Comparison of two thioxopeptide bond photoswitches in insect kinin

<正>The photoisomerization abilities of secondary thioxopeptide bond(CS-NH) and thioxo prolyl bond(CS-N) incorporated into the C-terminal pentapeptide of insect kinin were compared.H-Phe-Phe-Ψ[CS-NH]-D-Ala-Trp-Gly-NH_2 and H-Phe-Tyr-Ψ[CS-N]- Pro-Trp-Gly-NH_2 were studied by UV-vis absorption.The isomerization energy barriers of the two segments,Ac-Phe-Ψ[CS-NH]- D-Ala-NH_2 and Ac-Tyr-Ψ[CS-N]-Pro-NH_2 picked from the two peptides,were calculated using ab initio method.The cis isomer of CS-N is more stable than that of CS-NH due to higher energy barrier,so the former is more suitable in peptide structure-activity relationship studies.     

Photoswitchable elements within a peptide backbone-ultrafast spectroscopy of thioxylated amides

A series of thioxo compounds, thioacetamide, N-methylthioacetamide, a cyclic thioxoamide [(S)-5-thioxopyrrolidine-2-carboxylic acid ethyl ester], two thioxylated dipeptides (Ala-Psi[CS-NH]-Ala and Phe-Psi[CS-NH]-Ala) and a thioxylated dodecapeptide (Lys-Glu-Thr-Ala-Ala-Ala-Lys-Phe-Glu-Arg-Gln-His-Psi[CS-NH]-Nle-Asp-Ser-Ser-Thr-Ser-Ala-Ala, or [thioxo-His(12)]-S-peptide; Nle = norleucine) are investigated by ultrafast spectroscopy in the visible and near UV. The different molecules show very similar absorption dynamics featuring a rise of a strong visible absorption band on the subpicosecond and picosecond time scale. The decay of the visible absorption occurs within 150-600 ps. The observations are interpreted by the ultrafast formation of triplet states and their decay on the subnanosecond time scale. Comparison with published IR experiments on N-methylthioacetamide indicates that the cis-trans isomerization around the thioxopeptide bond is terminated within less than 1 ns.     

Effect of thioxopeptide bonds on alpha-helix structure and stability

Thioxoamide (thioamide) bonds are nearly isosteric substitutions for amides but have altered hydrogen-bonding and photophysical properties. They are thus well-suited backbone modifications for physicochemical studies on peptides and proteins. The effect of thioxoamides on protein structure and stability has not been subject to detailed experimental investigations up to date. We used alanine-based model peptides to test the influence of single thioxoamide bonds on alpha-helix structure and stability. The results from circular dichroism measurements show that thioxoamides are strongly helix-destabilizing. The effect of an oxo-to-thioxoamide backbone substitution is of similar magnitude as an alanine-to-glycine substitution resulting in a helix destabilization of about 7 kJ/mol. NMR characterization of a helical peptide with a thioxopeptide bond near the N-terminus indicates that the thioxopeptide moiety is tolerated in helical structures. The thioxoamide group is engaged in an i, i+4 hydrogen bond, arguing against the formation of a 3(10)-helical structure as suggested for the N-termini of alpha-helices in general and for thioxopeptides in particular.     

First-principle computational study on the full conformational space of L-threonine diamide, the energetic stability of cis and trans isomers

First-principle computations were carried out on the conformational space of trans and cis peptide bond isomers of HCO-Thr-NH2. Using the concept of multidimensional conformational analysis (MDCA), geometry optimizations were performed at the B3LYP/6-31G(d) level of theory, and single-point energies as well as thermodynamic functions were calculated at the G3MP2B3 level of theory for the corresponding optimized structures. Two backbone Ramachandran-type potential energy surfaces (PESs) were computed, one each for the cis and trans isomers, keeping the side chain at the fully extended orientation (chi1=chi2=anti). Similarly, two side chain PESs for the cis and trans isomers were generated for the (phi=psi=anti) orientation corresponding to approximately the betaL backbone conformation. Besides correlating the relative Gibbs free energy of the various stable conformations with the number of stabilizing hydrogen bonds, the process of trans-->cis isomerization is discussed in terms of intrinsic stabilities as measured by the computed thermodynamic functions.     

