Efficient Conformational Searching of by e295e75ae2526297


									Efficient Conformational Searching of
          Gas-Phase Peptides
                                   O                      O                O
                            CH     C        N       CH    C   N      CH    C
                            CH3                     CH3              CH3


                                   CH       O
                                                              H 2N    CH       C
                            H 3C                O
                                   H        CH3                       CH3

        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
       Mentor’s 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

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