Bioisis

PARTICLE MASS DETERMINATION ... by Robert P. Rambo, Ph.D.

SCÅTTER can estimate the mass of the scattering particle using a method from Rambo and Tainer Nature 496, 477-481 2013. This method requires an accurate assessment of I(0), Rg and Vc. Given that I(0) and Rg can be estimated from real and reciprocal space, we calculate mass using both methods. Based on the paper, the mass is determined from the QR ratio defined as the ratio of Vc2 to Rg. To determine the particle mass of your sample, perform the following steps:

  1. Perform a Guinier analysis or use "Auto Rg".
  2. Perform a real space analysis determining the P(r) distribution.
  3. Determine the volume-of-correlation via "Vc" button.

Figure 1 | (adapted from Rambo and Tainer Nature 496, 477-481 2013)

Protein_mass_figure_1

The mass parameter QR follows a power-law relationship with particle mass (Figure 1). For each type of particle (e.g. protein, RNA, or DNA), the power-law relationship can be parameterized from a set of known samples. In Figure 1 is the power-law relationship for protein (black), mixed nucleic acid protein complexes (cyan) and RNA (red) structures from the PDB. QR was calculated from in water SAXS simulations by D. Svergun's program CRYSOL.

Figure 2 | (adapted from Rambo and Tainer Nature 496, 477-481 2013)

Protein_mass_figure_2

QR is linear over a large mass range. Using actual protein and RNA samples (Figure 2), QR was calculated using highly purified and determined samples resulting in the determination of k and c from Figure 1. These parameters can be used to determine mass of either protein or RNA samples, independent of instrumentation or buffer composition.

SAXS MoW is an alternative method for estimating protein molecular mass directly from a SAXS curve. This method requires GNOM output from ATSAS version 2.4.2.