Β-turn Type Research Articles

Incorporation of Conformationally Constrained β-Amino Acids into Peptides

The use of norbornene units to induce the formation of β-sheet and β-turn type structures in peptides is discussed. The norbornene unit is readily prepared by a desymmetrization reaction and is easily incorporated into a peptide chain. Depending upon the exact nature of the norbornene unit, it is possible to form structures which resemble parallel β-sheets, antiparallel β-sheets or β-turns. Similar peptide analogues incorporating a cis-2-amino-cyclopropane carboxylic acid unit can also be prepared. As an illustration of the application of this chemistry, a short, asymmetric synthesis of conformationally constrained metalloprotease inhibitors is presented. Copyright © 2000 European Peptide Society and John Wiley & Sons, Ltd.

Free energy landscapes of peptides by enhanced conformational sampling

The free energy landscapes of peptide conformations in water have been observed by the enhanced conformational sampling method, applying the selectively enhanced multicanonical molecular dynamics simulations. The conformations of the peptide dimers, -Gly-Gly-, -Gly-Ala-, -Gly-Ser-, -Ala-Gly-, -Asn-Gly-, -Pro-Gly-, -Pro-Ala-, and -Ala-Ala-, which were all blocked with N-terminal acetyl and C-terminal N-methyl groups, were individually sampled with the explicit TIP3P water molecules. From each simulation trajectory, we obtained the canonical ensemble at 300 K, from which the individual three-dimensional landscape was drawn by the potential of mean force using the three reaction coordinates: the backbone dihedral angle, ψ, of the first amino acid, the backbone dihedral angle, φ, of the second amino acid, and the distance between the carbonyl oxygen of the N-terminal acetyl group and the C-terminal amide proton. The most stable state and several meta-stable states correspond to extended conformations and typical β-turn conformations, and their free energy values were accounted for from the potentials of mean force at the states. In addition, the contributions from the intra-molecular energies of peptides and those from the hydration effects were analyzed. Consequently, the stable β-turn conformations in the free energy landscape were consistent with the empirically preferred β-turn types for each amino acid sequence. The thermodynamic values for the hydration effect were decomposed and they correlated well with the empirical values estimated from the solvent accessible surface area of each molecular conformation during the trajectories. The origin of the architecture of protein local fragments was analyzed from the viewpoint of the free energy and its decomposed factors.

Effect of Solution Conformation on Antibody Recognition of a Protein Core Epitope from Gastrointestinal Mucin (MUC2)

Antibody recognition of the tandem repeat unit of MUC2 glycoprotein was investigated. To clarify the role of secondary structure, the immunoreactivity and conformation of overlapping and truncated peptides were investigated. For this several MUC2 peptides have been synthesized and their secondary structure has been analyzed by circular dichroism and Fourier transform infrared spectroscopical methods. For the binding studies a MUC2 mucin protein core-specific monoclonal antibody was used in competition RIA experiments. The minimal size peptide functioning as epitope was peptide18PTGTQ22. Within the immunodominant13TPTPTPTGTQTPTT26region we found that all peptides recognized by the 996 monoclonal antibody adopted β-turns secondary structure. Peptides15TPTPTGTQ22and16PTPTGTQ22, containing the most prominent β-turn(s), had the strongest immunoreactivity. It was also observed that peptides with Pro on their N-termini (16PTPTGTQ22,18PTGTQ22) adopt a different type of β-turn in TFE than peptides with Thr at their N-terminal. Based on the antibody binding, molecular dynamics calculations, and secondary structure analysis, we propose a model for the epitope structure of the MUC2 mucin tandem repeat.

The solution structure of human endothelin-2 a 1H-NMR and CD study.

The solution structure of the vasoactive endogenous 21-amino-acid human endothelin-2 has been determined by NMR and CD techniques, in a mixed solvent of 100 mM aqueous acetic acid and 25% (by vol.) 1,1,1,3,3,3-hexafluoro-2-propanol. From NMR-derived restraints on upper limit distances and dihedral angles, distance geometry structures were calculated using the program DADAS90, and refined by simulated annealing in X-PLOR. The structure of endothelin-2 consists of an alpha-helix of residues 9 to 17, orientated anti-parallel to a short beta-strand of residues 1 to 3, linked together by a possible beta-turn type I of residues 5-8. These secondary structural elements are stabilised and positioned by two disulphide bonds between residues 1 and 15, and 3 and 11, respectively. The average root mean square deviation over residues 1-17 of 15 accepted low-energy conformers chosen to reflect the solution structure of endothelin-2, was 0.73 A for the backbone and 1.41 A for all heavy atoms. The data on endothelin-2 will be discussed and compared with what has been published on other endothelin/sarafotoxin peptides.

