Anomalous dispersion of sulfur in quinidine sulfate, (C(20)H(25)N(2)O(2))(2)SO(4).2H(2)O: Implications for structure analysis

A Patterson-type map computed with Bijvoet differences squared as coefficients, (F(h) - F(-h))(2), as recommended by Rossmann, readily yielded the position of the S atom. The experiment was performed with Cu Kalpha radiation which is far from the absorption edge for sulfur. The coordinates of the remainder of the 54C, N, and O atoms were derived by means of partial structure development by use of the tangent formula. The latter was used only to effect phase extension, not phase refinement. A main purpose of this experiment was to reaffirm, as first shown in the investigation of the protein crambin by Hendrickson and Teeter, that, in the presence of a large number of lighter atoms, sulfur atoms can be located by use of anomalous dispersion at wave-lengths far from the absorption edge. The space group is P2(1) with a = 26.718(8) A, b = 6.987(3) A, c = 10.857(6) A, and beta = 99.51(4) degrees and contains two quinidyl ions, one sulfate ion, and two water molecules per asymmetric unit. The conformations of the two independent quinidyl ions differ mainly in the torsional angle of the bond between the vinyl side chain and the quinuclidine moiety. The R factor is 4.9% for all 2869 data.

Conformation of cyclo(Gly-L-Pro-L-Pro-Gly-L-Pro-L-Pro)(2)Mg complex crystallized from CH(3)CN solution

The cyclic hexapeptides (Gly-L-Pro-L-Pro-Gly-L-Pro-L-Pro) in the (peptide-Mg-peptide)(2+) complex have nearly identical asymmetric conformations. Each has two cis Pro-Pro linkages and lacks any intraring hydrogen bonds. The Mg(2+) ion forms six ligands in a regular octahedral array with the carbonyl oxygen atoms of the two Gly residues and one Pro residue of each peptide. The "sandwich" complex has an approximate 2-fold rotation axis through the Mg(2+) relating the two peptide moieties. Cyclo(Gly-Pro-Pro-Gly-Pro-Pro)(2)Mg(ClO(4))(2). 4C(2)H(3)CN crystallizes in space group P3(1) with a = b = 15.744(4) A, c = 24.002(6) A, gamma = 120 degrees , and Z = 3. A highlight of the structure determination is the ready location of the Mg self-vector in a Harker section and the development of the entire structure by use of the tangent formula starting with the known position of the Mg atom.

Conformations of the li-antamanide complex and na-[phe, val]antamanide complex in the crystalline state

Antamanide, a cyclic decapeptide isolated from the poisonous mushroom Amanita phalloides, preferably complexes with Na(+), but in less polar solvents, e.g., acetonitrile, also with Li(+) or K(+). The selectivity of complexation makes it an important model for the study of conformational requirements of ion binding. The conformations of the lithium antamanide complex and the Na-[Phe(4), Val(6)]antamanide complex have been established by x-ray diffraction analyses of single crystals. The two compounds are isostructural, but not isomorphous. The complexes are folded into a globular shape with an approximate 2-fold axis. Two of the peptide linkages are in the cis conformation, Pro(2)-Pro(3) and Pro(7)-Pro(8). There are only two intramolecular hydrogen bonds. Four C==O groups have their O atoms directed inward to form four Li-O or Na-O ligands. The fifth ligand to the metal ion is provided by a solvent molecule. The conformation found in the crystalline state is different from any of the conformations proposed for the sodium antamanide complex in solution on the basis of nuclear magnetic resonance data.

Conformation of uncomplexed natural antamanide crystallized from CH(3)CN/H(2)O

Natural antamanide, a cyclic decapeptide from Amanita phalloides, has been shown to have the same conformation for the backbone and comparable side groups as the biologically active synthetic [Phe(4), Val(6)]antamanide. Packing in the crystal is quite different for the two compounds. Large channels with a polar lining are formed in the crystals of [Phe(4), Val(6)]antamanide, whereas in natural antamanide large channels in the crystal are completely surrounded by the lipophilic side groups of the Pro, Phe, and Ala residues. Antamanide, C(64)H(78)N(10)O(10).8H(2)O.X, crystallizes in space group P2(1)2(1)2(1) with a = 15.88 A, b = 34.88 A, and c = 13.61 A.

A combined extended and helical backbone for Boc-(Ala-Leu-Ac7c-)2-OMe*

The structure of the peptide Boc-Ala-Leu-Ac7c-Ala-Leu-Ac7c-OMe (Ac7c,1-aminocycloheptane-1-carboxylic acid) is described in crystals. The presence of two Ac7c residues was expected to stabilize a 3(10)-helical fold. Contrary to expectation the structural analysis revealed an unfolded amino terminus, with Ala(1) adopting an extended beta-conformation (Phi=-93 degrees, psi=112 degrees). Residues 2-5 form a 3(10)-helix, stabilized by three successive intramolecular hydrogen bonds. Notably, two NH groups Ala(1) and Ac7c(3) do not form any hydrogen bonds in the crystal. Peptide assembly appears to be dominated by packing of the cycloheptane rings that stack against one another within the molecule and also throughout the crystal in columns.

