荧光研究表明去辅基天青蛋白突变体M121L至少存在两种不同的构象

以往对绿脓杆菌去辅基天青蛋白变性机制的研究认为它经历了一个复杂的反应过程,相比之下,锌离子替代的天青蛋白的变性符合简单的二态模型。以脲为变性剂对去辅基天青蛋白突变体M121L的变性过程进行了研究。结果表明,虽然稳态条件下突变体的变性／复性符合二态模型,但其动力学过程复杂,并可用溶液中存在着两种可以相互转化的构象的变性／复性来解释。天然态N1去折叠的速度快,其重折叠的速度也快,N1的折叠机制可用存在着折叠途径上的快速折叠中间体模型来描述;天然态N2的去折叠速度慢,其重折叠主要是首先生成天然态N1,然后再缓慢地转化成N2。添加Zn^2 能够把两种构象整合成一种构象,相应地,Zn^2 替代的天青蛋白突变体的变性过程简化为单指数过程。对该突变体的研究加深了对天青蛋白去折叠机制的理解。     

鸡肝二氢叶酸还原酶在盐酸胍溶液中构象的序变与激活

用蛋白质内源荧光、疏水荧光探针TNS及蛋白酶K限制性酶解等方法研究了二氢叶酸还原酶在盐酸胍变性过程中的构象变化及动力学,并与活力变化进行了比较.TNS可以监测到与激活同步的构象变化;盐酸胍浓度大于0.75mol/L时,二氢叶酸还原酶被蛋白酶K水解速度增大;当盐酸胍浓度大于1.2mol/L时,才能监测到酶分子整体构象的变化.以上结果表明二氢叶酸还原酶在盐酸胍溶液中的变性并不符合标准的二态模型,而是先经历构象逐步松散的序变过程,然后发生协同的构象伸展.二氢叶酸还原酶在低浓度盐酸胍溶液中的激活是由于酶活性部位构象的微小变化引起的.酶活性部位构象的变化虽然降低了酶与废物的结合能力,但加快了酶促反应限速步骤,即底物解离速度而使酶活力升高.     

去辅基天青蛋白两种天然构象共存的热力学证据 ———差热温度扫描和圆二色的研究

天然态蛋白质能否在溶液中存在多种构象是一个有争议的问题 . 在前报道中已经鉴定出绿脓杆菌去辅基天青蛋白突变体 M121L 可以多种构象共存 . 用差热扫描量热和圆二色性的方法研究了野生型去辅基天青蛋白的热变性 . 结果表明在 pH 从 4.0 到 9.0 的范围内存在着两个摩尔热容最大值 . 较低温度下的去折叠反应在所研究 pH 范围内均部分可逆,而较高温度下的去折叠反应均不可逆 . 蛋白质去折叠的热容变化双峰用可相互转化的两种构象共存模型进行拟合 . 较低温度下能够去折叠的构象在 pH 4.0 时占 64% ,在 pH 9.0 时占 55%. 监测热变性过程中圆二色谱在 219 nm 处的信号变化也可以观测到两个独立的去折叠变化 . 信号变化的比值与在相同条件下差热扫描法测得的两种构象摩尔比一致 . 上述结果进一步支持了前文提出的去辅基天青蛋白在溶液中至少存在着两种构象的设想 .     

磷酸丙糖异构酶的折叠及稳定性研究

从鸡胸肌中纯化出磷酸丙糖异构酶(triosephosphateisomerase,TIM),通过蛋白质内源荧光,圆二色性,紫外吸收二阶导数光谱等多种研究溶液构象的方法,对TIM被盐酸胍和热变性过程进行了详细的研究.结果表明,用不同测量方法得到TIM的变性过程均高度协同,没有观察到折叠中间态,应用单分子二态去折叠模型计算了TIM去折叠的热力学参数.通过圆二色光谱在222nm处的变化监测的TIM热变性过程也是高度协同的二态过程,天然态TIM的表观Tm为64.6℃.在低浓度盐酸胍存在下,TIM的热稳定性降低.讨论了二体蛋白质的可能去折叠机制,证明在使用的实验条件下磷酸丙糖异构酶去折叠过程中二级结构与三级结构的变化是同时发生的,其去折叠遵循观察不到二体解离的表观二态过程.     