β-Turn modulation by the cyclohexane analogues of phenylalanine

X-ray diffraction experiments have evidenced that the orientation of the aromatic side chain determine the folding tendencies of tBuCO-Pro-c 6Phe-NH iPr, where c 6Phe denotes the (S,S) and (R,R) cyclohexane analogues of phenylalanine. In the solid state, both dipeptides are β-folded, the β-turn type being dictated by the stereochemistry of the cyclohexane ring.

Demonstration ofendo-cis-(2S,3R)-Bicyclo[2.2.1]hept-5-en-2,3- dicarbonyl Unit as a Reverse-Turn Scaffold and Nucleator of Two-Stranded Parallel β-Sheets: Design, Synthesis, Crystal Structure, and Self-Assembling Properties of Norborneno Peptide Analogues

endo-cis-(2S,3R)-Bicyclo[2.2.1]hept-5-en (norbornene) dicarbonyl unit with a built-in U-architecture has been demonstrated to be an excellent reverse-turn molecular scaffold. A large variety of endo-cis-(2S,3R)-norborneno bispeptides containing almost all of the coded amino acids were synthesized and examined for conformational preferences by 1H NMR, FT-IR, CD, and X-ray crystallographic studies. While FT-IR and 1H NMR variable-temperature studies ruled out the presence of any significant amount of intramolecular hydrogen bonding in simple bispeptides (3a−h) (except in Aib bispeptide), the CD studies were clearly in favor of a β-turn type structure. Single-crystal X-ray studies on Aib, Val and Leu containing norborneno bispeptides (3b−d) provided convincing proof for the presence of reverse-turn conformation. While the interstrand Cα−Cα‘ distances (5.2−5.7 A) were well within the range of those for β-turn structures, no interstrand intramolecular hydrogen bonding was seen in Val and Leu bispeptides; the A...

Conformational properties of a model alanyl dipeptide and of alanine-derived oligopeptides: Effects of solvation in water and in organic solvents—A combined SIBFA/continuum reaction field, ab initio self-consistent field, and density functional theory investigation

A ϕ/ψ conformational energy map of a model alanyl dipeptide is first drawn using the SIBFA (Sum of Interactions Between Fragments Ab initio computed) procedure [N. Gresh, P. Claverie and A. Pullman (1979) International Journal of Quantum Chemistry Symposium, Vol. 13, pp. 243–253; N. Gresh, P. Claverie and A. Pullman (1982) International Journal of Quantum Chemistry, Vol. 22, pp. 199–215; N. Gresh, P. Claverie and A. Pullman (1984) Theoretical Chimica Acta, Vol. 66, pp. 1–20; N. Gresh, P. Claverie and A. Pullman (1985) Theoretical Chimica Acta, Vol. 67, pp. 11–32; N. Gresh, A. Pullman and P. Claverie (1985) International Journal of Quantum Chemistry, Vol. 28, pp. 757–771; N. Gresh, P. Claverie and A. Pullman (1986) International Journal of Quantum Chemistry, Vol. 29, pp. 101–118; N. Gresh (1995) Journal of Computational Chemistry, Vol. 16, pp. 856–882; N. Gresh and D.R. Garmer (1996) Journal of Computational Chemistry, Vol. 17, pp. 1481–1495; N. Gresh, M. Leboeuf and D.R. Salahub (1994) in Modelling the Hydrogen Bond, Vol. 569, American Chemical Society Symposia, Smith, D.A., Ed., pp. 82–112; N. Gresh (1997) Journal de Chim.-Phys. (Paris), Vol. 94, pp. 1365–1416]. A new formulation of the intramolecular (conformational) energy is used, consistent with the refinements that were recently published for the intermolecular interaction energies in joint SIBFA/ab initio supermolecule Self-Consistent Field/Moller-Plesset (SCF/MP2) and Density Functional Theory (DFT) studies of cation-ligand [see Gresh (1995) and Gresh and Garmer (1996) above], and H-bonded [see Gresh et al. (1994) above] complexes. The accuracy of the procedure is assessed, on fourteen conformers selected from the map, by comparing their relative conformational energies with those obtained from SCF/MP2 and DFT computations. Conformational energy maps are then recomputed in the presence of water, dimethyl sulfoxide, chloroform, and carbon tetrachloride, the solvation energies being computed with the Continuum reaction field procedure due to J. Langlet et al. [(1988) Journal of Physical Chemistry, Vol. 92, pp. 1617–1631], and recently integrated into SIBFA [J. Langlet, N. Gresh and C. Giessner-Prettre (1995) Biopolymers, Vol. 36, pp. 765–780]. Such an integrated procedure is next extended to a comparison of the relative stabilities of, on the one hand, the competing types of β-turns (I, I′, II, II′) that are prevalent in Ala/Gly-based model tetrapeptides, and, on the other hand, α- vs 310-helices in alanine oligomers. © 1998 John Wiley & Sons, Inc. Biopoly 45: 405–425, 1998

