光谱法研究钙调素与蜂毒肽片断及其类似物的相互作用

设计合成了蜂毒肽片断及其类似物:Mel15,Mel15(8F)和Mel15(7P),这些多肽与钙调素有很强的结合力,而且链段很短,因此它们可作为钙调素可结合蛋白质的结合部位的模型.本文采用光谱法研究了它们与钙调素的相互作用.荧光发射光谱法结果表明,多肽Mel15在与钙调素相互作用时,肽链中的Trp基团的微环境变得更加疏水,说明Mel15中的Trp残基可能与钙调素的疏水性表面靠近.紫外差谱测试表明,只有当钙调素分子结合2个Ca~(2+)后,才可以与多肽Mel15(8F)结合.圆二色谱法研究表明,多肽与钙调素结合后多肽分子和钙调素分子的α-螺旋结构的含量都被诱导而增加,结合力越大,则越多的残基被诱导形成α-螺旋结构.     

莲藕多酚氧化酶与底物或抑制剂相互作用的光谱学研究

本文研究了纯化的莲藕多酚氧化酶(PPO)与底物和抑制剂相互作用时的二级结构变化。园二色谱分析表明莲藕PPO主要含有α-螺旋和β-折叠结构。与抑制剂作用后,莲藕PPO活性显著降低,同时伴随其二级结构中α-螺旋结构明显减少,表明莲藕PPO的活性中心可能位于α-螺旋结构中。荧光分析表明,莲藕PPO与邻苯三酚(pyrogallic acid,PA)作用后,酪氨酸残基荧光强度略有降低,λmax位移不明显,色氨酸残基荧光强度略有降低,λmax红移2 nm;而与莲藕多酚(Lotus root polyphenol,LRP)作用后,莲藕PPO分子中酪氨酸(Tyr)和色氨酸(Trp)残基荧光强度显著提高,且其最大发射波长分别蓝移6nm和红移5nm。当加入异Vc钠后,Tyr和Trp残基最大发射峰显著红移,说明Trp和Tyr残基位于一定的疏水环境对维持PPO催化活性的优势构象至关重要。     

多肽对钙调素亲和力的预测

根据前文提出的钙调素可结合多肽的钙调素结合部位的模型,并综合钙调素可结合多肽的报道,提出一种简单方法来预测多肽的钙调素结合部位和其复合物的解离常数,研究了多肽的疏水性、形成α螺旋结构的倾向、碱性等因素对解离常数的影响.为了进一步检验模型和预测方法,设计合成了模型肽,合成的模型肽与钙调素的复合物的解离常数的实测值与预测值相符.     

硅钨杂多酸与牛血红蛋白相互作用的研究

多金属氧酸盐作为抗艾滋病病毒、抗流感病毒和抗肿瘤的药物,引起了人们对多金属氧酸与蛋白质之间相互作用的极大关注。蛋白质空间结构的任何变化引起的构象变化都意味着蛋白质分子的活性改变,因此,蛋白质与内源性化合物及许多药物分子之间相互作用的研究一直受到人们关注[1￣3]。血红蛋白是动物及人体内执行输氧任务的蛋白质,是生命机体进行各种生理活动的主要承担者。血红蛋白分子中每条α链和β链含有的色氨酸(Trp)残基分别为α-14Trp、β-15Trp、β-37Trp。Alpert[4]等认为位于疏水腔内的β-37Trp是血红蛋白内源荧光的主要来源,同时β…     

光谱法与分子对接法研究山柰酚对牛血清白蛋白二级结构的影响

采用分子对接技术和同步荧光光谱法、红边激发荧光位移法(REES法)及圆二色谱法(CD)共同研究了山柰酚与牛血清白蛋白(BSA)在pH7.40的缓冲溶液中的相互作用。分子对接的结果表明,山柰酚的B环插入到BSA的ⅡA结构域中的疏水腔内,与色氨酸残基(Trp212)的距离为12.96,维系药物与蛋白质的主要作用力为疏水作用。通过荧光光谱法测得二者之间相互作用力主要为疏水性相互作用,结合位点为1,与分子模拟结果一致。同步荧光光谱及REES法的研究表明,发生相互作用的过程中BSA的色氨酸残基处于运动受限的微环境中,而适当增加山柰酚的浓度能够改变色氨酸微环境的流动性,进而对BSA的构象产生一定影响;同时,圆二色谱的定量计算结果也表明,一定浓度的山柰酚与BSA的相互作用引起了α-螺旋含量的显著降低,从11.91%降低到1.67%,对BSA的二级结构产生一定影响。     

