Abstract
Carbon nanotubes (CNTs) have recently received considerable attention because of their possible applications in various branches of nanotechnology. For their cogent application, knowledge of their interactions with biological macromolecules, especially proteins, is essential and computer simulations are very useful for such studies. Classical all-atom force fields limit simulation time scale and size of the systems significantly. Therefore, in this work, we implemented CNTs into the coarse-grained UNited RESidue (UNRES) force field. A CNT is represented as a rigid infinite-length cylinder which interacts with a protein through the Kihara potential. Energy conservation in microcanonical coarse-grained molecular dynamics simulations and temperature conservation in canonical simulations with UNRES containing the CNT component have been verified. Subsequently, studies of three proteins, bovine serum albumin (BSA), soybean peroxidase (SBP), and α-chymotrypsin (CT), with and without CNTs, were performed to examine the influence of CNTs on the structure and dynamics of these proteins. It was found that nanotubes bind to these proteins and influence their structure. Our results show that the UNRES force field can be used for further studies of CNT-protein systems with 3–4 order of magnitude larger timescale than using regular all-atom force fields.Graphical abstractBovine serum albumin (BSA), soybean peroxidase (SBP), and α-chymotrypsin (CT), with and without CNTsᅟ
Highlights
Since the discovery of fullerenes and carbon nanotubes (CNTs) [1], nanotechnology has been one of the fastest developing branches in modern industry and medicine [2]
The total energy fluctuation over 400 μs (400 ns UNited RESidue (UNRES) time) simulation is less than 1.5 kcal mol-1 and no systematic energy drift can be observed; only a small energy jump occurs at about 60 μs
We proved that the total energy is conserved in microcanonical simulations of a system composed of a protein and a nanotube and the set temperature is kept in canonical simulations with the Berendsen, Nose-Hoover, and Langevin thermostats
Summary
Since the discovery of fullerenes and carbon nanotubes (CNTs) [1], nanotechnology has been one of the fastest developing branches in modern industry and medicine [2]. Nanoparticles are extensively investigated in the context of the delivery of potential drugs to their targets via surrounding of CNT or fullerene by ligand (corona effect) [8, 9] and their interaction with proteins and receptors. Such studies have been performed extensively both experimentally [10, 11] and theoretically [12,13,14]. Nanomaterials play a key role in nanomedicine and extensive research has been carried out on their use, e.g., in cancer cell treatment [15, 16]
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call