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Conformational Dynamics of Asparagine at Coiled-Coil Interfaces

Franziska Thomas^1,2, Ai Niitsu¹, Alain Oregioni³

¹School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K.

|November 23, 2017

Summary

Protein coiled coils (CCs) are dynamic, especially polar asparagine (Asn) residues at interfaces. These Asn side chains can move, not always forming hydrogen bonds, impacting CC stability and design.

Area of Science:

Protein structure and dynamics
Biophysics
Computational biology

Background:

Coiled coils (CCs) are common protein structures.
Their structural dynamics are not fully understood.
Polar asparagine (Asn) residues in CC interfaces are key for stability and recognition.

Purpose of the Study:

To investigate the structural dynamics of polar Asn residues in parallel CC dimers.
To explore the role of Asn side-chain conformations and hydrogen bonding in CC interfaces.

Main Methods:

Analysis of parallel CC dimers in the Protein Data Bank.
Multidimensional nuclear magnetic resonance (NMR) spectroscopy on a de novo-designed CC homodimer (CC-Di).
Model-free dynamical analysis and relaxation-dispersion experiments.
Molecular dynamics (MD) simulations.

Main Results:

Asn side chains exhibit diverse conformations at CC interfaces.
NMR data reveal millisecond-timescale dynamic exchange of Asn conformers.
MD simulations show picosecond-to-nanosecond exchange between hydrogen-bonded states.
Asn residues are not always buried or hydrogen-bonded in the CC core.

Conclusions:

CCs, particularly Asn residues at interfaces, are more dynamic than previously thought.
Interfacial Asn residues can adopt non-hydrogen-bonded conformations.
Understanding Asn dynamics is crucial for accurate modeling, engineering, and design of CCs.

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