SAXSMoW 2.0: Online calculator of the molecular weight of proteins in dilute solution from experimental SAXS data measured on a relative scale

Abstract

Knowledge of molecular weight, oligomeric states, and quaternary arrangements of proteins in solution is fundamental for understanding their molecular functions and activities. We describe here a program SAXSMoW 2.0 for robust and quick determination of molecular weight and oligomeric state of proteins in dilute solution, starting from a single experimental small-angle scattering intensity curve, I(q), measured on a relative scale. The first version of this calculator has been widely used during the last decade and applied to analyze experimental SAXS data of many proteins and protein complexes. SAXSMoW 2.0 exhibits new features which allow for the direct input of experimental intensity curves and also automatic modes for quick determinations of the radius of gyration, volume, and molecular weight. The new program was extensively tested by applying it to many experimental SAXS curves downloaded from the open databases, corresponding to proteins with different shapes and molecular weights ranging from ~10 kDa up to about ~500 kDa and different shapes from globular to elongated. These tests reveal that the use of SAXSMoW 2.0 allows for determinations of molecular weights of proteins in dilute solution with a median discrepancy of about 12% for globular proteins. In case of elongated molecules, discrepancy value can be significantly higher. Our tests show discrepancies of approximately 21% for the proteins with molecular shape aspect ratios up to 18.

Keywords: SAXS; molecular weight; on-line calculator; proteins.

Figure 1

SAXSMoW 2.0 interface displaying results associated to the SASDA32 dataset https://www.sasbdb.org/data/SASDA32/.

Figure 2

Discrepancy distributions for different expected molecular weights. (■) Option 1: q_max = 8/R_g; (▵) Option 2: derived from equation I(0)/I(q_max) = 10^2.25.

Figure 3

Discrepancy distributions in molecular weights computed for a set of globular proteins using different q _max values: (a) q_max = 8/R_g and (b) q _max from equation $\log \frac{I\left(0\right)}{I\left(q_{\mathit{max}}\right)}=2.25$.

Figure 4

Discrepancies in molecular weights associated to elongated proteins with different aspect ratios for both suggested options for q _max values. Option 1 (■) q_max = 8/R_g. Option 2 (▵) derived from equation I(0)/I(q_max) = 10^2.25.

Figure 5

Plots of polynomials that define (a) A(q_max) and (b) B(q_max), for all q _max values from 0.1 Å⁻¹ to 0.5 Å⁻¹.