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Simulations of the solvent structure for macromolecules. I. Solvation of B‐DNA double helix at T = 300 K
Author(s) -
Corongiu Giorgina,
Clementi Enrico
Publication year - 1981
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.1981.360200309
Subject(s) - chemistry , molecule , solvation , helix (gastropod) , counterion , monte carlo method , solvation shell , macromolecule , dna , solvent , hydrogen bond , protein filament , crystallography , molecular dynamics , chemical physics , computational chemistry , ion , organic chemistry , ecology , biochemistry , statistics , mathematics , snail , biology
Monte Carlo simulations are reported for a system of 447 water molecules enclosing a B‐DNA double‐helix fragment with 12 base pairs and the corresponding sugar and phosphate units. From a detailed analysis on the interaction energies and probability distributions (at a simulated temperature of 300 K), the water molecules can be partitioned into clusters strongly interacting with (1) the phosphates, (2) the sugars, (3) the sugars and the bases, and (4) the base pairs. In addition, transgroove and interphosphate filament of hydrogen‐bonded water molecules have been detected. From simulations performed with variable numbers of water molecules, a theoretical isotherm has been obtained, with the characteristic sigmoidal shape, known from absorption–desorption experiments on related systems. The expected main features for the structure of water molecules solvating B‐DNA with Na + counterions are briefly discussed at the end of the paper.