Study of non-covalent complexation between catechin derivatives and peptides by electrospray ionization mass spectrometry

The recent development of electrospray ionization mass spectrometry (ESI-MS) has allowed its use to study molecular interactions driven by non-covalent forces. ESI-MS has been used to detect non-covalent complexes between proteins and metals, ligands and peptides and interactions involving DNA, RNA, oligonucleotides and drugs. Surprisingly, the study of the interaction between polyphenolic molecules and peptides/proteins is still an area where ESI-MS has not benefited. With regard to the important influence of these interactions in the biological and food domains, ESI-MS was applied to the detection and the characterization of soluble polyphenol-peptide complexes formed in model solution. The ability to observe and monitor the weak interactions involved in such macromolecular complexation phenomena was demonstrated for monomeric and dimeric flavonoid molecules (catechin-derived compounds) largely encountered in plants and plant derived products. Intact non-covalent polyphenol-peptide complexes were observed by ESI-MS using different experimental conditions. Utilizing mild ESI interface conditions allowed the detection of 1 : 1 polyphenol-peptide complexes in all tested solutions and 2 : 1 complexes for the dimers and galloylated polyphenols (flavanols). These results show that there is a preferential interaction between polymerized and/or galloylated polyphenols and peptide compared with that between monomeric polyphenols and peptides. Thus, ESI-MS shows potential for the study of small polyphenolic molecule-peptide interactions and determination of stoichiometry.     

ATP与氨基酸弱相互作用的质谱与理论计算研究

利用电喷雾质谱、荧光、核磁和理论计算研究了ATP与19种氨基酸的弱相互作用.在质谱中发现除甘氨酸(Gly)、丙氨酸(Ala)、缬氨酸(Val)外,其它氨基酸均可观测到与ATP因弱相互作用形成的复合物离子.利用不同质谱锥孔电压下复合物稳定性的不同,分析了侧链基团对ATP与19种氨基酸弱相互作用的影响.并利用荧光光谱和核磁共振波谱法研究了芳香性氨基酸与ATP的弱相互作用.结果表明,氨基酸与ATP的弱相互作用强弱顺序为:色氨酸(Trp)＞苯丙氨酸(Phe)＞具有R‖C-NH2的氨基酸＞具有-RCOOH、-R-NH2的氨基酸＞具有-RSH、-ROH的氨基酸＞R为长链的氨基酸＞R为短链的氨基酸.不同官能团的氨基酸与ATP的弱相互作用的模拟计算也证实了此结论,并发现氨基酸的主侧链基团与ATP分子基团间的多个分子间因氢键作用使复合物能稳定存在.这一结果将为预测蛋白与ATP结合位点及研究ATP的识别机理提供依据.     

The Investigation of Interaction Competition Between ATP and DIPP-Ala,Boc-Ala,or Ala by ESI-MS/MS and Theoretical Calculation

The interactions between ATP and N-(O,O-diisopropyl) phosphoryl-L-alanine (DIPP-Ala), N-(tert-butoxycarbonyl)-L-alanine (Boc-Ala), or L-alanine (Ala) were investigated by electrospray ionization tandem mass spectrometry (ESI-MS/MS). The non-covalent complexes between ATP and Boc-Ala or DIPP-Ala were observed, while the complex between ATP and Ala was not found in the mass spectra. The affinity of DIPP-Ala for ATP was confirmed to be stronger than that of Boc-Ala by competition experiment. Through molecular modeling calculations, it was found that the non-covalent complexes were stabilized by intermolecular hydrogen bonds, and the affinity sequence for ATP was DIPP-Ala > Boc-Ala > Ala by comparing their binding energy, ?35.407 kcal/mol, ?15.634 kcal/mol, ?6.555 kcal/mol, respectively. The results implied that a phosphoryl group was a very important functional group to provide an interaction site between amino acids and ATP, and that N-phosphoryl amino acids can be used as a good model of protein in the studies of molecular recognition of ATP.     