中华仓鼠二氢叶酸还原酶的酶学性质研究

测定中华仓鼠二氢叶酸还原酶（ＤＨＦＲ,Ｅ．Ｃ．１．５．１．３．）催化反应的各个动力学常数,对其反应机制进行了研究。测定了不同浓度脲溶液中酶与底物的解离常数Ｋｄ和表观米氏常数Ｋｍ,结果表明酶与底物二氢叶酸（ＤＨＦ）和还原型尼克酰胺腺嘌呤二核苷酸磷酸（ＮＡＤＰＨ）的结合能力相差很小,都随脲浓度增加而减弱,而且一种底物的结合会削弱酶与另一底物的结合能力。研究了ＤＨＦＲ在脲变性过程中活力和构象的变化,结果表明低浓度脲可使稳态酶活力增强,此时酶的内源荧光发射光谱和ＣＤ谱变化很小;随脲浓度的增加,酶逐渐失活,同时荧光光谱的最大发射峰位红移,荧光强度和椭圆率也明显下降,说明酶活力的变化先于酶分子整体构象的变化,酶活性部位位于比酶分子整体更易受变性剂影响的有限区域,而且酶分子这种相对的和一定限度内的柔性是其表现生物活性所必需的     

超氧化物歧化酶全酶和脱辅基酶胍变性时失活与去折叠的比较研究

利用紫外差吸收光谱和荧光发射光谱等监测手段研究天然铜锌ＳＯＤ和脱铜锌ＳＯＤ在不同浓度胍溶液中的去折叠及活力变化。结果表明ｈｏｌｏ－ＳＯＤ和ａｐｏ－ＳＯＤ分别在４．０和２．０ｍｏｌ／Ｌ胍溶液中去折叠,而分别在２．０和０．５ｍｏｌ／Ｌ胍溶液中其构象尚未发生明显改变时活性几乎完全丧失。提示金属离子对维持酶的整体及活性部位构象具有重要作用,脱去金属离子的酶分子的构象特别是活性部位的构象更易受到变性剂的破坏     

重组单链胰岛素在含有巯基试剂的变性剂中的解折叠

重组单链胰岛素(PIP)含有3对二硫键。在含有巯基试剂的变性剂中,PIP产生二硫键交换从而形成一系列具有不同解折叠程度的二硫键异构体混合物。分别用高压液相色谱（HPLC）和圆二色性（CD）光谱分析了PIP在含有0．2mmol/L2－巯基乙醇的尿素和盐酸胍中的解中的解折叠程度。PIP二硫键异构体混合物通过胰蛋白酶酶解并用质谱测定酶解片段的分子量,证明PIP确实产生了二硫键交换。同时还分离纯化了PIP的一种主要非天然二硫键异构体并研究了它重新折叠成天然构象的情况。观察到PIP只有一种热力学稳定的二硫键配对方式,PIP的非天然二硫键异构体在巯基试剂存在的条件下可以高效转化为天然二硫键配对。还将PIP解折叠和再折叠的情况与胰岛素样生长因子－I（IGF－I）及胰岛素做了比较：胰岛素和PIP只折叠成一种热力学稳定的三级结构,IGF－I却折叠成两种热力学稳定的二硫键异构体;胰岛素的双链重组需缓慢进行,而PIP却可以快速折叠。     

绿脓杆菌apoazurin在溶液中存在两种天然构象

如何解释绿脓杆菌apoazurin变性过程的复杂机制是一个有争议的问题.最近的研究表明apoazurin的复杂变性机制可以归结为其天然态存在着至少两种构象.利用内源荧光发射谱和圆二色谱进一步研究了apoazurin的脲变性机制,发现其稳态脲变性符合表观的二态过程,但其动力学为双相过程.在高浓度脲中快反应在几秒钟内完成,而慢反应要经过几个小时.快反应和慢反应的mu值分别为2.24和2.45kJ·mol-1·M-1,去折叠活化能的差值为22kJ·mol-1.时间分辨的荧光发射谱和圆二色谱可以用天然态和完全变性态的谱图通过一个固定的比例参数进行重建.结果表明,过去被广泛接受的存在着变性中间体的机制是不正确的,而apoazurin在天然态存在至少两种构象的假设是合理的.     

