Fig. 5. Example of the application of metainference in integrative structural biology.

(A) Comparison of the metainference and maximum entropy approaches by modeling the structural fluctuations of the protein ubiquitin in its native state using NMR chemical shifts and RDC data. (B) The metainference ensemble supports the finding (36) that a major source of dynamics involves a flip of the backbone of residues D⁵²-G⁵³ (B; left scatterplot), which interconverts between an α state with a 65% population and a β state with a 35% population. This flip is coupled with the formation of a hydrogen bond between the side chain of E²⁴ and the backbone of G⁵³ (B; right scatterplot); the state in which the hydrogen bond is present (β_HB+) is populated 30% of the time, and the state in which the hydrogen bond is absent (β_HB−) is populated 5% of the time. By contrast, the NMR structure (Protein Data Bank code 1D3Z) provides a static picture of ubiquitin in this region in which the α state is the only populated one (black triangle). (C) Validation of the metainference (MI; red) and maximum entropy principle (MEP; green) ensembles, along with the NMR structure (blue) and the MD ensemble (purple), by the backcalculation of experimental data not used in the modeling: ³J_HNC and ³J_HNHA scalar couplings and two independent sets of RDCs (RDC sets 2 and 3).