Efficient Conformational Searching of Gas-Phase Peptides

 

 

††††††††††† Investigations of the structural and energetic properties of biomolecules in the gas phase represent an important new direction for scientific research.† The critical role of mass spectrometry in the field of proteomics has led to the regular study of gaseous, ionized peptides.† Modeling such molecules using the majority of contemporary empirical force fields for proteins would prove problematic, as these have been optimized for the study of proteins in condensed phases.† Furthermore, these molecules carry charges in nonstandard places, such as on atoms along the peptide backbone.† Motivated by these limitations, we have developed and validated parameters for conformational searching techniques for ionized peptides in the gas phase.† Specifically, we are studying the conformations of protonated peptides.† As the first step toward successful modeling of peptide ions in the gas phase, force field parameters for the protonated peptide backbone, based on the CHARMM22 protein force field, are being developed.† We will also compare results of modeled fragmentation reactions with mass spectral data.

 

Author Information

††††††††††† Name:††††††††††††††††††††††††† Christopher R. Kinsinger

††††††††††† Mentorís name:††††††††††† Karl K. Irikura

††††††††††† Division:†††††††††††††††††††††† Physical and Chemical Properties, 838

††††††††††† Laboratory:††††††††††††††††† CSTL

††††††††††† Room/Building: 358B/221

††††††††††† Mail Stop:††††††††††††††††††† 8380

††††††††††† Telephone #:†††††††††††††††† 301-975-2526

††††††††††† Fax #:†††††††††††††††††††††††††† 301-869-4020

††††††††††† Email:†††††††††††††††††††††††††† Christopher.kinsinger@nist.gov

††††††††††† Sigma Xi:††††††††††††††††††††† not a member

††††††††††† Category:†††††††††††††††††††† Chemistry