Application of SAXS to characterize the structural dynamics of proteins

Project Abstract

Small angle X-ray scattering (SAXS) is a powerful method to define the structural dynamics of large proteins such as antibodies and protein complexes in solution.  The use of SAXS to characterize antibody structures has yet to be established and this project involves demonstrating the applicability of this approach.  To this end, it is essential to perform the first experiments, test different SAXS methods, and determine what data analysis software is most suitable for this application.  Sample preparation requires highly monodisperse samples and we will work with size exclusion chromatography and multi-angle light scattering (SEC-MALS) as well as dynamic light scattering to develop protocols and ultimately pipelines to optimize buffer conditions and validate monodispersity.  Data can be collected remotely and processed at the home laboratory, but optimized methods for shipping and coordination with beamline staff needs to be worked out.  Data will be collected at the SIBYLS beamline at the ALS because the Chazin lab already has established an excellent working relationship with the staff.  For the purposes of this short summer internship, results will be analyzed only to the point of determining if high quality data have been obtained.

Training plan

Yongseok will work with Clayton Wandishin in the Crowe Lab on developing protocols to characterize the solution structural dynamics of proteins/antibodies by small angle X-ray scattering (SAXS).  Clayton and Yongseok in turn will be trained in the theory and all of the technical/practical aspects of SAXS sample preparation, data acquisition and analysis by Chazin lab senior postdoctoral fellow Matthew Thompson.  In the beginning, Yongseok will meet each Clayton multiple times each day and eventually will be come sufficiently independent to work on his own each day after a meeting to discuss priorities at the beginning of each day.  I will meet with Yongseok formally each week on Friday mornings to discuss his progress, scientific interests and plans for the future.  Yongseok will prepare a written report summarizing his project at the end of the internship and also an oral presentation for the Chazin lab and the Program.

Mentors

Primary: Walter Chazin

Secondary: James Crowe, Jr.