A proposed bioactive conformation of Peptide T

The conformational profiles of Peptide T, (5–8)Peptide T, [Abu⁵](4–8)Peptide T and (4–8)Peptide T were computed independently to assess the geometrical characteristics of the bioactive conformation of Peptide T. The conformational profiles of the peptides were computed within the molecular mechanics framework using an effective dielectric constant of 80. The conformational space was thoroughly sampled using an iterative simulated annealing protocol. The bioactive conformation was assessed by pairwise cross comparisons of each of the unique low energy conformations found for each of the different analogs studied. After a putative bioactive conformation was selected, in order to further validate our hypothesis the conformational profile of the potent compound cyclo(Thr-Thr-Asn-Tyr-Thr-Asp) was computed and the putative bioactive conformation was found. The conformation exhibits a pseudo -turn involving the side chain of Thr⁵ and the carbonyl oxygen of Tyr⁷ forming a C12 ring.     

Impact of azaproline on amide cis-trans isomerism: conformational analyses and NMR studies of model peptides including TRH analogues

The beta-turn is a well-studied motif in both proteins and peptides. Four residues, making almost a complete 180 degree-turn in the direction of the peptide chain, define the beta-turn. Several types of the beta-turn are defined according to Phi and Psi torsional angles of the backbone for residues i + 1 and i + 2. One special type of beta-turn, the type VI-turn, usually contains a proline with a cis-amide bond at residue i + 2. In an aza-amino acid, the alpha-carbon of the amino acid is changed to nitrogen. Peptides containing azaproline (azPro) have been shown to prefer the type VI beta-turn both in crystals and in organic solvents by NMR studies. MC/MD simulations using the GB/SA solvation model for water explored the conformational preferences of azPro-containing peptides in aqueous systems. An increase in the conformational preference for the cis-amide conformer of azPro was clearly seen, but the increased stability was relatively minor with respect to the trans-conformer as compared to previous suggestions. To test the validity of the calculations in view of the experimental data from crystal structures and NMR in organic solvents, [azPro(3)]-TRH and [Phe(2), azPro(3)]-TRH were synthesized, and their conformational preferences were determined by NMR in polar solvents as well as the impact of the azPro substitution on their biological activities.     

Conformational preferences and cis-trans isomerization of azaproline residue

The conformational study of N-acetyl-N'-methylamide of azaproline (Ac-azPro-NHMe, the azPro dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the effects of the replacement of the backbone CHalpha group by the nitrogen atom on the conformational preferences and prolyl cis-trans isomerization in the gas phase and in solution (chloroform and water). The incorporation of the Nalpha atom into the prolyl ring results in the different puckering, backbone population, and barriers to prolyl cis-trans isomerization from those of Ac-Pro-NHMe (the Pro dipeptide). In particular, the azPro dipeptide has a dominant backbone conformation D (beta2) with the cis peptide bond preceding the azPro residue in both the gas phase and solution. This may be ascribed to the favorable electrostatic interaction or intramolecular hydrogen bond between the prolyl nitrogen and the amide hydrogen following the azPro residue and to the absence of the unfavorable interactions between electron lone pairs of the acetyl carbonyl oxygen and the prolyl Nalpha. This calculated higher population of the cis peptide bond is consistent with the results from X-ray and NMR experiments. As the solvent polarity increases, the conformations B and B* with the trans peptide bond become more populated and the cis population decreases more, which is opposite to the results for the Pro dipeptide. The conformation B lies between conformations D and A (alpha) and conformation B* is a mirror image of the conformation B on the phi-psi map. The barriers to prolyl cis-trans isomerization for the azPro dipeptide increase with the increase of solvent polarity, and the cis-trans isomerization proceeds through only the clockwise rotation with omega' approximately +120 degrees about the prolyl peptide bond for the azPro dipeptide in the gas phase and in solution, as seen for the Pro dipeptide. The pertinent distance d(N...H-NNHMe) and the pyramidality of imide nitrogen can describe the role of this hydrogen bond in stabilizing the transition state structure and the lower rotational barriers for the azPro dipeptide than those for the Pro dipeptide in the gas phase and in solution.     

Variety of the molecular conformation in Peptide nanorings and nanotubes

Possible molecular conformations in peptide nanorings and nanotubes were theoretically investigated by a mathematical conformation analysis as well as ab initio Hartree-Fock calculations. The mathematical analysis predicts not only the conventional nanorings having an extended-type (E-type) backbone (trans zigzag) but also the novel ones having bound-type (B-type) backbones with a smaller internal diameter. Ab initio calculations for the amino acid substitution reveal that all 20 encoded residues can form both types of the above nanorings as a local minimum. However, the energetically stable type is determined in accordance with the kind of the replaced side chains. Moreover, the present work theoretically reveals that both types of nanorings stack to form nanotubes through inter-ring hydrogen bonds, i.e., larger E-type nanotubes and smaller B-type nanotubes. Electronically, the HOMO and LUMO states of the nanoring and nanotube backbones are formed by the in-plane pi state. The replacement by the appropriate residues is furthermore predicted to intrude additional levels in the energy gap and to form the frontier states localized at the side chains.     

