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Biomolecular Modeling in Biomaterials
Published in Heather N. Hayenga, Helim Aranda-Espinoza, Biomaterial Mechanics, 2017
Sai J. Ganesan, Silvina Matysiak
A 12-peptide repeating sequence pattern of –HHPP– folds into a helix without any bias. Since hydrophilic loops are common in proteins, we use polar turning residues for both helix and sheet bundles [46–48]. Folding of a 33-residue helix bundle sequence (HHPP)3HH-(T)5-(PPHH)3PP from a completely extended conformation is shown in Figure 8.3a. The chain folds into two distinct helices on either ends in a hierarchical manner, followed by the collapse of the chain to form the α-helix bundle. Folding of the helices on either ends is induced by backbone dipole interactions and their subsequent orientations, which is a local effect. Therefore, the secondary structure is sufficiently stable in the absence of tertiary interactions, and the formation of secondary and supersecondary structures is uncoupled. Hierarchical folding has been observed for several proteins, such as the engrailed homeodomain [49,50]. However, once backbone dipole particles are removed, the peptide does not fold into a helix bundle and remains collapsed, with no helicity. Without dipole particles, the folded fraction computed as a measure of helical dihedrals remains at 0.1 for all temperatures between 300 and 600 K (red curve in Figure 8.3b). When backbone dipoles are present, the folding process becomes cooperative, achieving a folded fraction of 0.6 at 300 K, as evident from the sigmoidal shape of the blue folding curve in Figure 8.3b. Folding of helix bundles is driven by both dipolar interactions and pairwise LJ interactions, that is, a combination of the sequence patterning and electrostatic interactions. However, the role of electrostatics is more significant in the systems we explored. The macrodipoles of each of the two helices, which is computed by adding the microdipoles of each helix (denoted in Figure 8.3a), signal an antiparallel dipole orientation that might provide additional favorable electrostatic interaction energy for the formation of helix bundles. The known helix bundles of protein structures in the literature exhibit similar antiparallel orientation [51].
A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer
Published in Molecular Physics, 2018
Kazutomo Kawaguchi, Satoshi Nakagawa, Isman Kurniawan, Koichi Kodama, Muhammad Saleh Arwansyah, Hidemi Nagao
GCN4-pLI is one of the GCN4 leucine zipper mutants and a coiled-coil composed of four α-helices wrapped around each other to bury a hydrophobic core [1]. The formation of GCN4-pLI tetramer is dominated by both hydrophobic and electrostatic interaction between monomers. While the association of the tetramer is dominated by hydrophobic interaction, the helix orientation is dominated by the salt bridge arising from the electrostatic interaction between charged amino acid residues [2]. In their experiment, only all-parallel helices have been observed after 36 h because of the salt bridge between charged amino acid residues, although anti-parallel four-helix bundle conformations have been prepared in solution.