超氧化物歧化酶全酶和脱辅基酶胍变性时失活与去折叠的比较研究

利用紫外差吸收光谱和荧光发射光谱等监测手段研究天然铜锌ＳＯＤ（ｈｏｌｏ－ＳＯＤ）和脱铜锌ＳＯＤ（ａｐｏ－ＳＯＤ）在不同浓度胍溶液中的去折叠及活力变化．结果表明ｈｏｌｏ－ＳＯＤ和ａｐｏ－ＳＯＤ分别在４．０和２．０ｍｏｌ／Ｌ胍溶液中去折叠,而分别在２．０和０．５ｍｏｌ／Ｌ胍溶液中其构象尚未发生明显改变时活性几乎完全丧失．提示金属离子对维持酶的整体及活性部位构象具有重要作用,脱去金属离子的酶分子的构象特别是活性部位的构象更易受到变性剂的破坏．     

江浙蝮蛇毒酸性与碱性磷脂酶A_2溶液构象变化的差示扫描量热法研究

运用差示扫描量热法,在不同ｐＨ值的缓冲溶液内和各种浓度的碱土族氯化物溶液内,研究了来自江浙蝮蛇（ＡｇｋｉｓｔｒｏｄｏｎｈａｌｙｓＰａｌｌａｓ）毒的酸性与碱性磷脂酶外Ａ２（ＰＬＡ２）的热变性过程。得到表征这两种酶溶液构象变化的热力学参数。依据这些参数研究了两者的溶液构象及其变化。在ｐＨ４．５以下,分子净荷正电的这两种酶在溶液中不形成可热致伸展的有序构象;ｐＨ高于４．５时,Ａｓｐ和Ｇｌｕ的侧链羧基以负离子形式存在有利于有序构象的稳定。Ｈｉｓ是决定ＰＬＡ２活力和热稳定性的重要残基。磷酸根离子和这两种酶有结合作用而降低有序构象的热稳定性。碱土族阳离子除和这两种酶结合外,还以依赖于离子强度的方式复杂地影响酶的溶液构象,但其作用不完全是静电性的,是或多或少地随离子的不同而不同的。计算给出酸性ＰＬＡ２的△Ｈｃｄ．     

Folding of dihydrofolate reductase from Escherichia coli

The urea-induced equilibrium unfolding transition of dihydrofolate reductase from Escherichia coli was monitored by UV difference, circular dichroism (CD), and fluorescence spectroscopy. Each of these data sets were well described by a two-state unfolding model involving only native and unfolded forms. The free energy of folding in the absence of urea at pH 7.8, 15 degrees C is 6.13 +/- 0.36 kcal mol-1 by difference UV, 5.32 +/- 0.67 kcal mol-1 by CD, and 5.42 +/- 1.04 kcal mol-1 by fluorescence spectroscopy. The midpoints for the difference UV, CD, and fluorescence transitions are 3.12, 3.08, and 3.18 M urea, respectively. The near-coincidence of the unfolding transitions monitored by these three techniques also supports the assignment of a two-state model for the equilibrium results. Kinetic studies of the unfolding and refolding reactions show that the process is complex and therefore that additional species must be present. Unfolding jumps in the absence of potassium chloride revealed two slow phases which account for all of the amplitude predicted by equilibrium experiments. Unfolding in the presence of 400 mM KCl results in the selective loss of the slower phase, implying that there are two native forms present in equilibrium prior to unfolding. Five reactions were observed in refolding: two slow phases designated tau 1 and tau 2 that correspond to the slow phases in unfolding and three faster reactions designated tau 3, tau 4, and tau 5 that were followed by stopped-flow techniques. The kinetics of the recovery of the native form was monitored by following the binding of methotrexate, a tight-binding inhibitor of dihydrofolate reductase, at 380 nm.(ABSTRACT TRUNCATED AT 250 WORDS)     

