Matrix-assisted laser desorption/ionization mass spectra reflect solution-phase zinc finger peptide complexation

Cu and Zn Interactions with Peptides Revealed by High-Resolution Mass Spectrometry

Alzheimer’s disease (AD) is a progressive neurodegenerative disease characterized by abnormal extracellular amyloid-beta (Aβ) peptide depositions in the brain. Among amorphous aggregates, altered metal homeostasis is considered a common risk factor for neurodegeneration known to accelerate plaque formation. Recently, peptide-based drugs capable of inhibiting amyloid aggregation have achieved unprecedented scientific and pharmaceutical interest. In response to metal ions binding to Aβ peptide, metal chelation was also proposed as a therapy in AD. The present study analyzes the interactions formed between NAP octapeptide, derived from activity-dependent neuroprotective protein (ADNP), amyloid Aβ(9–16) fragment and divalent metal ions such as Cu and Zn. The binding affinity studies for Cu and Zn ions of synthetic NAP peptide and Aβ(9–16) fragment were investigated by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), electrospray ion trap mass spectrometry (ESI-MS) and atomic force microscopy (AFM). Both mass spectrometric methods confirmed the formation of metal–peptide complexes while the AFM technique provided morphological and topographic information regarding the influence of metal ions upon peptide crystallization. Our findings showed that due to a rich histidine center, the Aβ(9–16) fragment is capable of binding metal ions, thus becoming stiff and promoting aggregation of the entire amyloid peptide. Apart from this, the protective effect of the NAP peptide was found to rely on the ability of this octapeptide to generate both chelating properties with metals and interactions with Aβ peptide, thus stopping its folding process.

New insights into the zinc-α2-glycoprotein (ZAG) scaffold and its metal ions binding abilities using spectroscopic techniques

AIMS

Zinc-α2-glycoprotein (ZAG) is soluble lipid mobilizing protein and a noval adipokine associated with cancer cachexia. ZAG is an omnipresent protein and represent a fold of MHC class I proteins. Although ZAG's metal binding capacity has already been reported, no other metal has been mapped to date besides the complex formation with zinc.

MAIN METHODOLOGY

In this study, fluorescence emission spectroscopy and mass spectrometry (MALDI-TOF) were employed to define the putative interaction sites and their accessibility for the biologically important metals of Irving William Series.

KEY FINDINGS

Several hotspot residues in the ZAG scaffold involved in these interactions were mapped and their binding affinity score for each metal has been determined. Thebinding abilities of these sites and aggregation propensities of ZAG were monitored by fluorescence emission spectroscopy.

SIGNIFICANCE

The prediction of such binding affinity with metals on the active sites and its impact on the conformational states to accelerate aggregation was discussed as an important finding that may be involved in several other biochemical processes such as lipid binding, β-adrenergic receptors, cancer cachexia and association with plasma cholesterol and obesity.

Mechanistic Studies on Cationization in MALDI-MS Employing a Split Sample Plate Set-up

In the analysis of polymers by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), a commonly observed ionization pathway is cation-adduct formation, as polymers often lack easily ionizable (basic/acidic) functional groups. The mechanism of this process has been hypothesized to involve gas-phase cation attachment. In previous experiments, a split sample plate set-up has been introduced, enabling separate deposition of the components on individual MALDI plates. The plates are divided by a small gap of a few micrometers, allowing simultaneous laser irradiation from both plates, while precluding the possibility of any other interactions prior to ablation. Here, we extend on these studies by using different polymer-salt combinations to test the generalizability of a gas-phase ionization process. Clear evidence for in-plume ionization is presented for the model polymers poly (methyl methacrylate) and polystyrene. Furthermore, the contribution of in-plume processes to the overall ion formation by cationization is gauged, providing a first estimate for the importance of this pathway.

