Studies on the inactivation of bovine liver enoyl-CoA hydratase by (methylenecyclopropyl)formyl-CoA: elucidation of the inactivation mechanism and identification of cysteine-114 as the entrapped nucleophile

The inhibitory properties of (methylenecyclopropyl)formyl-CoA (MCPF-CoA), a metabolite derived from a natural amino acid, (methylenecyclopropyl)glycine, against bovine liver enoyl-CoA hydratase (ECH) were characterized. We have previously demonstrated that MCPF-CoA specifically targets ECHs, which catalyze the reversible hydration of alpha,beta-unsaturated enoyl-CoA substrates to the corresponding beta-hydroxyacyl-CoA products. Here, we synthesized (R)- and (S)-diastereomers of MCPF-CoA to examine the stereoselectivity of this inactivation. Both compounds were shown to be competent inhibitors for bovine liver ECH with nearly identical second-order inactivation rate constants (k(inact)/K(I)) and partition ratios (k(cat)/k(inact)), indicating that the inactivation is nonstereospecific with respect to ring cleavage. The inhibitor, upon incubation with bovine liver ECH, labels a tryptic peptide, ALGGGXEL, near the active site of the protein, where X is the amino acid that is covalently modified. Cloning and sequence analysis of bovine liver ECH gene revealed the identity of the amino acid residue entrapped by MCPF-CoA as Cys-114 (mature sequence numbering). On the basis of gHMQC (gradient heteronuclear multiple quantum coherence) analysis with [3-(13)C]-labeled MCPF-CoA, the ring cleavage is most likely induced by the nucleophilic attack at the terminal carbon of the exomethylene group (C(2)'). We propose a plausible inactivation mechanism that involves relief of ring strain and is consistent with examples found in the literature. In addition, these studies provide important clues for future design of more efficient and selective inhibitors to control and/or regulate fatty acid metabolism.     

DFT study on the geometric, electronic structure and Raman spectra of 5,15-diphenylporphine

The ground state geometric, electronic structure and Raman spectra of 5,15-diphenylporphine (H(2)DPP) have been studied using B3LYP/6-31G(d) method and compared with that of well-studied free base porphine (H(2)P) and meso-tetraphenylporphine (H(2)TPP). Calculation shows that 5,15-substitution causes remarkable in-plane distortion, whereas the resulting out-of-plane distortion is negligible. The calculated electronic structure of H(2)DPP is consistent with the absorption spectra compared with H(2)P and H(2)TPP. The calculated vibrational frequencies of H(2)DPP scaled with a single factor of 0.971 agree well with experimental data (the rms error is 8.0 cm(-1)). The assignment of experimental Raman bands of H(2)DPP was discussed on the basis of theoretical calculation and the comparison with that of H(2)P and H(2)TPP. The splitting of some vibrational modes involving the motion of C(m) atom, such as nu(1), nu(8), and nu(10), was observed and was attributed to the diversification of the environment around C(m) atoms. As the shift of absorption peaks, the shift of some structure-sensitive Raman bands of H(2)DPP form that of H(2)TPP and H(2)P was attributed to the in-plane nuclear reorganization (IPNR) induced by phenyl-substitution, though the contribution of nonplanarity mechanism could not be excluded completely.     

Synthesis and characterization of chitosan-graft-polycaprolactone copolymers

The graft copolymers of chitosan with polycaprolactone (PCL) were prepared through a protection-graft-deprotection route using phthaloylchitosan as intermediate. PCL macromonomers terminated with isocyanate groups reacted with hydroxyl groups of phthaloyl-protected chitosan regioselectively, and then phthaloyl groups were deprotected to give the free amino groups. The graft reaction was carried out in homogeneous system and yielded copolymers with high grafting content due to solubilization. FTIR, NMR and XRD were detected to characterize the resultant chitosan-graft-PCL copolymers.     

Synthesis of 1-triphenylgermylpropiono-4-substituted semicarbazides,thiosemicarbazides and their heterocyclic derivatives

Twenty-one new organogermanium compounds with the formulae Ph₃GeCHR¹CH₂CONHNHC(X)NHR² (1) (R¹=H, Ph; = Ph, p-CH₃Ph, O -CH₃Ph, p-ClPh, COPh, X = S, O) and (R¹ = H, Ph; R² = Ph, p-CH₃Ph, o-CH₃Ph, p-ClPh; X=S, O) were synthesized and characterized by elemental analysis, ¹H NMR, IR, MS and X-ray diffraction techniques. Compounds l were prepared by the reactions of Ph₃GeCHR¹CH₂CONHNH₂ with R²NCX in chloroform in 77-94% yields, and 2 were obtained by refluxing l with sodium hydroxide (8%) with yields of 55-94%.     

Quantum chemistry study on B32 and B32H2–32

The structures of B32 and B₃₂H^2–₃₂ with I_h symmetry have been investigated by means of ab initio calculations at STO-3G level. The relationship between molecular orbitals of them has been analyzed and their bonding properties have been discussed. Then the possibility of their existence, as well as the similarity and difference between B₃₂ (B₃₂H^2–₃₂) and C₆₀ (C₆₀H₆₀) have been inferred.     