Ligand binding to a high‐energy partially unfolded protein

The conformational energy landscape of a protein determines populations of all possible conformations of the protein and also determines the kinetics of the conversion between the conformations. Interaction with ligands influences the conformational energy landscapes of proteins and shifts populations of proteins in different conformational states. To investigate the effect of ligand binding on partial unfolding of a protein, we use Escherichia coli dihydrofolate reductase (DHFR) and its functional ligand NADP⁺ as a model system. We previously identified a partially unfolded form of DHFR that is populated under native conditions. In this report, we determined the free energy for partial unfolding of DHFR at varying concentrations of NADP⁺ and found that NADP⁺ binds to the partially unfolded form as well as the native form. DHFR unfolds partially without releasing the ligand, though the binding affinity for NADP⁺ is diminished upon partial unfolding. Based on known crystallographic structures of NADP⁺‐bound DHFR and the model of the partially unfolded protein we previously determined, we propose that the adenosine‐binding domain of DHFR remains folded in the partially unfolded form and interacts with the adenosine moiety of NADP⁺. Our result demonstrates that ligand binding may affect the conformational free energy of not only native forms but also high‐energy non‐native forms.     

Folding mechanism of the (H3-H4)2 histone tetramer of the core nucleosome

To further understand oligomeric protein assembly, the folding and unfolding kinetics of the H3-H4 histone tetramer have been examined. The tetramer is the central protein component of the core nucleosome, which is the basic unit of DNA compaction into chromatin in the eukaryotic nucleus. This report provides the first kinetic folding studies of a protein containing the histone fold dimerization motif, a motif observed in several protein-DNA complexes. Previous equilibrium unfolding studies have demonstrated that, under physiological conditions, there is a dynamic equilibrium between the H3-H4 dimer and tetramer species. This equilibrium is shifted predominantly toward the tetramer in the presence of the organic osmolyte trimethylamine-N-oxide (TMAO). Stopped-flow methods, monitoring intrinsic tyrosine fluorescence and far-UV circular dichroism, have been used to measure folding and unfolding kinetics as a function of guanidinium hydrochloride (GdnHCl) and monomer concentrations, in 0 and 1 M TMAO. The assignment of the kinetic phases was aided by the study of an obligate H3-H4 dimer, using the H3 mutant, C110E, which destabilizes the H3-H3' hydrophobic four-helix bundle tetramer interface. The proposed kinetic folding mechanism of the H3-H4 system is a sequential process. Unfolded H3 and H4 monomers associate in a burst phase reaction to form a dimeric intermediate that undergoes a further, first-order folding process to form the native dimer in the rate-limiting step of the folding pathway. H3-H4 dimers then rapidly associate with a rate constant of > or =10(7) M(-1)sec(-1) to establish a dynamic equilibrium between the fully assembled tetramer and folded H3-H4 dimers.     

Quantitative analysis of the kinetics of denaturation and renaturation of barstar in the folding transition zone.

The fluorescence-monitored kinetics of folding and unfolding of barstar by guanidine hydrochloride (GdnHCl) in the folding transition zone, at pH 7, 25 degrees C, have been quantitatively analyzed using a 3-state mechanism: U(S)<-->UF<-->N. U(S) and UF are slow-refolding and fast-refolding unfolded forms of barstar, and N is the native protein. U(S) and UF probably differ in possessing trans and cis conformations, respectively, of the Tyr 47-Pro 48 bond. The 3-state model could be used because the kinetics of folding and unfolding of barstar show 2 phases, a fast phase and a slow phase, and because the relative amplitudes of the 2 phases depend only on the final refolding conditions and not on the initial conditions. Analysis of the observed kinetics according to the 3-state model yields the values of the 4 microscopic rate constants that describe the transitions between the 3 states at different concentrations of GdnHCl. The value of the equilibrium unfolded ratio U(S):UF (K21) and the values of the rate constants of the U(S)-->UF and UF-->U(S) reactions, k12 and k21, respectively, are shown to be independent of the concentration of GdnHCl. K21 has a value of 2.1 +/- 0.1, and k12 and k21 have values of 5.3 x 10(-3) s-1 and 11.2 x 10(-3) s-1, respectively. Double-jump experiments that monitor reactions that are silent to fluorescence monitoring were used to confirm the values of K21, k12, and k21 obtained from the 3-state analysis and thereby the validity of the 3-state model.(ABSTRACT TRUNCATED AT 250 WORDS)     

