CG2AT2: an Enhanced Fragment-Based Approach for Serial Multi-scale Molecular Dynamics Simulations
Year: 2021
Type: article
Abstract: Coarse-grained molecular dynamics provides a means for simulating the assembly and interactions of macromolecular complexes at a reduced level of representation, thereby allowing both longer timescale and larger sized simulations. Here, we describe an enhanced fragment-based protocol for converting macromolecular complexes from coarse-grained to atomistic resolution, for further refinement and analysis. While the focus is upon systems that comprise an integral membrane protein embedded in a phospholipid bilayer, the technique is also suitable for membrane-anchored and soluble protein/nucleotide complexes. Overall, this provides a method for generating an accurate and well-equilibrated atomic-level description of a macromolecular complex. The approach is evaluated using a diverse test set of 11 system configurations of varying size and complexity. Simulations are assessed in terms of protein stereochemistry, conformational drift, lipid/protein interactions, and lipid dynamics.
Authors: Owen N. Vickery, Phillip J. Stansfeld
Institution: University of Warwick
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $5,000
Awards: Computational tools for enzyme engineering: bridging the gap between enzymologists and expert simulation, The UK High-End Computing Consortium for Biomolecular Simulation, Inquire: Software for real-time analysis of binding, The UK High-End Computing Consortium for Biomolecular Simulation, Assembly and Dynamics of Bacterial Chemosensory Signaling Arrays, Proposal for a Tier 2 Centre - HPC Midlands Plus, CCP-BioSim: Biomolecular Simulation at the Life Sciences Interface, CCP-BioSim: Biomolecular simulation at the life sciences interface, The Lipoprotein Biogenesis Pathway: An Emerging Structural Target for Novel Antibiotics, The Lipoprotein Biogenesis Pathway: An Emerging Structural Target for Novel Antibiotics, G5066350998, G5580141040, G5927648607, G6396470543, Adaptive Multi-Resolution Massively-Multicore Hybrid Dynamics, Predicting drug-target binding kinetics through multiscale simulations, BristolBridge: Bridging the Gaps between the Engineering and Physical Sciences and Antimicrobial Resistance, Multiscale Ensemble Computing for Modelling Biological Catalysts, Computational biochemistry: predictive modelling for biology and medicine, G8243181047, The UK High-End Computing Consortium for Biomolecular Simulation, Triggering assembly of the twin-arginine translocase, G881534351, G9000158989, Functional dynamics of the KATP channel
OpenAlex ID: W3197665808