Rotamer jumps, proton exchange, and amine inversion dynamics of dimethylated lysine residues in proteins resolved by ph-dependent 1h and 13c nmr relaxation dispersion
Weininger, Ulrich LU ; Modig, Kristofer LU
; Ishida, Hiroaki
; Vogel, Hans J.
and Akke, Mikael
LU
(2019)
In Journal of Physical Chemistry B
123(46).
p.9742-9750
- Abstract
Post-translational methylation of lysine side chains is of great importance for protein regulation, including epigenetic control. Here, we present specific 13CHD2 labeling of dimethylated lysines as a sensitive probe of the structure, interactions, and dynamics of these groups, and outline a theoretical and experimental framework for analyzing their conformational dynamics using 1H and 13C CPMG relaxation dispersion experiments. Dimethylated lysine side chains in calcium-loaded calmodulin show a marked pH dependence of their Carr-Purcell-Meiboom-Gill (CPMG) dispersion profiles, indicating complex exchange behavior. Combined analysis of 1H and 13C CPMG relaxation... (More)
Post-translational methylation of lysine side chains is of great importance for protein regulation, including epigenetic control. Here, we present specific 13CHD2 labeling of dimethylated lysines as a sensitive probe of the structure, interactions, and dynamics of these groups, and outline a theoretical and experimental framework for analyzing their conformational dynamics using 1H and 13C CPMG relaxation dispersion experiments. Dimethylated lysine side chains in calcium-loaded calmodulin show a marked pH dependence of their Carr-Purcell-Meiboom-Gill (CPMG) dispersion profiles, indicating complex exchange behavior. Combined analysis of 1H and 13C CPMG relaxation dispersions requires consideration of 12-state correlated exchange of the two methyl groups due to circular three-state rotamer jumps around the Cϵ-Nζ axis combined with proton exchange and amine inversion. Taking into account a number of fundamental constraints, the exchange model can be reduced to include only three fitted parameters, namely, the geometric average of the rotamer-jump rate constants, the rate constant of deprotonation of Nζ, and the chemical shift difference between the trans and gauge positions of the 13C or 1H nuclei. The pH dependence indicates that protonation of the end group dramatically slows down rotamer exchange for some lysine residues, whereas deprotonation leads to rapid amine inversion coupled with rotamer scrambling. The observed variation among residues in their exchange behavior appears to depend on the structural environment of the side chain. Understanding this type of exchange process is critical to correctly interpreting NMR spectra of methylated lysine side chains. The exchange model presented here forms the basis for studying the structure and dynamics of epigenetically modified lysine side chains and perturbations caused by changes in pH or interactions with target proteins.
(Less)
- author
- Weininger, Ulrich
LU
; Modig, Kristofer
LU
; Ishida, Hiroaki
; Vogel, Hans J.
and Akke, Mikael
LU
- organization
- publishing date
- 2019-11-21
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Journal of Physical Chemistry B
- volume
- 123
- issue
- 46
- pages
- 9 pages
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- scopus:85075031525
- pmid:31580078
- ISSN
- 1520-6106
- DOI
- 10.1021/acs.jpcb.9b06408
- language
- English
- LU publication?
- yes
- id
- 46844206-91eb-48a5-9a5d-ee3431ee8e31
- date added to LUP
- 2019-12-10 11:12:59
- date last changed
- 2024-05-01 02:24:13
@article{46844206-91eb-48a5-9a5d-ee3431ee8e31,
abstract = {{<p>Post-translational methylation of lysine side chains is of great importance for protein regulation, including epigenetic control. Here, we present specific <sup>13</sup>CHD<sub>2</sub> labeling of dimethylated lysines as a sensitive probe of the structure, interactions, and dynamics of these groups, and outline a theoretical and experimental framework for analyzing their conformational dynamics using <sup>1</sup>H and <sup>13</sup>C CPMG relaxation dispersion experiments. Dimethylated lysine side chains in calcium-loaded calmodulin show a marked pH dependence of their Carr-Purcell-Meiboom-Gill (CPMG) dispersion profiles, indicating complex exchange behavior. Combined analysis of <sup>1</sup>H and <sup>13</sup>C CPMG relaxation dispersions requires consideration of 12-state correlated exchange of the two methyl groups due to circular three-state rotamer jumps around the Cϵ-Nζ axis combined with proton exchange and amine inversion. Taking into account a number of fundamental constraints, the exchange model can be reduced to include only three fitted parameters, namely, the geometric average of the rotamer-jump rate constants, the rate constant of deprotonation of Nζ, and the chemical shift difference between the trans and gauge positions of the <sup>13</sup>C or <sup>1</sup>H nuclei. The pH dependence indicates that protonation of the end group dramatically slows down rotamer exchange for some lysine residues, whereas deprotonation leads to rapid amine inversion coupled with rotamer scrambling. The observed variation among residues in their exchange behavior appears to depend on the structural environment of the side chain. Understanding this type of exchange process is critical to correctly interpreting NMR spectra of methylated lysine side chains. The exchange model presented here forms the basis for studying the structure and dynamics of epigenetically modified lysine side chains and perturbations caused by changes in pH or interactions with target proteins. </p>}},
author = {{Weininger, Ulrich and Modig, Kristofer and Ishida, Hiroaki and Vogel, Hans J. and Akke, Mikael}},
issn = {{1520-6106}},
language = {{eng}},
month = {{11}},
number = {{46}},
pages = {{9742--9750}},
publisher = {{The American Chemical Society (ACS)}},
series = {{Journal of Physical Chemistry B}},
title = {{Rotamer jumps, proton exchange, and amine inversion dynamics of dimethylated lysine residues in proteins resolved by ph-dependent <sup>1</sup>h and <sup>13</sup>c nmr relaxation dispersion}},
url = {{http://dx.doi.org/10.1021/acs.jpcb.9b06408}},
doi = {{10.1021/acs.jpcb.9b06408}},
volume = {{123}},
year = {{2019}},
}