Gas-Phase Conformation of Biological Molecules: Bradykinin

Abstract

Several cationized forms of bradykinin (BK) were generated in the gas phase using matrix assisted laser desorption ionization (MALDI). Accurate collision cross sections were obtained using the ion chromatography method. The species studied include (BK + H) +, (BK + Na) +, and (BK − H + 2Na) + . It was found that all three species had very similar cross sections of 245 ± 3 Å 2, and these cross sections were independent of temperature from 300 to 600 K. It could be concluded from these data that BK wraps itself around the charge center(s) in a globular shape whose time average size changes little up to 600 K. The arrival time distributions of all three systems were narrow, only slightly broader than expected for a single species indicating cationized BK exists in only a few low-energy conformers at low temperature. A detailed analysis of the data was done using molecular mechanics/dynamics of the AMBER 4.0 suite of programs. The calculations were in excellent agreement with experiment in that scatter plots indicated cross sections of 100 member structural sets of (BK + H) +, (BK + Na) +, and (BK − H + 2Na) + were very similar. Further, very extensive dynamics studies over the range 200 to 600 K indicated the lowest energy conformers exhibited cross sections independent of temperature in agreement with experiment and supported the indication that only a few conformers are involved. The absolute magnitudes of the AMBER generated 0 K structures were ∼10% smaller than experiment. The discrepancy decreased to ∼5% when the systems were thermally averaged at 300 K. Selected 0 K conformers of (BK + H) + were calculated using AM1 and PM3 from AMBER starting structures. It was found that the 0 K cross sections increased by ∼5% over the AMBER structures providing better agreement with experiment. The extensive conformer sets generated in the scatter plots were analyzed to see which parts of BK preferred to bind to the charge sites. As expected the binding was global, but each isomer or system had different preferred binding sites. We looked for a preference of BK forming a β-turn in the Ser 6 -Pro 7 -Phe 8 -Arg 9 sequence since such a feature had been proposed in solution NMR studies. We found little evidence for β-turns in our 500 conformers of variously cationized BK in the gas phase.