Machine Learning Approaches for Metalloproteins

Metalloproteins are a family of proteins characterized by metal ion binding, whereby the presence of these ions confers key catalytic and ligand-binding properties. Due to their ubiquity among biological systems, researchers have made immense efforts to predict the structural and functional roles of metalloproteins. Ultimately, having a comprehensive understanding of metalloproteins will lead to tangible applications, such as designing potent inhibitors in drug discovery. Recently, there has been an acceleration in the number of studies applying machine learning to predict metalloprotein properties, primarily driven by the advent of more sophisticated machine learning algorithms. This review covers how machine learning tools have consolidated and expanded our comprehension of various aspects of metalloproteins (structure, function, stability, ligand-binding interactions, and inhibitors). Future avenues of exploration are also discussed.     

Tandem mass spectroscopy as a tool for investigation of complexes of PNP‐lariat ether derivative with metal ions

The novel PNP‐lariat ether L with cyclotriphosphazene ring incorporated in the macrocyclic structure was synthesized and checked by the electrospray mass spectrometry (ESI‐MS) method for the ability to bind different types of ions Ag⁺, Ca²⁺, Cd²⁺, Cu²⁺, and Pb²⁺. Furthermore, the stability constants of the abovementioned ion complexes with the investigated ligand have been determined by direct and competitive potentiometric methods. To evaluate the stability of various complex types and to confirm the way of metal cation binding, the tandem mass spectra of the investigated ligand and its complexes were taken. As a result, we obtained quite a good relationship between the number and main types of complex species observed in ESI‐MS experiments and the forms of complexes for which the stabilization constants were determined by potentiometric methods. Moreover, we also concluded that in case of big discrepancies of stability constants, ESI‐MS experiments could provide information about the most stable form of the complexes, but they fail when the differences between the strength of the coordination binding are slightly different.     

计算机辅助的金属蛋白设计与改造研究进展

金属蛋白是一类含有金属离子的蛋白的统称,具有特殊的催化活性,在生物体中发挥着重要作用,其结构与功能的关系已经得到了较为充分的研究。在此基础上,通过模拟已知金属蛋白的活性位点,利用计算机辅助设计的方法可以人工设计得到具有特定结构和功能的金属蛋白。本文综述了近期计算机辅助金属蛋白设计与改造领域的研究进展,概括了引入金属离子结合位点和改造蛋白活性的一般规律,总结了计算机辅助设计的优势以及目前存在的问题和挑战,并展望了此领域未来发展的方向和可能的突破点。     

Applications of electrospray ionization mass spectrometry to neutral organic molecules including fullerenes

The use of electrospray ionization mass spectrometry (ESI/MS) for the detection of neutral organic molecules becomes possible by their derivation with specific ESI/MS tagging reagents that have either proton or metal ion binding sites. We used the neutral crown ether group in several reagents to attach a metal binding site to substrate molecules. Application of this method to steroids, amino acids, vitamin D, fatty acids, and fullerenes is described. Besides characterization, tagged molecules can be used for studying organic reactions by ESI/MS. This work demonstrates that ESI/MS provides a unique window on fullerene solution chemistry. ESI/MS is not only an excellent tool for the analysis of biopolymers but is also useful for studying the organic chemistry of small neutral molecules.     

Insights into partially folded or unfolded States of metalloproteins from nuclear magnetic resonance

Nuclear magnetic resonance (NMR) provides detailed insights into the conformational features of unfolded and partially folded proteins. In the case of metalloproteins, special attention should be devoted to the characterization of the properties of the metal binding sites, and specific approaches need to be developed depending on the nature of the metal ion and its coordination environment. At the same time, metal-based NMR parameters may help in getting a better picture of the average structural properties of the metalloprotein. A critical evaluation of the limits of applicability of paramagnetic effects for solution structure determination in partially folded or unfolded proteins is presented. The coupling between NMR characterization of structure and dynamic of the polypeptide chain and of the metal environment provides insights into the stabilizing role of metal ions in metalloproteins. The overall approach is illustrated for some case examples of increasing flexibility obtained far from native conditions for cytochrome c and superoxide dismutase, two metalloproteins that have been extensively studied in our lab and whose misfolded forms may be relevant for important biological processes.     

