Molecular level understanding of the role of aldehyde in vegetable‐aldehyde–collagen cross‐linking reaction

The role of formaldehyde (HCHO) in vegetable‐aldehyde–collagen cross‐linking reaction was investigated at the B3LYP/6‐31+G(d) level, where lysine (LYS) was used as model of collagen and catechin (EC) as model of condensed vegetable tannin. Atomic charge and Frontier molecular orbital analysis show that intermediates formed by HCHO reacting with LYS or EC, that is, M_LYS, M_EC‐6, and M_EC‐8, still have both nucleophilic and electrophilic sites, which are elements to form ternary cross‐linking in vegetable‐aldehyde–collagen system. The analysis of energy gap between HOMO (highest occupied molecular orbit) and LUMO (lowest unoccupied molecular orbit) indicate that the intermediate of HCHO–LYS residues (M_LYS) can further react with free HCHO to form product P‐N(CH₂OH)₂ (P‐N‐represents amino acid residue; N represents nitrogen atom on side chain), but the reaction of intermediate M_LYS with free EC is difficult to take place. So, the probability of forming ternary cross‐linking structure of amino acid residue–HCHO–EC is small, if HCHO is added before vegetable tannin in vegetable‐aldehyde–collagen system. However, the reactions of EC–HCHO intermediates (M_EC‐6 and M_EC‐8) with free amino acids, HCHO–amino acid residue intermediate (M_LYS), as well as with other EC–HCHO intermediates (M_EC‐6 and M_EC‐8), are very easy to take place. The reaction enthalpy also shows that the cross‐linking tendency is favorable in thermodynamics. So, it can be deduced that covalent cross‐linking among amino side chain of collagen and vegetable tannin may take place when aldehyde is added after vegetable tannin. In this way, a multiple point cross‐linking reaction occurs to create a high stabilization of collagen. © 2011 Wiley Periodicals, Inc.     

Exclusive Use of High Pressure Liquid Chromatography for the Determination of the Complete Amino Acid Sequence of the 12K Fragment of Avian Sarcoma Virus Structural Protein p27

Abstract

Using exclusively high pressure liquid chromatography for the protein and peptide separation complete primary structure of the 12,000 molecular weight (12K) amino terminal (1–87 residues) fragment obtained by mild acid hydrolysis of p27 (Avian Sarcoma Virus structural protein) has been determined. The sequence was established by direct degradation of the native molecule and its (12K) peptides isolated by molecular exclusion and reverse phase HPLC.     

Role of catechin on collagen type I stability upon oxidation: a NMR approach

Abstract

The study focuses on the understanding, at molecular level, the mechanism of interaction between protein and flavonoids. Collagen and catechin interactions were investigated by NMR in solution and solid state. The effect of catechin on the stability of collagen to oxidation was also explored. Collagen was treated with two concentrations of catechin solutions. Oxidation was carried out by incubation of collagen solution with three oxidation systems: Fe(II)/H₂O₂, Cu(II)/H₂O₂, and NaOCl/H₂O₂. The effects of oxidation systems were evaluated by high resolution 1?D and 2?D proton spectroscopy and solid state NMR (¹³C CP MAS) experiments. Interactions between collagen and catechin preferentially occur between catechin B ring and the amino acids Pro and Hyp of collagen. Results showed that both iron and copper oxidation systems were able to interact with collagen by site specific attack. Moreover, catechin protects collagen proline from oxidation by metal/H₂O₂ systems, preventing copper and iron approach to collagene molecule;this behaviour was more evident for the copper/H₂O₂ system.     

Quantum chemical study of cyclic dipeptides

The preferred conformations of cyclic dipeptides were first studied systemically using the density functional theory (DFT) B3LYP method at the 6‐31G(d) level. The structural characteristics of cyclic dipeptides were revealed, most of which have not been confirmed until now. Our studies showed that the six‐member main circles of cyclic dipeptides composed of natural L ‐amino acid residues appeared as boat conformations. The important factors that influence conformations of cyclic dipeptides, such as molecular total energy, nuclear repulsion energy, molecular orbit, spatial effects, and reactive mechanism, are discussed in detail. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Synthesis and structural study of carbocyclic analogues of 1,2-disubstituted nucleosides

The compounds (±)-cis- and (±)-trans-9-[(2-hydroxymethyl) cyclopentyl]guanine (1 and 2 respectively) were efficiently synthesized by the construction of the purine base on the primary amino group of cis- and trans-2-aminocyclopentylmethanol. The 3D structures of these two 1,2-disubstituted carbanucleosides in DMSO were determined using molecular dynamics calculations with experimental NMR restraints on the basis of the information obtained from a ROESY spectrum. These structures were compared with those obtained in vacuo using molecular dynamics and AM1 semiempirical calculations. The global structures of the two compounds are very similar in the two environments studied, meaning that the structural determination in the gas phase can be extrapolated to molecular simulation studies in solution for compounds of this type.     

