Association studies of N-acetyl-amino acid N,N-dimethylamides in carbon tetrachloride

The self-association of N-acetylglycine N,N-dimethylamide, N-acetyl-L -valine N,N-dimethylamide, and N-acetyl-L -phenylalanine N,N-dimethylamide in carbon tetrachloride was investigated by using ir and ¹H-nmr methods. It was concluded from ir measurements that the associated species is the dimer formed as a result of the simultaneous formation of two intermolecular hydrogen bonds. This is supported by the results of ¹H-nmr measurements. Thermodynamic quantities for the association were determined from the temperature and concentration dependence of the NH proton chemical shifts of the sample solutions. Compared with the Gly derivative, L -Val and L -Phe derivatives have larger values of ?ΔH for association, which shows good correlation with Δv_NH values, the difference between the maxima of the monomer and dimer bands, obtained from ir spectra. This is due to the less stable monomer conformation and to the stronger intermolecular hydrogen bonding of the dimers in L -Val and L -Phe derivatives. The line shapes of both methyl proton resonances of L -Val residue and methylene proton resonances of L -Phe residue were found to vary with concentration and temperature of the sample solutions. These data indicate that the rotation about the C^α—C^β bond is restricted by the steric hindrance present in the associated dimers. All these experimental results can be related to the fact that L -Val and L -Phe derivatives have a warped framework because of the bulky side chains, whereas the Gly derivative has a planar framework.     

Purification and Characterization of a Co(II)-Sensitive α-Mannosidase from Ginkgo biloba Seeds

An α-mannosidase was purified from developing Ginkgo biloba seeds to apparently homogeneity. The molecular weight of the purified α-mannosidase was estimated to be 120 kDa by SDS–PAGE in the presence of 2-mercaptoethanol, and 340 kDa by gel filtration, indicating that Ginkgo α-mannosidase may function in oligomeric structures in the plant cell. The N-terminal amino acid sequence of the purified enzyme was Ala–Phe–Met–Lys–Tyr–X–Thr–Thr–Gly–Gly–Pro–Val–Ala–Gly–Lys–Ile–Asn–Val–His–Leu–. The α-mannosidase activity for Man₅GlcNAc₁ was enhanced by the addition of Co²⁺, but the addition of Zn²⁺, Ca²⁺, or EDTA did not show any significant effect. In the presence of cobalt ions, the hydrolysis rate for pyridylaminated Man₆GlcNAc₁ was significantly faster than that for pyridylaminated Man₆GlcNAc₂, suggesting the possibility that this enzyme is involved in the degradation of free N-glycans occurring in developing plant cells (Kimura, Y., and Matsuo, S., J. Biochem., 127, 1013–1019 (2000)). To our knowledge, this is the first report showing that plant cells contain an α-mannosidase, which is activated by Co²⁺ and prefers the oligomannose type free N-glycans bearing only one GlcNAc residue as substrate.     

1H-N.m.r. and c.d. investigation of the histidine side chain conformation in small peptides

Three series of model peptides containing histidine have been examined by ¹H-n.m.r. and c.d. spectroscopy: X-His peptides with X = Gly, Ala, Leu; His-X peptides with X = Gly, Ala, Leu, Ser, Lys, Phe, Tyr; and Pro-His-X peptides with X = Gly; Ala; Leu; Val; Phe; Tyr, C.d. spectra were obtained for pH values between 1 and 11 to give titration curves [θ] vs. pH; ¹H-n.m.r. spectra were recorded at four selected pH values corresponding to defined ionic species. ¹H-n.m.r. spectra in Me₂SO of the NH₃⁺, Imid⁺, COO^? ionic state (pH 4.5) were also obtained. The histidine side chain conformation in the various peptides and the changing ionic states is reflected in the ³J_αβ,β′ coupling constants, the Δδ ββ′ anisochrony values and the c.d. histidine chromophore contribution at 215 nm, and qualitative and semiquantitative correlations can be established between these parameters. Whereas the histidine side chain conformation is quite different in each of the three series, and varies with the ionic state and environment, it is practically identical for each peptide within a series: the nature of the X-residue does not exert any influence on the histidine side chain conformational behaviour. Thus, the classical rotamer distribution R I > R II > R III which is due to steric factors is usually observed unless specific intramolecular interactions such as hydrogen or ionic bonds override these.     

