Flexibility of "polyunsaturated fatty acid chains" and peptide backbones: A comparative ab initio study

The conformational properties of omega-3 type of polyunsaturated fatty acid (PUFA) chains and their fragments were studied using Hartree-Fock (RHF/3-21G) and DFT (B3LYP/6-31G(d)) methods. Comparisons between a unit (U) fragment of the PUFA chain and a mono N-Ac-glycine-NHMe residue show that both structures have the same sequence of sp2-sp3-sp2 atoms. The flexibility of PUFA originates in the internal rotation about the above pairs of sigma bonds. Therefore, potential energy surfaces (PESs) were generated by a scan around the terminal dihedral angles (phi t1 and phi t2) as well as the phi 1 and psi 1 dihedrals of both 1U congeners (Me-CHCH-CH2-CHCHMe and MeCONH-CH2-CONHMe) at the RHF/3-21G level of theory. An interesting similarity was found in the flexibility between the cis allylic structure and the trans peptide models. A flat landscape can be seen in the cis 1U (hepta-2,5-diene) surface, implying that several conformations are expected to be found in this (PES). An exhaustive search carried out on the 1U and 2U models revealed that straight chain structures such as trans and cis beta (phi 1 approximately psi 1 approximately 120 degrees; phi 2 approximately psi 2 approximately -120 degrees) or trans and cis extended (phi 1 approximately psi 1 approximately phi 2 approximately psi 2 approximately 120 degrees) can be formed at the lowest energy of both isomers. However, forming helical structures, such as trans helix (phi 1 approximately -120 degrees, psi 1 approximately 12 degrees; phi 2 approximately -120 degrees, psi 2 approximately 12 degrees) or cis helix (phi 1 approximately -130 degrees, psi 1 approximately 90 degrees; phi 2 approximately -145 degrees, psi 2 approximately 90 degrees) will require more energy. These six conformations, found in 2U, were selected to construct longer chains such as 3U, 4U, 5U, and 6U to obtain the thermochemistry of secondary structures. The variation in the extension or compression of the chain length turned out to be a factor of 2 between the helical and nonhelical structures. The inside diameter of the "tube" of cis helix turned out to be 3.5 A after discounting the internal H atoms. Thermodynamic functions were computed at the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d). The cis-trans isomerization energy of 1.7 +/- 0.2 kcal mol(-1) unit(-1) for all structure pairs indicates that the conformer selection was consistent. A folding energy of 0.5 +/- 0.1 kcal mol(-1) unit(-1) has been extracted from the energy comparison of the helices and most extended nonhelical structures. The entropy change associated with the folding (Delta S(folding)) is decreases faster with the degree of polymerization (n) for the cis than for the trans isomer. As a consequence, the linear relationships between (Delta G(folding)) and n for the cis and trans isomer crossed at about n = 3. This suggested that the naturally occurring cis isomer less ready to fold than the trans isomer since a greater degree of organization is exhibited by the cis isomer during the folding process. The result of this work leads to the question within the group additivity rule: could the method applied in our study of the folding of polyallylic hydrocarbons be useful in investigating the thermochemistry of protein folding?     

UV Raman spatially resolved melting dynamics of isotopically labeled polyalanyl peptide: slow alpha-helix melting follows 3(10)-helices and pi-bulges premelting

