Harold W Hatch, Christina Bergonzo, Marco A Blanco, Guangcui Yuan, Sergei Grudinin, Mikael Lund, Joseph E Curtis, Alexander V Grishaev, Yun Liu, Vincent K Shen
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引用次数: 0
Abstract
We develop a multiscale coarse-grain model of the NIST Monoclonal Antibody Reference Material 8671 (NISTmAb) to enable systematic computational investigations of high-concentration physical instabilities such as phase separation, clustering, and aggregation. Our multiscale coarse-graining strategy captures atomic-resolution interactions with a computational approach that is orders of magnitude more efficient than atomistic models, assuming the biomolecule can be decomposed into one or more rigid bodies with known, fixed structures. This method reduces interactions between tens of thousands of atoms to a single anisotropic interaction site. The anisotropic interaction between unique pairs of rigid bodies is precomputed over a discrete set of relative orientations and stored, allowing interactions between arbitrarily oriented rigid bodies to be interpolated from the precomputed table during coarse-grained Monte Carlo simulations. We present this approach for lysozyme and lactoferrin as a single rigid body and for the NISTmAb as three rigid bodies bound by a flexible hinge with an implicit solvent model. This coarse-graining strategy predicts experimentally measured radius of gyration and second osmotic virial coefficient data, enabling routine Monte Carlo simulation of medically relevant concentrations of interacting proteins while retaining atomistic detail. All methodologies used in this work are available in the open-source software Free Energy and Advanced Sampling Simulation Toolkit.
期刊介绍:
The Journal of Chemical Physics publishes quantitative and rigorous science of long-lasting value in methods and applications of chemical physics. The Journal also publishes brief Communications of significant new findings, Perspectives on the latest advances in the field, and Special Topic issues. The Journal focuses on innovative research in experimental and theoretical areas of chemical physics, including spectroscopy, dynamics, kinetics, statistical mechanics, and quantum mechanics. In addition, topical areas such as polymers, soft matter, materials, surfaces/interfaces, and systems of biological relevance are of increasing importance.
Topical coverage includes:
Theoretical Methods and Algorithms
Advanced Experimental Techniques
Atoms, Molecules, and Clusters
Liquids, Glasses, and Crystals
Surfaces, Interfaces, and Materials
Polymers and Soft Matter
Biological Molecules and Networks.