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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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A molecular simulation protocol to avoid sampling redundancy and discover new states.

Marco Bacci¹, Andreas Vitalis¹, Amedeo Caflisch¹

¹University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.

Biochimica Et Biophysica Acta

|September 7, 2014

Summary

This study introduces Progress Index Guided Sampling (PIGS), a novel algorithm for molecular dynamics simulations. PIGS enhances phase space exploration and identifies metastable states more efficiently than conventional methods.

Keywords:

Biomolecules Enhanced sampling Molecular dynamics Scalable algorithm Simulation convergence Transition path

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Area of Science:

Computational Chemistry
Biophysics
Molecular Dynamics Simulations

Background:

Experimental data for biomacromolecules often captures only specific states, leading to ambiguity in simulations.
Exploring complex molecular systems is challenging due to unknown phase space domains and difficulties in achieving sampling recurrence.
Rugged free energy surfaces in molecular dynamics hinder unbiased phase space exploration, making sampling inefficient.

Purpose of the Study:

To develop a heuristic algorithm for improving phase space exploration in molecular dynamics simulations.
To address the limitations of conventional sampling schemes in discovering relevant states and pathways.
To reduce unquantifiable errors arising from incomplete exploration of phase space.

Main Methods:

A heuristic algorithm, Progress Index Guided Sampling (PIGS), was developed to terminate and reseed parallel trajectories.
The method utilizes a snapshot ordering technique to identify "interesting" and "unique" simulations.
Criteria are defined to guide reseeding from more informative simulation points in overlapping phase space regions.

Main Results:

The PIGS method significantly amplifies the rate of phase space exploration.
Metastable states, previously undiscovered by conventional methods, were identified using a pedagogical example and an α-helical peptide.
Accurate kinetic information and reaction pathways were successfully extracted from the simulations.

Conclusions:

Progress Index Guided Sampling (PIGS) is an unsupervised, scalable method that improves with more replicas.
The underlying principles of PIGS are sufficient to enhance sampling efficiency in molecular simulations.
This protocol offers a valuable tool for researchers to mitigate errors associated with incomplete phase space exploration.