Label‐free detection of binary mixtures of proteins using surface‐enhanced Raman scattering

The surface‐enhanced Raman scattering (SERS) spectra of five binary mixtures of proteins were studied, including mixtures of apomyoglobin (apMb) and lysozyme, insulin and lysozyme, Mb and cytochrome c (cyt c), Mb and apoMb, and cyt c and human serum albumin. For mixtures in which both proteins did not contain chromophores, the variations in the intensities of SERS signals with changes in the relative concentration of the two proteins were largely proportional to the relative concentration of the protein mixtures. Similar results were obtained for mixtures in which both the proteins contained chromophores. However, for mixtures in which one protein contained chromophores and the other did not, the SERS intensities of the protein mixtures showed a bell‐shaped variation with changes in the compositions of the mixtures. The present study provides new insights into the application of SERS spectroscopy to label‐free detection in a binary of mixture of proteins. The complexities in both SERS phenomena and protein structures should be considered in the analysis of the SERS spectra of protein mixtures. By monitoring the heme band of a protein containing a heme and the NO₃^– band of a protein without a heme, the simultaneous detection of both proteins in a binary mixture may be possible. It has also been found that the larger the size of the protein, the smaller is the SERS intensity of that protein. Copyright © 2011 John Wiley & Sons, Ltd.     

Interaction and energy transfer between carbon dots and serum human transferrin

Human serum transferrin has been used as a potential drug carrier to transport anticancer drugs to tumor cells, where transferrin receptors are overexpressed on the surface. Carbon dots are biocompatible, and have potential application to drug delivery. The interaction mechanism of human serum transferrin with carbon dots was investigated by fluorescence spectra, ultraviolet–visible absorption spectroscopy, circular dichroism, at extracellular pH 7.4 and endosomal pH 4.8, at varying temperatures. We observed a quenching of fluorescence of human serum transferrin in the presence of carbon dots by a static quenching mechanism and also analyzed the quenching results using the Stern–Volmer equation and obtained high-affinity binding to human serum transferrin dominated by hydrogen bonds or van der Waals forces. An isoemissive point was seen, indicating that quenching of human serum transferrin depends on the formation of human serum transferrin–carbon dots complex. Binding distance between carbon dots and human serum transferrin substantiated that the photoinduced electron transfer and Föster nonradiative resonance energy transfer mechanism were also involved in the quenching of protein. Furthermore, the circular dichroism also showed that carbon dots changed the secondary structure of human serum transferrin to some extent with decreased α-helix content or peak wavelength red-shifted. This study provides some theoretical foundation for carbon dots as a promising probe to monitor the process of delivering drugs to human serum transferrin in the future.     

The human brain hexacoordinated neuroglobin three-dimensional structure

Neuroglobin, mainly expressed in vertebrate brain and retina, is a recently identified member of the globin superfamily. Augmenting O2 supply, neuroglobin promotes survival of neurons upon hypoxic injury, potentially limiting brain damage. In the absence of exogenous ligands, neuroglobin displays a six-coordinated heme. O2 and CO bind to the heme-iron, displacing the endogenous HisE7 heme distal ligand. Hexacoordinated human neuroglobin displays a classical globin fold, adapted to host the reversible bis-histidyl heme complex, and an elongated protein matrix cavity, held to facilitate O2 diffusion to the heme. The structure of neuroglobin suggests that the classical globin fold is endowed with striking adaptability, indicating that hemoglobin and myoglobin are just two examples within a wide and functionally diversified protein homology superfamily.     

