1. Atomic Level Study of Adsorption, Conformational Change and Dimerization of an α-helical Peptide at Graphene Surface
Luchun Ou, Yin Luo, and Guanghong Wei
Phys. Dept., Fudan Univ., Shanghai, People’s Republic of China
Protein-surface interaction has drawn significant attention due to its important role in many fields. Surface may perturb or stabilize the native structure of proteins. Experimental studies reported some protein would transform from α-helix to β-sheet structure at surface1,2. But the detailed adsorption and structural dynamics at surfaces are not well understood. The purpose of this work is to help understanding the mechanism of conformational transition at graphene surface using MD simulations.
Methods and details of MD runs
Model: all-atom molecular dynamics simulation
Software: Gromacs Force Field: OPLS
Temperature and pressure coupling: Berendsen
Peptide: (DELERRIRELEARIK)3
Results with graphene
These data indicate that the interactions of graphene with the peptides prevent inter-peptide hydrophobic interactions and facilitate non-native hydrophilic (or electrostatic) interactions, thus inducing local or more extensive unfolding.
The peptide undergoes obvious structural changes at graphene.
Results without graphene
The -helix to 310-helix/turn/bend transition and the formation of amorphous dimer may play important role on the aggregation of the peptides into -sheet assemblies.
The adsorption is initiated from C-terminus and exhibits stepwise behavior.
The greater the residue-graphene interaction strength, the more the loss of -helical structure.
The two chains form a α-helical dimer in solution.
Conclusions
The formation of -helical dimer in solution is mostly driven and stabilized by inter-peptide hydrophobic interactions;
the adsorption and the -helix unfolding of the peptide at graphene surface is initiated from the C-terminal region due to strong interactions between residues Arg13-Ile14-Lys15 and graphene surface;
the extent of helix unfolding strongly depends on the interaction strength between the peptide and graphene surface;
the dimerization of two unfolded peptide chains at graphene surface results from the interplay between peptide-graphene and peptide-peptide interactions.
References
Sethuraman, A.; Vedantham, G.; Imoto, T.; Przybycien, T.; Belfort, G. Proteins: Struct., Funct., Bioinf. 2004, 56, 669.
Mao, X. B.; Wang, Y. B.; Liu, L.; Niu, L.; Yang, Y. L.; Wang, C. Langmuir 2009, 25, 8849.
Burkhard, P.; Meier, M.; Lustig, A. Protein Sci. 2000, 9, 2294