细胞色素b5-蛋白质相互作用研究

蛋白质-蛋白质相互作用在生命过程中发挥至关重要的作用,特别是血红素类蛋白。细胞色素b5(Cyt b5)是血红素蛋白的一个典型代表,在生物体内通过多种蛋白质-蛋白质相互作用来执行其生物功能。目前所揭示的与Cyt b5相关的蛋白质相互作用包括:细胞色素b5-细胞色素b5还原酶,细胞色素b5-细胞色素P450,细胞色素b5-细胞色素c,细胞色素b5-肌红蛋白或血红蛋白,细胞色素b5-融合蛋白(谷胱甘肽S-转移酶GST和绿色荧光蛋白GFP)和细胞色素b5-转运蛋白(蔗糖转运蛋白SUT1和山梨醇转运蛋白SOT6)等。同一蛋白能与众多不同蛋白相互作用的事实,使我们认识到某些特定蛋白的生物学重要性。另一方面,研究同一蛋白与不同蛋白质间的相互作用将会进一步加深我们对蛋白质结构与功能关系的理解,以及指导新颖蛋白的理性设计与最终应用。     

Designed Heme-Cage β-Sheet Miniproteins

The structure and function of naturally occurring proteins are governed by a large number of amino acids (≥100). The design of miniature proteins with desired structures and functions not only substantiates our knowledge about proteins but can also contribute to the development of novel applications. Excellent progress has been made towards the design of helical proteins with diverse functions. However, the development of functional β-sheet proteins remains challenging. Herein, we describe the construction and characterization of four-stranded β-sheet miniproteins made up of about 19 amino acids that bind heme inside a hydrophobic binding pocket or “heme cage” by bis-histidine coordination in an aqueous environment. The designed miniproteins bound to heme with high affinity comparable to that of native heme proteins. Atomic-resolution structures confirmed the presence of a four-stranded β-sheet fold. The heme–protein complexes also exhibited high stability against thermal and chaotrope-induced unfolding.     

Electrochemical property and analysis application of biosensors in miscible nonaqueous media—Room-temperature ionic liquid

Stable heme proteins entrapped in dimethylformamide (DMF)–chitosan organohydrogel films modified electrodes were operated in neat hydrophilic room-temperature ionic liquid (IL) [bmim][BF₄] for the first time. The modified electrodes possess outstanding electrochemical response in [bmim][BF₄] without adding water. The morphology studies of films were demonstrated by atomic force microscopy (AFM). UV–Vis and FTIR spectroscopy showed that the heme proteins retained their native structure in organohydrogel films. Direct electrochemistry and bioelectrocatalysis of heme protein–organohydrogel films were investigated. Several electrochemical parameters such as the charge transfer coefficients (α) and the apparent electron transfer rate constant (k_s) of these processes were calculated by performing nonlinear regression analysis of square wave voltammetry (SWV) experimental dates. Furthermore, high electrocatalytic activity to hydrogen peroxide (H₂O₂) was observed, indicating that heme proteins entrapped in organohydrogel films retained their bioelectrocatalytic activities in [bmim][BF₄]. Kinetic analysis of the cyclic voltammetry dates shows that heme protein–organohydrogel films operated in IL bring up to an enhancement of the biosensor sensitivity and a high affinity for H₂O_2.     

Profiling the Heme-Binding Proteomes of Bacteria Using Chemical Proteomics

Heme is a cofactor with myriad roles and essential to almost all living organisms. Beyond classical gas transport and catalytic functions, heme is increasingly appreciated as a tightly controlled signalling molecule regulating protein expression. However, heme acquisition, biosynthesis and regulation is poorly understood beyond a few model organisms, and the heme-binding proteome has not been fully characterised in bacteria. Yet as heme homeostasis is critical for bacterial survival, heme-binding proteins are promising drug targets. Herein we report a chemical proteomics method for global profiling of heme-binding proteins in live cells for the first time. Employing a panel of heme-based clickable and photoaffinity probes enabled the profiling of 32–54 % of the known heme-binding proteomes in Gram-positive and Gram-negative bacteria. This simple-to-implement profiling strategy could be interchangeably applied to different cell types and systems and fuel future research into heme biology.     

