酸诱导拥挤条件下肌红蛋白及突变体去折叠过程

采用紫外-可见吸收光谱、同步荧光光谱和圆二色(CD)光谱法研究拥挤试剂葡聚糖70 (Dextran70)和聚蔗糖70 (Ficoll70)存在条件下, 酸诱导野生型肌红蛋白Mb(WT)及其突变体Mb(D60K)的去折叠过程. 结果显示: 在Dextran70 和Ficoll70 两种拥挤环境下, Mb(WT)的变性中点pH值由4.25 分别降低到3.78 与3.76, 拥挤试剂加入后增强了Mb(WT)的耐酸能力; 肌红蛋白60位天冬氨酸(Asp)突变为赖氨酸(Lys)后, 变性中点pH值由4.25 降低到4.19, 耐酸性比野生型肌红蛋白有所增强, Mb(D60K)在Dextran70 和Ficoll70 两种拥挤环境下变性中点pH值由4.19 分别降至3.74 和3.12. 以上实验说明肌红蛋白表面氨基酸突变和拥挤试剂的添加起到了稳定血红素微环境、芳香族氨基酸及二级结构和保护蛋白天然状态的作用.     

光谱与停流荧光法研究肌红蛋白及其突变体D60K与表面活性剂的相互作用

用停流荧光法、紫外光谱法、荧光光谱法和圆二色(CD)光谱法研究了肌红蛋白(Mb)及其突变体Mb(D60K)分别与两种表面活性剂的相互作用.停流荧光数据表明不同浓度的十二烷基硫酸钠(SDS)和十六烷基三甲基溴化铵(CTAB)与Mb及Mb(D60K)相互作用均为(准)一级反应,虽然Mb(D60K)只是将肌红蛋白表面的60位天冬氨酸突变为赖氨酸,但二者性质差异显著,说明60位氨基酸对蛋白质性质影响较大.紫外、荧光与圆二色谱的结果也表明在上述表面活性剂作用下肌红蛋白及其突变体结构与功能均发生变化,其适应性和稳定性有一定差异.综合数据分析得知,肌红蛋白突变体D60K在表面活性剂溶液中性质更加稳定.     

D60K Mb定点突变对肌红蛋白结构及荧光量子产率的影响

为了探究肌红蛋白表面60位的Asp突变为Lys后对蛋白荧光强度的影响,在模拟生理条件下,利用荧光法和圆二色法对WT Mb及D60K Mb的结构及荧光光谱特性进行了对照研究,结果表明D60K Mb的荧光量子产率远大于WT Mb。通过研究pH值和结构对荧光量子产率的影响,发现Mb 60位天冬氨酸(Asp)突变为赖氨酸(Lys)后,蛋白表面电荷发生改变,导致蛋白的荧光量子产率明显增强;同时使蛋白内部的芳香族氨基酸较原来更暴露,极性增强,激发态分子的去激发过程由原来的无辐射能量转移为主转变为辐射能量转移为主,最终导致荧光强度增强。     

荧光法对光诱导野生型肌红蛋白和突变体(D44K)去氧的对照研究

用荧光法对光诱导野生型肌红蛋白(Mb)和突变体(D44K)去氧的过程进行对照研究。发现430nm是研究Mb(WT)和Mb(D44K)光照去氧的最佳激发波长。430nm激发时,Mb(D44K)在597.9nm和628.8nm处出现两个荧光发射峰,不同于Mb(WT)仅在597nm处出现一个荧光发射峰。经研究证明,628.8nm处荧光峰是Mb3 -H2O型中的H2O峰。光照也使此峰的荧光强度下降,但比去氧的速率慢。研究发现,597nm处Mb(D44K)的荧光效率比Mb(WT)的荧光效率低。传能实验表明Mb表面44位氨基酸由天冬氨酸突变为赖氨酸后,不影响Mb(D44K)中色氨酸和酪氨酸残基传递给铁卟啉的荧光效率,但使Mb(D44K)中色氨酸和酪氨酸残基的荧光效率变高。     

