Computational analysis of amino acids\u2019 adhesion to the graphene surface

Anders Frederiksen,Ilia A Solov’Yov

doi:10.1140/epjd/e2020-100109-8

Abstract

The mechanisms of cellular growth have attracted scientists’ attention for a long time, leading to recent efforts in establishing cellular growth on specific functionalized substrates. In order to fully understand the supported cellular growth mechanisms, one needs first to comprehend how individual amino acids interact with the substrate material as cells are known to attach to surfaces through specific proteins designed to improve adhesion. In this study, we have considered graphene as a candidate material for support-assisted cellular growth and simulated the interaction of all 20 naturally occurring amino acids deposited on graphene. Investigations utilized classical molecular dynamics (MD) for amino acids in aqueous solution and in vacuo, in tandem with quantum chemical calculations. The MD simulations were carried out for classical and polarizable CHARMM force fields. The simulations performed with the polarizable force field confirmed that adhesion of amino acids to the graphene surface may be significantly enhanced due to the polarization forces, which was further supported by quantum chemical calculations. The performed analysis thus revealed the role of polarization on amino acids’ adhesion to the graphene surface.Graphical abstract

Highlights

Living organisms are connected through the extracellular matrix (ECM), which apart from providing structural support is believed to be important in initial growth and differentiation of stem cells [1,2,3]
The molecular dynamics (MD) simulations reveal that different amino acids, such as e.g. arginine or tryptophan, exhibit strong binding configurations to the graphene surface while some other amino acids, such as e.g. glycine or valine, bind rather weakly
Those probability density distributions represent the sampled energies defined in equations (1) and (2) for the solvated and in vacuo simulations. Every subplot in these figures features a single amino acid type where the main peak corresponds to a binding configuration of an amino acid on graphene surfaces, while the increase in the interaction energy binding probability at around 0 kcal/mol indicates non-bound configurations

Summary

Introduction

Living organisms are connected through the extracellular matrix (ECM), which apart from providing structural support is believed to be important in initial growth and differentiation of stem cells [1,2,3]. ECM consists of a variety of fiber-like shaped structures, such as e.g. fibrils of the protein fibronectin schematically shown in Figure 1 (as green bars), which are responsible for binding of the cells together [4]. We have employed a palette of computational tools to model the interactions between graphene and amino acids which in turn determine the binding and unbinding rates to the graphene surface

Methods

Results

Conclusion