Slow internal protein dynamics from water (1)H magnetic relaxation dispersion.
To probe internal motions in proteins on the 10(-8)-10(-5) s time scale by NMR relaxation, it is necessary to eliminate protein tumbling. Here, we examine to what extent magnetic relaxation dispersion (MRD) experiments on the water (1)H resonance report on protein motions in this time window. We also perform a critical test of two physically distinct mechanisms that have been proposed to explain and interpret (1)H MRD profiles from immobilized proteins: the exchange-mediated orientational randomization (EMOR) mechanism and the two-phase spin-fracton (2PSF) mechanism. For these purposes, we report the (1)H MRD profiles from protonated and partially deuterated ubiquitin, cross-linked by glutaraldehyde. The EMOR approach, with the crystal structure of ubiquitin as input, accounts quantitatively for the MRD data and shows that hydroxyl-bearing side chains undergo large-amplitude motions on the microsecond time scale. In contrast, the 2PSF model, which attributes (1)H relaxation to small-amplitude backbone vibrations that propagate in a low-dimensional fractal space, fails qualitatively in describing the effect of H-->D substitution. These findings appear to resolve the long-standing controversy over the molecular basis of water-(1)H relaxation in systems containing rotationally immobilized macromolecules, including biological tissue.
Sunde
Erik P
EP
Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden.
Halle
Bertil
B
D003903:Deuterium; D005976:Glutaral; D055767:Immobilized Proteins; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009038:Motion; D011506:Proteins / Q000737:chemistry*; D025801:Ubiquitin; D014867:Water / Q000737:chemistry*
D055767:Immobilized Proteins; D011506:Proteins; D025801:Ubiquitin; D014867:Water; D003903:Deuterium; D005976:Glutaral