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310-Helix, A-Helix, and A8-Bend Ribbon (X-Ray Structure Analysis/Hydrogen Bonds/Parallel Packing of Heilces/Peptaibophol Antibiotics) ISABELLA L

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310-Helix, A-Helix, and A8-Bend Ribbon (X-Ray Structure Analysis/Hydrogen Bonds/Parallel Packing of Heilces/Peptaibophol Antibiotics) ISABELLA L Proc. Natl. Acad. Sci. USA Vol. 84, pp. 5087-5091, August 1987 Chemistry Conformation of a 16-residue zervamicin IIA analog peptide containing three different structural features: 310-helix, a-helix, and a8-bend ribbon (x-ray structure analysis/hydrogen bonds/parallel packing of heilces/peptaibophol antibiotics) ISABELLA L. KARLE*, JUDITH FLIPPEN-ANDERSON*, MUPPALLA SUKUMARt, AND PADMANABHAN BALARAMt *Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, DC 20375-5000, and tMolecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India Contributed by Isabella L. Karle, April 6, 1987 ABSTRACT Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib- Pro-Ala-Aib-Pro-Aib-Pro-Phe-OMe (where Boc is t-butoxy- carbonyl and Aib is a-aminoisobutyric acid), a synthetic apolar analog of the membrane-active fungal peptide antibiotic zer- vamycin IIA, crystallizes in space group P1 with Z = 1 and cell parameters a = 9.086 ± 0.002 A, b = 10.410 ± 0.002 A, c = 28.188 ± 0.004 A, a = 86.13 + 0.01°, 18 = 87.90 ± 0.010, and Y = 89.27 ± 0.010; overall agreement factor R = 7.3% for 7180 data (Fo > 3o) and 0.91-A resolution. The peptide backbone makes a continuous spiral that begins as a 310-helix at the N-terminus, changes to an et-helix for two turns, and ends in FIG. 1. Schematic representation of 8-bend ribbon, with three a in NH-.O==C hydrogen bonds, that winds into an approximate 3jo- spiral of three fl-bends a ribbon. Each of the fl-bends helix. See Fig. 2 for conformation in the complete molecule drawn by contains a proline residue at one of the corners. The torsion computer using experimentally determined coordinates for the at- angles Hi range from -51° to -91° (average value -64°), and oms. Note that the proline residues occur either at the i + 1 or i + the torsion angles Pif range from -1° to -46° (average value 2 position in the 3-bends. -31°). There are 10 intramolecular NH-..OC hydrogen bonds in the helix and two direct head-to-tail hydrogen bonds between successive molecules. Two H20 and two CH3OH solvent ribbon was proposed for the conformation of Z-(Aib-Pro)4- molecules fill additional space with appropriate hydrogen OMe (Z, benzyloxycarbonyl) in solution (4, 5). Bent a-helices bonding in the head-to-tail region, and two additional 1120 caused by steric hindrance due to the presence of one central molecules form hydrogen bonds with carbonyl oxygens near the proline residue have been observed in proteins [e.g., see curve in the helix at Pro-10. Since there is only one peptide glyceraldehyde-phosphate dehydrogenase residues 146-161 molecule per cell in space group P1, the molecules repeat only (6) and melittin (7)]. by translation, and consequently the helices pack parallel to each other. EXPERIMENTAL PROCEDURES Transmembrane pore formation by alamethicin and related The 16-residue peptide was synthesized by conventional membrane-modifying peptides containing a-aminoisobutyric solution-phase procedures and crystallized from CH30H/ acid (Aib) most likely involves lipid phase aggregation of H20. The colorless crystals were fragile and crumbly. An helical peptide molecules, since individual 310-helices or irregular fragment, with maximum dimensions of 0.15 x 0.25 a-helices have an inner pore much too small for the passage x 0.40 mm, was mounted in a thin glass capillary with some of ions (1). The role of specific side chains in promoting helix mother liquor. The profiles of the individual x-ray reflections aggregation and the mode of aggregation are being studied by were sharp and symmetric. The data were collected with a means of crystal-structure analyses of membrane-active four-circle automated diffractometer using Cu Ka radiation peptides. The study began with a synthetic apolar analog of and a graphite monochromator. The 0-20 scan technique was zervamicin IIA (2) in which Gln, Thr, and Hyp (Hyp is used with a 2.0° scan, 15'/min scan rate, and 20max = 115°, 4-hydroxyproline) have been replaced with Ala, Val, and Pro, for a total of 8082 independent reflections and 7180 reflec- respectively; the N-terminus has been blocked with t- tions with intensities >3a(F) to a resolution of 0.91 A. Three butoxycarbonyl (Boc) rather than acetyl; and the C-terminal reflections monitored after every 60 measurements remained alcohol function has been replaced by a methyl ester. The constant within 4% during the data collection. Lorentz, 5 polarization, and absorption corrections were applied to the structure of the hexadecapeptide Boc-Trp-Ile-Ala-Aib-Ile- 10 15 data. The space group is P1 with the cell dimensions shown Val-Aib-Leu-Aib-Pro-Ala-Aib-Pro-Aib-Pro-Phe-OMe is re- in the Abstract. The calculated density was 1.186 g/cm3, ported in this paper. The crystal structure of the decapeptide based on a molecular weight of 1763.22 + 136.15 for fragment composed of residues 1-10 has been published (3). C9oH139N17Oj9-4H202CH3OH, one formula unit per cell, and A helical conformation (for residues 9-16) containing three cell volume V = 2658.5 A3. p-bend reversals (for Prol'-Ala", Aib12-Prol3, and Aib14- Since the structure of the peptide fragment containing the Pro'5; Fig. 1) has been confirmed by crystal-structure anal- first 10 residues was already known (3), the assumption was ysis. A similar approximate 310-helix containing a p-bend made, which proved to be correct, that the helical backbone for residues 1-9 is quite similar in the two molecules. Residue The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" Abbreviations: Aib, a-aminoisobutyric acid, Boc, t-butoxycarbonyl; in accordance with 18 U.S.C. §1734 solely to indicate this fact. Hyp, 4-hydroxyproline. 5087 Downloaded by guest on September 30, 2021 5088 Chemistry: Karle et al. Proc. Natl. Acad. Sci. USA 84 (1987) Table 1. Fractional coordinates and thermal factors (A2 x 102) Mean value (SD x 104) Mean value (SD x 104) Atomt x y Z Uteq Atomt x y z Ueq O(OBu') -0.0913 (9) -0.4300 (7) 1.2835 (3) 9.1 Cy(8) -0.2618 (11) 0.4240 (10) 0.9224 (4) 7.5 C(OBu')-2 -0.1330 (18) -0.5556 (12) 1.2723 (5) 12.3 C81(8) -0.3797 (14) 0.4837 (16) 0.8976 (5) 13.0 C(OBu')-3 -0.2863 (31) -0.5533 (19) 1.2625 (7) 23.7 C82(8) -0.2308 (18) 0.4932 (17) 0.9659 (5) 14.7 C(OBut)-4 -0.1184 (22) -0.6362 (14) 