A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family

Abstract

Conformational ensembles are increasingly recognized as a useful representation to describe fundamental relationships between protein structure, dynamics and function. Here we present an ensemble of ubiquitin in solution that is created by sampling conformational space without experimental information using “Backrub” motions inspired by alternative conformations observed in sub-Angstrom resolution crystal structures. Backrub-generated structures are then selected to produce an ensemble that optimizes agreement with nuclear magnetic resonance (NMR) Residual Dipolar Couplings (RDCs). Using this ensemble, we probe two proposed relationships between properties of protein ensembles: (i) a link between native-state dynamics and the conformational heterogeneity observed in crystal structures, and (ii) a relation between dynamics of an individual protein and the conformational variability explored by its natural family. We show that the Backrub motional mechanism can simultaneously explore protein native-state dynamics measured by RDCs, encompass the conformational variability present in ubiquitin complex structures and facilitate sampling of conformational and sequence variability matching those occurring in the ubiquitin protein family. Our results thus support an overall relation between protein dynamics and conformational changes enabling sequence changes in evolution. More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics.

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

“…For additional analysis, we have used two Backrub ensembles described in ref. 47 (two ensembles of 50 structures with maximum segment length 3 and 12 and kT ϭ 2.4 and 1.2, respectively) that also reproduce the RDC data well. However, if not further specified, our analysis refers to the EROS ensemble.…”

“…We have carried out a detailed analysis based on an NMR ensemble (39,41) that is, to the best of our knowledge, the most detailed available structural description of ubiquitin dynamics, covering a dynamical range from ps to s. However, it is known that different structural ensembles can reproduce the NMR data to a similar extent, including ensembles that were generated through refinement (39,41,47) or even represent different structural models obtained by other methods such as X-ray crystallography The KS P value analysis conducted on a dataset from all 19 structural pairs pooled together into one distribution for each distance range. (B) Mapping of the calculated KS P values onto a representative ubiquitin surface [structure of ubiquitin bound to ADP-ribosylation-factor-binding protein GGA3 (gray); PDB ID code 1YD8], capturing the P value dependence on the distance from the binding site.…”

“…(48). For this reason, we have repeated our complete analysis on two additional NMR ensembles generated from the same RDC data as the EROS ensemble [Backrub ensembles generated via Monte Carlo simulations (47) Text). For example, 47% of the structures in the Backrub 1.2 ensemble (Table S1) without the tail, and 58% with the tail included, exhibit significantly greater fluctuations (P Ͻ 0.1) in the region Ͻ1.5 Å away from the binding site compared with the molecule as a whole.…”

“…For example, 47% of the structures in the Backrub 1.2 ensemble (Table S1) without the tail, and 58% with the tail included, exhibit significantly greater fluctuations (P Ͻ 0.1) in the region Ͻ1.5 Å away from the binding site compared with the molecule as a whole. However, here one should emphasize that the original EROS ensemble still slightly better reproduces the original RDC data (47) and may potentially be somewhat more realistic as it was generated by using time-dependent molecular dynamics simulations.…”

“…We focus on the NMR ensemble by Lange and coworkers, but to confirm our findings, we also analyzed two other structural ensembles (Backrub ensembles from ref. 47) that were refined based on the same RDC data.…”