Structural versatility of peptides from Cα, α-disubstituted glycines: Crystal-state conformational analysis of homopeptides from Cα-methyl,Cα-benzylglycine [(αMe)Phe]n

The molecular and crystal structures of one derivative and three homopeptides (from the di-to the tetrapeptide level) of the chiral, C^{α, α}-disubstituted glycine C^α-methyl, C^α-benzylglycine [(αMe)Phe], have been determined by x-ray diffraction. The derivative is mClAc-D -(αMe)Phe-OH, and the peptides are pBrBz-[D -(αMe)Phe]₂-NHMe, pBrBz-[D -(αMe)Phe]₃-OH hemihydrate, and pBrBz-[D -(αMe)Phe]₄-OtBu sesquihydrate. All (αMe)Phe residues prefer ?,ψ torsion angles in the helical region of the conformational map. The dipeptide methylamide and the tripeptide carboxylic acid adopt a β-turn conformation with a 1 ← 4 C?O…?H? N intramolecular H bond. The structure of the tripeptide carboxylic acid is further stabilized by a 1 ← 4 C?O…?H? O intramolecular H bond, forming an “oxy-analogue” of a β-turn. The tetrapeptide ester is folded in a regular (incipient) 3₁₀-helix. In general, the relationship between (αMe)Phe chirality and helix screw sense is opposite to that exhibited by protein amino acids. A comparison is made with the conclusions extracted from published work on homopeptides from other C^α-methylated α-amino acids. © 1993 John Wiley & Sons, Inc.     

Conformational dependence of vicinal 13C′NCαH coupling constants in peptides: A dirac vector model investigation

Theoretical calculations of the heteronuclear vicinal coupling constant ³J(¹³C′NC^αH) in peptides have been carried out using the Dirac vector model. The results showed an angular dependence for this coupling constant, which can be expressed in the form ³J(¹³C′NC^αH) = A cos² θ + B cos θ + C, where A, B, and C are constants and θ is related to the torsional angle ? of the peptide backbone. The results of the present calculations are in very good agreement with those obtained using finite perturbation theory at the INDO level of approximation.     

Influence of substituents on conformational preferences of helix foldamers of γ‐dipeptides

Conformational preferences of 9‐ and 14‐helix foldamers have been studied for γ‐dipeptides of 2‐aminocyclohexylacetic acid (γAc₆a) residues such as Ac‐(γAc₆a)₂‐NHMe ( 1 ), Ac‐(C^α‐Et‐γAc₆a)₂‐NHMe ( 2 ), Ac‐(γAc₆a)₂‐NHBn ( 3 ), and Ac‐(C^α‐Et‐γAc₆a)₂‐NHBn ( 4 ) at the M06‐2X/cc‐pVTZ//M06‐2X/6‐31 + G(d) level of theory to explore the influence of substituents on their conformational preferences. In the gas phase, the 9‐helix foldamer H9 and 14‐helix foldamer H14‐z are found to be most preferred for dipeptides 2 and 4 , respectively, as for dipeptides 1 and 3 , which indicates no remarkable influence of the C^α‐ethyl substitution on conformational preferences. The benzyl substitution at the C‐terminal end lead H14‐z to be the most preferred conformer for dipeptides 3 and 4 , whereas it is H9 for dipeptides 1 and 2 , which can be ascribed to the favored C? H···π interactions between the cyclohexyl group of the first residue and the C‐terminal benzyl group. There are only marginal changes in backbone structures and the distances and angles of H‐bonds for all local minima by C^α‐ethyl and/or benzyl substitutions. Although vibrational frequencies and intensities of the dipeptide 4 calculated at both M06‐2X/6‐31 + G(d) and M05‐2X/6‐31 + G(d) levels of theory are consistent with observed results in the gas phase, H14‐z is predicted to be most preferred by ΔG only at the former level of theory. Hydration did not bring the significant changes in backbone structures of helix foldamers for both dipeptide 1 and 4 . It is expected that the different substitutions at the C‐terminal end lead to the different helix foldamers, which may increase the resistance of helical structures to proteolysis and provide the more surface to the helical structures suitable for molecular recognition. © 2014 Wiley Periodicals, Inc. Biopolymers 101: 1077–1087, 2014.     

