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.     

Hg2+在大鼠组织器官中的分布及其存在形态研究

汞是环境中重要的污染物之一,对人类的健康构成了巨大的威胁。文章通过建立电感耦合等离子体质谱及凝胶排阻色谱分离法与紫外和电感耦合等离子体质谱在线检测的联用技术,研究大鼠灌喂HgCl2后Hg在大鼠中的分布累积规律和及其与蛋白的结合,实验结果表明肝脏和肾脏中在Hg刺激下诱导产生大量硫蛋白,大量产生的金属硫蛋白可能因此而优先与通过胃肠吸收摄入的Hg结合,减少了Hg对其它蛋白的正常作用的干扰,从而大大降低了Hg^2＋的毒性。     

Electron spin-lattice relaxation rates for high-spin Fe(III) complexes in glassy solvents at temperatures between 6 and 298 K

The temperature dependence of spin-lattice relaxation rates was analyzed for four high-spin nonheme iron proteins between 5 and 20 K, for three high-spin iron porphyrins between 5 and 118 K, and for four high-spin heme proteins between 5 and 150 to 298 K. For the nonheme proteins the zero-field splittings, D, are less than 0.7 cm(-1), and the relaxation is dominated by the Orbach and Raman processes. For the iron porphyrins and heme proteins D is between 4 and 12 cm(-1) and the relaxation is dominated by the Orbach process between about 5 and 100 K and by a local mode at higher temperatures. The relaxation rates for the heme proteins in glassy matrices extrapolated to values at room temperature that are similar to values obtained by NMR relaxivity in fluid solution. This similarity suggests that for high-spin Fe(III) heme proteins with effective intramolecular spin-lattice relaxation processes, the additional motional freedom gained when a relatively large protein goes from glassy solid to liquid solution at room temperature has little impact on spin-lattice relaxation.     

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.     

Out‐of‐plane deformations of the heme group in different ferrocytochrome c proteins probed by resonance Raman spectroscopy

We measured the low‐wavenumber polarized resonance Raman spectra of horse heart (hhc), chicken (chc) and yeastC102T (yc) ferrocytochromes c with Soret excitation. We examined the out‐of‐plane (oop) deformations of the heme groups by virtue of relative intensities and depolarization ratios of a variety of oop and in‐plane (ip) Raman active bands. Analysis of relative Raman intensities shows differences in deviation from planarity of the heme groups of yeast, horse heart and chicken cytochromes c. The heme groups in cytochrome c proteins have been shown by normal coordinate static deformation (NSD) analysis from crystal structures to exhibit a dominant ruffling (B_1u) deformation. As a consequence the B_1u modes, γ₁₀ − γ₁₂, become resonance Raman active. We used normalized Raman intensity ratios and depolarization ratios of oop Raman active modes, whose intensities are attributable to specific nonplanar deformations, to estimate and compare their Franck‐Condon‐type and Jahn‐Teller‐type coupling magnitudes for horse heart, chicken and yeast ferrocytochrome c at neutral pH. These coupling magnitudes allow for a quantitative comparison of oop deformations between individual heme groups. Chicken ferrocytochrome was found to have the largest ruffling deformation of the three investigated proteins, followed by horse heart and yeast cytochrome c. The heme group of the former is slightly more ruffled than the corresponding active site of the latter, while saddling in both proteins is substantially larger than in chicken ferrocytochrome c. The Raman data are sensitive enough to allow a comparison of lesser deformations. Doming, which is a kinetic coordinate in many heme proteins, is largest in chicken and smallest in yeast cytochrome c. Waving is largest in yeast, followed by horse heart and chicken cytochrome c. Propellering deformations could be compared for chicken and horse heart cytochrome c and were found to be substantially larger in the latter. A comparison with heme deformations obtained from X‐ray structures (for horse heart and yeast cytochrome c) and from molecular dynamics simulations (MDS) (performed for all three proteins) yields some agreement with the main ruffling and saddling deformations derived from the crystal structures, whereas the heme conformations produced by MDS seem to account better for smaller deformations like doming and propellering. The present study demonstrates the usefulness of resonance Raman spectroscopy for the analysis of nonplanar deformations in heme proteins. Copyright © 2008 John Wiley & Sons, Ltd.     

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.     

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.     

Induced long-range attractive potentials of human serum albumin by ligand binding

Small-angle x-ray scattering and dielectric spectroscopy investigation on the solutions of recombinant human serum albumin and its heme hybrid revealed that heme incorporation induces a specific long-range attractive potential between protein molecules. This is evidenced by the enhanced forward intensity upon heme binding, despite no hindrance to rotatory Brownian motion, unbiased colloid osmotic pressure, and discontiguous nearest-neighbor distance, confirming monodispersity of the proteins. The heme-induced potential may play a trigger role in recognition of the ligand-filled human serum albumins in the circulatory system.     