We used UV resonance Raman (UVRR) to examine the spatial dependence of the T-jump secondary structure relaxation of an isotopically labeled 21-residue mainly Ala peptide, AdP. The AdP penultimate Ala residues were perdeuterated, leaving the central residues hydrogenated, to allow separate monitoring of melting of the middle versus the end peptide bonds. For 5 to 30 degrees C T-jumps, the central peptide bonds show a approximately 2-fold slower relaxation time (189 +/- 31 ns) than do the exterior peptide bonds (97 +/- 15 ns). In contrast, for a 20 to 40 degrees C T-jump, the central peptide bond relaxation appears to be faster (56 +/- 6 ns) than that of the penultimate peptide bonds (131 +/- 46 ns). We show that, if the data are modeled as a two-state transition, we find that only exterior peptide bonds show anti-Arrhenius folding behavior; the middle peptide bonds show both normal Arrhenius-like folding and unfolding. This anti-Arrhenius behavior results from the involvement of pi-bulges/helices and 3(10)-helix states in the melting. The unusual temperature dependence of the (un)folding rates of the interior and exterior peptide bonds is due to the different relative (un)folding rates of 3(10)-helices, alpha-helices, and pi-bulges/helices. Pure alpha-helix unfolding rates are approximately 12-fold slower (approximately 1 micros) than that of pi-bulges and 3(10)-helices. In addition, we also find that the alpha-helix is most stable at the AdP N-terminus where eight consecutive Ala occur, whereas the three hydrophilic Arg located in the middle and at the C-terminus destabilize the alpha-helix in these regions and induce defects such as pi-bulges and 3(10)-helices.     

A theoretical study of conformational properties of N-methyl azapeptide derivatives

The conformational properties of azapeptide derivatives, Ac-azaGly-NHMe (1), Ac-azaAla-NHMe (2), Ac-NMe-azaGly-NHMe (3), Ac-NMe-azaAla-NHMe (4), Ac-azaGly-NMe(2) (5), Ac-azaAla-NMe(2) (6), Ac-NMe-azaGly-NMe(2) (7), and Ac-NMe-azaAla-NMe(2) (8), were systematically examined by using ab initio MO and DFT methods. Structural perturbations in azapeptides resulting from cyclic substitution of a methyl group at three N-positions of an azaamino acid were studied on the basis of the structure of the simplest model azapeptide, 1. Potential energy surfaces were generated at the HF/6-31G level for 1-4 and at the HF/6-31G//HF/3-21G level for 5-8 by rotating two key dihedral angles (phi, psi) in increments of 30 degrees. The backbone (phi, psi) angles of the minima for 1-4 are observed at the i + 2 position to form the betaI(I')-, betaII(II')-, betaVI-turns or the polyproline II structure according to the orientation of the acetyl group and the positions of the N-methyl groups. Compounds 5-8 coupled to a secondary amine were found to preferentially adopt polyproline II, betaI(III)-turn, or alpha-helical structure or even extended conformations depending on the orientation of the acetyl group and the positions of the N-methyl groups. Furthermore, N-methyl groups, depending on their positions, were found to affect the orientation of the amide group in the lowest energy conformations, the pyramidality of the N2 atom, and the bond length in azapeptide derivatives. These unique theoretical conformations of N-methyl azapeptide derivatives could be utilized in the definite design of secondary structure for peptides and proteins, and in the development of new drugs and molecular machines.     

Secondary structures of peptides and proteins via NMR chemical-shielding anisotropy (CSA) parameters

Complete nuclear magnetic resonance (NMR) chemical-shielding tensors, sigma, have been computed at different levels of density-functional theory (DFT), within the gauge-including atomic orbital (GIAO) formalism, for the atoms of the peptide model For-L-Ala-NH2 as a function of the backbone dihedral angles phi and psi by employing a dense grid of 10 degrees. A complete set of rigorously orthogonal symmetric tensor invariants, {sigma iso, rho, tau}, is introduced, where sigma iso is the usual isotropic chemical shielding, while the newly introduced rho and tau parameters describe the magnitude and the orientation/shape of the chemical-shielding anisotropy (CSA), respectively. The set {sigma iso, rho, tau} is unaffected by unitary transformations of the symmetric part of the shielding tensor. The mathematically and physically motivated {rho, tau} anisotropy pair is easily connected to more traditional shielding anisotropy measures, like span (Omega) and skew (kappa). The effectiveness of the different partitions of the CSA information in predicting conformations of peptides and proteins has been tested throughout the Ramachandran space by generating theoretical NMR anisotropy surfaces for our For-L-Ala-NH2 model. The CSA surfaces, including Omega(phi, psi), kappa(phi, psi), rho(phi, psi), and tau(phi, psi) are highly structured. Individually, none of these surfaces is able to distinguish unequivocally between the alpha-helix and beta-strand secondary structural types of proteins. However, two- and three-dimensional correlated plots, including Omega versus kappa, rho versus tau, and sigma iso versus rho versus tau, especially for 13Calpha, have considerable promise in distinguishing among all four of the major secondary structural elements.     