Capillary electrophoresis-mass spectrometry for the analysis of intact proteins

Developments in the fields of protein chemistry, proteomics and biotechnology have increased the demand for suitable analytical techniques for the analysis of intact proteins. In 1989, capillary electrophoresis (CE) was combined with mass spectrometry (MS) for the first time and its potential usefulness for the analysis of intact (i.e. non-digested) proteins was shown. This article provides an overview of the applications of CE-MS within the field of intact protein analysis. The principles of the applied CE modes and ionization techniques used for CE-MS of intact proteins are shortly described. It is shown that separations are predominantly carried out by capillary zone electrophoresis and capillary isoelectric focusing, whereas electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) are the most popular ionization techniques used for interfacing. The combination of CE with inductively coupled plasma (ICP) MS for the analysis of metalloproteins is also discussed. The various CE-MS combinations are systematically outlined and tables provide extensive overviews of the applications of each technique for intact protein analysis. Selected examples are given to illustrate the usefulness of the CE-MS techniques. Examples include protein isoform assignment, single cell analysis, metalloprotein characterization, proteomics and biomarker screening. Finally, chip-based electrophoresis combined with MS is shortly treated and some of its applications are described. It is concluded that CE-MS represents a powerful tool for the analysis of intact proteins yielding unique separations and information.     

The potential of organic (electrospray- and atmospheric pressure chemical ionisation) mass spectrometric techniques coupled to liquid-phase separation for speciation analysis

The use of mass spectrometry based on atmospheric pressure ionisation techniques (atmospheric pressure chemical ionisation, APCI, and electrospray ionisation, ESI) for speciation analysis is reviewed with emphasis on the literature published in and after 1999. This report accounts for the increasing interest that atmospheric pressure ionisation techniques, and in particular ESI, have found in the past years for qualitative and quantitative speciation analysis. In contrast to element-selective detectors, organic mass spectrometric techniques provide information on the intact metal species which can be used for the identification of unknown species (particularly with MS–MS detection) or the confirmation of the actual presence of species in a given sample. Due to the complexity of real samples, it is inevitable in all but the simplest cases to couple atmospheric pressure MS detection to a separation technique. Separation in the liquid phase (capillary electrophoresis or liquid chromatography in reversed phase, ion chromatographic or size-exclusion mode) is particularly suitable since the available techniques cover a very wide range of analyte polarities and molecular mass. Moreover, derivatisation can normally be avoided in liquid-phase separation. Particularly in complex environmental or biological samples, separation in one dimension is not sufficient for obtaining adequate resolution for all relevant species. In this case, multi-dimensional separation, based on orthogonal separation techniques, has proven successful. ESI-MS is also often used in parallel with inductively coupled plasma MS detection. This review is structured in two parts. In the first, the fundamentals of atmospheric pressure ionisation techniques are briefly reviewed. The second part of the review discusses recent applications including redox species, use of ESI-MS for structural elucidation of metal complexes, characterisation and quantification of small organometallic species with relevance to environment, health and food. Particular attention is given to the characterisation of biomolecules and metalloproteins (metallothioneins and phytochelatins) and to the investigation of the interaction of metals and biomolecules. Particularly in the latter field, ESI-MS is the ideal technique due to the softness of the ionisation process which allows to assume that the detected gas-phase ions are a true representation of the ions or ion–biomolecule complexes prevalent in solution. It is particularly this field, important to biochemistry, physiology and medical chemistry, where we can expect significant developments also in the future.     