多肽抑制剂抑制淀粉质多肽42构象转换的分子动力学模拟和结合自由能计算

应用分子动力学模拟和结合自由能计算方法研究了多肽抑制剂KLVFF、VVIA和LPFFD抑制淀粉质多肽42 (Aβ42)构象转换的分子机理. 结果表明, 三种多肽抑制剂均能够有效抑制Aβ42的二级结构由α-螺旋向β-折叠的构象转换. 另外, 多肽抑制剂降低了Aβ42分子内的疏水相互作用, 减少了多肽分子内远距离的接触, 有效抑制了Aβ42的疏水塌缩, 从而起到稳定其初始构象的作用. 这些抑制剂与Aβ42之间的疏水和静电相互作用(包括氢键)均有利于它们抑制Aβ42的构象转换. 此外, 抑制剂中的带电氨基酸残基可以增强其和Aβ42之间的静电相互作用(包括氢键), 并降低抑制剂之间的聚集, 从而大大增强对Aβ42构象转换的抑制能力. 但脯氨酸的引入会破坏多肽的线性结构, 从而大大降低其与Aβ42 之间的作用力. 上述分子模拟的结果揭示了多肽抑制剂KLVFF、VVIA和LPFFD抑制Aβ42构象转换的分子机理, 对于进一步合理设计Aβ的高效短肽抑制剂具有非常重要的理论指导意义.     

影响多肽与花粉钙调素亲和性的因素──多肽的圆二色性及核磁共振研究

钙调素 ( Ca M)存在于所有真核细胞生物体内 ,它可与很多天然的生物活性肽结合 ,如 β-内啡肽、胰高血糖素和某些昆虫毒液肽等 [1] .有关 Ca M与多肽相互作用的研究普遍认为 ,对 Ca M有高亲和性的多肽应该具有形成α螺旋结构的显著倾向[2 ] .为进一步确认多肽的主链构象对 Ca M亲和能力的影响 ,我们采用圆二色性光谱和核磁共振波谱分析了荞麦花粉碱性十二肽 BPP-1和它的类似物 BPP-3的结构特征 ,配合多肽对花粉钙调素 ( p Ca M)的结合能力 ,发现肽链的可塑性和 C端的极性是影响多肽与 p Ca M亲和能力的因素 ,而形成 α螺旋结构的倾…     

蜂毒肽与CT-DNA的相互作用

通过圆二色光谱、紫外光谱、荧光光谱以及等温滴定量热等技术研究了蜂毒肽(Mel)与小牛胸腺DNA(CT-DNA)之间的相互作用以及构象变化。结果表明Mel可以与CT-DNA形成复合物。复合物的形成使得Mel的构象发生变化,由无规卷曲转变为α-helix,Mel中色氨酸残基处于更加疏水的环境。同时,CT-DNA的结构发生变化,解链温度(T_m)从64.3℃增加到66.2℃。Mel与CT-DNA的结合常数(K_a)约为10⁵L·mol^-1,复合物的形成是吸热的过程,主要依靠静电作用,其次是疏水作用。     

罗非昔布与牛血清白蛋白之间相互作用的研究

在模拟人体生理条件下,通过荧光光谱法、紫外光谱法、红外光谱法和分子对接等技术探究罗非昔布(RFB)与牛血清白蛋白(BSA)之间相互作用的化学本质。研究结果表明,RFB与BSA的Trp/Tyr残基之间的π-π堆积作用诱导了BSA的荧光发生猝灭,其猝灭机制为静态猝灭并且伴随着非辐射能量的转移;热力学参数表明RFB-BSA可以自发地通过氢键与范德华力进行结合,二者之间的结合距离r_0=3.50 nm,且结合位点数为1;同步荧光和分子对接结果证明RFB与BSA在结合位点Ⅰ结合;三维荧光光谱与红外光谱揭示了RFB导致BSA蛋白质二级结构发生变化,其中α-螺旋和β-片层结构含量下降,β-折叠和β-转角含量上升。     

