Increasing charge while preserving noncovalent protein complexes for ESI-MS

Increased multiple charging of native proteins and noncovalent protein complexes is observed in electrospray ionization (ESI) mass spectra obtained from nondenaturing protein solutions containing up to 1% (vol/vol) m-nitrobenzyl alcohol (m-NBA). The increases in charge ranged from 8% for the 690 kDa α₇β₇β₇α₇ 20S proteasome complex to 48% additional charge for the zinc-bound 29 kDa carbonic anhydrase-II protein. No dissociation of the noncovalently bound ligands/subunits was observed upon the addition of m-NBA. It is not clear if the enhanced charging is related to altered surface tension as proposed in the “supercharging” model of Iavarone and Williams (Iavarone, A. T.; Williams, E. R. J. Am. Chem. Soc. 2003, 125, 2319–2327). However, more highly charged noncovalent protein complexes have utility in relaxing slightly the mass-to-charge (m/z) requirements of the mass spectrometer for detection and will be effective for enhancing the efficiency for tandem mass spectrometry studies of protein complexes.     

Using ESI-MS to probe protein structure by site-specific noncovalent attachment of 18-crown-6

A new method for probing the equilibrium structures and folding states of proteins utilizing electrospray ionization mass spectrometry is described. Protein structure is explored as a function of side-chain availability as determined by a specific interaction between lysine and 18-crown-6 ether (18C6). Various intramolecular interactions are competitive with the lysine/18C6 interaction and can prevent noncovalent attachment of 18C6. Changes to protein structure modify these inhibiting intramolecular interactions, which leads to a change in the number of 18C6s that attach to the protein. Experiments conducted with cytochrome c, ubiquitin, and melittin reveal that the method is sensitive to changes in both tertiary and secondary structure. In addition, the structure of each charge state can be examined independently. Experiments can be performed under conditions where the pH and amount of organic cosolvent are varied. Control experiments conducted with pentalysine, which lacks structural organization, are also presented.     

The structural analysis of large noncovalent oxygen binding proteins by MALLS and ESI-MS: a review on annelid hexagonal bilayer hemoglobin and crustacean hemocyanin

Understanding the function of macromolecular complexes is related to a precise knowledge of their structure. These large complexes are often fragile high molecular mass noncovalent multimeric proteins. Classical biochemical methods for determination of their native mass and subunit composition were used to resolve their quaternary structure, sometimes leading to different models. Recently, the development of mass spectrometry and multi-angle laser light scattering (MALLS) has enabled absolute determination of native masses and subunit masses. Electrospray ionization mass spectrometry (ESI-MS) was used in denaturing and native conditions to probe subunit composition and noncovalent assemblies masses up to 2.25 MDa. In a complementary way, MALLS provides mass and size estimation in various aqueous solvents. ESI-MS method can also give insights into post-translational modifications (glycosylation, disulfide bridges ). By combining native mass and subunit composition data, structural models can be proposed for large edifices such as annelid extracellular hexagonal bilayer hemoglobins (HBL Hb) and crustacean hemocyanins (Hc). Association/dissociation mechanisms, protein-protein interactions, structural diversity among species and environmental adaptations can also be addressed with these methods. With their absolute mass determination, the very high precision of spectrometry and the versatile nature of light scattering, ESI-MS and MALLS have provided a wealth of data helping to resolve parts of controversies for HBL-Hb models and opening access to new fields of investigation in structural diversity and molecular adaptation. In this review we will focus on annelid HBL-Hb and on crustacean Hc and on the original contributions of ESI-MS and MALLS in this field.     

Quantitative classification of covalent and noncovalent H-bonds

The covalent nature of interactions within various hydrogen bonded molecular aggregates has been characterized by the two entirely different computational methods: Bader analysis of the electron density and variation-perturbation partitioning of the intermolecular interaction energy. Analysis of 34 complexes representing different types of hydrogen bonds indicates that the proton-acceptor distance approximately 1.8 A and the ratio of delocalization and electrostatic terms approximately 0.45 constitutes approximately a borderline between covalent and noncovalent hydrogen bonds. The latter ratio could be used to characterize quantitatively the degree of the covalent nature of transition state interactions with active site residues, a quantity essential for an enzyme catalytic activity.     