Collagen stability: insights from NMR spectroscopic and hybrid density functional computational investigations of the effect of electronegative substituents on prolyl ring conformations

Collagen-like peptides of the type (Pro-Pro-Gly)(10) fold into stable triple helices. An electron-withdrawing substituent at the H(gamma)(3) ring position of the second proline residue stabilizes these triple helices. The aim of this study was to reveal the structural and energetic origins of this effect. The approach was to obtain experimental NMR data on model systems and to use these results to validate computational chemical analyses of these systems. The most striking effects of an electron-withdrawing substituent are on the ring pucker of the substituted proline (Pro(i)) and on the trans/cis ratio of the Xaa(i-1)-Pro(i) peptide bond. NMR experiments demonstrated that N-acetylproline methyl ester (AcProOMe) exists in both the C(gamma)-endo and C(gamma)-exo conformations (with the endo conformation slightly preferred), N-acetyl-4(R)-fluoroproline methyl ester (Ac-4R-FlpOMe) exists almost exclusively in the C(gamma)-exo conformation, and N-acetyl-4(S)-fluoroproline methyl ester (Ac-4S-FlpOMe) exists almost exclusively in the C(gamma)-endo conformation. In dioxane, the K(trans/cis) values for AcProOMe, Ac-4R-FlpOMe, and Ac-4S-FlpOMe are 3.0, 4.0, and 1.2, respectively. Density functional theory (DFT) calculations with the (hybrid) B3LYP method were in good agreement with the experimental data. Computational analysis with the natural bond orbital (NBO) paradigm shows that the pucker preference of the substituted prolyl ring is due to the gauche effect. The backbone torsional angles, phi and psi, were shown to correlate with ring pucker, which in turn correlates with the known phi and psi angles in collagen-like peptides. The difference in K(trans/cis) between AcProOMe and Ac-4R-FlpOMe is due to an n-->pi interaction associated with the Bürg-Dunitz trajectory. The decrease in K(trans/cis) for Ac-4S-FlpOMe can be explained by destabilization of the trans isomer because of unfavorable electronic and steric interactions. Analysis of the results herein along with the structures of collagen-like peptides has led to a theory that links collagen stability to the interplay between the pyrrolidine ring pucker, phi and psi torsional angles, and peptide bond trans/cis ratio of substituted proline residues.     

All-cis helical polypeptides

The possibility of all-cis open-chain polypeptides is rarely addressed, owing to three main reasons, namely, (i) the extreme scarcity of cis peptide bonds in naturally occurring proteins and peptides, (ii) the lesser thermodynamic stability (by about 2.5 kcal/mol) of cis amide bonds with respect to their trans counterparts, and (iii) widely held preconceptions about the so-called "steric clash" between lateral chains borne by two successive alpha carbons. Quantum-chemistry calculations performed on alanine tridecamers show how the latter constraints can be efficiently relieved through proper phi/psi adjustments along the backbone, leading to several helical arrangements--presumably the only permitted regular structures. Four more-or-less regular helices were thus characterized, one of them, a superhelix, exhibiting intramolecular hydrogen bonds. Understanding and anticipating all-cis open-chain structures not only make use of the classical Ramachandran maps at each C alpha i, relating to E = f(phi i,psi i), but also require the profile of a new kind of conformational dependence, the plaque maps, relating to E = f(phi i,psi i-1). The obvious coupling between two such maps enforces conformational dependence between two consecutive C alpha's, somewhat questioning in this context the customary "local effects", and presumably reducing the whole chain plasticity. Whereas cis thermodynamic penalty cannot be abolished locally, energy clues indicate that assembling cis-prepared building units is an exothermic process. Besides, once built up, the all-cis backbone should be difficult to unlock, thus affording reasonable kinetic stability.     

