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MELD-Path Efficiently Computes Conformational Transitions, Including Multiple and Diverse Paths.

Alberto Perez¹, Florian Sittel², Gerhard Stock²

¹Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 1179 4, United States.

Journal of Chemical Theory and Computation

|March 17, 2018

Summary

We developed MELD-path, a fast computational method to map protein reaction pathways. This approach efficiently explores molecular dynamics, revealing complex routes and kinetics for biomolecular mechanisms.

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Area of Science:

Computational Biology
Biophysics
Molecular Dynamics

Background:

Protein molecular actions are governed by reaction coordinates.
Current computational methods struggle to explore these pathways effectively.

Purpose of the Study:

To introduce MELD-path, a novel computational protocol for efficient exploration of molecular reaction pathways.
To enable rapid mapping of biomolecular mechanistic processes.

Main Methods:

MELD-path combines MELD (Molecular Enhanced Dynamics) for state sampling with Markov State Models (MSMs).
It seeds multiple short Molecular Dynamics (MD) trajectories from sampled states.
MSMs are constructed to determine reaction routes and kinetics.

Main Results:

MELD-path successfully mapped the right-handed to left-handed helix transition of an AIB peptide.
The method identified all metastable states, their populations, and a broad ensemble of reaction routes.
Computational results showed convergence with extensive MD simulations.

Conclusions:

MELD-path provides a highly parallelizable and efficient method for exploring biomolecular mechanisms.
This protocol can rapidly generate comprehensive maps of molecular reaction pathways.
It offers a generalizable approach for studying complex biological processes computationally.