Study of alkali metal cations binding selectivity of beta-cyclodextrin by ESI-MS

Cyclodextrins (CDs), cyclic oligosaccharides commonly composed of six, seven or eight (alpha, beta, and gamma respectively) D-glucopyranosyl units connected by alpha-(1,4)- glycosidic linkages, have the ability to form inclusion complexes with a wide range of substrates in aqueous solution. This property has led to their applications in different areas such as enzyme mimics, catalysis and the encapsulation. of drugs. ESI-MS has begun to be viewed as a useful tool for investigating the general area of molecular recognition thus providing a powerful mean for the analysis of a wide array of host-guest complexes and other non covalent complexes present in solution. The evaluation of the binding selectivity of beta-cyclodextrin towards the first group alkali cations is reported. The estimation of the affinity degrees has been achieved by competition ESI-MS experiments. In these experiments beta-CD was incubated at the presence of two different cations at the same time, and the ratio of the mass peaks corresponding to the two complexes was calculated. In general, it appears a much larger affinity of the beta-cyclodextrin molecule with sodium with respect to all the other alkaline cations, thus giving evidence that it is the size of the beta-cyclodextrin ring in relation with the cationic radius, which drives the formation of what, at this point, could be defined as an inclusion complex.     

Multivalent binding motifs for the noncovalent functionalization of graphene

Single-layer graphene is a newly available conductive material ideally suited for forming well-defined interfaces with electroactive compounds. Aromatic moieties typically interact with the graphene surface to maximize van der Waals interactions, predisposing most compounds to lie flat on its basal plane. Here we describe a tripodal motif that binds multivalently to graphene through three pyrene moieties and projects easily varied functionality away from the surface. The thermodynamic and kinetic binding parameters of a tripod bearing a redox-active Co(II) bis-terpyridyl complex were investigated electrochemically. The complex binds strongly to graphene and forms monolayers with a molecular footprint of 2.3 nm(2) and a ΔG(ads) = -38.8 ± 0.2 kJ mol(-1). Its monolayers are stable in fresh electrolyte for more than 12 h and desorb from graphene 1000 times more slowly than model compounds bearing a single aromatic binding group. Differences in the heterogeneous rate constants of electron transfer between the two compounds suggest that the tripod projects its redox couple away from the graphene surface.     

Top-down ESI-ECD-FT-ICR mass spectrometry localizes noncovalent protein-ligand binding sites

Mass spectrometry (MS) with electrospray ionization (ESI) has the capability to measure and detect noncovalent protein-ligand and protein-protein complexes. However, information on the sites of ligand binding is not easily obtained by the ESI-MS methodology. Electron capture dissociation (ECD) favors cleavage of covalent backbone bonds of protein molecules. We show that this characteristic of ECD translates to noncovalent protein-ligand complexes, as covalent backbone bonds of protein complexes are dissociated, but the noncovalent ligand interaction is retained. For the complex formed from 140-residue, 14.5 kDa alpha-synuclein protein, and one molecule of polycationic spermine (202 Da), ECD generates product ions that retain the protein-spermine noncovalent interaction. Spermine binding is localized to residues 106-138; the ECD data are consistent with previous solution NMR studies. Our studies suggest that ECD mass spectrometry can be used to determine directly the sites of ligand binding to protein targets.     

Synthesis and binding properties of a noncovalent molecularly imprinted testosterone-specific polymer

In this study, molecular imprinting was used to develop a method based on noncovalent interactions for synthesis of a testosterone-specific polymer. The effect of the different template–monomer ratios, the particle sizes of polymers, and chromatographic mobile phases on steroid–polymer interactions are discussed. The polymer obtained was found to interact specifically with testosterone, while other steroids under study were eluted close to the void volume in the HPLC experiments. Batch rebinding studies in acetonitrile were undertaken to quantitatively evaluate the affinity of the polymer for testosterone. During this experiment, the testosterone concentration was measured in two ways: spectrophotometrically and by HPLC on a column with testosterone-specific imprinted polymer synthesized by us. Both methods resulted in similar values of association constants and the number of binding sites. However, the second method has obvious advantages when the analyzed solution contains a mixture of optically dense compounds. The results obtained focus on the two-point binding nature of the imprinted polymer–testosterone interaction and the significant role of hydrogen bonds between the OH group of testosterone and carboxy group of methacrylic acid residues inside specific recognition sites of the imprinted polymer. © 1998 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 36: 1725–1732, 1998     