Synthesis and Characterization of a Ruthenium(II) Complex for Photovoltaic Cells

We have designed and synthesized a new ruthenium complex, [(5‐amino‐1,10‐phenanthroline)bis(4,4′‐dicarboxylic acid‐2,2′‐bipyridine)]ruthenium(II) by introducing two types of ligands, 5‐amino‐1,10‐phenanthroline and 4,4′‐dicarboxylic acid‐2,2′‐bipyridine. We investigated the electronic, spectroscopic, electrochemical, and photovoltaic properties of the Ru(II) complex. The short‐circuit current density and overall solar‐to‐electric energy conversion efficiency of photovoltaic cells made with this Ru(II) complex were found to be 8.9 mA/cm² and 2.1%, respectively. A series of analogous Ru(II) complexes have also been synthesized and investigated to compare the effects of functional groups on various ligands. HOMO‐LUMO energies and molecular orbital surfaces have been investigated using semiempirical quantum chemical methods.     

Highly selective fluorescent recognition of amino alcohol based on chiral calix[4]arenes bearing L-tryptophan unit

Four two-armed chiral calix[4]arenes (1a–1d) functionalised at the lower ring with amino acid units have been synthesised and the structures of these compounds were characterised by IR, MS, ¹H NMR, ¹³C NMR spectra and elemental analysis. Their molecular recognition abilities towards amino alcohol were examined by fluorescence titration experiment in three kinds of solution. The results indicated that these receptors exhibited excellent fluorescent response to phenylglycinol and could distinguish phenylglycinol from phenylalaninol rapidly through the obvious difference in the fluorescent response. Solvent comparative experiments also indicated that acetonitrile was the best solvent to detect these phenomena.     

Molecularly Imprinted Overoxidized Polypyrrole Colloids: Promising Materials for Molecular Recognition

This article reviews a novel approach to molecular imprinting technology developed by the authors. Preparation, characterization, and performance of the molecularly imprinted overoxidized polypyrrole colloids is discussed to discriminate amino acid enantiomers and structural isomers of naphthalene compounds by using electrochemical and spectroscopic techniques. An overoxidized colloid, which was prepared with L-lactate as a dopant, shows a higher affinity for L-alanine than for D-alanine, and an uptake ratio (L/D) of as high as 11 was observed under optimum conditions. Furthermore, an overoxidized colloid with a cavity created by 1-naphthalenesulfonate (1-NS) showed a higher uptake for 1-NS than 2-NS. Thus, the shape-complementary cavity created at the colloid surface can precisely recognize the difference in the spatial configuration of enantiomers and structural isomers.     

Synthesis of chiral SalenZn(II) and its coordination with imidazole derivatives and amino acid ester derivatives

A chiral complex, SalenZn(II) (S), was synthesized and characterized. Its coordination with imidazole derivatives and amino acid ester derivatives was studied by UV-vis spectrophotometric titrations and CD spectroscopy. The binding constants decreased in the order K (Im)>K (2-MeIm)>K (2-Et-4-MeIm)>K (N-MeIm) for imidazole derivatives, and K (AlaOMe)>K (PheOMe)>K (ValOMe) for amino acid ester derivatives with the same configuration and K _D >K _L for amino acid esters with different configuration. CD spectra can quantify the strength of SalenZn(II)-ligand interactions, giving results consistent with the magnitudes of the binding constants. Moreover the minimum energy conformations of the adducts were obtained by simulated annealing, and quantum chemical calculations were performed based on those conformations to explain experimental results at the molecular level.     

Crystal structures of inclusion complexes of cholic acid with aniline,mono- and difluorinated anilines: Guest information expressed by molecular assembly

The crystal structures of cholic acid (CA), a naturally occurring bile acid, complexed with aniline, and its mono- and difluorinated derivatives were elucidated by X-ray crystallography. Comparison of the structures obtained shows that the molecular assembly pattern and the related structural change of the CA molecule vary among different complexes. These structural changes are the molecular information of the guests. Supplementary Data relating to this article are deposited with the British Library as Supplementary Publication No. SUP 82197 (27 pages).     

