灵芝线粒体及其对菌丝生长、主要活性成分影响的分析

线粒体是为细胞提供能量（ATP）的细胞器,携带着自己的DNA——mtDNA,已有多种灵芝属菌株的线粒体基因组相继报道,但对于种内的线粒体基因组的分析较少,对核相同、线粒体不同的菌株间差异的研究也鲜有报道。本研究对两株灵芝线粒体基因组进行组装注释,根据差异片段构建分子标记进行种间分类。结果显示：两株灵芝线粒体基因组大小分别为49 233bp、61 563bp的闭环结构,含有15个常见蛋白编码基因,rRNA大小亚基基因及26个携带氨基酸的tRNA基因,其差异区段主要为内含子序列、大亚基及基因间区。根据cob、cox2基因序列能够进行灵芝种间区分,用于灵芝种间鉴定。本研究还根据灵芝119、灵芝无孢的单核菌株构建同核异质体（TY-119、TY-W）,分析线粒体对菌落形态、菌丝生长速度及多糖、三萜成分的影响,结果显示：同核异质体TY-W与TY-119菌落形态上有一定差异,同核异质体TY-W菌丝生长速度为4.77mm/d,是TY-119菌丝生长速度4.50mm/d的1.06倍,同核异质体TY-119菌丝、子实体阶段多糖含量分别为4.45mg/g、12.14mg/g是TY-W菌丝体多糖含量（3.23mg/g）的1.38倍、子实体多糖含量（10.24mg/g）的1.19倍;同核异质体TY-W菌丝、子实体阶段的三萜含量分别为6.82mg/g、11.45mg/g是同核异质体TY-119菌丝体三萜含量（9.26mg/g）的0.74倍,子实体三萜含量（9.10mg/g）的1.26倍。利用高效液相色谱分析同核异质体中灵芝酸含量显示同核异质体TY-W灵芝酸A、灵芝酸E、灵芝酸F含量分别为3.77μg/mL、14.29μg/mL、12.91μg/mL;是TY-119灵芝酸A含量（2.59μg/mL）的1.46倍、灵芝酸E含量（13.65μg/mL）的1.17倍、灵芝酸F含量（12.72μg/mL）的1.06倍。对同核异质体菌丝、子实体阶段多糖、三萜合成通路关键基因（pgm、ugp、gls、hmgs、hmgr、mvd、fps、sqs）表达量进行检测,显示两菌株间多数基因具有显著性差异。结果表明线粒体的不同会影响灵芝菌落形态、菌丝生长速度及多糖、三萜的含量,有助于我们进一步研究线粒体基因组。     

Solvation study of the non-specific lipid transfer protein from wheat by intermolecular NOEs with water and small organic molecules

Intermolecular nuclear Overhauser effects (NOEs) were measured between the protons of various small solvent or gas molecules and the non-specific lipid transfer protein (ns-LTP) from wheat. Intermolecular NOEs were observed with the hydrophobic pocket in the interior of wheat ns-LTP, which grew in intensity in the order cyclopropane (saturated solution) < methane (140 bar) < ethane (40 bar) < acetonitrile (5% in water) < cyclohexane (saturated solution) < benzene (saturated solution). No intermolecular NOEs were observed with dioxane (5% in water). The intermolecular NOEs were negative for all of the organic molecules tested. Intermolecular NOEs between wheat ns-LTP and water were weak or could not be distinguished from exchange-relayed NOEs. As illustrated by the NOEs with cyclohexane versus dioxane, the hydrophobic pocket in wheat ns-LTP preferably binds non-polar molecules. Yet, polar molecules like acetonitrile can also be accommodated. The pressure dependence of the NOEs between methane and wheat ns-LTP indicated incomplete occupancy, even at 190 bar methane pressure. In general, NOE intensities increased with the size of the ligand molecule and its vapor pressure. NMR of the vapor phase showed excellent resolution between the signals from the gas phase and those from the liquid phase. The vapor concentration of cyclohexane was fivefold higher than that of the dioxane solution, supporting the binding of cyclohexane versus uptake of dioxane.     

