Molecular Interactions at the Interface of C - Reactive Protein (CRP) and Poly Vinyl Alcohol (PVA) in the Presence of Carbon Nanotubes

Many diseases typically trigger an immune response producing biomarkers, which are largely proteins present in blood, other body fluids or tissues indicating the presence of that disease. A common detection method for certain diseases is therefore, the detection of abnormal amount of a certain protein in the body. One example of this is a cardiac inflammatory C-reactive protein (CRP), which is commonly seen to result from a heart disease. Nanotechnology and biosensors can be used to detect the levels of CRP in blood plasma before they get to more extreme levels, leading to an early detection of the disease as pointed out by previous studies. The goal of this project is to simulate the interactions between the inflammatory protein, CRP, a polymer, Polyvinyl Alcohol (PVA), and Carbon Nanotubes (CNTs) using molecular dynamics through simulation software called Visual Molecular Dynamics (VMD) and nanoscale molecular dynamics (NAMD). Atomic-level models (coordinates) of the CRP protein and PVA are acquired through the protein data bank database while the pristine 20nm long CNTs with chirality (15,15) and (12,20) are modeled through the Nanotube builder modeling program within VMD. Molecular simulations of the individual PVA, CRP and CNT controls as well as an entire system with PVA and CRP interacting between the two CNTs are carried out based on the CHARMM (Chemistry at HARvard Molecular Mechanics) parameters. Furthermore, TIP3 water model along with neutralizing salt concentration is used to create a waterbox for real-time interactions as currently such data is lacking in the literature. Stability analysis is performed using RMSD (root mean square deviation), distance between center of mass, salt bridges, hydrogen bonds, secondary structure analysis and conformational energies of the system using VMD plugins and TCL scripts. Exhaustive analysis involving electrostatic energy evaluation of individual molecules, Van der Waals energies between the molecules, optimal adsorption cut-offs using the criteria of interaction energies and number of participating adsorbed atoms as well as interfacial water molecules and their hydrogen bonds is also performed on the simulated molecular trajectories at the nano-bio interface. It is expected that the information obtained from these simulations will be used to develop electrospun PVA/CNT nanofibrous scaffold based electrochemical biosensor to detect biomarkers similar to CRP.