pH协同血清白蛋白对单个活态人红细胞作用的拉曼光谱研究

红细胞是维持生命最重要的细胞之一,pH是影响其结构功能的重要因素。 结合人血液中存在血清白蛋白,且可能会对红细胞起作用的特点,在模拟人体内血液中血清白蛋白与血红蛋白摩尔比值的条件下,研究pH协同血清白蛋白对单个活态人红细胞的形态,细胞膜变形能力及胞内血红蛋白结构变化的影响。 结果显示,不同pH下,红细胞的表面形态、 膜变形能力的变化规律与其胞内血红蛋白结构的变化有关：在pH 4.14,4.76,10.18时,红细胞胞内血红蛋白螺旋结构的减少、 疏水性氨基酸的暴露,血红素珠蛋白结合状态的改变,影响了血红蛋白结构的稳定性,从而导致红细胞的结构发生变化,其形态、 膜变形能力与正常值相比,变化结果显著。 而在pH 6.51和7.80下,血红蛋白的拉曼谱结果并未发现有上述变化情况,胞内血红蛋白的结构没有发生改变,红细胞的形态、 膜变形能力也接近于正常值。 在pH 5.49和8.76下,红细胞的表面形态和膜变形能力都有不同程度的变差,但其胞内血红蛋白的结构并没有改变,提示红细胞的形态和变形能力的改变可能是可逆的。 结果表明,pH协同血清白蛋白的作用下,血清白蛋白能对红细胞起保护作用,增强红细胞调节、 缓冲环境pH变化的能力。 研究结果全面地揭示了在模拟人体内血液中血清白蛋白与血红蛋白摩尔比值的情况下,红细胞结构功能的变化情况,不仅有助于阐明红细胞在有关生理、 病理状态下的结构与功能的变化,而且对其临床表现与有关防治对策都有重要的指导意义。     

Potential of protoporphyrin IX and metal derivatives for single molecule fluorescence studies

Metalloporphyrins are cofactors of a variety of proteins, and are often used as spectroscopic probes of the active site. Many high resolution techniques, such as single molecule spectroscopy, are based on fluorescence contrast and require the replacement of the native metalloporphyrin by a fluorescent analog. We have investigated the potential of several fluorescent analogs of heme, namely free-base protoporphyrin IX and its metal derivatives containing Zn, Sn, and Mg, for single molecule fluorescence studies by determining their room-temperature molecular absorption cross sections and fluorescence quantum yields. According to these data, free-base protoporphyrin IX and its Zn derivative, which have the highest fluorescence quantum yields, are the most suitable heme analogs for single molecule fluorescence studies.     

粗糙银电极上高铁血红素的非共振表面增强拉曼光谱研究

以632.8nm为激发线,研究了高铁血红素的非共振表面增强拉曼光谱。结果表明,高铁血红素的氧化和还原状态的拉曼谱图以B_(1g)振动模式为主;血红素以丙酸侧基直接吸附于电极表面,叶啉环则以垂直于电极表面的形式存在。B_(1g)振动模式v_(15)对血红素中心铁的氧化还原状态十分敏感,被指认为非共振条件下血红素氧化还原状态的特征谱峰。     

57Fe quadrupole splitting and isomer shift in various oxyhemoglobins: study using Mössbauer spectroscopy

A comparative study of normal human, rabbit and pig oxyhemoglobins and oxyhemoglobin from patients with chronic myeloleukemia and multiple myeloma using Mössbauer spectroscopy with a high velocity resolution demonstrated small variations of the ⁵⁷Fe quadrupole splitting and isomer shift. These variations may be a result of small structural differences in the heme iron stereochemistry of various hemoglobins.     

Low-field nuclear magnetic resonance spectrometer for non-invasive monitoring of fluctuations in blood glucose in the human finger

A low-field nuclear magnetic resonance spectrometer for non-invasive monitoring of human finger blood glucose fluctuations was developed. Saline solution and blood serum samples with different glucose concentrations were first detected by the spectrometer and it has been found that there was a high-linear correlation between the glucose concentration and the transverse relaxation time. Then, the spectrometer was employed to noninvasively measure a finger from each of the several volunteers. The experiment results showed that the transverse relaxation time of the human finger increases with human blood glucose concentration. In conclusion, the human finger nuclear magnetic resonance spectrometer could be a potential tool to noninvasive monitoring of human body’s blood glucose fluctuations in the future.     

Sub‐picosecond Raman spectrometer for time‐resolved studies of structural dynamics in heme proteins

