Molecular Dynamics Investigation Of Single-Walled Carbon Nanotube Interactions With Soluble Proteins
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Type of WorkText
ProgramMaster of Science
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Many biotechnology applications rely on immobilization of macromolecules to inert surfaces or the detection of biological reactions on biosensor surfaces. Thus, due to their unique physical, chemical and electrical properties, carbon nanotubes have attracted a lot in interest in the scientific community. This study was aimed at elucidating mechanisms for potential interactions between proteins and single-walled carbon nanotubes (SWCNTs). Through use of atomistic molecular dynamics simulations, the non-bonded interactions of the well-characterized green fluorescent protein (GFP) and cellulose hydrolyzing enzyme cellobiohydrolase I (CEL7A) with a SWCNT of small diameter have been investigated. After 100 ns simulations, a residue-based method was applied to subsequent energy calculations in order to better characterize the mechanisms of adsorption between a SWCNT and each protein. For both simulations, it was observed that adsorption to SWCNT was preferred along flexible sections of turn and bend residues in between more recognizable secondary structure features. For GFP, residues adjacent to turn 2 of the protein's crystal structure were found to mediate interactions which maintained conformation of the protein when SWCNT was present. Altered dynamics of conserved residues in the chromophore region suggested that presence of SWCNT might impede fluorescent activity of the protein. For CEL7A, residues of the N-terminus were found to contribute to migration of the N-terminal end from a position adjacent to the enzyme to a position along the nanotube sidewall. This migration prevented equilibration of the enzyme within the simulation time frame, suggesting that cellulolytic activity of CEL7A could be compromised in the presence of SWCNT. Observation of the SWCNT preference for localization along flexible turn/bend residues of soluble proteins may serve to inform the design of protein-nanotube conjugates. The study has also established methods and procedures for simulating and modeling protein-SWCNT interactions.