The synthetic peptide Gly-L-Ala-L-Val (C10H19N3O4.3H2O; GAV) crystallizes in the monoclinic space group P21, with a = 8.052(2), b = 6.032(2), c = 15.779(7) A, beta = 98.520(1) degree, V = 757.8 A3, Dx = 1.312 g cm-3, and Z = 2. The peptide Gly-L-Ala-L-Leu (C11H21N3O4.3H2O; GAL) crystallizes in the orthorhombic space group P212121, with a = 6.024(1), b = 8.171(1), c = 32.791(1) A, V = 1614 A3, Dx = 1.289 g cm-3, and Z = 4. Their crystal structures were solved by direct methods using the program SHELXS-86, and refined to an R index of 0.05 for 1489 reflections for GAV and to an R index of 0.05 for 1563 reflections for GAL. The tripeptides exist as a zwitterion in the crystal and assume a near alpha-helical backbone conformation with the following torsion angles: psi 1 = -150.7 degrees; phi 2, psi 2 = -68.7 degrees, -38.1 degrees; phi 3, psi 32 = -74.8 degrees, -44.9 degrees, 135.9 degrees for GAV; psi 1 = -150.3 degrees; phi 2, psi 2 = -67.7 degrees, -38.9 degrees; phi 3, psi 31, psi 32 = -72.2 degrees, -45.3 degrees, 137.5 degrees for GAL. Both the peptide units in both of the tripeptides show significant deviation from planarity [omega 1 = -171.3(6) degrees and omega 2 = -172.0(6) degrees for GAV; omega 1 = -171.9(5) degrees and omega 2 = -173.2(6) degrees for GAL]. The side-chain conformational angles chi 21 and chi 22 are -61.7(5) degrees and 175.7(5) degrees, respectively, for valine, and the side-chain conformations chi 12 and chi 23's are -68.5(5) degrees and (-78.4(6) degrees, 159.10(5) degrees) respectively, for leucine. Each of 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 alpha-helix.
We have designed, synthesized, crystallized, and performed x-ray analysis of several hydrophobic tripeptides that show an extended near a-helical structure in the crystalline state. All of the tripeptides that show this remarkably stable helix crystallize with two or three water molecules; they all have glycine at the N terminus and have increasing hydrophobicity as one moves from the N to C terminus. Even though three residues in the oligomer are not sufficient to complete a turn, one of the water molecules acts as an added residue and links up adjacent tripeptide segments along the helix axis so that in the crystal, the helix appears effectively as one long continuous helix. Two of these tripeptides are stabilized by two water molecules that enable the peptides to complete a turn of the helix and extend the helical structure throughout the crystal by linking translationally related peptides by hydrogen bonds. In two other peptides, these roles are played by three rather than two water molecules. Though these tripeptides have different crystal symmetry, they all show the basic pattern of hydrated helix and packing, indicating the strong conformational preference for a stable structure even for these tripeptides. Such conformationally stable hydrated structures for short specific related sequences illustrate their possible importance in nucleating protein folding and in the role water molecules play in such events.How proteins start to fold and what clues the primary structure itself gives to the folding process have long been a mystery. Though it was demonstrated as early as 1960 by Anfinsen, White, and Sela (for a review, see ref. 1) that polypeptide chains can refold in vitro, the mechanism of the folding process and how different amino acid sequences direct chains into unique conformations have not been elucidated. It is being increasingly realized (for recent short reviews on protein folding, see refs. 2 and 3) that not only do the amino acid sequences determine the final folded conformation, but they also influence the folding process to reach the final folded state rapidly and with near perfect fidelity. One of the key elements of the folding process, as originally suggested by Anfinsen (4) and later experimentally observed by Anfinsen and coworkers (5) and by many others (6, 7), is the presence of nucleating sites in the polypeptide. These nucleating sites are short fragments of the polypeptide chains that, during the folding process, can flicker in and out of the conformation that they assume in the final fold; if these fragments have well-defined conformations, they seed effectively the folding process. Anfinsen and coworkers detected the native-like folding of fragments of the polypeptide that have highly unfavorable equilibrium constants using a conformation-sensitive antibody technique. Early attempts to detect stable conformations (for example, a-helices) in short oligopeptides isolated from helix-containing regions of proteins gave negative results (8,9).It has been rather widely assumed t...
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.
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