Biomimetics use nature for insipration to design materials by application of engineering and various technological tools and it is essentially mimicking the naturally observed features to model novel materials. One of such natural materials are protein-based biopolymer fibers, silk protein, which possesses exceptional mechanical properties such as ultimate tensile strength more than steel, elasticity etc. There have been several attempts to mimic the molecular assembly of silk protein on an industrial scale, yet it remained challenging owing to a lack of complete understanding of design principles relating silk sequence to its structural properties. Silk fiber owes its extraordinary mechanical strength to the hierarchical arrangement of laminated antiparallel β-sheet nanocrystals embedded in an amorphous matrix composed of predominantly short stretches of regular or nonregular secondary structures. The key to silk fiber strength lies in β-sheet nanocrystals. In our lab, we are interested in addressing following questions:

• Can sequence of silk nanocrystal be rationally modified to improve its ultimate tensile strength?
• Can strength or elasticity of silk protein be modulated by changing sequence(s) of its amorphpus region?
• Investigating the sequence features of silk proteins from multiple spiders?

The mechanical features are mostly attributed to the hierarchical arrangement of antiparallel β-sheet nanocrystals in the crystalline region. In these nanocrystals, the β-strand length, arrangements, and H-bond interactions are crucual in determining ultimate tensile strenght of silk. We investigated the role of amino acid sequence of β-sheet nanocrystals in determing the ultimate silk fiber strength. We modeled various representative amino acid homopolymers β-sheet nanocrystals and computationally determined the sequence motifs having superior mechanical properties. We used already well-known established mechanism of nanocrystal rupture study by constant velocity pulling SMD simulations to determine ultimate tensile strength of modeled silk nanocrystals.

We modeled homopolymer consisting of amino sequences. Based on physiochemical properties the models are cataegorized into Small Amino acid models: poly(Ala), poly(Ala-Gly), poly(Gly); Hydrophobic amino acid models: poly(Ile), poly(Val) and Polar amino acid models: poly(Thr) and poly(Asn). We investigated the modeled nanocrystals for amino acid sequences for packing of side chain and geometry of nanocrystals. In general, (see figure below) the packing remains similar among models. However, nanocrystals adopt twisted cubodial geometry for bulky amino acid side chains.

The constant velocity pulling SMD simulations were performed in triplicate and determined ultimate tensile force as well as toughness (see figure below).

As can be seen, natually occuring sequence motids of (Ala/Ala-Gly) have superior mechanical properties than other modeled sequence motifs. Surprisingly, the enhanced side-chain interactions in homo(poly)-polar/hydrophobic amino acid models are unable to augment backbone hydrogen bond cooperativity to increase mechanical strength. We analyzed the rupture of hydrogen bonds in various modeled structure and observed lack of hydrogen bond cooperativity in poly-hydrophobic and poly-polar amino acid models. An example of hydrogen bond ruputure in poly-Ala models is shown below: Further, detailed analyses of hydrogen bond dynamics and side-chain packing suggested that these are optimized in naturally occuring sequence motifs for mechanical strength. This study provides insight into the silk’s molecular design principle with implications in the genetically modified artificial synthesis of silk-like biomaterials. The above project and studies will compensate for reducing the structural gap between the strength design attributes and protein quaternary organization. We believe that this will provide insights into the under-appreciated role of maintaining quaternary and tertiary packing efficiency while designing materiomics driven protein fibers and design units. The present work is in collaboration with the femtosecond lab (Dr. KP singh, Department of Physical Sciences, IISER-M) .