Direct observation of a series of non-covalent complexes formed by phosphorylated flavonoid-protein interactions through electrospray ionization tandem mass spectroscopy

In the work described in this paper, 7-hydroxyflavone and chrysin were phosphoylated by a modified Atheron-Todd reaction. Three new phosphorylated flavonoids (PF) were obtained, and the structures of the target products were determined by X-ray and NMR data and electrospray ionization (ESI) tandem mass spectroscopy (MS). The mixed solutions of the phosphorylated flavonoids and different proteins such as insulin, lysozyme, and cytochrome c were injected in an ion trap mass spectrometer. The results show that all the phosphorylated flavonoids could form non-covalent complexes with the proteins mentioned above, while non-covalent complexes were not detected from the mixed solution of the chrysin or 7-hydroxyflavone with proteins. The research shows that the phosphorylated flavonoids could enhance the interaction with proteins. It may imply their important role in biological processes. The method described in this paper provides us additional information for studying such interactions for phosphorylated flavonoids in this important field.     

Using solution phase hydrogen/deuterium (H/D) exchange to determine the origin of non-covalent complexes observed by electrospray ionization mass spectrometry: in solution or in vacuo?

Electrospray ionization (ESI) is a soft ionization technique that is able to transfer intact ions, as well as solution phase non-covalent complexes into the gas phase. With small molecules that have a high tendency to form hydrogen bonds, the observation of non-covalent complexes by ESI-MS can be the result of a non-specific interaction, due to the nature of the electrospray process. Special precautions and additional steps should be performed to identify the origin of the complexes observed with ESI-MS, and we have utilized solution phase hydrogen/deuterium (H/D) exchange as a method to determine the specificity of the complexes. By comparing the average number of exchanges for the monomer subunits to the average number of exchanges for the complex, one can distinguish if a specific complex is formed in solution. In this paper we have investigated non-covalent complexes of some common chemotherapy agents: paclitaxel, doxorubicin, and etoposide by ESI-MS. By using the solution phase H/D exchange, we were able to identify several specific drug-drug complexes. Thus, solution phase H/D exchange combined with ESI-MS provides for a convenient method in ascertaining the specificity of non-covalent complexes as being formed in solution or in vacuo.     

Gas-phase binding of non-covalent protein complexes between bovine pancreatic trypsin inhibitor and its target enzymes studied by electrospray ionization tandem mass spectrometry

The potential of electrospray ionization (ESI) mass spectrometry (MS) to detect non-covalent protein complexes has been demonstrated repeatedly. However, questions about correlation of the solution and gas-phase structures of these complexes still produce vigorous scientific discussion. Here, we demonstrate the evaluation of the gas-phase binding of non-covalent protein complexes formed between bovine pancreatic trypsin inhibitor (BPTI) and its target enzymes over a wide range of dissociation constants. Non-covalent protein complexes were detected by ESI-MS. The abundance of the complex ions in the mass spectra is less than expected from the values of the dissociation constants of the complexes in solution. Collisionally activated dissociation (CAD) tandem mass spectrometry (MS/MS) and a collision model for ion activation were used to evaluate the binding of non-covalent complexes in the gas phase. The internal energy required to induce dissociation was calculated for three collision gases (Ne, Ar, Kr) over a wide range of collision gas pressures and energies using an electrospray ionization source. The order of binding energies of the gas-phase ions for non-covalent protein complexes formed by the ESI source and assessed using CAD-MS/MS appears to differ from that of the solution complexes. The implication is that solution structure of these complexes was not preserved in the gas phase.     

Separation-based approach to study dissociation kinetics of noncovalent DNA-multiple protein complexes

Noncovalent binding of DNA with multiple proteins is pivotal to many regulatory cellular processes. Due to the lack of experimental approaches, the kinetics of assembly and disassembly of DNA-multiple proteins complexes have never been studied. Here, we report on a first method capable of measuring disassembly kinetics of such complexes. The method is based on continuous spatial separation of different complexes. The kinetics of multiple complex dissociation processes are also spatially separated, which in turn facilitates finding their rate constants. Our separation-based approach was compared with a conventional no-separation approach by using computer simulation of dissociation kinetics. It proved to be much more accurate than the no-separation approach and to be a powerful tool for testing hypothetical mechanisms of the disassembly of DNA-multiple proteins complexes. An experimental implementation of the separation-based approach was finally demonstrated by using capillary electrophoresis as a separation method. The interaction between an 80 nucleotide long single-stranded DNA and single-stranded DNA binding protein was studied. DNA-protein complexes with one and two proteins were observed, and rate constants of their dissociation were determined. We foresee that a separation approach will be also developed to study the kinetics of the formation of DNA-multiple protein complexes.     