Inversion of 310-helix screw sense in a (D-αMe)Leu homotetrapeptide induced by a guest D-(αMe)val residue

The terminally blocked tetrapeptide pBrBz-[D -(αMe)Leu]₂-D -(αMe)Val-D -(αMe)Leu-OtBu is folded in the crystal state in a left-handed 3₁₀-helical structure stabilized by two consecutive 1 ← 4 C?O ?H? N intramolecular H-bonds, as determined by X-ray diffraction analysis. A CD study strongly supports the view that this conformation is also that largely prevailing in MeOH solution. A comparison with the published conformation of pBrBz-[D -(αMe)Leu]₄-OtBu indicates that incorporation of a single internal β-branched (αMe)Val guest residue into the host homo-tetrapeptide from the γ-branched (αMe)Leu residue is responsible for a dramatic structural perturbation, i.e. an inversion of the 3₁₀ screw sense from right to left-handed.     

Structural versatility of peptides from Cα,α-disubstituted glycines: Preferred conformation of the chiral isovaline residue

The molecular structures of four protected isovaline- (Iva-) containing peptides to the pentamer level have been determined by x-ray diffraction. The peptides are t-Boc-Ala-(S)-Iva-Ala-OMe (t-Boc : tert-butyloxycarbonyl; OMe : methoxy) and its (R)-Iva diastereomer, and t-Boc-[Ala-(R)-Iva]₂-Ala-OH and its (S)-Iva diastereomeric methyl ester analogue. The two tripeptides are folded in an open type II β-bend conformation. The fully developed right-handed 3₁₀-helix formed by the (R)-Iva pentapeptide, which includes an unusual intramolecular (acid) O? H ?O?C(peptide) H bond, is partially unfolded (near the C-terminus) in the (S) -Iva pentapeptide. ¹H-nmr and Fourier transform ir absorption studies suggest that in CDCl₃ solution (a) the two tripeptides maintain a type II β-bend conformation of comparable stability and (b) both diastereomeric pentapeptide sequences adopt a fully developed 3₁₀-helix. A comparison with the preferred conformation of other extensively investigated C^α,α-disubstituted glycines is made and the implications for the use of the Iva residue in designing conformationally constrained analogues of bioactive peptides are briefly discussed.     

ω‐Turn: A novel β‐turn mimic in globular proteins stabilized by main‐chain to side‐chain CH···O interaction

Mimicry of structural motifs is a common feature in proteins. The 10‐membered hydrogen‐bonded ring involving the main‐chain C?O in a β‐turn can be formed using a side‐chain carbonyl group leading to Asx‐turn. We show that the N? H component of hydrogen bond can be replaced by a C^γ‐H group in the side chain, culminating in a nonconventional C? H···O interaction. Because of its shape this β‐turn mimic is designated as ω‐turn, which is found to occur ～three times per 100 residues. Three residues (i to i + 2) constitute the turn with the C? H···O interaction occurring between the terminal residues, constraining the torsion angles ?_{i + 1}, ψ_{i + 1}, ?_{i + 2} and χ′_{1(i + 2)} (using the interacting C^γ atom). Based on these angles there are two types of ω‐turns, each of which can be further divided into two groups. C^β‐branched side‐chains, and Met and Gln have high propensities to occur at i + 2; for the last two residues the carbonyl oxygen may participate in an additional interaction involving the S and amino group, respectively. With Cys occupying the i + 1 position, such turns are found in the metal‐binding sites. N‐linked glycosylation occurs at the consensus pattern Asn‐Xaa‐Ser/Thr; with Thr at i + 2, the sequence can adopt the secondary structure of a ω‐turn, which may be the recognition site for protein modification. Location between two β‐strands is the most common occurrence in protein tertiary structure, and being generally exposed ω‐turn may constitute the antigenic determinant site. It is a stable scaffold and may be used in protein engineering and peptide design. Proteins 2015; 83:203–214. © 2014 Wiley Periodicals, Inc.     

