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https://github.com/lamm-mit/spiderpdb

PDB files of spider silk structures
https://github.com/lamm-mit/spiderpdb

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PDB files of spider silk structures

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# SpiderPDB: Atomistic model of the spider silk nanostructures



Spider silk is an ultrastrong and extensible self-assembling biopolymer that outperforms the mechanical characteristics of many synthetic materials including steel. Here we report atomic-level structures that represent aggregates of MaSp1 proteins from the N. Clavipes silk sequence based on a bottom-up computational approach using replica exchange molecular dynamics. We discover that poly-alanine regions predominantly form distinct and orderly beta-sheet crystal domains while disorderly structures are formed by poly-glycine repeats, resembling 

-helices. These could be the molecular source of the large semicrystalline fraction observed in silks, and also form the basis of the so-called “prestretched” molecular configuration. Our structures reported in [1] are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content (Figure 1).



In a follow-up paper [2] we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 3₁-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions (Figure 2). Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre.



The MaSp1 sequence is (in one-letter amino acid codes): GGAGQGGYGGLGSQGAGRGGLGGQGAGAAAAAAGGAGQGGYGGLGSQGAGRGGLGGQGAG

The MaSp2 sequence is: GPGQQGPGGYGPGQQGPGGYGPGQQGPSGPGSAAAAAAAAGPGQQGPGGYGPGQQGPGGYGPGQQGPSGPGS



This repository includes PDB files of spider silk structures reported and studied in the papers [1, 2].



References:



[1] S. Keten and M.J. Buehler, Atomistic model of the spider silk nanostructure, Appl. Phys. Lett. 96, 153701 (2010), DOI: https://doi.org/10.1063/1.3385388

URL: https://pubs.aip.org/aip/apl/article/96/15/153701/338788/Atomistic-model-of-the-spider-silk-nanostructure



[2] S. Keten and M.J. Buehler, Nanostructure and molecular mechanics of spider dragline silk protein assemblies, Roy. Soc. Interface (2010), DOI: 10.1098/rsif.2010.0149

URL: https://royalsocietypublishing.org/doi/10.1098/rsif.2010.0149



![image](https://github.com/lamm-mit/SpiderPDB/assets/101393859/4da0f82d-bb14-4589-b6b6-f6a0452bc025)



Figure 1: Simulation protocol and representative results. (a) Summary of the approach used here to predict the nanostructure of spider silk proteins, here focusing on the MaSp1 silk sequence from the N. Clavipes spider. Monomers consisting of a single poly-Ala repeat and 2 Gly-rich regions are used as the basic building block. (b) Representative structures from replica exchange simulations. Percentages of different secondary structures are illustrated in each subpanel (I–III). The coloring is based on residue names. The insets show the stacking formation of the beta-sheets in the poly-Ala regions. The results consistently illustrate that poly-Ala regions (center of the molecule) form highly orderly beta-sheet crystals whereas the Gly-rich repeat units are less orderly, forming more amorphous domains.



![image](https://github.com/lamm-mit/SpiderPDB/assets/101393859/f054d2e8-a715-4637-90de-d461890452c1)



Figure 2: Force–displacement curves for selected structures. Figure shown illustrates the response of selected structures to shear forces applied to alternating strands. Force values shown are the loads applied per polypeptide strand. Illustration of the plots obtained from MaSp1 (a) and MaSp2 (b). The forces cause tensile stretching of the strands, in which a strain stiffening behaviour is evident once the chain reaches a certain length, independent of the chain's initial stretch state. The responses are similar for MaSp1 and MaSp2; however, it depends on the secondary structure content of the system. MaSp1 structures have a large variation on beta-sheet versus turn content, which leads to distinctly different mechanical responses (c). Solid lines indicate cases having the largest turn content, whereas dashed lines indicate structures with more beta-sheets. As the turn ratio increases, an initial stiff regime, followed by softening, followed by a stiff bond stretching regime is observed. For extended structures, the initial stiff regime disappears and the typical strain stiffening behaviour of polypeptide chains can be observed. The source of this difference is the existence of denser hydrogen bonding in amorphous regions owing to turn formation, which leads to higher stiffness and energy dissipation for structures containing more turns. The lower variation of turn and beta-sheet content in MaSp2 leads to the reduced variation of the mechanical response for this structure. As can be inferred from (d), the failure strength of both structures is more or less the same, as expected from the sequence similarity of the alanine-rich crystalline regions controlling the onset of failure.