An asymmetric conformation of 1,3,5-benzene tricarbonyl [Aib4OMe]3

Molecules of 1,3,5-benzene tricarbonyl [Aib(4)OMe](3) do not possess any internal symmetry, neither exact nor approximate, in the crystalline state. The Aib(4)OMe moieties each form a 3(10)-helix with an appropriate pair of hydrogen bonds but the sense of rotation is right-handed for two of the helices and left-handed for the third one. The helices are not evenly positioned around the benzene ring, and their helix axes are inclined toward one side of the plane of the benzene ring, giving the molecule the shape of a shallow bowl with an irregular periphery. The molecules are largely surrounded by water and dimethyl sulfoxide (DMSO) solvent molecules that form hydrogen bonds with the CO and NH moieties that protrude from the surfaces of the peptide molecule. The space group is Cc with a = 23.618(4) A, b = 19.708(6) A, c = 17.939(7) A and beta = 100.09(3) degrees.

Controls exerted by the Aib residue: helix formation and helix reversal

The helix forming properties of the achiral alpha-amino isobutyric residue (Aib) have been demonstrated by numerous crystal structure analyses of designed and naturally occurring peptides containing one or more Aib residues in the sequence. Experimental and computational results concerning the type of helix obtained, whether the 3(10)-helix with 4 --> 1 type hydrogen bonds or the alpha-helix with 5 --> 1 hydrogen bonds or mixtures of the two, have been published. This paper deals with residues that, if inserted into a sequence, could perturb the helix-forming propensity afforded by the presence of Aib residues. Examples of structures will be presented in which Pro, Hyp, Gly-Gly, d-Ala-Gly, and Lac have been centrally placed in the sequence. In addition to the formation of helices, detailed experimentally obtained conformation information is presented for the role of the Aib residue in reversing the sense of the helix (the Schellman motif) with the consequent formation of the 6 --> 1 type hydrogen bond or a solvated 6 --> 1 hydrogen bond. Data are presented for 13 molecules with helix reversals at the C-terminus or near the center of the sequence.

Effects of hydrogen-bond deletion on peptide helices: structural characterization of depsipeptides containing lactic acid

The insertion of alpha-hydroxy acids into peptide chains provides a convenient means for investigating the effects of hydrogen bond deletion on polypeptide secondary structures. The crystal structures of three oligopeptides containing L-lactic acid (Lac) residue have been determined. Peptide 1, Boc-Val-Ala-Leu-Aib-Val-Lac-Leu-Aib-Val-Ala-Leu-OMe (Boc: tert-butyloxycarbonyl; Aib: alpha- aminoisobutyric acid; OMe: methyl ester), and peptide 2, Boc-Val-Ala-Leu-Aib-Val-Lac-Leu-Aib-Val-Leu-OMe, adopt completely helical conformations in the crystalline state with the Lac(6) residue comfortably accommodated in the center of a helix. The distance between the O atoms of Leu(3) CO group and the Lac(6) O (ester) in both the structures is 3.1-3.3 A. The NMR and CD studies of peptide 1 and its all-amide analogue 4, Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe, provide firm evidence for a continuous helical conformation in solution in both the cases. In a 14-residue peptide 3, Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Val-Ala-Leu-Aib-Val-Lac-Leu-OMe, residues Val(1)-Leu(10) adopt a helical conformation. Aib(11) is the site of chiral reversal resulting in helix termination by formation of a Schellman motif. Residues 12-14 adopt nonhelical conformations. The loss of the hydrogen bond near the C-terminus appears to facilitate the chiral reversal at Aib(11). Published 2001 John Wiley & Sons, Inc. Biopolymers 59: 276-289, 2001

One-step transformation of tricyclopentabenzene (trindane, C(15)H(18)) to bicyclo(10.3.0)pentadec-1(12)ene- 2,6,7,11-tetrone (C(15)H(18)O(4)) and its aldol product, 12-hydroxy-16-oxatetracyclo(10.3.1.0.(1,5)0(7,11))hexadec-7(11)ene-2,6-dione (C(15)H(18)O(4))

[reaction: see text] Ozonolysis of 1 largely results in 2 and 3, having features similar to several classes of natural products. The retention of the C(15) pericycle suggests preference for the cleavage of pi-bonds endo to the cyclopentane ring. This unique property of trindane offers opportunities for synthesis of complex natural products from this hydrocarbon that can be made in quantity by acid-catalyzed trimerization of cyclopentanone.

Self-assembling, cystine-derived, fused nanotubes based on spirane architecture: design, synthesis, and crystal structure of cystinospiranes

A novel family of cystine-based spirobicyclic peptides (cystinospiranes) has been synthesized by a single-step procedure involving condensation of pentaerythritol-derived tetrachloride with either the simple L-cystine dimethyl ester or its C,C'-extended bispeptides leading to a variety of 19-membered spirobicyclic peptides or its N,N'-extended bispeptides affording the ring-expanded 25-membered cystinospiranes. The design is flexible with respect to the ring size that can be adjusted depending upon the length of the N,N'-extended cystine bispeptide, and the choice of an amino acid, as illustrated here with the preparation of a large number of cystinospiranes containing a wide variety of amino acids. X-ray crystal structure of the parent spirane (5a) revealed nanotube formation by vertical stacking of relatively flat spirobicyclic molecules through contiguous NH- - -O==C hydrogen bonding. The fused pair of parallel nanotubes is open-ended, hollow, and extends to infinity. Crystallographic parameters are the following: C(33)H(52)N(4)O(16)S(4), space group C2, a = 42.181(3) A, b = 5.1165(7) A, c = 11.8687(9) A, beta = 106.23(1) degrees.

