Distribution of Pico- and Nanosecond Motions in Disordered Proteins from Nuclear Spin Relaxation

Abstract

Intrinsically disordered proteins and intrinsically disordered regions (IDRs) are ubiquitous in the eukaryotic proteome. The description and understanding of their conformational properties require the development of new experimental, computational, and theoretical approaches. Here, we use nuclear spin relaxation to investigate the distribution of timescales of motions in an IDR from picoseconds to nanoseconds. Nitrogen-15 relaxation rates have been measured at five magnetic fields, ranging from 9.4 to 23.5 T (400-1000 MHz for protons). This exceptional wealth of data allowed us to map the spectral density function for the motions of backbone NH pairs in the partially disordered transcription factor Engrailed at 11 different frequencies. We introduce an approach called interpretation of motions by a projection onto an array of correlation times (IMPACT), which focuses on an array of six correlation times with intervals that are equidistant on a logarithmic scale between 21 ps and 21 ns. The distribution of motions in Engrailed varies smoothly along the protein sequence and is multimodal for most residues, with a prevalence of motions around 1 ns in the IDR. We show that IMPACT often provides better quantitative agreement with experimental data than conventional model-free or extended model-free analyses with two or three correlation times. We introduce a graphical representation that offers a convenient platform for a qualitative discussion of dynamics. Even when relaxation data are only acquired at three magnetic fields that are readily accessible, the IMPACT analysis gives a satisfactory characterization of spectral density functions, thus opening the way to a broad use of this approach.

A Small Molecule Causes a Population Shift in the Conformational Landscape of an Intrinsically Disordered Protein

“…Application of large amplitude ω eff 1 H N RD methods in the future will allow detection of low microsecond motions within other IDPs, IDRs, and unfolded proteins ( e.g. , as has been proposed to exist in a recent report for the IDP Engrailed 21 ) and unfolded proteins that exhibit elevated transverse relaxation rates. 8,12,13,52 This approach can complement studies that utilize conventional relaxation methods that probe picosecond to nanosecond motions.…”

Sequence-dependent correlated segments in the intrinsically disordered region of ChiZ

“…For disordered proteins, global and local motions are no longer separable, and interpreting relaxation data becomes a challenge. One can still model the relaxation data by fitting the NH bond vector time-correlation functions CNH(t) to a sum of exponentials but the assignment of the resulting time constants to specific types of motions can be ambiguous (37)(38)(39). MD simulations can help elucidate these connections.…”

What Drives 15N Spin Relaxation in Disordered Proteins? Combined NMR/MD Study of the H4 Histone Tail

“…The first one employs a continuous distribution of correlation times, which is modeled by a certain simple function or, alternatively, parameterized through distribution moments (14)(15)(16). The second utilizes a predefined grid of correlation times (17). The access to different 15 N relaxation rates-including cross-correlated cross-relaxation ratesas well as the availability of data recorded at multiple magnetic field strengths (17,18) makes it possible to obtain a rather accurate and well-validated representation of the backbone correlation functions.…”

“…The second utilizes a predefined grid of correlation times (17). The access to different 15 N relaxation rates-including cross-correlated cross-relaxation ratesas well as the availability of data recorded at multiple magnetic field strengths (17,18) makes it possible to obtain a rather accurate and well-validated representation of the backbone correlation functions. This leaves us, however, with the remaining important question: how to relate the temporal correlation function, which is representative of the reorientational motion of the NH bond, to specific forms of motion occurring in disordered proteins?…”