Molecular Simulations of Recognitive Polymer Networks Prepared by Biomimetic Configurational Imprinting as Responsive Bi
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Molecular Simulations of Recognitive Polymer Networks Prepared by Biomimetic Configurational Imprinting as Responsive Biomaterials David B. Henthorna, and Nicholas A. Peppasa,b a
Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA b Department of Biomedical Engineering and Division of Pharmaceutics, The University of Texas at Austin, Austin, TX, USA
Abstract Proteins, enzymes, and antibodies have the ability to discern specific molecules out of a whole host of species and selectively bind them with remarkable affinity. A route that would enable the creation of synthetic polymers with this binding ability would be a great advance with subsequent applications in chemical sensors, single-molecule separations, and even artificial enzymes. In this work we study the molecular imprinting process whereby a controlled nanostructure consisting of distinct binding sites is created in a polymer network through a templating procedure. Simulations were done to better understand the underlying network structure that gives rise to the increased uptake. An all-atom molecular dynamics simulation was coupled with a kinetic gelation approach to study network formation in the presence of a template. The monomers used were first studied with density-functional theory in order to parameterize a force field for various methacrylates. Simulation results showed three key functional group interactions that lead to successful imprinting and subsequent rebinding.
1. Introduction Enzymes and other proteins have dedicated binding sites capable of recognizing and discerning specific molecules out of many possible ones. It is therefore of interest to researchers to design materials with this same recognitive ability [1]. Applications are broad and include, among others; analyte specific separations [2] , microsensors for the detection of specific molecules, and artificial enzymes. However, the challenge lies in building this precise structural alignment into materials. While the prospect of synthesizing whole proteins may one day be possible – it is still out of reach in both understanding how a chain of amino acids will fold into a given conformation and in laboratory methods for synthesis of a whole protein. Alternative techniques are therefore desired, preferably using readily available materials. While understanding how a protein folds into its native conformation from a given amino acid is still being studied, it is known that much of the protein structure exists as a support for these binding or catalytic sites. In the case of streptavidin (molecular weight 64 kDa), several binding sites are present solely for the binding of the relatively small (molecular weight 244 Da) biotin molecule. This complex is of great interest since it has the highest interaction affinity of any non-covalent system known.
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In the three dimensional structure of a protein, amino acid residues are located in the binding site that have functional groups complementary to those of the molecule to be bound. In additio
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