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Quantifying protein dynamics in the ps–ns time regime by NMR relaxation

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Abstract

Both 15N chemical shift anisotropy (CSA) and sufficiently rapid exchange linebroadening transitions exhibit relaxation contributions that are proportional to the square of the magnetic field. Deconvoluting these contributions is further complicated by residue-dependent variations in protein amide 15N CSA values which have proven difficult to accurately measure. Exploiting recently reported improvements for the implementation of T1 and T1ρ experiments, field strength-dependent studies have been carried out on the B3 domain of protein G (GB3) as well as on the immunophilin FKBP12 and a H87V variant of that protein in which the major conformational exchange linebroadening transition is suppressed. By applying a zero frequency spectral density rescaling analysis to the relaxation data collected at magnetic fields from 500 to 900 MHz 1H, differential residue-specific 15N CSA values have been obtained for GB3 which correlate with those derived from solid state and liquid crystalline NMR measurements to a level similar to the correlation among those previously reported studies. Application of this analysis protocol to FKBP12 demonstrated an efficient quantitation of both weak exchange linebroadening contributions and differential residue-specific 15N CSA values. Experimental access to such differential residue-specific 15N CSA values should significantly facilitate more accurate comparisons with molecular dynamics simulations of protein motion that occurs within the timeframe of global molecular tumbling.

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Acknowledgments

We acknowledge the use of the NMR facility and Applied Genomic Technologies cores at the Wadsworth Center. This work was supported in part by National Institutes of Health [GM 088214]. The NMR data collected at NYSBC was made possible by a grant from NYSTAR and ORIP/NIH facility improvement Grant CO6RR015495. The 900 MHz NMR spectrometers were purchased with funds from NIH Grant P41GM066354, the Keck Foundation, New York State Assembly, and U.S. Department of Defense.

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  1. Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, School of Public Health, University at Albany - SUNY, Empire State Plaza, Albany, NY, 12201, USA

    Griselda Hernández & David M. LeMaster

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  1. Griselda Hernández
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  2. David M. LeMaster
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Correspondence to David M. LeMaster.

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Hernández, G., LeMaster, D.M. Quantifying protein dynamics in the ps–ns time regime by NMR relaxation. J Biomol NMR 66, 163–174 (2016). https://doi.org/10.1007/s10858-016-0064-7

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