Multiscale modeling and simulation of deformation and failure mechanisms of hierarchical alpha-helical protein materials

Alpha-helical (AH) protein structures are critical building blocks of life, representing the key constituents of biological materials such as cells, hair, hoof and wool, where they assemble to form hierarchical structures. AHs play an important mechanical role in biological processes such as mechanotransduction, cell mechanics, tissue mechanics and remodeling. Whereas the mechanics of engineered materials has been widely investigated, the deformation and failure mechanisms of biological protein materials remain largely unknown, partly due to a lack of understanding of how individual protein building blocks respond to mechanical load and how the hierarchical features participate in the function of the overall biological system. In this Thesis, we develop, calibrate, validate and apply two computational models to predict the elasticity, deformation, strength and failure mechanisms of AH protein arrangements and eukaryotic cells over multiple orders of magnitude in time- and lengthscales. Our AH protein model is based on the formulation of tensile double-well mesoscale potentials and intermolecular adhesion Lennard-Jones potentials derived directly from results of full atomistic simulations. We report a systematic analysis of the influence of key parameters on the strength properties and deformation mechanisms, including structural and chemical parameters, and compare it with theoretical strength models. We find a weakening effect as the length of AH proteins increases, followed by an asymptotic regime in which the strength remains constant. We also show that interprotein sliding is a dominating mechanism that persists for a variety of geometries and realistic biologically occurring amino acid sequences. The model reported here is generally applicable to other protein filaments that feature a serial array of domains that unfold under applied strain. Although simple, our coarse-grained cell model agrees well with experiments and illustrates how the multiscale approach developed here can be used to describe more complex biological structures. We further show that cytoskeletal intermediate filaments contribute to cell stiffness and deformation and thus play a significant role to maintain cell structural integrity in response to stress. These studies lay the foundation to improve our understanding of pathological pathways linked to AH proteins such as muscular dystrophies.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Civil and Environmental Engineering.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2009

Author dc:creator

• Bertaud, Jeremie

Advisor dc:contributor.advisor

• Markus J. Buehler.

• Civil and Environmental Engineering.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/55153

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/55153