Convergent synthesis of homogeneous Glc1Man9GlcNAc2-protein and derivatives as ligands of molecular chaperones in protein quality control

A detailed understanding of the molecular mechanism of chaperone-assisted protein quality control is often hampered by the lack of well-defined homogeneous glycoprotein probes. We describe here a highly convergent chemoenzymatic synthesis of the monoglucosylated glycoforms of bovine ribonuclease (RNase) as specific ligands of lectin-like chaperones calnexin (CNX) and calreticulin (CRT) that are known to recognize the monoglucosylated high-mannose oligosaccharide component of glycoproteins in protein folding. The synthesis of a selectively modified glycoform Gal(1)Glc(1)Man(9)GlcNAc(2)-RNase was accomplished by chemical synthesis of a large N-glycan oxazoline and its subsequent enzymatic ligation to GlcNAc-RNase under the catalysis of a glycosynthase. Selective removal of the terminal galactose by a β-galactosidase gave the Glc(1)Man(9)GlcNAc(2)-RNase glycoform in excellent yield. CD spectroscopic analysis and RNA-hydrolyzing assay indicated that the synthetic RNase glycoforms maintained essentially the same global conformations and were fully active as the natural bovine ribonuclease B. SPR binding studies revealed that the Glc(1)Man(9)GlcNAc(2)-RNase had high affinity to lectin CRT, while the synthetic Man(9)GlcNAc(2)-RNase glycoform and natural RNase B did not show CRT-binding activity. These results confirmed the essential role of the glucose moiety in the chaperone molecular recognition. Interestingly, the galactose-masked glycoform Gal(1)Glc(1)Man(9)GlcNAc(2)-RNase also showed significant affinity to lectin CRT, suggesting that a galactose β-1,4-linked to the key glucose moiety does not significantly block the lectin binding. These synthetic homogeneous glycoprotein probes should be valuable for a detailed mechanistic study on how molecular chaperones work in concert to distinguish between misfolded and folded glycoproteins in the protein quality control cycle.     

Calorimetric evidence for conformational transitions of RNase A in the presence of cytidine 2′,3′-cyclic phosphate

Thermal denaturation of ribonuclease A (RNase A) complex with cytidine 3′-monophosphate (3′CMP) was studied by differential scanning calorimetry (DSC). The kinetic and binding studies of RNase A with cytidine 2′,3′-cyclic phosphate (cCMP) as a substrate, and 3′CMP as a ligand were also investigated by difference spectrophotometry. The obtained kinetic saturation curve reveals the occurrence of an anomalous non-hyperbolic shape at high substrate concentrations, and a biphasic binding isotherm. These phenomena indicate that a conformational change is occurring with RNase A during the hydrolysis of cCMP. A combination of kinetic and thermodynamic studies tends to elucidate the reasons for the formation of a non-hyperbolic behavior in a kinetic saturation curve. The thermal profile of the enzyme-3′CMP complexes shows a splitting of two distinct peaks with different structural stabilities of melting points (T_m) of 325 and 337 K. The bifurcate appearance of DSC profile of RNase A-3′CMP complexes manifests a physical view of a light kinetic structural transition. It is worthy to note, the direct binding (not via enzymatic reaction) of enzyme with 3′CMP indicates single DSC profile and monophasic binding isotherm.     

Dioxotungsten 1,2-benzenedithiolate complex stabilized by NH...S hydrogen bonds

Novel dioxo-tungsten(VI) bis(1,2-benzenedithiolate) complexes with neighboring amide groups, as models for tungsten enzymes, (NEt4)2[W(VI)O2{1,2-S(2)-3,6-(RCONH)2C6H2}2] (R = CH3, t-Bu), were designed and synthesized. The presence of the NH...S hydrogen bond was confirmed through IR spectrometry and X-ray crystallographic analysis. In the W(VI)O2 complexes, the NH...S hydrogen bond trans to the oxo ligand is stronger than that cis to oxo. On the basis of comparisons with [W(VI)O2(1,2-S2C6H4)2](2-), the NH...S hydrogen bond positively shifted the W(VI)/W(V) redox potentials and depressed the reduction by benzoin or triphenylphosphine. These results suggest that the NH...S hydrogen bond stabilizes the oxo ligand through trans influence and regulates O-atom transfer in tungsten and molybdenum enzymes.     