Kinetics and Mechanism of the Peptide Synthesis in Solution

The kinetics of the reaction of Boc-Xaa fluorophenyl esters (where Xaa = Ala, Val, Phe, Ser, Leu, Gly, Met, Pro, or Ile) with leucinamide was studied in order to measure changes in fluorescence emission at 375 nm of the fluorophenyl chromophore accompanying the reaction. It was found that the experimental kinetic data could not be described by a simple scheme of the second order reaction. Measurements of the kinetic parameters of the reaction at various initial concentrations of reagents indicated that the reaction rate can be expressed as: = kC _N ^a C _AE ^b , where k is the reaction rate constant, C _N is the concentration of leucinamide, and C _AE is the concentration of fluorophenyl ester. The a and b reaction orders were close to 1/2 and 3/2 for Xaa = Ala, Val, Phe, Ser, or Leu, 1/2 and 1 for Gly, Met, or Pro, and 1 and 2 for Ile. The experimental equations for the reaction rate can theoretically be derived from a single scheme of chain reactions with various deactivation ways for active intermediates.     

Further studies on the antiviral activity of alloferon and its analogues

The subject of our studies was the synthesis, biological evaluation, and conformational studies of insect tridecapeptide alloferon (H‐His‐Gly‐Val‐Ser‐Gly‐His‐Gly‐Gln‐His‐Gly‐Val‐His‐Gly‐OH) and its analogues such as: [des‐His¹]‐, [Lys¹]‐, [Arg¹]‐, and [Ala¹]‐alloferon. These peptides were synthesized to check the influence of the His residue at position 1 of the alloferon chain on its antiviral activity. Two aspects of the biological effects of these peptides were determined: (i) the cytotoxicity in vitro in the Vero, LLC‐MK2, and HEp‐2 cell lines, and (ii) the antiviral activity in vitro in respect to DNA and RNA viruses. We found that alloferon inhibited the herpes virus multiplication and failed to affect the coxsackie virus replication, whereas [Lys¹]‐alloferon exhibited a high inhibitory action towards both viruses. Moreover, the peptides did not show any cytotoxic activity against the Vero, LLC‐MK2, and HEp‐2 cells. The preliminary circular dichroism conformational studies showed that the peptides investigated seem to prefer an unordered conformation. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

Cation-binding cyclic peptides with lipophilic tails

We have synthesized and characterized a series of cation-binding cyclic octapeptides which may function as potential ionophoric substances. The materials contain varying degrees of hydrophobic character, which was controlled systematically through the incorporation of N-alkylglycine residues where N-alkyl = methyl, n-hexyl, cyclohexyl, or n-decyl. The peptides reported include cyclo(Phe-Sar-Gly-Sar)₂, cyclo(Glu(OBzl)-Sar-Gly-Sar-Glu(OBzl)-Sar-Gly-(N-decyl)Gly), cyclo(Glu(OBzl)-Sar-Gly-(N-decyl)Gly)₂, cyclo(Glu(OBzl)-Sar-Gly-(N-hexyl)Gly)₂, cyclo(Glu(OBzl)-Sar-Gly-(N-cyclohexyl)Gly)₂, and the corresponding free diacid forms of the Glu-containing compounds. Using ¹³C- and ¹H-nmr spectra, we demonstrated that the mixture of cis/trans peptide bond-isomer conformers, characteristic of the free-peptide benzyl esters in solution, was converted to unique C₂-symmetric, presumably all-trans conformers on complexation with calcium ions. Cation-transport experiments, using the thick-liquid model of transport in a Pressman cell, established that these compounds transport a variety of cations and that one peptide examined in detail, cyclo(Glu(OBzl)-Sar-Gly-(N-decyl)Gly)₂ (selectivity Ca²⁺ > Na⁺ > K⁺ > Mn²⁺ > Cu²⁺ > Mg²⁺ > Co²⁺ > Zn²⁺), transports calcium about an order of magnitude more efficiently than magnesium.     

