Apparent sedimentation coefficient distribution

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 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. 

An extended analysis of data using the time-derivative method provides for simultaneous determination of apparent sedimentation, and apparent diffusion coefficient, values at a particular concentration and temperature [9]. The apparent diffusion coefficient was calculated from the apparent sedimentation coefficient distribution by the following relationship ... 

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.

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... 

A sedimentation coefficient distribution—either c s) versus 5 or g (s) vs. s—for a polysaccharide can also be converted into an apparent molecular weight distribution if the conformation of the polysaccharide is known or can... 

In order to apply Eqs. (6.3) or (6.4) to the sediment zone subject to bioturbation or physical disturbance, a number of researchers have suggested that the effects of biogenic or physical reworking on pore-water distributions be lumped into an effective or apparent transport coefficient (Hammond eta/., 1975 Vanderborght eta/., 1977 Goldhaber eta/., 1977). D is arbitrarily adjusted until the observed pore-water profile is fit to the appropriate solution, say, to Eq. (6.4). This approach has been found to work reasonably well in sediments where biogenic or physical disturbance is limited to the upper few centimeters (Vanderborght et al., 1977 Aller,... 

Fig. 6.4 Calculated, estimated, or apparent salting out constants for various chemicals (a) selected aromatic compounds, (b) selected aliphatic compounds, (c) natural or surrogate hgands, (d) anthropogenic ligands, (e) sediment organic matter (SOM), (f) transition metal complexes, (g) trace metal complexes in the Mersey Estuary. Reprinted with permission from Turner A, Martino M, Le Roux SM (2002) Trace metal distribution coefficients in the Mersey Estuary UK Evidence for salting out of metal complexes. Environ Sci Technol 36 4578-4584. Copyright 2002 American Chemical Society...

Equilibrating a gas two or more times with an aqueous sample (waters, sediment slurries, biological fluids) permits calculation of distribution coefficients and measurements of volatile organic compounds, such as hydrocarbons and halocarbons at sub-fxg/L concentrations. Classes of volatile organic compounds have different distribution coefficients, which aids in their separation and identification. The multiple gas-phase equilibration method has been used to measure the solubilities of pure hydrocarbons in waters of various salinities and of volatile hydrocarbons in oils and in water from the Cook Inlet, Gulf of Mexico, and Santa Barbara Channel It was first to detect small amounts of chloroform and other contaminants in New Orleans drinking water it measured the loss of C1-C10 hydrocarbons from oil slicks on the ocean surface and the apparent absence of dissolved hydrocarbons under the slicks in less than 8 hr. It has simultaneously measured up to 8 anesthetic gases in blood and plasma. 

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