Understanding the role of stereoelectronic effects in determining collagen stability. 1. A quantum mechanical study of proline, hydroxyproline, and fluoroproline dipeptide analogues in aqueous solution.

The importance of local (intraresidue) effects in determining the stability of the collagen triple helix has been investigated with special reference to the role played by hydroxyproline. To this end the dipeptide analogues of L-proline (ProDA), 4(R)-hydroxy-L-proline (HypDA), and 4(R)-fluoro-L-proline (FlpDA) have been studied by means of quantum mechanical ab initio calculations, taking into account solvent effects by the polarizable continuum model (PCM). Our results confirm that the relative stability of up puckerings of the pyrrolidine ring increases with the electronegativity of the 4(R) substituent (X), whereas down puckerings are favored by 4(S) electronegative substituents. Calculations on model compounds show that this effect is due to the interaction between vicinal C-H bonding and C-X antibonding orbitals. Electronegative substituents on the pyrrolidine ring affect cis-trans isomerism around the peptidic bond, with trans isomers stabilized by 4(R) substituents and cis isomers by 4(S) substituents. Also the hydrogen bonding power of the carbonyl moiety following the pyrrolidine ring is affected by 4(R) substituents, but this effect is tuned by the polarity of the embedding medium. Finally, up puckering favors smaller values of the backbone dihedrals phi and psi. All these results strongly support the proposal that the stability of triple helices containing fluorinated or hydroxylated prolines in Y positions is related to the necessity of having up puckerings in those positions.     

Time-resolved infrared spectroscopy of thiopeptide isomerization and hydrogen-bond breaking

The photoisomerization of the protected tetrathioxopeptide Boc-Ala-Gly(=S)-Ala-Aib-OMe was followed using time-resolved infrared spectroscopy in the amide I region in combination with isotope labeling. In acetonitrile at room temperature, approximately half of the molecules are found in a loop conformation, restrained by an intramolecular hydrogen bond, while the other half adopts more extended conformations. UV-excitation of the thioxopeptide unit immediately weakens the intramolecular hydrogen bond. After the molecules have relaxed to the electronic ground state with a 130 ps time-constant, a delayed re-formation of the intramolecular hydrogen bond is observed for molecules returning to the initial trans conformation of the thioamide bond, while the loop structure is permanently broken when the molecules isomerize to the cis conformation.     

Allylpalladium dimers with metals connected by binucleating dithiooxamidates in two different coordination modes: solution behavior and solid-state structure