Full 1H NMR assignment of a 24-nucleotide RNA hairpin: Application of the 1H 3D-NOE/2QC experiment

The subject RNA models the binding site for the coat protein of the R17 virus, as well as the ribosome recognition sequence for the R17 replicase gene. With an RNA of this size, overlaps among the sugar protons complicate assignments of the ¹H NMR spectrum. The cross peaks that overlap significantly in 2D-NOE spectra can frequently be resolved by introducing a third, in our approach the double-quantum, frequency axis. In particular the planes in a 3D-NOE/2QC spectrum perpendicular to the 2Q axis are extremely useful, showing a highly informative repeating NOE-2Q pattern. In this experiment substantial J-coupling confers special advantages. This always occurs for geminal pairs (H5/H5 for RNA plus H2/H2 for DNA), as well as for H5/H6, for H3/H4 in sugars with substantial populations of the N-pucker, for H1/H2 for S-puckered sugars, and usually for H2/H3. For the 24-mer RNA hairpin the additional information from the 3D-NOE/2QC spectrum allowed assignment of all of the non-exchangeable protons, eliminating the need for stable-isotope labeling.     

Membrane-bound structure and alignment of the antimicrobial β-sheet peptide gramicidin S derived from angular and distance constraints by solid state 19F-NMR

The antimicrobial properties of the cyclic -sheet peptide gramicidin S are attributed to its destabilizing effect on lipid membranes. Here we present the membrane-bound structure and alignment of a derivative of this peptide, based on angular and distance constraints. Solid-state ¹⁹F-NMR was used to study a ¹⁹F-labelled gramicidin S analogue in dimyristoylphosphatidylcholine bilayers at a lipid:peptide ratio of 80:1 and above. Two equivalent leucine side chains were replaced by the non-natural amino acid 4F-phenylglycine, which serves as a highly sensitive reporter on the structure and dynamics of the peptide backbone. Using a modified CPMG multipulse sequence, the distance between the two ¹⁹F-labels was measured from their homonuclear dipolar coupling as 6 Å, in good agreement with the known backbone structure of natural gramicidin S in solution. By analyzing the anisotropic chemical shift of the ¹⁹F-labels in macroscopically oriented membrane samples, we determined the alignment of the peptide in the bilayer and described its temperature-dependent mobility. In the gel phase, the ¹⁹F-labelled gramicidin S is aligned symmetrically with respect to the membrane normal, i.e., with its cyclic -sheet backbone lying flat in the plane of the bilayer, which is fully consistent with its amphiphilic character. Upon raising the temperature to the liquid crystalline state, a considerable narrowing of the ¹⁹F-NMR chemical shift dispersion is observed, which is attributed the onset of global rotation of the peptide and further wobbling motions. This study demonstrates the potential of the ¹⁹F nucleus to describe suitably labelled polypeptides in membranes, requiring only little material and short NMR acquisition times.     

Hydration of the partially folded peptide RN-24 studied by multidimensional NMR

Summary Peptide-water interactions of a ribonuclease C-peptide analogue, RN-24 (Suc-AETAAAKFLRAHA-NH₂), which exhibits significant helicity, have been studied in solution using homonuclear 2D and 3D NMR cross-relaxation experiments. Dipolar peptide proton-water proton interactions are indicated by a large number of NOESY-type cross peaks at the H₂O resonance frequency, most of them with opposite sign relative to the diagonal. Some cross peaks arise from intrapeptide cross relaxation to labile protons of histidine, threonine, lysine and arginine side chains. The observed peptide-water interactions are rather uniformly distributed, involving peptide backbone and side chains equally. The data are consistent with rapid fluctuations of the conformational ensemble and the absence of peptide regions that are highly shielded from bulk solvent, even in a peptide that exhibits high propensities for formation of helical secondary structure.     

