光谱法对照研究肌红蛋白及其突变体Mb(D60K)与H_2O_2的相互作用

为了解肌红蛋白(Mb)表面60位天冬氨酸(Asp)突变为赖氨酸(Lys)后对蛋白结构稳定性的影响,本文通过紫外-可见吸收光谱、荧光光谱和停流荧光光谱对照研究了模拟生理条件下野生型肌红蛋白Mb(WT)及其突变体Mb(D60K)与过氧化氢(H2O2)的相互作用。结果表明:在Mb(D60K)与H2O2发生相互作用过程中,铁卟啉部位的紫外和荧光发射光谱数据与Mb(WT)相比,性质与功能均表现出显著差异。虽然只有一个氨基酸的改变,但其结构和性质发生明显变化,说明60位氨基酸在稳定蛋白结构中有重要的作用。同步荧光光谱和停流光谱的结果同样表明Mb(D60K)的结构与功能受H2O2的影响较小,Mb(WT)受H2O2影响明显。综合分析表明,Mb(D60K)在与H2O2相互作用过程中,蛋白结构稳定性提高。     

光谱及分子探针方法研究番茄Metacaspase蛋白与Ca~(2+)的相互作用

Metacaspases(MCPs)是发现于植物、真菌、原生动物体内的一种结构上类似多细胞动物Caspase的半胱氨酸蛋白酶家族,其大多数成员的激活依赖于钙离子,但钙离子如何影响MCPs的激活机制有待深入研究。借助圆二色谱技术、Terbium/Stains-all探针技术以及荧光光谱技术,以番茄Ⅱ型Metacaspase(LeMCA1)重要位点突变的三种体外原核表达重组蛋白,包括LeMCA1C139A(活性催化位点突变体)、LeMCA1K223G(自降解位点突变体)以及预测的Ca2+结合位点突变体LeMCA1D116A/D117A为研究材料,探究了MCPs与Ca2+相互作用机制。实验结果表明,Ca2+与LeMCA1之间既不存在强烈的结合作用,也不影响蛋白的二级结构,但Ca2+通过相互作用改变LeMCA1的三级结构来实现对LeMCA1的酶原激活过程。其中,LeMCA1蛋白的Asp-116,Asp-117氨基酸残基作为预测的与Ca2+作用的重要位点,其缺失将导致蛋白与Ca2+相互作用能力下降。利用圆二色谱、荧光光谱结合离子探针技术研究了典型茄科植物番茄中Ca2+与LeMCA1的相互作用特性,结合之前同源序列比对、位点突变结果确定了LeMCA1中的Asp-116,Asp-117氨基酸残基影响着Ca2+与蛋白质的相互作用。该结果对后续LeMCA1的生化特性及晶体结构的解析研究有着重要的参考价值。     

光谱法结合分子动力学模拟研究臭氧对肌红蛋白结构的作用机制

臭氧(O₃)是一种具有强氧化性作用的杀菌消毒剂,因其安全无害等特点已被广泛用于肉制品生产加工的减菌处理,但O₃减菌处理对红肉色泽具有较强的负面作用,且其作用机制尚缺乏研究。针对肌红蛋白（Mb）存在状态是决定红色肉色泽关键因素的基础,通过紫外-可见吸收光谱法、荧光光谱法和圆二色光谱法（CD）研究O₃作用下Mb的光谱特性变化,结合蛋白质氧化特征指标分析和分子动力学模拟技术探究O₃对Mb分子的作用效果与机制。光谱研究结果表明,O₃处理可使Mb的紫外-可见光谱图在412 nm左右处的铁卟啉环特征峰及540和580 nm附近的氧合肌红蛋白（OMb）特征峰的强度减弱,其中铁卟啉环特征峰发生蓝移;利用固定激发波长280 nm下测定Mb内源性荧光和同步荧光光谱表明O₃会降低Mb的荧光强度,增大铁卟啉基团贡献的荧光峰强度和造成酪氨酸残基荧光光谱特征峰的蓝移;O₃作用使Mb三维荧光光谱特征峰强度的下降及光散射强度的增加。以上变化推断出O₃会促进Mb的氧化,造成其氨基酸残基疏水基团裸露,使Mb所处微环境及其蛋白构象改变;CD分析表明O₃与肌红蛋白接触时间越久,蛋白质二级结构变化越明显,造成α-螺旋的含量下降,无规则卷曲增加。辅以检测不同强度O₃处理Mb的含量及性质的变化,可知O₃处理使OMb含量下降,高铁肌红蛋白（MMb）含量增加,同时O₃处理Mb的羰基含量增加和巯基含量下降,这也进一步证实O₃作用促进了Mb的氧化,此外,O₃处理Mb表面疏水性的增强,说明O₃造成Mb体系微环境的极性变化。分子动力学模拟结果显示O₃会提高Mb肽链的RMSD值,影响Mb肽链的稳定性,减弱铁卟啉环与Mb肽链的相互作用;RMSF结果表明Mb活性口袋附近氨基酸残基的变化较大;蛋白质二级结构分析与光谱学试验研究结果一致,Mb的α-螺旋的含量下降,无规则卷曲增加。总而言之,O₃可作用于Mb的氨基酸残基,导致蛋白质二级结构和疏水性改变,并发生蛋白氧化及铁卟啉环暴露,进而引起红色肉色泽发生改变。该研究可为生鲜红肉护色技术制定等提供一定理论依据。     