Folding of staphylococcal nuclease A studied by equilibrium and kinetic circular dichroism spectra

The urea-induced unfolding of staphylococcal nuclease A has been studied by circular dichroism both at equilibrium and by the kinetics of unfolding and refolding (pH 7.0 and 4.5 degrees C), as a function of Ca2+ and thymidine 3',5'-diphosphate (pdTp) concentration. The results are as follows. (1) The unfolding transition is shifted to higher concentrations of urea by Ca2+ and pdTp, and the presence of both ligands further stabilizes the protein. (2) In the first stage of kinetic refolding, the peptide ellipticity changes rapidly within the dead time of stopped-flow measurement (15 ms), indicating accumulation of a transient intermediate. This intermediate is remarkably less stable than those of other globular proteins previously studied. (3) Dependence of the folding and unfolding rate constants on urea concentration indicates that the critical activated state of folding ("transition state") has considerable structural organization. The transition state does not, however, have the capacity to bind Ca2+ and pdTp, as indicated by the effects of these ligands on the unfolding rate constant. (4) There are at least four different phases in the refolding kinetics in native conditions below 1 M urea. In the absence of pdTp, there are two phases in unfolding, while in the presence of pdTp the unfolding kinetics show a single phase. Some characteristics of the transient intermediate and of the transition state for folding are discussed.     

Formation of on- and off-pathway intermediates in the folding kinetics of Azotobacter vinelandii apoflavodoxin

The folding kinetics of the 179-residue Azotobacter vinelandii apoflavodoxin, which has an alpha-beta parallel topology, have been followed by stopped-flow experiments monitored by fluorescence intensity and anisotropy. Single-jump and interrupted refolding experiments show that the refolding kinetics involve four processes yielding native molecules. Interrupted unfolding experiments show that the two slowest folding processes are due to Xaa-Pro peptide bond isomerization in unfolded apoflavodoxin. The denaturant dependence of the folding kinetics is complex. Under strongly unfolding conditions (>2.5 M GuHCl), single exponential kinetics are observed. The slope of the chevron plot changes between 3 and 5 M denaturant, and no additional unfolding process is observed. This reveals the presence of two consecutive transition states on a linear pathway that surround a high-energy on-pathway intermediate. Under refolding conditions, two processes are observed for the folding of apoflavodoxin molecules with native Xaa-Pro peptide bond conformations, which implies the population of an intermediate. The slowest of these two processes becomes faster with increasing denaturant concentration, meaning that an unfolding step is rate-limiting for folding of the majority of apoflavodoxin molecules. It is shown that the intermediate that populates during refolding is off-pathway. The experimental data obtained on apoflavodoxin folding are consistent with the linear folding mechanism I(off) <==> U <==> I(on) <== > N, the off-pathway intermediate being the molten globule one that also populates during equilibrium denaturation of apoflavodoxin. The presence of such on-pathway and off-pathway intermediates in the folding kinetics of alpha-beta parallel proteins is apparently governed by protein topology.     

Testing the role of chain connectivity on the stability and structure of dihydrofolate reductase from E. coli: fragment complementation and circular permutation reveal stable, alternatively folded forms

The effects of chain cleavage and circular permutation on the structure, stability, and activity of dihydrofolate reductase (DHFR) from Escherichia coli were investigated by various spectroscopic and biochemical methods. Cleavage of the backbone after position 86 resulted in two fragments, (1--86) and (87--159) each of which are poorly structured and enzymatically inactive. When combined in a 1 : 1 molar ratio, however, the fragments formed a high-affinity (K(a) = 2.6 x 10(7) M(-1)) complex that displays a weakly cooperative urea-induced unfolding transition at micromolar concentrations. The retention of about 15% of the enzymatic activity of full-length DHFR is surprising, considering that the secondary structure in the complex is substantially reduced from its wild-type counterpart. In contrast, a circularly permuted form with its N-terminus at position 86 has similar overall stability to full-length DHFR, about 50% of its activity, substantial secondary structure, altered side-chain packing in the adenosine binding domain, and unfolds via an equilibrium intermediate not observed in the wild-type protein. After addition of ligand or the tight-binding inhibitor methotrexate, both the fragment complex and the circular permutant adopt more native-like secondary and tertiary structures. These results show that changes in the backbone connectivity can produce alternatively folded forms and highlight the importance of protein-ligand interactions in stabilizing the active site architecture of DHFR.     