Gas‐Phase Spectroscopy of Ferric Heme?NO Complexes

Weakly bound complexes between ferric heme cations and NO were synthesised in the gas phase from ion–molecule reactions, and their absorption measured based on photodissociation yields. The Soret band, which serves as an important marker band for heme‐protein spectroscopy, is maximal at 357±5 nm and significantly blue‐shifted compared to ferric heme nitrosyl proteins (maxima between 408 and 422 nm). This is in stark contrast to the Q‐band absorption where the protein microenvironment is nearly innocent in perturbing the electronic structure of the porphyrin macrocycle. Photodissociation is primarily through loss of NO. In contrast to the Q‐band region, two‐photon absorption was seen in the Soret band despite NO loss only requiring ～1 eV. A model based on intersystem crossing to a long‐lived triplet state where a barrier has to be surmounted is suggested. Finally, we summarise the measured absorption maxima of heme and its complexes with amino acids and NO.     

Structural and functional properties of designed globins

De novo design of artificial proteins is an essential approach to elucidate the principles of protein architecture and to understand specific functions of natural proteins and also to yield novel molecules for medical and industrial aims. We have designed artificial sequences of 153 amino acids to fit the main-chain framework of the sperm whale myoglobin structure based on the knowledge-based energy functions to evaluate the compatibility between protein tertiary structures and amino acid sequences. The synthesized artificial globins bind a single heme per protein molecule as designed, which show well-defined electrochemical and spectroscopic features characteristic of proteins with a low-spin heme. Redox and ligand binding reactions of the artificial heme proteins were investigated and these heme-related functions were found to vary with their structural uniqueness. Relationships between the structural and functional properties are discussed.     

Direct meso‐Alkynylation of Metalloporphyrins Through Gold Catalysis for Hemoprotein Engineering

A method was developed for the direct functionalization of metalloporphyrins at the methine protons (meso positions) to yield asymmetric alkynylated derivatives by using gold catalysis and hypervalent iodine reagents. This single‐step procedure was applied to b‐type heme and the product was incorporated into a gas‐sensor heme protein. The terminal alkyne allows fluorophore labeling through copper(I)‐catalyzed azide–alkyne cycloaddition (CuAAC). Hemoproteins with this type of engineered cofactor have several potential applications in labeling and imaging technologies. Additionally, the alkyne provides a handle for modulating porphyrin electron density, which affects cofactor redox potential and ligand affinity. This method will be helpful for investigating the chemistry of natural heme proteins and for designing artificial variants with altered properties and reactivities.     

Regulating the Coordination State of a Heme Protein by a Designed Distal Hydrogen-Bonding Network

Heme coordination state determines the functional diversity of heme proteins. Using myoglobin as a model protein, we designed a distal hydrogen-bonding network by introducing both distal glutamic acid (Glu29) and histidine (His43) residues and regulated the heme into a bis-His coordination state with native ligands His64 and His93. This resembles the heme site in natural bis-His coordinated heme proteins such as cytoglobin and neuroglobin. A single mutation of L29E or F43H was found to form a distinct hydrogen-bonding network involving distal water molecules, instead of the bis-His heme coordination, which highlights the importance of the combination of multiple hydrogen-bonding interactions to regulate the heme coordination state. Kinetic studies further revealed that direct coordination of distal His64 to the heme iron negatively regulates fluoride binding and hydrogen peroxide activation by competing with the exogenous ligands. The new approach developed in this study can be generally applicable for fine-tuning the structure and function of heme proteins.     

Non-exponential non-Arrhenius relaxation in the course of CO rebinding to heme proteins

The dispersive transport model for relaxation of photolyzed heme proteins has been improved to take into account the coupling of the ligand-heme geminate recombination and the non-Gaussian diffusive dynamics of conformational changes in heme proteins. Contrary to the earlier deterministic version of the model, the present more rigorous formulation is based on the stochastic approach to the problem. This implies that the time evolution of protein conformations should be described in terms of the transient distribution which satisfies the Smoluchowski-type differential equation with a time-dependent diffusion coefficient. The obtained analytical solution of this equation enables us to relate main kinetic parameters of the geminate recombination and quantities characterizing the ligand-heme interaction. The derived expressions demonstrate that the reaction barrier shifts with time towards higher values following the near-stretched exponential behavior in agreement with experiment. Such a behavior is governed by the non-exponential non-Arrhenius conformational relaxation. The latter process can be identified by the characteristics “footprint” left on the experimental rebinding curve and is shown to be responsible for some kinetically different phases of the ligand-heme geminate recombination observed within distinct temperature ranges.     

