Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

TLDR

Protein dynamics are essential for protein function, yet accessing atomic motions on nanosecond‑to‑microsecond timescales in solution remains challenging. The study aims to present a structural ensemble of ubiquitin refined against residual dipolar couplings to capture solution dynamics up to microseconds. The authors refined this ensemble against RDCs to resolve dynamics on the microsecond scale. The ensemble reproduces the full heterogeneity of 46 ubiquitin crystal structures, shows that conformational selection—not induced fit—drives recognition, reveals strong correlations between flexibility and complex contacts, and identifies a dominant concerted mode that explains most recognition heterogeneity while minimizing entropic cost.

Abstract

Protein dynamics are essential for protein function, and yet it has been challenging to access the underlying atomic motions in solution on nanosecond-to-microsecond time scales. We present a structural ensemble of ubiquitin, refined against residual dipolar couplings (RDCs), comprising solution dynamics up to microseconds. The ensemble covers the complete structural heterogeneity observed in 46 ubiquitin crystal structures, most of which are complexes with other proteins. Conformational selection, rather than induced-fit motion, thus suffices to explain the molecular recognition dynamics of ubiquitin. Marked correlations are seen between the flexibility of the ensemble and contacts formed in ubiquitin complexes. A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost.