Crystal structure of the α‐helical undecapeptide Boc‐<scp>L</scp>‐Ala‐Aib‐Ala‐Aib‐Ala‐Glu(OBzl)‐Ala‐Aib‐Ala‐Aib‐Ala‐OMe

Bosch, R.; Jung, Günther; Schmitt, H.; Winter, Werner

doi:10.1002/bip.360240605

Cited by 82 publications

(26 citation statements)

References 31 publications

(10 reference statements)

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“…The columns of head-to-tail-bonded helices must necessarily pack in a parallel fashion. This parallel packing of the a-helices is in contrast to the antiparallel packing generally observed in proteins and in other small a-helical structures (9)(10)(11).…”

contrasting

confidence: 82%

“…The closest contacts between molecules in the lateral direction are 0(10). C(1) = 3.28 A and Cpl (9)...N(1) = 3.91 A near the bottom of one molecule and C81(2) ..C82(8) = 3.89 A near the top of the same molecule. All the other nearest approaches in the lateral directions are greater than 4.1 A.…”

mentioning

confidence: 98%

“…Although peaks for many other H atoms also were found in difference maps, idealized calculated positions were used for all the H atoms on C atoms. Least (10) 7379 (10) 10443 (9) 9193 (11) 10069 (9) 8425 (8) 8591 (4) 8129 (5) 7861 (6) 7516 (5) 8259 (4) 6898 (4) 6549 (5) 7583 (4) 5545 (5) 6899 (4) 5921 (5) 7064 (4) 5552 (3) 6294 (3) 4122 (5) 7069 (4) 4008 (5) 8236 (4) 4142 (6) 9102 (5) 3992 (5) 10050 (4) 3692 (6) 9816 (4) 3382 (7) 10503 (5) 3120 (9) 10040 (6) 3100 (8) 8902 (7) 3388 (7) 8225 (5) 3697 (5) 8683 (4) 6704 (4) 8085 (3) 7076 (5) 8282 (4) 7916 (5) 7480 (4) 7858 (4) 7189 (3) 7773 (6) 9541 (4) 7888 (7) 9801 (5) 9140 (7) 9916 (5) 6573 (9) 9580 (6) 8715 (4) 7143 (3) 9511 (5) 6381 (4) 8629 (5) 5241 (4) 8908 (4) 4756 (3) 10432 (6) 6226 (5) 7529 (4) 4788 (3) 6536 (5) 3712 (4) 5974 …”

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confidence: 99%

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Parallel packing of alpha-helices in crystals of the zervamicin IIA analog Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe.2H2O.

Karle¹,

Sarojadevi²,

Balaram³

1986

Proc. Natl. Acad. Sci. U.S.A.

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An apolar synthetic analog of the first 10 residues at the NH2-terminal end of zervamicin HA crystallizes in the triclinic space group P1 with cell dimensions a = 10. Ac-Trp-Ile-Gln-Aib-Ile-Thr-Aib-Leu-Aib-Hyp- 15-Gln-Aib-Hyp-Aib-Pro-Phe-ol.(Hyp is 4-hydroxyproline; Phe-ol is phenylalaninol.) The decapeptide whose structure is reported in this paper is the apolar analog of the first 10 residues in which Gln-3, Thr-6, and Hyp-10 have been replaced with Ala, Val, and Pro, respectively; the NH2 terminus has been blocked with t-butoxycarbonyl (Boc) rather than acetyl; and the COOH terminus has been esterified with methanol:Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe.EXPERIMENTAL PROCEDURE Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe was synthesized by conventional solution-phase procedures, and crystals were grown from dimethyl sulfoxide/H20 in the form of triangular prisms. X-ray diffraction data were measured from a crystal that was 0.10 mm thick and 0.30 mm on each side of the triangular face. The crystal was sealed in a capillary with a small amount of mother liquor. The data were collected with a four-circle automated diffractometer using Cu Ka radiation and a graphite monochromator (A = 1.54178 A). The 0-20 scan technique was used with a 2.00 scan, 15'/min scan rate, and 2ma,,x = 1150, for a total of 5294 independent reflections and 4378 reflections with intensities >3a(F) to a resolution of 0.91 A. Three reflections monitored after every 60 measurements remained constant within 3% during the data collection. Lorentz, polarization, and absorption corrections were applied to the data. The structure was solved by direct phase determination using the random-tangent formula procedure in the SHELXTL computer programt. Initially, the positions of 36 atoms, mainly in the backbone, were found. The positions of the remainder of the C, N, and 0 atoms were found by means of partial structure development. Eight of the nine H atoms on amide groups were found in difference maps after partial least-squares refinement, and subsequently their coordinates and isotropic thermal factors were refined by least-squares. Hydrogen atoms for the two water molecules were not found. Although peaks for many other H atoms also were found in difference maps, idealized calculated positions were used for all the H atoms on C atoms. Least-squares refinement with anisotropic thermal factors for the C, N, and 0 atoms; isotropic thermal factors for eight amide H atoms; and 88 H atoms on C atoms kept fixed in idealized positions yielded an agreement factor of R = 5.61% for the 4378 reflections measured >3a(F). Fractional coordinates for the C, N, and o atoms and the amide H atoms are listed in Table 1

