b00288
DO - 10.1021/acs.jpcb.8b00288
M3 - Article
AN - SCOPUS:85045459481
SN - 1520-6106
VL - 122
SP - 3801
EP - 3814
JO - Journal of Physical Chemistry B
JF - Journal of Physical Chemistry B
IS - 14
ER -