Determination of molecular parameters by fitting sedimentation data to finite-element solutions of the Lamm equation.
A method for fitting experimental sedimentation velocity data to finite-element solutions of various models based on the Lamm equation is presented. The method provides initial parameter estimates and guides the user in choosing an appropriate model for the analysis by preprocessing the data with the G(s) method by van Holde and Weischet. For a mixture of multiple solutes in a sample, the method returns the concentrations, the sedimentation (s) and diffusion coefficients (D), and thus the molecular weights (MW) for all solutes, provided the partial specific volumes (v) are known. For nonideal samples displaying concentration-dependent solution behavior, concentration dependency parameters for s(sigma) and D(delta) can be determined. The finite-element solution of the Lamm equation used for this study provides a numerical solution to the differential equation, and does not require empirically adjusted correction terms or any assumptions such as infinitely long cells. Consequently, experimental data from samples that neither clear the meniscus nor exhibit clearly defined plateau absorbances, as well as data from approach-to-equilibrium experiments, can be analyzed with this method with enhanced accuracy when compared to other available methods. The nonlinear least-squares fitting process was accomplished by the use of an adapted version of the "Doesn't Use Derivatives" nonlinear least-squares fitting routine. The effectiveness of the approach is illustrated with experimental data obtained from protein and DNA samples. Where applicable, results are compared to methods utilizing analytical solutions of approximated Lamm equations.
Demeler
B
B
Department of Biochemistry, University of Texas Health Sciences Center at San Antonio, 78284-7760, USA. demeler@bioc02.uthscsa.edu
Saber
H
H
D003198:Computer Simulation; D004247:DNA / Q000737:chemistry / Q000302:isolation & purification*; D016018:Least-Squares Analysis; D008838:Microcomputers; D008962:Models, Theoretical; D008970:Molecular Weight; D012984:Software; D012996:Solutions; D014461:Ultracentrifugation
D012996:Solutions; D004247:DNA