Phosphorylation of Fibronectin Influences the Structural Stability of the Predicted Interchain Domain

Abstract

As a key player in cell adhesion, the glycoprotein fibronectin is involved in the complex mechanobiology of the extracellular matrix. Although the function of many modules in the fibronectin molecule has already been understood, the structure and biological relevance of the C-terminal cross-linked region (CTXL) still remains unclear. It is known that fibronectin is only phosphorylated in the CTXL domain, but no results have been presented to date, which indicate a biological function based on this phosphorylation. For the first time, we introduce a structural model of the CTXL region in fibronectin, which we obtained by exhaustive replica exchange molecular dynamics simulations (TIGER2hs). The sampling revealed a conformational landscape of the dimerization module, and the global minimum state showed an umbrella-like module body and conspicuous structural region with two feet. We observed that the CTXL foot region exhibits a structural stability in its physiological state, which disappears upon changes in the phosphorylation state. Thus, our in silico studies enabled us to show that the flexibility of the CTXL region is guided by phosphorylation. These results indicate an in vivo function of the CTXL domain in protein binding and cell adhesion, which is controlled by phosphorylation.

Tethering of the IgG1 Antibody to Amorphous Silica for Immunosensor Development: A Molecular Dynamics Study

“…Accordingly, the aqueous environment was represented using the generalized Born implicit solvent (GBIS) . The GBIS implicit model, which approaches the polar solvent as a dielectric continuum, is extensively used for modeling large systems like the one studied in this work. − Figure shows the IgG1 antibody immobilized on amorphous silica, which is the system to be simulated.…”

Structure–Property Relationships of Elastin-like Polypeptides: A Review of Experimental and Computational Studies

“…These simulations calculate numerical solutions for classical many-body problems in which atoms are considered as point masses that interact with each other following Newtonian equations of motion. Full atomistic MD simulations have been successfully applied to many biomolecular systems. ,− To that end, force fields that accurately calculate the forces and energies in these systems are needed. Some examples of extensively validated force fields for biomolecular simulations include CHARMM, ,, AMBER, − or OPLS. − The secondary structure of proteins is key to the mechanical properties, but predicting it for de novo polypeptide designs via full atomistic MD simulations is challenging, especially if solvent molecules are explicitly represented in the simulation.…”

Fundamental Redesign of the TIGER2hs Kernel to Address Severe Parameter Sensitivity

“…Pressures and temperatures were maintained by a Langevin piston barostat (100 fs period and 200 fs decay time) and Langevin thermostat (10 ps −1 damping coefficient), respectively. For all replica exchange simulations a pseudo-NVT ensemble 29 was implemented by adjusting the target pressure at the desired temperature. The Antoine equation 44 (A = 8.14019, B = 1810.94 °C, C = 244.485 °C) multiplied by a factor of three sets the target pressure to maintain solvent density and suppress vapor.…”

“…A heavily reduced replica number was sufficient to retain accurate results. Recent studies have successfully proven the application of TIGER2h(s) to enhance sampling of various molecular systems, − but effects of different replica numbers or temperature scales have not yet been investigated in detail. Applied replica counts and temperature ranges to a maximum of 600 K, typically used in protein folding simulations, resulted in only minor deviations that we previously accounted to insufficient convergence. , …”