A comparative study of various computational approaches in calculating the structure of pyridoxal 5'-phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment

Various computational approaches, using molecular mechanics (Amber), semiempirical (AM1), density functional (B3LYP), and various ONIOM methods, have been comparatively investigated for the structure of Escherichia coli NifS CsdB protein. The structure of the entire monomer containing 407 amino acid residues and 579 surrounding water molecules has been optimized. The full geometry optimization in the "active site-only" approach (including only active site atoms) has been found to give the largest root-mean-square (RMS) deviation from the X-ray structure; a much better agreement has been achieved by keeping the atoms leading to the backbones of some amino acids frozen in their positions in the X-ray structure. The best agreement has been attained by including the surrounding protein in the calculations using the two-layer ONIOM (B3LYP:Amber) approach. The results presented in this study conclusively demonstrate the importance of the protein/active-site interaction on the active-site structure of the enzyme. The present theoretical study represents the largest system studied at the ONIOM level to date, containing 7992 atoms, including 84 atoms in the QM region and rest in the MM region.     

Studies on the refolding of the reduced-denatured insulin with size exclusion chromatography

The refolding of the reduced-denatured insulin from bovine pancreas was investigated with the size exclusion chromatography (SEC). It was shown that the reduced-denatured insulin originally denatured with 7.0 mol·L-1 guanidine hydrochloride (GuHCI) or 8.0 mol·L-1 urea could not be refolded with a non-oxidized mobile phase. Although the oxidized and reduced glutathione (GSSG and GSH) were employed in the oxidized mobile phase, the reduced-denatured insulin still could not be renatured. However, in the presence of 2.0 mol·L-1 urea in the oxidized mobile phase employed, the reduced-denatured insulin can be refolded with SEC, and the aggregation of denatured insulin can be diminished by urea. In addition, the disul-fide exchange of reduced-denatured insulin also can be accelerated with GSSG/GSH in the oxidized mobile phase. The three disulfide bridges of insulin were formed correctly and the reduced-unfolded insulin can be renatured completely. The results were further tested with re-versed-phase liquid chromatography (RPLC) and hydrophobic interaction chromatography (HIC).     

In Vitro Determination of Dobesilate in Medicine and Human Urine with Chemiluminescence Detection

A unique flow injection chemiluminescence (CL) method for the determination of calcium dobesilate in pharmaceutical preparations and human urine is presented in this paper. The analytical reagents involved in the CL reaction, luminol and ferricyanide, were both immobilized on an anion-exchange column in an FI system. The CL signal produced by the reaction of luminol with ferricyanide (the reagents had been eluted from the column through sodium phosphate injection) decreased in the presence of dobesilate. The decreased CL intensity was linear to the dobesilate concentration in the range 0.2100.0ngmL^–1. At a flow rate of 2.0mLmin^–1, one analytical cycle can be completed in 1.5min, including sampling and washing, resulting in a throughput of 40 cycles per hour. The proposed method was applied successfully to the determination of dobesilate in pharmaceutical preparations and human urine without any pre-treatment. It was found that, after oral administration, the dobesilate concentration reached its maximum after three hours, and the dobesilate metabolism ratio in 24 hours was 57.1% in the bodies of volunteers.Received September 14, 2002; accepted March 11, 2003 Published online July 16, 2003     

Molecular basis for antifreeze activity difference of two insect antifreeze protein isoforms

The insect spruce budworm(Choristoneura fumiferana) produces antifreeze protein(AFP) to assist in the protection of the over-wintering larval stage and contains multiple isoforms. Structures for two isoforms,known as CfAFP-501 and CfAFP-337,show that both possess similar left-handed β-helical structure,although thermal hysteresis activity of the longer isoform CfAFP-501 is three times that of CfAFP-337. The markedly enhanced activity of CfAFP-501 is not proportional to,and cannot be simply accounted for,by the increased ice-binding site resulting from the two extra coils in CfAFP-501. In or-der to investigate the molecular basis for the activity difference and gain better understanding of AFPs in general,we have employed several different computational methods to systematically study the structural properties and ice interactions of the AFPs and their deletion models. In the context of intact AFPs,a majority of the coils in CfAFP-501 has better ice interaction and causes stronger ice lattice disruption than CfAFP-337,strongly suggesting a cooperative or synergistic effect among β-helical coils. The synergistic effect would play a critical role and make significant contributions to the anti-freeze activity β-helical antifreeze proteins. This is the first time that synergistic effect and its implica-tion for antifreeze activity are reported for β-helical antifreeze proteins.     

