红外光谱和圆二色光谱法研究氰根配位的辣根过氧化物酶(HRP)的热伸展过程

典型的辣根过氧化物酶同功酶 C(HRP)是用于过氧化物酶生物化学研究的原型酶 .HRP的血红素辅基的铁是五配位的 ,血红素口袋的远端和近端位点都存在一个氢键网络 .HRP结构的稳定性已用随温度变化的 FTIR光谱法 [1]和圆二色及荧光光谱法 [2 ]进行了研究 ,并与细胞色素 c过氧化物酶进行了比较 . HRP的氰根加合物的活性位点的动力学稳定性和分子结构也用二维核磁共振法进行了表征[3] .但是关于氰根配体对 HRP在热伸展过程中的结构影响尚未见到报道 .本文用傅里叶变换红外光谱(FTIR)和圆二色 (CD)光谱法详细研究了氰根配位的 HRP随温…     

红外光谱和圆二色光谱研究氰根配位的辣根过氧化物酶（HRP）的热伸展过程

典型的辣根过氧化物酶同功酶C（HRP）是用于过氧化物酶生物化学研究的原型酶。HRP的血红素辅基的铁是五配位的,血红素口袋的远端和近端位点都存在一个氢键网络。HRP结构的稳定性已用随温度变化的FTIR光谱法^[1]和圆二色及荧光光谱法^[2]进行了研究,并与细胞色素c过氧化物酶进行了比较。HRP的氰根加合物的活性位点的动力学稳定性和分子结构也用二维核磁共振法进行了表征^[3]。但是关于氰根配体对HRP在热伸展过程中的结构影响未见到报道。本文用傅里叶变换红外光谱（FTIR）和圆二色（CD）光谱法详细研究了氰根配位的HRP随温度的热伸展过程。研究发现氰根（CN－）取代后,酶中血红素铁的自旋状态和配位状态都与天然态完全不同,氰根取代水分子成为血红素Fe(Ⅲ）的第六配体,这时血红素周围的氢键也会遭受一定程度的破坏,从而使HRP的热稳定性急剧下降。FTIR和Soret-CD的光谱分析表明HRP－CN的热变性过程与天然态HRP完全不同,其途径可表示为：Ⅰ→Ⅰ′→U→A,存在二级和三级结构同时部分破坏的伸展中间态（Ⅰ′）和完全伸展后蛋白质的聚集态（A）。     

共振喇曼光谱研究稀土离子Er3对肌红蛋白结构的影响

随着稀土金属开发应用的不断深入 ,它的安全性已引起人们的广泛关注 .Evans[1]曾报道稀土化合物由于其类 Ca2 + 性导致各种负面生物效应 ,包括影响心血管功能及溶血 ,然而有关稀土离子影响血红素蛋白结构的研究尚很少见报道 .肌红蛋白由含 1 5 2个残基的单一多肽链 (珠蛋白 )和血红素组成 .在生物体中 ,它为肌肉组织贮存氧 ,以供细胞呼吸的需要 ,因此它在人体中具有极其重要的生理作用 .研究稀土离子对肌红蛋白的影响对了解稀土离子降低血红素蛋白载氧能力的作用机理具有实际意义[2 ] .由于血红素在可见和近紫外区有很强的吸收带 ,以氩离子…     

分子动力学模拟残基突变对芳香烃受体配体结合区的影响

芳香烃受体(Aryl hydrocarbon receptor,AhR)属于配体依赖性的转录因子蛋白。本文通过对AhR配体结合区域(Ligand binding domain,LBD)的结构功能及物种特异性分析,发现在其结合腔口有一些关键残基可能起到"门控"作用,进一步将野生型(WT)和3个突变模型(Phe289Ala、Tyr316Ala、Ile319Ala)进行分子动力学模拟,从蛋白稳定性、蛋白结构变化、蛋白结合腔变化及蛋白和配体结合能力4个方面分析3个残基的门控作用。研究发现,Phe289、Tyr316、Ile319氨基酸残基通过形成疏水作用为AhR LBD起到"门控"作用;而将这些氨基酸分别突变后,其蛋白稳定性降低,整体运动性增加,配体亲和力减弱,其中Tyr316、Ile319对腔内体积影响较大,Phe289使腔内环境稳定性降低。本研究可为基于芳香烃受体的药物设计提供相关理论指导。     