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confidence: 82%

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confidence: 98%

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confidence: 99%

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Parallel packing of alpha-helices in crystals of the zervamicin IIA analog Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe.2H2O.

Karle¹,

Sarojadevi²,

Balaram³

1986

Proc. Natl. Acad. Sci. U.S.A.

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“…Helical peptides (with more than 6 residues) in crystals have almost always been observed to pack in a head-to-tail motif that results in forming long rods or columns of helices throughout the crystal (Bosch et al, 1985a(Bosch et al, , 1985bFrancis et al, 1985;Marshall et al, 1990). In crystals where the succeeding a-helices in a column are in good register with respect to each other, 3 intermolecular NH.…”

Section: Head-to-tail Hydrogen Bondingmentioning

confidence: 99%

Facile transition between 3₁₀‐ and α‐helix: Structures of 8‐, 9‐, and 10‐residue peptides containing the ‐(Leu‐Aib‐Ala)₂‐Phe‐Aib‐fragment

Karle¹,

Flippen‐Anderson²,

Gurunath³

et al. 1994

Protein Science

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A structural transition from a 3,0-helix to an a-helix has been characterized at high resolution for an octapeptide begins as a 3,,-helix and abruptly changes to an a-helix at carbonyl 0(3), which is the acceptor for both a 4 + 1 hydrogen bond with N(6)H and a 5 + 1 hydrogen with N(7)H, even though the last 8 residues have the same sequence in all 3 peptides. The average q5,$ angles in the decapeptide are -58", -28" for residues 1-3 and -63", -41 O for residues 4-10. The packing of helices in the crystals does not provide any obvious reason for the transition in helix type. Fourier transform infrared studies in the solid state also provide evidence for a 310-to a-helix transition with the amide I band appearing at 1,656-1,657 cm" in the 9-and 10-residue peptides, whereas in shorter sequences the band is observed at 1,667 cm-l.

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“…More recently, by theoretical (7)(8)(9)(10)(11) as well as experimental (12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27) investigations, it has been shown that the 4,q, angles ofthe achiral a-aminoisobutyric acid residue (Aib), the prototype of Caa-dialkylated a-amino acids, are restricted to values near those associated either with right-or left-handed a-or 310-helices, unless it is part of a strained cyclic compound (28). The x-ray diffraction structures of aaminoisobutyric acid homopeptides to the pentamer have provided examples of short (less than two complete turns) 310-helical conformations in the solid state (14,15,22,23).…”

mentioning

confidence: 99%

Long polypeptide 3 ₁₀ -helices at atomic resolution

Bavoso

Benedetti

Blasio

et al. 1986

Proc. Natl. Acad. Sci. U.S.A.