Peptide hybrids containing alpha - and beta-amino acids: structure of a decapeptide beta-hairpin with two facing beta-phenylalanine residues

A beta-hairpin conformation has been characterized in crystals of the decapeptide t-butoxycarbonyl-Leu-Val-beta Phe-Val-(D)Pro-Gly-Leu-beta Phe-Val-Val-methyl ester [beta Phe; (S)-beta(3) homophenylalanine] by x-ray diffraction. The polypeptide chain reversal is nucleated by the centrally positioned (D)Pro-Gly segment, which adopts a type-I' beta-turn conformation. Four intramolecular cross-strand hydrogen bonds stabilize the peptide fold. The beta Phe(3) and beta Phe(8) residues occupy facing positions on the hairpin, with the side chains projecting on opposite faces of the beta-sheet. At the site of insertion of beta-residues, the polarity of the peptide units along each strand reverses, as compared with the alpha-peptide segments. In this analog, a small segment of a polar sheet is observed, where adjacent CO and NH groups line up in opposite directions in each strand. In the crystal, an extended beta-sheet is formed by hydrogen bonding between strands of antiparallel pairs of beta-hairpins. The crystallographic parameters for C(65)H(102)N(10)O(13) x 3H(2)O are: space group P2(1)2(1)2(1); a = 19.059(8) A, b = 19.470(2) A, c = 21.077(2) A; Z = 4; agreement factor R(1) = 9.12% for 3,984 data observed >4 sigma(F) and a resolution of 0.90 A.

Designed beta-hairpin peptides with defined tight turn stereochemistry

The conformational analysis of two synthetic octapeptides, Boc-Leu-Val-Val-D-Pro-L-Ala-Leu-Val-Val-OMe (1) and Boc-Leu-Val-Val-D-Pro-D-Ala-Leu-Val-Val-OMe (2) has been carried out in order to investigate the effect of beta-turn stereochemistry on designed beta-hairpin structures. Five hundred megahertz (1)H NMR studies establish that both peptides 1 and 2 adopt predominantly beta-hairpin conformations in methanol solution. Specific nuclear Overhauser effects provide evidence for a type II' beta-turn conformation for the D-Pro-L-Ala segment in 1, while the NMR data suggest that the type I' D-Pro-D-Ala beta-turn conformation predominates in peptide 2. Evidence for a minor conformation in peptide 2, in slow exchange on the NMR time scale, is also presented. Interstrand registry is demonstrated in both peptides 1 and 2. The crystal structure of 1 reveals two independent molecules in the crystallographic asymmetric unit, both of which adopt beta-hairpin conformations nucleated by D-Pro-L-Ala type II' beta-turns and are stabilized by three cross-strand hydrogen bonds. CD spectra for peptides 1 and 2 show marked differences, presumably as a consequence of the superposition of spectral bands arising from both beta-turn and beta-strand conformations.

Channel-forming, self-assembling, bishelical amphiphilic peptides: design, synthesis and crystal structure of Py(Aibn)2, n=2,3,4

The design, synthesis, characterization and self-assembling properties of a new class of amphiphilic peptides, constructed from a bifunctional polar core attached to totally hydrophobic arms, are presented. The first series of this class, represented by the general structure Py(Aibn)2 (Py=2,6-pyridine dicarbonyl unit; Aib=alpha, alpha'-dimethyl glycine; n=1-4), is prepared in a single step by the condensation of commercially available 2,6-pyridine dicarbonyl dichloride with the methyl ester of homo oligoAib peptide (Aibn-OMe) in the presence of triethyl amine. 1H NMR VT and ROESY studies indicated the presence of a common structural feature of 2-fold symmetry and an NH...N hydrogen bond for all the members. Whereas the Aib3 segment in Py(Aib3)2 showed only the onset of a 3(10)-helical structure, the presence of a well-formed 3(10)-helix in both Aib4 arms of Py(Aib4)2 was evident in the 1H NMR of the bispeptide. X-ray crystallographic studies have shown that in the solid state, whereas Py(Aib2)2 molecules organize into a sheet-like structure and Py(Aib3)2 molecules form a double-stranded string assembly, the tetra Aib bispeptide, Py(Aib4)2, is organized to form a tetrameric assembly which in turn extends into a continuous channel-like structure. The channel is totally hydrophobic in the interior and can selectively encapsulate lipophilic ester (CH3COOR, R=C2H5, C5H11) molecules, as shown by the crystal structures of the encapsulating channel. The crystal structure parameters are: 1b, Py(Aib2)2, C25H37N5O8, sp. gr. P2(1)2(1)2(1), a=9.170(1) A, b=16.215(2) A, c=20.091(3) A, R=4.80; 1c, Py(Aib3)2, C33H51N7O10H2O, sp. gr. P1, a=11.040(1) A, b=12.367(1) A, c=16.959(1) A, alpha =102.41 degrees, beta =97.29 degrees, gamma =110.83 degrees, R1=6.94; 1 da, Py(Aib4)2.et ac, C41H65N9O12.1.5H2O.C4H8O2, sp. gr. P1, a=16.064(4) A, b=16.156 A, c=21.655(5) A, alpha =90.14(1)degrees, beta=101.38(2) degrees, gamma=97.07(1)degrees, Z=4, R1=9.03; 1db, Py(Aib4)2.amylac, C41H65N9O12.H2O.C7H14O2, P2(1)/c, a=16.890(1) A, b=17.523(1)A, c=20.411(1) A, beta=98.18 degrees, Z=4, R=11.1 (with disorder).

