肌红蛋白力致去折叠的全原子分析（英文）

位于脊椎动物骨骼肌中的肌红蛋白在生命过程中扮演着重要角色,其折叠过程依赖于血红素的绑定.本文着重于肌红蛋白在力的作用下去折叠过程的全原子统计分析.结果表明血红素不仅具有生物学上的功能,而且决定其去折叠的动力学过程.在血红素不存在的情况下,肌红蛋白的力致去折叠过程存在一个中间态,其构象不同于化学变性剂所导致的去折叠中间态,发现新的中间态.结论与相关实验结果相符,揭示了肌红蛋白力致去折叠的一般机制.     

基于光谱法研究盐酸胍诱导的人血红蛋白去折叠过程

借助于紫外-可见吸收光谱法、荧光光谱法以及停流-荧光光谱法研究了盐酸胍(GdmHcl)诱导人血红蛋白的去折叠过程。实验发现,盐酸胍诱导的血红蛋白去折叠有两个不同的过程,即随着GdmHcl浓度增加到1.0 mol·L-1左右时,血红蛋白亚基发生解聚,形成中间态;持续增加其浓度时,各亚基发生内部去折叠,最终导致血红素发生崩解。加入还原剂(β-巯基乙醇)对血红蛋白亚基解聚、血红素崩解有协同作用且直接引起亚基和全分子同步变构。血红蛋白去折叠过程从“三态模型”转变为“二态模型”。     

钙离子调控微丝切割蛋白中A6亚基解折叠的单分子力谱研究

在生命活动中,金属离子扮演了非常重要的角色.微丝切割蛋白(adseverin)需要钙离子的活化才能行使其切割肌动蛋白微丝的功能.本文通过基于原子力显微镜的单分子力谱研究了微丝切割蛋白C端末的A6亚基在结合钙离子前后的力学解折叠机理.实验结果显示:在未结合钙离子时,A6的解折叠表现为两态过程;在结合钙离子后A6力学稳定性显著提高;同时,钙离子的结合使得A6解折叠过程中出现稳定的中间态.通过对中间态的链长的分析,我们推测了中间态对应着A6的N端部分解折叠.而这一部分的解折叠可以使得掩藏在该结构后的A5亚基中肌动蛋白微丝结合位点暴露,从而促使微丝切割蛋白执行功能.我们的实验结果为理解微丝切割蛋白的工作原理提供了新的实验证据.     

新天花粉蛋白的盐酸胍去折叠过程

本文利用荧光光谱和园二色光谱研究了新天花粉蛋白的盐酸胍去折叠过程.结果显示:新天花粉蛋白的盐酸胍去折叠是一个只包含天然蛋白和变性终态的二态过程,与已经报道的天花粉蛋白的盐酸胍去折叠过程不同.     

可见光谱法研究肌红蛋白血红素铁与金属离子相互作用(Ⅰ)

肌红蛋白(Myoglobin,Mb)是哺乳动物细胞主要是肌细胞贮存和分配氧的蛋白质, 由一条多肽链和一个血红素辅基构成,其血红素铁在氧气的传递和运输中起到关键作用。文章利用紫外-可见光谱法对肌红蛋白的血红素铁和外加金属离子M(Ⅱ)[Cu(Ⅱ), Zn(Ⅱ)和Co(Ⅱ)] 的直接相互作用进行了研究。结果发现, 金属离子M(Ⅱ)与肌红蛋白活性中心的Fe(Ⅱ)发生了直接相互作用,外加金属离子将铁离子从肌红蛋白中“拖拽”出来,形成部分空位肌红蛋白衍生物。同时研究了外界条件,如离子浓度对这种相互作用的影响,发现随着外加金属离子量的增加这种相互作用逐渐增强,其作用强度依次为Co(Ⅱ)＞Zn(Ⅱ)＞Cu(Ⅱ)。 研究证实了肌红蛋白的血红素铁与金属离子之间存在直接相互作用,并且离子浓度对这种相互作用有影响。     

新开花粉蛋白的盐酸胍去折叠过程

本文利用荧光光谱和园二色光谱了新开花粉蛋白的盐酸胍去折叠过程。结果显示：新开花粉蛋白的盐酸胍去折叠是一个只包含天然蛋白和变性终态的二态过程,与已经报道的天花粉蛋白的盐酸胍去折叠的过程不同。     

