The role of phosphorylated residues in peptide-peptide noncovalent complexes formation

Electrospray mass spectrometry (ESI-MS) has become the tool of choice for the study of noncovalent complexes. Our previous work has highlighted the role of phosphorylated amino acid residues in the formation of noncovalent complexes through electrostatic interaction with arginine residues’ guanidinium groups. In this study, we employ tandem mass spectrometry to investigate the gas-phase stability and dissociation pathways of these noncovalent complexes. The only difference in the three phosphopeptides tested is the nature of the phosphorylated amino acid residue. In addition the absence of acidic residues and an amidated carboxyl terminus insured that the only negative charge came from the phosphate, which allowed for the comparison of the noncovalent bond between arginine residues and each of the different phosphorylated residues. Dissociation curves were generated by plotting noncovalent complex ion intensities as a function of the nominal energy given to the noncovalent complex ion before entering the collision cell. These results showed that noncovalent complexes formed with phosphorylated tyrosine were the most stable, followed by serine and threonine, which had similar stability.     

Dissociation of tetrameric ions of noncovalent streptavidin complexes formed by electrospray ionization

The noncovalent tetrameric association of the protein streptavidin formed by electrospray ionization (ESI) mass spectrometry has been observed intact and dissociated in the gas phase. An extended mass-to-charge ratio range quadrupole mass spectrometer was employed to examine the effects of harsher conditions in the ESI atmosphere-vacuum interface region on the streptavidin tetramer. Thermally induced dissociation caused the mass spectra to exhibit a series of complementary monomer and trimer ions that correspond to decomposition of the tetrameric species. Similar results were obtained with tandem mass spectrometric experiments on a Fourier transform ion cyclotron resonance mass spectrometer by application of sustained off-resonance irradiation (SORI) on a selected tetrameric charge state. The technique of single-frequency quadrupole excitation was used to accomplish selected-ion accumulation of the 14 + charge state of the tetramer during ion injection. Subsequent low energy SORI combined with broadband quadrupole cooling produced the 7 + monomer and 7 + trimer species, as well as the 6 + monomer and 8 + trimer complementary ions. The observed asymmetric breakup of the tetramer is qualitatively explained by using physical models.     

Detection of noncovalent complex between alpha-amylase and its microbial inhibitor tendamistat by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) is now routinely used for detection of noncovalent complexes. However, detection of noncovalent protein-protein complexes is not a widespread practice and still produces some challenges for mass spectrometrists. Here we demonstrate the detection of a noncovalent protein-protein complex between alpha-amylase and its microbial inhibitor tendamistat using ESI-MS. Crude porcine pancreatic alpha-amylase was purified using a glycogen precipitation method. Noncovalent complexes between porcine pancreatic alpha-amylase and its microbial inhibitor tendamistat are probed and detected using ESI-MS. The atmosphere-vacuum ESI conditions along with solution conditions and the ratio of inhibitor over enzyme strongly affect the detection of noncovalent complexes in the gas phase. ESI mass spectra of alpha-amylase at pH 7 exhibited charge states significantly lower than that reported previously, which is indicative of a native protein conformation necessary to produce a noncovalent complex. Detection of noncovalent complexes in the gas phase suggests that further use of conventional biochemical approaches to provide a qualitative, and in some cases even quantitative, characterization of equilibria of noncovalent complexes in solution is possible.     

Observation of noncovalent complexes to the avidin tetramer by electrospray ionization mass spectrometry

Intact avidin-biotin and avidin-biotin maleimide noncovalent complexes have been observed by electrospray ionization mass spectrometry (ESI-MS) by using an extended mass range quadrupole mass spectrometer. By utilizing mild ES1 interface conditions, the expected solution behavior of four biotin or biotin maleimide molecules noncovalently binding to each avidin tetramer can be preserved in the gas phase. The ESI-MS results show the appropriate mass additions of 973 ± 60 Da for biotin and 1802 ± 40 Da for biotin maleimide to the avidin tetramer species. These results support the hypothesis that substantial retention of higher order structure is possible in the gas phase by using gentle ESI conditions.     