Peptide conformation in gas phase probed by collision-induced dissociation and its correlation to conformation in condensed phases

A kinetic peptide fragmentation model for quantitative prediction of peptide CID spectra in an ion trap mass spectrometer has been reported recently. When applying the model to predict the CID spectra of large peptides, it was often found that the predicted spectra differed significantly from their experimental spectra, presumably due to noncovalent interactions in these large polypeptides, which are not considered in the fragmentation model. As a result, site-specific quantitative information correlated to the secondary/tertiary structure of an ionized peptide may be extracted from its CID spectrum. To extract this information, the kinetic peptide fragmentation model was modified by incorporating conformation-related parameters. These parameters are optimized for best fit between the predicted and the experimental spectrum. A conformational stability map is then generated from these conformation-related parameters. Analysis of a few bioactive alpha-helical peptides including melittin, glucagon and neuropeptide Y by this technique demonstrated that their stability maps in the gas phase correlate strongly to their secondary structures in the condensed phases.     

Impact of molecular conformation on barriers to internal methyl rotation: the rotational spectrum of m-methylbenzaldehyde

The ground state spectrum of m-methylbenzaldehyde (m-MBA) was measured with a chirped-pulse Fourier transform microwave (CP-FTMW) spectrometer. The methyl rotor on m-MBA introduces an internal rotation barrier, which leads to splitting of the torsional energy level degeneracy into A and E states. Ab initio calculations predict a low torsional barrier for both the O-cis and O-trans conformers, resulting in a large doublet splitting up to several gigahertz in the frequency spectrum. The rotational constants, distortion terms, and V(3) values for both species have been determined from the ground state rotational spectrum using the BELGI-C(s) fitting program. There are significant differences in the torsional potential for the O-cis and O-trans m-MBA conformers. Molecular orbitals and resonance structures for each conformer are analyzed to understand the difference in torsional barrier height as well as the irregular shape of the O-trans torsional potential.     

Impact of Peptide Micropatterning on Endothelial Cell Actin Remodeling for Cell Alignment under Shear Stress

HSVEC behavior under physiological shear stress in vitro is investigated on PET surfaces micropatterned with both RGDS and WQPPRARI peptides. This technique allows (i) creating geometries on surface to guide cell orientation under shear stress and (ii) controlling surface chemical composition in order to modulate cell behavior. Under shear stress, endothelial cells adhere on patterned PET surfaces and present a more rapid orientation in flow direction in comparison to cells cultured on homogeneous surfaces. Micropatterned surfaces presenting a large surface area ratio of RGDS/WQPPRARI peptides induce fibrillar adhesion, while surfaces presenting an equal RGDS/WQPPRARI peptides surface area ratio preferentially induce focal adhesion.

     

Impact of lone pairs on the conformation and configuration statistics of poly(lactic acid) chains

Nonbonded interaction energies have been calculated for various conformations of the diester giving explicit consideration to the lone-pair electrons. As suspected from an earlier calculation on the dipeptide, such inclusion of the lone-pair effect leads to significant differences in the conformational potential energy map. The diester is shown to be more constrained than the dipeptide. The impact of this constrained geometry and the possible occurrence of cis residues on configuration statistics of poly(lactic acid) chains have been studied. Contrary to expectation the inclusion of cis isomers does not explain the paradoxical high negative temperature coefficient of ln C∞.     

Peptide conformation, 24 homo- and heteronuclear 2D NMR spectroscopy of cyclic pentapeptides containing the active sequenceof somatostatin

2D NMR methods such as SECSY and 2D-¹H-¹³C-shift correlations enable assignments of the NMR signals in three cyclic peptides of the constitution cyclo | Phe-Trp-Lys-Thr-Pro |     

Influence of pressure on protein conformation

The pressure effects in aqueous solutions of biopolymers are presented. It is shown, that pressure in the range of 300 to 800 MPa leads for small monomeric proteins to irreversible denaturation. Larger oligomeric enzymes and structural proteins dissociate reversibly in the pressure range around 100 MPa. The sign of the volume effects of the various noncovalent interactions contributing to the observed reaction and activation volumes is discussed.     

多肽片段连接方法及肽硫酯和肽醛的合成*

本文综述了多肽和蛋白质合成中的片段连接方法,这是近年来多肽和蛋白质合成领域中方法学上的重要进展.该方法使用非保护的多肽片段,无需酶或化学活化试剂,在缓冲溶液中能够高产率地获得多肽和蛋白质.还介绍了与多肽片段连接有关的肽硫酯和肽醛的合成方法.     