氰根桥联Fe(Ⅲ)-Cu(Ⅱ)双金属配合物的合成及磁性研究

基于五氰构筑单元[Fe(CN)₅L]^2-[L=1-甲基咪唑(1-Meim), 咪唑(Him)]和铜大环配离子合成了3个氰根桥联Fe(Ⅲ)-Cu(Ⅱ)双金属配合物, 并研究了它们的晶体结构和磁性. 单晶结构分析表明, 3个化合物为一维链状的Fe^Ⅲ-Cu^Ⅱ配合物, 铜离子的配位构型为拉长八面体结构, 轴向由2个[Fe(CN)₅L]^2-上的氰根氮原子配位, 而每个[Fe(CN)₅L]^2-用2个氰根桥联2个铜离子, 得到1个交替一维链结构. 磁性研究表明, 其中2个配合物呈铁磁相互作用, 1个呈少见的反铁磁耦合.     

一种在含水介质和食物样品中快速和高灵敏度的双通道检测氰根的化学传感器（英文）

众所周知,氰根离子(CN-)是最具有毒性的阴离子之一,它能够对环境和生物体造成很多不良的影响,因此,研究氰根离子的检测方法是非常有必要的,尤其是在水中以及食物中进行检测.然而,由于游离态的氰根离子半衰期短,但很多氰根离子检测方法所需分析时间较长并且容易受到其他阴离子的干扰,这些都成为精确检测氰根离子的挑战.利用氰根离子特殊的亲核性,合成了一个基于萘并呋喃酰氯和2-氨基苯并咪唑的新型传感器分子Q1-2,其设计原理在于通过调节分子内的氢键来影响分子的π-共轭效应.当加入氰根离子之后,传感器Q1-2的紫外光谱出现红移现象,并且荧光也立刻猝灭.计算得到该传感器通过紫外和荧光检测氰根离子的最低检测限分别为8.0769×10~(-7)和1.0510×10~(-9) mol/L.其他共存的阴离子几乎不能干扰该识别过程.不仅如此,Q1-2可成功地应用于可见光和365 nm紫外灯照射下,肉眼识别食物样品中和硅胶板上的氰根.     

分子动力学模拟研究点突变(Met108→Leu108)对树胶醛糖结合蛋白与配体作用的影响

为了研究点突变(Met108→Leu108)对树胶醛糖结合蛋白(ABP)与配体结合能力的影响,对ABP、ABP结合树胶醛糖复合物及ABP结合半乳糖复合物以及它们各自的突变体分别进行60 ns的分子动力学模拟.模拟结果表明,108号残基突变前后,电子等排体的两个氨基酸残基,使蛋白与配体间的范德华相互作用发生明显变化,同时导致蛋白的内部运动也发生变化,进而影响蛋白与配体的相互作用.进一步分析表明,突变前后的蛋白构象变化都趋向于两个结构域张开,而与配体的结合可减缓张开程度.     

DNA G-四链体的结构完整性对催化性质的影响

DNA酶中的G-四链体-血红素(G4-hemin)DNA酶结构具有较高的设计性和化学稳定性,因此格外受研究者关注.G-平面作为辅酶因子hemin的结合位点,不仅提供大π平面与hemin结合,而且其平面上的G碱基还可以充当近端配位基团与hemin进行配位.因此,研究G-平面完整性在G4-DNA酶体系中的作用具有重要意义....     

