TY - JOUR
T1 - Hydrophobicity-driven unfolding of Trp-cage encapsulated between graphene sheets
AU - Cai, Zhikun
AU - Zhang, Yang
N1 - Funding Information:
This work is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division , under Award Number DE-SC-0014804. We thank the Beckman Institute and the Illinois Campus Cluster Program for providing the computing resources.
Funding Information:
This work is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, under Award Number DE-SC-0014804. We thank the Beckman Institute and the Illinois Campus Cluster Program for providing the computing resources.
Publisher Copyright:
© 2018 Elsevier B.V.
PY - 2018/8/1
Y1 - 2018/8/1
N2 - Understanding the interaction between proteins and graphene not only helps elucidate the behaviors of proteins in confined geometries, but is also imperative to the development of a plethora of graphene-based biotechnologies, such as the graphene liquid cell transmission electron microscopy. To discuss the overall geometrical-thermal effects on proteins, we performed molecular dynamics simulations of hydrated Trp-cage miniprotein sandwiched between two graphene sheets and in the bulk environment at the temperatures below and above its unfolding temperature. The structural fluctuations of Trp-cage were characterized using the backbone root mean square displacement and the radius of gyration, from which the free energy landscape of Trp-cage was further constructed. We observed that at both temperatures the confined protein became adsorbed to the graphene surfaces and exhibited unfolded structures. Residue-specific analyses clearly showed the preference for the graphene to interact with the hydrophobic regions of Trp-cage. These results suggested that the conformation space accessible to the protein results from the competition between the thermodynamic driving forces and the geometrical restraints. While confinement usually tends to restrict the conformation of proteins by volume exclusion, it may also induce the unfolding of proteins by hydrophobic interactions.
AB - Understanding the interaction between proteins and graphene not only helps elucidate the behaviors of proteins in confined geometries, but is also imperative to the development of a plethora of graphene-based biotechnologies, such as the graphene liquid cell transmission electron microscopy. To discuss the overall geometrical-thermal effects on proteins, we performed molecular dynamics simulations of hydrated Trp-cage miniprotein sandwiched between two graphene sheets and in the bulk environment at the temperatures below and above its unfolding temperature. The structural fluctuations of Trp-cage were characterized using the backbone root mean square displacement and the radius of gyration, from which the free energy landscape of Trp-cage was further constructed. We observed that at both temperatures the confined protein became adsorbed to the graphene surfaces and exhibited unfolded structures. Residue-specific analyses clearly showed the preference for the graphene to interact with the hydrophobic regions of Trp-cage. These results suggested that the conformation space accessible to the protein results from the competition between the thermodynamic driving forces and the geometrical restraints. While confinement usually tends to restrict the conformation of proteins by volume exclusion, it may also induce the unfolding of proteins by hydrophobic interactions.
KW - Confined protein
KW - Graphene
KW - Hydrophobic interface
KW - Molecular dynamics simulation
UR - http://www.scopus.com/inward/record.url?scp=85044867454&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85044867454&partnerID=8YFLogxK
U2 - 10.1016/j.colsurfb.2018.03.039
DO - 10.1016/j.colsurfb.2018.03.039
M3 - Article
C2 - 29627125
AN - SCOPUS:85044867454
VL - 168
SP - 103
EP - 108
JO - Colloids and Surfaces B: Biointerfaces
JF - Colloids and Surfaces B: Biointerfaces
SN - 0927-7765
ER -