Conformational Analysis of the Highly Potent Bradykinin Antagonist Hoe-140 by Means of Two Different Computational Methods

The AMBER 4.0 force field was used to perform the characterization of the conformational profile of the highly potent bradykinin antagonist Hoe-140 (D-Arg0-Arg1-Pro2-Hyp3-Gly4- Thi5-Ser6-D-Tic7-Oic8-Arg9). The structural features of the peptide were assessed using two different computational methods, both capable to provide a good sampling of the low-energy conformations of the molecule. Specifically, the conformational space of the peptide was explored: i) computing molecular dynamics trajectories in cycles of high (900 K) and low (300 K) temperature and ii) using simulated annealing (SA) in an iterative fashion. Analysis of the structures characterized indicates that most of the low-energy conformations of the peptide exhibit a βII′-turn motif at its C-terminus, in agreement with previous experimental and theoretical studies. On the other hand, about a 50% of the low-energy conformations characterized also exhibit different β-turn type motifs at the N-terminus, whereas the rest of the conformations can be described as bends. Finally, in order to get new insights into the structural requirements necessary to design more potent and selective antagonists of bradykinin, present results were compared with those previously reported by this laboratory on the conformational preferences of the native nonapeptide and its DPhe7 analog.

Formula omitted]: X-ray structure, energy minimization and calorimetric determinations

A solid-state study of N- acetyl- l-prolyl- l-leucyl-glycinamide hemihydrate (NAPLGA), C 15H 26N 4O 4·0.5H 2O has been performed using single crystal X-ray diffraction method and calorimetric determinations of the fusion thermodynamic parameters. Conformational energy map of AcProLeuGlyNH 2 molecule has also been evaluated. In the crystal, the molecular backbone is folded back between Leu and Gly residues and the conformation is stabilized by a 1 ← 4 intramolecular H-bond. In this manner a ten-membered cyclic structure with β-turn type II conformation is formed. Prolyl residue is in a slightly distorted CsC β- exo form and Leu side-chain adopts the energetically favoured t( g + t) conformation. Crystal packing is characterized by four intermolecular hydrogen bonds which involve all the donor groups. The crystallization water placed on a binary axis acts as a bridge, through two H-bonds, between two-fold related peptide molecules. All the hydrogen bonds assemble in wide layers extending parallel to the ab plane of a C2 space group. Along the c direction, adjacent layers are separated by regions characterized by loose van der Waals interactions. Potential energy calculations have been carried out using procedures as in ecepp (empirical conformational energy program for peptides) and amber programs and the most favoured conformations have been analysed in comparison with the one observed in the hydrated crystal. The observed conformation is very close to a relative minimum, whose energy is only 4 kJ mol −1 ( ecepp procedure) higher than that of the calculated absolute minimum. Thermodynamic properties concerning the fusion, when compared with those of other correlated N-acetyl peptidoamides, suggest that the intramolecular hydrogen bond is probably maintained also in NAPLGA molten, partially limiting the conformational freedom of each peptide molecule.

Secondary structure in oligomers of carbohydrate amino acids

Short oligomeric chains of tetrahydrofuran amino acids exhibit a novel repeating β-turn type secondary structure in solution stabilised by hydrogen bonds and provide clear evidence that carbopeptoids will allow control of conformation in peptidomimetics.