一种消毒样品的电喷雾质谱分析

从《禁止化学武器公约》1997年4月正式生效以来,化学核查方法研究不断深入,从鉴定化学战剂原体逐步向降解、消毒等相关化学品方向发展,且扩展到复杂的环境基质样品。为了确保各缔约国履约,对于已被"禁止化学武器组织"(简称OPCW)指定和正在寻求指定的实验室,每年至少要参加一次水平考试,分析公约附表化学品及它们的前体和降解产物,并取得优异的成绩,只有这样,才有资格分析真实样品(从被怀疑的产品或者储藏地点或者是从宣布使用过化学武器的环境中采集的)。本文样品是OPCW组织的第十四次水平考试的"消毒"废液样品D及其空白对照DB,采用液相色谱-电喷雾质谱联用技术(HPLC-ESI-MS)对样品进行定性检测,结合其他分析方法,结果与配样清单完全一致,见表1。     

The use of ESI-MS to probe the binding of divalent cations to calmodulin

Proteins have evolved with distinct sites for binding particular metal ions. This allows metalloproteins to perform a myriad of specialized tasks with conformations tailor-made by the combination of its primary sequence and the effect on this of the ligated metal ion. Here we investigate the selectivity of the calcium trigger protein calmodulin for divalent metal ions. This ubiquitous and highly abundant protein exists in equilibrium between its apo and its holo form wherein four calcium ions are bound. Amongst its many functions, calmodulin modulates the calcium concentration present in cells, but this functional property renders it a target for competition from other metal ions. We study the competition posed by four other divalent cations for the calcium binding sites in calmodulin using electrospray ionization mass spectrometry (ESI-MS). We have chosen two other group II cations Mg²⁺, Sr²⁺, and two heavy metals Cd²⁺, Pb²⁺. The ease with which each of these metals binds to apo and to holo CaM[4Ca] is described. We find that each metal ion has different properties with respect to calmodulin binding and competition with calcium. The order of affinity for apo CaM is Ca²⁺ ≫ Sr²⁺ ∼ Mg²⁺ > Pb²⁺ ∼ Cd²⁺. In the presence of calcium the affinity alters to Pb²⁺ > Ca²⁺ > Cd²⁺ > Sr²⁺ > Mg²⁺. Once complexes have been formed between the metal ions and protein (CaM:[xM]) we investigate whether the structural change which must accompanies calcium ligation to allow target binding takes place for a given CaM:[xM] system. We use a 20 residue target peptide, which forms the CaM binding site within the enzyme neuronal nitric-oxide synthase. Our earlier work (Shirran et al. 2005) [1] has demonstrated the particular selectivity of this system for CaM:4Ca²⁺. We find that along with Ca²⁺ only Pb²⁺ forms complexes of the form CaM:4M²⁺:nNOS. This work demonstrates the affinity for calcium above all other metals, but also warns about the ability of lead to replace calcium with apparent ease.     

Characterization of noncovalent complexes formed between minor groove binding molecules and duplex DNA by electrospray ionization-mass spectrometry

The noncovalent complex formed in solution between minor groove binding molecules and an oligonucleotide duplex was investigated by electrospray ionization-mass spectrometry (ESI-MS). The oligonucleotide duplex formed between two sequence-specific 14-base pair oligonucleotides was observed intact by ESI-MS and in relatively high abundance compared to the individual single-stranded components. Only sequence-specific A:B duplexes were observed, with no evidence of random nonspecific aggregation (i.e., A:A or B:B) occurring under the conditions utilized. Due to the different molecular weights of the two 14-base pair oligonucleotides, unambiguous determination of each oligonucleotide and the sequence-specific duplex was confirmed through their detection at unique mass-to-charge ratios. The noncovalent complexes formed between the self-complementary 5′-dCGCAAATTTGCG-3′ oligonucleotide and three minor groove binding molecules (distamycin A, pentamidine, and Hoechst 33258) were also observed. Variation of several electrospray ionization interface parameters as well as collision-induced dissociation methods were utilized to characterize the nature and stability of the noncovalent complexes. The noncovalent complexes upon collisional activation dissociated into single-stranded oligonucleotides and single-stranded oligonucleotides associated with a minor groove binding molecule. ESI-MS shows potential for the study of small molecule-oligonucleotide duplex interactions and determination of small molecule binding stoichiometry.     