Transient intermediates in the folding of dihydrofolate reductase as detected by far-ultraviolet circular dichroism spectroscopy

The kinetics of the reversible folding and unfolding of Escherichia coli dihydrofolate reductase have been studied by stopped-flow circular dichroism in the peptide region at pH 7.8 and 15 degrees C. The reactions were induced by concentration jumps of a denaturant, urea. The method can detect various intermediates transiently populated in the reactions although the equilibrium unfolding of the protein is apparently approximated by a two-state reaction. The results can be summarized as follows. (1) From transient circular dichroism spectra measured as soon as the refolding is started, a substantial amount of secondary structure is formed in the burst phase, i.e., within the dead time of stopped-flow mixing (18 ms). (2) The kinetics from this burst-phase intermediate to the native state are multiphasic, consisting of five phases designated as tau 1, tau 2, tau 3, tau 4, and tau 5 in increasing order of the reaction rate. Measurements of the kinetics at various wavelengths have provided kinetic difference circular dichroism spectra for the individual phases. (3) The tau 5 phase shows a kinetic difference spectrum consistent with an exciton contribution of two aromatic residues in the peptide CD region. The absence of the tau 5 phase in a mutant protein, in which Trp 74 is replaced by leucine, suggests that Trp 74 is involved in the exciton pair and that the tau 5 phase reflects the formation of a hydrophobic cluster around Trp 74. From the similarity of the kinetic difference spectrum to the difference between the native spectra of the mutant and wild-type proteins, it appears that Trp 47 is the partner in the exciton pair and that the structure formed in the tau 5 phase persists during the later stages of folding. (4) The later stages of folding show kinetic difference spectra that can be interpreted by rearrangement of secondary structure, particularly the central beta sheet of the protein. The pairwise similarities in the spectrum between the tau 3 and tau 4 phases, and between the tau 1 and tau 2 phases, also suggest the presence of two parallel folding channels for refolding. (5) The unfolding kinetics show three to four phases and are interpreted in terms of the presence of multiple native species. The total ellipticity change in kinetic unfolding reaction, however, agrees with the ellipticity difference between the native and unfolding states, indicating the absence of the burst phase in unfolding.(ABSTRACT TRUNCATED AT 400 WORDS)     

Structure of a partially unfolded form of Escherichia coli dihydrofolate reductase provides insight into its folding pathway

Proteins frequently fold via folding intermediates that correspond to local minima on the conformational energy landscape. Probing the structure of the partially unfolded forms in equilibrium under native conditions can provide insight into the properties of folding intermediates. To elucidate the structures of folding intermediates of Escherichia coli dihydrofolate reductase (DHFR), we investigated transient partial unfolding of DHFR under native conditions. We probed the structure of a high‐energy conformation susceptible to proteolysis (cleavable form) using native‐state proteolysis. The free energy for unfolding to the cleavable form is clearly less than that for global unfolding. The dependence of the free energy on urea concentration (m‐value) also confirmed that the cleavable form is a partially unfolded form. By assessing the effect of mutations on the stability of the partially unfolded form, we found that native contacts in a hydrophobic cluster formed by the F‐G and Met‐20 loops on one face of the central β‐sheet are mostly lost in the partially unfolded form. Also, the folded region of the partially unfolded form is likely to have some degree of structural heterogeneity. The structure of the partially unfolded form is fully consistent with spectroscopic properties of the near‐native kinetic intermediate observed in previous folding studies of DHFR. The findings suggest that the last step of the folding of DHFR involves organization in the structure of two large loops, the F‐G and Met‐20 loops, which is coupled with compaction of the rest of the protein.