朗之万方程及其在蛋白质折叠动力学中的应用

研究了朗之万方程的动力学性质,并用它模拟了蛋白质分子的折叠过程.首先在相空间中对朗之万方程做连续映射,发现做布朗运动的粒子在位置坐标上存在明显的概率分布,这表明蛋白质折叠过程中分子空间构型是非遍历的.此外,本文还通过数值模拟得到了去折叠态蛋白质的紧密度指标,并验证了它与实验结果以及其他理论方法的一致性.本文还提出了一种利用重整化方法研究熔球体状态蛋白质的理论模型,并提供了考虑疏水基影响的蛋白质折叠过程的模拟思路. 关键词： 朗之万方程 蛋白质折叠非遍历性 紧密度指标 重整化     

荧光光谱法研究氨基改性介孔泡沫对DhaA的稳定化机理

采用F-4600荧光光谱仪,对尿素和二甲基亚砜两种变性剂中烷基卤脱卤酶DhaA在氨基改性介孔泡沫固定化前后的荧光光谱特征进行测定。运用荧光相图分析DhaA在两种变性剂中的去折叠过程,并结合活性残留率进行了变性过程热力学参数计算,比较固定化前后DhaA去折叠过程和热力学参数的区别。实验结果表明,DhaA催化活性随变性剂浓度增加而降低。相同变性剂浓度下,固定化DhaA能够比游离态DhaA保持更高的催化活性,在变性剂到达临界浓度之前（尿素浓度5.5 mol·L-1,DMSO浓度7 mol·L-1）,氨基改性介孔泡沫的稳定化作用显著。DhaA在尿素诱导下的变性过程符合“二态模型”,而在DMSO诱导下符合“三态模型”,DhaA中间态出现在浓度为5.6 mol·L-1。氨基改性介孔泡沫固定化不改变DhaA变性过程,但能够提高DhaA的去折叠热力学参数。在尿素诱导下,计算得到的DhaA初始吉布斯自由能变ΔG(H₂O)为8.51 kcal·mol-1,固定化后ΔG(H₂O)提高为9.55 kcal·mol-1;但由于尿素分子容易通过静电作用进入氨基介孔泡沫孔道,固定化后DhaA的溶液可及面积m由3.69 kcal·(mol·mol·L-1)-1增大到4.00 kcal·(mol·mol·L-1)-1,孔道内的氨基、羟基能够通过氢键作用增强DhaA的刚性,从而有效的降低了尿素可及面积增加带来的影响,提高了DhaA的尿素耐受性。在DMSO诱导下,计算发现游离态与固定化DhaA在折叠态向中间态转变过程中的ΔG(H₂O)均为12.12 kcal·mol-1,由于孔道内的氨基、羟基能够有效阻碍非极性DMSO分子的进入,造成m从3.39 kcal·(mol·mol·L-1)-1降低为2.30 kcal·(mol·mol·L-1)-1;当DhaA从中间态向去折叠态转化时,DhaA内部疏水基团暴露导致m增加,由于孔道内极性微环境作用,固定化DhaA的m值（4.40 kcal·(mol·mol·L-1)-1）仍然低于游离态DhaA（4.94 kcal·(mol·mol·L-1)-1）。荧光光谱法研究固定化对DhaA去折叠过程及热力学参数的影响是深入研究DhaA稳定性的有效手段,能够为其他生物酶的稳定化机理研究提供方法指导。     

快速获得蛋白质晶体的X射线劳厄像

构成生物体新陈代谢的几乎全部的化学反应都是在活性蛋白质——酶的催化下进行的.酶作为催化剂,有高度的专一性、效率高及条件温和等一般催化剂不可比拟的优点.蛋白质的结构以及酶催化反应过程中中间态的结构,对催化机制的了解有着重要意义.X射线衍射方法在蛋白质的空间结构测量中一直占有重要地位.一般说来,最令人信服的结果是来自X射线衍射法. 酶催化反应或肌红蛋白与血红蛋白的配位结合反应中的结构中间态,在生理温度下典型的寿命是毫秒或更短.这些瞬变的中间态不可能形成稳定的结晶体,于是不可能用X射线晶体学的方法直接研究,但是可以…     