Carbon Nanotubes and Graphene Promote Pyrolysis of Free-Base Phthalocyanine

Unsubstituted phthalocyanines (including free-base H₂Pc and many of its metal complexes) are among the most stable organic compounds. They can sublime without decomposition under reduced pressure and temperatures of up to 550 °C. This property was previously employed to design a novel approach to noncovalent functionalization of pristine single-walled carbon nanotubes (SWNTs) with 3d metal(II) phthalocyanine complexes. However, when we attempted to use the same sublimation protocol to prepare a SWNTs-H₂Pc hybrid, an unexpected side effect of partial H₂Pc pyrolysis was detected, phthalonitrile being a main decomposition product, under the conditions when H₂Pc is supposed to be totally stable. By using density functional theory calculations, we offer an explanation for the thermal behavior of H₂Pc based on its covalent attachment to the pentagonal-ring topological defects, which are very common in all graphene-derived carbon nanomaterials and capable of reacting with amines via nucleophilic addition process.

The Application of Curve Fitting on the Voltammograms of Various Isoforms of Metallothioneins-Metal Complexes

The translation of metallothioneins (MTs) is one of the defense strategies by which organisms protect themselves from metal-induced toxicity. MTs belong to a family of proteins comprising MT-1, MT-2, MT-3, and MT-4 classes, with multiple isoforms within each class. The main aim of this study was to determine the behavior of MT in dependence on various externally modelled environments, using electrochemistry. In our study, the mass distribution of MTs was characterized using MALDI-TOF. After that, adsorptive transfer stripping technique with differential pulse voltammetry was selected for optimization of electrochemical detection of MTs with regard to accumulation time and pH effects. Our results show that utilization of 0.5 M NaCl, pH 6.4, as the supporting electrolyte provides a highly complicated fingerprint, showing a number of non-resolved voltammograms. Hence, we further resolved the voltammograms exhibiting the broad and overlapping signals using curve fitting. The separated signals were assigned to the electrochemical responses of several MT complexes with zinc(II), cadmium(II), and copper(II), respectively. Our results show that electrochemistry could serve as a great tool for metalloproteomic applications to determine the ratio of metal ion bonds within the target protein structure, however, it provides highly complicated signals, which require further resolution using a proper statistical method, such as curve fitting.

Deciphering metal ion preference and primary coordination sphere robustness of a designed zinc finger with high-resolution mass spectrometry

Small zinc finger (ZnF) motifs are promising molecular scaffolds for protein design owing to their structural robustness and versatility. Moreover, their characterization provides important insights into protein folding in general. ZnF motifs usually possess an exceptional specificity and high affinity towards Zn(II) ion to drive folding. While the Zn(II) ion is canonically coordinated by two cysteine and two histidine residues, many other coordination spheres also exist in small ZnFs, all having four amino acid ligands. Here we used high-resolution mass spectrometry to study metal ion binding specificity and primary coordination sphere robustness of a designed zinc finger, named MM1. Based on the results, MM1 possesses high specificity for zinc with sub-micromolar binding affinity. Surprisingly, MM1 retains metal ion binding affinity even in the presence of selective alanine mutations of the primary zinc coordinating amino acid residues.

MALDI-ToF mass spectrometry for studying noncovalent complexes of biomolecules

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been demonstrated to be a valuable tool to investigate noncovalent interactions of biomolecules. The direct detection of noncovalent assemblies is often more troublesome than with electrospray ionization. Using dedicated sample preparation techniques and carefully optimized instrumental parameters, a number of biomolecule assemblies were successfully analyzed. For complexes dissociating under MALDI conditions, covalent stabilization with chemical cross-linking is a suitable alternative. Indirect methods allow the detection of noncovalent assemblies by monitoring the fading of binding partners or altered H/D exchange patterns.

Matrix-free laser desorption/ionization of ions landed on plasma-treated metal surfaces

We report new experiments in which laser desorption/ionization time-of-flight mass spectrometry (LDI-TOF-MS) was applied to detection and characterization of gramicidin S and IgG pentapeptide (DSDPR) that were reactively landed on plasma-treated stainless steel surfaces. The distributions of [M+H](+), [M+Na](+) and [M + K](+) ion species in LDI-TOF for gramicidin S and IgG pentapeptide (DSDPR) were found to be markedly different from those in conventional MALDI-TOF spectra of the same samples. LDI-TOF mass spectra showed a strong preference for [M+K](+) adducts even in the presence of a large excess of sodium cations, or following surface treatment with trifluoroacetic acid. Alkali metal cations (K(+) and Cs(+)) can be exchanged in reactively landed peptide samples to provide the corresponding cationized peptide ions by LDI. Multiple charged trypsin cations were reactively landed into a layer of 2-(4-hydroxyphenylazo)benzoic acid and ionized by LDI. The ionization mechanisms for LDI of surface-deposited peptides are briefly discussed.