NMR spectrometric assay for determining enzymatic hydrolysis of β-lactam antibiotics with bacteria in aqueous solution

Abstract An application of a nuclear magnetic resonance (NMR) spectrometer for the measurement of β-lactamase activity in clinical material containing bacteria is presented. By means of proton (¹H)-NMR, it was easy to measure quantitatively β-lactamase activity in human bacteriuria, without performing any such pretreatment as isolation of bacteria or extraction of crude enzymes and without preparing special reagents for the detection. This is the first report on the application of ¹H-NMR analysis of structural changes for determining hydrolysis of β-lactam antibiotics with β-lactamase-producing bacteria in aqueous solution.     

Selective structural change of bulged-out region of double-stranded RNA containing bulged nucleotides by spermidine

Polyamines are essential for cell growth due to effects mainly at the level of translation. These effects likely involve a structural change, induced by polyamines, of the bulged-out region of double-stranded RNA that is different from changes induced by Mg²⁺. Structural changes were studied using U6-34, a model RNA of U6 small nuclear RNA containing bulged nucleotides. Binding of NS1-2 peptide derived from the RNA binding site of NS1 protein, to U6-34 was inhibited by spermidine but not by Mg²⁺. A selective conformational change of the bases in the bulged-out region of U6-34 induced by spermidine was observed by NMR. The selective effect of spermidine was lost when the bulged-out region of U6-34 was removed in U6-34(Δ5). The binding of NS1-2 peptide to U6-34(Δ5) was inhibited both by spermidine and Mg²⁺. The selective structural change of U6-34 by spermidine was confirmed by circular dichroism.     

Line narrowing in spectra of proteins dissolved in a dilute liquid crystalline phase by band-selective adiabatic decoupling: Application to 1HN-15N residual dipolar coupling measurements

Residual heteronuclear dipolar couplings obtained from partially oriented protein samples can provide unique NMR constraints for protein structure determination. However, partial orientation of protein samples also causes severe ¹ H line broadening resulting from residual ¹ H-¹H dipolar couplings. In this communication we show that band-selective ¹H homonuclear decoupling during data acquisition is an efficient way to suppress residual ¹H-¹H dipolar couplings, resulting in spectra that are still amenable to solution NMR analysis, even with high degrees of alignment. As an example, we present a novel experiment with improved sensitivity for the measurement of one-bond ¹ H^N-¹⁵N residual dipolar couplings in a protein sample dissolved in magnetically aligned liquid crystalline bicelles.     

Analysis of peptide rotational diffusion by homonuclear NMR

The analysis of the rotational diffusion of a molecule using homonuclear NMR is investigated. The homonuclear longitudinal and transverse cross-relaxation rates, which can be quantitatively measured using off-Resonance Rotating frame nuclear Overhauser Effect Spectroscopy (ROESY), are used to build a distribution, which exhibits a solid-state-like pattern characteristic of the diffusion tensor. The distributions of the antimicrobial peptide ranalexin in water and in 30% of trifluoracetic acid (TFE) are compared, and the peptide rotational diffusion is shown to be more isotropic in water than in 30% TFE. This difference is further supported by the analysis of NMR ranalexin conformers in 30% TFE, and by the analysis of a molecular dynamics simulation of peptide in water.     

Urinary excretion products of formaldehyde in the rat

Thymidine was reacted in methanol with four epoxides of varying mutagenicities: propylene oxide, glycidol, epichlorohydrin and trichloropropylene oxide. A single product was detected with each epoxide, and these products had the same retention times on silica high pressure liquid chromatography (HPLC). UV spectra of the products identified them as 3-alkylthymidines, and this was confirmed by infrared (IR) and nuclear magnetic resonance (NMR) spectra. Mass spectra (MS) analysis showed the products to be consistent with attachment at the least substituted carbon of the epoxide. Formation of 3-alkylthymidines correlated to Taft σ¹ electron withdrawing values for the substituents on the epoxides and mutagenicities in strain TA100 of the Ames Assay.