Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling.

By Peter Schuck. Biophysical Journal, 2000

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A new method for the size-distribution analysis of polymers by sedimentation velocity analytical ultracentrifugation is described. It exploits the ability of Lamm equation modeling to discriminate between the spreading of the sedimentation boundary arising from sample heterogeneity and from diffusion. Finite element solutions of the Lamm equation for a large number of discrete noninteracting species are combined with maximum entropy regularization to represent a continuous size-distribution. As in the program CONTIN, the parameter governing the regularization constraint is adjusted by variance analysis to a predefined confidence level. Estimates of the partial specific volume and the frictional ratio of the macromolecules are used to calculate the diffusion coefficients, resulting in relatively high-resolution sedimentation coefficient distributions c(s) or molar mass distributions c(M). It can be applied to interference optical data that exhibit systematic noise components, and it does not require solution or solvent plateaus to be established. More details on the size-distribution can be obtained than from van Holde-Weischet analysis. The sensitivity to the values of the regularization parameter and to the shape parameters is explored with the help of simulated sedimentation data of discrete and continuous model size distributions, and by applications to experimental data of continuous and discrete protein mixtures.

Subfields: Computational Mechanics, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/fa36d616bc2cabcc0490eed9a318747fe5812aba

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Citations in the corpus

Structure of the Pf12 and Pf41 heterodimeric complex of Plasmodium falciparum 6-cysteine proteins (2022, methodology): “The sedimenting boundaries were fitted to a model that describes the sedimentation of a distribution of sedimentation coefficients with no assumption of heterogeneity (c(s)) using the program SEDFIT (Schuck 2000).”
Size-distribution analysis of proteins by analytical ultracentrifugation: strategies and application to model systems. (2002, methodology): “…of the conformational changes 34 of the rotavirus nonstructural protein NSP2 (Schuck et al., 2000), or the known shape and sizedependence of the partial-specific volume of the emulsion particles (M.A. Perugini, P. Schuck, G.J. Howlett, submitted), or a known diffusion coefficient (Schuck, 2000).”
Optimization of the preparation process for human serum albumin (HSA) nanoparticles. (2003, methodology): “In parallel, in part of the samples the size distribution was studied by sedimentation velocity analysis in the analytical ultracentrifuge (Vogel et al., 2002), making use of the superior resolving power of this technique (Schuck, 2000; Schuck and Rossmanith, 2000; Schuck et al., 2002).”
On the analysis of protein self-association by sedimentation velocity analytical ultracentrifugation. (2003, methodology): “As has been pointed out before (67, 68), the deconvolution is based on the assumption of non- interacting species, and for interactions that are reversible on the timescale of the sedimentation experiment, the peaks in the c(s) distribution do not correspond to the svalues of sedimenting species.”
Sedimentation equilibrium analysis of protein interactions with global implicit mass conservation constraints and systematic noise decomposition. (2004, methodology): “The MC constraint is used here similarly as is the prior knowledge in regularization terms for ill-conditioned inverse problems (27, 28).”
Revisit of reconstituted 30-nm nucleosome arrays reveals an ensemble of dynamic structures (2018, methodology): “The absorbance was monitored at 260 nm or 280 nm. Data were analyzed in SEDFIT [58] in terms of a continuous c(s) distribution spanning a sedimentation coefficient range of 0 to 100 (or 150) S with a resolution of 200 (or 300) points and a confidence interval of 68%.”