EPR和NMR自旋标记法研究部分折叠蛋白质构象

部分折叠蛋白质的特征是在溶液中有部分二级结构,但是三级结构接触比较松散或者较少,其意义可能是蛋白质折叠过程的中间态,或者有重要的生理功能. 利用EPR和NMR波谱可以表征其构象特征,从而构建其二级结构、三级结构、四级结构以及构象变化的结构模型. 利用分子生物学的点突变技术可以在蛋白质主链上插入1个或2个半胱氨酸残基,然后把顺磁自旋标记物特异地共价结合在半胱氨酸的侧链巯基上来制备自旋标记样品. 位点特异性自旋标记电子顺磁共振（SDSL-EPR）波谱是通过测定2个自旋标记间的偶极相互作用,从而推测2个硝基氧自由基间的距离. 核磁共振（NMR）波谱则是通过测定单个自旋标记中心对周围原子核驰豫效应增强（PRE）的效应,推测出顺磁中心相对于周围原子核的距离. 连续波EPR和NMR自旋标记方法可以测定2.5 nm左右的偶极相互作用距离,属于长程的距离约束,这对于确定部分折叠蛋白质的构象至关重要. 该文将就蛋白质部分折叠态研究的生物学意义,自旋标记方法以及EPR和NMR方法研究其构象特征举例描述.     

Mössbauer spectroscopic evidence on the heme binding to the proximal histidine in unfolded carbonmonoxy myoglobin by guanidine hydrochloride

The unfolded heme structure in myoglobin is controversial because of no chance of direct X-ray structure analyses. The unfolding of carbonmonoxy myoglobin (MbCO) by guanidine hydrochloride (GdnHCl) was studied by the Mössbauer spectroscopy. The spectra show the presence of a sort of spectrum in the unfolded MbCO, independent on the concentration of GdnHCl from 1 to 6 M and the increase of the fraction of unfolded MbCO, depending on the GdnHCl concentration. The isomer shift of the iron of heme in the unfolded MbCO was identified to be different from that of the native MbCO as the globin structure in Mb collapses under the unfolded conditions. This result and the existing related Mössbauer data proved that the heme in the unfolded MbCO may remain coordinated to the proximal histidine.     

Comparison of ligand migration and binding in heme proteins of the globin family

The binding of small diatomic ligands such as carbon monoxide or dioxygen to heme proteins is among the simplest biological processes known. Still, it has taken many decades to understand the mechanistic aspects of this process in full detail. Here, we compare ligand binding in three heme proteins of the globin family, myoglobin, a dimeric hemoglobin, and neuroglobin. The combination of structural, spectroscopic, and kinetic experiments over many years by many laboratories has revealed common properties of globins and a clear mechanistic picture of ligand binding at the molecular level. In addition to the ligand binding site at the heme iron, a primary ligand docking site exists that ensures efficient ligand binding to and release from the heme iron. Additional, secondary docking sites can greatly facilitate ligand escape after its dissociation from the heme. Although there is only indirect evidence at present, a preformed histidine gate appears to exist that allows ligand entry to and exit from the active site. The importance of these features can be assessed by studies involving modified proteins(via site-directed mutagenesis) and comparison with heme proteins not belonging to the globin family.     

Conformational changes in hemoglobin triggered by changing the iron charge

In this work the hemoglobin conformational changes induced by changing the iron charge have been studied and compared with Myoglobin. Mössbauer spectroscopy was used to follow the change of the iron conformation. In order to compare the conformational relaxation of hemoglobin and myoglobin, and to study a possible influence of the quaternary structure, an intermediate metastable state of hemoglobin has been created by low temperature X-ray irradiation of methemoglobin. The irradiation reduces the Fe(III) of the heme groups to Fe(II) Low Spin, where the water is still bound on the sixth coordination. Heating cycles performed at temperatures from 140 K to 200 K allow the molecules to overcome an activation energy barrier and to relax into a stable conformation such as deoxy-hemoglobin or carboxy-hemoglobin, if CO is present. Slightly different structures (conformational substates) reveal themselves as a distribution of energy barriers (ΔG^#). The distribution of the activation energy, for the decay of the Fe(II) Low Spin intermediate, has been fitted with a Gaussian. For comparison, published myoglobin data were re-analysed in the same way. The average energy value at characteristic temperature is very similar in case of myoglobin and hemoglobin. The larger Gaussian energy distribution for myoglobin with respect to hemoglobin shows that more conformational substates are available. This may be caused by a larger area exposed to water. In hemoglobin, part of the surface of the chains is not water accessible due to the quaternary structure.     