Charge transfer in polypeptides: effect of secondary structures on charge-transfer integral and site energies

We have theoretically studied the charge transfer in glycine polypeptide using quantum mechanical models based on a tight-binding Hamiltonian approach. The charge-transfer integrals and site energies involved in the transport of positive charge through the peptide bond in glycine polypeptide have been calculated. The charge-transfer integrals and site energies have been calculated directly from the matrix elements of the Kohn-Sham Hamiltonian defined in terms of the molecular orbitals of the individual fragments of the glycine polypeptide. In addition to this, we have calculated the rate of charge transfer between a neighboring amino acid subgroup through the Marcus rate equation. These calculations have been performed for the different secondary structures of the glycine model peptide such as linear, alpha-helix, 3(10)-helix, and antiparallel beta-sheet by varying the dihedral angles omega, varphi, and psi along the Calpha-carbon of amino acid subgroup. Present theoretical results confirm that the charge transfer through the peptide bond is strongly affected by the conformations of the oligopeptide.     

Alpha-gamma hybrid peptides that contain the conformationally constrained gabapentin residue: characterization of mimetics of chain reversals

The crystal structures of four dipeptides that contain the stereochemically constrained gamma-amino acid residue gabapentin (1-(aminomethyl)cyclohexaneacetic acid Gpn) are described. The molecular conformation of Piv-Pro-Gpn-OH (1), reveals a beta-turn mimetic conformation, stabilized by a ten atom C[bond]H...O hydrogen bond between the Piv CO group and the pro S hydrogen of the Gpn CH(2)[bond]CO group. The peptides Boc-Gly-Gpn-OH (2), Boc-Aib-Gpn-OH (3), and Boc-Aib-Gpn-OMe (4) form compact, folded structures, in which a distinct reversal of polypeptide chain direction is observed. In all cases, the Gpn residue adopts a gauche,gauche (g,g) conformation about the C(gamma)[bond]C(beta) (theta(1)) and C(beta)[bond]C(alpha) (theta(2)) bonds. Two distinct Gpn conformational families are observed. In peptides 1 and 3, the average backbone torsion angle values for the Gpn residue are phi=98 degrees, theta(1)=-62 degrees, theta(2)=-73 degrees, and psi=79 degrees, while in peptide 2 and 4 the average values are phi=-103 degrees, theta(1)=-46 degrees, theta(2)=-49 degrees, and psi=-92 degrees. In the case of 1 and 3, an intramolecular nine-membered O[bond]H...O hydrogen bond is formed between the C[double bond]O of the preceding residue and the terminal carboxylic acid OH group. All four alpha-gamma dipeptide sequences yield compact folded backbone conformations; this suggests that the Gpn residue may be employed successfully in the design of novel folded structures.     

Chirality and helix stability of polyglutamic acid enantiomers

In this work the chirality and the relative thermal stability of ordered micellar aggregates of poly-L- and poly-D-glutamic acids with the cationic surfactant C14TAB is examined. The complexed mesophases poly-L-Glu/C14TAB and poly-d-Glu/C14TAB were characterized by circular dichroism (CD) in the temperature range 10-70 degrees C for their chirality and thermal stability as well as by X-ray diffraction (XRD) for the micellar ordered structure. Low angle XRD analysis showed that both micellar aggregates poly-L-Glu/C14TAB and poly-D-Glu/C14TAB are hexagonally packed in a MCM-41 fashion with an intermicellar distance identical and equal to 3.55+/-0.10 nm. The CD spectra indicated that both complexes poly-L-Glu/C14TAB and poly-D-Glu/C14TAB possess a mainly alpha-helix structure and are exact mirror images to each other. The same mirror images and a mainly alpha-helix configuration were also observed by CD for the free poly-l- and poly-d-glutamic acids at room temperature. As the temperature increases from 10 up to 70 degrees C the alpha-helix of the poly-l-glutamic acid is gradually transformed to a mixture containing increased amounts of the 3(10)-helix while the alpha-helix structure of the poly-d-glutamic acid is constantly degenerated. In contrast the alpha-helices of the corresponding complexes poly-L-Glu/C14TAB and poly-d-Glu/C14TAB are degenerated upon heating without appreciable increase of the 3(10)-helices as an intermediate configuration. This difference in helix conservation is attributed to increase protection of the l-enantiomers, compared to d-enantiomers, which might be related to the survival of l-aminoacids in the living world.     