The biotin-streptavidin interaction can be reversibly broken using water at elevated temperatures

The biotin-streptavidin system is the strongest noncovalent biological interaction known, having a dissociation constant, K(d), in the order of 4x10(-14) M. The strength and specificity of the interaction has led it to be one of the most widely used affinity pairs in molecular, immunological, and cellular assays. However, it has previously been impossible to re-use any streptavidin solid support, since the conditions needed to break the interaction with biotin has led to the denaturation of the streptavidin. Here, we show that a short incubation in nonionic aqueous solutions at temperatures above 70 degrees C can efficiently break the interaction without denaturing the streptavidin tetramer. Both biotin and the streptavidin remain active after dissociation and both molecules can therefore be re-used. The efficiency of the regeneration allowed solid supports with streptavidin to be used many times, here exemplified with the multiple re-use of streptavidin beads used for sample preparation prior to automated DNA sequencing. The results suggest that streptavidin regeneration can be introduced as an improvement in existing methods and assays based on the streptavidin system as well as emerging solid phase applications in fields, such as microfluidics and nanotechnology.     

Mass and charge state assignment for proteins and peptide mixtures via noncovalent adduction in electrospray mass spectrometry

A method has been developed that takes advantage of the formation of noncovalent compounds in electrospray mass spectrometry. Mixtures of proteins and peptides are shown to produce an intense ion that corresponds to a 1:1 complex with a crown ether (18-crown-6). Although the crown ether may be added directly to the solution, for the current experiments it is introduced via the methanol liquid sheath. The spacing of these complexed species in the mass spectrum allows unambiguous determination of the charge state of the ions and their actual mass. Through constant neutral loss scans, charge state may be determined, mass assigned, spectra simplified, and chemical noise may be reduced for the analysis of complex peptide samples without chromatographic separation. Finally, the prevalence of single complexation permits mass assignments based on the mass difference of a single protein ion and its complexed form at any charge state. In essence, the method performs a separation based on charge state. It can be used to complement chromatographic separation and deconvolution algorithms for the electrospray mass spectrometry analysis of peptide-protein mixtures.     

Electrostatic polarization is critical for the strong binding in streptavidin‐biotin system

The origin of strong affinity of biotin and its analogs binding to (strept)avidin is still the subject of an ongoing controversy. In this work, thermodynamic integration is carried out to study of the difference of binding free energies between biotin and iminobiotin to streptavidin. Three atomic charge schemes are implemented and compared. One is the traditional AMBER charge, and the other two, termed the polarized protein‐specific charge, are based on a linear scaling quantum mechanical method and a continuous solvation model and have polarization effect partially or fully included. The result indicates that when nonpolarized AMBER force field is applied, the result is much underestimated. When electronic polarization is gradually included, the difference of binding affinity increases along with it. Using the linear‐response approximation to eliminate the error in self‐charging process, the corrected binding affinity agrees well with the experimental observation. This study is direct evidence indicating that polarization effect is critical for the strong binding in streptavidin‐biotin system. © 2012 Wiley Periodicals, Inc.     

Qualitative comparison between the quantum calculations and electrospray mass spectra o complexes of polyammonium macrotricyclic ligands with dicarboxylic acids

The host-guest interactions play a very important role in chemical and biological processes. It is therefore important to be able to characterize these complexes. Electrospray mass spectrometry can be used to characterize the complex formation. It provides information on the mass and the charge of these ionic complexes. In this article, we show that the use of ab initio and semiempirical calculations, in addition to the results obtained by electrospray mass spectrometry, reveal to be a promising tool for the study of these noncovalent complexes. In this article, host-guest complexes formed by macropolycyclic polyammonium host molecules and dicarboxylic acids are studied.     

Electrochemical rectification by redox-labeled bioconjugates: molecular building blocks for the construction of biodiodes

In the present work, we describe the properties of a bifunctional redox-labeled bioconjugate at electrode surfaces mediating the electron transfer across the electrode-electrolyte interface. We show that the assembly of ferrocene-labeled streptavidin on biotinylated electrodes results in a reproducible unidirectional current flow in the presence of electron donors in solution. Such rectifying films were built up by spontaneous binding of tetrameric streptavidin molecules to biotin centers immobilized on the electrode surface. Due to the high affinity of biotin to streptavidin, such bifunctional films completely bind any biotinylated compounds. The charge transport between donors in solution and the Au electrode is mediated by the ferrocene moieties, allowing us to develop a molecular rectifier. Our experimental results suggest that such redox-labeled proteins with a high binding capacity constitute a promising alternative to organic compounds used in molecular electronics.     