Coordination ability of 3-pyridinyl coumarins with palladium(II) and platinum(II)

The coordination ability of two 3-pyridinyl coumarins with Pd(II) and Pt(II) both in solution and in solid state is elucidated by conventional and linear-polarized IR-spectroscopy of oriented colloid suspensions in nematic liquid crystal, ¹H- and ¹³C-NMR, UV-Vis spectroscopy, positive and negative ion mass spectrometry (ESI), HPLC tandem mass spectrometry (HPLC ESI MS/MS), TGV, and DSC methods. The four metal complexes are compared with free ligands. Density functional theory calculations are performed to obtain the electronic structure and vibrational properties of the compounds to support the experimental data.     

Exploring the chemical profile of designer drugs by ESI(+) and PSI(+) mass spectrometry—An approach on the fragmentation mechanisms and chemometric analysis

The consumption of design drugs, frequently known as new psychoactive substances (NPS), has increased considerably worldwide, becoming a severe issue for the responsible governmental agencies. These illicit substances can be defined as synthetic compounds produced in clandestine laboratories in order to act as analogs of schedule drugs mimetizing its chemical structure and improving its pharmacological effects while hampering the control and making regulation more complicated. In this way, the development of new methodologies for chemical analysis of NPS drugs is indispensable to determine a novel class of drugs arising from the underground market. Therefore, this work shows the use of high‐resolution mass spectrometry Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR MS) applying different ionization sources such as paper spray ionization (PSI) and electrospray ionization (ESI) in the evaluation of miscellaneous of seized drugs samples as blotter paper (n = 79) and tablet (n = 100). Also, an elucidative analysis was performed by ESI(+)MS/MS experiments, and fragmentation mechanisms were proposed to confirm the chemical structure of compounds identified. Besides, the results of ESI(+) and PSI(+)‐FT‐ICR MS were compared with those of GC–MS, revealing that ESI(+)MS showed greater detection efficiency among the methodologies employed in this study. Moreover, this study stands out as a guide for the chemical analysis of NPS drugs, highlighting the differences between the techniques of ESI(+)‐FT‐ICR MS, PSI(+)‐FT‐ICR MS, and GC–MS.     

Metal displacement and stoichiometry of protein‐metal complexes under native conditions using capillary electrophoresis/mass spectrometry

Increases in the study of protein‐metal complexes, as well as in metal displacement in protein‐metal complexes under native conditions for optimum catalytic properties in drug research and catalyst design, demands a separation/detection technology that can accurately measure metal displacement and stoichiometry in protein‐metal complexes. Both nuclear magnetic resonance (NMR) and X‐ray diffraction techniques have been used for this purpose; however, these techniques lack sensitivity. Electrospray ionization mass spectrometry (ESI‐MS) using direct infusion offers higher sensitivity than the former techniques and provides molecular distribution of various protein‐metal complexes. However, since protein‐metal complexes under native conditions usually are dissolved in salt solutions, their direct ESI‐MS analysis requires off‐line sample clean‐up prior to MS analysis to avoid sample suppression during ESI. Moreover, direct infusion of the salty solution promotes non‐specific salt adduct formation by the protein‐metal complexes under ESI‐MS, which complicates the identification and stoichiometry measurements of the protein‐metal complexes. Because of the high mass of protein‐metal complexes and lack of sufficient resolution by most mass spectrometers to separate non‐specific from specific metal‐protein complexes, accurate protein‐metal stoichiometry measurements require some form of sample clean up prior to ESI‐MS analysis. In this study, we demonstrate that capillary electrophoresis/electrospray ionization in conjunction with a medium‐resolution (～10 000) mass spectrometer is an efficient and fast method for the measurement of the stoichiometry of the protein‐metal complexes under physiological conditions (pH ～7). The metal displacement of Co²⁺ to Cd²⁺, two metal ions necessary for activation in the monomeric AHL lactonase produced by B. thuringiensis, has been used as a proof of concept. Copyright © 2010 John Wiley & Sons, Ltd.     