Influence of local interactions on protein structure. IV. Conformational energy studies of N-acetyl-N′-mehylamides of Ser-X- and X-Ser dipeptides

Conformational energy calculations using an empirical conformatinol energy program for peptides (ECEPP) werer carried out on 16 N-acetyl-N′-methylamides of Ser-X and X- Ser dipeptides, where X = Ala, Asn, Asn, Asp, Gly, Phe, Ser, Thr, and Val, and on Pro-Ser. As with the other dipeptides studied in this serites, intraresidue interactions found to dominate over interresidue interactions in determining conformational properties. The Ser-containing dipeptides (except for those with a pro or Gly residue) were found to have unusually low calculated bend probailities, in disagreement observations on proteins; this discrepancy probably arises becuse of sovent effects (not included in the computations). The Ser-X dipeptides were calculated to have a lower preference for bends than the X-Ser dipeptides.     

Influence of local interactions on protein structure. II. Conformational energy studies of N-acetyl-N′-methylamides of Ala-X and X-Ala dipeptides

Conformational energy calculations using an empirical conformational energy program for peptides (ECEPP) were carried out on 17 N-acetyl-N′-methylamides of Ala-X and X-Ala dipeptides, Where X = Ala, Asn, Asp, Gly, Phe, Ser, Tyr, Val, and Pro. Each dipeptide was found to have many low-energly minima, some of which corresponded to bend structures. The stability of bends was found to depend on the amino acid composition and sequence, with the Ala-X dipeptide generally favoring bends more than the X-Ala dipeptide for a particular X. In bends and nonbends alike, intraresidue interactions dominate over interresidue interactions in determining conformational propeties. The calcutions were shown to be in good agreement with available experimental data.     

Toward engineering efficient peptidomimetics. Screening conformational landscape of two modified dehydroaminoacids

Effective peptidomimetics should posses structural rigidity and appropriate interaction pattern leading to potential spatial and electronic matching to the target receptor site. Rational design of such small bioactive molecules could push chemical synthesis and molecular modeling toward faster progress in medicinal chemistry. Conformational properties of N‐t‐butoxycarbonyl‐glycine‐(E/Z)‐dehydrophenylalanine N′,N′‐dimethylamides (Boc‐Gly‐(E/Z)‐ΔPhe‐NMe₂) in chloroform were studied by NMR and IR spectroscopy. The experimental findings were supported by extensive calculations at DFT(B3LYP, M06‐2X) and MP2 levels of theory and the β‐turn tendency for both isomers of the studied dipeptide were determined in vacuum and in solution. The theoretical data and experimental IR results were used as an additional information for the NMR‐based determination of the detailed solution conformations of the peptides. The obtained results reveal that N‐methylation of C‐terminal amide group changes dramatically the conformational properties of studied dehydropeptides. Theoretical conformational analysis reveals that the tendency to adopt β‐turn conformations is much weaker for the N‐methylated Z isomer (Boc‐Gly‐(Z)‐ΔPhe‐NMe₂), both in vacuum and in polar environment. On the contrary, N‐methylated E isomer (Boc‐Gly‐(E)‐ΔPhe‐NMe₂) can easily adopt β‐turn conformation, but the backbone torsion angles (φ₁, ψ₁, φ₂, ψ₂) are off the limits for common β‐turn types. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 28–40, 2014.     

Quantification of hydroxyl radical-derived oxidation products in peptides containing glycine, alanine, valine, and proline

Proteins are a major target for oxidation due to their abundance and high reactivity. Despite extensive investigation over many years, only limited quantitative data exist on the contributions of different pathways to the oxidation of peptides and proteins. This study was designed to obtain quantitative data on the nature and yields of oxidation products (alcohols, carbonyls, hydroperoxides, fragment species) formed by a prototypic oxidant system (HO^?/O₂) on small peptides of limited, but known, amino acid composition. Peptides composed of Gly, Ala, Val, and Pro were examined with particular emphasis on the peptide Val-Gly-Val-Ala-Pro-Gly, a repeat motif in elastin with chemotactic activity and metalloproteinase regulation properties. The data obtained indicate that hydroperoxide formation occurs nonrandomly (Pro > Val > Ala > Gly) with this inversely related to carbonyl yields (both peptide-bound and released). Multiple alcohols are generated at both side-chain and backbone sites. Backbone fragmentation has been characterized at multiple positions, with sites adjacent to Pro residues being of major importance. Summation of the product concentrations provides clear evidence for the occurrence of chain reactions in peptides exposed to HO^?/O₂, with the overall product yields exceeding that of the initial HO^? generated.     

