Determination of molecular parameters by fitting sedimentation data to finite-element solutions of the Lamm equation

Biophysical Journal
Borries Demeler, H Saber

Abstract

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 ava...Continue Reading

References

Jan 1, 1992·Methods in Enzymology·M L Johnson, L M Faunt
Nov 1, 1981·Proceedings of the National Academy of Sciences of the United States of America·G P Todd, R H Haschemeyer
Sep 1, 1979·Biophysical Chemistry·L A Holladay

❮ Previous
Next ❯

Citations

Mar 18, 2009·European Biophysics Journal : EBJ·Alexandra S SolovyovaMark J Banfield
Mar 20, 2009·European Biophysics Journal : EBJ·Helmut CölfenBorries Demeler
Sep 11, 2002·Journal of Molecular Biology·Pamela L LumJoel F Schildbach
Feb 24, 2006·Biochemistry·Franklin A HaysBorries Demeler
Apr 11, 2007·Journal of the American Chemical Society·Omid KhakshoorJames S Nowick
Jul 1, 2009·Proceedings of the National Academy of Sciences of the United States of America·Eri ChataniYuji Goto
Apr 5, 2012·The Journal of Biological Chemistry·Andjelka S ĆelićTitus J Boggon
Aug 13, 2008·The Journal of Biological Chemistry·Andjelka CelićTitus J Boggon
Aug 23, 2002·Protein Science : a Publication of the Protein Society·Jacob LebowitzPeter Schuck
Apr 23, 2002·Protein Science : a Publication of the Protein Society·Stephen J KingTrina A Schroer
Apr 7, 2004·European Journal of Biochemistry·Eman BashaElizabeth Vierling
Dec 29, 2010·Methods : a Companion to Methods in Enzymology·John P Gabrielson, Kelly K Arthur
Jan 27, 2010·Developmental and Comparative Immunology·Beatrice MindykowskiHeinz Decker
Nov 24, 2004·Analytical Biochemistry·Borries Demeler, Kensal E van Holde
Mar 31, 2004·Journal of Molecular Biology·Ignacio E SánchezRudi Glockshuber
Apr 6, 2006·Journal of Structural Biology·Heike SummerEilika Weber-Ban
Aug 9, 2005·Journal of Molecular Biology·Udayar IlangovanAndrew P Hinck
Jun 26, 2001·Biophysical Journal·C DekkerB de Kruijff
Oct 19, 2006·Methods in Enzymology·Yee-Foong Mok, Geoffrey J Howlett
Sep 8, 2010·Nanoscale·Karel L Planken, Helmut Cölfen
Aug 17, 2004·The Journal of Biological Chemistry·Jacqueline M BenjaminThomas J McGarry
Oct 22, 2002·The Journal of Biological Chemistry·Srikumar M RajaChristopher J Froelich
Apr 25, 2003·The Journal of Biological Chemistry·Hui-Chuan Chang, Gu-Gang Chang
Jun 23, 2018·European Biophysics Journal : EBJ·Cornelia M Schneider, Helmut Cölfen

❮ Previous
Next ❯

Related Concepts

Related Feeds

Bacterial Cell Wall Structure (ASM)

Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by unusual peptides containing D-amino acids. Here is the latest research on bacterial cell wall structures.

Bacterial Cell Wall Structure

Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by unusual peptides containing D-amino acids. Here is the latest research on bacterial cell wall structures.