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Mechanics of Protein Crystals: Atomistic Modeling of Elasticity and Fracture

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The structure, behavior, and mechanical properties of proteins plays an overarching role in biological systems. In recent years, materials based on proteins have also been proposed as a basis of new materials for medical and technological applications. In this article, we report classical molecular dynamics modeling of the elasticity and fracture behavior of protein crystals. We consider two proteins, a small protein α-conotoxin PnIB from conus pennaceus and lysozyme, a well-studied enzyme that catalyzes breaking of glycosidic bonds. We calculate pressure–strain curves for different loading conditions, including uniaxial strain in three crystallographic directions and equitriaxial loading. Our modeling yields insight into the deformation mechanisms inside the protein molecules. We find that changes in internal displacements of backbone C α -atoms, referred to as characteristic deformation profiles, can be linked with the macroscopic elastic response of the protein crystal. We demonstrate that simple sequence mutations may have a strong impact on elastic properties, indicating the potential of using amino acid mutations to tailor mechanical properties. We observe that such sequence mutations induce changes in the characteristic displacement profiles, which lead to modified elastic response. We also report a study of mode I fracture of protein crystals, showing some molecular details of dynamical crackpropagation in protein crystals.
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Keywords: BIOLOGY; DEFORMATION; ELASTICITY; ENZYME; FORCE FIELD; FRACTURE; MECHANICS; MOLECULAR MODELING; PROTEIN CRYSTALS

Document Type: Research Article

Publication date: October 1, 2006

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  • Journal of Computational and Theoretical Nanoscience is an international peer-reviewed journal with a wide-ranging coverage, consolidates research activities in all aspects of computational and theoretical nanoscience into a single reference source. This journal offers scientists and engineers peer-reviewed research papers in all aspects of computational and theoretical nanoscience and nanotechnology in chemistry, physics, materials science, engineering and biology to publish original full papers and timely state-of-the-art reviews and short communications encompassing the fundamental and applied research.
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