Co-C bond dissociation energy and reaction volume change of 2',5'-dideoxyadenosylcobalamin studied by laser-induced time-resolved photoacoustic calorimetry

Time resolved photoacoustic calorimetry (PAC) was applied to a study of the photolysis of a coenzyme B(12) analog 2',5'-dideoxyadenosylcobalamin, which lacks an -OH group at the 2' position of ribofuranose ring. In aqueous solution, we report for the first time the quantum yield Phi(d) (0.25+/-0.02), Co-C bond dissociation energy (BDE; 31.8+/-2.5 kcal mol(-1)) and reaction volume change deltaV(R) (6.5+/-0.5 ml mol(-1)) due to conformation changes of the corrin ring and its side chains accompanying the cleavage of the Co-C bond. These values for the analog are very similar to those for the natural cofactor. Based our results and previous studies, a possible explanation for the similarity in their structure and properties versus the large difference in their enzymatic activity is discussed.     

Single molecule force spectroscopy reveals the context dependent folding pathway of the C-terminal fragment of Top7

Top7 is a de novo designed protein with atomic level accuracy and shows a folded structure not found in nature. Previous studies showed that the folding of Top7 is not cooperative and involves various folding intermediate states. In addition, various fragments of Top7 were found to fold on their own in isolation. These features displayed by Top7 are distinct from those of naturally occurring proteins of a similar size and suggest a rough folding energy landscape. However, it remains unknown if and how the intra-polypeptide chain interactions among the neighboring sequences of Top7 affect the folding of these Top7 fragments. Here we used single-molecule optical tweezers to investigate the folding–unfolding pathways of full length Top7 as well as its C-terminal fragment (CFr) in different sequence environments. Our results showed that the mechanical folding of Top7 involves an intermediate state that likely involves non-native interactions/structure. More importantly, we found that the folding of CFr is entirely dependent upon its sequence context in which it is located. When in isolation, CFr indeed folds into a cooperative structure showing near-equilibrium unfolding–folding transitions at ∼6.5 pN in OT experiments. However, CFr loses its autonomous cooperative folding ability and displays a folding pathway that is dependent on its interactions with its neighboring sequence/structure. This context-dependent folding dynamics and pathway of CFr are distinct from those of naturally occurring proteins and highlight the critical importance of intra-chain interactions in shaping the overall energy landscape and the folding pathway of Top7. These new insights may have important implications on the de novo design of proteins.

Optical tweezers experiments reveal that the folding of the C-terminal fragment of Top7 (cFr) is context-dependent. Depending on its neighboring sequence, cFr shows very different folding pathways and folding kinetics.      

Trihydroxy-2-thiaquinolizidine derivatives as a new class of bicyclic glycosidase inhibitors

Trihydroxy-2-thiaquinolizidines, a new class of bicyclic dideoxy-iminohexitol glycosidase inhibitor derivatives with nominally the d-gluco, l-ido, d-manno and l-gulo configurations were synthesized. X-ray analyses indicated that the preferred conformation for d-gluco and d-manno derivatives was a flat trans-fused system. Unlike deoxynojirimycin, the compound with d-gluco configuration was selective for α-glucosidases (yeast and rice) and showed no inhibitory activity towards β-glucosidase (almond), α-galactosidase (green coffee beans), α-galactosidase (E. coli) and α-mannosidase (jack bean), while the l-ido derivative was specific for β-glucosidase (almond).     

Incorporation of rare-earth ions in Mg-Al layered double hydroxides: intercalation with an [Eu(EDTA)] chelate

Reaction of an aqueous slurry of an Mg₂Al-NO₃ layered double hydroxide with a four-fold excess of Na[Eu(EDTA)] gives a material which analyses for Mg_0.68Al_0.32(OH)₂[Eu(EDTA)]_0.10(CO₃)_0.11·0.66H₂O. The interlayer spacing of the material is 13.8 Å, corresponding to a gallery height of 9.0 Å, which accords with the maximal dimensions (9-10 Å) of the anion in metal-EDTA complex salts as determined by single crystal X-ray diffraction. Geometrical considerations show that the charge density on the layered double hydroxide layers is too high to be balanced by intercalation of [Eu(EDTA)]⁻ alone, necessitating the co-intercalation of carbonate ions which have a much higher charge density.     

DNA-templated self-assembly of protein and nanoparticle linear arrays

Self-assembling DNA tiling lattices represent a versatile system for nanoscale construction. Self-assembled DNA arrays provide an excellent template for spatially positioning other molecules with increased relative precision and programmability. Here we report an experiment using a linear array of DNA triple crossover tiles to controllably template the self-assembly of single-layer or double-layer linear arrays of streptavidin molecules and streptavidin-conjugated nanogold particles through biotin-streptavidin interaction. The organization of streptavidin and its conjugated gold nanoparticles into periodic arrays was visualized by atomic force microscopy and scanning electron microscopy.