13C NMR signal detection of iron-bound cyanide ions in ferric cyanide complexes of heme proteins

13CN ion appears to have the greatest potential to probe the heme environment of the ferric heme proteins; however, a resonance of the iron-bound (13)CN ion in ferric heme proteins has not yet been located. We show here the first detection of (13)C NMR signals of the iron-bound (13)CN for heme proteins and their model complexes in an unexpectedly large upfield region. This study demonstrates that the (13)C NMR signal of the iron-bound (13)CN is a sensitive probe to study the nature of the proximal ligand in ferric heme protein.     

HNO binding in a heme protein: structures, spectroscopic properties, and stabilities

HNO can interact with numerous heme proteins, but atomic level structures are largely unknown. In this work, various structural models for the first stable HNO heme protein complex, MbHNO (Mb, myoglobin), were examined by quantum chemical calculations. This investigation led to the discovery of two novel structural models that can excellently reproduce numerous experimental spectroscopic properties. They are also the first atomic level structures that can account for the experimentally observed high stabilities. These two models involve two distal His conformations as reported previously for MbCNR and MbNO. However, a unique dual hydrogen bonding feature of the HNO binding was not reported before in heme protein complexes with other small molecules such as CO, NO, and O(2). These results shall facilitate investigations of HNO bindings in other heme proteins.     

Direct Electrochemistry and Catalytic Activity of Hemoglobin and Myoglobin Entrapped in PEG Film

Abstract

Direct electrochemistry and electrocatalysis of two heme proteins, hemoglobin (Hb) and myoglobin (Mb), incorporated in polyethylene glycol (PEG) films, were studied by cyclic voltammetry. The two proteins exhibited a pair of well‐defined, quasi‐reversible cyclic voltammetric peaks with the apparent formal potential at about ?0.21 V (Hb) and ?0.22 V (Mb), respectively, vs. saturated calomel electrode (SCE) in pH 5.0 acetate buffer solution, characteristic of the h eme Fe(III)/Fe(II) redox couples, indicating enhanced electron transfer between the proteins and the substrate electrode in the PEG film environment. The protein–PEG films could also exhibit excellent stability. Meanwhile, positions of Soret absorption band of the proteins in the PEG films suggested that the heme proteins kept their secondary structure similar to their native state in the medium pH range. Oxygen, trichloroacetic acid, nitric oxide, and hydrogen peroxide could all be catalytically reduced by Hb or Mb in PEG films.     

Resonance raman investigation of the specific sensing mechanism of a target molecule by gas sensory proteins

Specific sensing of gas molecules such as CO, NO, and O2 is a unique function of gas sensory hemoproteins, while hemoproteins carry out a wide variety of functions such as oxygen storage/transport, electron transfer, and catalysis as enzymes. It is important in gas sensory proteins that the heme domain not only recognizes its target molecule but also discriminates against other gases having similar molecular structures. Coordination of a target molecule to the heme is assumed to alter the protein conformation in the vicinity of heme, and the conformation change is propagated to the effector domain where substrate turnover, DNA binding, or interaction with a signal transduction protein is performed differently than the binding of other gases. To understand the appearance of such a specificity, we focus our attention on the ligand-protein interactions in the distal side of heme. In practice, the metal-ligand vibrations as well as internal modes of ligand and heme are measured with resonance Raman spectroscopy for wild-type and some mutant proteins with full-length or limited sensory regions. On the basis of such observations together with the knowledge currently available, we discuss the mechanism of specific sensing of a diatomic molecule in gas sensory proteins.     

Electrochemical and spectroscopic investigations of immobilized de novo designed heme proteins on metal electrodes.

On the basis of rational design principles, template-assisted four-helix-bundle proteins that include two histidines for coordinative binding of a heme were synthesized. Spectroscopic and thermodynamic characterization of the proteins in solution reveals the expected bis-histidine coordinated heme configuration. The proteins possess different binding domains on the top surfaces of the bundles to allow for electrostatic, covalent, and hydrophobic binding to metal electrodes. Electrostatic immobilization was achieved for proteins with lysine-rich binding domains (MOP-P) that adsorb to electrodes covered by self-assembled monolayers of mercaptopropionic acid, whereas cysteamine-based monolayers were employed for covalent attachment of proteins with cysteine residues in the binding domain (MOP-C). Immobilized proteins were studied by surface-enhanced resonance Raman (SERR) spectroscopy and electrochemical methods. For all proteins, immobilization causes a decrease in protein stability and a loosening of the helix packing, as reflected by a partial dissociation of a histidine ligand in the ferrous state and very low redox potentials. For the covalently attached MOP-C, the overall interfacial redox process involves the coupling of electron transfer and heme ligand dissociation, which was analyzed by time-resolved SERR spectroscopy. Electron transfer was found to be significantly slower for the mono-histidine-coordinated than for the bis-histidine-coordinated heme. For the latter, the formal heterogeneous electron-transfer rate constant of 13 s(-1) is similar to those reported for natural heme proteins with comparable electron-transfer distances, which indicates that covalently bound synthetic heme proteins provide efficient electronic communication with a metal electrode as a prerequisite for potential biotechnological applications.     