Cryoradiolytic reduction of crystalline heme proteins: analysis by UV‐Vis spectroscopy and X‐ray crystallography

The X‐ray crystallographic analysis of redox‐active systems may be complicated by photoreduction. Although radiolytic reduction by the probing X‐ray beam may be exploited to generate otherwise short‐lived reaction intermediates of metalloproteins, it is generally an undesired feature. Here, the X‐ray‐induced reduction of the three heme proteins myoglobin, cytochrome P450cam and chloroperoxidase has been followed by on‐line UV‐Vis absorption spectroscopy. All three systems showed a very rapid reduction of the heme iron. In chloroperoxidase the change of the ionization state from ferric to ferrous heme is associated with a movement of the heme‐coordinating water molecule. The influence of the energy of the incident X‐ray photons and of the presence of scavengers on the apparent reduction rate of ferric myoglobin crystals was analyzed.     

Chemical synthesis of TASP arrays and their application in protein design

A combinatorial synthesis of de novo proteins is described. The concept of template-assembled synthetic proteins (TASP) has been adapted to an orthogonal assembly of small libraries of purified peptide building blocks. It is combined with the spot synthesis of peptides which is exploited to array cyclic decapeptide templates on cellulose membranes. A cleavable linker on the cellulose allows control of the synthesis. The hydrophilic proteins are constructed by successive cleavage of orthogonal protecting groups on the template, followed by coupling of amphipathic helices in a predefined orientation and finally by incorporation of a cofactor. Libraries of peptides with variation of the amino acids expected to be close to the cofactor were coupled to the cellulose-bound template in all combinations, yielding up to 500 variants of a protein. Cofactors have been inserted either at non-covalent binding sites as heme and Cu2+ or by covalent modification of amino acids as Ru-bipyridine or flavin. The proteins were screened by recording their UV-vis spectra directly on the solid support. The properties screened include the redox potential of heme proteins, charge transfer bands indicating the ligation of Cu-centers, enzymatic activity, and folding stability. Synthesis of the best hits as soluble variants was used for detailed characterization. Iterative improvement in a second screening cycle was efficient in finding novel copper proteins. We discuss the prospects of synthesizing proteins by extending the concept to beta-sandwich proteins and construction of efficient peptide libraries with computer-supported design, as well as the possible usage of improved solid phase materials.     

Effective methods for preparation and characterization of HNO‐adducts of heme proteins

Driven by the documented effectiveness of cryoradiolysis coupled with resonance Raman spectroscopy for the preparation and structural characterization of unstable peroxo and hydroperoxo intermediates of catalytic and oxidative enzymes, similar strategies have now been applied to prepare and study the still relatively unexplored chemistry of nitrosyl hydride (HNO) adducts of heme proteins and their derivatives. Previously, such HNO derivatives of heme proteins were prepared by chemical addition of reducing agents or by direct addition of an HNO donor. Here, for the first time, we report effective cryoradiolytic preparation of Fe–N(H)O species of myoglobin and their structural characterization by resonance Raman spectroscopy. Our results are in excellent agreement with those previously reported for chemically prepared derivatives and with computational results. Furthermore, the present study provides new data for the deuterated analogue; i.e. bearing a nitrosyl deuteride (DNO) fragment. Copyright © 2012 John Wiley & Sons, Ltd.     

Resonance Raman determination of vinyl group disposition in different derivatives of native myoglobin and its heme‐disoriented form

In heme‐reconstituted heme proteins, the heme inserts such that some of the heme is rotated 180° about the α–γ meso axis, eventually equilibrating to native conformations. Also, proteins from different species may naturally possess both conformers. Resonance Raman (RR) spectroscopy is effective in signaling this conformational heterogeneity, detecting altered interactions with active site residues. While shifts of the vibrational modes of the two vinyl groups could be readily detected, they could not be assigned to a particular vinyl group. This deficiency is alleviated by employing a specifically labeled protoheme isotopomer, wherein only the 4‐vinyl group is labeled (i.e. –CH=C²H₂), providing a spectral editing mechanism for selectively tracking the individual vinyl groups. The RR spectral data acquired here for the met‐, deoxy‐, and ferrous CO adduct of myoglobin, along with their ‘flipped heme’ isomers, provide convincing evidence for the anticipated effects of ‘swapping’ the environments of the two vinyl groups; i.e., in the native form, the 2‐vinyl group assumes a more out‐of‐plane orientation with respect to the pyrrole plane than does the (nearly in‐plane) 4‐vinyl group, whereas in the ‘reversed’ orientation, the 4‐vinyl group now assumes a position that is more out‐of‐plane than the newly positioned 2‐vinyl group. The ability of RR spectroscopy to document such differences in the orientation of the vinyl substituents is made important by the fact that changes in the disposition of these groups has long been known to carry functional consequences. Copyright © 2014 John Wiley & Sons, Ltd.     