From strong van der Waals complexes to hydrogen bonding: From CO⋯H2O to CS⋯H2O and SiO⋯H2O complexes

Structures and interaction energies of complexes valence isoelectronic to the important CO?H(2)O complex, namely SiO?H(2)O and CS?H(2)O, have been studied for the first time using high-level ab initio methods. Although CO, SiO, and CS are valence isoelectronic, the structures of their complexes with water differ significantly, owing partially to their widely varied dipole moments. The predicted dissociation energies D(0) are 1.8 (CO?H(2)O), 2.7 (CS?H(2)O), and 4.9 (SiO?H(2)O) kcal∕mol. The implications of these results have been examined in light of the dipole moments of the separate moieties and current concepts of hydrogen bonding. It is hoped that the present results will spark additional interest in these complexes and in the general non-covalent paradigms they represent.     

电喷雾质谱法研究谷胱甘肽与L型芳香性氨基酸非共价复合物

为探索谷胱甘肽和L型芳香性氨基酸的非共价相互作用, 将一定化学剂量比的还原型γ-谷胱甘肽分别与L型芳香性氨基酸(包括苯丙氨酸、酪氨酸和色氨酸)在室温和生理pH条件下混合后, 温育1 h, 生成非共价复合物, 并使反应完全. 电喷雾质谱测量结果揭示谷胱甘肽和L型芳香性氨基酸反应可以生成非共价复合物. 在二级串级质谱MS2测得的复合物碎片离子峰中, 除芳香性氨基酸离子峰外, 还包括谷胱甘肽及其它再次碎裂产生的b2和y2碎片离子, 进一步确认了非共价复合物的形成. 紫外光谱也证实了电喷雾质谱的实验结果. 为避免严重的离子化效率差异和质谱信号的相互抑制作用, 定量评估了谷胱甘肽和酪氨酸的相互作用, 结果显示反应物的初始浓度应该选择在5×10-5~3.00×10-4 mol/L范围内. 用质谱滴定法测定了谷胱甘肽与3个芳香性氨基酸非共价复合物的解离常数, 结果表明, 谷胱甘肽复合物的稳定性按Tyr, Trp和Phe次序依次增大.     

Substituent Effects on the Hydrogen Bonding between 4-Substituted Phenols and HF, H2O, NH3

Density function theory UB3LYP/6-31 g(d) calculations were performed to study the hydrogen bonds between para-substituted phenols and HF, H2O, or NH3. It revealed that many properties of the non-covalent complexes, such as the interaction energies, donor-acceptor distances, bond lengths and vibration frequencies, showed well-defined substituent effects. Therefore, from the substituent effects not only the mechanism of a certain non-covalent interaction can be better understood, but also the interaction energies and structures of a certain non-covalent complex, which otherwise might be very hard or resource-consuming to estimate, can be easily predicted.     

Computer modeling of the dynamic properties of the cAMP-dependent protein kinase catalytic subunit

The structural dynamics of the cAMP-dependent protein kinase catalytic subunit were modeled using molecular dynamics computational methods. It was shown that the structure of this protein as well as its complexes with ATP and peptide ligand PKI(5-24) consisted of a large number of rapidly inter-converting conformations which could be grouped into subsets proceeding from their similarity. This cluster analysis revealed that conformations which correspond to the “opened” and “closed” structures of the protein were already present in the free enzyme, and most surprisingly co-existed in enzyme–ATP and enzyme–PKI(5-24) complexes as well as in the ternary complex, which included both of these ligands. The results also demonstrated that the most mobile structure segments of the protein were located in the regions of substrate binding sites and that their dynamics were most significantly affected by the binding of the ATP and peptide ligand.     

Coordination and organometallic compounds in the functionalization of carbon nanotubes

Various methods for functionalization of carbon nanotubes (CNTs) using classic coordination complexes, as well as organometallic compounds as precursors, are discussed. CNTs can form hybrids via covalent or non-covalent interaction with metal complexes of crown ethers, carboxylates, amines, polypyridyl compounds, a host of N,O-containing ligands, derivatives of phosphonic acid, porphyrins, phthalocyanines, carbonyls, cyclopentadienyls, pyrene-containing moieties, and other aromatic structures. Several applications of synthesized composites/hybrids are emphasized.     

