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Peptide Self-Assembly pp 23–68Cite as

Solid-State NMR Structural Characterization of Self-Assembled Peptides with Selective 13C and 15N Isotopic Labels

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1777))

Abstract

For the structural characterization methods discussed here, information on molecular conformation and intermolecular organization within nanostructured peptide assemblies is discerned through analysis of solid-state NMR spectral features. This chapter reviews general NMR methodologies, requirements for sample preparation, and specific descriptions of key experiments. An attempt is made to explain choices of solid-state NMR experiments and interpretation of results in a way that is approachable to a nonspecialist. Measurements are designed to determine precise NMR peak positions and line widths, which are correlated with secondary structures, and probe nuclear spin–spin interactions that report on three-dimensional organization of atoms. The formulation of molecular structural models requires rationalization of data sets obtained from multiple NMR experiments on samples with carefully chosen 13C and 15N isotopic labels. The information content of solid-state NMR data has been illustrated mostly through the use of simulated data sets and references to recent structural work on amyloid fibril-forming peptides and designer self-assembling peptides.

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Notes

  1. 1.

    Nuclear magnetization is induced by population differences in nuclear spin states.

  2. 2.

    Shorter values for d 1 are sometimes used for faster scanning and better signal-to-noise, at the expense of some distortion in relative peak intensities.

  3. 3.

    The energy splitting between nuclear spin energy levels is \( \Delta E=h{\gamma}_n\cdot \left|\overrightarrow{B_0}\right| \), where h is Planck’s constant and γ n is the gyromagnetic ratio. Local nuclear magnetic interactions have very small (but measurable) effects on these energy splittings.

  4. 4.

    The Larmor frequency \( {\nu}_{\mathrm{L}}=\frac{\Delta E}{h}={\gamma}_n\cdot \left|\overrightarrow{B_0}\right| \). It is common to refer to a magnet in terms of its 1H Larmor frequency rather than its magnetic field strength.

  5. 5.

    Pulse, duration, power, and phase are independent parameters that define a radio frequency pulse. Pulse duration is the time over which the pulse is applied. Pulse power (energy input to the probe per unit time) is proportional to the second power of the voltage (or current) input to the probe. Pulse phase is the phase of the radio frequency waveform (sinusoid) for the pulse. Unless otherwise specified, the frequency of the pulse waveform is set to the spectrometer carrier frequency. In some experiments, pulse frequencies, phases, and powers can vary during the pulse.

  6. 6.

    This description does not capture the implications of “off-resonance” pulses that are not perfectly at the Larmor frequency. The Bloch equations capture the effects of off-resonant pulses on nuclear spin magnetization in the absence of local spin interactions [81, 84].

  7. 7.

    Pulse power in frequency units is proportional to \( \left|\overrightarrow{B_1}\right| \) and the current in the coil during the pulse. Pulse power in Watts would be proportional to \( {\left|\overrightarrow{B_1}\right|}^2 \).

  8. 8.

    It is common to refer to static magnetic field strength in terms of the 1H NMR Larmor frequency. For example, an 11.75 Tesla magnet would often be called a 500 MHz magnet.

  9. 9.

    Frequency in ppm is defined as the frequency of an NMR signal in Hz divided by a reference frequency (near the spectrometer carrier) in MHz. In ppm frequency units, many features of NMR spectra become independent of \( \left|\overrightarrow{B_0}\right| \).

  10. 10.

    The NMR spectra of RADA16-I nanofibers exhibited three sets of NMR peaks for each 13C atom labeled within alanine residues. These spectral features indicate the coexistence of multiple distinct molecular structures. We have simplified the schematic representations of NMR data in Figs. 4 and 5 to indicate only one set of alanine 13C NMR peaks.

  11. 11.

    It is possible to detect crosspeaks in 2D spectra even if dipolar recoupling is not employed during mixing periods, since MAS does not completely eliminate spin–spin couplings.

  12. 12.

    The most expensive FMOC -protected amino acids are those with acidic or basic sidechains, because of the need for sidechain production during peptide synthesis .

  13. 13.

    Isotopic labeling with 13C or 15N sites within sidechain aromatic or functional groups is often advantageous, because these sites often correspond to spectrally isolated NMR signals.

  14. 14.

    In our experience, 2D-fpRFDR tends to more selectively produce crosspeaks between directly bonded 13C atoms at MAS speeds above 20 kHz, when compared to 2D-DARR experiments with short (10 ms) mixing times. It is also possible to observe these crosspeaks at shorter mixing times (2 ms) with 2D-fpRFDR, such that overall signal is stronger due to less T 2 relaxation.

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Acknowledgements

This work was supported by the National Institute on Aging of the National Institutes of Health (award number R01AG045703). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. A portion of the work is financially supported by the National Science Foundation (DMR-105221 to AKP) and the startup at Georgia Institute of Technology. The authors also gratefully acknowledge Terrone L. Rosenberry, Ankita Gupta, and Smaranda Birlea for the proofreading of this manuscript.

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Authors and Affiliations

  1. School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA

    Danting Huang, Benjamin C. Hudson, Yuan Gao, Evan K. Roberts & Anant K. Paravastu

Authors
  1. Danting Huang
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  2. Benjamin C. Hudson
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  3. Yuan Gao
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  4. Evan K. Roberts
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  5. Anant K. Paravastu
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Correspondence to Anant K. Paravastu .

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Editors and Affiliations

  1. Department of Chemistry, University of Rochester, Rochester, New York, USA

    Bradley L. Nilsson

  2. Department of Medicinal Chemistry, Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota, USA

    Todd M. Doran

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Huang, D., Hudson, B.C., Gao, Y., Roberts, E.K., Paravastu, A.K. (2018). Solid-State NMR Structural Characterization of Self-Assembled Peptides with Selective 13C and 15N Isotopic Labels. In: Nilsson, B., Doran, T. (eds) Peptide Self-Assembly. Methods in Molecular Biology, vol 1777. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7811-3_2

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  • DOI: https://doi.org/10.1007/978-1-4939-7811-3_2

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