title: On the structure elucidation using ion mobility spectrometry and molecular dynamics.
abstract: A new approach is described for the elucidation of gas-phase peptide ion structures combining ion mobility spectrometry (IMS) data and molecular dynamics (MD)-cluster analysis (CA) prediction. The new approach is based on the determination of the gas-phase ion structure identity vectors (e.g., structure and population vectors) that generate the total conformational space of the gas-phase ion as a function of the IMS experimental conditions (e.g., field strength, pressure, bath gas temperature, and IM cell geometry). Two methods to efficiently sample the gas-phase conformational space of molecular ions as a function of the effective ion temperature characteristic of the IMS experiments are described: (i) a simulated annealing MD-CA-constant temperature MD-CA, and (ii) a generalized non-Boltzmann sampling MD-free energy analysis-CA. The new theoretical method has been successfully applied to two model peptide ions (Bradykinin fragments 1-5 and 1-8, RPPGF and RPPGFSPF, respectively) for which multiple conformations sensitive to the effective ion temperature have been suggested in previous studies.
authors: Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA.
authors: F A
authors: FA
authors: Fernandez-Lima
authors: H
authors: H
authors: Wei
authors: Y Q
authors: YQ
authors: Gao
authors: D H
authors: DH
authors: Russell
mesh_terms: D000595:Amino Acid Sequence; D001920:Bradykinin / Q000737:chemistry; D016000:Cluster Analysis; D005740:Gases / Q000737:chemistry; D008958:Models, Molecular; D009038:Motion; D010446:Peptide Fragments / Q000737:chemistry; D011312:Pressure; D011487:Protein Conformation; D013057:Spectrum Analysis; D013696:Temperature; D013816:Thermodynamics
chemical_list: D005740:Gases; D010446:Peptide Fragments; C079000:bradykinin (1-5); D001920:Bradykinin