细胞色素b5 S64X突变体对蛋白结构及稳定性的影响

为了深入了解细胞色素b₅(Cyt b₅)64位氨基酸残基(Ser64)对血红素辅基微环境及蛋白性质的影响,我们分别对Cyt b₅ Ser64进行了保守性突变(S64T)以及非保守性突变(S64K、S64N和S64H),均为亲水性氨基酸残基。对野生型细胞色素b₅及其突变体蛋白S64X(X：T,K,N或H)的热、酸、盐酸胍变性的稳定性研究表明：4个突变体蛋白的稳定性相对于野生型都大大降低了;CD光谱表明,细胞色素b₅ S64X突变体中的α-螺旋明显减少,芳香性氨基酸残基所处的肽链结构受到了影响;盐酸胍变性荧光光谱表明,Trp22周围的蛋白肽链受到了影响,Trp22暴露于水溶液的程度加大。我们认为Ser64不仅对血红素辅基有稳定作用,同时还对维持蛋白Core 1中的第5个α-螺旋结构有重要的作用,在64位引入其他氨基酸残基影响了第5个α-螺旋的结构,并通过蛋白肽链的相互作用,使得Trp22所在的Core 2结构也受到了较为明显的扰动。     

细胞色素c突变研究进展

在简述细胞色素c的生物功能和结构特征的基础上,综述了细胞色素c突变研究的进展,重点论述了对血红素辅基(heme)的轴向配体Met80、heme所在腔的保守氨基酸残基Tyr67以及蛋白表面的保守氨基酸残基Phe82的突变研究,并对一些突变体蛋白表现出来的特殊性质给予解释。     

苏丹红Ⅱ与肌红蛋白相互作用的分子模拟与实验

用荧光光谱法研究了苏丹红Ⅱ与肌红蛋白(Mb)之间的相互作用, 实验结果表明,二者结合位点数近似为1, 结合常数K=3.84×107L/mol, 有很强的相互作用. 用分子柔性对接技术模拟确定了它们之间的作用位点、作用力类型及相互作用能. 理论计算的结果表明,苏丹红Ⅱ和Mb相互作用的势能为-9419.9 kJ/mol, 静电能为-7468.8 kJ/mol, 范德华能为-1951.0 kJ/mol. 苏丹红Ⅱ与Mb中His64残基形成氢键, 苏丹红Ⅱ也能与疏水氨基酸残基, 如能产生内源荧光的Phe33、Phe43、Phe106 和 Phe138等发生作用, 这与苏丹红Ⅱ能使Mb荧光猝灭的实验结果是一致的.     

表面带负电荷氨基酸残基的突变对细胞色素b5与细胞色素c结合和识别的影响

利用核磁共振方法研究表面带不同负电荷氨基酸残基突变后的细胞色素b5与细胞色素c的结合与识别. 结果表明, 静电作用在细胞色素b5与细胞色素c的结合过程中有着重要的贡献, 而且这些静电贡献在一定程度上具有累加性, E48的贡献略大于E44. 同时还证明Brownian dynamics simulations优化出的\{Glu48-Lys13\}, Glu56-Lys87, Asp60-Lys86和heme 6-propionate-Tml72(细胞色素b5的残基排在前面)的结合方式在溶液中的确存在. 细胞色素b5突变体(E48, E56/A, D60/A)及 [Cr(oxalate)3]3-对细胞色素c的表面结合竞争实验表明, 细胞色素c表面结合区Site Ⅲ仍然同细胞色素b5突变体(E48, E56/A, D60/A)有结合作用, 只是结合强度上相对于野生细胞色素b5同细胞色素c的结合有所降低. 这表明除上述的Brownian dynamics simulations模型外, 尚有其它如Salemme模型等的结合方式, 这也揭示出细胞色素b5和细胞色素c之间的结合是比较动态的.     

