Computing translational diffusion and sedimentation coefficients: an evaluation of experimental data and programs

Mattia Rocco, Olwyn Byron

Research output: Contribution to journalArticle

Abstract

Hydrodynamic characterisation of (bio)macromolecules is a well-established field. Observables linked to translational friction, such as the translational diffusion (Dt0(20,w)) and sedimentation (Formula presented.) coefficients, are the most commonly used parameters. Both can be computed starting from high-resolution structures, with several methods available. We present here a comprehensive study of the performance of public-domain software, comparing the calculated Dt0(20,w) and (Formula presented.) for a set of high-resolution structures (ranging in mass from 12,358 to 465,557 Da) with their critically appraised literature experimental counterparts. The methods/programs examined are AtoB, SoMo, BEST, Zeno (all implemented within the US-SOMO software suite) and HYDROPRO. Clear trends emerge: while all programs can reproduce Dt0(20,w) on average to within ±5 % (range −8 to +7 %), SoMo and AtoB slightly overestimate it (average +2 and +1 %, range −2 to +7 and −4 to +5 %, respectively), and BEST and HYDROPRO underestimate it slightly more (average −3 and −4 %, range −7 to +2 and −8 to +2 %, respectively). Similar trends are observed with (Formula presented.), but the comparison is likely affected by the necessary inclusion of the partial specific volume in the computations. The somewhat less than ideal performances could result from the hydration treatment in BEST and HYDROPRO, and the bead overlap removal in SoMo and AtoB. Interestingly, a combination of SoMo overlapping bead models followed by Zeno computation produced better results, with a 0 % average error (range −4 to +4 %). Indeed, this might become the method of choice, once computational speed considerations now favouring the 5 Å-grid US-SOMO AtoB approach are overcome.

Original languageEnglish
Pages (from-to)417-431
Number of pages15
JournalEuropean Biophysics Journal
Volume44
Issue number6
DOIs
Publication statusPublished - Jun 12 2015

Keywords

  • Analytical ultracentrifugation
  • Dynamic light scattering
  • Hydrodynamics
  • Multi-resolution modelling

ASJC Scopus subject areas

  • Biophysics

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