Relationship between ion pair geometries and electrostatic strengths in proteins.
The electrostatic free energy contribution of an ion pair in a protein depends on two factors, geometrical orientation of the side-chain charged groups with respect to each other and the structural context of the ion pair in the protein. Conformers in NMR ensembles enable studies of the relationship between geometry and electrostatic strengths of ion pairs, because the protein structural contexts are highly similar across different conformers. We have studied this relationship using a dataset of 22 unique ion pairs in 14 NMR conformer ensembles for 11 nonhomologous proteins. In different NMR conformers, the ion pairs are classified as salt bridges, nitrogen-oxygen (N-O) bridges and longer-range ion pairs on the basis of geometrical criteria. In salt bridges, centroids of the side-chain charged groups and at least a pair of side-chain nitrogen and oxygen atoms of the ion-pairing residues are within a 4 A distance. In N-O bridges, at least a pair of the side-chain nitrogen and oxygen atoms of the ion-pairing residues are within 4 A distance, but the distance between the side-chain charged group centroids is greater than 4 A. In the longer-range ion pairs, the side-chain charged group centroids as well as the side-chain nitrogen and oxygen atoms are more than 4 A apart. Continuum electrostatic calculations indicate that most of the ion pairs have stabilizing electrostatic contributions when their side-chain charged group centroids are within 5 A distance. Hence, most (approximately 92%) of the salt bridges and a majority (68%) of the N-O bridges are stabilizing. Most (approximately 89%) of the destabilizing ion pairs are the longer-range ion pairs. In the NMR conformer ensembles, the electrostatic interaction between side-chain charged groups of the ion-pairing residues is the strongest for salt bridges, considerably weaker for N-O bridges, and the weakest for longer-range ion pairs. These results suggest empirical rules for stabilizing electrostatic interactions in proteins.
Kumar
Sandeep
S
Laboratory of Experimental and Computational Biology, National Cancer Institute, Frederick Cancer Research and Development Center, Frederick, Maryland 21702 USA.
Nussinov
Ruth
R
D055592:Biophysical Phenomena; D001703:Biophysics; D018360:Crystallography, X-Ray; D019992:Databases as Topic; D007477:Ions; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009584:Nitrogen / Q000737:chemistry; D010100:Oxygen / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity; D013816:Thermodynamics
D007477:Ions; D011506:Proteins; D009584:Nitrogen; D010100:Oxygen