How stable is a collagen triple helix? An ab initio study on various collagen and β‐sheet forming sequences

Collagen forms the well characterized triple helical secondary structure, stabilized by interchain H-bonds. Here we have investigated the stability of fully optimized collagen triple helices and beta-pleated sheets by using first principles (ab initio and DFT) calculations so as to determine the secondary structure preference depending on the amino acid composition. Models composed of a total of 18 amino acid residues were studied at six different amino acid compositions: (i) L-alanine only, (ii) glycine only, (iii) L-alanines and glycine, (iv) L-alanines and D-alanine, (v) L-prolines with glycine, (vi) L-proline, L-hydroxyproline, and glycine. The last two, v and vi, were designed to mimic the core part of collagen. Furthermore, ii, iii, and iv model the binding and/or recognition sites of collagen. Finally, i models the G-->A replacement, rare in collagen. All calculated structures show great resemblance to those determined by X-ray crystallography. Calculated triple helix formation affinities correlate well with experimentally determined stabilities derived from melting point (T(m)) data of different collagen models. The stabilization energy of a collagen triple helical structure over that of a beta-pleated sheet is 2.1 kcal mol(-1) per triplet for the [(-Pro-Hyp-Gly-)(2)](3) collagen peptide. This changes to 4.8 kcal mol(-1) per triplet of destabilization energy for the [(-Ala-Ala-Gly-)(2)](3) sequence, known to be disfavored in collagen. The present study proves that by using first principles methods for calculating stabilities of supramolecular complexes, such as collagen and beta-pleated sheets, one can obtain stability data in full agreement with experimental observations, which envisage the applicability of QM in molecular design.     

Complexes of mono- and bis(2-carboxyethyl)-2-picolylamine: Synthesis and crystal and molecular structures

N-(2-Pyridylmethyl)iminodipropionic (I) and N-(2-pyridylmethyl)-3-aminopropionic acids (II) were obtained. A reaction of acid I with a Cu(II) salt gave a 2: 2 complex (III); a reaction of acid II with a Ni(II) salt yielded a 1 : 2 complex (IV). The crystal structures of these complexes were determined by X-ray diffraction. The abilities of compounds I and II to form complexes were compared with the literature data for other ligands containing the N-(2-pyridylmethyl)amino fragment. The structural features of the chelate complexes with 2-aminomethylpyridine derivatives were revealed, depending on the other substituents and the metal center.     

Heterocyclic Synthesis Using Nitrilimines,Part 12: Synthesis and Bioactivity of 5-Carboxymethylthio-1,2,4-triazoles

The reaction of 4-amino-5-phenyl-3,5-thiaaza-4-pentenoic acid 3 with various nitrilimines 2 led to the formation of substituted carboxymethylthio derivatives of 1,2,4-triazoles (4a–l) rather than the amino derivatives 5 or imidazole derivatives 6. The spectral data of the synthesized compounds are in full agreement with its molecular structure.     

Chiral discrimination in biliverdin (S)-amino acids,II: Structural variations of the amino acid functional groups

The Biliverdin-(S)-amino acid derivatives2–21 have been synthesized, and are subject to a thorough c. d. and u. v.-vis. electronic absorption analysis in the bilatriene chromophoric region. It is shown that the extent of chiral discrimination of the bilatriene helices is particularly sensitive towards structural variations of the amino acids bound to the propionic side chains. Thus, a pronounced decrease of chiral induction occurs if hydrogen bonding between one of the two essential coordination sites of the amino acid entity and the bilatriene backbone is disturbed. Accordingly, derivatives of (S)-amino acidt-butyl esters (3,5,7,16 and17) andN-substituted (S)-amino acids (8–10, 20 and21) generally display weak c. d. spectra. If additional polar groups are present in bis(amino acid) derivatives mutual interferences of the adjacent side chains must be taken into account. The attenuations of -values observed for the bis(serine) and bis(aspartic acid) compounds14 and15 thus are mainly due to intramolecular interchain interactions. The results provide evidence in support of the proposed mechanism of chiral discrimination in biliverdin amino acids.Dedicated to Prof. Dr.Kurt L. Komarek on the occasion of his 60th birthday.     

Theoretical studies on conformational preferences of model modified nucleic acid base N6-(N-alanylcarbonyl) adenine

Conformational preferences of model modified nucleic acid base N⁶-(N-alanylcarbonyl) adenine, ac⁶Ade, have been investigated using the quantum chemical PCILO (perturbative configuration interaction using localized orbitals) method. The multidimensional conformational space has been searched using selected grid points formed by combining the various torsion angles that take favored values derived from energy variation with respect to each torsion angle individually. The preferred molecular structure is stabilized by an intramolecular hydrogen bond from N(11)H of the amino acid to N(1) of the adenine. The observed crystal structure conformations for the naturally occurring, anticodon adjacent, threonyl analogs, tc⁶Ade, correspond to the predicted most stable conformation for the model modified base ac⁶Ade. Three stable, low energy conformations differing in the orientations of the carboxyl group and the amino acid side chain are predicted within 1 kcal/mol of the most stable structure. The possible bifurcated hydrogen bonding of N(11)H with N(1) and either of the carboxyl oxygens is of minor significance. The indicated orientational flexibility for the carboxyl group and the amino acid side chain may enable convenient probing of the molecular environment, in the vicinity of the anticodon in tRNA, by the amino acid substituent, with only modest changes in energy stabilization.     