八肋游仆虫中心蛋白N端半分子Loop区首个氨基酸的作用

本文通过分子生物学方法将八肋游仆虫中心蛋白N端半分子loop区的首个氨基酸,天冬氨酸Asp37和Asp73,分别突变为带相反电荷的赖氨酸。使用铽敏化荧光、TNS疏水探针研究了八肋游仆虫中心蛋白N端半分子loop区的首个氨基酸的作用。结果表明：当中心蛋白loop Ⅰ区37位的天冬氨酸突变为赖氨酸后,loop Ⅰ丧失了金属离子结合能力,进而影响了中心蛋白依赖于金属离子的构象变化;而loop Ⅱ区73位的天冬氨酸突变为赖氨酸后仍保持金属离子结合能力,依赖于金属离子的构象变化减小。中心蛋白发挥大部分生物功能都依赖于金属离子,这就表明loop Ⅰ区37位的天冬氨酸在中心蛋白发挥生物功能时起着重要作用,是不可缺少的。在10 mmol·L^-1 Hepes、pH 7.4、20 mmol·L^-1 KCl条件下,八肋游仆虫中心蛋白N端半分子loop Ⅱ与金属离子Tb³⁺和Ca²⁺的结合常数分别为：K_Ⅱ(Tb³⁺)=(8.31±0.18)×10⁴ L·mol^-1和K_Ⅱ(Ca²⁺)=(0.94±0.12)×10² L·mol^-1,中心蛋白N端半分子的两个金属结合部位结合能力顺序为：Ⅰ>Ⅱ。     

表面带负电荷氨基酸残基的突变对细胞色素bs与细胞色素c结合和识别的影响

利用核磁共振方法研究表面带不同负电荷氨基酸残基突变后的细胞色素b5与细胞色素c的结合与识别，结果表明，静电作用在细胞色素b5与细胞色素c的结合过程中有着重要的贡献，而且这些静电贡献在一定程度上具有 加性，E48的贡献略大于E44。同时还证明Brownian dyanmics simulations优化出的Glu48-Lys13,Clu56-Lys87,Asp60-Lys86和heme 6-propionate-Tml72（细胞色素b5的残基排在前面）的结合方式在溶液中的确存在，细胞色素b5突变体9E48，E56／A，D60／A）及[Cr(oxalate)3]^3－对细胞色素c的表面竞争实验表明，细胞色素c表面结合区SiteⅢ仍然同细胞色素b5突变体9E48，E56／A，D60／A）有结合作用，只是结合强度上相对于野生细胞色素b5同细胞色素c的结合有所降低，这表明除上述的Browni-an dynamics simulations模型外，尚有其它如Salemme模型等的结合方式，这也揭示出细胞色素b5和细胞色素c之间的结合是比较动态的。     

An analysis of ATP binding with kinase catalytic subunit by molecular dynamics simulation of the CDK2 active kinase crystal lattice

Molecular dynamics simulation was used to analyze changes in the functionally significant structural elements of the crystal lattices of pT160-CDK2/cyclin and A/ATP-Mg²⁺/substrate complexes of the native (CDK2-G16) and mutant (CDK2-S16) active kinases at physiological temperatures (300 K). The structural rearrangement of ATP caused by changes in the kinase catalytic domain was studied. ATP was fixed by the ionic and H-bond interactions of several residues, including Lys33, Asp145, and side-chain amides of the G loop between β1 and β2. The binding of the kinases to complexes with cyclin and the phosphorylation of T160 in the active complex of the CDK2 kinase result in the ATP orientation more convenient for the transfer of the phosphate group to the substrate. An analysis of interatomic distances in the ATP active site region and Asp145, Asn132, Lys33 catalytic sites participating in the orientation of ATP phosphates revealed that the Asp 145 amino acid residue was situated noticeably closer to the ATP molecule in the native complex than in its mutant counterpart. The same is true of the arrangement of the Lys33 residue with respect to ATP.     

The correct molecular weight of myoglobin, a common calibrant for mass spectrometry.

Myoglobins from horse heart muscle, horse skeletal muscle and sperm whale are widely used as calibration standards or test compounds for various mass spectrometric methodologies. In all such cases reported in the literature, a molecular weight value is used (16,950.5 and 17,199, respectively) which is based on the assumption that amino acid 122 in this 153 amino-acid-long protein is asparagine, overlooking a published suggestion that it is aspartic acid instead. Since the mass assignment accuracy for matrix-assisted laser desorption mass spectrometry is reported to be +/- 0.01% and for electrospray ionization +/- 0.0025%, and error of one mass unit in approximately 17,000 would be significant. The mass-to-charge ratio of ions of the tryptic peptide encompassing amino acid 122 derived from commercially available horse heart and horse skeletal myoglobins, the apomyoglobin of the latter, and the tryptic and chymotryptic peptide of sperm whale myoglobin proved that in both proteins amino acid 122 is indeed aspartic acid, rather than asparagine. This finding was further confirmed by the collision-induced dissociation spectra of the [M + H]+ ions of the tryptic peptides from the horse myoglobins and the chymotriptic peptide from sperm whale myoglobin. Thus, the correct molecular weight of horse myoglobin is 16,951.49 and that of the sperm whale protein is 17,199.91.     

