Statistical Analysis of Ion Mobility Spectrometry. II. Adaptively Biased Methods and Shape Correlations
Following a recent effort [J. Am. Soc. Mass Spectrom. 23, 386-396 (2012)], we continue to explore computational methodologies for generating molecular conformations to support collisional cross sections suggested by ion mobility measurements. Here, adaptively biased molecular dynamics (ABMD) simulations are used to sample the configuration space and to achieve flat-histogram sampling along the reaction coordinates of the first two moments of the gyration tensor. The method is tested and compared with replica-exchange simulations on triply-protonated bradykinin and on a larger 25-residue peptide. It is found to have a much higher efficiency for producing large sets of conformations in a broad range of diffusion cross-sections, whereas it does not compete with conventional replica-exchange molecular dynamics in locating the lowest-energy structure. Nevertheless, the broad sampling obtained from the ABMD method allows to quantitatively correlate the diffusion cross-section Omega with other geometric order parameters that have simpler interpretation. The strong correlations found between the diffusion cross-section and the radius of gyration, the surface area and the volume of the convex hull suggest an optimal template for accurately mimicking the variations of Omega in a broad range of conformations, using only geometrical information and doing so at a very moderate computational cost. The existence of such a correlation is confirmed on the much larger protein alpha-lactalbumin.
Keywords: Ion mobility spectrometry ; Structure determination ; Molecular dynamics ; Exchange Molecular-Dynamics ; Free-Energy Calculations ; Gas-Phase ; Mass-Spectrometry ; Bradykinin ; Algorithm ; Protein ; States ; Model ; Dissociation
Record created on 2012-06-21, modified on 2016-08-09