Nitric oxide heme interactions in nitrophorin 7 investigated by nuclear inelastic scattering

Nitrophorins (NPs) occur in the blood-sucking insect Rhodnius prolixus. These proteins use ferric heme to store nitric oxide (NO) in the salivary glands of the insects and transport it to the victim’s tissues, resulting in vasodilation and reduced blood coagulation. In this work we present a nuclear inelastic scattering (NIS) study in order to characterize the iron-NO interaction in the isoform nitrophorin 7 (NP7). The NIS data obtained for NP7 complexed with NO show a strong band at ～589 cm^?1 which is due to modes with significant Fe-NO stretching and bending character. Another conspicuous feature is a significant peak at ～280 cm^?1 in the region where the heme modes occur. Based on a hybrid calculation method, which uses density functional theory and molecular mechanics, the band at ～280 cm^?1 is assigned to heme modes with substantial doming character.     

Observation of persistent α‐helical content and discrete types of backbone disorder during a molten globule to ordered peptide transition via deep‐UV resonance Raman spectroscopy

The molten globule (MG) state can aid in the folding of a protein to a functional structure and is loosely defined as an increase in structural disorder with conservation of the ensemble secondary structure content. Simultaneous observation of persistent secondary structure content with increased disorder has remained experimentally problematic. As a consequence, modeling how the MG state remains stable and how it facilitates proper folding remains difficult due to a lack of amenable spectroscopic techniques to characterize this class of partially unfolded proteins. Previously, deep‐UV resonance Raman (dUVRR) spectroscopy has proven useful in the resolution of global and local structural fluctuations in the secondary structure of proteins. In this work, dUVRR was employed to study the MG to ordered transition of a model four‐helix bundle protein, HP7. Both the average ensemble secondary structure and types of local disorder were monitored, without perturbation of the solvent, pH, or temperature. The MG to ordered transition is induced by stepwise coordination of two heme molecules. Persistent dUVRR spectral features in the amide III region at 1295–1301 and 1335–1338 cm⁻¹ confirm previous observations that HP7 remains predominantly helical in the MG versus the fully ordered state. Additionally, these spectra represent the first demonstration of conserved helical content in a MG protein. With successive heme binding, significant losses are observed in the spectral intensity of the amide III₃ and S regions (1230–1260 and 1390 cm⁻¹, respectively), which are known to be sensitive to local disorder. These observations indicate that there is a decrease in the structural populations able to explore various extended conformations with successive heme binding events. DUVRR spectra indicate that the first heme coordination between two helical segments diminishes exploration of more elongated backbone structural conformations in the inter‐helical regions. A second heme coordination by the remaining two helices further restricts protein motion. Copyright © 2013 John Wiley & Sons, Ltd.     

Structural properties of cyanobacterial hemoglobins: the unusual heme-protein cross-link of Synechocystis sp. PCC 6803 Hb and Synechococcus sp. PCC 7002 Hb

The truncated hemoglobins from Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7002 ligate the heme iron with two axial histidines (HisF8 and HisE10). In addition, these two proteins are able to form a heme-protein cross-link between a vinyl substituent and a histidine at position 16 of the H helix. The product is a protein with improved resistance to thermal and acid denaturation.     

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.     

Impact of Mercury(II) on proteinase K catalytic center: investigations via classical and Born-Oppenheimer molecular dynamics

Mercury(II) has a strong affinity for the thiol groups in proteins often resulting in the disruption of their biological functions. In this study we present classical and first-principles, DFT-based molecular dynamics (MD) simulations of a complex of Hg(II) and proteinase K, a well-known serine protease with a very broad and diverse enzymatic activity. It contains a catalytic triad formed by Asp39, His69, and Ser224, which is responsible for its biological activity. It was found previously by X-ray diffraction experiments that the presence of Hg(II) inhibits the enzymatic action of proteinase K by affecting the stereochemistry of the triad. Our simulations predict that (i) the overall structure as well as the protein backbone dynamics are only slightly affected by the mercury cation, (ii) depending on the occupied mercury site, the hydrogen bonds of the catalytic triad are either severely disrupted (both bonds for mercury at site 1, and the His69–Ser224 contact for mercury at site 2) or slightly strengthened (the Asp39–His69 bond when mercury is at site 2), (iii) the network of hydrogen bonds of the catalytic triad is not static but undergoes constant fluctuations, which are significantly modified by the presence of the Hg(II) cation, influencing in turn the triad’s ability to carry out the enzymatic function—these facts explain the experimental findings on the inhibition of proteinase K by Hg(II).     