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The crystal-state preferred conformation of the terminally blocked homooctapeptide from the Ca'adimethylated a-aminoisobutyric acid (Aib) residue, pBrBz-(Aib)8-OBu', in which pBrBz is para-bromobenzoyl and OBu' is tert-butoxy, determined by x-ray diffraction analysis using direct methods, was found to be a 310-helix stabilized by six consecutive intramolecular N-H O=C hydrogen bonds of the C10-llI (or E') type. This is the first observation at atomic resolution of a regular 310-helix longer than two complete turns.The solid-state structural analysis was extended to the terminally blocked, a-aminoisobutyric acid-rich octapeptide corresponding to the 2-9 sequence of the peptaibol antibiotics emerimicins Im and IV, pBrBz-Aib3-L-Val-Gly-L-Leu-Aib2-OMe. Again, this peptide adopts a (right-handed) 310-helical structure, although slightly distorted at the level of the Lleucine residue. The role of specific amino acid sequence and peptide main-chain length in stabilizing either the 310-or the a-helical conformation and their possible implications on the nature of the channel formed by peptaibol antibiotics in the membrane are also briefly discussed.The polypeptide 310-helix, first proposed by Donohue in the early 1950s (1), has a three-residue repeat and a hydrogen bond between the C=O group of residue i and the N-H group of residue i + 3 [type III (III') C10 form or 3-bend (2, 3)]. Its 4,qi torsion angles are approximately ±60°,±300, within the same energy minimum in the conformational map as the a-(3.613)helix (4, 5). However, the H-bonding schemes are different in the two types of helices, being of the i +-i + 4 type [C13 form or a-bend (3)] in the a-helix.For a long periodic structure formed by Ca-monoalkylated a-amino acid residues with the same chirality at the a-carbon, the 310-helix is energetically considerably less favorable than the a-helix (4, 5). Therefore, it is not surprising that only short pieces of approximately 310-helix (particularly at the C end of an a-helix) have been found in protein crystal analyses (4-6).More recently, by theoretical (7-11) as well as experimental (12-27) investigations, it has been shown that the 4,q, angles ofthe achiral a-aminoisobutyric acid residue (Aib), the prototype of Caa-dialkylated a-amino acids, are restricted to values near those associated either with right-or left-handed a-or 310-helices, unless it is part of a strained cyclic compound (28). The x-ray diffraction structures of aaminoisobutyric acid homopeptides to the pentamer have provided examples of short (less than two complete turns) 310-helical conformations in the solid state (14,15,22,23).Our recent solution conformational analysis of monodispersed, terminally blocked (Aib), homooligopeptides to the dodecamer is strongly in favor of the formation of fully developed, stable 310-helices in chloroform, starting from the octamer (26).In this paper we present the results of a crystal structure analysis of pBrBz-Aib8-OBu' (pBrBz, para-bromobenzoyl; OBu', tert-butoxy) by x-ray diffraction using direct...

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Crystal structure of the α‐helical undecapeptide Boc‐L‐Ala‐Aib‐Ala‐Aib‐Ala‐Glu(OBzl)‐Ala‐Aib‐Ala‐Aib‐Ala‐OMe

Cited by 82 publications

References 31 publications

Parallel packing of alpha-helices in crystals of the zervamicin IIA analog Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe.2H2O.

Parallel packing of alpha-helices in crystals of the zervamicin IIA analog Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe.2H2O.

Facile transition between 3₁₀‐ and α‐helix: Structures of 8‐, 9‐, and 10‐residue peptides containing the ‐(Leu‐Aib‐Ala)₂‐Phe‐Aib‐fragment

Long polypeptide 3 ₁₀ -helices at atomic resolution

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Crystal structure of the α‐helical undecapeptide Boc‐L‐Ala‐Aib‐Ala‐Aib‐Ala‐Glu(OBzl)‐Ala‐Aib‐Ala‐Aib‐Ala‐OMe

Cited by 82 publications

References 31 publications

Parallel packing of alpha-helices in crystals of the zervamicin IIA analog Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe.2H2O.

Parallel packing of alpha-helices in crystals of the zervamicin IIA analog Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe.2H2O.

Facile transition between 310‐ and α‐helix: Structures of 8‐, 9‐, and 10‐residue peptides containing the ‐(Leu‐Aib‐Ala)2‐Phe‐Aib‐fragment

Long polypeptide 3 10 -helices at atomic resolution

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Facile transition between 3₁₀‐ and α‐helix: Structures of 8‐, 9‐, and 10‐residue peptides containing the ‐(Leu‐Aib‐Ala)₂‐Phe‐Aib‐fragment

Long polypeptide 3 ₁₀ -helices at atomic resolution