Femtomolar Zn(II) affinity in a peptide-based ligand designed to model thiolate-rich metalloprotein active sites

Metal-ligand interactions are critical components of metalloprotein assembly, folding, stability, electrochemistry, and catalytic function. Research over the past 3 decades on the interaction of metals with peptide and protein ligands has progressed from the characterization of amino acid-metal and polypeptide-metal complexes to the design of folded protein scaffolds containing multiple metal cofactors. De novo metalloprotein design has emerged as a valuable tool both for the modular synthesis of these complex metalloproteins and for revealing the fundamental tenets of metalloprotein structure-function relationships. Our research has focused on using the coordination chemistry of de novo designed metalloproteins to probe the interactions of metal cofactors with protein ligands relevant to biological phenomena. Herein, we present a detailed thermodynamic analysis of Fe(II), Co(II), Zn(II), and[4Fe-4S]2(+/+) binding to IGA, a 16 amino acid peptide ligand containing four cysteine residues, H2N-KLCEGG-CIGCGAC-GGW-CONH2. These studies were conducted to delineate the inherent metal-ion preferences of this unfolded tetrathiolate peptide ligand as well as to evaluate the role of the solution pH on metal-peptide complex speciation. The [4Fe-4S]2(+/+)-IGA complex is both an excellent peptide-based synthetic analogue for natural ferredoxins and is flexible enough to accommodate mononuclear metal-ion binding. Incorporation of a single ferrous ion provides the FeII-IGA complex, a spectroscopic model of a reduced rubredoxin active site that possesses limited stability in aqueous buffers. As expected based on the Irving-Williams series and hard-soft acid-base theory, the Co(II) and Zn(II) complexes of IGA are significantly more stable than the Fe(II) complex. Direct proton competition experiments, coupled with determinations of the conditional dissociation constants over a range of pH values, fully define the thermodynamic stabilities and speciation of each MII-IGA complex. The data demonstrate that FeII-IGA and CoII-IGA have formation constant values of 5.0 x 10(8) and 4.2 x 10(11) M-1, which are highly attenuated at physiological pH values. The data also evince that the formation constant for ZnII-IGA is 8.0 x 10(15) M-1, a value that exceeds the tightest natural protein Zn(II)-binding affinities. The formation constant demonstrates that the metal-ligand binding energy of a ZnII(S-Cys)4 site can stabilize a metalloprotein by -21.6 kcal/mol. Rigorous thermodynamic analyses such as those demonstrated here are critical to current research efforts in metalloprotein design, metal-induced protein folding, and metal-ion trafficking.     

新型包覆Pd纳米粒子液相色谱-串联质谱法用于鉴定沙特阿拉伯原油中的含氧化合物(英文)

Saudi Arabian crude oil is a super complex mixture and,up to now,there has been little research into its heteroatom-containing compounds.First,oxygenated compounds(OCs)were isolated from Saudi Arabian oil using a Pd nanoparticle exchange complex,which formed between the nano-Pds and the oxygenated ligands.Normally,polycyclic aromatic sulphur heterocycles(S-PAHs)are separated from petroleum oil via the same method.The obtained results reveal that all the OC formulations with S-PAHs can be separated from the pre-isolated aromatic fraction of crude oil via this approach.S-PAHs are mixtures of benzothiophene and dibenzothiophene congeners.The isolated OCs are composed mainly of hydroxyl compounds.The liquid chromatography(LC)/electrospray ionization(ESI)in positive ion mode ESI(+)/tandem mass spectrometry(MS/MS)technique was used to assign the molecular weight distribution and identify the isolated OCs.The LC/ESI(+)-MS/MS technique differentiates S-PAHs and OCs using protonated ions.Thus,LC/ESI(+)-MS/MS can be used to assign molecular weight distributions for both the groups as a single mixture.MS/MS in precursor ion mode was used for the immediate identification of the target S or O analytes.     