Assessment of dispersion corrections in DFT calculations on large biological systems

The performance of empirical dispersion corrections in DFT calculations has been assessed for several large, genuine biological systems that include MbAB, H64L(AB), and V68N(AB) (AB?=?CO, O₂), where Mb stands for a wild-type myoglobin, H64L is the (histidine64?→?leucine) mutated myoglobin, and V68N is the (valine68?→?asparagine) mutated myoglobin. The effects of the local protein environment are accounted for by including the five nearest surrounding residues in the calculated systems and they are examined by comparing the binding energies of AB to the myoglobin and to the porphyrin (Por) without residues. Three versions of Grimme's dispersion correction methods, labeled as DFT-D1, DFT-D2, and DFT-D3, were all tested. In the first version (-D1), the dispersion correction (E_disp) is calculated only for noncovalent interactions between molecular fragments and E_disp within a covalent molecule is not calculated. For the DFT functionals, for which the calculated Por–AB binding energies are already too large, only further overestimation occurs when a dispersion correction is made. The geometry optimizations show that the DFT-D2 and DFT-D3 approaches give too short distances between the residues and the heme moiety in the myoglobins and their calculated relative binding energies ΔE_bind(myoglobin-AB/Por–AB) are in poor agreement with experiment in most cases. DFT-D1 performs very well, ensuring structural and energetic features in close agreement with experiment.     

Unfolding proteins under external forces: a solvable model under the self-consistent pair contact probability approximation

We extend a model of Micheletti et al. [Phys. Rev. Lett. 87, 088102 (2001)]] used to study protein con-formations to the case in which there is an external force field. Under the self-consistent pair contact probability approximation, this residue-level resolution model can still be solved under pulling forces. We implement the algorithm using heterogeneous parameters and study the force-induced unfolding of a helical segment from the protein transformylase and of the beta-stranded domains from the protein titin. The results are qualitatively consistent with the results from more expensive, atomistic dynamics simulation. Despite the mean-field-like approach, we observed a sharp and cooperative unfolding transition.     

Long-range reactive dynamics in myoglobin

We report the complete vibrational spectrum of the probe nucleus 57Fe at the oxygen-binding site of the protein myoglobin. The Fe-pyrrole nitrogen stretching modes of the heme group, identified here, probe asymmetric interactions with the protein environment. Collective oscillations of the polypeptide, rather than localized heme vibrations, dominate the low frequency region. We conclude that the heme "doming" mode is significantly delocalized, so that distant sites respond to oxygen binding on vibrational time scales. This has ramifications for understanding long-range interactions in biomolecules, such as those that mediate cooperativity in allosteric proteins.     

The effect of protein internal cavities on ligand migration and binding in myoglobin

Using Fourier Transform Infrared Spectroscopy at cryogenic temperatures, we have studied carbon monoxide (CO) migration in the interior of sperm whale myoglobin and binding to teh heme iron. The effect of protein internal cavities was examined by comparing the wild-type protein with mutants in which the cavities were blocked by bulky amino acid sidechains. After photodissociation at 3 K, CO ligands reside in the primary docking site (B) from where they can migrate to other sites (C, D) that were identified as the Xe4 and Xe1 cavities. These studies were complemented by flash photolysis experiments at room temperature, which revealed that the protein cavities enable efficient excape of ligands from the protein after dissociation from the heme iron.     

Force-dependent fragility in RNA hairpins

We apply Kramers theory to investigate the dissociation of multiple bonds under mechanical force and interpret experimental results for the unfolding and refolding force distributions of an RNA hairpin pulled at different loading rates using laser tweezers. We identify two different kinetic regimes depending on the range of forces explored during the unfolding and refolding process. The present approach extends the range of validity of the two-states approximation by providing a theoretical framework to reconstruct free-energy landscapes and identify force-induced structural changes in molecular transition states using single molecule pulling experiments. The method should be applicable to RNA hairpins with multiple kinetic barriers.     

圆二色谱研究Asp44在稳定肌红蛋白结构中的作用

为了了解肌红蛋白Mb分子表面44位天冬氨酸对稳定肌红蛋白结构的影响,用PCR定点突变的技术将肌红蛋白(Mb)基因上的第44位天冬氨酸的密码子GAT突变成赖氨酸的密码子AAA,获得突变体D44K基因,将突变体基因克隆在肌红蛋白表达质粒pGYM上,转化大肠杆菌BL21,突变蛋白D44K在大肠杆菌中大量表达,收集菌体。酶法裂解细菌,依次用硫酸铵沉淀、离子交换柱层析、凝胶柱层析分离纯化得突变肌红蛋白D44K。用圆二色谱分别研究野生型肌红蛋白及其突变体(D44K)的耐热及耐酸的变性过程。实验结果表明：用碱性氨基酸Lys取代酸性氨基酸Asp44残基,增强了肌红蛋白耐热变性能力,导致蛋白质的热变性中点温度T_m由71.9 ℃增加到75.1 ℃,但对肌红蛋白耐酸变性的能力影响不大。