Electron-nuclear interactions as probes of domain motion in proteins

Abstract

Long range interactions between nuclear spins and paramagnetic ions can serve as a sensitive monitor of internal motion of various parts of proteins, including functional loops and separate domains. In the case of interdomain motion, the interactions between the ion and NMR-observable nuclei are modulated in direction and magnitude mainly by a combination of overall and interdomain motions. The effects on observable parameters such as paramagnetic relaxation enhancement ͑PRE͒ and pseudocontact shift ͑PCS͒ can, in principle, be used to characterize motion. These parameters are frequently used for the purpose of structural refinements. However, their use to probe actual domain motions is less common and is lacking a proper theoretical treatment from a motional perspective. In this work, a suitable spin Hamiltonian is incorporated in a two body diffusion model to produce the time correlation function for the nuclear spin-paramagnetic ion interactions. Simulated observables for nuclei in different positions with respect to the paramagnetic ion are produced. Based on these simulations, it demonstrated that both the PRE and the PCS can be very sensitive probes of domain motion. Results for different nuclei within the protein sense different aspects of the motions. Some are more sensitive to the amplitude of the internal motion, others are more sensitive to overall diffusion rates, allowing separation of these contributions. Experimentally, the interaction strength can also be tuned by substitution of different paramagnetic ions or by varying magnetic field strength ͑in the case of lanthanides͒ to allow the use of more detailed diffusion models without reducing the reliability of data fitting.

Expanding the utility of NMR restraints with paramagnetic compounds: Background and practical aspects

“…For large amplitude motions also the distance dependence of the PCSs is affected. A mathematical description for structural averaging is just emerging in the literature [69]. …”

Paramagnetic relaxation enhancement for the characterization of the conformational heterogeneity in two-domain proteins

“…29,30,36,38 The same approach has been used here to analyse the PRE, with the advantage that the large distance between the unpaired electrons and the nucleus makes the contribution of fast local motions negligible, thus enhancing the effect of domain motions. 39 According to this model, eqn ( 6) and ( 7) are obtained. The correlation times t r and t s can be determined from amide relaxation measurements, 30,38 or estimated through HYDRONMR calculations.…”

NMR study of eukaryotic translation termination

“…However, we still cannot rule out the possibility of allostery regulation via helix α4 of N-domain and the linker peptide. It would be interesting in the future to look into the inter-domain motion of NM-domain using other state-of-the-art experimental methods (Chen and Tjandra, 2008, Monkenbusch et al, 2010, Shapira and Prestegard, 2010. Based on the available data, peptidyl-tRNA hydrolysis achieved by NMdomain alone may not be allosteric regulated by stop codon recognition.…”