Aib-rich peptides containing lactam-bridged side chains as models of the 3(10)-helix.

Aib-rich side chain lactam-bridged oligomers with n =1, 2, 3, were designed and synthesized as putative models of the 3(10)-helix. These peptides were conformationally characterized in aqueous solution containing SDS micelles by CD, NMR, and computer simulations. The lactam bridge between the side chains of L-Glu and L-Lys in (i) and (i+3) positions was introduced in order to enhance the conformational preference toward the right-handed 3(10)-helix. The NMR results clearly indicate that there is an increase of 3(10)-helix formation upon chain elongation. In the dimer and trimer (n = 2 and n = 3, respectively, in the structure reported above) the observed NOE connectivities are compatible with the 3(10)-helical arrangement, confirmed by the temperature coefficients of the amide proton resonances which suggest the presence of a hydrogen-bonded structure. The phi and psi dihedral angles of the structures obtained by molecular dynamics calculations are also compatible with the 3(10)-helix. Identification of the hydrogen-bond pattern indicate that C=O(i)- - -HN(i+3) hydrogen bonds, typical of the 3(10)-helical conformation, are highly probable in all low-energy structures. The CD spectra of these Aib-rich lactam-bridged oligopeptides, obtained in the same solvent system used for NMR experiments, provide important insight into the spectroscopic characteristics of the 3(10)-helix.     

Structure determination of a peptide model of the repeated helical domain in Samia cynthia ricini silk fibroin before spinning by a combination of advanced solid-state NMR methods

Fibrous proteins unlike globular proteins, contain repetitive amino acid sequences, giving rise to very regular secondary protein structures. Silk fibroin from a wild silkworm, Samia cynthia ricini, consists of about 100 repeats of alternating polyalanine (poly-Ala) regions of 12-13 residues in length and Gly-rich regions. In this paper, the precise structure of the model peptide, GGAGGGYGGDGG(A)(12)GGAGDGYGAG, which is a typical repeated sequence of the silk fibroin, was determined using a combination of three kinds of solid-state NMR studies; a quantitative use of (13)C CP/MAS NMR chemical shift with conformation-dependent (13)C chemical shift contour plots, 2D spin diffusion (13)C solid-state NMR under off magic angle spinning and rotational echo double resonance. The structure of the model peptide corresponding to the silk fibroin structure before spinning was determined. The torsion angles of the central Ala residue, Ala(19), in the poly-Ala region were determined to be (phi, psi) = (-59 degrees, -48 degrees ) which are values typically associated with alpha-helical structures. However, the torsion angles of the Gly(25) residue adjacent to the C-terminal side of the poly-Ala chain were determined to be (phi, psi) = (-66 degrees, -22 degrees ) and those of Gly(12) and Ala(13) residues at the N-terminal of the poly-Ala chain to be (phi, psi) = (-70 degrees, -30 degrees ). In addition, REDOR experiments indicate that the torsion angles of the two C-terminal Ala residues, Ala(23) and Ala(24), are (phi, psi) = (-66 degrees, -22 degrees ) and those of N-terminal two Ala residues, Ala(13) and Ala(14) are (phi, psi) = (-70 degrees, -30 degrees ). Thus, the local structure of N-terminal and C-terminal residues, and also the neighboring residues of alpha-helical poly-Ala chain in the model peptide is a more strongly wound structure than found in typical alpha-helix structures.     