Design, synthesis, and crystal structure of self-assembling norbornene (NBE)-supported two-helix bundles: a unique example of Janus helicity in the solid-state structure of NBE(Aib(5))(2)

Norbornene-supported bis-helical peptides with the general structure NBE(Aib(n) )(2) (NBE: 2,3-trans-norbornene dicarbonyl unit; Aib: alpha,alpha'-dimethyl glycine unit; n = 4,5) have been synthesized and examined for self-assembly preferences in the solid state. An x-ray study has revealed a phenomenon of Janus helicity in the solid state structure of NBE(Aib(5))(2). The lower homologue NBE(Aib(4))(2), however, shows an identical screw sense for both the helical arms. The difference in the handedness of left and right arms is reflected in the self-assembly patterns. Thus, while the NBE(Aib(4))(2) molecule self-assembles to form an infinite hydrogen-bonded superhelical ladder, the Janus molecule NBE(Aib(5))(2) crystallizes as individual units surrounded by water molecules. The structures of Z-Aib(4)-OMe and Z-Aib(5)-OMe are also presented to compare their conformations with the helical arms of the title compound and also to the already known structures of other X-Aib(n) -Y compounds. The helices in all the molecules are the 3(10)-type.

Design and synthesis of AB(3)-type (A = 1,3,5-benzenetricarbonyl unit; B = Glu diOME or Glu(7) octa OMe) peptide dendrimers: crystal structure of the first generation

The first generation molecule of glutamic acid-based dendrons on a 1, 3,5-benzenetricarbonyl core leads to a cylindrical assembly as demonstrated by single crystal x-ray diffraction. The benzene pi-pi stack (A) is stabilized by vertical NH...O===C hydrogen bonding with each subunit participating in three intermolecular hydrogen bonds related by three-fold rotation symmetry.

Double-helical cyclic peptides: design, synthesis, and crystal structure of figure-eight mirror-image conformers of adamantane-constrained cystine-containing cyclic peptide cyclo (Adm-Cyst)(3)

A large number of macrocycles containing alternating repeats of cystine diOMe(-NH-CH(CO(2)Me)-CH(2)-S-)(2) and either a conformationally rigid aromatic/alicyclic moiety or a flexible polymethylene unit (X) in the cyclic backbone with ring size varying from 13- to 78-membered have been examined by spectral ((1)H NMR, FT-IR, CD) and X-ray crystallography studies for unusual conformational preferences. While (1)H NMR measurements indicated a turnlike conformation for all macrocycles, stabilized by intramolecular NH.CO hydrogen bonding, as also supported by FT-IR spectra in chloroform, convincing proof for beta-turn structures was provided by circular dichroism studies. Single-crystal X-ray studies on 39-membered cyclo (Adm-L-Cyst)(3) revealed a double-helical fold (figure-eight motif) for the macrocycle. Only a right-handed double helix was seen in the macrocycle constructed from L-cystine. The mirror-image macrocycle made up of D-cystine units exhibited a double helix with exactly the opposite screw sense, as expected. The enantiomeric figure-eights were stabilized by two intramolecular NH. CO hydrogen bonds and exhibited identical (1) H NMR and FT-IR spectra. The CD spectra of both isomers had a mirror-image relationship. The present results have clearly brought out the importance of cystine residues in inducing turn conformation that may be an important deciding factor for the adoption of topologically important structures by macrocycles containing multiple S-S linkages.

De novo protein design: Crystallographic characterization of a synthetic peptide containing independent helical and hairpin domains

The Meccano (or Lego) set approach to synthetic protein design envisages covalent assembly of prefabricated units of peptide secondary structure. Stereochemical control over peptide folding is achieved by incorporation of conformationally constrained residues like alpha-aminoisobutyric acid (Aib) or DPro that nucleate helical and beta-hairpin structures, respectively. The generation of a synthetic sequence containing both a helix and a hairpin is achieved in the peptide BH17, Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Gly-Gly-Leu-Phe-Val-DPro-Gly-Leu- Phe-Val-OMe (where Boc is t-butoxycarbonyl), as demonstrated by a crystal structure determination. The achiral -Gly-Gly- linker permits helix termination as a Schellman motif and extension to the strand segment of the hairpin. Structure parameters for C(89)H(143)N(17)O(20) x 2H(2)O are space group P2(1), a = 14.935(7) A, b = 18.949(6) A, c = 19.231(8) A, beta = 101.79(4) degrees, Z = 2, agreement factor R(1) = 8.50% for 4,862 observed reflections > 4 sigma(F), and resolution of approximately 0.98 A.