A series of allylpalladium dimers having metals connected by binucleating dialkyldithiooxamidate [N(R)SC-CS(R)N](2-) [R = methyl, ethyl, isopropyl, benzyl, isoamyl, (S)-1-(1-phenyl)ethyl, meso-(1-phenyl)ethyl, and rac-(1-phenyl)ethyl] were prepared by reacting the monochelate [(η(3)-allyl)Pd(N(R)SC-CS(R)NH κ-S,S Pd)] with [(η(3)-allyl)PdCl](2) in chloroform. At low temperature (20 °C), the bimetallic complexes [(η(3)-allyl)Pd](2)(μ-dialkyldithiooxamidate κ-N,N' Pd, κ-S,S' Pd') (kinetic compounds) are formed in a short reaction time (10 min). At a higher temperature (50 °C) and a longer reaction time (24 h), the corresponding bimetallic isomers [(η(3)-allyl)Pd](2)(μ-dialkyldithiooxamidate κ-N,S Pd, κ-N',S' Pd') (thermodynamic compounds) are obtained. Both kinetic and thermodynamic compounds can exist as endo or exo isomers, depending on the reciprocal orientation of the allyl cuspids. Both endo and exo isomers are only detectable in solution when the alkyl substituents are chiral alkyl groups. Moreover, diffractometric modeling agrees with the presence of both isomers in the solid state even when the alkyl substituent is an achiral alkyl group. In a chloroform solution, endo and exo isomers undergo isomeric conversion owing to the apparent allyl rotation that follows the Pd-N bond rupture in the (η(3)-allyl)Pd(N^N) frame of kinetic compounds or in the (η(3)-allyl)Pd(N^S) frame of thermodynamic compounds. The dithiooxamidate [N(R)SC-CS(R)N](2-), when engaged in a κ-N,S Pd, κ-N',S' Pd' coordination mode, behaves as a hybrid hemilabile binucleating ligand. At room temperature and in a chloroform solution, the kinetic compounds rearrange into the thermodynamically more stable isomers in about 3 or 4 days. The higher stability of the thermodynamic species was evaluated by means of computational studies in accordance with the maximum hardness principle. Finally, the crystal structures of [(η(3)-allyl)Pd](2)(μ-diethyldithiooxamidate κ-N,S Pd, κ-N',S' Pd'), [(η(3)-allyl)Pd](2)(μ-meso-(1-phenyl)ethyldithiooxamidate κ-N,S Pd, κ-N',S' Pd'), and [(η(3)-allyl)Pd](2)(μ-rac-(1-phenyl)ethyldithiooxamidate κ-N,N' Pd, κ-S,S' Pd') are reported.     

Density functional study on dihydrogen activation at the H cluster in Fe-only hydrogenases

Models simulating the catalytic diiron subcluster [FeFe](H) in Fe-only hydrogenases have often been designed for computational exploration of the catalytic mechanism of the formation and cleavage of dihydrogen. In this work, we extended the above models by explicitly considering the electron reservoir [4Fe-4S](H) which is linked to the diiron subcluster to form a whole H cluster ([6Fe-6S] = [4Fe-4S](H) + [FeFe](H)). Large-scale density functional theory (DFT) computations on the complete H cluster, together with simplified models in which the [4Fe-4S](H) subcluster is not directly involved in the reaction processes, have been performed to probe hydrogen activation on the Fe-only hydrogenases. A new intermediate state containing an Fe(p)...H...CN two-electron three-center bond is identified as a key player in the H2 formation/cleavage processes.     

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.     

Efficient RNase H-directed cleavage of RNA promoted by antisense DNA or 2'F-ANA constructs containing acyclic nucleotide inserts

The ability of modified antisense oligonucleotides (AONs) containing acyclic interresidue units to support RNase H-promoted cleavage of complementary RNA is described. Manipulation of the backbone and sugar geometries in these conformationally labile monomers shows great benefits in the enzymatic recognition of the nucleic acid hybrids, while highlighting the importance of local strand conformation on the hydrolytic efficiency of the enzyme more conclusively. Our results demonstrate that the duplexes support remarkably high levels of enzymatic degradation when treated with human RNase HII, making them efficient mimics of the native substrates. Furthermore, interesting linker-dependent modulation of enzymatic activity is observed during in vitro assays, suggesting a potential role for this AON class in an RNase H-dependent pathway of controlling RNA expression. Additionally, the butyl-modified 2'F-ANA AONs described in this work constitute the first examples of a nucleic acid species capable of eliciting high RNase H activity while possessing a highly flexible molecular architecture at predetermined sites along the AON.     

