Molecular dynamics simulations reveal internal tension in native state collagen fibrils

TL;DR

This study addresses whether native collagen fibrils carry internal stresses under physiological hydration. Using large-scale all-atom MD of a collagen type I microfibril across hydration levels, it uncovers a native hydration around $0.78$ g/g where zero lateral stress coexists with a substantial longitudinal stress of about $210$ MPa, arising from an overstretched protein backbone rather than hydration. The work shows that relaxing these stresses reduces the longitudinal modulus by about $22\%$ and shortens the fibril by ~$7\%$, highlighting the out-of-equilibrium nature of fibril assembly and its impact on mechanics. These findings have implications for tissue engineering, suggesting native fibrils are mechanically primed by residual stresses that influence anisotropy and design of biomimetic materials.

Abstract

Collagen fibrils are the building block of many biological tissues, which viability depend on the fibrils properties. Altered properties of collagen fibrils are central to the appearance of many diseases, and physiological or native properties must be reproduced for tissue engineering. Yet, the self-assembly, the structure, and therefore the properties of collagen fibrils remain elusive. One main reason is the extreme sensitivity of the fibrils to their environmental conditions, and in particular hydration which is only loosely bound by experimental measurements. Furthermore, mechanics are an integral part of the self-assembly process and may result in internal stresses in collagen fibrils in native conditions. Here, we propose to investigate internal stresses in collagen fibrils by means of molecular dynamics simulations of the collagen microfibril model. Our simulations reveal the quantitative evolution of internal stresses in collagen fibrils with hydration. We establish a value of native hydration of collagen fibrils at 0.78 g/g based on an absence of cross-sectional stresses. In turn, we determine a quantitative estimate of internal longitudinal stresses in collagen fibrils in native conditions of 210 MPa. We find that internal longitudinal stresses are caused by an over-extended protein backbone rather than partial hydration, which appears remnant of the local forces driving collagen self-assembly. We also demonstrate the consequences of internal longitudinal stresses on the mechanical properties of collagen fibrils, which the absence of induces more than a 20% decrease in the Young's modulus. Overall, our findings provide insights into the native structure and properties of collagen fibrils. More than ever, collagen fibrils appear to be assembled via an out-of-equilibrium process key for the synthesis of viable tissues.

Figures (4)

• Figure 1: Hydration and internal stresses. (a) Evolution of the internal stresses in the microfibril sampled at $308$ K at varying hydration levels. The three diagonal components of the stress tensor $\sigma_{xx}$, $\sigma_{yy}$, and $\sigma_{zz}$ are drawn in blue, orange and green, respectively. The internal stresses vary from tension to compression with increasing hydration. (c) Time-evolution of the internal stresses at $0.78$ g/g ($12600$ water molecules) up to equilibration, with lateral stresses converging to zero. At zero lateral stresses, the longitudinal stress is positive, that is the microfibril is under tension. (c) Visualisation of the structure of the microfibril at zero lateral stresses.
• Figure 2: Ablation of the microfibril. Influence of the removal of covalent bonds in the tropocollagen molecules in the whole cross-section for $z$ ranging from $32$ to $32.5$ nm. Visualisations of the microfibril in the region of the cut, (a) before and (b) after relaxation of the microfibril. Evolution of the average $z$ position $\langle u_z \rangle$ of the atoms initially located (c) above the cut ($z$ ranging from $32.5$ to $33$ nm) and (d) below the cut ($z$ ranging from $31.5$ to $32$ nm). The evolution of $\langle u_z \rangle$ is compared in presence ("cut") and in absence ("intact") of the removal of covalent bonds.
• Figure 3: Release the stresses. Comparison of the structures of the microfibril from X-ray fiber diffraction (initial), after equilibration (NVT-ensemble) and after ambient-pressure stress relaxation (NPT-ensemble). (a) Visualisation of the atomistic structure for each of the three states of the microfibril (initial, NVT equilibration, NPT relaxation). Ramachandran plots of the torsion (dihedral) angles ($\phi$ and $\psi$) of the amino acids in tropocollagen molecules. The distributions of the torsion angles are computed for (b) a short 30 amino acid long peptide of collagen (PDB: 7CWK) and the (c) initial, (d) equilibrated and (e) relaxed structures of the microfibril. Cyan, dark blue and red dots represent torsion angles of favoured, allowed and disallowed regions respectively. Contour lines delimit the different regions based on energy calculations. Dots represent residues other than glycine, while triangles indicate glycine residues. (f) Evolution of the local stress $\sigma^{loc}_{zz}$ in the protein only along the longitudinal $z$-dimension in the microfibril before (NVT) and after (NPT) ambient-pressure relaxation.
• Figure 4: Deformation of the microfibril. Simulations of constant rate deformation applied to the microfibril in the longitudinal $z$ direction. (a) Comparison between the relaxed and the internally stressed initial state for (left) the evolution of the length $L_z$ of the microfibril with time; (middle) the evolution of the longitudinal stress $\sigma_{zz}$ with time; (right) evolution of the stress $\sigma_{zz}$ with the strain $\epsilon_{zz}$. Influence on the longitudinal stress $\sigma_{zz}$ of (b) the presence of lateral constraints (free vs. fixed), (c) the strain rate ($\dot{\epsilon_{zz}} = 0.01$ ns$^{-1}$ vs. $\dot{\epsilon_{zz}} = 0.0025$ ns$^{-1}$), or (d) an extended strain amplitude up to $20$ %.