Role of Side-Chain Conformational Entropy in Transmembrane Helix Dimerization of Glycophorin A

Dimerization of the transmembrane domain of glycophorin A is mediated by a seven residue motif LIxxGVxxGVxxT through a combination of van der Waals and hydrogen bonding interactions. One of the unusual features of the motif is the large number of β-branched amino acids that may limit the entropic cost of dimerization by restricting side-chain motion in the monomeric transmembrane helix. Deuterium NMR spectroscopy is used to characterize the dynamics of fully deuterated Val80 and Val84, two essential amino acids of the dimerization motif. Deuterium spectra of the glycophorin A transmembrane dimer were obtained using synthetic peptides corresponding to the transmembrane sequence containing either perdeuterated Val80 or Val84. These data were compared with spectra of monomeric glycophorin A peptides deuterated at Val84. In all cases, the deuterium line shapes are characterized by fast methyl group rotation with virtually no motion about the C_α-C_β bond. This is consistent with restriction of the side chain in both the monomer and dimer due to intrahelical packing interactions involving the β-methyl groups, and indicates that there is no energy cost associated with dimerization due to loss of conformational entropy. In contrast, deuterium NMR spectra of Met81 and Val82, in the lipid interface, reflected greater motional averaging and fast exchange between different side-chain conformers.     

Afc can adopt either the fully extended or a turn conformation

Summary We have synthesized by solution methods and fully characterized two sets of terminally protected peptides based on the tricyclic C^α,α-disubstituted glycine Afc. The conformational preferences of the Afc/Gly peptides were examined by FT-IR absorption and¹H NMR techniques, while those of the Afc/TOAC peptides were primarily investigated by using fluorescence spectroscopy. The X-ray diffraction structure of an Afc derivative was also analyzed. The body of solution and crystal-state experimental data conclusively confirms previous findings that the Afc residue may either adopt the fully extended (C₅) or a turn conformation.     

Dimerization effects on coacervation property of an elastin‐derived synthetic peptide (FPGVG)5

Elastin, a core protein of the elastic fibers, exhibits the coacervation (temperature‐dependent reversible association/dissociation) under physiological conditions. Because of this characteristic, elastin and elastin‐derived peptides have been considered to be useful as base materials for developing various biomedical products, skin substitutes, synthetic vascular grafts, and drug delivery systems. Although elastin‐derived polypeptide (Val‐Pro‐Gly‐Val‐Gly)_n also has been known to demonstrate coacervation property, a sufficiently high (VPGVG)_n repetition number (n > 40) is required for coacervation. In the present study, a series of elastin‐derived peptide (Phe‐Pro‐Gly‐Val‐Gly)₅ dimers possessing high coacervation potential were newly developed. These novel dimeric peptides exhibited coacervation at significantly lower concentrations and temperatures than the commonly used elastin‐derived peptide analogs; this result suggests that the coacervation ability of the peptides is enhanced by dimerization. Circular dichroism (CD) measurements indicate that the dimers undergo similar temperature‐dependent and reversible conformational changes when coacervation occurs. The molecular dynamics calculation results reveal that the sheet‐turn‐sheet motif involving a type II β‐turn‐like structure commonly observed among the dimers and caused formation of globular conformation of them. These synthesized peptide dimers may be useful not only as model peptides for structural analysis of elastin and elastin‐derived peptides, but also as base materials for developing various temperature‐sensitive biomedical and industrial products. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.     