External accumulation of ions for enhanced electrospray ionization fourier transform ion cyclotron resonance mass spectrometry

Electrospray ionization (ESI) in combination with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry provides for mass analysis of biological molecules with unrivaled mass accuracy, resolving power and sensitivity. However, ESI FTICR MS performance with on-line separation techniques such as liquid chromatography (LC) and capillary electrophoresis has to date been limited primarily by pulsed gas assisted accumulation and the incompatibility of the associated pump-down time with the frequent ion beam sampling requirement of on-line chromatographic separation. Here we describe numerous analytical advantages that accrue by trapping ions at high pressure in the first rf-only octupole of a dual octupole ion injection system before ion transfer to the ion trap in the center of the magnet for high performance mass analysis at low pressure. The new configuration improves the duty cycle for analysis of continuously generated ions, and is thus ideally suited for on-line chromatographic applications. LC/ESI FTICR MS is demonstrated on a mixture of 500 fmol of each of three peptides. Additional improvements include a fivefold increase in signal-to-noise ratio and resolving power compared to prior methods on our instrument.     

Electrospray Ionization Mass Spectrometry: A Powerful Platform for Noble‐Metal Nanocluster Analysis

Electrospray ionization mass spectrometry (ESI‐MS) is an analytical technique that measures the mass of a sample through “soft” ionization. Recent years have witnessed a rapid growth of its application in noble‐metal nanocluster (NC) analysis. ESI‐MS is able to provide the mass of a noble‐metal NC analyte for the analysis of their composition (n, m, q values in a general formula [M_nL_m]^q), which is crucial in understanding their properties. This review attempts to present various developed techniques for the determination of the composition of noble metal NCs by ESI‐MS. Additionally, advanced applications that use ESI‐MS to further understand the reaction mechanism, complexation behavior, and structure of noble metal NCs are introduced. From the comprehensive applications of ESI‐MS on noble‐metal NCs, more possibilities in nanochemistry can be opened up by this powerful technique.     

Characterization of the pH-dependent dissociation of a multimeric metalloprotein Streptomyces rubiginosus xylose isomerase by ESI FT-ICR mass spectrometry

We report an analysis of the pH-dependent dissociation of a multimeric metalloprotein, xylose isomerase from Streptomyces rubiginosus (XI), by electrospray ionization (ESI) Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. Xylose isomerases are industrially significant enzymes that catalyze interconversion of aldose and ketose sugars. XI is biologically active as a approximately 173-kDa tetrameric complex, comprised of four identical approximately 43-kDa subunits and eight metal cations, unequivocally identified as the Mg(2+) cations in this work. ESI FT-ICR mass spectra of XI measured in the pH range of 3.0-6.9 indicated that the dissociation of the intact holo-tetramer is initiated by the loss of all eight Mg(2+) cations at pH 相似文献   

气相条件下金属离子/肽复合物电喷雾串联质谱研究

研究蛋白质与金属离子之间的相互作用的本质一直是生物学家感兴趣的课题。但蛋白结构的复杂性使得二者之间相互作用的研究难度很大,常选用氨基酸或小肽作为模型化合物进行研究^[1-4]。目前该方法的研究甩缺乏系统性。     

液相色谱-电喷雾质谱法分析脂肪醇聚氧乙烯醚硫酸钠

采用电喷雾质谱(ESI/MS)技术建立了脂肪醇聚氧乙烯醚硫酸钠(AES)的烷基碳链分布、乙氧基分布及平均EO数、平均相对分子质量的测定方法;采用液相色谱-电喷雾质谱(LC-ESI/MS)测定了AES中的游离十二烷基硫酸钠(SDS)的含量。将本方法应用于实际样品的测定,并与核磁共振法测得的平均EO数进行比较,二者的测定结果相当吻合,从而验证了本法的可靠性。     

