### Abstract

Monte Carlo simulations of a small protein, carmbin, were carried out with and without hydration energy. The methodology presented here is characterized, as compared with the other similar simulations of proteins in solution, by two points: (1) protein conformations are treated in fixed geometry so that dihedral angles are independent variables rather than cartesian coordinates of atoms; and (2) instead of treating water molecules explicitly in the calculation, hydration energy is incorporated in the conformational energy function in the form of Σg_{i}A_{i}, where A_{i} is the accessible surface area of an atomic group i in a given conformation, and g_{i} is the free energy of hydration per unit surface area of the atomic group (i.e., hydration-shell model). Reality of this model was tested by carrying out Monte Carlo simulations for the two kinds of starting conformations, native and unfolded ones, and in the two kinds of systems, in vacuo and solution. In the simulations starting from the native conformation, the differences between the mean properties in vacuo and solution simulations are not very large, but their fluctuations around the mean conformation during the simulation are relatively smaller in solution than in vacuo. On the other hand, in the simulations starting from the unfolded conformation, the molecule fluctuates much more largely in solution than in vacuo, and the effects of taking into account the hydration energy are pronounced very much. The results suggest that the method presented in this paper is useful for the simulations of proteins in solution.

Original language | English |
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Pages (from-to) | 733-747 |

Number of pages | 15 |

Journal | Journal of Protein Chemistry |

Volume | 8 |

Issue number | 6 |

DOIs | |

Publication status | Published - 1989 Dec 1 |

### Keywords

- Monte Carlo simulation
- conformational energy analysis
- crambin
- hydration energy

### ASJC Scopus subject areas

- Biochemistry