1.3187 (5) 15.2 C'(8) 0.0044 (10) 0.3393 (9) 0.8182 (3) 6.1 C(OBut)-5 -0.0459 (27) -0.6069 (15) 1.2324 (6) 19.4 0(8) 0.0132 (8) 0.4348 (6) 0.7911 (2) 7.5 CI(O) -0.0904 (11) -0.3328 (9) 1.2518 (4) 7.3 N(9) 0.1083 (8) 0.2485 (7) 0.8217 (2) 5.7 O(O) -0.1273 (8) -0.3356 (7) 1.2103 (2) 8.0 Ca(9) 0.2567 (10) 0.2637 (10) 0.8013 (3) 6.2 N(1) -0.0476 (9) -0.2232 (8) 1.2694 (3) 7.3 C131(9) 0.3397 (11) 0.1368 (12) 0.8086 (4) 8.4 Ca(1) -0.0576 (11) -0.1013 (9) 1.2422 (4) 6.7 Cf32(9) 0.3356 (13) 0.3677 (12) 0.8242 (4) 9.0 C,8(1) -0.0196 (11) 0.0113 (9) 1.2719 (4) 7.2 C'(9) 0.2545 (10) 0.2976 (9) 0.7470 (3) 6.2 Cy(l) 0.1300 (11) 0.0127 (9) 1.2905 (3) 7.1 0(9) 0.3491 (6) 0.3722 (6) 0.7287 (2) 6.7 C81(1) 0.1700 (13) -0.0305 (12) 1.3351 (4) 8.8 N(10) 0.1557 (8) 0.2435 (7) 0.7206 (2) 6.1 C82(1) 0.2652 (12) 0.0555 (9) 1.2661 (3) 7.2 Ca(10) 0.1625 (12) 0.2792 (11) 0.6678 (3) 7.8 Ce2(1) 0.3790 (12) 0.0362 (11) 1.2974 (4) 7.9 Cf3(10) 0.0372 (15) 0.1987 (13) 0.6513 (4) 10.4 CE3(1) 0.2958 (12) 0.1142 (9) 1.2199 (3) 7.2 Cy(10) 0.0186 (14) 0.0901 (11) 0.6858 (4) 9.6 CQ2(1) 0.5226 (13) 0.0676 (13) 1.2842 (4) 9.8 C8(10) 0.0455 (12) 0.1449 (10) 0.7327 (4) 7.6 Co3(1) 0.4407 (12) 0.1446 (10) 1.2076 (4) 8.2 C'(10) 0.1446 (11) 0.4185 (11) 0.6549 (3) 7.9 C-q2(1) 0.5513 (13) 0.1217 (12) 1.2403 (4) 10.0 0(10) 0.1855 (9) 0.4647 (9) 0.6151 (2) 10.4 NE1(1) 0.3185 (11) -0.0180 (10) 1.3388 (3) 10.0 N(11) 0.0752 (9) 0.4935 (8) 0.6859 (3) 7.3 C'(1) 0.0389 (10) -0.0964 (9) 1.1964 (3) 6.1 Ca(11) 0.0571 (11) 0.6293 (11) 0.6755 (4) 8.3 0(1) 0.0071 (8) -0.0196 (6) 1.1628 (2) 7.5 C13(11) -0.0491 (14) 0.6877 (13) 0,7100 (5) 11.9 N(2) 0.1535 (8) -0.1772 (7) 1.1931 (2) 5.7 C'(11) 0.2072 (11) 0.7042 (11) 0.6734 (4) 7.9 Ca(2) 0.2439 (10) -0.1725 (9) 1.1501 (3) 6.3 0(11) 0.2222 (8) 0.8028 (7) 0.6482 (3) 8.3 CB(2) 0.3804 (10) -0.2642 (10) 1.1535 (4) 7.2 N(12) 0.3085 (9) 0.6582 (8) 0.7037 (3) 6.9 Cyl(2) 0.3401 (11) -0.4013 (11) 1.1658 (5) 9.9 Ca(12) 0.4416 (11) 0.7325 (10) 0.7112 (3) 7.2 Cy2(2) 0.4910 (13) -0.2121 (12) 1.1865 (5) 9.9 Cpi(12) 0.4000 (14) 0.8594 (13) 0.7337 (5) 10.6 C81(2) 0.4505 (19) -0.4962 (14) 1.1525 (7) 15.7 C,82(12) 0.5384 (12) 0.6498 (12) 0.7462 (4) 8.8 C'(2) 0.1502 (10) -0.2025 (9) 1.1069 (3) 6.5 C'(12) 0.5292 (11) 0.7636 (10) 0.6636 (4) 7.3 0(2) 0.1855 (7) -0.1563 (7) 1.0676 (2) 7.7 0(12) 0.5772 (9) 0.8709 (7) 0.6541 (3) 9,9 N(3) 0.0360 (8) -0.2812 (7) 1.1157 (3) 6.3 N(13) 0.5539 (9) 0.6684 (7) 0.6333 (3) 6.3 Ca(3) -0.0527 (11) -0.3165 (9) 1.0774 (3) 7.0 Ca(13) 0.6416 (11) 0.7014 (10) 0.5885 (4) 7.6 C,3(3) -0.1704 (14) -0.4089 (12) 1.0946 (4) 9.4 C13(13) 0.7140 (12) 0.5702 (12) 0.5769 (4) 9.2 C'(3) -0.1279 (10) -0.1924 (11) 1.0532 (4) 7.8 Cy(13) 0.6114 (20) 0.4763 (14) 0.5996 (6) 15.0 0(3) -0.1407 (8) -0.1832 (8) 1.0100 (2) 8.4 CS(13) 0.5369 (12) 0.5310 (11) 0.6398 (4) 8.4 N(4) -0.1743 (9) -0.1020 (9) 1.0818 (3) 7.6 C'(13) 0.5450 (11) 0.7477 (11) 0.5466 (3) 7.5 Ca(4) -0.2460 (11) 0.0178 (12) 1.0636 (4) 8.6 0(13) 0.6081 (9) 0.7784 (8) 0.5091 (3) 9.3 C,B1(4) -0.2700 (15) 0.1075 (14) 1.1039 (4) 11.6 N(14) 0.4018 (10) 0.7508 (10) 0.5542 (3) 9.0 C/32(4) -0.3923 (12) -0.0119 (15) 1.0425 (5) 12.1 Ca(14) 0.2954 (13) 0.7652 (13) 0.5142 (4) 10.1 C'(4) -0.1436 (11) 0.0874 (11) 1.0251 (4) 7.9 Cp1(14) 0.1419 (15) 0.7749 (18) 0.5364 (5) 14.1 0(4)
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