三个包含酰胺型配体铜/锌配合物的合成、结构及荧光性质（英文）

合成并通过单晶衍射表征了3个配合物[Cu LCl2]·CH3CN(1),[Cu LBr2]·CH3CN(2)和[Zn L(NO3)2]·CH3CN(3)(L=2-(5-氯-8-喹啉氧基)-1-(吡咯烷-1-基)乙酮)。在配合物1和2中,五配位的铜离子采取扭曲的四方锥配位构型,与来自配体L的2个氧原子和1个氮原子及2个卤离子配位。而在配合物3中,锌离子与1个三齿配位的配体L,1个单齿配位的硝酸根和1个双齿配位的硝酸根配位,配位构型为扭曲的八面体。乙腈溶液中,配合物1和2在410 nm处的最大荧光发射峰与配体L的相似,强度有所降低。而配合物3由于配体到锌离子之间的能量转移,最大荧光发射峰红移至430 nm。     

人顶体酶活性腔性质及与抑制剂的结合模式

顶体酶是目前抗生育药物的一个潜在靶点. 在前期同源模建人顶体酶三维结构复合物的基础上, 采用多重拷贝同时搜寻(MCSS)等方法对人顶体酶活性腔进行分析. 结果显示, 活性腔的P1,P2和G 3个区域均具有较大极性, 且P1对抑制剂结合尤为重要. 另外, G和P1边缘及P2底部还具有一定疏水性, 且其中的部分重要残基还能与配体形成氢键作用和静电作用. MCSS计算结果确定的关键配体结合位点与人顶体酶复合物结构和定点突变实验结果相吻合. 在此基础上用分子对接方法将6个人顶体酶代表性抑制剂对接入活性腔, 阐明其结合模式, 确定与配体结合相关的关键残基.     

Structural Identification of Spectroscopic Substates in Neuroglobin

The structural origins of infrared absorptions of photodissociated CO in murine neuroglobin (Ngb) are determined by combining Fourier transform infrared (FTIR) spectroscopy and molecular dynamics (MD) simulations. Such an approach allows to identify and characterize both the different conformations of the Ngb active site and the transient ligand docking sites. To capture the influence of the protein environment on the spectroscopy and dynamics, experiments and simulations are carried out for the wild type protein and its F28L and F28W mutants. It is found that a voluminous side chain at position 28 divides site B into two subsites, B’ and B”. At low temperatures, CO in wt Ngb only migrates to site B’ from where it can rebind, and B” is not populated. The spectra of CO in site B’ for wt Ngb from simulations and experiments are very similar in spectral shift and shape. They both show doublets, red‐shifted with respect to gas‐phase CO and split by≈8 cm^?1. The FTIR spectra of the F28L mutant show additional bands which are also found in the simulations and can be attributed to CO located in substate B”. The different bands are mainly related to different orientations of the His64 side chain with respect to the CO ligand. Large red‐shifts arise from strong interactions between the Histidine? NH and the CO oxygen. After dissociation from the heme iron, the CO ligand visits multiple docking sites. The locations of the primary docking site B and a secondary site C, which corresponds to the Mb Xe4 cavity, could be identified unambiguously. Finally, by comparing experiment and simulations it is also possible to identify protonation of its ε position (His_ε64 NgbCO) as the preferred heme‐bound conformation in the wild type protein with a signal at 1935 cm^?1.     

Theory and simulation of diffusion-influenced, stochastically gated ligand binding to buried sites

We consider the diffusion-influenced rate coefficient of ligand binding to a site located in a deep pocket on a protein; the binding pocket is flexible and can reorganize in response to ligand entrance. We extend to this flexible protein-ligand system a formalism developed previously [A. M. Berezhkovskii, A, Szabo, and H.-X. Zhou, J. Chem. Phys. 135, 075103 (2011)] for breaking the ligand-binding problem into an exterior problem and an interior problem. Conformational fluctuations of a bottleneck or a lid and the binding site are modeled as stochastic gating. We present analytical and Brownian dynamics simulation results for the case of a cylindrical pocket containing a binding site at the bottom. Induced switch, whereby the conformation of the protein adapts to the incoming ligand, leads to considerable rate enhancement.     

