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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

Enhanced unbiased sampling of protein dynamics using evolutionary coupling information.

Zahra Shamsi¹, Alexander S Moffett², Diwakar Shukla^3,4,5,6

¹Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL, 61801, USA.

Scientific Reports

|October 7, 2017

Summary

Evolutionary couplings help predict protein dynamics. Using distances between coupled residues accelerates simulations for protein activation, folding, and association, significantly reducing computation time.

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Area of Science:

Computational biology
Biophysics
Protein dynamics

Background:

Atomistic simulations face challenges in sampling rare protein conformational transitions.
Evolutionary couplings infer residue contacts, aiding protein structure prediction.

Purpose of the Study:

To assess evolutionary couplings as reaction coordinates for enhanced sampling in molecular simulations.
To predict protein functional conformations and transition pathways.

Main Methods:

Utilized distances between evolutionarily coupled residues.
Incorporated these distances into Markov state model-based adaptive sampling schemes.
Applied methods to beta 2-adrenergic receptor activation, FiP35 WW domain folding, and molybdopterin synthase dimerization.

Main Results:

Significantly reduced simulation time for beta 2-adrenergic receptor activation and WW domain folding.
Successfully identified potential association pathways for molybdopterin synthase.
Predicted near-crystal structure complexes from protein-protein association simulations.

Conclusions:

Evolutionary couplings provide effective reaction coordinates for accelerated molecular simulations.
This approach enhances the prediction of protein conformational changes, folding, and associations.
The method offers a powerful tool for understanding complex biological processes at an atomic level.