Illuminate Proteins and Peptides by Elemental Tag for HPLC-ICP-MS Detection

Abstract

High-performance liquid chromatography–inductively coupled plasma mass spectrometry (HPLC-ICP-MS) is becoming a significant complementary technique of HPLC–molecular mass spectrometry for proteins and peptides quantification. However, the naturally occurring heteroelements inside proteins and peptides, such as sulfur, phosphor, and selenium, are not sensitive enough in ICP-MS for low-abundance proteins and peptides, due to their low ionization efficiency or polyatomic spectral interference. In order to make the low-abundance proteins and peptides “visible” by HPLC-ICP-MS, a foreign elemental tag can be employed. The foreign elemental tags are highly sensitive in ICP-MS and almost absent in common biological matrices, which leads to significantly low limits of detection. This review summarizes the major applications of elemental tags in combination with HPLC-ICP-MS detection. The organic mercury tags, iodine tags, ferrocene tags, and macrocyclic metal chelate complex tags are discussed in detail. The recent development of HPLC-ICP-MS in combination with elemental tags demonstrates the great potential in sensitive and accurate proteins and peptides quantification.     

紫外-可见光谱法研究二茂铁衍生物与血红素的相互作用

采用紫外-可见光谱法(UV-Vis)研究三种二茂铁衍生物[Fc(COOH)₂(λ_max=286 nm), Fc(OBt)₂(λ_max=305 nm), Fc(Cys)(λ_max=289 nm)]与血红素(heme, λ_max=386 nm)的相互作用。实验结果表明：当固定heme浓度时,heme的吸光度随着Fc(COOH)₂和Fc(Cys)浓度的增加而增大,而heme的吸光度随着Fc(OBt)₂的浓度的增加几乎没有增大;当分别固定Fc(COOH)₂, Fc(Cys)和Fc(OBt)₂的浓度时,Fc(COOH)₂和Fc(Cys)的吸光度随着heme浓度的增加而增大,而Fc(OBt)₂的吸光度随着heme浓度的增加没有变化,说明Fc(COOH)₂和Fc(Cys)与heme存在分子间的相互作用,主要是由于Fc(COOH)₂和 Fc(Cys)与heme能形成氢键,分子链增长,吸收的能量增加,导致吸光度增大;而Fc(OBt)₂与heme没有分子间的相互作用,是由于Fc(OBt)₂没有自由的氢,不能与heme形成分子间的氢键。同时考察了三种二茂铁衍生物与heme 的吸光度随时间的变化,Fc(COOH)₂和 Fc(Cys)与heme的吸光度随着时间的增加而减少,而Fc(OBt)₂与heme的吸光度随时间的变化几乎没有变化。Fc(COOH)₂与Fc(Cys)和heme的反应时间为0.5,18和48 h,当固定Fc(COOH)₂浓度时,在λ_max=384 nm处的吸光度由2.64分别变为2.53和2.51;当固定heme的浓度时,在λ_max=384 nm处的吸光度由1.76分别变为1.72和1.68;当固定Fc(Cys)浓度时,在λ_max=397 nm处的吸光度由2.74分别变为2.63和2.55;当固定heme的浓度时,在λ_max=397 nm处的吸光度由1.82分别变为1.58和1.49。     

Vibrational dynamics of biological molecules: Multi-quantum contributions

High-resolution X-ray measurements near a nuclear resonance reveal the complete vibrational spectrum of the probe nucleus. Because of this, nuclear resonance vibrational spectroscopy (NRVS) is a uniquely quantitative probe of the vibrational dynamics of reactive iron sites in proteins and other complex molecules. Our measurements of vibrational fundamentals have revealed both frequencies and amplitudes of ⁵⁷Fe vibrations in proteins and model compounds. Information on the direction of Fe motion has also been obtained from measurements on oriented single crystals, and provides an essential test of normal mode predictions. Here, we report the observation of weaker two-quantum vibrational excitations (overtones and combinations) for compounds that mimic the active site of heme proteins. The predicted intensities depend strongly on the direction of Fe motion. We compare the observed features with predictions based on the observed fundamentals, using information on the direction of Fe motion obtained either from DFT predictions or from single crystal measurements. Two-quantum excitations may become a useful tool to identify the directions of the Fe oscillations when single crystals are not available.