[RASMB] SEDANAL - Issue with Claverie Simulations ans Stable Fits - Heterologus Protein-Protein Interaction Model

Richard Itwaru richard.itwaru at regeneron.com
Thu Mar 1 05:12:21 PST 2018


Good morning all!  I'm a relatively new user of SEDANAL (v6.67) and I'm trying to extract some kinetic data from a model system.

I'm trying to fit 6 sets of absorbance data of Protein A and Protein B to a 1-1 binding model.  This is a fairly heterogenous system, where there are sites for up to a 6:1 complex of proteins. 2D distributions show a fair bit of heterogeneity (both by s- and f/f0), but the distribution shows that the majority complex is 1-1 by c(s), with some incompetent Protein A.  I want to use this 1-1 model as a first guess for parameter estimation.    I know the kinetic off-rate is fairly fast (>0.00001 1/s), but in my attempts to fit for this parameter, I run into trouble.  I find that my Claverie simulations are not robust enough to generate good fits.  I either end up with the fit crashing, or end up having to force the finite-element simulations to continue with negative concentrations and end up with "CHECK GRID" errors.

How can I generate better, more stable models?  I understand that CHECK GRID has to do with coarseness of the simulation grid, where I've tried 200 and 400 points. Should I try to increase the number of points even more? For reference, I'm using Newton-Raphson at the initial equilibrium to fit.  I'm assuming this non-analytical algorithm can help to calculate and redistribute the loading concentration of Protein A into its competent and incompetent forms.  Should I instead add another component to my model, Protien A', that is non-interacting?  My simulation then moves on to  SEulEx for equilibration during run and ends with Newton-Raphson again.

Thanks for your help in this matter.  At this point, I've run my head into the wall!

Richard Itwaru
Research Associate II - Protein Biochemistry
Regeneron Pharmaceuticals
Work: 914 - 847-3594
Email: Richard.itwaru at regeneron<mailto:Richard.itwaru at regeneron>.com


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