Investigation of single-site zirconium azaborolinyl complexes by laser desorption ionization time of flight mass spectrometry

Laser desorption ionization mass spectrometry (LDI-MS) was performed on selected azaborolinyl zirconium complexes in order to study them as potential industrial polyolefin catalyst compounds. UV-vis absorption data in conjunction with negative and positive ionization analyses revealed the mechanistic workings of the compounds when such single-site catalysts function in olefin polymerization reactions. Results presented highlight the many benefits of LDI-MS in the study of single-site zirconium azaborolinyl catalyst complexes including minimal sample preparation, the absence of matrix/pH/solvation effects, a lower degree of fragmentation as compared to EI ionization, high sensitivity and the ability to observe interesting and unique gas phase chemistry including ring slippage, and distinctive metal coordination and oxidation states. The extreme lability of the chlorine ligands was apparent, as well as the reactivity of the resulting zirconium metal center as demonstrated by the appearance of numerous similar four-coordinate zirconium species along with di-chloro-bridged dimers. LDI-MS permits analysis at low molecular weights, improving spectral characterization of these zirconium complexes.

Matrix-assisted laser desorption/ionization studies on transition metal complexes of benzimidazole thiosemicarbazones

The transition metal (M=Fe, Co, Ni, Cu, Zn, Cd and Hg) complexes of 2- acetylbenzimidazolethiosemicarbazone (L(1)) and 1-methyl 2-acetylbenzimidazole-thiosemicarbazone (L(2)) are analyzed by MALDI using HCCA, THP, MMNPD and DMN as the matrices. All the MALDI spectra are clean without any contribution from the complex ions resulted by multiple proton addition/removal. All the complexes, except Cu, irrespective of the matrix used, show 1:2 complex ions wherein two ligands (neutral or deprotonated) complex with the metal ion depending on the nature and stable oxidation state of the central metal ion viz., [M + 2L - 2H](+) ion for Fe and Co complexes (+3 oxidation state) and [M + 2L - H](+) ion for Ni, Zn, Cd and Hg (+2 oxidation state). The Cu complex show 1:1 complex ion corresponding to [2M + 2L - 2H](+) ions. When HCCA is used as a matrix, the complex ions due to ligand exchange by matrix are also found, and this process is relatively more if a neutral ligand is bound to the metal ion in the original complex ion. The type of complex ions found under MALDI experiments are similar to those found under ESI experiments. However, the complex ions due to reduction of Cu are found only in the MALDI analysis of Cu complexes.

Characterization of specific noncovalent complexes between guanidinium derivatives and single-stranded DNA by MALDI

Noncovalently bound complexes between highly basic sites of 12 guanidinium compounds and single-stranded DNA were studied using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. 6-Aza-2-thiothymine (ATT) was used as the matrix in the presence of ammonium citrate, and spectra were recorded in the positive ion mode. Detailed control experiments confirmed unambiguously the high selectivity and specificity of the guanidinium moiety for phosphate groups of DNA. The results verify the binding stoichiometry and show preferential binding of hydrophobic binders (pyrene and anthracene guanidinium derivatives) to all sequences examined. In addition, we demonstrate that electrostatic noncovalent interactions are strengthened with phosphorothioate analogs of DNA. These results clearly highlight the structure-directing role of the self-assembling organic species and strongly emphasize the significance of concentration, hydrophobicity, hydrogen-bonding, and pi-pi interactions of the artificial receptor in the formation of these noncovalent complexes. Because of the ability of DNA-binding compounds to influence gene expression, and therefore cell proliferation and differentiation, the interactions described above could be important in providing a better understanding of the mechanism of action of these noncovalent genetic regulators.

