Multi-speed sedimentation velocity implementation in UltraScan-III

Gary E. Gorbet, Subhashree Mohapatra, Borries Demeler

Research output: Contribution to journalArticlepeer-review

11 Scopus citations

Abstract

A framework for the global analysis of multi-speed analytical ultracentrifugation sedimentation velocity experiments is presented. We discuss extensions to the adaptive space–time finite element fitting methods implemented in UltraScan-III to model sedimentation velocity experiments where a single run is performed at multiple rotor speeds, and describe extensions in the optimization routines used for fitting experimental data collected at arbitrary multi-speed profiles. Our implementation considers factors such as speed dependent rotor stretching, the resulting radial shifting of the finite element solution’s boundary conditions, and changes in the associated time-invariant noise. We also address the calculation of acceleration rates and acceleration zones from existing radial acceleration and time records, as well as utilization of the time state object available at high temporal resolution from the new Beckman Optima AUC instrument. Analysis methods in UltraScan-III support unconstrained models that extract reliable information for both the sedimentation and the diffusion coefficients. These methods do not rely on any assumptions and allow for arbitrary variations in both sedimentation and diffusion transport. We have adapted these routines for the multi-speed case, and developed optimized and general grid based fitting methods to handle changes in the information content of the simulation matrix for different speed steps. New graphical simulation tools are presented that assist the investigator to estimate suitable grid metrics and evaluate information content based on edit profiles for individual experiments.

Original languageEnglish (US)
Pages (from-to)825-835
Number of pages11
JournalEuropean Biophysics Journal
Volume47
Issue number7
DOIs
StatePublished - Oct 1 2018

Keywords

  • Analytical ultracentrifugation
  • Finite element modelling
  • Multi-speed analysis

ASJC Scopus subject areas

  • Biophysics

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