Preparation and properties of methoxycarbonylsulfenyl isocyanate, CH(3)OC(O)SNCO

Pure methoxycarbonylsulfenyl isocyanate, CH3OC(O)SNCO, is quantitatively prepared by the metathesis reaction between CH3OC(O)SCl and AgNCO. This novel species has been obtained in its pure form and characterized by 1H and 13C NMR, UV-vis, FTIR, and FT-Raman spectroscopy. The conformational properties of the gaseous molecule have been studied by vibrational spectroscopy and quantum chemical calculations (B3LYP and MP2 methods). The compound exhibits a conformational equilibrium at room temperature having the most stable form CS symmetry with the C=O double bond synperiplanar with respect to the S-N single bond. A second form was observed in the IR spectrum and corresponds to a conformer possessing the C-S bond antiperiplanar with respect to the N=C double bond of the isocyanate group. The structure of a single crystal of CH3OC(O)SNCO was determined by X-ray diffraction analysis at low temperature using a miniature zone melting procedure. The crystalline solid (triclinic, P1, a = 8.292(6) A, b = 9.839(7) A, c = 11.865(8) A, alpha = 67.290(2) degrees , beta = 71.5570(10) degrees , gamma = 83.4850(10) degrees and Z = 6) shows the presence of molecules having exclusively a synperiplanar conformation with respect to the three phi(CO-C=O), phi(O=C-SN), and phi(CS-N=C) dihedral angles.     

Onset of 3(10)-helical secondary structure in aib oligopeptides probed by coherent 2D IR spectroscopy

We have investigated the onset of the secondary structure and the evolution of two-dimensional infrared (2D IR) spectral patterns as a function of chain length with a study of 3(10)-helical peptides. The results show that 2D IR is highly sensitive to peptide conformation, disorder, and size. An extensive set of 2D IR spectra of C (alpha)-methylated homopeptides, Z-(Aib) n -O tBu ( n = 3, 5, 8, and 10), in CDCl 3 was measured in the amide-I region. The 2D spectral patterns of the tripeptide are quite different from those of the longer peptides. The spectral signatures begin to converge at the pentapeptide and become almost the same for the octa- and decapeptide. Simulations employing a vibrational exciton model were performed, with the local mode frequency shifts estimated from the intramolecular hydrogen bond electrostatic energies. The 2D spectra are well simulated using dihedral angle distributions around the average values (phi, psi) approximately (-57 degrees , -31 degrees) with a width of approximately 21 degrees. The simulated site-dependent amide-I local mode frequencies are in agreement with those from scaled semiempirical AM1 calculations. The tripeptide exhibits a more noticeable discrepancy between the experimental and simulated cross-peak patterns. This behavior suggests the presence of a peptide population outside the single beta-turn conformation. The onset of the 3(10)-helical secondary structure appears to already occur at the pentapeptide level.     

Free energy surfaces for the alpha(1 --> 4)-glycosidic linkage: implications for polysaccharide solution structure and dynamics

We present a potential of mean force surface for rotation about phi and psi dihedral angles of the alpha(1 --> 4)-glycosidic linkage in the maltose disaccharide (4-O-alpha-d-glucopyranosyl-d-glucopyranose) in aqueous solution. Comparison of the vacuum and solution free energy surfaces for maltose shows the principal effects of water to be an increase in the rotational freedom of the alpha(1 --> 4) linkage brought about by lowering the energy barrier for syn to anti conformational changes as well as expansion of the range of low-energy phi,psi conformations. This free energy analysis thus provides a thermodynamic and conformational rationale for the effects of water on alpha(1 --> 4)-linked polysaccharides and carbohydrate glasses.     

Direct UV Raman monitoring of 3(10)-helix and pi-bulge premelting during alpha-helix unfolding

We used UV resonance Raman (UVRR) spectroscopy exciting at approximately 200 nm within the peptide bond pi --> pi* transitions to selectively study the amide vibrations of peptide bonds during alpha-helix melting. The dependence of the amide frequencies on their Psi Ramachandran angles and hydrogen bonding enables us, for the first time, to experimentally determine the temperature dependence of the peptide bond Psi Ramachandran angle population distribution of a 21-residue mainly alanine peptide. These Psi distributions allow us to easily discriminate between alpha-helix, 3(10)-helix and pi-helix/bulge conformations, obtain their individual melting curves, and estimate the corresponding Zimm and Bragg parameters. A striking finding is that alpha-helix melting is more cooperative and shows a higher melting temperature than previously erroneously observed. These Psi distributions also enable the experimental determination of the Gibbs free energy landscape along the Psi reaction coordinate, which further allows us to estimate the free energy barriers along the AP melting pathway. These results will serve as a benchmark for the numerous untested theoretical studies of protein and peptide folding.     