A convenient synthesis of substituted pyrazolidines and azaproline derivatives through highly regio- and diastereoselective reduction of 2-pyrazolines

The synthesis of substituted N-acetyl- and N-aroyl-2-pyrazolines via intramolecular Michael addition of alpha,beta-unsaturated hydrazones generated through olefination of phosphinyl and phosphonyl hydrazones with carbonyl compounds is reported. The regioselective reduction of the C-N double bond in these 2-pyrazolines using Superhydride (Et3BHLi) gives pirazolidine derivatives with excellent levels of cis-diastereoselectivity. These 2-pyrazolines can also be obtained in one-pot reaction from allenes, hydrazides, and aldehydes; and pyrazolidines, after reduction, from allenes, hydrazides, and aldehydes. This synthetic route was developed to provide a new approach to substituted azaproline derivatives in a diastereoselective fashion.     

Theoretical studies on the conformation of saccharides

Conformations of 2-methoxytetrahydropyran as a model for the six-membered ring in aldopyranosides have been calculated by the PCILO method using the algorithm of the conjugated gradient to optimize the geometry. The calculated geometry of the fourteen basic forms of 2-methoxytetrahydropyran was found to be in agreement with the available data obtained by X-ray diffraction of pyranosides. The results indicate differences in the geometry of 2-methoxytetrahydropyran resulting from the change of the axial vs. equatorial position of the methoxyl group. These changes are particularly meaningful in the values of bond angles and they are in agreement with the anomeric and exoanomeric effects. The experimentally found differences in the energies of an axial (⁴ C ₁) and equatorial (¹ C ₄) conformer, G = 2.9–3.7 kJ/mol, and the dipole moment, = 1.20 ± 0.05 D (1D = 3.33 10^–30mAs) agree well with the calculated values E = 3.18 kJ/mol and <> = 1.18 D which, in turn, suggest that the axial conformer is preferred over the equatorial one by a ratio a:e = 78:22.     

Influence of backbone conformation on protein aggregation

Effect(s) of organic solvents on an all beta-sheet protein are investigated to understand the influence of backbone conformation on protein aggregation. Results obtained in the present study reveal that protein aggregation is accompanied by the formation of non-native beta-sheet conformation. In contrast, induction of non-native helical segments in the protein is found to inhibit aggregation. The differential effects of the secondary structures on protein aggregation are proposed to stem from the disparity in the nature of the hydrogen bonds and packing of the side chains of hydrophobic residues in the beta-sheet and alpha-helix conformation. In our opinion, the results of the present study provide useful hints to develop methods to alleviate the problems of both in vitro and in vivo protein aggregation.     

Theoretical studies on the conformation of saccharides

The stereochemistry of d-glucopyranose has been studied theoretically in 11 solvents. The stability of the individual conformers in solution has been compared using a method in which the total energy is divided into the energy of an isolated molecule and the solvation energy. The structure and the energy of the isolated molecule have been estimated by geometry optimization using the PCILO quantum chemical method. The solvation energy consists of electrostatic, dispersion, and cavity terms which have been determined from calculated properties of the solute and physiochemical properties of the solvents. The influence of the solvent on rotation of the individual pendant groups and the stability of anomers have been investigated. The calculated composition of the anomeric mixture of d-glucopyranose in various solvents at 25°C (e.g., in pyridine 49% is -anomer, in dimethyl sulfoxide 46%, and in water 32%) is in good agreement with the available experimental data and clearly demonstrates that the solvation properties of - and -d-glucopyranose differ. Based on the calculated abundances of anomers the magnitude of the anomeric effect has been estimated and compared with the results of corresponding calculations on other compounds.     

在肽库中进行小肽筛选的初步研究

以合成六肽ＤＧＧＳＡＡ为模型对在噬菌体肽库中进行小肽筛选做了初步研究。结果表明，含有可形成氢键和离子键残基的小肽能够在噬菌体肽库中进行筛选。并用明显提高了筛选的专一性。     

Peptide synthesis on fluorous support

New fluorous supports were synthesized and used to prepare a peptide having a C-terminal COOH based on fluorous chemistry. The hexakisfluorous chain-type support was suitable for the synthesis of a pentapeptide or a peptide derivative on a fluorous support whose fluorine content is over 40 w/w%. A bioactive peptide, Leu-enkephalin, was easily synthesized using an Fmoc-strategy based on fluorous chemistry.     

Peptide

Ohne Zusammenfassung     

Influence of solvents on the conformation of benzoin

The conformation of benzoin in several organic solvents is investigated by infrared spectrometry and dipolometry. The frequencies, intensities, and band shapes of the ν(OH), ν(CO), and aromatic ring vibrations indicate that in solvents of low proton acceptor ability, the cis conformer with intramolecular OH···O hydrogen bonding is preserved. In solvents of large proton acceptor ability there is equilibrium between the cis and trans conformers. The dipole moments are less sensitive to conformational changes, but indicate the same trends. The results are discussed as a function of the specific solvation of the O atoms or OH groups of benzoin.