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Peptide bond formation via dehydration reaction. When two amino acids form a dipeptide through a peptide bond, [1] it is a type of condensation reaction. [2] In this kind of condensation, two amino acids approach each other, with the non-side chain (C1) carboxylic acid moiety of one coming near the non-side chain (N2) amino moiety of the other.
Hydrogen bonds contribute to the stability of ion pairs with e.g. protonated ammonium ions, and with anions is formed by deprotonation as in the case of carboxylate, phosphate etc; then the association constants depend on the pH. Entropic driving forces for ion pairing (in absence of significant H-bonding contributions) are also found in ...
Secondary structure is defined by hydrogen bonding, so the exact definition of a hydrogen bond is critical. The standard hydrogen-bond definition for secondary structure is that of DSSP, which is a purely electrostatic model. It assigns charges of ±q 1 ≈ 0.42e to the carbonyl carbon and oxygen, respectively, and charges of ±q 2 ≈ 0.20e to ...
According to one definition, a turn is a structural motif where the C α atoms of two residues separated by a few (usually 1 to 5) peptide bonds are close (less than 7 Å [0.70 nm]). [1] The proximity of the terminal C α atoms often correlates with formation of an inter main chain hydrogen bond between the corresponding residues. Such hydrogen ...
The peptide backbone dihedral angles (φ, ψ) are about (–140°, 135°) in antiparallel sheets. In this case, if two atoms C α i and C α j are adjacent in two hydrogen-bonded β-strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds.
The β pleated sheet is a structure that forms with the backbone bending over itself to form the hydrogen bonds (as displayed in the figure to the left). The hydrogen bonds are between the amide hydrogen and carbonyl oxygen of the peptide bond. There exists anti-parallel β pleated sheets and parallel β pleated sheets where the stability of ...
[1] [2] [3] The hydrogen bonding pattern in an alpha sheet is similar to that of a beta sheet, but the orientation of the carbonyl and amino groups in the peptide bond units is distinctive; in a single strand, all the carbonyl groups are oriented in the same direction on one side of the pleat, and all the amino groups are oriented in the same ...
Carbon atoms grey, oxygen atoms red and nitrogen atoms blue. The defining hydrogen bond is shown as a magenta line. The hydrogen bond criterion for beta turns, applied to polypeptides whose amino acids are linked by trans peptide bonds, gives rise to just four categories, as shown by Venkatachalam in 1968. They are called types I, II, I’ and ...