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Cited by 33Protein Structure and DynamicsAdvanced NMR Techniques and ApplicationsChemical Synthesis and Analysis

Conformational Dynamics of Asparagine at Coiled-Coil Interfaces

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Thomas, Franziska, Niitsu, Ai, Oregioni, Alain, Bartlett, Gail J., Woolfson, Derek N.·2017·Biochemistry
DOI 10.1021/acs.biochem.7b00848PMC PMC5916467
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Abstract

Coiled coils (CCs) are among the best-understood protein folds. Nonetheless, there are gaps in our knowledge of CCs. Notably, CCs are likely to be structurally more dynamic than often considered. Here, we explore this in an abundant class of CCs, parallel dimers, focusing on polar asparagine (Asn) residues in the hydrophobic interface. It is well documented that such inclusions discriminate between different CC oligomers, which has been rationalized in terms of whether the Asn can make side-chain hydrogen bonds. Analysis of parallel CC dimers in the Protein Data Bank reveals a variety of Asn side-chain conformations, but not all of these make the expected inter-side-chain hydrogen bond. We probe the structure and dynamics of a de novo-designed coiled-coil homodimer, CC-Di, by multidimensional nuclear magnetic resonance spectroscopy, including model-free dynamical analysis and relaxation–dispersion experiments. We find dynamic exchange on the millisecond time scale between Asn conformers with the side chains pointing into and out of the core. We perform molecular dynamics simulations that are consistent with this, revealing that the side chains are highly dynamic, exchanging between hydrogen-bonded-paired conformations in picoseconds to nanoseconds. Combined, our data present a more dynamic view for Asn at CC interfaces. Although inter-side-chain hydrogen bonding states are the most abundant, Asn is not always buried or engaged in such interactions. Because interfacial Asn residues are key design features for modulating CC stability and recognition, these further insights into how they are accommodated within CC structures will aid their predictive modeling, engineering, and design.

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  • The burial of more than two Asn residues at the hydrophobic peptide core is not tolerated in higher oligomerization states, rendering the trimer and tetramer states less favorable.

    “However, the burial of more than two Asn residues is not tolerated in higher oligomerization states, rendering the trimer and tetramer states less favorable.33,112”

    From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [112]

    The Abstract and Discussion (pages unavailable) say that a central Asn pair favors dimer formation, and that Asn side chains point out of the hydrophobic core when one studied peptide forms trimers. They do not establish a general limit of two buried Asn residues or show that both trimers and tetramers become less favorable for that reason. (LLM, conf=0.86)

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Cited by

Sorted by citations

Authors
Thomas, F., Niitsu, A., Oregioni, A., Bartlett, G. J., & Woolfson, D. N.
Affiliations
  • University of Bristol (GB)
  • The Francis Crick Institute (GB)
Corresponding author
  • Thomas, Franziska
  • Woolfson, Derek N.
ORCID
Venue
Biochemistry
Publisher
American Chemical Society (ACS)
Published
2017-11-22
Volume
56
Issue
50
Pages
6544-6554
ISSN
  • 0006-2960 (ISSN-L)
  • 1520-4995
DOI
10.1021/acs.biochem.7b00848
PMC
PMC5916467
OpenAlex
W2768605858
Cited by
33
References
5
Citations by year
2026: 4 · 2025: 2 · 2024: 4 · 2023: 5 · 2022: 2 · 2021: 2 · 2020: 5 · 2019: 3 · 2018: 6
FWCI
1.56
Type
journal article
Language
en
Open access
Licence
Locations
  • Biochemistry (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • Bristol Research (University of Bristol) (publishedVersion, other-oa)
  • Explore Bristol Research (acceptedVersion, other-oa)
  • Figshare (submittedVersion, cc-by)
Funders
  • Wellcome Trust (FC001142, FC10029)
  • H2020 European Research Council (340764)
  • Medical Research Council (NA)
  • Biotechnology and Biological Sciences Research Council (BB/J009784/1)
  • Leverhulme Trust (RPG-2012-536)
  • Royal Society (WM140008)
  • Cancer Research UK (NA)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced NMR Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
Keywords
coiled coil, asparagine, side-chain conformation, hydrophobic interface, conformational exchange, protein dynamics, relaxation dispersion, molecular dynamics simulation
MeSH terms
Amino Acid Sequence, Asparagine, Computer Simulation, Hydrogen Bonding, Magnetic Resonance Spectroscopy, Protein Conformation, Proteins, Protein Structure, Secondary, Dimerization, Databases, Protein, Molecular Dynamics Simulation, Hydrophobic and Hydrophilic Interactions

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