γ loop

A γ loop is a secondary structural element in proteins that allows a polypeptide chain to change direction completely . Among the loop structures in proteins, the γ loop denotes an interaction between an amino acid and an amino acid two positions apart, i.e. H. in the γ position.

The γ-loop is able to connect two anti-parallel β-sheet structures using three amino acid residues . In addition, the γ loop contains two hydrogen bonds , which are located between the first and third amino acid residues. An inverse γ-loop is a mirror image of the classic γ-loop.

Structure of the classical γ loop

The γ loop contains two hydrogen bonds. A hydrogen bond is formed between the carbonyl group (–C = O) of the first amino acid residue ( n ) and the amide proton (–NH) of the third amino acid residue ( n +2), which leads to the formation of a seven-membered ring. This ring structure with torsion angles of and has been proposed as a stable conformation in several studies. Although this hydrogen bond is very bent, it has a normal H ^... O length . Nevertheless, it has a considerable influence on the stability of the folded, seven-membered ring (see Table 2). The folding of the second amino acid residue also allows the formation of a second hydrogen bond between the amide proton of the first amino acid residue and the carbonyl oxygen of the third amino acid residue. This bond is almost straight and has an optimal bond strength (see Table 2), which is consistent with the hydrogen bonds of the anti-parallel β-sheet structure. ${\displaystyle \phi _{i+1}\approx 60^{\circ }}$ ${\displaystyle \psi _{i+1}\approx -60^{\circ }}$

Ribbon model of the classical γ loop of thermolysin (in orange) from Bacillus thermoproteolyticus , which is formed by residues 25-27 (Ser-Thr-Tyr), according to PDB  2A7G . The hydrogen bonds are shown in yellow.

Table 1: Torsion angle of the stable conformations of the γ-loop ¹

sequence	amino acid residue	φ in degrees	Ψ in degrees	ω in degrees
- L -Ala 3 -	n	172	128	-170
	n +1	68	-61	172
	n +2	-131	162	-
- Gly 3 -	n	171	125	-170
	n +1	70	-61	172
	n +2	-129	165	-

¹ defined according to the standard conventions of the IUPAC-IUB

Table 2: Characteristic properties of the hydrogen bonds in the γ loop

properties	N 1 H 1 ... O 3 C 3	N 3 H 3 ... O 1 C 1
H … O length in Å	1.82	1.78
Total energy in kcal / mol	-5.5	-4.5
NHO angle in degrees	166	138
HOC angle in degrees	166	102

Inverse γ loop

Ribbon model of the inverse γ-loop of proteinase A (in green) of S. griseus , which is formed by residues 113–115 (Ala-Ala-Asp), according to PDB  5SGA . The hydrogen bond is shown in yellow.

The inverse γ-loop has different torsion angles and is related to the classic γ-loop in that, by reversing the sign of the - and - angle, the respective backbone conformations are mirror images of each other. The mean values ​​for the torsion angles of the inverse γ loop are and . An example of an inverse γ-loop can be seen in the enzyme proteinase A from S. griseus at positions 113-115 (Ala-Ala-Asp). ${\displaystyle \phi }$ ${\displaystyle \psi }$ ${\displaystyle \phi _{i+1}=-79^{\circ }}$ ${\displaystyle \psi _{i+1}=69^{\circ }}$

Individual evidence

1. ↑ VF Bystrov, SL Port Nova, VI Tsetlin, VT Ivanov, YA Ovchinnikov: conformational studies of peptide system. The rotational states of the NH-CH fragment of alanine dipeptides by nuclear magnetic resonance. In: Tetrahedron. Volume 25, Number 3, February 1969, pp. 493-515, doi: 10.1016 / s0040-4020 (01) 83261-0 , PMID 5352158 .
2. ↑ GM Crippen, HA Scheraga: MINIMIZATION OF POLYPEPTIDE ENERGY, VIII. APPLICATION OF THE DEFLATION TECHNIQUE TO A DIPEPTIDE. In: Proceedings of the National Academy of Sciences. Volume 64, number 1, September 1, 1969, p. 42, doi: 10.1073 / pnas.64.1.42 .
3. ^ Bernard Maigret, Bernard Pullman, David Perahia: Molecular orbital calculations on the conformation of polypeptides and proteins. In: Journal of Theoretical Biology. Volume 31, number 2, May 1971, p. 269, doi: 10.1016 / 0022-5193 (71) 90187-1 .
4. ↑ ^{a b c} George Némethy, Morton P. Printz: The γ Turn, a Possible Folded Conformation of the Polypeptide Chain. Comparison with the β turn. In: Macromolecules. Volume 5, Number 6, November 1, 1972, p. 755, doi: 10.1021 / ma60030a017 .
5. ^ MA Holmes, BW Matthews: Structure of thermolysin refined at 1.6 A resolution. In: Journal of molecular biology. Volume 160, Number 4, October 1982, pp. 623-639, doi: 10.1016 / 0022-2836 (82) 90319-9 , PMID 7175940 .
6. ^ C. Mueller-Dieckmann, S. Panjikar, PA Tucker, MS Weiss: On the routine use of soft X-rays in macromolecular crystallography. Part III. The optimal data-collection wavelength. In: Acta crystallographica. Section D, Biological crystallography. Volume 61, Number 9, September 2005, pp. 1263-1272, doi: 10.1107 / S0907444905021475 , PMID 16131760 .
7. ^ IUPAC-IUB Commission on Biochemical Nomenclature. Abbreviations and symbols for the description of the conformation of polypeptide chains. In: Journal of molecular biology. Volume 52, Number 1, August 1970, pp. 1-17, PMID 5485910 .
8. ↑ ^{a b} M. NG James, AR Sielecki, GD Brayer, LTJ Delbaere, CA Bauer: Structures of product and inhibitor complexes of Streptomyces griseus protease A at 1.8 Å resolution. In: Journal of Molecular Biology. Volume 144, number 1, November 25, 1980, p. 43, doi: 10.1016 / 0022-2836 (80) 90214-4 .
9. ↑ E. Milner-White, BM Ross, R. Ismail, K. Belhadj-Mostefa, R. Poet: One type of gamma-turn, rather than the other gives rise to chain-reversal in proteins. In: Journal of molecular biology. Volume 204, Number 3, December 1988, pp. 777-782, doi: 10.1016 / 0022-2836 (88) 90368-3 , PMID 3225851 .