Comparison of helix-stabilizing effects of alpha,alpha-dialkyl glycines with linear and cycloalkyl side chains

The ability of alpha, alpha-di-n-alkyl glycines with linear and cyclic alkyl side chains to stabilize helical conformations has been compared using a model heptapeptide sequence. The conformations of five synthetic heptapeptides (Boc-Val-Ala-Leu-Xxx-Val-Ala-Leu-OMe, Xxx = Ac8c, Ac7c, Aib, Dpg, and Deg, where Ac8c = 1-aminocyclooctane-1-carboxylic acid, Ac7c = 1-aminocycloheptane-1-carboxylic acid, Aib = alpha-aminoisobutyric acid, Dpg = alpha,alpha-di-n-propyl glycine, Deg = alpha,alpha-di-n-ethyl glycine) have been investigated. In crystals, helical conformations have been demonstrated by x-ray crystallography for the peptides, R-Val-Ala-Leu-Dpg-Val-Ala-Leu-OMe, (R = Boc and acetyl). Solution conformations of the five peptides have been studied by 1H-nmr. In the apolar solvent CDCl3, all five peptides favor helical conformations in which the NH groups of residues 3-7 are shielded from the solvent. Successive NiH<-->Ni + 1H nuclear Overhauser effects over the length of the sequence support a major population of continuous helical conformations. Solvent titration experiments in mixtures of CDCl3/DMSO provide evidence for solvent-dependent conformational transitions that are more pronounced for the Deg and Dpg peptides. Solvent-dependent chemical shift variations and temperature coefficients in DMSO suggest that the conformational distributions in the Deg/Dpg peptides are distinctly different from the Aib/Acnc peptides in a strongly solvating medium. Nuclear Overhauser effects provide additional evidence for the population of extended backbone conformations in the Dpg peptide, while a significant residual population of helical conformations is still detectable in the isomeric Ac7c peptide in DMSO.

Isomorphous replacement combined with anomalous dispersion in the linear equations: application to a crystal containing four nonapeptide conformers

The investigation of the structure of the four conformers of the nonapeptide described here has an additional purpose: to illustrate a method for combining isomorphous replacement information with anomalous dispersion information within the linear equations that have found use in the analysis of multiple-wavelength anomalous dispersion data. In the present application, isomorphous replacement data were obtained from the replacement of naturally occurring S atoms in the nonapeptide with Se atoms. Only one wavelength was used for the analysis: Cu Kalpha radiation. Details of the analysis are presented, as well as the structural results obtained. It was found that the four independent molecules in the structure have similar, but not identical, conformations. The backbones fold into predominantly alpha-helices with one or two 310-type hydrogen bonds and have extended side chains. Three to four water molecules are associated with each of the four head-to-tail regions between the peptides. Optimal packing between hydrophobic surfaces may account for the existence of four molecules in an asymmetric unit.

Crystal structure of the channel-forming polypeptide antiamoebin in a membrane-mimetic environment

Crystals of an ion-channel-forming peptaibol peptide in a partial membrane environment have been obtained by cocrystallizing antiamoebin with n-octanol. The antiamoebin molecule has a bent helical conformation very similar to that established for Leu-zervamicin, despite a significantly different sequence for residues 1-8. The bent helices assemble to form a polar channel in the shape of an hour glass that is quite comparable to that of Leu-zervamicin. The molecules of cocrystallized octanol are found in two different areas with respect to the assembly of peptide molecules. One octanol molecule mimics a membrane segment along the hydrophobic exterior of the channel assembly. The other octanol molecules fill the channel in such a way that their OH termini satisfy the C==O moieties directed into the interior of the channel. Structure parameters for C82 H27 N17 O20(.3) C8H18O are space group P2(1) 2(1) 2(1), a = 9.143(2) A, b = 28.590(8) A, c = 44.289(8) A, Z = 4, agreement factor R1 = 11.95% for 4,113 observed reflections [>4sigma(F)], resolution approximately 1.0 A.

Self-assembling bis-dendritic peptides: design, synthesis and characterization of oxalyl-linked bis-glutamyl peptides [Glu(n)(CO2Me)n + 1-CO-]2; n = 1,3,7

Three generations of glutamic acid dendrons [Glu(n),(CO2Me)n + 1; n = 1, 3, 7] have been joined together head-to-head by an oxalyl unit to form highly sterically congested bis-Glu-dendritic peptides with gelling properties. The single crystal X-ray structure of the first generation bis-dendritic peptide showed an extended hydrogen-bonded chiral tape with modest nonlinear optical activity.

Design of two-helix motifs in peptides: crystal structure of a system of linked helices of opposite chirality and a model helix-linker peptide

BACKGROUND

An attempt is being made to produce two-helix bundles that are soluble in apolar media, without the use of a rigid template. The approach relies on the use of stereochemically constrained amino acids for helix construction, while a flexible linker is obtained by the use of an epsilon-aminocaproic acid residue (Acp). The Acp linker has appropriate NH and COOH termini to connect to the N and C termini of the helices, a flexible (CH2)5 moiety and sufficient length to make the desired assembly.

