Protein Interaction with Dendrimer Monolayers: Energy and Surface Topology

Claudiu N Lungu,Mihai V Putz,Ireneusz P Grudziński,Melinda E Füstös,Gabriel Olteanu

doi:10.3390/sym12040641

Abstract

Protein interaction with polymers layers is a keystone in designing bio-nano devices. Polyamidoamines (PAMAMs) are well-known polymers. Zero aromatic core dendrimers (ZAC) are molecules with no proven toxic effect in cultured cells. When coating nanodevices with enzymatic systems, active sites are disturbed by an interaction with the biosystem surface. Computational methods were used in order to simulate, characterize, and quantify protein–polymer interaction. Protein corona, i.e., surface proteins disposed on a viral membrane or nanodevice outer surface, are crucial in interactions with a potential pharmacological target or receptor. Corona symmetry has been observed in the Middle East respiratory syndrome-related coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As a protein alpha 1 antitrypsin’s a crystallographic structure was chosen. Protein–mono dendrimer layer systems were generated using in silico methods in order to simulate their interaction. Interactions were quantified using topological and quantum mechanical strategies. Results showed that PAMAM and ZAC interact differently with alpha 1 antitrypsin. Energy and topological surfaces of protein vary accordingly with the dendrimer monolayer. Topological surfaces have a higher sensibility in describing the interactions.

Highlights

Circulating blood proteins interact with polymers, especially with nanostructures coated by a polymer mesh [1]
The phenomenon of protein interaction with the surface of nanomaterials is a very complicated process, because of the dynamics of the observed changes, a similar effect to the effect of Vroman, which can never reach an equilibrium in vivo, but especially the complexity of the parameters of the tested system that determines the processes of adsorption of the course and forming the layer of biomolecular composition [24]
The results demonstrate that in comparison with the rest of the dendrimer monolayers, PAMAM G0 exercises fewer changes in conformation regarding the binding in any two consecutive atoms

Summary

Introduction

Circulating blood proteins interact with polymers, especially with nanostructures coated by a polymer mesh [1]. Proteins tend to form a protein corona around the molecule [2]. Such coronas were observed in liposomes, gold, and fullerenes coated with polymers. Proteins tend to fix at the polymer layer and to circulate along with the coated structure interfering with its function [3]. Protein stability in the environment can be influenced by the polymer system resulting in protein precipitation [4]. Proteins interact with molecular surfaces by their functional groups present at the medium interface. In the case of enzymes, these interactions conduct enzyme inactivation as described in Symmetry 2020, 12, 641; doi:10.3390/sym12040641 www.mdpi.com/journal/symmetry

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