Weak Long-Range Correlated Motions in a Surface Patch of Ubiquitin Involved in Molecular Recognition

Abstract

Long-range correlated motions in proteins are candidate mechanisms for processes that require information transfer across protein structures, such as allostery and signal transduction. However, the observation of backbone correlations between distant residues has remained elusive, and only local correlations have been revealed using residual dipolar couplings measured by NMR spectroscopy. In this work, we experimentally identified and characterized collective motions spanning four β-strands separated by up to 15 Å in ubiquitin. The observed correlations link molecular recognition sites and result from concerted conformational changes that are in part mediated by the hydrogen-bonding network.

Correlated motions are a fundamental property of β-sheets

“…1b, we provide a summary of the correlation analysis, where the crankshaft motion, a rotation of the peptide plane about the C a i À 1 -C a i axis that leads to the anti-correlation of c i À 1 and f i often observed in MD simulations, is shown in italics 24 . The crankshaft motion is equivalent to that put forward in the onedimensional Gaussian axial fluctuation model (1D-GAF) of the protein backbone and to the g motion of the related 3D-GAF motional model, the amplitudes of which have been extensively studied by NMR spectroscopy 20,21,[25][26][27] . The anti-correlation is due to the rigidity of the peptide plane, which couples the motion Figure 1 | b-sheet ensemble correlations observed within and between the strands.…”

“…This correlation was also observed in a high-quality conformational ensemble termed ERNST (ensemble refinement for native proteins using a single alignment tensor) that was determined for the small a/b protein ubiquitin by restraining MD simulations with a large set of residual dipolar couplings measured using NMR. This correlation, which we termed b-lever, is caused by concerted crankshaft motions of peptide planes of neighbouring strands in a manner that preserves the inter-strand hydrogen bonds that stabilize the b-sheet 21 . The correlation is stronger between the f torsion angle of residues in neighbouring strands, with rE0.…”

“…In a complementary fashion, theoretical methods have also provided insights into the mechanistic details of how interresidue interactions can lead to correlated motions spanning long distances 18 . Finally, hybrid experimental/computational approaches have also been used to study this phenomenon [19][20][21][22][23] .…”

Protein dynamics and function from solution state NMR spectroscopy

“…Another ubiquitin ensemble that was constructed by refinement against RDCs and is sensitive to motions on a ps-to-ms time scale is described in some detail in Section 4 (Lange et al 2008). Ensemble approaches have also been used to visualize transient encounter complexes (Bashir et al 2010;Tang et al 2006), quantify enzyme dynamics , describe the solution structures of intrinsically disordered proteins (Jensen et al 2013(Jensen et al , 2014Silvestre-Ryan et al 2013), and probe correlated motions in proteins (Bouvignies et al 2005;Bryn Fenwick et al 2014;Clore & Schwieters, 2004a;Fenwick et al 2011).…”

ProCS15: A DFT-based chemical shift predictor for backbone and C β atoms in proteins

“…The PM6-D3H+ optimizations are done using the GAMESS program (Schmidt et al, 1993) with a convergence criterion of 5 × 10 −4 atomic units, while the CHARMM22/CMAP optimizations are done using TINKER (Ponder and Richards, 1987) with the default convergence criterion of 0.01 kcal/mole/Å. In addition the following NMR-derived structural ensembles are used without further refinement: 1D3Z (Cornilescu et al, 1998), 2K39 (Lange et al, 2008), 1XQQ (Lindorff-Larsen et al, 2005), 2LJ5 (Montalvao et al, 2012), 2KOX (Fenwick et al, 2011). In all calculation we used charged protonation states for the acidic and basic side-chains, but in the NMR ensembles Histidine were left neutral (with either Nδ 1 or Nε2 protonated) as published.…”