Synthesis,and crystal and molecular structure of the 310-helical α,β-dehydro pentapeptide Boc-Leu-Phe-Ala-ΔPhe-Leu-Ome

α,β-Dehydro amino acid residues are known to constrain the peptide backbone to the β-bend conformation. A pentapeptide containing only one α,β dehydrophenylalanine (ΔPhe) residue has been synthesized and crystallized, and its solid state conformation has been determined. The pentapeptide Boc-Leu-Phe-Ala-ΔPhe-Leu-OMe (C₃₉H₅₅N₅O₈, M_w = 721.9) was crystallized from aqueous methanol. Monoclinic space group was P2₁, a = 10.290(2)°, b = 17.149(2)°, c = 12.179(2) Å, β = 96.64(1)° with two molecules in the unit cell. The x-ray (Mo K_α, λ = 0.7107A) intensity data were collected using a CAD4 diffractometer. The crystal structure was determined by direct methods and refined using least-squares technique. R = 4.4% and R_w = 5.4% for 4403 reflections having |F₀| ≥ 3σ(|F₀|). All the peptide links are trans and the pentapeptide molecule assumes 3₁₀-helical conformation. The mean ?,ψ values, averaged over the first four residues, are ?64.4°, ?22.4° respectively. There are three 4 → 1 intramolecular hydrogen bonds, characteristic of 3₁₀,-helix. In the crystal, the peptide helices interact through two head-to-tail. N? H? O intermolecular hydrogen bonds. The peptide molecules related by 2₁, screw symmetry form a skewed assembly of helices. © 1995 John Wiley & Sons, Inc.     

The β association of (DLLys)10–(LVal)20–(DLLys)10: An nmr study

(DL Lys)₁₀–(L Val)₂₀–(DL Lys)₁₀, a copolymer of a valine block in the β conformation with randomly coiled flanking blocks of lysine [Kubota, S. & Fasman, G. D. (1975) Biopolymers 14 , 605–631], was studied by nuclear magnetic resonance. The peak areas of the N? H and C? H resonances of valine and lysine are concentration-dependent with little chemical shift change. A model is presented describing the aggregation of the copolymer. Additional evidence, obtained by monitoring the spin-lattice relaxation times of amino, amide, γ-methyl-valine, and ?-methylene-lysine, is consistent with the aggregation model. Hydrodynamic studies are presented which show monomer → oligomer aggregation of four or five subunits.     

An NMR investigation of putative interresidue H-bonding in methyl α-cellobioside in solution

Methyl α-cellobioside (methyl β-d-glucopyranosyl-(1→4)-α-d-glucopyranoside) was labeled with ¹³C at C4′ for use in NMR studies in DMSO-d₆ solvent to attempt the detection of a trans-H-bond J-coupling (^3hJ_CCOH) between C4′ and OH3. Analysis of the OH3 signal at 600 MHz revealed only the presence of two homonuclear J-couplings: ³J_H3,OH3 and a smaller, longer range J_HH. No evidence for ^3hJ_C4′,OH3 was found. The longer range J_HH was traced to ⁴J_H4,OH3 based on 2D ¹H–¹H COSY data and inspection of the H2 and H4 signal lineshapes. A limited set of DFT calculations was performed on a methyl cellobioside mimic to evaluate the structural dependencies of ⁴J_H2,O3H and ⁴J_H4,O3H on the H3–C3–O3–H torsion angle. Computed couplings range from about −0.7 to about +1.1 Hz, with maximal values observed when the C–H and O–H bonds are roughly diaxial.     

Crystallographic characterization of the α,γ C12 helix in hybrid peptide sequences

