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Int J Ion Mobil Spectrom. 2015 Jun;18(1):23-29. Epub 2015 Mar 7.

Theoretical predictor for candidate structure assignment from IMS data of biomolecule-related conformational space.

Author information

1
Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
2
Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.

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.

KEYWORDS:

candidate structure generation; collision cross section; ion mobility spectrometry; molecular dynamic simulations; structural motifs

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