RESULTS

The conformations in crystals (determined by X-ray diffraction analyses) are described for a partial assembly consisting of a 7-residue helix with Acp (helix-Acp) and for two assemblies of 7-residue helices with Acp (helix-Acp-helix) in which the chiralities of the helices are L,L (already published) and L,D (this publication). The Acp linker is extended away from the helix in the L,L analog in a zig-zag manner, but assumes a helical conformation in the L,D analog. The two helices in the L,L and L,D analogs are displaced laterally by the linker, but in neither case has the linker folded the molecule into the desired U-conformation. Cell parameters for Boc-L-Val-L-Ala-L-Leu-Aib-L-Val-L-Ala-L-Leu-Acp-D-Val-D -Ala-D-Leu-Aib-D-Val-D-Ala-D-Leu-OMe are space group P4(1) with a = b = 10.094(6) A and c = 93.383(12) A.

CONCLUSIONS

Strong hydrogen bonds (NH...O=C) between the displaced helices of one molecule and the displaced helices of a neighboring molecule, which form near the linker of each helix-linker-helix assembly, appear to dominate in both the L,L and L,D crystal. The (CH2)5 segment of the linker readily adopts different conformations that result in the L and D helices packing in a similar spatial motif. Greater conformational control at the linking segment or introduction of specific interhelix interactions may be necessary in order to achieve U-type folding between neighboring helices in a single molecule.

A designed beta-hairpin peptide in crystals

Beta-hairpin structures have been crystallographically characterized only in very short acyclic peptides, in contrast to helices. The structure of the designed beta-hairpin, t-butoxycarbonyl-Leu-Val-Val-D-Pro-Gly-Leu-Val-Val-OMe in crystals is described. The two independent molecules of the octapeptide fold into almost ideal beta-hairpin conformations with the central D-Pro-Gly segment adopting a Type II' beta-turn conformation. The definitive characterization of a beta-hairpin has implications for de novo peptide and protein design, particularly for the development of three- and four-stranded beta-sheets.

Peptide design: crystal structure of a helical peptide module attached to a potentially nonhelical amino terminal segment

The peptide Boc-Gly-Dpg-Gly-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe has been designed to examine the structural consequences of placing a short segment with a low helix propensity at the amino terminus of a helical heptapeptide module. The Gly-Dpg-Gly segment is a potential connecting element in the synthetic construction of a helix-linker-helix motif. Crystal parameters for the peptide are P21, a = 8.651 (3) A, b = 46.826 (13) A, c = 16.245 A, beta = 90.13 (3) degrees, Z = 4; 2 independent molecules/asymmetric unit. The structure reveals almost identical conformations for the two independent molecules. The backbone is completely helical for residues 2-9, with on 4 --> 1 hydrogen bond and six 5 --> 1 hydrogen bonds. The alpha, alpha-di-n-propylglycine residue adopts a helica conformation. Gly (1) adopts an extended conformation resulting in a nonhelical N-terminus, with the Boc group swinging away from the helix. the lateral association of helices in the beta axis direction is unusual in that the helix axes are directed up or down (parallel or antiparallel) by pairs: decrease decrease increase increase decrease decrease, etc.

Crystal structures of a nonapeptide helix containing alpha, alpha-di-n-butylglycine (Dbg), Boc-Gly-Dbg-Ala-Val-Ala-Leu-Aib-Val-Leu-OMe

Two crystal structures of a nonapeptide (anhydrous and hydrated) containing the amino acid residue alpha, alpha-di-n-butylglycyl, reveal a mixed 3(10)-/alpha-helical conformation. Residues 1-7 adopt phi, psi values in the helical region, with Val(8) being appreciably distorted. The Dbg residue has phi, psi values of -40, -37 degrees and -46, -40 degrees in the two crystals with the two butyl side chains mostly extended in each. Peptide molecules in the crystals pack into helical columns. The crystal parameters are: C50H91N9O12, space group P2(1), with a = 9.789(1) A, b = 20.240(2) A, c = 15.998(3) A, beta = 103.27(1); Z = 2, R = 10.3% for 1945 data observed > 3 sigma (F) and C50H91N9O12.3H2O, space group P2(1), with a = 9.747(3) A, b = 21.002(8) A, c = 15.885(6) A, beta = 102.22(3) degrees, Z = 2, R = 13.6% for 2535 data observed > 3 sigma (F). The observation of a helical conformation at Dbg suggests that the higher homologs in the alpha, alpha-dialkylated glycine series also have a tendency to stabilize peptide helices.