The solid‐state conformations of two αγ hybrid peptides Boc‐[Aib‐γ⁴(R)Ile]₄‐OMe 1 and Boc‐[Aib‐γ⁴(R)Ile]₅‐OMe 2 are described. Peptides 1 and 2 adopt C₁₂‐helical conformations in crystals. The structure of octapeptide 1 is stabilized by six intramolecular 4 → 1 hydrogen bonds, forming 12 atom C₁₂ motifs. The structure of peptide 2 reveals the formation of eight successive C₁₂ hydrogen‐bonded turns. Average backbone dihedral angles for αγ C₁₂ helices are peptide 1 , Aib; φ (°) = ?57.2 ± 0.8, ψ (°) = ?44.5 ± 4.7; γ⁴(R)Ile; φ (°) = ?127.3 ± 7.3, θ₁ (°) = 58.5 ± 12.1, θ₂ (°) = 67.6 ± 10.1, ψ (°) = ?126.2 ± 16.1; peptide 2 , Aib; φ (°) = ?58.8 ± 5.1, ψ (°) = ?40.3 ± 5.5; ψ⁴(R)Ile; φ (°) = ?123.9 ± 2.7, θ₁ (°) = 53.3 θ 4.9, θ ₂ (°) = 61.2 ± 1.6, ψ (°) = ?121.8 ± 5.1. The tendency of γ⁴‐substituted residues to adopt gauche–gauche conformations about the C^α–C^β and C^β–C^γ bonds facilitates helical folding. The αγ C₁₂ helix is a backbone expanded analog of α peptide 3₁₀ helix. The hydrogen bond parameters for α peptide 3₁₀ and α‐helices are compared with those for αγ hybrid C₁₂ helix. Copyright © 2016 European Peptide Society and John Wiley & Sons.     

The conformational properties of α,β‐dehydroamino acids with a C‐terminal ester group

α,β‐Dehydroamino acid esters occur in nature. To investigate their conformational properties, a systematic theoretical analysis was performed on the model molecules Ac‐ΔXaa‐OMe [ΔXaa = ΔAla, (E)‐ΔAbu, (Z)‐ΔAbu, ΔVal] at the B3LYP/6‐311+ + G(d,p) level in the gas phase as well as in chloroform and water solutions with the self‐consistent reaction field‐polarisable continuum model method. The Fourier transform IR spectra in CCl₄ and CHCl₃ have been analysed as well as the analogous solid state conformations drawn from The Cambridge Structural Database. The ΔAla residue has a considerable tendency to adopt planar conformations C5 (?, ψ ≈ ? 180°, 180°) and β2 (?, ψ ≈ ? 180°, 0°), regardless of the environment. The ΔVal residue prefers the conformation β2 (?, ψ ≈ ? 120°, 0°) in a low polar environment, but the conformations α (?, ψ ≈ ? 55°, 35°) and β (?, ψ ≈ ? 55°, 145°) when the polarity increases. The ΔAbu residues reveal intermediate properties, but their conformational dispositions depend on configuration of the side chain of residue: (E)‐ΔAbu is similar to ΔAla, whereas (Z)‐ΔAbu to ΔVal. Results indicate that the low‐energy conformation β2 is the characteristic feature of dehydroamino acid esters. The studied molecules constitute conformational patterns for dehydroamino acid esters with various side chain substituents in either or both Z and E positions. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

Helix–coil transition in poly(γ-benzyl-L-glutamate) and poly-ε-carbobenzoxy-L-lysine

In this paper two points are considered: the methods of evaluating the helical content θ and the calculation of the parameters of the transition from experimental data and its interpretation. The parameter ΔH obtained is in good agreement with the calorimetric one and v is found to be independent of temperature and solvent and in agreement with the ordinarily accepted value for poly(γ-benzyl-L -glutamate). The different methods of estimating θ are discussed for both polypeptides.     

Structural versatility of peptides from Cα,αdialkylated glycines: Linear Ac3c homo-oligopeptides

The crystal-state molecular structures of five linear Ac₃c homo-oligopeptides to the tetramer were determined by x-ray diffraction. The oligomers are H-(Ac₃c)₂-OMe, Fmoc-(Ac₃c)₂-OMe MeOH, Ac-(Ac₃c)₂-OMe, pBrBz-(Ac₃c)₃-OMe · H₂O, and t-Boc-(Ac₃c)₄-OMe · 2H₂O. The results indicate the propensity of the tri- and tetrapeptides to fold into type I β-bends and distorted 3₁₀-helices, respectively, in partial contrast to Aib, Ac₅c, and Ac₆c homo-peptides of comparable main-chain length, where regular type III β-bends and 3₁₀-helical structures were found. When the influence of the constraints produced by the intramolecular H bonds of the C₁₀-type is absent, other less common structural features may be observed. The average geometry of the cyclopropyl group of the Ac₃c residue is found to be asymmetric and the N? C^α? C′ bond angle significantly expanded from the regular tetrahedral value.     