Stereospecific capillary electrophoresis assays using pentapeptide substrates for the study of Aspergillus nidulans methionine sulfoxide reductase A and mutant enzymes

Stereospecific capillary electrophoresis‐based methods for the analysis of methionine sulfoxide [Met(O)]‐containing pentapeptides were developed in order to investigate the reduction of Met(O)‐containing peptide substrates by recombinant Aspergillus nidulans methionine sulfoxide reductase A (MsrA) as well as enzymes carrying mutations in position Glu99 and Asp134. The separation of the diastereomers of the N‐acetylated, C‐terminally 2,4‐dinitrophenyl (Dnp)‐labeled pentapeptides ac‐Lys‐Phe‐Met(O)‐Lys‐Lys‐Dnp, ac‐Lys‐Asp‐Met(O)‐Asn‐Lys‐Dnp and ac‐Lys‐Asn‐Met(O)‐Asp‐Lys‐Dnp was achieved in 50 mM Tris‐HCl buffers containing sulfated β‐CD in fused‐silica capillaries, while the diastereomer separation of ac‐Lys‐Asp‐Met(O)‐Asp‐Lys‐Dnp was achieved by sulfated β‐CD‐mediated MEKC. The methods were validated with regard to range, linearity, accuracy, limits of detection and quantitation as well as precision. Subsequently, the substrates were incubated with wild‐type MsrA and three mutants in the presence of dithiothreitol as reductant. Wild‐type MsrA displayed the highest activity towards all substrates compared to the mutants. Substitution of Glu99 by Gln resulted in the mutant with the lowest activity towards all substrates except for ac‐Lys‐Asn‐Met(O)‐Asp‐Lys‐Dnp, while replacement Asn for Asp134 lead to a higher activity towards ac‐Lys‐Asp‐Met(O)‐Asn‐Lys‐Dnp compared with the Glu99 mutant. The mutant with Glu instead of Asp134 was the most active among the mutant enzymes. Molecular modeling indicated that the conserved Glu99 residue is buried in the Met‐S‐(O) groove, which might contribute to the correct placing of substrates and, consequently, to the catalytic activity of MsrA, while Asp134 did not form hydrogen bonds with the substrates but only within the enzyme.     

Unusual ligand discrimination by a myoglobin reconstituted with a hydrophobic domain-linked heme

New, reconstituted horse heart myoglobins possessing a hydrophobic domain at the terminal of the two heme propionate side chains were constructed. The O2 and CO bindings for the reconstituted deoxymyoglobins were examined in detail by laser flash photolysis and stopped-flow rapid mixing techniques. The artificially created domain worked as a barrier against exogenous ligand penetration into the heme pocket, whereas the bound O2 was stabilized in the reconstituted myoglobin as well as in the native one. In contrast, the CO dissociation rate for the reconstituted myoglobin increased by 20-fold compared to the native protein, suggesting that the incorporation of the hydrophobic domain onto the heme pocket perturbs the distal-site structure of the reconstituted myoglobin. As a result, the substantial ligand selectivity for the reconstituted myoglobin significantly increases in favor of O2 over CO with the M' value (= KCO/KO2) of 0.88, whereas, to the best of our knowledge, there is no myoglobin mutant in which the O2 affinity exceeds the CO one. The present work concludes that the O2 selectivity of myoglobin over CO is markedly improved by chemically modifying the heme propionates without any mutation of the amino acid residues in the distal site.     