光谱学结合分子动力学研究秋水仙碱与血红蛋白之间相互作用机制

本文通过分子光谱、分子对接以及分子动力学模拟等技术手段探究了秋水仙碱与血红蛋白(Hb)之间相互作用的模式与机制。分子光谱和非辐射能量转移理论研究结果表明秋水仙碱通过范德华力与Hb结合,并导致Hb的构象发生改变。分子对接和分子动力学研究发现秋水仙碱在Hb的中央空腔与其形成稳定的复合物,并导致Hb的结构变得紧密,从而驱动Hb二级结构中的α-螺旋、β-转角、弯曲、无规则卷曲等结构的含量发生显著变化。Hb的某些氨基酸残基如:Trp37(β2)、Ala130(α2)、Pro90(α1)、Thr137(α1)、Tyr35(β2)等在它们结合的过程中发挥着至关重要的作用。实验数据和模拟研究结果相互印证,为进一步揭示秋水仙碱在生物体内的作用机制提供重要信息和参考依据。     

A new way to understand quaternary structure changes of hemoglobin upon ligand binding on the basis of UV-resonance Raman evaluation of intersubunit interactions

The single residue vibrational spectra of tryptophan (Trp) and tyrosine (Tyr) residues in human adult hemoglobin (HbA), which play important roles in cooperative oxygen binding, were determined for the deoxy and CO-bound forms by applying UV resonance Raman spectroscopy to various variant Hbs. It was found that Trpβ37, Tyrα42, Tyrα140, and Tyrβ145 at the α(1)-β(2) subunit interface underwent transitions between two contact states (named as T and R) upon ligand binding, while Trpα14, Trpβ15, and Tyrβ35 displayed little changes. The corresponding spectral changes were identified only for the α(2)β(2) tetramer, but not the isolated α and β chains in the oligomeric forms, and therefore were exclusively attributed to a quaternary structure change. Ligand binding as well as allosteric effectors and pH altered only the number of the T-contacted Tyr and Trp residues without varying the two contact states themselves. A new method to semiquantitatively evaluate the amount of T-contacted Tyr and Trp residues in a given liganded form is here proposed, and with it a quaternary structure was determined for various symmetrically half-liganded forms obtained with ligand-hybrid, metal-hybrid, and valency-hybrid Hbs. It was found that ligand binding to the α or β subunits yielded different subunit contacts and that the contact changes of the Trp and Tyr residues were not always concerted. The contact changes at the α(1)-β(2) (α(2)-β(1)) interface are correlated with the proximal strain exerted on the Fe-His(F8) bond, which is noted to be much larger in the α than β subunits in the α(2)β(2) tetramer.     

Two-dimensional fluorescence correlation spectroscopy IV: resolution of fluorescence of tryptophan residues in alcohol dehydrogenase and lysozyme

Generalized two-dimensional (2D) fluorescence correlation spectroscopy has been used to resolve the fluorescence spectra of two tryptophan (Trp) residues in alcohol dehydrogenase and lysozyme. In each protein, one Trp residue is buried in a hydrophobic domain of the protein matrix and the other Trp residue is located at a hydrophilic domain close to the protein-water interface. Fluorescence quenching by iodide ion, a hydrophilic quencher, was employed as a perturbation to induce the intensity change in the spectra. The Trp residue which is located at the hydrophilic domain is effectively quenched by the quencher, while the Trp residue located at the hydrophobic domain is protected from the quenching. Therefore, the fluorescence of these two Trp residues have a different sensitivity to the quenching, showing a different response to the concentration of the quencher. Fluorescence spectra of the two Trp residues in alcohol dehydrogenase, which are heavily overlapped in conventional one-dimensional spectra, have been successfully resolved by the 2D correlation technique. From the asynchronous correlation map, it was revealed that the quenching of Trp located at the hydrophobic part was brought about after that of Trp located at the hydrophilic part. In contrast, the fluorescence spectra of the two Trp residues could not be resolved after the alcohol dehydrogenase was denatured with guanidine hydrochloride. These results are consistent with the well-known structure of alcohol dehydrogenase. Furthermore, it was elucidated that the present 2D analysis is not interfered by Raman bands of the solvent, which sometimes bring difficulty into the conventional fluorescence analysis. Fluorescence spectra of the Trp residues in lysozyme could not be resolved by the 2D correlation technique. The differences between the two proteins are attributed to the fact that the Trp residue in the hydrophobic site of lysozyme is not sufficiently protected from the quenching.     