Analysis of antioxidants in insulation cladding of copper wire: a comparison of different mass spectrometric techniques (ESI–IT,MALDI–RTOF and RTOF–SIMS)

Commercial copper wire and its polymer insulation cladding was investigated for the presence of three synthetic antioxidants (ADK STAB AO412S, Irganox 1010 and Irganox MD 1024) by three different mass spectrometric techniques including electrospray ionization–ion trap–mass spectrometry (ESI–IT–MS), matrix‐assisted laser desorption/ionization reflectron time‐of‐flight (TOF) mass spectrometry (MALDI–RTOF–MS) and reflectron TOF secondary ion mass spectrometry (RTOF–SIMS). The samples were analyzed either directly without any treatment (RTOF–SIMS) or after a simple liquid/liquid extraction step (ESI–IT–MS, MALDI–RTOF–MS and RTOF–SIMS). Direct analysis of the copper wire itself or of the insulation cladding by RTOF–SIMS allowed the detection of at least two of the three antioxidants but at rather low sensitivity as molecular radical cations and with fairly strong fragmentation (due to the highly energetic ion beam of the primary ion gun). ESI–IT‐ and MALDI–RTOF–MS‐generated abundant protonated and/or cationized molecules (ammoniated or sodiated) from the liquid/liquid extract. Only ESI–IT–MS allowed simultaneous detection of all three analytes in the extract of insulation claddings. The latter two so‐called ‘soft’ desorption/ionization techniques exhibited intense fragmentation only by applying low‐energy collision‐induced dissociation (CID) tandem MS on a multistage ion trap‐instrument and high‐energy CID on a tandem TOF‐instrument (TOF/RTOF), respectively. Strong differences in the fragmentation behavior of the three analytes could be observed between the different CID spectra obtained from either the IT‐instrument (collision energy in the very low eV range) or the TOF/RTOF‐instrument (collision energy 20 keV), but both delivered important structural information. Copyright © 2009 John Wiley & Sons, Ltd.     

SNP的电喷雾串联质谱研究

采用电喷雾串联质谱技术对两组单核苷酸多态性(SNP)样品进行了研究,初步研究结果显示应用串联质谱可快速鉴定SNP分型以及确定SNP位点。采用16.3 mmol/L三乙胺(TEA)-400 mmol/L六氟异丙醇(HFIP)缓存溶液,电喷雾负离子模式下,长度为20 bp的寡核苷酸的MS扫描谱图显示其母离子呈较宽的多电荷态分布。选择低电荷态[M-4H]4-母离子,碰撞能为54 eV时,MS/MS扫描得到丰富的碎片离子,通过鉴定特征离子碎片(w和a-B离子系列)可确定其序列。     

Comparison of the pH‐dependent formation of His and Cys heptapeptide complexes of nickel(II), copper(II), and zinc(II) as determined by ion mobility‐mass spectrometry

The analog methanobactin (amb) peptide with the sequence ac‐His₁‐Cys₂‐Gly₃‐Pro₄‐Tyr₅‐His₆‐Cys₇ (amb_5A) will bind the metal ions of zinc, nickel, and copper. To further understand how amb_5A binds these metals, we have undertaken a series of studies of structurally related heptapeptides where one or two of the potential His or Cys binding sites have been replaced by Gly, or the C‐terminus has been blocked by amidation. The studies were designed to compare how these metals bind to these sequences in different pH solutions of pH 4.2 to 10 and utilized native electrospray ionization (ESI) with ion mobility‐mass spectrometry (IM‐MS) which allows for the quantitative analysis of the charged species produced during the reactions. The native ESI conditions were chosen to conserve as much of the solution‐phase behavior of the amb peptides as possible and an analysis of how the IM‐MS results compare with the expected solution‐phase behavior is discussed. The oligopeptides studied here have applications for tag‐based protein purification methods, as therapeutics for diseases caused by elevated metal ion levels or as inhibitors for metal‐protein enzymes such as matrix metalloproteinases.