Small-Angle X-Ray Scattering Signatures of Conformational Heterogeneity and Homogeneity of Disordered Protein Ensembles

TL;DR

This study investigates whether small-angle X-ray scattering (SAXS) can distinguish between homogeneous and heterogeneous disordered protein ensembles, revealing that SAXS form factors often cannot uniquely characterize ensemble heterogeneity.

Contribution

The paper demonstrates through simulations that SAXS molecular form factors have limited discriminatory power for conformational heterogeneity in disordered proteins, challenging previous assumptions.

Findings

SAXS MFFs can be similar for heterogeneous and homogeneous ensembles.

Heterogeneous ensembles with different shapes can produce nearly identical SAXS signatures.

The ensemble-to-MFF mapping is many-to-one and non-smooth.

Abstract

Physically, disordered ensembles of non-homopolymeric polypeptides are expected to be heterogeneous; i.e., they should differ from those homogeneous ensembles of homopolymers that harbor an essentially unique relationship between average values of end-to-end distance $R_{\rm EE}$ and radius of gyration $R_{\rm g}$. It was posited recently, however, that small-angle X-ray scattering (SAXS) data on conformational dimensions of disordered proteins can be rationalized almost exclusively by homopolymer ensembles. Assessing this perspective, chain-model simulations are used to evaluate the discriminatory power of SAXS-determined molecular form factors (MFFs) with regard to homogeneous versus heterogeneous ensembles. The general approach adopted here is not bound by any assumption about ensemble encodability, in that the postulated heterogeneous ensembles we evaluated are not restricted to those entailed by simple interaction schemes. Our analysis of MFFs for certain heterogeneous ensembles with more narrowly distributed $R_{\rm EE}$ and $R_{\rm g}$ indicates that while they deviates from MFFs of homogeneous ensembles, the differences can be rather small. Remarkably, some heterogeneous ensembles with asphericity and $R_{\rm EE}$ drastically different from those of homogeneous ensembles can nonetheless exhibit practically identical MFFs, demonstrating that SAXS MFFs do not afford unique characterizations of basic properties of conformational ensembles in general. In other words, the ensemble to MFF mapping is practically many-to-one and likely non-smooth. Heteropolymeric variations of the $R_{\rm EE}$--$R_{\rm g}$ relationship were further showcased using an analytical perturbation theory developed here for flexible heteropolymers. Ramifications of our findings for interpretation of experimental data are discussed.