Cytochrome c heme lyase can mature a fusion peptide composed of the amino-terminal residues of horse cytochrome c

It is shown that cytochrome c heme lyase (CCHL) attaches heme covalently to peptides composed of the N-terminal segment of cyt c fused to a non-heme containing protein, lending insight into the substrate specificity of CCHL and providing a new route to artificial heme proteins.     

Fourier transform infrared spectroscopy as a tool to study structural properties of cytochromes P450 (CYPs)

Cytochrome P450 proteins (CYPs) are a big class of heme proteins which are involved in various metabolic processes of living organisms. CYPs are the terminal catalytically active components of monooxygenase systems where the substrate binds and is hydroxylated. In order to be functionally competent, the protein structures of CYPs possess specific properties that must be explored in order to understand structure–function relationships and mechanistic aspects. Fourier transform infrared spectroscopy (FTIR) is one tool that is used to study these structural properties. The application of FTIR spectroscopy to the secondary structures of CYP proteins, protein unfolding, protein–protein interactions and the structure and dynamics of the CYP heme pocket is reviewed. A comparison with other thiolate heme proteins (nitric oxide synthase and chloroperoxidase) is also included. Figure The protein secondary structure, protein unfolding, redox-partner protein–protein interaction, structural changes induced by the reduction of the heme iron, and the structure and dynamics of the active site of cytochromes P450 (CYP) can be studied using Fourier transform infrared spectroscopy (FTIR). FTIR spectroscopy is a good approach for gaining a deeper insight into structure–function relationships in CYPs. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Exploring the interaction between “site-markers,aspirin and esterase-like activity” ternary systems on the human serum albumin: direct evidence for modulation of catalytic activity of the protein in different inhibition modes

Albumin which is the most abundant drug carrier protein in plasma controls the distribution aspect of drug pharmacokinetics. The aim of this study has been to elucidate the concurrent binding behavior of indomethacin/ibuprofen/heme to HSA under the effect of aspirin-mediated protein acetylation and also to explore the esterase-like catalytic property of the unmodified/modified proteins, as binary or ternary systems, by using various spectroscopic and molecular docking techniques. We found that aspirin-based modification of HSA affects the protein conformation as well as ligand binding at sites I–III. Decrease in pNPA-mediated esterase activity of HSA in different reversible inhibition modes, upon the protein–ligand interactions, was also documented, an issue that may receive considerable attention for computational prodrug design in near future.     

Ligand probes for heme proteins

Heme-containing proteins are one of the most structurally and functionally diverse groups of proteins in nature. Central to our understanding of their function is an appreciation of the fundamental inorganic and physical properties of the heme prosthetic group itself. Many spectroscopic techniques have been used to probe heme proteins but these alone often cannot reveal all of the key information required. Many exogeneous heme-iron ligands have been shown to be highly sensitive to the electronic and physical properties of protein-bound heme groups. Such ligands, used in combination with spectroscopic and/or crystallographic analyses, have proved to be particularly useful in probing not only the heme prosthetic group itself but also the surrounding structure and dynamics of the protein active-site. In this perspective, we introduce five diverse families of heme-proteins and discuss how the use of heme-coordinating ligands has provided immensely important information about the physical and structural properties of each heme-protein family.     

PROTEIN GLOBULE SPEEDS UP THE HEME PHOTOREDUCTION

Abstract— To answer the question whether the external electron can be transferred through the protein globule, the rate of photoreduction of the free heme with dye radicals was compared with that of the heme in various protein environments, in cytochrome c, myoglobin and in heme-HSA complex. In all cases the globular part of proteins did not prevent the photoreduction of the heme; in fact, it speeded up the process. As determined by flash-photolysis, the rate constants(1–5) x 10⁸ M^-1 s^-1 are close to that of the diffusion controlled reactions between molecules of similar size. The experimental data confirm the hypothesis that the native protein globule can transfer external unpaired electrons rather effectively. We make the supposition that this ability is a general feature of proteins but not a function related to electron carriers only.