Structural and thermodynamic properties of group 13 imidometallanes and their heavier analogues

Systematic theoretical studies of the [XMYH](n) inorganic rings and clusters (M = Al, Ga, In; Y = N, P, As; X = H, F, Cl, Br, I; n = 1-6) have been carried out using hybrid Hartree-Fock density functional theory. A consistent set of the structural and thermodynamic properties has been obtained. The stability of the MY bond decreases in the order Al > Ga >or= In; N > P > As. Terminal groups X have a minor influence on the subsequent elimination enthalpies of the clusters. In the case of X = H, hydrogen elimination makes formation of the [HMYH](6) oligomers from MH(3) and YH(3) thermodynamically favorable; while in the case of halide substituents, formation of [XMYH](6) is thermodynamically unfavorable, except for the system with the strongest MY bond (AlN). Substitution of the acidic hydrogen by X is favorable energetically for all [HMYH](6) clusters, but is complicated by the processes of cluster destruction to form the [X(2)MYH(2)](2) dimers. The high stability of the [HMNH](6) clusters makes them attractive single-source precursors for the production of 13-15 composites.     

The first triple thiol-thiolate hydrogen bond versus triple diselenide bond that bridges two metal centers

Treatment of fac(S)-[Rh(aet)3] (aet = 2-aminoethanethiolate) with aqueous HBF4 in air led to the protonation at coordinated thiolato groups to give a rhodium(III) dimer, [{Rh(aet)2(Haet)}{Rh(aet)(Haet)2}](BF4)3 ([1](BF4)3). On the other hand, similar treatment of fac(Se)-[Rh(aes)3] (aes = 2-aminoethaneselenolate) produced a dinuclear rhodium(III) complex, [Rh2(selenocystamine)3](BF4)6 ([2](BF4)6), because of the autoxidation of coordinated selenolato groups by air. The crystal structures of [1](BF4)3, DeltaDelta-[1](BF4)3, and [2](BF4)6 were determined by X-ray crystallography. In [1]3+ two RhIII octahedrons are connected through a strong triple thiol-thiolate S-H...S hydrogen bond, while two RhIII octahedrons are directly joined by a triple diselenide bond in [2]6+. The cyclic voltammetry indicated that in acidic media the RhIII center in fac(Se)-[Rh(aes)3] is more easily oxidized to RhIV than that in fac(S)-[Rh(aet)3], which is responsible for the formation of coordinated diselenide bonds.     

Enzymatic mechanism of Fe-only hydrogenase: density functional study on H-H making/breaking at the diiron cluster with concerted proton and electron transfers

The mechanism of the enzymatic hydrogen bond forming/breaking (2H(+) + 2e<==>H(2)) and the plausible charge and spin states of the catalytic diiron subcluster [FeFe](H) of the H cluster in Fe-only hydrogenases are probed computationally by the density functional theory. It is found that the active center [FeFe](H) can be rationally simulated as [[H](CH(3)S)(CO)(CN(-))Fe(p)(CO(b))(mu-SRS)Fe(d)(CO)(CN(-))L], where the monovalence [H] stands for the [4Fe4S](H)(2+) subcluster bridged to the [FeFe](H) moiety, (CH(3)S) represents a Cys-S, and (CO(b)) represents a bridging CO. L could be a CO, H(2)O, H(-), H(2), or a vacant coordination site on Fe(d). Model structures of possible redox states are optimized and compared with the X-ray crystallographic structures and FTIR experimental data. On the basis of the optimal structures, we study the most favorable path of concerted proton transfer and electron transfer in H(2)-forming/breaking reactions at [FeFe](H). Previous mechanisms derived from quantum chemical computations of Fe-only hydrogenases (Cao, Z.; Hall, M. B. J. Am. Chem. Soc. 2001, 123, 3734; Fan, H.; Hall, M. B. J. Am. Chem. Soc. 2001, 123, 3828) involved an unidentified bridging residue (mu-SRS), which is either a propanedithiolate or dithiomethylamine. Our proposed mechanism, however, does not require such a ligand but makes use of a shuttle of oxidation states of the iron atoms and a reaction site between the two iron atoms. Therefore, the hydride H(b)(-) (bridged to Fe(p) and Fe(d)) and eta(2)-H(2) at Fe(p) or Fe(d) most possibly play key roles in the dihydrogen reversible oxidation at the [FeFe](H) active center. This suggested way of H(2) formation/splitting is reminiscent of the mechanism of [NiFe] hydrogenases and therefore would unify the mechanisms of the two related enzymes.