Time-Resolved Protein Side-Chain Motions Unraveled by High-Resolution Relaxometry and Molecular Dynamics Simulations

Abstract

Motions of proteins are essential for the performance of their functions. Aliphatic protein side chains and their motions play critical roles in protein interactions: for recognition and binding of partner molecules at the surface or serving as an entropy reservoir within the hydrophobic core. Here, we present a new NMR method based on high-resolution relaxometry and high-field relaxation to determine quantitatively both motional amplitudes and time scales of methyl-bearing side chains in the picosecond-to-nanosecond range. We detect a wide variety of motions in isoleucine side chains in the protein ubiquitin. We unambiguously identify slow motions in the low nanosecond range, which, in conjunction with molecular dynamics computer simulations, could be assigned to transitions between rotamers. Our approach provides unmatched detailed insight into the motions of aliphatic side chains in proteins and provides a better understanding of the nature and functional role of protein side-chain motions.

Structural and dynamic origins of ESR lineshapes in spin-labeled GB1 domain: the insights from spin dynamics simulations based on long MD trajectories

“…This result is consistent with the known magnitude of rotational barriers in alkanes, 3-5 kcal/mol 82 , and more specifically, in the R1 residue 76 . It is also consistent with MD/ NMR data on side-chain dynamics 83 . We conclude that for solvent-facing R1 tag on the surface of α-helix the rotameric jumps involving χ 1 and χ 2 should not necessarily be viewed as a slow form of motion.…”

Predicting NMR relaxation of proteins from molecular dynamics simulations with accurate methyl rotation barriers

“…The descriptive power of spectral densities from NMR relaxation experiments can be increased by measuring at multiple field strengths, which yields additional spectral density points, or by field shuttling. [26][27][28] However, these approaches are demanding and necessarily constrained to a limited number of discrete points.…”

Determining isoleucine side-chain rotamer-sampling in proteins from 13C chemical shift

“…The structure and conformational sampling of side chains are often derived from a combination of several NMR measurements, such as nuclear Overhauser effects (NOEs), three-bond scalar couplings, 4,5 residual dipolar couplings and spin-relaxation measurements. 6 Although these measurements are feasible for most proteins smaller than 20 kDa, an accurate description of side-chain behaviour of larger systems often becomes challenging. Moreover, characterising the conformational sampling of side chains in low-populated states 2,7 is still more difficult, because neither NOEs nor scalar couplings can currently be obtained.…”