Conformational dynamics of ATP∕Mg:ATP in motor proteins via data mining and molecular simulation

The conformational diversity of ATP∕Mg:ATP in motor proteins was investigated using molecular dynamics and data mining. Adenosine triphosphate (ATP) conformations were found to be constrained mostly by inter cavity motifs in the motor proteins. It is demonstrated that ATP favors extended conformations in the tight pockets of motor proteins such as F(1)-ATPase and actin whereas compact structures are favored in motor proteins such as RNA polymerase and DNA helicase. The incorporation of Mg(2+) leads to increased flexibility of ATP molecules. The differences in the conformational dynamics of ATP∕Mg:ATP in various motor proteins was quantified by the radius of gyration. The relationship between the simulation results and those obtained by data mining of motor proteins available in the protein data bank is analyzed. The data mining analysis of motor proteins supports the conformational diversity of the phosphate group of ATP obtained computationally.     

N-磷酰化肽酯及小肽与氨基酸相互作用的ESI-MS研究

采用ESI-MS研究了一系列结构具有可比性的N-二异丙氧基磷酰化肽酯及小肽同20种蛋白氨基酸及3种D型氨基酸(D-Ala、D-Ser、D-Phe)的非共价相互作用.结果表明,可形成π-π共轭体系的芳香环,可显著增强磷酰化肽酯及小肽与氨基酸的相互作用力,π-π堆积力是首要的非共价相互作用力;可形成氢键的极性基团有利于形成复合物,但能否形成氢键还要受到分子柔顺性的影响;另外,分子大小、空间位阻对复合物的形成也有影响;而氨基酸的手性对它们的相互作用在质谱条件下没有表现出影响.     

Charge state effect on the zwitterion influence on stability of non-covalent interaction of single-stranded DNA with peptides

Negative ion ESI mass spectrometry was used to study the gas-phase stability and dissociation pathways of peptide-DNA complexes. We show that bradykinin and three modified peptides containing the basic residue arginine or lysine form stable interactions with single-stranded oligonucleotides. ESI-MS/MS of complexes of T(8) with PPGFSPFRR resulted in a major dissociation pathway through cleavage of the peptide covalent bond. The stability of the complex is due to electrostatic interaction between the negatively charged phosphate group and the basic side chain of the arginine and lysine residues as demonstrated by Vertes et al. and Woods et al. In fact, the present work establishes the role played by zwitterions on complex stabilisation. The presence of protons in nucleobase and/or amino acid contributes in reinforcing the strength of the salt bridge (SB) interaction. The zwitterionic form of the most basic of amino acid residues, arginine, is assumed to form a strong SB interaction to the negatively charged phosphate groups of DNA. This non-covalent complex is stable enough to withstand disruption of the non-covalent interaction and to first break the covalent bond. Moreover, the dependence of fragmentation patterns upon the complex charge state is explained by the fact that the net number of negative charges modulates the number of zwitterionic sites, which stabilise the complexes. Finally, the weak influence of the nucleobase is assumed by the existence of competition for proton addition between the nucleobase and the R/K side chain leading to a decrease in the stabilisation of the SB interaction.     

Analysis of Proteins,Protein Complexes,and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry

Native mass spectrometry (MS) is a rapidly advancing field in the analysis of proteins, protein complexes, and macromolecular species of various types. The majority of native MS experiments reported to-date has been conducted using direct infusion of purified analytes into a mass spectrometer. In this study, capillary zone electrophoresis (CZE) was coupled online to Orbitrap mass spectrometers using a commercial sheathless interface to enable high-performance separation, identification, and structural characterization of limited amounts of purified proteins and protein complexes, the latter with preserved non-covalent associations under native conditions. The performance of both bare-fused silica and polyacrylamide-coated capillaries was assessed using mixtures of protein standards known to form non-covalent protein–protein and protein–ligand complexes. High-efficiency separation of native complexes is demonstrated using both capillary types, while the polyacrylamide neutral-coated capillary showed better reproducibility and higher efficiency for more complex samples. The platform was then evaluated for the determination of monoclonal antibody aggregation and for analysis of proteomes of limited complexity using a ribosomal isolate from E. coli. Native CZE-MS, using accurate single stage and tandem-MS measurements, enabled identification of proteoforms and non-covalent complexes at femtomole levels. This study demonstrates that native CZE-MS can serve as an orthogonal and complementary technique to conventional native MS methodologies with the advantages of low sample consumption, minimal sample processing and losses, and high throughput and sensitivity. This study presents a novel platform for analysis of ribosomes and other macromolecular complexes and organelles, with the potential for discovery of novel structural features defining cellular phenotypes (e.g., specialized ribosomes).