Structure and photochemistry of nitrocobalt(III) tetraphenylporphyrin with axial triphenylphosphine in toluene solutions

Thermal and photochemical reactions of nitroaquacobalt(III) tetraphenylporphyrin, (NO(2))(H(2)O)Co(III)TPP, have been investigated in toluene solutions containing triphenylphosphine, P phi(3). It is found that Pphi(3) thermally abstracts an oxygen atom from the NO(2) moiety of (NO(2))(H(2)O)Co(III)TPP with a rate constant 0.52 M(-1) s(-1), resulting in the formation of nitrosylcobalt porphyrin, (NO)CoTPP. The 355-nm laser photolysis of (NO(2))(H(2)O)Co(III)TPP at low concentrations of P phi(3) (<1.0 x 10(-4) M) gives Co(II)TPP and NO(2) as intermediates. The recombination reaction of Co(II)TPP and NO(2) initially forms the coordinately unsaturated nitritocobalt(III) tetraphenylporphyrin, (ON-O)Co(III)TPP, which reacts with P phi(3) to yield nitro(triphenylphosphine)cobalt(III) tetraphenylporphyrin, (NO(2))(P phi(3))Co(III)TPP. Subsequently, the substitution reaction of the axial P phi(3) with H(2)O leads to the regeneration of (NO(2))(H(2)O)Co(III)TPP. From the kinetic studies, the substitution reaction is concluded to occur via a coordinately unsaturated nitrocobalt(III) porphyrin, (NO(2))Co(III)TPP. At higher concentrations of P phi(3) (>4 x 10(-3) M), (NO(2))(H(2)O)Co(III)TPP reacts with P phi(3) to form (NO(2))(P phi(3))Co(III)TPP: the equilibrium constant is obtained as K = 4.3. The X-ray structure analysis of (NO(2))(P phi(3))Co(III)TPP reveals that the P-Co-NO(2) bond angle is 175.0(2) degrees and the bond length Co-NO(2) is 2.000(7) A. In toluene solutions of (NO(2))(H(2)O)Co(III)TPP containing P phi(3) (>4 x 10(-3) M), the major light-absorbing species is (NO(2))(P phi(3))Co(III)TPP, which yields (NO)CoTPP by continuous photolysis. The laser photolysis of (NO(2))(P phi(3))Co(III)TPP gives Co(II)TPP, NO(2), and P phi(3) as initial products. The NO(2) molecule is suggested to be reduced by P phi(3) to yield NO, and the reaction between NO and Co(II)TPP gives (NO)CoTPP. The quantum yield for the photodecomposition of (NO(2))(P phi(3))Co(III)TPP is determined as 0.56.     

Conformational analysis of thiopeptides: (ϕ,ψ) maps of thio‐substituted dipeptides