We describe a pump–probe Raman spectrometer based on a femtosecond Ti:sapphire laser, an optical parametric generator and two optical parametric amplifiers for time‐resolved studies, with emphasis on the structural dynamics in heme proteins. The system provides a 100‐fs pump pulse tunable in the range 500–600 nm and a transform‐limited sub‐picosecond probe pulse tunable in the range 390–450 nm. The spectrometer has spectral (25 cm⁻¹) and temporal (∼0.7 ps) resolutions which constitute an effective compromise for identifying transient heme protein species and for following their structural evolution by spontaneous Raman scattering in the time range 0.5 ps to 2 ns. This apparatus was applied to time‐resolved studies of a broad range of heme proteins, monitoring the primary dynamics of photoinduced heme coordination state and structural changes, its interaction with protein side‐chains and diatomic gaseous ligands, as well as heme vibrational cooling. The treatment of transient Raman spectra is described in detail, and the advantages and shortcomings of spontaneous resonance Raman spectroscopy for ultrafast heme proteins studies are discussed. We demonstrate the efficiency of the constructed spectrometer by measuring Raman spectra in the sub‐picosecond and picosecond time ranges for the oxygen‐storage heme protein myoglobin and for the oxygen‐sensor heme protein FixLH in interaction with the diatomic gaseous ligands CO, NO, and O₂. Copyright © 2010 John Wiley & Sons, Ltd.     

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.     

Nanobionics of Pharmacologically Active Derivatives of Fullerene C60

The physical–chemical mechanisms of pharmacologic functioning of amino acid derivatives of fullerene C₆₀ (ADF) have been studied. ADF were shown to penetrate through the lipid bilayer of liposomes without destruction of membrane integrity. ADF are able to carry bivalent metal ions through phospholipid bilayer owing to the formation of complexes. It was shown that stereoisomers of ADF selectively penetrate into phospholipid membranes. In contrast to D-isomers, L-isomers penetrate through the phosphatidylcholine membrane into liposome interior. Stereo-specific effect of ADF enantiomers was also observed in reaction of peroxidation of lipids. Besides that, ADF bring about a substantial increase in the catalytic activity of monoaminoxidases A and B. The directed intraprotein electron transfer was studied by creating a donor–acceptor pair in a water solution in the presence of ADF. To realize the intraprotein electron transfer, the model system was produced on the base of apomyoglobin by incorporating ADF (electron acceptor) into the heme pocket of protein instead of removed heme. It was established that the fullerene C₆₀ and its derivatives did not produce specific anti-C₆₀ antibodies, both IgG and IgE classes, while ADF themselves are efficient adjuvants, i.e. they increased the antibody response to poor antigens. Some ADF were found to inhibit the human immunodeficiency virus and human cytomegalovirus infection.     

Studying high-spin ferric heme proteins by pulsed EPR spectroscopy: Analysis of the ferric form of the E7Q mutant of human neuroglobin

In this work, the high-spin ferric form of the E7Q mutant of human neuroglobin (E7Q-NGB) is studied by X-band continuous-wave electron paramagnetic resonance (CW EPR) and hyperfine sublevel correlation (HYSCORE) spectroscopy. It is shown that the use of matched pulses in the HYSCORE experiment is essential to observe the nitrogen spectral contributions. The validity of approximating the high-spin Fe(III) system (S=5/2) as an effectiveS=1/2 system is tested and the consequences for the HYSCORE simulations are highlighted. Comparative HYSCORE experiments combined with deuterium exchange experiments for aquometmyoglobin and ferric E7Q-NGB clearly show that the heme iron of the latter protein is pentacoordinated, lacking the distal water. Furthermore, CW EPR experiments show that, at high pH, the E10K residue is coordinating to the heme iron in this globin. These observations are corroborated by resonance Raman experiments and could also be reproduced for other E7 mutants of human and mouse neuroglobin. Finally, the proton and nitrogen hyperfine and nuclear quadrupole parameters obtained for ferric E7Q-NGB are discussed in detail.     

Transfer of pyrene-dietherphosphatidylcholine to serum lipoproteins

The nonhydrolyzable fluorescent diether analog of phosphatidylcholine, 1-O-hexadecyl-2-0-pyrenedecyl-sn-glycero-3-phosphocholine, has been synthesized as a stable probe for the determination of phospholipid transfer to different lipoprotein classes with potential phospholipase activities. After incubation of total human serum with the new probe at 37°C for 3 hours a characteristic partition equilibrium between the main lipoprotein fractions was observed. The fluorescent lipid was not degraded under these conditions and, therefore, served as a marker for choline glycerophospholipid distribution between and transport to serum lipoproteins.     

