Dragline spider silk composition is primarily a flexible amorphous and strong and stiff crystalline phase. This special combination is based on its molecular structure, resulting in an outstanding tough fiber. Three main regions compose the structure of dragline spider silk proteins (spidroins): a pH-dependent N-terminal domain (NT), a repetitive region rich in GGX motifs and poly-alanine repeats, and a C-terminal domain (CT).
Experimental results have shown that the assembly pathway at the spinning duct of the spider gland is mainly triggered by a pH-decreasing gradient that induces conformational changes in the NT and CT domains, and a flow along the duct [1,2]. It has been shown that the flow is relevant in guiding the assembly of spider silk, providing enhancement of the crystalline phase formation . However, the molecular mechanism of the role of the flow is unknown, and it is most likely involved in protein chain alignment and stretching in the initial stages of the assembly. Considering the hierarchy of the self-assembly of dragline silk from the nano-scale to the meso-scale, we studied the effect of a uniform flow in the assembly pathway of the silk fiber, combining classical atomistic and coarse-grained  Molecular Dynamics (MD) simulations of the repetitive fragments of spider silk peptides. The simulations allowed us to monitor the polyalanine beta-sheet content under different protein concentrations and flow rates. We also compare our simulations to results from a novel experimental setup for microscopic flow-induced assembly. More specifically, we monitored silk protein assembly by means of optical manipulation, microfluidics, and microscopy techniques at varying flow and pH conditions.
1. Rammensee, S., Slotta, U., Schiebel. T & Bausch, A.R. Proc. Natl. Acad. Sci. USA 105, 6590-6595 (2008).
2. Andersson, M. et al. PLoS Biol. 12, e1001921 (2014).
3. Pavel I. Zhuravlev et al. J. Mol. Biol. (2014) 426, 2653-2666.