Noncoded amino acids such as isobutyric acid have been used extensively in the process of drug design and protein engineering. This article focuses on a noncoded amino acid where the oxygen in the peptide unit is replaced with a sp² sulfur. It was hypothesized that the conformational space as well as the conformational preferences of thiopeptides will be more restricted and altered by the bulkier atom with different electrostatic properties. In vacuo conformational minima as well as associated energies for the thio‐substituted alanine dipeptides were calculated at the ab initio HF/6‐31G* level. When the bulkier sulfur atom acts as a hydrogen bond acceptor in the C₅ conformation or in the C$^{\mathrm{axial}}_{7}$ and C$^{\mathrm{equatorial}}_{7}$ conformations, the hydrogen bond lengths are much longer than that of normal peptides. Consequently, the ?, ψ dihedral angles of the C₅, C$^{\mathrm{axial}}_{7}$, and C$^{\mathrm{equatorial}}_{7}$ conformations change to accommodate the longer hydrogen bonds. The thiopeptide group is a poorer hydrogen bond acceptor and a better hydrogen bond donor than the normal peptide group. Therefore, thio‐substitution at the amino terminal leads to disfavoring of the C₇ conformations relative to the C₅ conformations and thio‐substitution at the carboxyl terminal leads to favoring of the C₇ conformations relative to the C₅ conformation. To simulate the conformations in solution, (?,ψ) conformational energy maps were calculated for the glycine and alanine dipeptides at various dielectric constants using the CFF91 force field with our previously derived parameters for the thioamide group. The results show that thio‐substitution does restrict the conformations available to amino acids residues in peptides. Thio substitution at the amino terminal introduces unfavorable interactions near ?=?120 and 120, where there are increased overlaps between S_n?1?H_β, and S_n?1?C_β atoms, respectively. Thio substitution at the carboxyl terminal restricts the conformations near ψ=60, ?60, and 180, which correspond with increase overlaps between S_n?C_β, S_n?H_β′ and S_n?N_n atoms, respectively. The effects of dithio substitutions of either the alanine or the glycine dipeptides are similar to the combined effects of the two single thio substitutions. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1026–1037, 2001     

Properties of chloroformyl peroxynitrate, ClC(O)OONO(2)

The synthesis of ClC(O)OONO(2) is accomplished by photolysis of a mixture of Cl(2), NO(2), and CO in large excess of O(2) at about -70 degrees C. The product is isolated after repeated trap-to-trap condensation. The solid compound melts at -84 degrees C, and the extrapolated boiling point is 80 degrees C. ClC(O)OONO(2) is characterized by IR, Raman, (13)C NMR, and UV spectroscopy. According to the IR matrix spectra, the compound exists at room temperature only as a single conformer. The molecular structure of ClC(O)OONO(2) is determined by gas electron diffraction. The molecule possesses a gauche structure with a dihedral angle of phi(COON) = 86.7(19) degrees , and the C=O bond is oriented syn with respect to the O-O bond. The short O-O bond (1.418(6) A) and the long N-O bond (1.511(8) A) are consistent with the facile dissociation of ClC(O)OONO(2) into the radicals ClC(O)OO and NO(2). The experimental geometry of ClC(O)OONO(2) is reproduced reasonably well by B3LYP/6-311+G(2df) calculations, whereas the MP2 approximation predicts the N-O bond considerably too long and the dihedral angle too small.     

The conformation of tetraalanine in water determined by polarized Raman, FT-IR, and VCD spectroscopy

The present article reports the conformation of cationic tetraalanine in aqueous solution. The determination of the dihedral angles of the two central amino acid residues was achieved by analyzing the amide I' band profile in the respective polarized visible Raman, Fourier transform-IR, and vibrational circular dichroism (VCD) spectra by means of a novel algorithm which utilizes the excitonic coupling between the amide I modes of nearest neighbor and second nearest peptide groups. It is an extension of a recently developed theory (Schweitzer-Stenner, R. Biophys. J., 2002, 83, 523-532). UV electronic circular dichroism (ECD) spectra of the peptides were used to validate the results of the structure analysis. The analyses yielded the dihedral angles (phi(12), psi(12)) = (-70 degrees, 155 degrees ) and (phi(23), psi(23)) = (-80 degrees, 145 degrees ). The obtained values are very close to the Ramachandran coordinates of the polyproline II helix (PPII). The data suggest that this is the conformation predominantly adopted by the peptide at room temperature. This notion was corroborated by the corresponding electronic circular dichroism spectrum. Tetraalanine exhibits a higher propensity for PPII than trialanine for which a 50:50 mixture of polyproline II and an extended beta-strand-like conformation was obtained from recent spectroscopic studies (Eker et al., J. Am. Chem. Soc. 2002, 124, 14330-14341). The temperature dependence of the CD spectra rule out that any cooperativity is involved in the strand if PPII transition. This led to the conclusion that solvent-peptide interactions give rise to the observed PPII stability. Our result can be utilized to understand why the denaturation of helix-forming peptides generally yields a PPII rather than a heterogeneous random conformation.     

