THE THERMODYNAMICS OF CRYSTAL PACKING: SOLVENT VERSUS STERIC EFFECTS. P. Shing Ho and Todd F. Kagawa, Dept. of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331

Molecular mechanics methods are useful tools for modeling the atomic details of molecular structures (1), but have not been generally successful at predicting global conformations. Solvent free energy (SFE) calculations, in contrast, have successfully modeled the contribution of hydrophobicity to the relative stability of protein (2) and DNA conformations (3, 4), but is not currently applicable at the atomic level. Here, we use a crystallographic assay to study the contribution of competing steric and hydrophobic effects on the orientation of an asymmetric DNA duplex within a crystal lattice. In these studies, we monitor the effect of single methyl groups of cytosine bases on the specific orientations of sequences of the type d(CGCCCG)-d(CGGGCG) (5). From this we determine the free energies of intermolecular interactions in the lattice. Both solvent and steric interactions appear to contribute to assembly of the lattice: the contribution of steric interactions, however, are overestimated by a factor of 4 using standard Lennard-Jones potentials. The assay provides a scaling factor between the two competing interactions and thus a means for incorporating hydrophobicity, as estimated from SFEs, into the more detailed molecular mechanics methods for predicting macromolecular folding and assembly. This should apply to any assembly process, including the packing of helices in polypeptides.

Finally, we have assessed the overall effect of crystal packing on oligonucleotide structures by comparing essentially identical six and eight-base-pair sequences that crystallize as A-DNA. The hexanucleotide conformation of d(GCGCGC) is that of canonical A-DNA, while that of the octanucleotide d(GCGCGCGC) is the longer and narrower structure that is typical of this length. The inter-duplex interactions are identical in both sequences. We therefore have introduced the concept of a "symmetry force" to account for this difference. Here, we define the need for duplexes to adopt a symmetric lattice as the primary force that drives the conformational distortions observed in the oligonucleotide crystals. We estimate the magnitude of these forces by comparing the conformational energies of the six and eight base pair sequences.