Abstract
By combining non-equilibrium molecular dynamics(NEMD), umbrella sampling, and weighted histogram analysis method(WHAM), we calculated the potential of mean force of histidine peptide moving over a self-assembly structure. The reaction coordinate is along the main chain direction of the histidine peptide in the self-assembly structure. It is found that the energy needed for the histidine peptide with 3 and 5 residues while moving along the reaction coordinate is around -2.2 kCal/mol and -7.4 kCal/mol, respectively. And the histidine peptide crawls along the reaction coordinate, performing a snake-like movement. This result could illustrate how histidine peptide adjusts its position during self-assembly process.
Highlights
Self-assembly phenomenon is common in nature and many materials with excellent optical, electrical, catalytic properties such as nonlinear optics, chemical biosensors, information storage materials, and tissue growth scaffolding materials, are produced by self-assembly
The potential of mean force profile is extracted by Weighted Histogram Analysis Method (WHAM)
We can calculate the energy needed for the histidine peptide to “crawl” on the reaction surface, which is 7.4kCal/mol for peptide with 5 residues of His and -2.2kCal/mol for peptide with 3 residues
Summary
Self-assembly phenomenon is common in nature and many materials with excellent optical, electrical, catalytic properties such as nonlinear optics, chemical biosensors, information storage materials, and tissue growth scaffolding materials, are produced by self-assembly. Noncovalent interactions (e.g., hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, π-π stacking, and/or electrostatic) are crucial to the self-assembly process. Histidine is an α-amino acid that is used in the biosynthesis of proteins It contains an αamino group, a carboxylic acid group, and an imidazole side chain (which is partially protonated), classifying it as a positively charged amino acid at physiological pH. The imidazole ring of histidine is aromatic at all pH values [2] and it can form π stacking interactions[3]. The self-assembly of histidine peptide is by hydrogen bonding between the backbone of the peptide, forming an antiparallel β-sheet second structure. To find out how histidine peptide adjust itself into neat structure is the target of this article. We perform the following simulation, trying to find out the energy needed for the histidine peptide to adjust its position over the assembly block
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