Two-dimensional infrared investigation of N-acetyl tryptophan methyl amide in solution

The linear infrared and two-dimensional infrared (2D IR) spectra in the amide-I region of N-acetyl tryptophan methyl amide (NATMA) in solvents of varying polarity are reported. The two amide-I transitions have been assigned unambiguously by using 13C isotopic substitution of the carbonyl group. The amide unit at the amino end shows a lower transition frequency in CH2Cl2 and methanol, while the acetyl end has a lower transition frequency in D2O. Multiple conformers exist in CH2Cl2 and methanol, but only one conformer is evident in D2O. The 2D IR cross peaks from the intermode coupling yield off-diagonal anharmonicities 2.5 +/- 0.5, 3.25 +/- 0.5, and 3.0 +/- 0.5 cm(-1) in CH2Cl2, methanol, and D2O, respectively, which by simple matrix diagonalization yield the coupling constants 8.0 +/- 0.5, 8.0 +/- 1.0, and 5.5 +/- 1.0 cm(-1). The major conformer in CH2Cl2 corresponds to a C7 structure, in agreement with that found in the gas phase [Dian, B. C.; Longarte, A.; Mercier, S.; Evans, D. A.; Wales, D. J.; Zwier, T. S. J. Chem. Phys. 2002, 117, 10688-10702] with intramolecular hydrogen bonding between the acetyl end C=O and the amino end N-H. The backbone dihedral angles (phi, psi) are determined to be in the ranges of (-55 +/- 5 degrees , 30 +/- 5 degrees ), (120 +/- 10 degrees , -20 +/- 10 degrees ), and (+/-160 +/- 10 degrees , +/-75 +/- 10 degrees ) in CH2Cl2, methanol, and D2O, respectively.     

Dihedral psi angle dependence of the amide III vibration: a uniquely sensitive UV resonance Raman secondary structural probe.

UV resonance Raman studies of peptide and protein secondary structure demonstrate an extraordinary sensitivity of the amide III (Am III) vibration and the C(alpha)H bending vibration to the amide backbone conformation. We demonstrate that this sensitivity results from a Ramachandran dihedral psi angle dependent coupling of the amide N-H motion to (C)C(alpha)H motion, which results in a psi dependent mixing of the Am III and the (C)C(alpha)H bending motions. The vibrations are intimately mixed at psi approximately 120 degrees, which is associated with both the beta-sheet conformation and random coil conformations. In contrast, these motions are essentially unmixed for the alpha-helix conformation where psi approximately -60 degrees. Theoretical calculations demonstrate a sinusoidal dependence of this mixing on the psi angle and a linear dependence on the distance separating the N-H and (C)C(alpha)H hydrogens. Our results explain the Am III frequency dependence on conformation as well as the resonance Raman enhancement mechanism for the (C)C(alpha)H bending UV Raman band. These results may in the future help us extract amide psi angles from measured UV resonance Raman spectra.     

LOCUSTRA: accurate prediction of local protein structure using a two-layer support vector machine approach

Constraint generation for 3d structure prediction and structure-based database searches benefit from fine-grained prediction of local structure. In this work, we present LOCUSTRA, a novel scheme for the multiclass prediction of local structure that uses two layers of support vector machines (SVM). Using a 16-letter structural alphabet from de Brevern et al. (Proteins: Struct., Funct., Bioinf. 2000, 41, 271-287), we assess its prediction ability for an independent test set of 222 proteins and compare our method to three-class secondary structure prediction and direct prediction of dihedral angles. The prediction accuracy is Q16=61.0% for the 16 classes of the structural alphabet and Q3=79.2% for a simple mapping to the three secondary classes helix, sheet, and coil. We achieve a mean phi(psi) error of 24.74 degrees (38.35 degrees) and a median RMSDA (root-mean-square deviation of the (dihedral) angles) per protein chain of 52.1 degrees. These results compare favorably with related approaches. The LOCUSTRA web server is freely available to researchers at http://www.fz-juelich.de/nic/cbb/service/service.php.