Helix‐forming tendencies of amino acids depend on the restrictions of side‐chain rotamer conformations: Crystal structure of the tripeptide GAI in two crystalline forms

Abstract

In our attempts to design crystalline alpha-helical peptides, we synthesized and crystallized GAI (C11H21N3O4) in two crystal forms, GAI1 and GAI2. Form 1 (GAI1) Gly-L-Ala-L-Ile (C11H21N3O4.3H2O) crystals are monoclinic, space group P2(1) with a = 8.171(2), b = 6.072(4), c = 16.443(4) A, beta = 101.24(2) degrees, V = 800 A3, Dc = 1.300 g cm-3 and Z = 2, R = 0.081 for 482 reflections. Form 2 (GAI2) Gly-L-Ala-L-Ile (C11H21N3O4.1/2H2O) is triclinic, space group P1 with a = 5.830(1), b = 8.832(2), c = 15.008(2) A, alpha = 102.88(1), beta = 101.16(2), gamma = 70.72(2) degrees, V = 705 A3, Z = 2, Dc = 1.264 g cm-3, R = 0.04 for 2582 reflections. GAI1 is isomorphous with GAV and forms a helix, whereas GAI2 does not. In GAI1, the tripeptide molecule is held in a near helical conformation by a water molecule that bridges the NH3+ and COO- groups, and acts as the fourth residue needed to complete the turn by forming two hydrogen bonds. Two other water molecules form intermolecular hydrogen bonds in stabilizing the helical structure so that the end result is a column of molecules that looks like an incipient alpha-helix. GAI2 imitates a cyclic peptide and traps a water molecule. The conformation angles chi 11 and chi 12 for the side chain are (-63.7 degrees, 171.1 degrees) for the helical GAI1, and (-65.1 degrees, 58.6 degrees) and (-65.0 degrees, 58.9 degrees) for the two independent nonhelical molecules in GAI2; in GAI1, both the C gamma atoms point away from the helix, whereas in GAI2 the C gamma atom with the g+ conformation points inward to the helix and causes sterical interaction with atoms in the adjacent peptide plane. From these results, it is clear that the helix-forming tendencies of amino acids correlate with the restrictions of side-chain rotamer conformations. Both the peptide units in GAI1 are trans and show significant deviation from planarity [omega 1 = -168(1) degrees; omega 2 = -171(1) degrees] whereas both the peptide units in both the molecules A and B in GAI2 do not show significant deviation from planarity [omega 1 = 179.3(3) degrees; omega 2 = -179.3(3) degrees for molecule A and omega 1 = 179.5(3) degrees; omega 2 = -179.4(3) degrees for molecule B], indicating that the peptide planes in these incipient alpha-helical peptides are considerably bent.

Probing alpha-helical secondary structure at a specific site in model peptides via restriction of tryptophan side-chain rotamer conformation

“…We anticipate that the ability to probe the conformational properties of a specific site in a protein or peptide will be a useful tool in structural investigations. In protein folding, for example, the restriction of side-chain conformation in the a-helix may be a significant factor in determining the helix forming tendencies of amino acids (Padmanabhan et al, 1990;Lya et al, 1991;Go et al, 1992). It is often important to be able to determine the location of helical regions within peptides and the correlation's we have demonstrated here will allow fluorescence spectroscopy (Willis and Szabo, 1992) to supplement data from other spectroscopic techniques (Dyson and Wright, 1991;Liff et al, 1991).…”

Crystal structure and a twisted β‐sheet conformation of the tripeptide L‐leucyl‐L‐leucyl‐L‐leucine monohydrate trimethanol solvate: Conformation analysis of tripeptides

“…'- 4 We also have found that when the amino acids in the above sequences are permuted or reversed, the tripeptides do not form helices even though they have the same amino acid compositions. In this process, we have discovered earlier five tripeptide sequences GAF, GAV, GGV, GAL, and GAI that exhibited helical conformation in the crystalline state.…”