Solid state and solution conformations of a helical peptide with a central Gly-Gly segment

The influence of amino acids with contrasting conformational tendencies on the stereochemistry of oligopeptides has been investigated using an octapeptide Boc-Leu-Aib-Val-Gly-Gly-Leu-Aib-Val-OMe, which contains two helix-promoting Aib residues and a central helix-destabilizing Gly-Gly segment. Single crystal x-ray diffraction studies reveal that a 3(10)-helix is formed up to the penultimate Aib residue, at which point there is a helix reversal in the backbone, reminiscent of a C-terminal 6-->1 hydrogen bond. The curious feature in the crystal is the solvation of the possible 6-->1 bond by a CH3OH molecule, where the OH is inserted between O(3) and N(8) and participates in hydrogen bonds with both. The cell parameters are as follows: space group P2(1)2(1)2(1), a = 10.649 (4) A, b = 15.694 (5) A, c = 30.181 (8) A, R = 6.7% for 3427 data (magnitude of F0 > 3 sigma F) observed to 0.9 A. Nuclear magnetic resonance studies in CDCl3 using NH group solvent accessibility and nuclear Overhauser effects as probes are consistent with a 3(10)-helical conformation. In contrast, in (CD3)2SO, unfolding of the central segment results in a multiple beta-turn structure, with beta-turn conformations populated at residues 1-2, 3-4, and 6-7. CD studies in methanol-2,2,2-trifluoroethanol (TFE) mixtures also provide evidence for a solvent-dependent structural transition. Helical conformations are populated in TFE, while type II beta-turn structures are favored in methanol.

Effects of end group and aggregation on helix conformation: crystal structure of Ac-(Aib-Val-Ala-Leu)2-Aib-OMe

The role of end groups in determining stereochemistry and packing in hydrophobic helical peptides has been investigated using an alpha-aminosobutyric acid (Aib) containing model nonapeptide sequence. In contrast to the Boc-analogue, Ac-(Aib-Val-Ala-Leu)2-Aib-OMe crystallizes with two independent molecules in a triclinic cell. The cell parameters are: space group P1, a = 10.100(2)A, b = 15.194(4)A, c = 19.948(5)A, alpha = 63.12(2) degrees, beta = 88.03(2) degrees, y = 88.16(2) degrees, Z = 2, R = 7.96% for 5140 data where magnitude of Fo > 3 rho(F). The two independent molecules alternate in infinite columns formed by head-to-tail hydrogen bonding. The helices in the two independent molecules are quite similar to each other but one molecule is rotated approximately 123 degrees about its helix axis with respect to the other. All the helical columns pack parallel to each other in the crystal. Replacement of the bulky Boc group does not lead to any major changes in conformation. Packing characteristics are also similar to those observed for similar helical peptides.

Flexibility in peptide molecules and restraints imposed by hydrogen bonds, the Aib residue, and core inserts

The first segments of this article review some of the early crystal structure determinations of beta-bends, gamma-bends, large conformational changes in cyclic peptides upon complexation with metal ions, and both the stability and drastic change in conformation as a function of the solvent used for growing crystals. More recent structure analyses have concerned helical peptides containing the Aib and/or Dpg residues and associated conformational problems such as 310-/alpha-helix transitions, helix aberrations, reversals, severe curving of the helix, unfolding, and hydration of backbone. Ion channels occurring in three crystal forms of zervamicin and possible ion transport and gating mechanisms are described. Finally, hydrogen bonding patterns are presented in supramolecular assemblies of retropeptides with core inserts consisting of oxalyl, adipoyl, suberoyl and polymethylene moieties.

Core directed self-assemblies in the solid state of retro Aib bis-peptide dicarboxylic acids; a design strategy for control of molecular orientation in peptides

Self-assembly patterns as a function of the central core insert in the retro bis-peptide dicarboxylic acids HO-Aib-X-Aib-OH, containing oxalyl (-CO-CO-; 1), fumaryl (-CO-CH = CH-CO-; 2), and adipoyl [-CO-(CH2)4-CO-; 3], have been characterized by single crystal x-ray diffraction analyses. Extensive hydrogen bonding occurs in each crystal but there are no OH ... O binds between acid groups. Only two types of hydrogen bonds occur in all the crystals: NH ... O (acid terminal), 2.84-2.98 A and OH (acid terminal) ... O (core carbonyl), 2.55-2.67 A (except for an additional intramolecular C5 type bond in the oxalyl moiety in 1). The self-assembly patterns are a beta-network in 1, separate layer assemblies (beta-networks) for two independent molecules in 2 that combine into a three-dimensional gamma network, and separate ribbon assembles (alpha networks) for two independent molecules in 3 that combine into an extended beta-network sheet with hydrophobic faces.

The delineation of hydrogen-bonding patterns in supramolecular self-assembly of several core oxalo retro-peptides and crystal structure of MeO-Ser-Leu-COCO-Leu-Ser-OMe

Pseudo-C5-type intramolecular hydrogen bonding, arising from the C2 disposition of the core NH-CO-CO-NH unit in oxalo retro-peptides, is formed in addition to extended hydrogen bonding with neighbors forming sheets in MeO-Aib-COCO-Aib-OMe (1), helices in MeO-Leu-COCO-Leu-OMe (2) and ribbons in MeO-Ser-Leu-COCO-Leu-Ser-OMe (3). In 3 the OH in the Ser side-chains form hydrogen bonds with the backbone carbonyl of Leu groups from neighboring molecules. Crystal parameters for 3 are: C22H38N4O10, monoclinic, space group P2(1), a = 7.374(1), b = 18.218(4), c = 10.661(3) A, beta = 95.72(2) degrees, R = 0.063 for 1738 observed reflections with [formula: see text].