Serine-Based Cyclodepsipeptides on an Adamantane Building Block: Design, Synthesis, and Characterization of a Novel Family of Macrocyclic Membrane Ion-Transporting Depsipeptides

A simple two-step synthetic strategy provides a straightforward entry to a large variety of adamantane-containing serine-based cyclodepsipeptides. The design is flexible with respect to the choice of an amino acid, the ring size, and the nature of the template as illustrated here with the preparation of a large variety of serine-based macrocycles, for example, 18-membered simple cyclo(Adm-Ser-)2 (4), 21-membered, S−S bridged, cyclo(Adm-Ser-Cyst-Ser-) (10), 24-membered cyclo(Adm-Ser-Val-)2 (5a), cyclo(Adm-Ser-Leu-)2 (5b), cyclo(Adm-Ser (Leu)-Val)2 (6), pyridine-containing cyclo(Adm-Ser-Val-Py-Val-Ser-) (13), 26-membered cyclo(Adm-Ser-Ser-)2 (8) and crown ether hybrid cyclo(Adm-Ser-TEG-Ser-) (12), and 36-membered cyclo(Adm-Ser-)4 (7) and provides built-in handles (in the form of protected NH2 and COOH groups) for attachment of suitable pendants leading to attractive models that may have multiple uses as membrane ionophores, scaffolds, or templates in the design of artificial proteins and for studying the structure−function relationship in biological receptors. This novel class of macrocyclic peptides are demonstrated to adopt β-turn type conformation and possess high efficiency in transporting Na+, Ca2+, and Mg2+ ions across model membranes. Amongst the cyclodepsipeptides reported here, the 24-membered macrocycle 6, containing two leucine residues symmetrically placed on the exterior of the ring, was found to be the most efficient ion-transporter in lipid bilayer membranes. Interestingly, no appreciable ion-transport was noticed by 18-membered cyclodepsipeptide (4) and by macrocycles 10, 12, and 13 possessing only one adamantane unit in their cyclic framework. These results show that a minimum of two adamantane units in a 24-membered ring size appears to be the optimum requirement for efficient membrane ion transport.

Molecular dynamics simulations of a simple tripeptide, N-acetyl-Pro-Gly-Phe in the crystalline states: distinction of the β-turn Type I from the Type II Form

Molecular dynamics simulations of a simple tripeptide, N-acetyl-Pro-Gly-Phe in the crystalline states: distinction of the β-turn Type I from the Type II Form

Molecular dynamics simulations of a simple tripeptide, N-acetyl-Pro-Gly-Phe in the crystalline states: distinction of the β-turn Type I from the Type II form

Molecular dynamics (MD) simulations of a simple tripeptide N-acetyl-Pro-Gly-Phe in the crystalline states show that this tripeptide exhibits two different β-turn conformations (Types I and II) in two different crystalline states. The combination of the one intramolecular and four intermolecular hydrogen bonds for each molecule in crystal plays an important role in determining a propensity to form either Type I or Type II conformation. Each of the conformations in crystals is found to be close to one of the local minima of the tripeptide itself, although more stable conformations appear in the MD simulation of the single tripeptide in vacuo. It is concluded that the conformations in crystal cannot be formed without the intermolecular interactions. The present MD simulation in one of the crystalline states demonstrates the presence of the puckering motion in the pyrrolidine ring, which is consistent with our previous finding by solid-state NMR.

Free Energy Determinants of Secondary Structure Formation: III. β-Turns and their Role in Protein Folding

The stability of β-turns is calculated as a function of sequence and turn type with a Monte Carlo sampling technique. The conformational energy of four internal hydrogen-bonded turn types, I, I′, II and II′, is obtained by evaluating their gas phase energy with the CHARMM force field and accounting for solvation effects with the Finite Difference Poisson- Boltzmann (FDPB) method. All four turn types are found to be less stable than the coil state, independent of the sequence in the turn. The free-energy penalties associated with turn formation vary between 1.6 kcal/mol and 7.7 kcal/mol, depending on the sequence and turn type. Differences in turn stability arise mainly from intraresidue interactions within the two central residues of the turn. For each combination of the two central residues, except for -Gly-Gly-, the most stable β-turn type is always found to occur most commonly in native proteins. The fact that a model based on local interactions accounts for the observed preference of specific sequences suggests that long-range tertiary interactions tend to play a secondary role in determining turn conformation. In contrast, for β-hairpins, long-range interactions appear to dominate. Specifically, due to the right-handed twist of β-strands, type I′ turns for -Gly-Gly- are found to occur with high frequency, even when local energetics would dictate otherwise. The fact that any combination of two residues is found able to adopt a relatively low-energy turn structure explains why the amino acid sequence in turns is highly variable. The calculated free-energy cost of turn formation, when combined with related numbers obtained for α-helices and β-sheets, suggests a model for the initiation of protein folding based on metastable fragments of secondary structure.