Synthesis and photochemistry of a new class of photocleavable protein cross-linking reagents

A new series of photocleavable protein cross-linking reagents based on bis(maleimide) derivatives of diaryl disulfides have been synthesised. They have been functionalised with cysteine and transient absorption spectra for the photolysis reaction have been recorded by using the pump-probe technique with a time resolution of 100 femtoseconds. Photolysis of the disulfide bond yields the corresponding thiyl radicals in less than a picosecond. There is a significant amount of geminate recombination, but some of the radicals escape the solvent cage and the quantum yield for photocleavage is 30 % in water.     

Enantioselectivity of 6-O-alkyldimethylsilyl-2,3-di-O-methyl-β-cyclodextrins as chiral stationary phases in capillary GC

Summary Clenbuterol has been determined in urine by solidphase extraction on a C₁₈ cartridge, diazotization of the eluate with nitrite, coupling of the diazonium ion with 1-(naphthyl)ethylenediamine, and separation of the azo dye formed by HPLC with a C₁₈ column and a micellar mobile phase containing 0.1 M sodium dodecyl sulphate, 12%n-butanol and 0.05 M citrate buffer, pH 3. Recoveries higher than 90% were obtained by mixing the samples with a 20% 0.2 M NaOH before extraction. Limits of detection of 51 and 6.7 ng L⁻¹ were obtained with spectrophotometric and thermal lens spectrometric detection, respectively; respective repeatabilities were 3.1% (5 μg mL⁻¹) and 5.6% (0.16 μg mL⁻¹).     

Conformational Studies on Polytripeptides as a Model of Collagen

To study the role of glycine residues in stabilizing the collagen triple helix, the glycine residues in the polytripeptide (Pro-Ala-Gly)_n were partially replaced by alanine. The proline content was kept constant. The stability of the helical conformation of these polypeptides was studied by IR- and X-ray measurements in the solid state and by ORD, CD and viscometry in solution. The renaturation was followed as a function of time. All the polytripeptides studied, with the exception of (-Pro-Ala-Ala-)_n attained the polyproline II conformation. However the stability decreased with increasing alanine content. Obviously the molecules of (-Pro-Ala-Gly-) are highly associated by intermolecular hydrogen bonds and one may therefore suppose that a triple-stranded helix aggregation occurs. The results of the refolding process show that the stability of the helices seems to also affect the refolding rate in terms of the optical rotation, Two transitions appeared: the first one is responsible for a rapid reversible change in conformation and the second one for a further slow and irreversible change in the hydrodynamic shape. The latter seems to be due to the partial helical nature, leading to higher chain mobility.     

Detection of potential membrane receptor proteins concerning circadian rhythmic leaf movement of legumes using novel photoaffinity probe compounds

Circadian rhythmic plant leaf movement, called nyctinasty, is controlled by a time-course change in the internal concentration of the leaf-movement factor in the plant body. We report that specific binding protein (210 and 180 kDa) for a leaf-movement factor, potassium lespedezate, is contained in the plasma membrane of the plant motor cell. These proteins would be potential receptors for leaf-movement factor to control the leaf movement.     

10°锥角台锥型液相色谱柱尺寸等比例放大和柱内谱带流型的可视化研究

摘要利用改进的可视化装置, 研究了10°锥角的台锥型液相色谱柱内的谱带流型与柱参数变化的关系. 将有机玻璃柱管加工成内圆台外方型的一体结构, 选择折射率一致的色谱固定相硅胶和流动相环己烷, 使整个色谱柱成为高度清晰的透明体, 能直接观察柱中彩色样品谱带的动态三维流型. 研究结果表明, 在实验条件范围内, 流动相流速对谱带流型无影响, 填料的形状和性质对塞子状流型有一定程度的影响. 比较了柱长为5cm和等比例放大后柱长为10cm锥型柱内的流型, 发现放大后的锥型柱内仍然保持塞子状流型, 总柱效等比例增加. 表明继续按比例放大成为工业规模色谱柱后仍能保持塞子状流型.     

DNA codes for nanoscience

The nanometer scale is a special place where all sciences meet and develop a particularly strong interdisciplinarity. While biology is a source of inspiration for nanoscientists, chemistry has a central role in turning inspirations and methods from biological systems to nanotechnological use. DNA is the biological molecule by which nanoscience and nanotechnology is mostly fascinated. Nature uses DNA not only as a repository of the genetic information, but also as a controller of the expression of the genes it contains. Thus, there are codes embedded in the DNA sequence that serve to control recognition processes on the atomic scale, such as the base pairing, and others that control processes taking place on the nanoscale. From the chemical point of view, DNA is the supramolecular building block with the highest informational content. Nanoscience has therefore the opportunity of using DNA molecules to increase the level of complexity and efficiency in self-assembling and self-directing processes.