Zn2+ binding to cysteine-rich domain of extracellular human immunodeficiency virus type 1 Tat protein is associated with Tat protein-induced apoptosis

The Tat protein has several functional domains, one of which is the cysteine-rich domain that is a highly conserved region in spite of the presence of many subtypes of human immunodeficiency virus type 1 (HIV-1). Although the cysteine-rich domain is a potential site for Zn(2+) binding, it is controversial whether Zn(2+) is substantially essential for the structure and activities of the Tat protein. To study the significance of Zn(2+) in the cysteine-rich domain of the Tat protein particularly released to the extracellular space, we raised the monoclonal antibody (MAb) 5A4, which has an attractive property of recognizing the Zn(2+)-binding Tat(20-41) peptide but not the apo-Tat(20-41) peptide. MAb 5A4 inhibited the trans-activation of the HIV long terminal repeat (LTR) in HeLa-CD4-LTR/beta-gal cells induced by treatment with the recombinant Tat protein, indicating that MAb 5A4 can recognize the full-length Tat protein and inhibit its trans-activity. The antibody also inhibited the apoptosis of Jurkat cells induced by treatment with the released native-Tat-protein-containing supernatant from the culture of HIV-1(JRFL)-infected cells. These results suggest that Zn(2+), whose structure is closely associated with not only the trans-activation of HIV-LTR but also the induction of apoptosis, binds to the extracellular native Tat protein. The Zn(2+)-binding cysteine-rich domain therefore can be a molecular target in the development of an anti-Tat vaccine and agents for the control of extracellular-Tat-protein-mediated pathogenesis leading to the progression of acquired immunodeficiency syndrome.

Cobalt inhibits the interaction between hypoxia-inducible factor-alpha and von Hippel-Lindau protein by direct binding to hypoxia-inducible factor-alpha

The hypoxia-inducible factor (HIF) activates the expression of genes that contain a hypoxia response element. The alpha-subunits of the HIF transcription factors are degraded by proteasomal pathways during normoxia but are stabilized under hypoxic conditions. The von Hippel-Lindau protein (pVHL) mediates the ubiquitination and rapid degradation of HIF-alpha (including HIF-1alpha and HIF-2alpha). Post-translational hydroxylation of a proline residue in the oxygen-dependent degradation (ODD) domain of HIF-alpha is required for the interaction between HIF and VHL. It has previously been established that cobalt mimics hypoxia and causes accumulation of HIF-1alpha and HIF-2alpha. However, little is known about the mechanism by which this occurs. In an earlier study, we demonstrated that cobalt binds directly to the ODD domain of HIF-2alpha. Here we provide the first evidence that cobalt inhibits pVHL binding to HIF-alpha even when HIF-alpha is hydroxylated. Deletion of 17 amino acids within the ODD domain of HIF-2alpha that are required for pVHL binding prevented the binding of cobalt and stabilized HIF-2alpha during normoxia. These findings show that cobalt mimics hypoxia, at least in part, by occupying the VHL-binding domain of HIF-alpha and thereby preventing the degradation of HIF-alpha.

Investigation of sample preparation and instrumental parameters in the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of noncovalent peptide/peptide complexes

The application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) to the direct detection and investigation of noncovalent solution-phase complexes is far from being routine and some principal problems and questions still exist. Therefore, this study systematically investigates several main problems, namely, the effect of sample preparation and some instrument-related parameters on the stability of the noncovalent complexes as well as the formation of nonspecific cluster ions in the case of the MALDI-MS analysis of specific peptide/peptide complexes. The complexes formed between biologically active fragments of human gastrin I, which contain the sequence motif EEEEE, and different peptides, which contain the interacting sequence motifs RR and RKR, were chosen as examples. A broad variety of MALDI matrices and sample preparation protocols were screened systematically and evaluated. The two 'less acidic' matrices 2,4,6-trihydroxyacetophenone and 6-aza-2-thiothymine, in combination with carefully selected solvents and additives, turned out to allow the reproducible detection of the solution-phase peptide/peptide complexes with good intensity, whereas the classical MALDI matrices could not be applied with the same success. Because both matrices also tend to induce the formation of nonspecific cluster ions, control experiments using nonbinding peptides were performed to definitely prove the specificity of the detected complexes. In contrast to the sensitivity of the peptide/peptide complexes to solution-phase conditions, the gas-phase stability during desorption/ionization was found to be extraordinary high. Neither the application of high laser fluence nor switching from continuous to delayed extraction mode as well as variation of the delay time up to 520 ns had considerable effect on the relative intensities of the specific peptide/peptide complexes.