Determination of the Three-Dimensional Structure of a New Crystalline Form of N-Acetyl-Pro-Gly-Phe As Revealed by 13C REDOR, X-Ray Diffraction, and Molecular Dynamics Calculation

The interatomic distances in the crystalline specimen of 13C,15N doubly labeled peptides [1-13C]N-acetyl-Pro-[15N]Gly-Phe (I), N-acetyl-[1-13C]Pro-Gly-[15N]Phe (II), and [1-13C]N-acetyl-Pro-Gly-[15N]Phe (III) evaluated from rotational echo double resonance (REDOR) data were compared with those from X-ray diffraction studies and justify our novel approach. The minimization of B1 inhomogeneity was critical to obtain accurate distances, which were achieved by confinement of the samples in the central portion (50% of the total filling volume of the rotor). The effect of the finite length of the π pulse was found to be negligible as long as the pulse length is less than 10% of the rotor cycle. The 13C···15N distances obtained from 13C REDOR were thus 3.24 ± 0.05, 3.43 ± 0.05, and 4.07 ± 0.05 A for I, II, and III, respectively. The REDOR-derived conformation of this peptide was β-turn type I, consistent with our X-ray diffraction study (orthorhombic crystal). The maximum deviation of the distances determined by...

A novel synthesis of ( R)- and ( S)-α-alkylated aspartic and glutamic acids: α-alkylated aspartic succinimides as new type of β-turn type II and II′ mimetics

A novel and efficient synthesis of optically pure ( R)- and ( S)-α-methyl glutamic acid ( 1), ( R)- and ( S)-α-methyl aspartic acid ( 2a) and ( R)- and ( S)-α-isobutyl aspartic acid ( 2b) using L-phenylalanine cyclohexylamide 4 as chiral auxiliary is described. Crystal structures show that the ( R)- and ( S)-α-methyl glutamic acid derivatives ( S,S)- 5 and ( R,S)- 6 adopt β-turn type I geometries, whereas the corresponding aspartimide derivatives ( R,S)- 12a,b form a β-turn type II and ( S,S)- 11a a β-turn type II′. These findings suggest, that the succinimide derivatives of ( R)- and ( S)-α-alkyl aspartic acids can serve as building blocks to stabilise β-turns of type II (or II′) in peptides depending on their absolute configuration.

Inter- and intra-molecular contributions of neighboring dipolar pairs to the precise determination of interatomic distances in a simple [ 13C, 15N]-peptide by 13C, 15N-REDOR NMR spectroscopy

Both 13C- and 15N-REDOR experiments were performed to determine the 13C- 15N interatomic distance in [ 1- 13C]N-acetyl-Pro-[ 15N]Gly-Phe crystal and to evaluate the inter- or intra-molecular dipolar contributions leading to its errors. The interatomic distance was determined to be 3.43 Å after removing the intermolecular contribution to the echo dephasing arising from the intermolecular dipolar interaction with labeled nuclei of the neighboring molecule. This contribution was estimated by extrapolation to infinite dilution of the labeled sample in unlabeled peptide. The theoretical formalism was developed for the nucleus coupled with two heteronuclei. The conformation of this peptide turned out to be β-turn type II on the basis of the abovementioned interatomic distance.

