COULOMBIC INTERACTIONS BETWEEN PARTIALLY CHARGED MAIN-CHAIN ATOMS NOTHYDROGEN-BONDED TO EACH OTHER INFLUENCE THE CONFORMATIONS OF ALPHA-HELICES AND ANTIPARALLEL BETA-SHEET - A NEW METHOD FOR ANALYZING THE FORCES BETWEEN HYDROGEN-BONDING GROUPS IN PROTEINS INCLUDES ALL THE COULOMBIC INTERACTIONS

An angle named gamma has been employed to describe the geometry at a h ydrogen bond between main-chain atoms of polypeptides. In antiparallel beta-sheet, gamma is normally positive, whereas, in parallel beta-she et and alpha-helices, it is negative. Although intriguing, no particul ar explanation has been offered to explain this result. We provide evi dence that, in each case, the angular preference maximises the favoura ble Coulombic interaction between the partial negative charge on the c arbonyl oxygen atom and the partial positive charge on the carbonyl ca rbon atom adjacent to the NH group to which it is hydrogen-bonded. Ana lyses of helices and beta-sheets in native proteins using Lennard-Jone s potentials suggest that these carbonyl-carbonyl interactions are sig nificant components of the attractive forces holding main-chain CONH g roups together and are even in some cases larger than the hydrogen bon ds themselves. A novel technique for analysing the forces holding toge ther hydrogen-bonding groups in proteins is presented. It tan be regar ded as a development of the Kabsch and Sander method of calculating th e energy of hydrogen bonds between main-chain atoms. In their program, electrostatic interactions are calculated between appropriate pairs o f atoms, i.e. NH binding to CO. Instead, in our method, the four N, H, C, and O atoms, in a pel!tide bond are taken as a unit and the intera ction between two NHCO groups calculated. We also use a Lennard-Jones potential, rather than just measuring the Coulombic interaction. With this approach, account is taken of all types of interactions between p artially charged atoms, not only the hydrogen bonds.