Mapping noncovalent ligand binding to stemloop domains of the HIV-1 packaging signal by tandem mass spectrometry

The binding modes and structural determinants of the noncovalent complexes formed by aminoglycoside antibiotics with conserved domains of the HIV-1 packaging signal (Psi-RNA) were investigated using electrospray ionization (ESI) Fourier transform mass spectrometry (FTMS). The location of the aminoglycoside binding sites on the different stemloop structures was revealed by characteristic coverage gaps in the ion series obtained by sustained off-resonance irradiation collision induced dissociation (SORI-CID) of the antibiotic-RNA assemblies. The site positions were confirmed using mutants that eliminated salient structural features of the Psi-RNA domains. The effects of the mutations on the binding properties of the different substrates served to validate the position of the aminoglycoside site on the wild-type structures. Additional information was provided by docking experiments performed on the different aminoglycoside-stemloop complexes. The results have shown that, in the absence of features disrupting the regular A-helix of the double-stranded stem, aminoglycosides tend to bind in an area situated between the upper stem and the loop regions, as demonstrated for stemloop SL3. The presence of a tandem wobbles motif in SL4 modifies the regular geometry of the upper stem, which does not affect the general site location, but greatly increases its solution binding affinity compared with SL3. The platform motif in SL2 locates the binding site in the stem midsection and confers upon this stemloop an intermediate affinity toward aminoglycosides. In SL3 and SL4, the extensive overlap of the antibiotic site with the region used to bind the nucleocapsid (NC) protein provides the basis for a competition mechanism that could explain the aminoglycoside inhibition of the NC.SL3 and NC.SL4 assemblies. In contrast, the minimal overlap between the aminoglycoside and the NC sites in SL2 accounts for the absence of inhibition of the NC.SL2 complex.     

Study of noncovalent enzyme—inhibitor complexes and metal binding stoichiometry of matrilysin by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) was used to study the noncovalent metallo-enzyme—inhibitor complexes of matrilysin (a matrix metalloproteinase of mass 18,720 u) under gentle experimental conditions and to determine the metal ion association stoichiometries in both the free enzyme and the complexes. The metal association stoichiometries of the free matrilysin were found to be highly sensitive to solution pH changes. At pH 2.2 the enzyme existed as metal-free apo-matrilysin and was not capable of binding an inhibitor. At pH 4.5–7.0 the enzyme associated specifically with zinc and calcium cations and became active in inhibitor binding. Although the stoichiometries of the metal cofactors varied (zero to two zinc and/or calcium ions) in the free enzyme dependent on solution pH, the predominant form of the enzyme—inhibitor complexes in the pH range of 4.5–7.0, in contrast, always had the metal association stoichiometry of 2Zn + 2Ca, which was the same stoichiometry the most active free metallo-enzyme had at the optimal pH of 7. At the activity onset pH of 4.5 matrilysin existed mostly as apo-enzyme (but in a conformation different from the denatured one at pH 2.2) and bound to an inhibitor slowly (time constant ～ 2.5 min) to form the noncovalent metallo-enzyme—inhibitor complex. Of the two inhibitors studied, the one with the higher solution binding constant also produced larger ion signals for the noncovalent complex in the solvent-free gas phase, which pointed to the feasibility of the use of ESI-MS for inhibitor screening studies.     

Uranium pyrrolylamine complexes featuring a trigonal binding pocket and interligand noncovalent interactions

The syntheses of tri- and tetravalent uranium complexes of the Ar(F)(3)TPA(3-) ligand [Ar(F) = 3,5-bis(trifluoromethyl)phenyl; TPA = tris(pyrrolyl-α-methylamine)] are described. Interligand noncovalent interactions between arene groups within the complexes are detected both in the solid state and in solution.     

XYG3 and XYGJ-OS performances for noncovalent binding energies relevant to biomolecular structures

XYG3 and XYGJ-OS doubly hybrid density functionals (DHDFs) are applied to calculate intermolecular interaction energies of biological relevance. The results are compared with those of the other types of DHDFs (MC3BB and B2PLYP), as well as their dispersion corrected variants (MC3BB-D B2PLYP-D, and B2PLYP-D3), in addition to those obtained from B3LYP, B3LYP-D and B3LYP-D3. The reference data are taken from the S22, S22x5 and JSCH-2005 benchmark sets consisting mainly of DNA base pairs and amino acid pairs. The overall good agreement with the reference values of the extrapolated CCSD(T) complete basis set limit suggests that the XYG3 and XYGJ-OS functionals are valuable tools for applications in biochemistry.