General Overview

There are several softwares for SAXS data analysis, most of them can be freely downloded from the internet,and there are a few that you need to buy. Below there is a list of these softwares along with a small explanation with the main characteristic of each one.

GENFIT

Among all softwares used in the SAXS data analysis, GENFIT is one of the most (if not the one!) complete. It has more them 60 theoretical models inside it, allowing the user to select among several biologically relevant systems, like proteins, micelles, vesicles, bilayers, and so on... SAS curves calculated from a theoretical model can be smeared to allow for the instrumental resolution. The user can fit the experimental data selecting one or more models from a list including more than 30 models, starting from simple asymptotic behaviours (Guinier's law, Porod's law, etc.) down to complete atomic structures. Besides, the software also allows the user to use the Global fitting procedure, where several Scattering curves can be analysed concomitantly, being also possible to link different parameter from different scattering curves. Some models, which are defined in terms of both form and structure factors, take into account the interactions between scattering particles in solution. GENFIT is able to simultaneously fit more SAS curves via a unique model or a mixture of models (the global fitting procedure). In the latter case, some specific model parameters can be shared by any selection of the experimental curves. Model parameters can be related to the experimental chemical-physical conditions (temperature, pressure, concentration, pH, etc.) by means of link functions, which can be freely defined by the user. On the other hand, GENFIT can be used to generate theoretical SAS curves from a given model and/or from the knowledge of the species in solution. It can hence be a useful instrument to find the optimum experimental conditions for a planned SAS experiment. GENFIT is written in Fortran. Versions 2.0 and higher make use of a graphical user interface (GUI) to manage input files and execute the calculations. The software was mainly developed by prof. Francesco Spinozzi, from Universita Politecnica delle Marche

References

1 - Mertens, H.D.T., Svergun, D.I., Structural characterization of proteins and complexes using small-angle X-ray solution scattering. J Struct.Biol . (2010) 172, 128–141. 2 - Trewhella, J., Insights into biomolecular function from small-angle scattering Curr. Opin. Struct. Biol. Curr. Opinion Struct. Biology, (1997). 7, 702-8 3 - Barbosa, L. R. S., Ortore, M. G., Spinozzi, F., Mariani, P., Bernstorff, S., Itri, R., The importance of protein-protein interactions on the pH-induced conformational changes of bovine serum albumin: a small-angle X-Ray scattering study. Biophys. J., (2010) 98(1). 147-157 4 - Zhang, F., Skoda, M.W.A., Jacobs, R.M.J., Martin, R.A., Martin, C.M., Schreiber, F., Effect of ionic strength and protein concentration for BSA in aqueous solutions. J. Phys. Chem. B., (2007)111, 251–259 5 - Ortore, M.G., Spinozzi, F., Mariani, P., Panciaroni, A., Barbosa, L. R. S., Amenitsch, H., Teinhart, M., Oliver, J., Russo, D., Combining structure and dynamics: non-denaturing high-pressure effect on lysozyme in solution. J. Royal Soc Interf, (2009) 6, S619-634 6 - Sinibaldi, R., M.G. Ortore, F.Spinozzi, F.Carsughi, H.Frielinghaus, S.Cinelli G.Onori, P. Mariani,. Preferential hydration of lysozyme in water/glycerol mixtures: A SANS study. J Chem. Phys. (2007)126: 235101 7 - Santos, S F ; Zanette, D. ; Fischer, H. ; Itri, R. . A systematic study of bovine serum albumin (BSA) and sodium dodecyl sulfate (SDS) interactions by electrical conductivity, surface tension and small angle x-ray scattering. J Coll and Interf Sci, (2003). 262, 400-408 8 - Hassan, N. Barbosa, L.R.S., Itri, R. Ruso, J.M. Fibrinogen stability under surfactant interaction. J. Col. Interf. Sci., (2011). In Press, 9 - Ospinal-Jiménez, M. and Pozzo D.C. Structural Analysis of Protein Complexes with Sodium Alkyl Sulfates by Small-Angle Scattering and Polyacrylamide Gel Electrophoresis. Langmuir, (2011)27(3), 928–935. 10 - Kathuria, S.V. Guo L., Graceffa, R. Barrea,R. Nobrega, P. Matthews. R., Irving, T. C., Bilsel. O. Structural Insights into Early Folding Events Using Continuous-Flow Time-Resolved Small-Angle X-Ray Scattering. Biopolymers (2011) 95(8) 550-558. 11 - Narayanan, T. High brilliance small-angle X-ray scattering applied to soft matter. Curr Opinion in Coll & Interf Sci (2009).14(6), 409-415. 12 - Arai,S and Hirai, M. Reversibility and Hierarchy of Thermal Transition of Hen Egg-White Lysozyme Studied by Small-Angle X-Ray Scattering Biophys. J., (1999)76, 2192.

USP IFUSP DFGE

Praça do Oceanográfico, Travessa E, S/N, Ala 1, sala 225 - Cidade Universitária

CEP 05508-090 - São Paulo - Brasil