Cytochrome P450 BM-3 in complex with its substrate: Temperature-dependent spin state equilibria in the oxidized and reduced states

In structural studies of cytochrome P450 enzymes, substrates have been seen to bind in a variety of modes; it is important to identify those with the closest resemblance to the configurations adopted during selective oxidation. We attempt here to identify conditions in which the catalytic binding mode of cytochrome P450 BM-3 saturated with N-palmitoylglycine is highly populated. When the substrate binds directly atop the heme, primed for oxidation, displacement of the water ligand is necessary, and thereby the ferric heme is generally converted from low-spin to high-spin. Using both optical spectroscopy and solid-state nuclear magnetic resonance, studying both the full-length enzyme and the isolated heme domain, we show that a high population of the high-spin form is seen at room temperature and above, but not at reduced temperatures. In contrast, the reduced state exhibits high spin throughout the temperature range. The isotropic chemical shift of deuterons in the substrate bound to the oxidized and reduced forms of the enzyme was temperature-dependent, consistent with the presence of a nearby paramagnetic center, but temperature-independent for the diamagnetic CO-bound form, and for the free form of the compound. The reduced (ferrous heme) species shows Curie law dependence of the²H substrate chemical shift with respect to temperature from ?54 to +35 °C, but the oxidized (ferric heme) species showed a pronounced non-Curie dependence in both the²H and the¹³C shift of the substrate’s methyl group, with the effect of the paramagnetic heme at low temperatures being much reduced. These data are consistent with a mixture of at least two binding modes in rapid equilibrium wherein the heme is high-spin at room temperature but low-spin at cryogenic temperatures.     

Normal coordinate structural decomposition of the heme distortions of hemoglobin in various quaternary states and bound to allosteric effectors

The distortions of the alpha1, alpha2, beta1, and beta2 hemes of human hemoglobin (HbA) in various quaternary states and as affected by the presence of allosteric effectors was investigated by subjecting CHARMM energy-minimized models to normal coordinate structural decomposition (NSD) analysis. NSD was applied to the individual hemes extracted from the R, T, and R2-state models of HbA and to HbA bound to DPG and to IHP. Overall, NSD results are indicative of characteristic distortions, not only for the hemes of the different HbA quaternary states, but also for the hemes of the HbA models bound to allosteric effectors. Comparing the distortions of the inequivalent alpha and beta hemes in T-state HbA, we show good correlation between NSD and the experimentally observed low-frequency nu52 (Eg) and gamma7 (A2u) modes reported in the literature for alpha and beta HbA hemes while noting substantial differences between these types for B2u and B1u distortions. For the R2 hemes, NSD yields heme distortions that are more comparable to those of the R-state, especially in magnitude. However, the R2 hemes do not exhibit inequivalence of alpha and beta heme distortions, a result that may contribute to an understanding of the functional importance of this state. Relative to T-state heme distortions, NSD results on the effector-bound hemes show that tertiary changes induced in T-state HbA as a result of binding DPG and IHP drastically affect heme distortions. In the alpha hemes extracted from the HbA-DPG model, most noteworthy are the increased wav(x) and wav(y) distortions and enhancement of ruf and dom deformations. In the beta hemes, the wav(y) is the most affected distortion with increase in sad. The NSD results are also different for the hemes of the HbA-IHP model, in that the beta sad and ruf deformations are more enhanced with increase of doming in the alpha hemes. Our results describe the effect of the subtle protein-induced changes on the nonplanarity of the HbA hemes that may play a role in the regulation of their oxygen affinity.     

P450血红素与CO、NO 和O2结合性质的密度泛涵研究

用两种模型在B3LYP/6-31G(d)水平上研究了双原子分子CO、NO和O2 (通称XO) 与P450血红素的结合性质. 在模型M2中考虑了双原子分子XO附近的丝氨酸残基对其的影响. 结果表明血红素附近的丝氨酸使得XO与血红素的结合更加牢固. 频率分析表明，当XO与血红素结合后X{O伸缩振动频率降低.同时讨论了复合物的HOMO和LUMO轨道的组成.     