改写生命密码

 利用基因工程设计生命体以获取蛋白质,需要编辑自然界的标准遗传密码--以字母C(胞嘧啶)、T(胸腺嘧啶)、A(腺嘌呤)、G(鸟嘌呤)表示--这个过程漫长复杂、代价高昂。美国耶鲁大学的艾萨克(Farren Isaacs)和同事找到一种方法,可以随心所欲地编辑遗传密码。
在DNA 中,每三个密码子组成一个基因。TAG或TAA 表示“停止”,其他组合则表达为各种氨基酸。研究者将酵母菌株中的TAG 替换为TAA,移除TAG 密码子后,他们有效地空出位置以容纳表达氨基酸(化学家制造出的几千种“非自然”氨基酸)的密码子,这就可以生产前所未有的蛋白质。这种方法可以构造非常奇异的生命体,对各种病毒均具有免疫力,而且不会与自然的生命体发生杂交现象。     

聚合酶链反应(PCR)的热性能对乙型肝炎病毒检测的影响

聚合酶链式反应(PCR)是由变性、退火及延伸三个步骤反复循环的DNA体外扩增技术.本文实验研究了PCR仪的三个阶段的热性能.结果显示,PCR实际温度与程序设置温度之间存在着较大的偏差;在变性阶段的温度差达3 K以上;而且处于平台温度±1℃范围内的时间也比设置的要短得多.本文同时用3.3 kb(扩增区150 bp)的乙型肝炎病毒(HBV-DNA)为试验材料(模板),实验研究了变性温度及变性时间对PCR扩增结果的影响.用电泳法分离PCR产物结果表明:当变性温度低于91℃,变性温度高于95℃,或者变性时间超过30 s都会导致乙型肝炎病毒PCR检验结果的假阴性.     

光谱法表征蛋白酶K的热变性过程

用不同温度处理蛋白酶K,以变性酪蛋白底物法测定酶活力,稳态/瞬态荧光光谱法和圆二色谱法测定空间构象和二级结构,研究温度对蛋白酶K酶活力和构象的影响。温度由25 ℃升高至65 ℃过程中,蛋白酶K的酶活力逐渐降低,半衰期缩短;发射光谱荧光强度降低,峰位由335 nm红移至354 nm;色氨酸残基同步荧光强度降低,酪氨酸残基同步荧光强度增大;色氨酸残基荧光寿命由4.427 1 ns降低至4.032 4 ns;α-螺旋百分含量降低。结果表明：采用稳态/瞬态荧光光谱法和圆二色谱法能较简便、准确的描述蛋白酶K的热稳定性变化;蛋白酶K的热变性过程符合三态模型,存在一个中间态;蛋白酶K分子内部存在酪氨酸残基对色氨酸残基的共振能量转移作用;α-螺旋是维系蛋白酶K活性中心构象稳定性的主要结构。     

用光子标记技术实时动态观测中性粒细胞吞噬病原体细胞

基因标记和光子学显象技术相结合,实时观测中性粒细胞吞噬病原体细胞骨架运动规律。利用致冷CCD系统组建了高灵敏度的荧光激发与测试装置。将带有绿色荧光蛋白(GFP)基因的PRSETB质粒转化大肠杆菌BL21,利用BL21高效表达GFP后发出强烈绿色荧光的特点,用光子显象技术连续记录荧光的变化,从而在不受干扰的条件下实时动态观察了中性粒细胞粘附、内吞、消化大肠杆菌的全过程。     

基于分子动力学的脂肪酶Lipase 5的热稳定性研究

天然的低温脂肪酶往往结构热稳定性比较差,制约了其长时间有效地发挥催化作用及保存. 该研究以来源于白色念珠菌（Candida albicans）的低温脂肪酶Lipase 5为对象,运用相关分子动力学方法进行研究,提出了提高其热稳定性的理论策略. 首先运用同源建模方法构建目标蛋白的三维结构模型;然后通过18ns分子动力学模拟,锚定目标蛋白不稳定区域中柔性氨基酸(甘氨酸)的位置,并将这些柔性氨基酸位点突变为刚性氨基酸(脯氨酸);最后利用分子动力学模拟来验证这些突变对蛋白质热稳定性的影响. 结果发现,将Lipase 5三维结构中的第279位甘氨酸突变为脯氨酸后,使得蛋白质热稳定性增强. 这为类似低温脂肪酶的热稳定性改造的实验设计提供了理论支持.     

