Murat Cetinkaya

Mechanical response of silk crystalline units from force-distribution analysis

The outstanding mechanical toughness of silk fibers is thought to be caused by embedded crystalline units acting as cross links of silk proteins in the fiber. Here, we examine the robustness of these highly ordered beta-sheet structures by molecular dynamics simulations and finite element analysis. Structural parameters and stress-strain relationships of four different models, from spider and Bombyx mori silk peptides, in antiparallel and parallel arrangement, were determined and found to be in good agreement with x-ray diffraction data. Rupture forces exceed those of any previously examined globular protein many times over, with spider silk (poly-alanine) slightly outperforming Bombyx mori silk ((Gly-Ala)(n)). All-atom force distribution analysis reveals both intrasheet hydrogen-bonding and intersheet side-chain interactions to contribute to stability to similar extent. In combination with finite element analysis of simplified beta-sheet skeletons, we could ascribe the distinct force distribution pattern of the antiparallel and parallel silk crystalline units to the difference in hydrogen-bond geometry, featuring an in-line or zigzag arrangement, respectively. Hydrogen-bond strength was higher in antiparallel models, and ultimately resulted in higher stiffness of the crystal, compensating the effect of the mechanically disadvantageous in-line hydrogen-bond geometry. Atomistic and coarse-grained force distribution patterns can thus explain differences in mechanical response of silk crystals, opening up the road to predict full fiber mechanics.

Silk Fiber Mechanics from Multiscale Force Distribution Analysis

Here we decipher the molecular determinants for the extreme toughness of spider silk fibers. Our bottom-up computational approach incorporates molecular dynamics and finite element simulations. Therefore, the approach allows the analysis of the internal strain distribution and load-carrying motifs in silk fibers on scales of both molecular and continuum mechanics. We thereby dissect the contributions from the nanoscale building blocks, the soft amorphous and the strong crystalline subunits, to silk fiber mechanics. We identify the amorphous subunits not only to give rise to high elasticity, but to also ensure efficient stress homogenization through the friction between entangled chains, which also allows the crystals to withstand stresses as high as 2 GPa in the context of the amorphous matrix. We show that the maximal toughness of silk is achieved at 10-40% crystallinity depending on the distribution of crystals in the fiber. We also determined a serial arrangement of the crystalline and amorphous subunits in lamellae to outperform a random or a parallel arrangement, putting forward what we believe to be a new structural model for silk and other semicrystalline materials. The multiscale approach, not requiring any empirical parameters, is applicable to other partially ordered polymeric systems. Hence, it is an efficient tool for the design of artificial silk fibers.

Recent advances in nanoscale bioinspired materials.

Natural materials have been a fundamental part of human life since the dawn of civilization. However, due to exploitation of natural resources and cost issues, synthetic materials replaced bio-derived materials in the last century. Recent advances in bio- and nano-technologies pave the way for developing eco-friendly materials that could be produced easily from renewable resources at reduced cost and in a broad array of useful applications. This feature article highlights structural and functional characteristics of bio-derived materials, which will expedite the design fabrication and synthesis of eco-friendly and recyclable advanced nano-materials and devices.

Segmented molecular design of self-healing proteinaceous materials

Hierarchical assembly of self-healing adhesive proteins creates strong and robust structural and interfacial materials, but understanding of the molecular design and structure–property relationships of structural proteins remains unclear. Elucidating this relationship would allow rational design of next generation genetically engineered self-healing structural proteins. Here we report a general self-healing and -assembly strategy based on a multiphase recombinant protein based material. Segmented structure of the protein shows soft glycine- and tyrosine-rich segments with self-healing capability and hard beta-sheet segments. The soft segments are strongly plasticized by water, lowering the self-healing temperature close to body temperature. The hard segments self-assemble into nanoconfined domains to reinforce the material. The healing strength scales sublinearly with contact time, which associates with diffusion and wetting of autohesion. The finding suggests that recombinant structural proteins from heterologous expression have potential as strong and repairable engineering materials.

Effects of crystalline subunit size on silk fiber mechanics

Here, we utilize a computational bottom-up approach to decipher the size effects of poly(alanine) crystalline subunits as they occur in most spider silks on silk fiber mechanics. We vary the crystal size in terms of their cross-sectional area, i.e. the number of layers of β-strands, S, in the crystal and the backbone length along the fiber axis, N. Meanwhile, other major parameters such as chemical composition, fiber crystallinity, and the relative orientation of the crystals in the fiber are constrained. The computational approach incorporates Molecular Dynamics and Finite Element simulations of the crystalline subunits along with Finite Element simulations of a two phase silk fiber model in order to determine the stress–strain behavior, elastic moduli and toughness properties. Overall, the fiber elastic modulus and toughness increase with the length of the crystals as given by the number of residues in the β-strands (N), and decrease with the crystal cross-section area, i.e. the number of β-strands per crystal (S). The smallest cross-sectional area investigated, a 3 × 3 crystal (∼1 nm2), shows the highest sensitivity of the mechanical properties towards the crystal length. The presented approach is a versatile tool in artificial fiber design since it does not require any empirical parameters and it is similarly applicable to other semicrystalline polymeric systems or composite materials.

Protein Simulations in Confined Environments

Materials surfaces mimic cell like architecture and proteins can be encapsulated by these material surfaces (e.g. a porous glass or gold). Depending on the number and types of surface interactions, this confine environment could destroy the protein or help it maintain its bioactivity. We developed computer models and simulation tools for the understanding of surface-protein interaction at the atomistic levels. At the molecular level, molecular dynamics simulations are very powerful, but the high computational cost of molecular simulations is a drawback. A viable alternative method to study protein-surface interactions is the coarse-grained molecular simulations of simplified models, such as elastic network model. At the atomic interaction level, we used ab initio simulations to calculate the potential between surface and protein atoms.