In-source H/D exchange and ion-molecule reactions using matrix assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry with pulsed collision and reaction gases

Controlled in-source ion-molecule reactions are performed for the first time in an external matrix assisted laser desorption ionization (MALDI) source of a Fourier transform ion cyclotron resonance mass spectrometer. The MALDI source with a hexapole ion guide that was originally designed to incorporate pulsed gas to collisionally cool ions (Baykut, G.; Jertz, R.; Witt, M. Rapid Commun. Mass Spectrom. 2000, 14, 1238-1247) has been modified to allow the study of in-source ion-molecule reactions. Upon laser desorption, a reaction gas was introduced through a second inlet and allowed to interact with the MALDI-generated ions trapped in the hexapole ion guide. Performing ion-molecule reactions in the high pressure range of the ion source prior to analysis in the ion cyclotron resonance (ICR) cell allows to maintain the ultra high vacuum in the cell which is crucial for high mass resolution measurements. In addition, due to the reaction gas pressure in the hexapole product ion formation is much faster than would be otherwise possible in the ICR cell. H/D exchange reactions with different peptides are investigated, as are proton-bound complex formations. A typical experimental sequence would be ion accumulation in the hexapole ion guide from multiple laser shots, addition of cooling gas during ion formation, addition of reaction gas, varied time delays for the ion-molecule reactions, and transmission of the product ions into the ICR cell for mass analysis. In this MALDI source H/D exchange reactions for different protonated peptides are investigated, as well as proton-bound complex formations with the reaction gas triethylamine. Amino acid sequence, structural flexibility and folding state of the peptides can be seen to play a part in the reactivity of such ions.

Progress in monitoring, modeling and control of bioprocesses during the last 20 years

The paper gives a review on the recent development of bioprocess engineering. It includes monitoring of product formation processes by flow injection analysis, various types of chromatographic and spectroscopic methods as well as by biosensors. The evaluation of mycelial morphology and physiology by digital image analysis is discussed also. It deals with advanced control of indirectly evaluated process variables by means of state estimation/observer, with the use of structured and hybrid models, expert systems and pattern recognition for process optimization and gives a short report on the state of the art of metabolic flux analysis and metabolic engineering.

Ionization in matrix-assisted laser desorption/ionization: singly charged molecular ions are the lucky survivors

A new model for the ionization processes in UV matrix-assisted laser desorption/ionization (MALDI) which accounts for the major phenomena observed is presented and discussed. The model retains elements of earlier approaches, such as photoionization and photochemical reactions, but it redefines these in the light of new working questions, most importantly why only singly charged ions are detected. Based on experimental evidence, the formation of singly and multiply charged clusters by a deficiency/excess of ions and also by photoionization and subsequent photochemical processes is pointed out to be the major ionization processes, which typically occur in parallel. The generation of electrons and their partial loss into the surrounding vacuum and solid, on the one hand, results in a positively charged ion-neutral plume facilitating a high overall ionization yield. On the other hand, these electrons, and also the large excess of protonated matrix ions in the negative ion mode, induce effective ion reneutralization in the plume. These neutralization processes are most effective for the highly charged cluster ions initially formed. Their fragmentation behaviour is evidenced in fast metastable fragmentation characteristics and agrees well with an electron capture dissociation mechanism and the enthalpy transfer upon neutralization forms the rationale for the prominent fragmentation and intense chemical noise accompanying successful MALDI. Within the course of the paper, cross-correlations with other desorption/ionization techniques and with earlier discussions on their mechanisms are drawn.

Matrix effects on selectivities of poly(ethylene glycol)s for alkali metal ion complexation in matrix-assisted laser desorption/ionization

The effect of the matrix on poly(ethylene glycol) (PEG) cationization was investigated using an equimolar mixture of CsCl and LiCl as cationizing agents. It was observed that for both carboxylic acid and non-carboxylic acid matrices used, PEG cationization by a given alkali metal ion depends on the matrix used. For example, cesiated PEG ion intensities were much stronger than those of the corresponding lithiated PEG ions when equimolar concentrations of Cs(+) and Li(+) were present and IAA (indolacrylic acid) was the matrix. However, an opposite result was obtained when the same experimental conditions were utilized, but with HABA (2-(4-hydroxyphenylazo)benzoic acid) in place of IAA as the matrix.