基于分子动力学的脂肪酶Lipase 5的热稳定性研究

天然的低温脂肪酶往往结构热稳定性比较差,制约了其长时间有效地发挥催化作用及保存.该研究以来源于白色念珠菌(Candida albicans)的低温脂肪酶Lipase 5为对象,运用相关分子动力学方法进行研究,提出了提高其热稳定性的理论策略.首先运用同源建模方法构建目标蛋白的三维结构模型;然后通过18ns分子动力学模拟,锚定目标蛋白不稳定区域中柔性氨基酸(甘氨酸)的位置,并将这些柔性氨基酸位点突变为刚性氨基酸(脯氨酸);最后利用分子动力学模拟来验证这些突变对蛋白质热稳定性的影响.结果发现,将Lipase 5三维结构中的第279位甘氨酸突变为脯氨酸后,使得蛋白质热稳定性增强.这为类似低温脂肪酶的热稳定性改造的实验设计提供了理论支持.     

Fe1.01Se0.4Te0.6单晶的超导电性研究

本文采用自助溶剂法生长得到Fe1.01Se0.4Te0.6单晶样品,超导零电阻温度Tczero=11.0 K,部分样品经400℃进行48小时退火之后,超导零电阻温度变为Tczero=7.0K.分析表明退火后样品的Fe含量变大,超导电性被部分抑制.通过磁场下电阻率-温度曲线的实验测量,用WHH(Werthamer-Helfand-Hohenberg)方法估算得到退火前后样品在0K附近的上临界场分别为83.2T和61.3T.上临界场μ0Hc2(T)随温度变化曲线在0T附近向高温方向上翘,说明样品具有"二流体"行为.直流磁化曲线在40K和120K分别出现向下弯曲,40K处的变化可能对应于过量Fe的自旋冻结.应变测量结果显示样品在117K时应变值发生一个突变,变化量约为晶格参数的0.06%,显示样品发生一个结构相变.因此,120K处的磁化下降对应于样品从四方相到正交相的结构转变.     

Similarities and differences in radiation damage at 100 K versus 160 K in a crystal of thermolysin

The temperature‐dependence of radiation damage in macromolecular X‐ray crystallography is currently much debated. Most protein crystallographic studies are based on data collected at 100 K. Data collection at temperatures below 100 K has been proposed to reduce radiation damage and above 100 K to be useful for kinetic crystallography that is aimed at the generation and trapping of protein intermediate states. Here the global and specific synchrotron‐radiation sensitivity of crystalline thermolysin at 100 and 160 K are compared. Both types of damage are higher at 160 K than at 100 K. At 160 K more residue types are affected (Lys, Asp, Gln, Pro, Thr, Met, Asn) than at 100 K (Met, Asp, Glu, Lys). The X‐ray‐induced relative atomic B‐factor increase is shown to correlate with the proximity of the atom to the nearest solvent channel at 160 K. Two models may explain the observed correlation: either an increase in static disorder or an increased attack of hydroxyl radicals from the solvent area of the crystal.     

Protonation state and free energy calculation of HIV-1 protease–inhibitor complex based on electrostatic polarisation effect

The protonation states of catalytic Asp25/25′ residues remarkably affect the binding mechanism of the HIV-1 protease–inhibitor complex. Here we report a molecular dynamics simulation study, which includes electrostatic polarisation effect, to investigate the influence of Asp25/25′ protonation states upon the binding free energy of the HIV-1 protease and a C₂-symmetric inhibitor. Good agreements are obtained on inhibitor structure, hydrogen bond network, and binding free energy between our theoretical calculations and the experimental data. The calculations show that the Asp25 residue is deprotonated, and the Asp25′ residue is protonated. Our results reveal that the Asp25/25′ residues can have different protonation states when binding to different inhibitors although the protease and the inhibitors have the same symmetry. This study offers some insights into understanding the protonation state of HIV-1 protease–inhibitor complex, which could be helpful in designing new inhibitor molecules.     