The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect

Recently, Baugh et al. discovered that a distal point mutation (F130L) in streptavidin causes no distinct variation to the structure of the binding pocket but a 1000‐fold reduction in biotin binding affinity. In this work, we carry out molecular dynamics simulations and apply an end‐state free energy method to calculate the binding free energies of biotin to wild type streptavidin and its F130L mutant. The absolute binding affinities based on AMBER charge are repulsive, and the mutation induced binding loss is underestimated. When using the polarized protein‐specific charge, the absolute binding affinities are significantly enhanced. In particular, both the absolute and relative binding affinities are in line with the experimental measurements. Further investigation indicates that polarization effect is indispensable in both the generation of structural ensembles and the calculation of interaction energies. This work verifies Baugh's conjecture that electrostatic polarization effect plays an essential role in modulating the binding affinity of biotin to the streptavidin through F130L mutation. © 2013 Wiley Periodicals, Inc.     

Strong ionic interactions in noncovalent complexes between poly(ethylene imine), a cationic electrolyte,and Cibacron Blue,a nucleotide mimic – implications for oligonucleotide vectors

Cationic polymers can bind DNA to form polyplexes, which are noncovalent complexes used for gene delivery into the targeted cells. For more insight on such biologically relevant systems, the noncovalent complexes between the cationic polymer poly(ethylene imine) (PEI) and the nucleotide mimicking dye Cibacron Blue F3G‐A (CB) were investigated using mass spectrometry methods. Two PEIs of low molecular weight were utilized (M_n ≈ 423 and 600 Da). The different types of CB anions produced by Na⁺/H⁺ exchanges on the three sulfonic acid groups of CB and their dehydrated counterparts were responsible for complex formation with PEI. The CB anions underwent noncovalent complex formation with protonated, but not with sodiated PEI. A higher proportion of cyclic oligomers were detected in PEI423 than PEI600, but both architectures formed association products with CB. Tandem mass spectrometry studies revealed a significantly stronger noncovalent interaction between PEI and dehydrated CB than between PEI and intact CB. Copyright © 2014 John Wiley & Sons, Ltd.     

Evaluation of Binding Between Electroactive Biotin Derivative and Streptavidin Immobilized on Chitin Film

Evaluation of the streptavidin‐biotin binding at the surface of chitin film was carried out with voltammetry. Immobilization of streptavidin was attempted to the protonated chitin film, based on an electrostatic interaction that hardly causes any change in the protein structure. The streptavidin‐biotin binding was estimated from changes in the electrode response of biotin labeled with an electroactive compound. Although the response of daunomycin as an electroactive compound did not change at an electrode covered with streptavidin/chitin film, the response of the labeled biotin decreased. This observation shows that streptavidin is immobilized on the chitin film and the biotin binds with immobilized streptavidin. Consequently, it was clear that the chitin film is useful as a reaction field for protein‐ligand binding. Generally, a binding event between protein and its ligand in the living body occurs on the cell surface. The electrochemical evaluation of protein‐ligand binding on a natural polysaccharide like chitin membrane surface is important.     

Nano-particle labelling of nucleic acids for enhanced detection by inductively-coupled plasma mass spectrometry (ICP-MS)

Oligonucleotides containing a biotin functionality were successfully labelled with a streptavidin nanogold conjugate and subsequently separated and analysed by high performance liquid chromatography-inductively coupled plasma-mass spectrometry (HPLC-ICP-MS).     

