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International Journal for Multiscale Computational Engineering
IF: 1.016 5-Year IF: 1.194 SJR: 0.452 SNIP: 0.68 CiteScore™: 1.18

ISSN Print: 1543-1649
ISSN Online: 1940-4352

International Journal for Multiscale Computational Engineering

DOI: 10.1615/IntJMultCompEng.v7.i3.70
pages 237-250

Atomistically Informed Mesoscale Model of Alpha-Helical Protein Domains

Jeremie Bertaud
Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Zhao Qin
Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Markus J. Buehler
Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

ABSTRACT

Multiscale mechanical properties of biological protein materials have been the focal point of extensive investigations over the past decades. In this article, we present the development of a mesoscale model of alpha-helical (AH) protein domains, key constituents in a variety of biological materials, including cells, hair, hooves, and wool. Our model, derived solely from results of full atomistic simulations, is suitable to describe the deformation and fracture mechanics over multiple orders of magnitude in time- and length scales. After validation of the mesoscale model against atomistic simulation results, we present two case studies, in which we investigate, first, the effect of the length of an AH protein domain on its strength properties, and second, the effect of the length of two parallel AH protein domain arrangement on its shear strength properties and deformation mechanisms. We find that longer AHs feature a reduced tensile strength, whereas the tensile strength is maximized for ultrashort protein structures. Moreover, we find that the shearing of two parallel AHs engenders sliding, rather than AH unfolding, and that the shear strength does not significantly depend on the length of the two AHs.