Controlled tissue emulsification produced by high intensity focused ultrasound shock waves and millisecond boiling

In high intensity focused ultrasound (HIFU) applications, tissue may be thermally necrosed by heating, emulsified by cavitation, or, as was recently discovered, emulsified using repetitive millisecond boiling caused by shock wave heating. Here, this last approach was further investigated. Experiments were performed in transparent gels and ex vivo bovine heart tissue using 1, 2, and 3 MHz focused transducers and different pulsing schemes in which the pressure, duty factor, and pulse duration were varied. A previously developed derating procedure to determine in situ shock amplitudes and the time-to-boil was refined. Treatments were monitored using B-mode ultrasound. Both inertial cavitation and boiling were observed during exposures, but emulsification occurred only when shocks and boiling were present. Emulsified lesions without thermal denaturation were produced with shock amplitudes sufficient to induce boiling in less than 20 ms, duty factors of less than 0.02, and pulse lengths shorter than 30 ms. Higher duty factors or longer pulses produced varying degrees of thermal denaturation combined with mechanical emulsification. Larger lesions were obtained using lower ultrasound frequencies. The results show that shock wave heating and millisecond boiling is an effective and reliable way to emulsify tissue while monitoring the treatment with ultrasound.     

On the Theory of Initiating Effect of Continuous Heating on Structural Transformations and Phase-Transition Temperature in Crystals

Physics of the Solid State - A model and kinetic theory of structural changes in crystals upon continuous heating are proposed; this theory takes into account nonadiabatic atomic transitions...     

An electron paramagnetic resonance study of conformational substate distribution in high spin heme-proteins

The electron paramagnetic resonance spectra of high spin ferric horse myoglobin and human hemoglobin have been analyzed by computer simulation in terms of a distribution of the metal ion crystal field energies Δ₁ and Δ₂. The widths of these distributions have been put into relation 0 to the distribution of the conformational substates which may be sampled by the biomolecules during their physiological activity and become eventually arrested at low temperature. These distributions are found to be dependent upon both the solvent used and the cooling history to which the samples were submitted. The results are discussed in connection with the physical analogies displayed by these biomolecules and the glassy systems in general.     

The study of heat stress in tomato fruits by NMR microimaging.

The ripening of the tomato fruit was delayed for several days (average 5 days) by a 1-day heat treatment at 42 degrees C. Ethylene production increased during the first 3 h, but, after 6 h inhibition was almost total in tomato fruit incubated at 42 degrees C. However, recovery of ethylene production was rapid if fruits were returned to a temperature of 25 degrees C after heating. In NMR microimaging, three imaging pulse sequences with different repetition and echo times at 42 degrees C were used to obtain the proton density (TR = 6000 ms, TE = 15 ms), the T1 weighted image (TR = 1000 ms, TE = 15 ms) and the T2-weighted image (TR = 6000 ms, TE = 120 ms). After 12 h heating, the water in locular tissues began to show shorter T1 and T2 values. Though the tomatos were returned to 25 degrees C and preserved one more day, the water having a shorter T2 value in locular tissues, did not change. These results show that tomato fruit do not fully recover from heating even after one day, although ethylene production is recovered almost immediately. For this reason, we suggest that some denaturation event inside the tomato, which goes on after the end of heating, is the cause of the delay in tomato ripening.     

Effects of metal ion binding on an oncomodulin mutant containing a novel calcium-binding loop

The Ca²⁺-binding protein oncomodulin was altered by cassette mutagenesis of the CD site (CDOM33) with a sequence that was derived by a consensus method using over 250 known Ca²⁺-binding loop sequences. This mutant was studied using time-resolved and steady-state fluorescence from the Trp residue included at position 7 of the loop (position 57 of the protein sequence). The fluorescence characteristics of this species in the absence and presence of metal ions were compared to those of a tetradecapeptide containing the loop and the single Trp mutant of oncomodulin, Y57W. The fluorescence properties of CDOM33 were quite different from the peptide, both in the apo form and in response to metal binding. The consensus CD loop in CDOM33 exhibited the characteristics of a Ca²⁺/Mg²⁺ site in contrast to the Ca²⁺ specificity of the wild-type CD loop. The Trp analogue, 5-hydroxytryptophan (5HW), was incorporated into both oncomodulin mutants to produce Y75(5HW) and 5HW-CDOM33. Results showed that this intrinsic probe was relatively insensitive to structural changes in the mutants upon metal binding compared to Trp itself.     

Raman spectroscopic differentiation of beef and horse meat using a 671 nm microsystem diode laser

A non-invasive Raman spectroscopic approach for meat species identification and quality detection was successfully demonstrated for the two closely related species beef and horse. Fresh beef and horse muscles were cut and ice-stored at 5 °C, and time-dependent Raman measurements were performed daily up to 12 days postmortem. Applying a 671 nm microsystem diode laser and a laser power of 50 mW, spectra were recorded with integration times of 1–4 s. A pronounced offset of the Raman spectra was observed between horse and beef, with high fluorescence background for horse compared to beef for all days of storage. Principal components analysis was applied for data evaluation revealing a clear distinction between beef and horse meat which can be attributed to differences in the myoglobin content of both species. Furthermore, separations according to aging and spoilage for the two species could be identified simultaneously. Therefore, Raman spectroscopy might be an efficient test method for meat species identification in combination with spoilage detection.