Ab initio and density functional theory based studies on collagen triplets

An understanding of the amino acid sequence dependent stability of polypeptides is of renowned interest to biophysicists and biochemists, in order to identify the nature of forces that stabilize the three-dimensional structure of proteins. In this study, the role of various collagen triplets influencing the stability of collagen has been addressed. It is found from this study that proline can stabilize the collagen triplet only when other residues are also in the polyproline II conformation. Solvation studies of various triplets indicate that the presence of polar residues increases the free energy of solvation. Especially the triplets containing arginine residues displays a higher solvation free energy. The chemical hardness of all the triplets in collagen-like conformation has been found to be higher than that in the extended conformation. Studies on Gly–X–Y, Gly–X–Hyp, and Gly–Pro–Y triplets confirm that there will be local variations in the stability of collagen along the entire sequence.     

A Chemical Ionization Mass Spectrometric Study of Fluorescamine and Fluorescamine - Amino Acid Derivatives

Abstract

The chemical ionization mass spectra of fluorescamine and fluorescamine - amino acid derivatives have been studied using methane and ammonia as reagent gases. Major ions in the spectra are protonated molecular ions, adduct ions and ions formed by loss of an oxygen atom.

Fluorescamine, 4-phenyl-spiro[furan-2(3H),1′-phthalan]3,3′-dione, is a powerful new fluorogenic reagent for assaying primary amines.¹ and EI² and EI³ mass spectrometric investigations of fluorescamine and its derivatives were carried out. Our present study reports the CI mass spectral analysis of fluorescamine and some of its amino acid derivatives.     

Tri-peptide reference structures for the calculation of relative solvent accessible surface area in protein amino acid residues

Relative amino acid residue solvent accessibility values allow the quantitative comparison of atomic solvent-accessible surface areas in different residue types and physical environments in proteins and in protein structural alignments. Geometry-optimised tri-peptide structures in extended solvent-exposed reference conformations have been obtained for 43 amino acid residue types at a high level of quantum chemical theory. Significant increases in side-chain solvent accessibility, offset by reductions in main-chain atom solvent exposure, were observed for standard residue types in partially geometry-optimised structures when compared to non-minimised models built from identical sets of proper dihedral angles abstracted from the literature. Optimisation of proper dihedral angles led most notably to marked increases of up to 54% in proline main-chain atom solvent accessibility compared to literature values. Similar effects were observed for fully-optimised tri-peptides in implicit solvent. The relief of internal strain energy was associated with systematic variation in N, C^α and C^β atom solvent accessibility across all standard residue types. The results underline the importance of optimisation of ‘hard’ degrees of freedom (bond lengths and valence bond angles) and improper dihedral angle values from force field or other context-independent reference values, and impact on the use of standardised fixed internal co-ordinate geometry in sampling approaches to the determination of absolute values of protein amino acid residue solvent accessibility. Quantum chemical methods provide a useful and accurate alternative to molecular mechanics methods to perform energy minimisation of peptides containing non-standard (chemically modified) amino acid residues frequently present in experimental protein structure data sets, for which force field parameters may not be available. Reference tri-peptide atomic co-ordinate sets including hydrogen atoms are made freely available.     

Sulphur in the Strategy of Natural Products Synthesis

Abstract

Syntheses of secondary metabolites of α-and β-mercapto aminoacids are described. The strategy in the first class of compounds consists of using N-hydroxy-α-amino acid derivatives as intermediates and of converting them into α-functionalized, in particular thiol-substituted amino acids; as examples serve syntheses in the gliotoxin and sporidesmin series. In the second class of compounds the cycloaddition products of indole derivatives, having sulfide substituents, and nitroso olefins are transformed into indole alkaloids, in particular tryptathionins, by rearrangement and further reactions. The antitumor agent sparsomycin has been synthesized via an amino sultine and its stereospecific nucleophilic ring opening. Bioassays done with this compound and sixteen of its structural analogs gave insight in the structural features that are required for sparsomycin's antitumor activity.