稀土离子对钙调蛋白与蜂毒素作用的影响

分别用钙调蛋白和蜂毒素的内源荧光光谱以及铽离子的敏化荧光光谱考察了铽离子对钙调蛋白构象变化以及对钙调蛋白与蜂毒素相互作用的影响 .结果表明 ,铽离子首先结合在钙调蛋白的第Ⅰ和第Ⅱ位点 ,铽离子不影响钙调蛋白与蜂毒素的相互作用 ,蜂毒素与钙调蛋白作用后不影响铽离子在钙调蛋白上的键合顺序 .傅里叶变换红外光谱结果表明三价的镧离子与钙调蛋白作用使钙调蛋白的α螺旋结构增加 ,β折叠结构减少 ,与钙离子对它的二级结构影响相类似 .稀土离子在钙调蛋白 -蜂毒素复合体系中主要与钙调蛋白作用 .     

Organic Ligand Binding by a Hydrophobic Cavity in a Designed Tetrameric Coiled‐Coil Protein

The design and characterization of a hydrophobic cavity in de novo designed proteins provides a wide range of information about the functions of de novo proteins. We designed a de novo tetrameric coiled‐coil protein with a hydrophobic pocketlike cavity. Tetrameric coiled coils with hydrophobic cavities have previously been reported. By replacing one Leu residue at the a position with Ala, hydrophobic cavities that did not flatten out due to loose peptide chains were reliably created. To perform a detailed examination of the ligand‐binding characteristics of the cavities, we originally designed two other coiled‐coil proteins: AM2, with eight Ala substitutions at the adjacent a and d positions at the center of a bundled structure, and AM2W, with one Trp and seven Ala substitutions at the same positions. To increase the association of the helical peptides, each helical peptide was connected with flexible linkers, which resulted in a single peptide chain. These proteins exhibited CD spectra corresponding to superhelical structures, despite weakened hydrophobic packing. AM2W exhibited binding affinity for size‐complementary organic compounds. The dissociation constants, K_d, of AM2W were 220 nM for adamantane, 81 μM for 1‐adamantanol, and 294 μM for 1‐adamantaneacetic acid, as measured by fluorescence titration analyses. Although it was contrary to expectations, AM2 did not exhibit any binding affinity, probably due to structural defects around the designed hydrophobic cavity. Interestingly, AM2W exhibited incremental structure stability through ligand binding. Plugging of structural defects with organic ligands would be expected to facilitate protein folding.     

家蝇幼虫抗菌肽MDL-1的构象分析

用红外光谱、圆二色谱和荧光光谱研究家蝇幼虫抗菌肽MDL-1的结构特征及其在不同条件下的构象变化. 红外光谱检测结果显示抗菌肽MDL-1结构中含有螺旋、无规卷曲、折叠构象的吸收特征; 圆二色谱显示抗菌肽MDL-1结构相对比较稳定, 抗菌肽在不同浓度溶液中的构象发生改变; 荧光光谱法研究发现家蝇幼虫抗菌肽MDL-1在280 nm波长的激发光下, 荧光光谱为Tyr残基和Trp残基共同提供, 而且Trp残基不是位于抗菌肽分子的表面, 而是位于分子的内部, 该研究结果为进一步探讨抗菌肽的抗菌机理奠定了基础.     

光谱法比较喜树碱与溶菌酶、过氧化氢酶的相互作用

采用紫外可见吸收、红外、荧光等多种光谱学方法研究了抗癌药物喜树碱和溶菌酶及过氧化氢酶两种蛋白之间的相互作用,结果表明,喜树碱与之均形成基态复合物并引起蛋白内源荧光猝灭。通过计算确定了喜树碱和蛋白相互作用的结合常数、结合位点数、主要作用力类型以及与蛋白中色氨酸的结合距离。喜树碱对过氧化氢酶具有较高的结合能力,这主要是由于喜树碱不仅与过氧化氢酶中的色氨酸存在相互作用,也与酶中的酪氨酸及血红素产生相互作用。喜树碱的存在可引起蛋白构象发生变化,使α-螺旋二级结构减少。     

Quenching of tryptophan fluorescence in various proteins by a series of small nickel complexes

A series of twelve anionic, cationic, and neutral nickel(II) complexes have been synthesized and characterized. The interaction of these complexes with bovine serum albumin (BSA), human serum albumin (HSA), lysozyme (Lyso), and tryptophan (Trp) has been studied using steady-state fluorescence spectroscopy. Dynamic and static quenching constants have been calculated, and the role played in quenching by the ligand and complex charge investigated. The nickel complexes showed selectivity towards the different proteins based on the environment surrounding the Trp residue(s). Only small neutral complexes with hydrophobic ligands effectively quenched protein fluorescence via static quenching, with association constants ranging from 10(2) M(-1) (free Trp) to 10(10) M(-1) (lysozyme), indicating a spontaneous and thermodynamically favorable interaction. The number of binding sites, on average, was determined to be one in BSA, HSA and free Trp, and two in lysozyme.     