Rational design of amyloid β peptide–binding proteins: Pseudo‐Aβ β‐sheet surface presented in green fluorescent protein binds tightly and preferentially to structured Aβ

Some neurodegenerative diseases such as Alzheimer disease (AD) and Parkinson disease are caused by protein misfolding. In AD, amyloid β‐peptide (Aβ) is thought to be a toxic agent by self‐assembling into a variety of aggregates involving soluble oligomeric intermediates and amyloid fibrils. Here, we have designed several green fluorescent protein (GFP) variants that contain pseudo‐Aβ β‐sheet surfaces and evaluated their abilities to bind to Aβ and inhibit Aβ oligomerization. Two GFP variants P13H and AP93Q bound tightly to Aβ, K_d = 260 nM and K_d = 420 nM, respectively. Moreover, P13H and AP93Q were capable of efficiently suppressing the generation of toxic Aβ oligomers as shown by a cell viability assay. By combining the P13H and AP93Q mutations, a super variant SFAB4 comprising four strands of Aβ‐derived sequences was designed and bound more tightly to Aβ (K_d = 100 nM) than those having only two pseudo‐Aβ strands. The SFAB4 protein preferentially recognized the soluble oligomeric intermediates of Aβ more than both unstructured monomer and mature amyloid fibrils. Thus, the design strategy for embedding pseudo‐Aβ β‐sheet structures onto a protein surface arranged in the β‐barrel structure is useful to construct molecules capable of binding tightly to Aβ and inhibiting its aggregation. This strategy may provide implication for the diagnostic and therapeutic development in the treatment of AD. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Conformations of peptides containing a chiral cyclic α, α‐disubstituted α‐amino acid within the sequence of Aib residues

A single chiral cyclic α,α‐disubstituted amino acid, (3S,4S)‐1‐amino‐(3,4‐dimethoxy)cyclopentanecarboxylic acid [(S,S)‐Ac₅c^dOM], was placed at the N‐terminal or C‐terminal positions of achiral α‐aminoisobutyric acid (Aib) peptide segments. The IR and ¹H NMR spectra indicated that the dominant conformations of two peptides Cbz‐[(S,S)‐Ac₅c^dOM]‐(Aib)₄‐OEt ( 1) and Cbz‐(Aib)₄‐[(S,S)‐Ac₅c^dOM]‐OMe (2) in solution were helical structures. X‐ray crystallographic analysis of 1 and 2 revealed that a left‐handed (M) 3₁₀‐helical structure was present in 1 and that a right‐handed (P) 3₁₀‐helical structure was present in 2 in their crystalline states. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.     

Type II β-turn conformation of pivaloyl-L-prolyl-α-aminoisobutyryl-N-methylamide: Theoretical,spectroscopic, and X-ray studies

Pivaloyl-L -Pro-Aib-N-methylamide has been shown to possess one intramolecular hydrogen bond in (CD₃)₂SO solution, by ¹H-nmr methods, suggesting the existence of β-turns, with Pro-Aib as the corner residues. Theoretical conformational analysis suggests that Type II β-turn conformations are about 2 kcal mol^?1 more stable than Type III structures. A crystallographic study has established the Type II β-turn in the solid state. The molecule crystallizes in the space group P2₁ with a = 5.865 Å, b = 11.421 Å, c = 12.966 Å, β = 97.55°, and Z = 2. The structure has been refined to a final R value of 0.061. The Type II β-turn conformation is stabilized by an intramolecular 4 → 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are ?_Pro = ?57.8°, ψ_Pro = 139.3°, ?_Aib = 61.4°, and ψ_Aib = 25.1°. The Type II β-turn conformation for Pro-Aib in this peptide is compared with the Type III structures observed for the same segment in larger peptides.     

