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Herrera Rodríguez, Ana María

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Silk fibers are outstandingly tough biomaterials, a result of the controlled self-assembly of their protein building blocks, spidroins. The combination of extensibility and high tensile strength relies on the microscopic composition within the fiber: small and strong beta-sheet crystals formed mainly by poly-alanine repeats enclosed into a flexible amorphous matrix of glycine-rich repeats. The internal molecular structure of silk proteins makes them sensitive to an elongational flow, which is a crucial factor for spider silk fiber spinning. However, the mechanism of flow-induced silk self-assembly, as well as the relevant dynamics of single silk proteins under flow remain largely unknown. In the present work, a bottom-up approach was used to study the dynamics and self-assembly of spider silk proteins under uniform flow conditions. We used non-equilibrium molecular dynamics (MD) simulations to study these processes at two scales, an atomistic model with explicit water, and a coarse-grained model with hydrodynamics incorporated by multi-particle collision dynamics. To be able to analyze the role of the flow on spider silk molecules atomistically, a prior implementation and systematic study of uniform flow MD simulations were carried out based on the GROMACS MD software. Subjecting a tethered single silk peptide to uniform flow leads to a coiled-to-stretch transition involving a multitude of intermediates states, the process of which depends on the mean flow velocity. The flow-induced structural changes of single spidroins exhibit a prominent tendency of alanine residues to be in beta-sheet conformation. All-atom simulations of the assembly process at low flow regimes revealed that the interchain contacts happen primarily in the poly-alanine repeats, which is a suitable condition for crystal formation and fibrillation. We also found beta-sheets formation at low flow regimes, confirming that flow promotes crystal formation. We complemented these findings to the more coarse-grained hydrodynamic simulations at aminoacid resolution, treating the silk proteins as semi-flexible block copolymers. We observed that the spidroins aggregate faster when they are less extended by monitoring oligomer formation in time. At medium peptide extensions (around 60-70%), the spidroin alignment increases, while their assembly slows down because of the reduced fluctuations orthogonal to the flow direction. The microscopic understanding of the spidroin dynamics provided in this work is likely relevant for other flow-dependent proteins.

Document type: Dissertation
Supervisor: Schwarz, Prof. Dr. Ulrich
Place of Publication: Heidelberg
Date of thesis defense: 8 January 2020
Date Deposited: 25 May 2020 07:11
Date: 2020
Faculties / Institutes: The Faculty of Physics and Astronomy > Institute of Physics
DDC-classification: 500 Natural sciences and mathematics
530 Physics
570 Life sciences
660 Chemical engineering
Controlled Keywords: spider silk, molecular dynamics, assembly
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