The conformational properties of dehydrobutyrine and dehydrovaline: theoretical and solid‐state conformational studies

Dehydrobutyrine is the most naturally occurring dehydroamino acid. It is also the simplest dehydroamino acid having the geometrical isomers E/Z. To investigate its conformational properties, a theoretical analysis was performed on N‐acetyl‐α,β‐dehydrobutyrine N′‐methylamides, Ac‐(E)‐ΔAbu‐NHMe and Ac‐(Z)‐ΔAbu‐NHMe, as well as the dehydrovaline derivative Ac‐ΔVal‐NHMe. The ?, ψ potential energy surfaces and the localised conformers were calculated at the B3LYP/6‐311 + + G(d,p) level of theory both in vacuo and with inclusion of the solvent (chloroform, water) effect (SCRF method). The X‐ray crystal structures of Ac‐(Z)‐ΔAbu‐NHMe and Ac‐ΔVal‐NHMe were determined at 85 and 100 K, respectively. The solid‐state conformational preferences for the studied residues have been analysed and compared with the other related structures. Despite the limitations imposed by the C^α = C^β double bond on the topography of the side chains, the main chains of the studied dehydroamino acids are more flexible than in standard alanine. The studied dehydroamino acids differ in their conformational preferences, which depend on the polarity of the environment. This might be a reason why the nature quite precisely differentiates between ΔVal and each of the ΔAbu isomers, and why, particularly so with the latter, they are used as a conformational tool to influence the biological action of usually small, cyclic dehydropeptides. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.     

Conformational characteristics of polypeptides containing isolated L-proline residues with cis peptide bonds

The conformational characteristics of the peptide sequence X-l-Pro, where X  Gly or l-Ala and the peptide bond joining X and l-Pro is cis, are evaluated. Semi-empirical potential functions are used to estimate the contributions to the conformational energy made by the non-bonded van der Waals' and electrostatic interactions and the intrinsic torsional potentials about the NC^a and C^aC′ bonds. Rotations φ₁ and ψ₁ about the NC^a and C^aC′ bonds in residue X and rotation ψ₂ about the C^aC′ bond in l-Pro are permitted, while the angle of rotation φ₂ about the NC^a bond in l-Pro is fixed at 120 ° by the pyrrolidine ring. The presence of the cis peptide bond connecting X and l-Pro renders the backbone rotations φ₁, ψ₁ in X dependent upon the rotation ψ₂ about the C^aC′ bond in l-Pro. (Interdependence of rotations in neighboring residues joined by a cis peptide bond was previously observed in l-alanine oligomers.) The number of energetically allowed conformations for the Gly and l-Ala residues preceding a cis peptide bond l-Pro residue are found to be substantially reduced from those permitted when the peptide bond is trans or when l-Pro is replaced by an amino acid residue. On the other hand, ψ₂ = 100 to 160 ° (cis′) and 300 to 0 ° (trans′) are found to be the lowest energy conformations of the l-Pro residue irrespective of the cis or trans conformation of the X-l-Pro peptide bond.     

Experimental conformational study of two peptides containing α-aminoisobutyric acid. Crystal structure of N-acetyl-α-aminoisobutyric acid methylamide

Some theoretical studies have predicted that the conformational freedom of the α-aminoisobutyric acid (H-Aib-OH) residue is restricted to the α-helical region of the Ramachandran map. In order to obtain conformational experimental data, two model peptide derivatives, MeCO-Aib-NHMe 1 and Bu^tCO-LPro-Aib-NHMe 2 , have been investigated. The Aib dipeptide 1 crystallizes in the monoclinic system (a = 12.71 Å, b = 10.19 Å, c = 7.29 Å, β = 110.02°, Cc space group) and its crystal structure was elucidated by x-ray diffraction analysis. The azimuthal angles depicting the molecular conformation (? = ?55.5°, ψ = ?39.3°) fall in the α-helical region of the Ramachandran map and molecules are hydrogen-bonded in a three-dimensional network. In CCl₄ solution, ir spectroscopy provides evidence for the occurrence of the so-called ₅ and C₇ conformers stabilized by the intramolecular i → i and i + 2 → i hydrogen bonds, respectively. The tripeptide 2 was studied in various solvents [CCl₄, CD₂Cl₂, CDCl₃, (CD₃)₂SO, and D₂O] by ir and pmr spectroscopies. It was shown to accommodate predominantly the βII folded state stabilized by the i + 3 → i hydrogen bond. All these experimental findings indicate that the Aib residue displays the same conformational behavior as the other natural chiral amino acid residues.     