Design of Peptides Using α,β-Dehydro-residues: Synthesis,Crystal Structure and Molecular Conformation of N-Boc-L-Val-ΔPhe–ΔPhe-L-Ala-OCH3

To obtain general rules of peptide design using α,β-dehydro-residues, a sequence with two consecutive ΔPhe-residues, Boc-L -Val-ΔPhe–ΔPhe- L -Ala-OCH₃, was synthesized by azlactone method in solution phase. The peptide was crystallized from its solution in an acetone/water mixture (70:30) in space group P6₁ with a=b=14.912(3) Å, c= 25.548(5) Å, V=4912.0(6) ų. The structure was determined by direct methods and refined by a full matrix least-squares procedure to an R value of 0.079 for 2891 observed [I?3σ(I)] reflections. The backbone torsion angles ?₁=?54(1)°, ψ₁= 129(1)°, ω₁=?177(1)°, ?₂ =57(1)°, ψ₂=15(1)°, ω₂ =?170(1)°, ?₃=80(1)°, ψ₃ =7(2)°, ω₃=?177(1)°, ?₄ =?108(1)° and ψ^T₄=?34 (1)° suggest that the peptide adopts a folded conformation with two overlapping β-turns of types II and III′. These turns are stabilized by two intramolecular hydrogen bonds between the CO of the Boc group and the NH of ΔPhe³ and the CO of Val¹ and the NH of Ala⁴. The torsion angles of ΔPhe² and ΔPhe³ side chains are similar and indicate that the two ΔPhe residues are essentially planar. The folded molecules form head-to- tail intermolecular hydrogen bonds giving rise to continuous helical columns which run parallel to the c-axis. This structure established the formation of two β-turns of types II and III′ respectively for sequences containing two consecutive ΔPhe residues at (i+2) and (i+3) positions with a branched β-carbon residue at one end of the tetrapeptide.     

Vibrational analysis of peptides,polypeptides, and proteins. XVIII. Conformational sensitivity of the α-helix spectrum: αI- and αII-Poly(L-alanine)

The α_II-helix (? = ?70.47°, ψ = ?35.75°) is a structure having the same n and h as the (standard) α_I-helix (? = ?57.37°, ψ = ?47.49°). Its conformational angles are commonly found in proteins. Using an improved α-helix force field, we have compared the vibrational frequencies of these two structures. Despite the small conformational differences, there are significant predicted differences in frequencies, particularly in the amide A, amide I, and amide II bands, and in the conformation-sensitive region below 900 cm^?1. This analysis indicates that α_II-helices are likely to be present in bacteriorhodopsin [Krimm, S. & Dwivedi, A. M. (1982) Science 216 , 407–408].     

Vibrational and chiroptical spectroscopic characterization of γ‐turn model cyclic tetrapeptides containing two β‐Ala residues

The optical spectroscopic characterization of γ‐turns in solution is uncertain and their distinction from β‐turns is often difficult. This work reports systematic ECD and vibrational circular dichroism (VCD) spectroscopic studies on γ‐turn model cyclic tetrapeptides cyclo(Ala‐β‐Ala‐Pro‐β‐Ala) ( 1 ), cyclo(Pro‐β‐Ala‐Pro‐β‐Ala) ( 2 ) and cyclo(Ala‐β‐Ala‐Ala‐β‐Ala) ( 3 ). Conformational analysis performed at the 6‐31G(d)/B3LYP level of theory using an adequate PCM solvent model predicted one predominant conformer for 1‐3 , featuring two inverse γ‐turns. The ECD spectra in ACN of 1 and 2 are characterized by a negative n→π* band near 230 nm and a positive π→π* band below 200 nm with a long wavelength shoulder. The ECD spectra in TFE of 1‐3 show similar spectra with blue‐shifted bands. The VCD spectra in ACN‐d₃ of 1 and 2 show a +/?/+/? amide I sign pattern resulting from four uncoupled vibrations in the case of 1 and a sequence of two positive couplets in the case of 2 . A ?/+/+/? amide I VCD pattern was measured for 3 in TFE‐d₂. All three peptides give a positive couplet or couplet‐like feature (+/?) in the amide II region. VCD spectroscopy, in agreement with theoretical calculations revealed that low frequency amide I vibrations (at ～1630 cm^?1 or below) are indicative of a C₇ H‐bonded inverse γ‐turns with Pro in position 2, while γ‐turns encompassing Ala absorb at higher frequency (above 1645 cm^?1). Chirality, 2010. © 2010 Wiley‐Liss, Inc.