Polymethylene spacer linked bis(Ala) peptides form modified beta-sheet structures. Crystal structure and self-assembly pattern of adipoyl and suberoyl analogues

The adipoyl- and suberoyl-linked bis(Ala) peptides have an extended backbone between the two C alpha atoms in each molecule. They self-assemble, through intermolecular hydrogen bonds and stacking of parallel strands, into highly ordered modified beta-sheet-like structures. Crystals data for adipoyl bis(Ala)diester are as follows: C14H24N2O6, monoclinic space group P2(1), a = 4.900(1), b = 29.093(10), c = 6.021(2) A, beta = 104.20(2) degrees, R = 0.053 for 1100 data > 3 sigma (F); for suberoyl bis(Ala)diester: C16H28N2O6, monoclinic space group P2(1), a = 4.887(2), b = 32.650(9), c = 6.004(2) A, beta = 103.79(3), R = 0.070 for 1065 data > 3 sigma (F).

Hydration and distortion of peptide helices in crystals. Alpha-helical structure of a dodecapeptide, Boc-(Ala-Leu-Aib)4-OMe

The dodecapeptide Boc-(Ala-Leu-Aib)4-OMe crystallized with two independent helical molecules in a triclinic cell. The two molecules are very similar in conformation, with a 3(10)-helix turn at the N-terminus followed by an alpha-helix, except for an elongated N(7)...O(3) distance in both molecules. All the helices in the crystal pack in a parallel motif. Eleven water sites have been found in the head-to-tail region between the apolar helices that participate in peptide-water hydrogen bonds and a network of water-water hydrogen bonds. The crystal parameters are as follows: 2(C58H104N12O15)+ca. 10H2O, space group P1 with a = 12.946(2), b = 17.321(3), c = 20.465(4) A, alpha = 103.12(2), beta = 105.63(2), gamma = 107.50(2) degrees, Z = 2, R = 10.9% for 5152 data observed > 3 sigma (F), resolution 1.0 A. In contrast to the shorter sequences [Karle et al. (1988) Proc. Natl. Acad. Sci. USA 85, 299-303] and Boc-(Ala-Leu-Aib)2-OMe [Karle et al. (1989) Biopolymers 28, 773-781], no insertion of a water molecule into the helix is observed. However, the elongated N---O distance between Ala7 NH and Aib3 CO in both molecules (molecule A, 3.40 A; molecule B, 3.42 A) is indicative of an incipient break in the helices.

Facile transition between 3(10)- and alpha-helix: structures of 8-, 9-, and 10-residue peptides containing the -(Leu-Aib-Ala)2-Phe-Aib- fragment

A structural transition from a 3(10)-helix to an alpha-helix has been characterized at high resolution for an octapeptide segment located in 3 different sequences. Three synthetic peptides, decapeptide (A) Boc-Aib-Trp-(Leu-Aib-Ala)2-Phe-Aib-OMe, nonapeptide (B) Boc-Trp-(Leu-Aib-Ala)2-Phe-Aib-OMe, and octapeptide (C) Boc-(Leu-Aib-Ala)2-Phe-Aib-OMe, are completely helical in their respective crystals. At 0.9 A resolution, R factors for A, B, and C are 8.3%, 5.4%, and 7.3%, respectively. The octapeptide and nonapeptide form ideal 3(10)-helices with average torsional angles phi(N-C alpha) and psi(C alpha-C') of -57 degrees, -26 degrees C and -60 degrees, -27 degrees for B. The 10-residue peptide (A) begins as a 3(10)-helix and abruptly changes to an alpha-helix at carbonyl O(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 phi, psi angles in the decapeptide are -58 degrees, -28 degrees for residues 1-3 and -63 degrees, -41 degrees 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 3(10)- to alpha-helix transition with the amide I band appearing at 1,656-1,657 cm-1 in the 9- and 10-residue peptides, whereas in shorter sequences the band is observed at 1,667 cm-1.

Conformation of the flexible bent helix of Leu1-zervamicin in crystal C and a possible gating action for ion passage

The membrane channel-forming polypeptide, Leu1-zervamicin, Ac-Leu-Ile-Gln-Iva-Ile5-Thr-Aib-Leu-Aib-Hyp10-Gln-Aib-Hyp-Aib-P ro15-Phol (Aib: alpha-aminoisobutyric acid; Iva: isovaline; Hyp: 4-hydroxyproline; Phol: phenylalininol) has been analyzed by x-ray diffraction in a third crystal form. Although the bent helix is quite similar to the conformations found in crystals A and B, the amount of bending is more severe with a bending angle approximately 47 degrees. The water channel formed by the convex polar faces of neighboring helices is larger at the mouth than in crystals A and B, and the water sites have become disordered. The channel is interrupted in the middle by a hydrogen bond between the OH of Hyp (10) and the NH2 of the Gln(11) of a neighboring molecule. The side chain of Gln(11) is wrapped around the helix backbone in an unusual fashion in order that it can augment the polar side of the helix. In the present crystal C there appears to be an additional conformation for the Gln(11) side chain (with approximately 20% occupancy) that opens the channel for possible ion passage. Structure parameters for C85H140N18O22.xH2O.C2H5OH are space group P2(1)2(1)2(1), a = 10.337(2) A, b = 28.387(7) A, c = 39.864(11) A, Z = 4, agreement factor R = 12.99% for 3250 data observed > 3 sigma (F), resolution = 1.2 A.