Study on the Gas Phase Stability of Heme-binding Pocket in Cytochrome Tb_5 and Its Mutants by Electrospray Mass Spectrometry

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Solution 1H NMR of the molecular and electronic structure of the heme cavity and substrate binding pocket of high-spin ferric horseradish peroxidase: effect of His42Ala mutation.

Solution 1H NMR has been used to assign a major portion of the heme environment and the substrate-binding pocket of resting state horseradish peroxidase, HRP, despite the high-spin iron(III) paramagnetism, and a quantitative interpretive basis of the hyperfine shifts is established. The effective assignment protocol included 2D NMR over a wide range of temperatures to locate residues shifted by paramagnetism, relaxation analysis, and use of dipolar shifts predicted from the crystal structure by an axial paramagnetic susceptibility tensor normal to the heme. The most effective use of the dipolar shifts, however, is in the form of their temperature gradients, rather than by their direct estimation as the difference of observed and diamagnetic shifts. The extensive assignments allowed the quantitative determination of the axial magnetic anisotropy, Deltachi(ax) = -2.50 x 10(-8) m(3)/mol, oriented essentially normal to the heme. The value of Deltachi(ax) together with the confirmed T(-2) dependence allow an estimate of the zero-field splitting constant D = 15.3 cm(-1), which is consistent with pentacoordination of HRP. The solution structure was generally indistinguishable from that in the crystal (Gajhede, M.; Schuller, D. J.; Henriksen, A.; Smith, A. T.; Poulos, T. L. Nature Structural Biology 1997, 4, 1032-1038) except for Phe68 of the substrate-binding pocket, which was found turned into the pocket as found in the crystal only upon substrate binding (Henriksen, A.; Schuller, D. J.; Meno, K.; Welinder, K. G.; Smith, A. T.; Gajhede, M. Biochemistry 1998, 37, 8054-8060). The reorientation of several rings in the aromatic cluster adjacent to the proximal His170 is found to be slow on the NMR time scale, confirming a dense, closely packed, and dynamically stable proximal side up to 55 degrees C. Similar assignments on the H42A-HRP mutant reveal conserved orientations for the majority of residues, and only a very small decrease in Deltachi(ax) or D, which dictates that five-coordination is retained in the mutant. The two residues adjacent to residue 42, Ile53 and Leu138, reorient slightly in the mutant H42A protein. It is concluded that effective and very informative 1H NMR studies of the effect of either substrate binding or mutation can be carried out on resting state heme peroxidases.     

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)

Protein binding sites undergo ligand specific conformational changes upon ligand binding. However, most docking protocols rely on a fixed conformation of the receptor, or on the prior knowledge of multiple conformations representing the variation of the pocket, or on a known bounding box for the ligand. Here we described a general induced fit docking protocol that requires only one initial pocket conformation and identifies most of the correct ligand positions as the lowest score. We expanded a previously used diverse "cross-docking" benchmark to thirty ligand-protein pairs extracted from different crystal structures. The algorithm systematically scans pairs of neighbouring side chains, replaces them by alanines, and docks the ligand to each 'gapped' version of the pocket. All docked positions are scored, refined with original side chains and flexible backbone and re-scored. In the optimal version of the protocol pairs of residues were replaced by alanines and only one best scoring conformation was selected from each 'gapped' pocket for refinement. The optimal SCARE (SCan Alanines and REfine) protocol identifies a near native conformation (under 2 angstroms RMSD) as the lowest rank for 80% of pairs if the docking bounding box is defined by the predicted pocket envelope, and for as many as 90% of the pairs if the bounding box is derived from the known answer with approximately 5 angstroms margin as used in most previous publications. The presented fully automated algorithm takes about 2 h per pose of a single processor time, requires only one pocket structure and no prior knowledge about the binding site location. Furthermore, the results for conformationally conserved pockets do not deteriorate due to substantial increase of the pocket variability.     