Molecular mechanism investigation on the interaction of Clothianidin with human serum albumin

Abstract

With the widespread application of neonicotinoid insecticides, Clothianidin has received much attention due to the potential harm to human health and ecological environment. However, the mechanism of Clothianidin's underlying toxicity to organisms remains unclear. In this work, the interaction between Clothianidin and human serum albumin was investigated and the intrinsic fluorescence of human serum albumin got quenched via static mechanisms upon the addition of Clothianidin. The binding constants between Clothianidin and human serum albumin at three different temperature were obtained to be 3.543?×?10⁴, 2.995?×?10⁴, and 2.490?×?10⁴ M^?1, respectively. Based on the van't Hoff equation, the thermodynamic parameters, ΔH⁰ and ΔS⁰ were estimated to be ?53.885?KJ mol^?1 and ?110.535?J mol^?1K^?1, respectively. A single binding site was predicted from the binding constants at different temperatures by multiple spectroscopic techniques and the negative values of ΔH⁰ and ΔS⁰ indicated the binding of human serum albumin with Clothianidin was driven by hydrogen bonds or van der Waals forces. Furthermore, the loose and unfolded secondary structure of human serum albumin along with the addition of clothianidin had been observed through ultraviolet-visible absorption and circular dichroism spectra. In addition, it was also found that Clothianidin had polar effects of structural microenviroment not only on Trp but also Tyr residues from synchronous fluorescence analysis. This study illuminates the molecular mechanism of the interaction between human serum albumin and clothianidin for the first time and helps to construct a specific pesticide biosensor system of human health.     

Resonance Raman spectroscopic investigation of structural changes of CO‐heme in soluble guanylate cyclase generated by effectors and substrate

The influence of the effectors YC‐1 and BAY on the CO‐heme structure of bovine lung soluble guanylate cyclase (sGC) was investigated with resonance Raman spectroscopy. The effectors produced a five‐coordinate (5c) CO‐heme in addition to the His‐bound six‐coordinate (6c) CO‐heme, and both their Soret maxima were determined by simulation. On the basis of the absorption intensity, the amount of the 5c species was not dominant, in contrast to the high activity. The heme structural features common to the 5c and 6c CO‐hemes generated by effectors are that the vinyl and propionate side chains are more coplanar to the pyrrole rings. The out‐of‐plane Raman bands were observed only for the 5c species, for which the saddling and propeller distortions of heme were deduced to be large. The Fe CO stretching bands of the 5c species at 522 cm⁻¹ and of the 6c species at 488 cm⁻¹ were most enhanced upon excitation at 407 and 422 nm, respectively, which is consistent with the simulated spectra. Unexpectedly, the ¹³C¹⁸O isotope sensitivity appeared in low wavenumber porphyrin modes. From these observations, we propose that the high catalytic activity of sGC‐CO in the presence of effectors is a result of the concerted effects of protein conformational changes triggered by certain local interactions between the heme side chains and effectors/substrate in the heme pocket, which partly induce the cleavage of the Fe Hisβ 105 bond. Copyright © 2010 John Wiley & Sons, Ltd.     

A switch in the electron transfer from heme a to binuclear centre of cytochrome c oxidase

New experimental evidence that a switch controls the reduction of the heme a₃－Cu_B binuclear centre has been observed in the N₂-dried thin film of purified cytochrome oxidase. When immersing the enzyme film into the acid phosphate buffer with extremely low concentration of dithionite, a spectrum was given to show a reduction of heme a with no electrons resting on Cu_A. By increasing dithionite, electrons could be accumulated gradually on Cu_A, but the binuclear centre still remains in the oxidized state. When the accumulation of electrons on Cu_A and/or heme a exceeded a threshold, a turnover of reduction of the binuclear centre and oxidation of heme a occurred abruptly. This switch-like action is pH-dependent.     

Molecular dynamics simulations of cytochrome c unfolding in AOT reverse micelles: The first steps

This paper explores the reduced form of horse cytochrome c confined in reverse micelles (RM) of sodium bis-(2-ethylhexyl) sulfosuccinate (AOT) in isooctane by molecular dynamics simulation. RMs of two sizes were constructed at a water content of W _o = [ H_2O ]/[AOT] = 5.5 and 9.1. Our results show that the protein secondary structure and the heme conformation both depend on micellar hydration. At low hydration, the protein structure and the heme moiety remain stable, whereas at high water content the protein becomes unstable and starts to unfold. At W _o = 9.1 , according to the X-ray structure, conformational changes are mainly localized on protein loops and around the heme moiety, where we observe a partial opening of the heme crevice. These findings suggest that within our time window (10ns), the structural changes observed at the heme level are the first steps of the protein denaturation process, previously described experimentally in micellar solutions. In addition, a specific binding of AOT molecules to a few lysine residues of the protein was found only in the small-sized RM.