Influence of local interactions on protein structure. III. Conformational energy studies of N-acety-N′-methylamides of Gly-X and X-Gly dipeptides

Conformational energy calculations using an empirical conformational energy program for peptides (ECEPP) were carried out on 20 N-acetyl- N′-methylamides of Gly-X and X-Gly depeptides, where X = Ala, Asn, Asp, Gly, Phe, Ser, Thr, Tyr, Val, and Pro, and also of Leu-Gly. Each depeptde was found to have 25 or more low-energy minima, except Gly-Thr, which had only 11 low-energy minima because of the stable side chian-backbone hydrogen present in all low-energy conformation. As a group, the stble chain-backbone hydrogen bonds present in all low-energy conformations. As a group, the Gly-containing dipeptides were calculated in all low-energy prpensity for formation of bends than the Ala-containing depeptides. The X- Gly dipeptides were calculated to favor bends more than the Gly-X dipeptides, primarlly because of the high stability of the type II bend in X-Gly dipeptides. These results are in agreement with obseved occurrences of bends in the x-ray structures of globular proteins. The calculated conformation properties were found to be in good agreement with experimental results.     

Optical anisotropies of amides and peptides in dioxane

The molar Kerr constants _mK, molar refractions _mR, and dipole moments μ are reported for the N-methylacetamides CX₃CONHCH₃ (X = H, CH₃, F. CI, Br) and acetamides CX₃CONH₂ (X = H, F, Cl, Br). The components of the polarizability tensor α are deduced for N-methylacetamide and acetamide on the basis of the bond additivity approximation. This α is found to be considerably more anisotropic than was indicated in previous determinations by other methods. The data for N-methylacetamide were used to calculate _mK, μ, and γ² (anisotropy squared) of N-acetyl-N′-methylglycine amide and N-acetyl-N′-methyl-alanine amide as functions of the torsional angles (?,Ψ). The statistical mechanical averages of _mK, μ, and γ² were calculated from conformational energies obtained by the methods of Scheraga.     

Influence of local interactions on protein structure. I. Conformational energy studies of N-acetyl-N′-methylamides of pro-X and X-pro dipeptides

Conformational energy calculations using an Empirical Conformational Energy Program for Peptides (ECEPP) were carried out on the N-acetyl-N′-methylamides of Pro-X, where X = Ala, Asn, Asp, Gly, Leu, Phe, Ser, and Val, and of X-Pro, where X = Ala, Asn, Gly, and Pro. The conformational energy was minimized from starting conformations which included all combinations of low-energy single-residue minima and several standard bend structures. It was found that almost all resulting minima are combinations of low-energy single-residue minima, suggesting that intra residue interactions predominate in determining conformation. The calculations also indicate, however, that inter residue interactions can be important. In addition, librational entropy was found to influence the relative stabilities of some minima. Because of the existence of 10–100 low-energy minima for each dipeptide, the normalized statistical weight of an individual minimum rarely exceeds 0.3, suggesting that these dipeptides have considerable conformational flexibility and exist as statistical ensembles of low-energy structures. The propensity of each dipeptide to form bend conformations was calculated, and the results were compared with available experimental data. It was found that bends are favored in Pro-X dipeptides because ?_Pro is fixed by the pyrrolidine ring in a conformation which is frequently found in bends, but that bends are not favored in X-Pro dipeptides because interactions between the X residue and the pyrrolidine ring restrict the X residue to conformations which are not usually found in bends.     

Preferred conformation of peptides from Cα,α-symmetrically disubstituted glycines: Aromatic residues

The conformational preference of C^α,α-diphenylglycinc (Døg) and C^α,α-dibenzylglycine (Dbz) residues was assessed in selected derivatives and small peptides by conformational energy computations, ir absorption, ¹H-nmr, and x-ray diffraction. Conformational energy computations on the two monopeptides strongly support the view that these C^α,α-symmetrically disubstituted glycines are conformationally restricted and that their minimum energy conformation falls in the fully extended (C₅) region. The results of the theoretical analyses appear to be in agreement with the solution and crystal-state structural propensities of three derivatives and seven di-and tripeptides.