Modulation of ligand-field parameters by heme ruffling in cytochromes c revealed by EPR spectroscopy

Electron paramagnetic resonance (EPR) spectra of variants of Hydrogenobacter thermophilus cytochrome c(552) (Ht c-552) and Pseudomonas aeruginosa cytochrome c(551) (Pa c-551) are analyzed to determine the effect of heme ruffling on ligand-field parameters. Mutations introduced at positions 13 and 22 in Ht c-552 were previously demonstrated to influence hydrogen bonding in the proximal heme pocket and to tune reduction potential (E(m)) over a range of 80 mV [Michel, L. V.; Ye, T.; Bowman, S. E. J.; Levin, B. D.; Hahn, M. A.; Russell, B. S.; Elliott, S. J.; Bren, K. L. Biochemistry 2007, 46, 11753-11760]. These mutations are shown here to also increase heme ruffling as E(m) decreases. The primary effect on electronic structure of increasing heme ruffling is found to be a decrease in the axial ligand-field term Δ/λ, which is proposed to arise from an increase in the energy of the d(xy) orbital. Mutations at position 7, previously demonstrated to influence heme ruffling in Pa c-551 and Ht c-552, are utilized to test this correlation between molecular and electronic structure. In conclusion, the structure of the proximal heme pocket of cytochromes c is shown to play a role in determining heme conformation and electronic structure.     

Cooperative motions of protein and hydration water molecules: molecular dynamics study of scytalone dehydratase

Two molecular dynamics (MD) simulations totaling 25 ns of simulation time of monomeric scytalone dehydratase (SD) were performed. The enzyme has a ligand-binding pocket containing a cone-shaped alpha+beta barrel, and the C-terminal region covers the binding pocket. Our simulations clarified the difference in protein dynamics and conformation between the liganded protein and the unliganded protein. The liganded protein held the ligand molecule tightly and the initial structure was maintained during the simulation. The unliganded protein, on the other hand, fluctuated dynamically and its structure changed largely from the initial structure. In the equilibrium state, the binding pocket was fully solvated by opening of the C-terminal region, and the protein dynamics was connected with hydration water molecules entry into and release from the binding pocket. In addition, the cooperative motions of the unliganded protein and the hydration water molecules produced the path through the protein interior for ligand binding.     

Strong ligand-protein interactions revealed by ultrafast infrared spectroscopy of CO in the heme pocket of the oxygen sensor FixL

In heme-based sensor proteins, ligand binding to heme in a sensor domain induces conformational changes that eventually lead to changes in enzymatic activity of an associated catalytic domain. The bacterial oxygen sensor FixL is the best-studied example of these proteins and displays marked differences in dynamic behavior with respect to model globin proteins. We report a mid-IR study of the configuration and ultrafast dynamics of CO in the distal heme pocket site of the sensor PAS domain FixLH, employing a recently developed method that provides a unique combination of high spectral resolution and range and high sensitivity. Anisotropy measurements indicate that CO rotates toward the heme plane upon dissociation, as is the case in globins. Remarkably, CO bound to the heme iron is tilted by ~30° with respect to the heme normal, which contrasts to the situation in myoglobin and in present FixLH-CO X-ray crystal structure models. This implies protein-environment-induced strain on the ligand, which is possibly at the origin of a very rapid docking-site population in a single conformation. Our observations likely explain the unusually low affinity of FixL for CO that is at the origin of the weak ligand discrimination between CO and O(2). Moreover, we observe orders of magnitude faster vibrational relaxation of dissociated CO in FixL than in globins, implying strong interactions of the ligand with the distal heme pocket environment. Finally, in the R220H FixLH mutant protein, where CO is H-bonded to a distal histidine, we demonstrate that the H-bond is maintained during photolysis. Comparison with extensively studied globin proteins unveils a surprisingly rich variety in both structural and dynamic properties of the interaction of a diatomic ligand with the ubiquitous b-type heme-proximal histidine system in different distal pockets.     