Binding of alkaloids into the S1 specificity pocket of α-chymotrypsin: evidence from induced circular dichroism spectra

Non-covalent binding of planar aromatic molecules into the S1 specificity pocket of the serine protease α-chymotrypsin (αCHT) can be detected by measuring induced circular dichroism (CD) spectroscopic signals. Utilizing this phenomenon, αCHT association of proflavine (PRF), the well known serine protease inhibitor has been investigated together with plant-derived compounds including isoquinoline, pyridocarbazole and indoloquinoline alkaloids, of which αCHT binding has never been reported. Non-degenerate exciton coupling between π-π* transitions of the ligand molecules and two tryptophan residues (Trp172 and Trp215) near to the binding site is proposed to be responsible for the induced CD activity. The association constants calculated from CD titration data indicated strong αCHT association of sanguninarine, ellipticine, desmethyl-isocryptolepine and isoneocryptolepine (K(a) ≈ 10(5) M(-1)) while berberine, coptisine and chelerythrine bind to the enzyme with lower, PRF-like affinity (K(a) ≈ 10(4) M(-1)). PRF-trypsin and ellipticine-trypsin binding interactions have also been demonstrated. The binding of the alkaloids into the S1 pocket of αCHT has been confirmed by CD competition experiments. Molecular docking calculations showed the inclusion of PRF as well as the alkaloid molecules in the S1 cavity where they are stabilized by hydrophobic and H-bonding interactions. These novel nonpeptidic scaffolds can be used for developing selective inhibitors of serine proteases having chymotrypsin-like folds. Furthermore, the results provide a novel, CD spectroscopic based approach for probing the ligand binding of αCHT and related proteases.     

Characterization of the tryptophan residues of human placental ribonuclease inhibitor and its complex with bovine pancreatic ribonuclease A by steady-state and time-resolved emission spectroscopy

Human placental ribonuclease inhibitor (hRI) containing six tryptophan (Trp) residues located at positions 19, 261, 263, 318, 375, and 438 and its complex with RNase A have been studied using steady-state and time-resolved fluorescence (298 K) as well as low-temperature phosphorescence (77 K). Two Trp residues in wild-type hRI and also in the protein-protein complex with RNase A are resolved optically. The accessible surface area values of Trp residues in the wild-type hRI and its complex and consideration of inter-Trp energy transfer in the wild-type hRI reveal that one of the Trp residues is Trp19, which is located in a hydrophobic buried region. The other Trp residue is tentatively assigned as Trp375 based on experimental results on wild-type hRI and its complex. This residue in the wild-type hRI is more or less solvent exposed. Both the Trp residues are perturbed slightly on complex formation. Trp19 moves slightly toward a more hydrophobic region, and the environment of Trp375 becomes less solvent exposed. The complex formation also results in a more heterogeneous environment for both the optically resolved Trp residues.     

Effect of temperature and pH on the aggregation and the surface hydrophobicity of bovine κ-casein

κ-Casein (κ-CN) aggregation by heating has been studied at pH 7.2 and 5.2 using UV-visible spectrophotometry, sodium dodecyl sulfate polyacrylamide gel electrophoresis, spectrofluorometric study of the 1–8 aniline naphtalene sulfonate (ANS)–κ-CN binding and circular dichroism (CD) spectroscopy. The aggregation process to form aggregates like micelles or submicelles and the structural characteristics of these aggregates were pH dependent. Far-UV CD showed that the aggregates obtained by heating presented changes in the κ-CN secondary structure. Near-UV CD spectra showed a certain degree of tertiary organization in the Tyr environment for the protein heated or unheated, only at pH 5.2. ANS binding at both pH was quite different and depends on the self-association process. Heating produced exposition of hydrophobic binding sites only at pH 7.2, including those in the neighborhood of the κ-CN Trp residue.