A molecular mechanics study of the effect of substitution in position 1 on the conformational space of the oxytocin/vasopressin ring

The effect of the substitution in position 1 on the low-energy conformations of the oxytocin/vasopressin 20-membered ring was investigated by means of molecular mechanics. Three representative substitutions were considered: β′-mercapto-β,β-dimethyl)propionic acid (Dmp), (β′-mercapto-β,β-cyclopentamethylene)propionic acid (Cpp), both forming strong antagonists, and (α,α-dimethyl-β-mercapto)propionic acid (α-Dmp), forming analogs of strongly reduced biological activity, with the β-mercaptopropionic (Mpa) residue taken as reference. Both ECEPP/2 (rigid valence geometry) and AMBER (flexible valence geometry) force fields were employed in the calculations. Three basic types of backbone conformations were taken into account which are distinguished by the type of β-turn at residues 3 and 4: β1/βIII, βII, and βI′/βIII′, all types containing one or two intra-annular hydrogen bonds. The allowed (ring-closed) disulfide-bridge conformations were searched by an algorithm formulated in terms of scanning the disulfide-bridge torsional angle Cβ-S-S-Cβ. The ECEPP/2 and AMBER energies of the obtained conformations were found to be in reasonable agreement. Two of the low-energy conformers of the [Mpa1]-compound agreed very well with the cyclic part of the two conformers found in the crystal structure of [Mpa1]-oxytocin. An analysis of the effect of β-substitution on relative energies showed that the conformations with the N-C′-CH2-CH2 (ψ′1) and C′-CH2-CH2-S (ϰ′1) angles of the first residue around (−100°, 60°) and (100°, −60°) are not affected; this in most cases implies a left-handed disulfide bridge. In the case of α-substitution the allowed values of ψ′1 are close to ± 60°. This requirement, being in contradiction to the one concerning β-substitution, could explain the very low biological activity of the α-substituted analogs. The conformational preferences of substituted compounds can largely be explained by the analysis of local interactions within the first residue. Based on the selection of the conformations which are low in energy for both the reference and β-substituted compounds, two distinct types of possible binding conformations were proposed, the first one being similar to the crystal conformer with a left-handed disulfide bridge, the second one having a right-handed bridge, but a geometry different from that of the crystal conformer with the right-handed bridge. The first type of disulfide-bridge arrangement is equally favorable for both βI/βIII and βII types of backbone structure, while the second one is allowed only for the βII type of backbone. No conformation of the βI′/βIII′ type has a low enough energy to be considered as a possible binding conformation for all of the active compounds studied in this work.

Diresidue-monopeptide (DRMP) model for analysis of peptide and protein conformation

The paired torsional angle representation φ i, ψ i in protein conformational analysis is only one type of correlation with a focus on a given C α residue and gives the relative orientation of a pair of peptide planes sandwiching a given residue (referred as mono-residue dipeptide model, MRDP). A shift of emphasis from a residue site to a given peptide plane (termed as diresidue monopeptide model, DRMP) leads to examination of pairs such as φ i, ψ i−1 and other parameters derived therefrom. General sum ( α n = φ i + ψ i−n) and the difference ( β n = φ i − ψ i−n) parameters are introduced, of which, n = 0 and n = 1 relate to MRDP models and DRMP models respectively. Apart from the helical regions, where ‘ α 0’ is found to be relatively stable, the sum parameters have been found to be more useful in the analysis of β-turns. The ‘ α 0’ at the second and third residue sites and ‘ α 1’ at the middle peptide plane of the four residue corner is found to offer a numerical triplet code for resolving various β-turn types. Besides these, an additional parameter introduced under the DRMP model is a virtual torsion angle ‘ σ 1’ involving C i−1 β ⋯ C′ i−1 − N i ⋯ C i β , which is expected to reflect the effect of interaction of the side chain atoms. The σ 1, α 1 pair is found to play a role parallel to φ, ψ at a given residue site. Various combinations of the sum and difference parameters, as two dimensional plots, like the α 0 vs β 0, α 0 vs α 1 and σ 1 vs α 1 bring out the conformational features related to secondary structures of proteins.

β-turn topography

The topography of the β-turn was investigated using 146 examples of β-turns reported in the literature. Common topographical features were observed across a wide variety of β-turn types. Based on this, it was proposed that β-turns could be described in terms of a single dihedral angle, which was defined as β , which provides a complete description of the spatial relationship between the entry and exit peptide bonds as well as the relative orientations of the intervening sidechains for any β-turn. This simplification was made possible by the reduction of the β-turn structure into two conformationally invariant units, the median geometries of which are reported herein. This description should prove particularly useful in the development and application of novel peptide mimetic drugs, compounds for which a classification based on a peptide backbone geometry may be entirely irrelevant.