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Graphical Abstract ?

     

Preservation of non-covalent associations in electrospray ionization mass spectrometry: Multiply charged polypeptide and protein dimers

The ‘softness’ of the electrospray ionization (ESI) method provides a direct link between solution chemistry and the inherent gas-phase environment of mass Spectrometry. Available results related to the preservation of non-covalent associations into the gas phase after ESI are reviewed. These associations include the possible retention of elements of higher order protein structure, non-covalent polypeptide–heme associations and enzyme complexes. Experimental results are presented showing that non-covalently bound polypeptide and protein dimer ions are relatively common as low level contributions to ESI mass spectra. It is argued that these dimers are reflective of multimeric species in solution since Coulombic barriers preclude dimerization after ESI although uncertainty remains regarding whether they exist prior to the formation of highly charged droplets. The dissociation of dimers is facile and for proteins can yield monomers having a broad distribution of charge states. The detection of non-covalently associated dimers requires gentle ESI mass spectrometer interface conditions, yielding relatively low levels of internal excitation. Under such conditions incomplete molecular ion desolvation can result in experimental artifacts for tandem mass spectrometric experiments. ESI mass Spectrometry may have broad potential for the study of noncovalent liquid phase associations.     

电喷雾质谱的非共价键蛋白质复合物研究

电喷雾质谱(ESI-MS)已经成为检测和研究生物分子弱相互作用,即非共价键作用的一个重要分析手段.ESI-MS除了具有快速、灵敏、专属的特点以外,还有能够直接得出复合物的分子量和化学计量比的优点.本文通过蛋白质与蛋白质、配体、金属离子的非共价复合物的例子阐述了ESI-MS技术的主要特性,综述了ESI-MS在非共价键蛋白质复合物方面的早期和近期应用研究成果.引用文献34篇.     

磷酰化对丙氨酸与溶菌酶相互作用的影响

在电喷雾离子阱质谱图中发现丙氨酸不能和溶菌酶形成二聚体, 而磷酰化丙氨酸(DIPP-Ala)能和溶菌酶形成二聚体. 进一步研究发现丙氨酸及其他氨基酸磷酰化后, 自身形成二聚能力大大增强. 在Silicon Graplics图形工作站上采用SYBYL 6.8软件, 利用Tripos力场和分子力学方法研究了DIPP-Ala最低能量构象, 并用分子对接(DOCK)研究了二聚体的形成. 结果说明磷氧双键的存在增强了分子间的相互作用.     

Impact of the Core Chemistry of Self-Assembled Spherical Nucleic Acids on their In Vitro Fate

Nucleic acid therapeutics (NATs), such as mRNA, small interfering RNA or antisense oligonucleotides are extremely efficient tools to modulate gene expression and tackle otherwise undruggable diseases. Spherical nucleic acids (SNAs) can efficiently deliver small NATs to cells while protecting their payload from nucleases, and have improved biodistribution and muted immune activation. Self-assembled SNAs have emerged as nanostructures made from a single DNA-polymer conjugate with similar favorable properties as well as small molecule encapsulation. However, because they maintain their structure by non-covalent interactions, they might suffer from disassembly in biologically relevant conditions, especially with regard to their interaction with serum proteins. Here, we report a systematic study of the factors that govern the fate of self-assembled SNAs. Varying the core chemistry and using stimuli-responsive disulfide crosslinking, we show that extracellular stability upon binding with serum proteins is important for recognition by membrane receptors, triggering cellular uptake. At the same time, intracellular dissociation is required for efficient therapeutic release. Disulfide-crosslinked SNAs combine these two properties and result in efficient and non-toxic unaided gene silencing therapeutics. We anticipate these investigations will help the translation of promising self-assembled structures towards in vivo gene silencing applications.