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European Biophysics Journal

, Volume 44, Issue 6, pp 417–431 | Cite as

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

  • Mattia RoccoEmail author
  • Olwyn Byron
Original Paper

Abstract

Hydrodynamic characterisation of (bio)macromolecules is a well-established field. Observables linked to translational friction, such as the translational diffusion (D t 0 (20,w)) and sedimentation (\( s_{(20,\text{w})}^{0} \)) 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 D t 0 (20,w) and \( s_{(20,\text{w})}^{0} \) 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 D t 0 (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 \( s_{(20,\text{w})}^{0} \), 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.

Keywords

Hydrodynamics Analytical ultracentrifugation Multi-resolution modelling Dynamic light scattering 

Notes

Acknowledgments

M.R. designed and performed research, and wrote the paper. O.B. contributed analytical tools and wrote the paper. We are indebted to Emre Brookes (University of Texas at San Antonio, TX, USA) for his continuous and timely efforts in improving the US-SOMO software. We thank Camillo Rosano (IRCCS AOU San Martino-IST, Genova, Italy) for completing several protein structures. M.R. was partially supported by the Italian Ministry of Health, “5 per mille 2011” funds. The authors declare no conflict of interest.

Supplementary material

249_2015_1042_MOESM1_ESM.xls (118 kb)
Supplementary material 1 (XLS 118 kb)

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Copyright information

© European Biophysical Societies' Association 2015

Authors and Affiliations

  1. 1.Biopolimeri e Proteomica, IRCCS AOU San Martino-ISTIstituto Nazionale per la Ricerca sul CancroGenovaItaly
  2. 2.School of Life Sciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK

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