IDENTIFICATION OF THE PROTON ACCEPTOR OF SCHIFF BASE DEPROTONATION IN BACTERIORHODOPSIN: A FOURIER-TRANSFORM-INFRARED STUDY OF THE MUTANT ASP85 → GLU IN ITS NATURAL LIPID ENVIRONMENT

Abstract— In order to assign the proton acceptor for Schiff base deprotonation in bacteriorhodopsin to a specific Asp residue, the photoreaction of the Asp85 → Glu mutant, as expressed in Halobacterium sp . GRB, was investigated by static low-temperature and time-resolved infrared difference spec-troscopy. Measurements were also performed on the mutant protein labeled with [4-¹³C]Asp which allowed discrimination between Asp and Glu residues. 14,15-di¹³C-retinal was incorporated to distinguish amide-II absorbance changes from changes of the ethylenic mode of the chromophore. In agreement with earlier UV-VIS measurements, our data show that from both the 540 and 610 nm species present in a pH-dependent equilibrium, intermediates similar to K and L can be formed. The 14 ms time-resolved spectrum of the 540 nm species shows that a glutamic acid becomes protonated in the M-like intermediate, whereas the comparable difference spectrum of the 610 nm species demonstrates that in the initial state a glutamic acid is already protonated. In conjunction with earlier observations of protonation of an Asp residue in wild-type M, the data provide direct evidence that the proton acceptor in the deprotonation reaction of the Schiff base is Asp85.     

Structural studies of the Maillard reaction products of a protein using ion trap mass spectrometry

The early stage products of the Maillard reaction of egg white lysozyme with D-glucose were studied. Incubation with D-glucose at 50 degrees C for 20 days caused reaction on the Lys and Arg residues of lysozyme as follows: all of the six Lys residues and 10 of the 11 Arg residues in lysozyme reacted with D-glucose; Arg 61 did not react with D-glucose. The Lys residues reacted with D-glucose with 1 mol of dehydration per mole of residue, and the Arg residues reacted with 2 mol of dehydration per mole of residue. The major constituent of the Amadori product with the epsilon-amino group of the Lys residue and the D-glucose was found to be the beta-pyranose form. The structure of the early stage product of the Maillard reaction of a protein with a sugar is the same as that of an amino acid with a sugar.     

A mechanistic study of electrospray mass spectrometry: Charge gradients within electrospray droplets and their influence on ion response

A model has been developed to account qualitatively for the effects of ion pairing, surface activity, and electrophoretic mobility in electrospray mass spectrometry. The model is tested with various salt and amino acid mixtures. The data suggest that the axial charge gradient arising from electrophoretic separation at droplet genesis may persist within the electrosprayed droplets at least until the first droplet fission, accounting for the field dependence of detected ion clustering of quaternary ammonium salts and for the relatively field-invariant charge distribution of horse heart myoglobin samples.     

STATISTICAL PROPERTIES OF LONG-RANGE CONTACTS IN GLOBULAR PROTEINS

The analysis of residue-residue contacts in protein structures can shed some light on our understanding of the folding and stability of proteins. In this paper, we study the statistical properties of long-range and short-range residue-residue contacts of 91 globular proteins using CSU software and analyze the importance of long-range contacts in globular protein structure. There are many short-range and long-range contacts in globular proteins, and it is found that the average number of long-range contacts per residue is 5.63 and the percentage of residue-residue contacts which are involved in long-range ones is 59.4%. In more detail, the distribution of long-range contacts in different residue intervals is investigated and it is found that the residues occurring in the interval range of 4-10 residues apart in the sequence contribute more long-range contacts to the stability of globular protein. The number of long-range contacts per residue, which is a measure of ability toform residue-residue contacts, is also calculated for 20 different amino acid residues. It is shown that hydrophobic residues (including Leu, Val, Ile, Met, Phe, Tyr, Cys and Trp) having a large number of long-range contacts easily form long-range contacts, while the hydrophilic amino acids (including Ala, Gly, Thr, His, Glu, Gln, Asp, Asn, Lys, Ser, Arg, and Pro) form long-range contacts with more difficulty. The relationship between the Fauchere-Pliska hydrophobicity scale (FPH) and the number of short-range and long-range contacts per residue for 20 amino acid residues is also studied. An approximately linear relationship between the Fauchere-Pliska hydrophobicity scale (FPH) and the number of long-range contacts per residue CL is found and can be expressed as