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Structure of guanosine‐3′,5′‐cytidine monophosphate. I. Semi‐empirical potential energy calculations and model‐building
Author(s) -
Stellman S. D.,
Hingerty B.,
Broyde S. B.,
Subramanian E.,
Sato T.,
Langridge R.
Publication year - 1973
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.1973.360121208
Subject(s) - dihedral angle , chemistry , crystallography , orientation (vector space) , molecule , monoclinic crystal system , potential energy , cytidine , crystal structure , geometry , hydrogen bond , physics , mathematics , quantum mechanics , enzyme , organic chemistry , biochemistry
The conformation and packing scheme for guanosine‐3′, 5′‐cytidine monophosphate, GpC, were computed by minimizing the classical potential energy. The lowest energy conformation of the isolated molecule had dihedral angles in the range of helical RNA's and the sugar pucker was C3′ endo . This was used as the starting conformation in a packing search over orientation space, the dihedral angles being flexible in this step also. The packing search was restricted by constraints from our x‐ray data, namely, (1) the dimensions of the monoclinic unit cell and its pseudo‐C2 symmetry (the real space group is P 2 1 ), (2) the location of the phosphorous atom, and (3) the orientation of the bases. In addition, a geometric function was devised to impose Watson‐Crick base pairing. Thus, a trial structure could be sought without explicit inclusion of intermolecular potentials. An interactive computer graphics system was used for visualizing the calculated structures. The packing searches yielded two lowest energy schemes in which the molecules had the same conformation (similar to double‐helical RNA) but different orientations within the unit cell. One of these was refined by standard x‐ray methods to a discrepancy index of 14.4% in the C2 pseudocell. This served as the starting structure for the subsequent refinement in the real P 2 1 cell. 5