Characterization of an opioid peptide-containing protein and of bovine α-lactalbumin by electrospray ionization and liquid secondary ion mass spectrometry

Mass spectrometry methods have been used to characterize two proteins: an opioid peptide-containing protein extracted from bovine pituitary, and bovine α-lactalbumin (BAL). A protein that contains β-endorphin was found in bovine pituitary, and that protein was characterized with electrospray ionization mass spectrometry (ESIMS), gel permeation chromatography, reversed-phase high performance liquid chromatography (RP-HPLC), radioimmunoassay, trypsinolysis, and liquid secondary ion mass spectrometry (LSIMS). BAL is a protein that was used as a model to develop analytical methods to study opioid peptide-containing proteins. Commercial BAL was purified by RP-HPLC, and its molecular weight (M.W.) was determined by ESIMS. The shift in mass observed following dithiothreitol (DTT) reduction estimated the number of disulfide bonds. For all of the data obtained for BAL with or without RP-HPLC separation, ESIMS determined the M.W. of the peptides produced by trypsin treatment of BAL, and LSIMS selected a precursor ion, the protonated molecule ion [M + H]⁺, of a tryptic peptide, which was analyzed by tandem mass spectrometry. Following DTT reduction, ESIMS and LSIMS detected each peptide that contained disulfide bonds in that mixture of tryptic peptides.     

In situ monitoring of the orientated assembly of strep-tagged membrane proteins on the gold surface by surface enhanced infrared absorption spectroscopy

Surface enhanced infrared absorption spectroscopy (SEIRAS) has been employed to monitor the orientated assembly of a strep-tagged membrane protein on the gold surface via a streptavidin/biotin interlayer. The high surface sensitivity of SEIRAS allows for tracking the individual assembling steps on the molecular level. The sequence of surface modification steps comprises: (i) cross-linking of biotin to the self-assembled monolayer of cysteamine along the gold surface; (ii) adsorption of streptavidin to and desorption from the biotin layer; and (iii) adsorption of the strep-tagged membrane protein ecgltP (glutamate transporter of E. coli) on the streptavidin/biotin layer. The analysis of the SEIRA spectra reveals that the biotin layer undergoes a phase transition from an isotropic orientation to a densely packed layer during coupling to the cysteamine monolayer. Formation of the densely packed layer weakens the interaction between streptavidin and the biotin layer but yields a binding specificity of 80%. The specificity of strep-tagged ecgltP to the streptavidin layer is with 60% only modest. Nevertheless, the streptavidin/biotin interlayer reveals a higher regeneration propensity than the His-tag/Ni-NTA interlayer.     

Characterization of noncovalent complexes of antimalarial agents of the artemisinin-type and Fe(III)-heme by electrospray mass spectrometry and collisional activation tandem mass spectrometry

In this study, we demonstrate, using electrospray ionization mass spectrometry (ESI-MS) and collision-induced dissociation tandem mass spectrometry (ESI-MS/CID/MS), that stable noncovalent complexes can be formed between Fe(III)-heme and antimalarial agents, i.e., quinine, artemisinin, and the artemisinin derivatives, dihydroartemisinin, alpha- and beta-artemether, and beta-arteether. Differences in the binding behavior of the examined drugs with Fe(III)-heme and the stability of the drug-heme complexes are demonstrated. The results show that all tested antimalarial agents form a drug-heme complex with a 1:1 stoichiometry but that quinine also results in a second complex with the heme dimer. ESI-MS performed on mixtures of pairs of various antimalarial agents with heme indicate that quinine binds preferentially to Fe(III)-heme, while ESI-MS/CID/MS shows that the quinine-heme complex is nearly two times more stable than the complexes formed between heme and artemisinin or its derivatives. Moreover, it is found that dihydroartemisinin, the active metabolite of the artemisinin-type drugs in vivo, results in a Na(+)-containing heme-drug complex, which is as stable as the heme-quinine complex. The efficiency of drug-heme binding of artemisinin derivatives is generally lower and the decomposition under CID higher compared with quinine, but these parameters are within the same order of magnitude. These results suggest that the efficiency of antimalarial agents of the artemisinin-type to form noncovalent complexes with Fe(III)-heme is comparable with that of the traditional antimalarial agent, quinine. Our study illustrates that electrospray ionization mass spectrometry and collision-induced dissociation tandem mass spectrometry are suitable tools to probe noncovalent interactions between heme and antimalarial agents. The results obtained provide insights into the underlying molecular modes of action of the traditional antimalarial agent quinine and of the antimalarials of the artemisinin-type which are currently used to treat severe or multidrug-resistant malaria.     

