Partial atomic charges of amino acids in proteins

Using a semiempirical quantum mechanical procedure (FCPAC) we have calculated the partial atomic charges of amino acids from 494 high‐resolution protein structures. To analyze the influence of the protein's environment, we considered each residue under two conditions: either as the center of a tripeptide with PDB structure geometry (free) or as the center of 13–16 amino acid clusters extracted from the PDB structure (buried). The partial atomic charges from residues in helices and in sheets were separated. The FCPAC partial atomic charges of the Cβ and Cα of most residues correlate with their helix propensity, positively for Cβ and negatively for Cα ( r 2 = 0.76 and 0.6, respectively). The main consequence of burying residues in proteins is the polarization of the backbone CO bond, which is more pronounced in helices than in sheets. The average shift of the oxygen partial charges that results from burying is −0.120 in helix and −0.084 in sheet with the charge of the proton as unit. Linear correlations are found between the average NMR chemical shifts and the average FCPAC partial charges of Cα ( r 2 = 0.8–0.85), N ( r 3 = 0.67–0.72), and Cβ (r 2 = 0.62) atoms. Correlations for helix and β‐sheet FCPAC partial charges show parallel regressions, suggesting that the charge variations due to burying in proteins differentiate between the dihedral angle effects and the polarization of backbone atoms. Proteins 2004. © 2004 Wiley‐Liss, Inc.