Preprints
https://doi.org/10.5194/mr-2020-38
https://doi.org/10.5194/mr-2020-38

  11 Jan 2021

11 Jan 2021

Status: this preprint has been withdrawn by the authors.

Protein dynamics insights from 15N-1H (TROSY) HSQC

Erik R. P. Zuiderweg1,a Erik R. P. Zuiderweg
  • 1University of Michigan Medical School, Department of Biological Chemistry, Ann Arbor, 5 MI 41109, USA
  • acurrent address: 6585XW Mook, the Netherlands

Abstract. Protein dynamic information is customarily extracted from 15N NMR spin-relaxation experiments. These experiments can only be applied to (small) proteins that can be dissolved to high concentrations. However, most proteins of interest to the biochemical and biomedical community are large and relatively insoluble. These proteins often have functional conformational changes, and it is particularly regretful that these processes cannot be supplemented by dynamical information from NMR.
We ask here whether (some) dynamic information can be obtained form the 1H line widths in 15N-1H HSQC spectra. Such spectra are widely available, also for larger proteins. We developed a computer program to predict amide proton line widths from (crystal) structures. As a calibration, we test our approach on BPTI. We find that we can predict most of the distribution of experimental amide proton line widths if we take the dipole-dipole interaction with at least 40 surrounding protons into account. When focusing our attention the outliers of the distribution, we find for BPTI a cluster of conformationally broadened 1HN resonances of residues in strands 10–15 and 36–40 of the beta sheet. Conformational exchange broadening of the 15NH resonances for these residues was previously reported using 15N relaxation measurements (Szyperski et al., J. Biomol. NMR 3, 151–164, 1993). There is little or no evidence for motional narrowing of the 1HN resonances, also in agreement with earlier data using 15N relaxation methods (Beeser et.al, J. Mol. Biol. 269, 154–164, 1997). We also apply our program to 42 kDa domain of the human Hsc70 protein. In this case, there is no previous 15N relaxation data to compare with, but we find, again from the outliers of the distribution, both exchange broadening and motional narrowing that appears to corroborate previous conformational insights for this domain.

This preprint has been withdrawn.

Erik R. P. Zuiderweg

Interactive discussion

Status: closed

Comment types: AC – author | RC – referee | CC – community | EC – editor | CEC – chief editor | : Report abuse
  • RC1: 'Comment on mr-2020-38', Anonymous Referee #1, 20 Jan 2021
  • AC1: 'Comment on mr-2020-38', Erik Zuiderweg, 21 Jan 2021
  • RC2: 'Comment on mr-2020-38', Anonymous Referee #2, 22 Jan 2021
  • RC3: 'Comment on mr-2020-38', Anonymous Referee #3, 23 Jan 2021
  • CEC1: 'Comment on mr-2020-38', Gottfried Otting, 27 Jan 2021

Interactive discussion

Status: closed

Comment types: AC – author | RC – referee | CC – community | EC – editor | CEC – chief editor | : Report abuse
  • RC1: 'Comment on mr-2020-38', Anonymous Referee #1, 20 Jan 2021
  • AC1: 'Comment on mr-2020-38', Erik Zuiderweg, 21 Jan 2021
  • RC2: 'Comment on mr-2020-38', Anonymous Referee #2, 22 Jan 2021
  • RC3: 'Comment on mr-2020-38', Anonymous Referee #3, 23 Jan 2021
  • CEC1: 'Comment on mr-2020-38', Gottfried Otting, 27 Jan 2021

Erik R. P. Zuiderweg

Erik R. P. Zuiderweg

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This preprint has been withdrawn.

Short summary
We show here that information about protein molecular dynamics can be directly extracted out of a single NMR spectrum. Understanding protein dynamics is essential to understanding its function, energetics and biology. We hope that this contribution helps bring this insight to a much broader application field and audience community than previously possible.