A novel kinetic trap for NO release from cytochrome c': a possible mechanism for NO release from activated soluble guanylate cyclase

Flash photolysis studies on the five-coordinate heme nitrosyl of Alcaligenes xylosoxidans cytochrome c' were carried out to investigate the ramifications of its proximal nitrosyl ligand on NO release. Delta absorbance spectra recorded 5 ms after photolysis indicate that approximately 5% of the photolyzed hemes are converted to a five-coordinate high spin ferrous state, revealing that reattachment of the endogenous His ligand is fast enough to trap some of the photolyzed heme. Analysis of NO rebinding suggests that the photolyzed ferrous protein is initially in a strained conformation, which relaxes on a millisecond time scale. The strained ferrous heme appears to contain a significantly labilized Fe-His bond, which allows direct second-order rebinding to the proximal face at high NO-concentrations. In contrast, the NO-binding properties of the relaxed conformation are similar to those previously observed in stopped-flow studies, which showed that a five-coordinate heme-nitrosyl is formed via a six-coordinate intermediate. The discovery of a rapid proximal His ligand reattachment to NO-dissociated heme reveals a novel "kinetic trap" mechanism for lowering the five-coordinate heme nitrosyl population in response to decreased ambient NO concentrations. Thus, NO dissociation from the five-coordinate heme nitrosyl, whether thermal or photochemical, is followed by rapid, and only slowly reversible, His reattachment which acts to kinetically trap the heme in its five-coordinate ferrous state. Because return to the five-coordinate heme nitrosyl requires two NO-dependent steps, the protein uses a kind of kinetic amplification of the thermodynamic dissociation that occurs in response to decreased NO concentrations. The implications of this "kinetic-trap" mechanism for NO release from soluble guanylate cyclase are discussed.     

Impact of proximal and distal pocket site-directed mutations on the ferric/ferrous heme redox potential of yeast cytochrome c peroxidase

Cytochrome c peroxidase (CCP) contains a five-coordinate heme active site. The reduction potential for the ferric to ferrous couple in CCP is anomalously low and pH dependent (Eo?=?~?180?mV vs. S.H.E. at pH 7). The contribution of the protein environment to the tuning of the redox potential of this couple is evaluated using site-directed mutants of several amino acid residues in the environment of the heme. These include proximal pocket mutation of residues Asp-235, Trp-191, Phe-202, and His-175, distal pocket mutation of residues Trp-51, His-52, and Arg-48; and a heme edge mutation of Ala-147. Where unknown, the structural changes resulting from the amino acid substitution have been studied by X-ray crystallography. In most cases, ostensibly polar or charged residues are replaced by large hydrophobic groups or alternatively by Ala or Gly. These latter have been shown to generate large, solvent-filled cavities. Reduction potentials are measured as a function of pH by spectroelectrochemistry. Starting with the X-ray-derived structures of CCP and the mutants, or with predicted structures generated by molecular dynamics (MD), predictions of redox potential changes are modeled using the protein dipoles Langevin dipoles (PDLD) method. These calculations serve to model an electrostatic assessment of the redox potential change with simplified assumptions about heme iron chemistry, with the balance of the experimentally observed shifts in redox potential being thence attributed to changes in the ligand set and heme coordination chemistry, and/or other changes in the structure not directly evident in the X-ray structures (e.g., ionization states, specific roles played by solvent species, or conformationally flexible portions of the protein). Agreement between theory and experiment is good for all mutant proteins with the exception of the mutation Arg 48 to Ala, and His 52 to Ala. In the former case, the influence of phosphate buffer is adduced to account for the discrepancy, with evidence for phosphate binding in the distal pocket, and measurements made in a bis?Ctris propane/2-(N-morpholino)ethanesulfonic acid buffer system agree well with theory. For the latter case, an unknown structural element relevant to His-52 and/or solvent influence in the mutant akin to anion binding in the distal pocket (though lacking proof that it is, and in this case lacking a phosphate effect) manifests in this mutant. The use of exogenous (sixth) ligands in dissecting the contributions to control of redox potential is also explored as a pathway for model building.