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Cited by 3Advanced NMR Techniques and ApplicationsProtein Structure and DynamicsElectron Spin Resonance Studies

The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.

Rapid Interpretation of Protein Backbone Rotation Dynamics Directly from Spin Relaxation Data

Open access
Nencini, Ricky, Mantzari, Efstathia, Sandelin, Amanda E., Ollila, O. H. Samuli·2024·The Journal of Physical Chemistry Letters
DOI 10.1021/acs.jpclett.4c01800PMC PMC11480883

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Abstract

Besides structure, protein dynamics is pivotal for their functions, particularly for intrinsically disordered proteins (IDPs) that do not fold to a fixed 3D structure. Rapid rotations of chemical bonds in proteins can be detected measuring NMR spin relaxation rates, but interpretation of protein dynamics from the experimental data is arduous for IDPs or molecular assemblies with complex dynamic landscape. Here we demonstrate numerically that the total effective correlation times of protein backbone N-H bond rotations, τeff , can be calculated from experimentally measured transverse 15N spin relaxation rates, R2, using linear relation. Using molecular dynamics (MD) simulations, we show this for wide range of proteins, from short peptides to partially dis- ordered proteins and peptides in micelles. Significant practical advance of the result is demonstrated by interpreting dynamics of partially disordered proteins that are beyond the scope of current approaches to interpret spin relaxation rate experiments.

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Crossref · 10.1021/acs.jpclett.4c01800

Cites

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Figures

Figure 1 (a) Representative conformations of proteins and peptides in MD simulations. (b) Effective correlation times, τeff, as functions of spin relaxation rates from MD simulations of different types of systems (dots) and 1-timescale approximation substituted into Redfield equations (blue solid lines). (c) Effective correlation times, τeff, as a function of R20 shown separately for different types of systems and different x-axis scales.
Figure 1 (a) Representative conformations of proteins and peptides in MD simulations. (b) Effective correlation times, τeff, as functions of spin relaxation rates from MD simulations of different types of systems (dots) and 1-timescale approximation substituted into Redfield equations (blue solid lines). (c) Effective correlation times, τeff, as a function of R20 shown separately for different types of systems and different x-axis scales.CC BY · PubMed Central
Figure 2 Effective correlation times of partially disordered proteins calculated from experimental R2 values from the literature (EN221 – blue, Pf-SH322 – orange, TDP-4323 – green, TonB3 – red, δ-subunit24 – violet, PDZ-linker25 – brown, and BRD426 – pink). Secondary structures of each protein are illustrated at the top of each panel with color coding (blue: α helix, green: β sheet; orange: disordered). All points are connected by colored lines. Residues that are manually assigned to belong to disordered regions are highlighted with green points, and residues assigned to folded regions are indicated with black points. Average correlation times for these folded and disordered regions as a function of their size, together with the Pearson correlation analysis, are shown in the bottom right corner. Color coding for proteins is the same as that in other plots.
Figure 2 Effective correlation times of partially disordered proteins calculated from experimental R2 values from the literature (EN221 – blue, Pf-SH322 – orange, TDP-4323 – green, TonB3 – red, δ-subunit24 – violet, PDZ-linker25 – brown, and BRD426 – pink). Secondary structures of each protein are illustrated at the top of each panel with color coding (blue: α helix, green: β sheet; orange: disordered). All points are connected by colored lines. Residues that are manually assigned to belong to disordered regions are highlighted with green points, and residues assigned to folded regions are indicated with black points. Average correlation times for these folded and disordered regions as a function of their size, together with the Pearson correlation analysis, are shown in the bottom right corner. Color coding for proteins is the same as that in other plots.CC BY · PubMed Central
Figure 3 Effective correlation times calculated using linear approximation for all proteins with R2 values available in four different magnetic fields in the BMRB database:29 azurin (BMRB: 6243,30 PDB: 1AZU(31)), B3 domain of protein G (BMRB: 26845,32 PDB: 1IGD(33)), human apo S100A1 (BMRB: 16360, PDB: 2L0P(34)), and CsPinA parvulin (BMRB: 18864,35 PDB: 2M1I). Protein structures are taken from the Protein Data Bank (PDB).36 Data points and structures are labeled with the same color for each protein. The black lines show equal values with both magnetic fields.
Figure 3 Effective correlation times calculated using linear approximation for all proteins with R2 values available in four different magnetic fields in the BMRB database:29 azurin (BMRB: 6243,30 PDB: 1AZU(31)), B3 domain of protein G (BMRB: 26845,32 PDB: 1IGD(33)), human apo S100A1 (BMRB: 16360, PDB: 2L0P(34)), and CsPinA parvulin (BMRB: 18864,35 PDB: 2M1I). Protein structures are taken from the Protein Data Bank (PDB).36 Data points and structures are labeled with the same color for each protein. The black lines show equal values with both magnetic fields.CC BY · PubMed Central
Figure 4 Effective correlation times for CsPinA determined from R2 at different fields (a) without and (b) with the correction term for chemical exchange. (c) The magnitude of the chemical exchange term at 500 MHz from our analysis and literature.35
Figure 4 Effective correlation times for CsPinA determined from R2 at different fields (a) without and (b) with the correction term for chemical exchange. (c) The magnitude of the chemical exchange term at 500 MHz from our analysis and literature.35CC BY · PubMed Central

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Research works printed but not linked: 1

  1. 10.26434/chemrxiv-2024-h3pmt · DOI

Metadata

Authors
Nencini, R., Mantzari, E., Sandelin, A. E., & Ollila, O. H. S.
Affiliations
University of Helsinki (FI)
Corresponding author
Ollila, O. H. Samuli
ORCID
Venue
The Journal of Physical Chemistry Letters
Publisher
American Chemical Society (ACS)
Published
2024-10-01
Volume
15
Issue
40
Pages
10204-10209
ISSN
1948-7185 (ISSN-L)
DOI
10.1021/acs.jpclett.4c01800
PMC
PMC11480883
OpenAlex
W4403018599
Cited by
3
References
38
Citations by year
2026: 1 · 2025: 2
FWCI
0.37
Type
journal article
Language
en
Open access
Licence
Locations
  • The Journal of Physical Chemistry Letters (publishedVersion, cc-by)
  • ChemRxiv (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Työväentutkimus Vuosikirja (submittedVersion)
Funders
Research Council of Finland (315596, 319902, 345631, 356568)
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced NMR Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Spectroscopy › Electron Spin Resonance Studies
Keywords
backbone dynamics, intrinsically disordered proteins, 15N spin relaxation, transverse relaxation rate, peptide micelles
MeSH terms
Micelles, Peptides, Protein Conformation, Proteins, Rotation, Nuclear Magnetic Resonance, Biomolecular, Intrinsically Disordered Proteins

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