Work

Fast calculation of small-angle scattering profiles of dense protein solutions modeled at the all-atom level

Year: 2025

Type: article

Abstract: The small-angle scattering (SAS) profile of a dense protein solution contains rich information about interprotein interactions, but extracting this information has been extremely challenging. In previous studies, we developed a fast Fourier transform-based method, FMAPB2, to compute protein pair interactions at the all-atom level. Here, we use FMAPB2 to precompute pair interaction energies and then use the latter to drive simulations of dense protein solutions. The resulting MAEPPI (many-protein atomistic energy from precomputed pair interaction) enables simulations of atomistic proteins at the speed of Lennard-Jones particles. On snapshots sampled from the simulations, we directly calculate the SAS profile. The results reveal artifacts generated by widely used spherical models and support a significant dimer population of bovine serum albumin at high concentrations. Our approach promises to modernize the prediction and interpretation of SAS profiles of dense protein solutions.

Source: Proceedings of the National Academy of Sciences

DOI: 10.1073/pnas.2519265122

Authors: Sanbo Qin, Huan-Xiang Zhou

Institutions: University of Illinois Urbana-Champaign, University of Illinois Chicago

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Funders: National Institutes of Health, National Institute of General Medical Sciences

Awards: G1383806369, G8203836530, G9000054294