Accurate geometries for "Mountain pass" regions of the Ramachandran plot using quantum chemical calculations

Unusual local arrangements of protein in Ramachandran space are not well represented by standard geometry tools used in either protein structure refinement using simple harmonic geometry restraints or in protein simulations using molecular mechanics force fields. In contrast, quantum chemical computations using small poly-peptide molecular models can predict accurate geometries for any well-defined backbone Ramachandran orientation. For conformations along transition regions-phi from 260 to 608 degrees-a very good agreement with representative high-resolution experimental X-ray (<= 1.5 A) protein structures is obtained for both backbone C21-N-Ca angle and the nonbonded O-1 center dot center dot center dot C distance, while "standard geometry" leads to the "clashing" of O center dot center dot center dot C atoms and Amber FF99SB predicts distances too large by about 0.15 angstrom. These results confirm that quantum chemistry computations add valuable support for detailed analysis of local structural arrangements in proteins, providing improved or missing data for less understood high-energy or unusual regions.