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Conformational study of the trinucleotide CpGpCp‐pentapeptide Gly 5 complex: The important role of bridging water in the complex formation
Author(s) -
Yoon Chang No,
Jhon Mu Shik
Publication year - 1986
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540070212
Subject(s) - intramolecular force , chemistry , hydrogen bond , molecular dynamics , ring (chemistry) , molecule , crystallography , stereochemistry , sugar , computational chemistry , organic chemistry
Conformational changes in the RNA‐protein interaction were studied by calculating the intramolecular interaction energy of a model complex with the use of potential functions. The model complex has hydrogen‐bonded water molecules bridging polypeptide NH groups to 2'‐hydroxyl groups and sugar ring oxygen atoms. Since the sugar ring is constrained by the bridging water, preliminary calculations with the model compounds, the sugar ring, mononucleoside diphosphates, pCp and pGp, were carried out, and the flexibility and energetics of the sugar ring were compared with the previous results of DNA. The shift of the phase angle of the sugar ring occurred in the complex formation because of the hydrogen bond through the bridging water and the flexibility of the sugar ring. The free energy difference at 298 K is about −74.0 kcal/mol which was obtained from the intramolecular interaction energy difference of −67.5 kcal/mol by adding the conformational entropy change of 21.9 e.u., which in turn was calculated from the evaluation of the determinant of the matrix containing variances and covariances of the internal coordinates.