Enhancing the quality of protein conformation ensembles with relative populations

Abstract

The function and dynamics of many proteins are best understood not from a single structure but from an ensemble. A high quality ensemble is necessary for accurately delineating protein dynamics. However, conformations in an ensemble are generally given equal weights. Few attempts were made to assign relative populations to the conformations, mainly due to the lack of right experimental data. Here we propose a method for assigning relative populations to ensembles using experimental residue dipolar couplings (RDC) as constraints, and show that relative populations can significantly enhance an ensemble's ability in representing the native states and dynamics. The method works by identifying conformation states within an ensemble and assigning appropriate relative populations to them. Each of these conformation states is represented by a sub-ensemble consisting of a subset of the conformations. Application to the ubiquitin X-ray ensemble clearly identifies two key conformation states, with relative populations in excellent agreement with previous work. We then apply the method to a reprotonated ERNST ensemble that is enhanced with a switched conformation, and show that as a result of population reweighting, not only the reproduction of RDCs is significantly improved, but common conformational features (particularly the dihedral angle distributions of ϕ 53 and ψ 52) also emerge for both the X-ray ensemble and the reprotonated ERNST ensemble.

Protein dynamics and function from solution state NMR spectroscopy

“…; Maciejewski et al 2011;Vammi et al 2014) in which an ensemble of conformers is generated and RDCs computed from this ensemble are compared with experimental values. This technique depends on the calculation of alignment tensors using tools such as prediction of alignment from structure (PALES) (Zweckstetter & Bax, 2000) or ALMOND programs (Almond & Axelsen, 2002), grouping of conformers into clusters, and careful analysis to avoid over-fitting of data.…”

Representing protein native states using weighted conformation ensembles

“…Two ESP ensembles were reported in our previous work (63) and 2MJB (30) and one crystal structure 1UBQ (69).…”

“…The anisotropic measurement can be obtained by the aid of various types of liquid crystalline media. Details regarding back-calculation of RDC's were given in the appendix of our previous work (63).…”

“…The RDCs used to determine the weights for the X-ray ensemble and enhanced ERNST ensemble are given in (63), along with the codes assigned to them according to (55). The Q-factors reported in this work use the newly determined RDC dataset in Squalamine and Pf1 media (30), in addition to the Ottiger dataset used in the determination of 1D3Z (56).…”

“…Except for a nominal increase in RMSD for amide hydrogens, enhanced ERNST (another ESP ensemble) also performs better than ERNST itself. Importance of the "switched" conformation: The "switched" conformation, represented by 2G45-E, was given a population weight of ~0.30 by our weighting protocol (63) in the enhanced ERNST ensemble. This weight was higher than the expected weight given in one previous work (85).…”