实时生物分子相互作用分析技术用于链霉亲和素-生物素化抗体的层层组装研究

使用生物分子相互作用分析（Biomolecular interaction analysis,BIA)技术实时监测了在链霉素和素表面层层组装亲和素－生物素化抗体多层膜的过程，结果表明，通过链霉素和素与生物素之间的强亲和作用，能够在表面形成均一的多层膜，并用实时BIA技术求得了每层蛋白质的表面浓度，对于生物素化抗体，单层吸附表面浓度为1.32ng/mm^2；对于链霉亲和素，单层吸附表面浓度为2.93ng/mm^2。同时对蛋白质在表面的排列状态进行了探讨。     

氨基酸-磷酸非共价复合物离子的电喷雾电离质谱研究

分子间的非共价相互作用对于理解分子复合物的结构和性质有着非常重要的意义。而电喷雾电离质谱(ESI-MS)是团簇化学研究的一种重要工具,广泛用于重要生物分子复合物的形成和性质研究,包括氨基酸、多肽和核糖等。该文将一定化学剂量比的磷酸分别与L型精氨酸和L型色氨酸混合,通过电喷雾电离的方法,利用傅立叶变换离子回旋共振质谱仪对精氨酸-磷酸以及色氨酸-磷酸的非共价复合物离子进行了研究。结果显示,精氨酸和色氨酸均可与磷酸分子产生种类丰富、价态为+1和+2的复合物离子。而对不同体系的生成离子分布进行分析,则显示出不同体系间的差别。     

Time-of-flight secondary ion mass spectrometry, fluorescence microscopy and scanning electron microscopy: combined tools for monitoring the process of patterning and layer-by-layer assembly of synthetic and biological materials

We have employed time-of-flight secondary ion mass spectrometry (TOF SIMS), fluorescence microscopy and scanning electron microscopy (SEM) to monitor the immobilization of biotinylated shell-crosslinked nanoparticles (SCKs) on biotin/streptavidin-functionalized, UV-photopatterned self-assembled monolayers (SAMs). TOF SIMS and fluorescence microscopy images showed that the streptavidin was immobilized primarily in the biotin-functionalized SAM areas. Biotinylated SCKs underwent both streptavidin-biotin recognition and electrostatic interactions to the underlying substrate. Upon adsorption, the biotinylated SCKs deformed significantly; their cross-sectional diameter increased by approximately 36% from 65+/-7 nm to 90+/-2 nm. Using the SCK contact area, we estimate that one SCK was bound between one and five streptavidin proteins. These data suggest that functionalized SCKs can be employed as biomolecule mimics to investigate the factors that control biomolecule adsorption on functionalized surfaces.     

The origins of femtomolar protein-ligand binding: hydrogen-bond cooperativity and desolvation energetics in the biotin-(strept)avidin binding site

The unusually strong reversible binding of biotin by avidin and streptavidin has been investigated by density functional and MP2 ab initio quantum mechanical methods. The solvation of biotin by water has also been studied through QM/MM/MC calculations. The ureido moiety of biotin in the bound state hydrogen bonds to five residues, three to the carbonyl oxygen and one for each--NH group. These five hydrogen bonds act cooperatively, leading to stabilization that is larger than the sum of individual hydrogen-bonding energies. The charged aspartate is the key residue that provides the driving force for cooperativity in the hydrogen-bonding network for both avidin and streptavidin by greatly polarizing the urea of biotin. If the residue is removed, the network is disrupted, and the attenuation of the energetic contributions from the neighboring residues results in significant reduction of cooperative interactions. Aspartate is directly hydrogen-bonded with biotin in streptavidin and is one residue removed in avidin. The hydrogen-bonding groups in streptavidin are computed to give larger cooperative hydrogen-bonding effects than avidin. However, the net gain in electrostatic binding energy is predicted to favor the avidin-bicyclic urea complex due to the relatively large penalty for desolvation of the streptavidin binding site (specifically expulsion of bound water molecules). QM/MM/MC calculations involving biotin and the ureido moiety in aqueous solution, featuring PDDG/PM3, show that water interactions with the bicyclic urea are much weaker than (strept)avidin interactions due to relatively low polarization of the urea group in water.