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Monte carlo simulation of the solvent structure in crystals of a hydrated cyclic peptide
Author(s) -
Hagler A. T.,
Moult J.,
Osguthorpe D. J.
Publication year - 1980
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.1980.360190214
Subject(s) - monte carlo method , chemistry , molecule , root mean square , hydrogen bond , solvent , molecular dynamics , crystal structure , structure factor , crystallography , crystal (programming language) , peptide , chemical physics , computational chemistry , physics , statistics , mathematics , organic chemistry , quantum mechanics , biochemistry , computer science , programming language
The Monte Carlo simulation of the structure of the 16 ordered and disordered waters in the unit cell of crystals of the cyclic peptide cyclo(‐ L ‐Ala‐ L ‐Pro‐ D ‐Phe) 2 is reported. The water structure has been characterized in terms of the statistically averaged positions of the individual molecules, their root‐mean‐square movements about these positions, the probability of finding a water in a given spatial position in the crystal (probability maps), and examination of individual configurations of the system. In this way a picture is obtained of the water structure, including water orientations (hydrogen positions), the hydrogen‐bonding network, and fluctuations in these structural features, to a degree hitherto unavailable either from experimental or theoretical studies. In addition, the variation in water structure in various peptide environments was studied and correlated with the energetics of the individual water molecules. Variations in the crystalline environment of different water molecules lead to energy differences of as much as 4–5 kcal/mol in their average energies. Similarly, differences are observed in the water–peptide and water–water components of the energy. Two different water potentials were tested. The results were compared with experimental data in terms of mean positions, root‐mean‐square movements, and the Fourier transform of the simulated water structure. The agreement factor ( R factor) calculated from the theoretical water probability distribution was 18.8% compared to the x‐ray value of 14.5%, and the value of 28% when the water is omitted.