Protein Shape Determination by Small Angle X-Ray Scattering

The 3-dimensional shape of Glucose Isomerase in solution was studied with the SAXSpace system. The solution structure of this protein was compared with the crystal structure obtained by X-ray crystallography.

SAXS and proteins in solution

Common methods for structure analysis on biological macromolecules are crystallography and Nuclear Magnetic Resonance (NMR). Small-angle X-ray scattering (SAXS) complements both these high-resolution techniques with valuable additional information and offers specific benefits compared to crystallography: SAXS allows to obtain the 3-dimensional structure of proteins and protein assemblies in solution which is essential for a better understanding of their biological function.
The low resolution 3D structure, calculated by ab-initio methods1 is indispensable additional information to the high resolution structures provided by protein crystallography and NMR.

Experimental and Results

A solution of Glucose Isomerase (1 % w/w) dissolved in TRIS buffer at pH 8 was measured with the SAXSpace system. The exposure time was 10 minutes. Fig. 1 shows the measured data and the desmeared curve (using GIFT) together with the fit from the ab-initio modeling.

Fig. 1 Background-subtracted scattering curves

The solution structure can be compared with the crystal structure. Fig. 2 shows a comparison of the Pair Distance Distribution Functions (PDDF) calculated from the SAXS data and the crystal structure of a Glucose Isomerase tetramer. The 3D model agrees well with the crystal structure available from the Protein Data Bank.

Fig. 2 Pair-Distance Distribution Functions

In the figure shown below, the ab-initio model based on the SAXS data is represented by white spheres, whereas the backbone of the crystal structure is shown in colors.
The SAXS data demonstrate convincingly that this protein exists as a tetramer in its native state.

1    P.V. Konarev,  M.V. Petoukhov, V.V. Volkov, D.I. Svergun, J. Appl. Cryst. 39 (2006) 277-286

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