title: Theoretical predictor for candidate structure assignment from IMS data of biomolecule-related conformational space.
abstract: The ability to correlate experimental ion mobility data with candidate structures from theoretical modeling provides a powerful analytical and structural tool for the characterization of biomolecules. In the present paper, a theoretical workflow is described to generate and assign candidate structures for experimental trapped ion mobility and H/D exchange (HDX-TIMS-MS) data following molecular dynamics simulations and statistical filtering. The applicability of the theoretical predictor is illustrated for a peptide and protein example with multiple conformations and kinetic intermediates. The described methodology yields a low computational cost and a simple workflow by incorporating statistical filtering and molecular dynamics simulations. The workflow can be adapted to different IMS scenarios and CCS calculators for a more accurate description of the IMS experimental conditions. For the case of the HDX-TIMS-MS experiments, molecular dynamics in the "TIMS box" accounts for a better sampling of the molecular intermediates and local energy minima.
authors.affiliation: Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
authors.forename: Emily R
authors.initials: ER
authors.lastname: Schenk
authors.affiliation: Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
authors.forename: Frederic
authors.initials: F
authors.lastname: Nau
authors.affiliation: Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
authors.forename: Francisco
authors.initials: F
authors.lastname: Fernandez-Lima
keywords: candidate structure generation; collision cross section; ion mobility spectrometry; molecular dynamic simulations; structural motifs