Peptide unit hydrogen bonds

Aida, M. 1993. Theoretical Studies on Hydrogen Bonding Interactions Between Peptide Units. Bull. Chem. Soc. Jpn. 66, 3423-3429. 

Fig. 10. Electron density projection along -strand direction—hydrogen-bonding direction (a-axis) horizontal, and intersheet direction (c-axis) vertical—and skeletal models of polyGln8 (Q8) and polyGln45 (Q45) assemblies. The unit cell for both peptides was monoclinic, with lattice constants a = 9.73 A, b = 7.14 A, c = 8.16 A, and y = 95.7° for Q8, and a = 9.66 A, b = 7.10 A, c = 8.33 A, and y = 94.0° for Q45. The side chains are nearly overlapped in the hydrogen-bonding direction. This difference in side chain conformation and disorder likely accounts for the differences in observed intensity between their diffraction patterns.

Tight turns were first recognized from a theoretical conformational analysis by Venkatachalam (1968). He considered what conformations were available to a system of three linked peptide units (or four successive residues) that could be stabilized by a backbone hydrogen bond between the CO of residue n and the NH of residue n + 3. He... 

Here Vij denotes the distance between atoms i and j and g(i) the type of the amino acid i. The Leonard-Jones parameters Vij,Rij for potential depths and equilibrium distance) depend on the type of the atom pair and were adjusted to satisfy constraints derived from as a set of 138 proteins of the PDB database [18, 17, 19]. The non-trivial electrostatic interactions in proteins are represented via group-specific dielectric constants ig(i),g(j) depending on the amino-acid to which atom i belongs). The partial charges qi and the dielectric constants were derived in a potential-of-mean-force approach [20]. Interactions with the solvent were first fit in a minimal solvent accessible surface model [21] parameterized by free energies per unit area (7j to reproduce the enthalpies of solvation of the Gly-X-Gly family of peptides [22]. Ai corresponds to the area of atom i that is in contact with a ficticious solvent. Hydrogen bonds are described via dipole-dipole interactions included in the electrostatic terms... 

Figure 11. (a) The chemical structure of a 24-membered macrocyclic molecule composed of alternating D- and L-amino acids, cyclo(Gln-(D-Leu-Trp)4-D-Leu 7. (b)A self-assembled tubular structure spanned across the bilayer lipid membrane. Flat ring-shaped units in the antiparallel configuration stack to form a tubular structure through extensive inter subunit hydrogen bonding and peptide side chain-lipid interactions. ... 

A hydrogen bond is formed between the N atom of the i-th peptide residue and the O atom of the (i + 4)-th residue if and only if the three peptide residues between them are distorted simultaneously to the a-helical conformation. Thus the shortest helical sequence consists of three h units, and the terminal C and N residues of the chain are never involved in a helical sequence. 

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