Apparent sedimentation coefficient distribution function

The apparent sedimentation coefficient distribution function, g(s ) vs. s, can be computed from the time derivative of the concentration profile using the following equation, in which the time derivative of the concentration profile has been corrected for the "plateau" contribution by an iterative procedure described previously (Stafford, 1992a Stafford, 1994a) ... 

Stafford, W. F. (1994b). "Sedimentation Boundary Analysis of Interacting Systems Use of the Apparent Sedimentation Coefficient Distribution Function" in MODERN ANALYTICAL ULTRACENTRIFUGATION Acquisition and Interpretation of Data for Biological and Synthetic Polymer Systems Eds. T. M. Schuster and T. M. Laue. Boston, Birkhauser Boston, Inc. 

Figure 4. Sedimentation Velocity Analysis of ZDD. A, Primary data collected at 1 mg/ml (10 scans). B, Apparent sedimentation coefficient distribution function, g(s ) versus s. The error bars represent the standard error of the mean. The solid line is the fit to equation 4. Apparent s, D, and Ms,D values were calculated as described.

It is recommended to carry out a set of SV measurements of the unfolded and the folded state ensembles as a function of RNA concentration as described earlier before collecting the data points for the entire equilibrium transition. The shape of the apparent sedimentation coefficient distribution curves (discussed in Section 5) derived from such measurements, indicate whether the initial and the final states are conformationally homogeneous. Appearance of more than one peak in such distributions would indicate the existence of distinct structural states with different hydrodynamic properties. 

The simplest way computationally of obtaining a sedimentation coefficient distribution is from time derivative analysis of the evolving concentration distribution profile across the cell [40,41]. The time derivative at each radial position r is d c r,t)/co /dt)r where cq is the initial loading concentration. Assuming that a sufficiently small time integral of scans are chosen so that Ac r t)/At= dc r t)ldt the apparent weight fraction distribution function g (s) n.b. sometimes written as (s ) can be calculated... 

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