A study of noncovalent complexes involving single-stranded DNA and polybasic compounds using nanospray mass spectrometry

Interactions of Protonated Guanidine and Guanidine Derivatives with Multiply Deprotonated RNA Probed by Electrospray Ionization and Collisionally Activated Dissociation

Interactions of ribonucleic acid (RNA) with guanidine and guanidine derivatives are important features in RNA-protein and RNA-drug binding. Here we have investigated noncovalently bound complexes of an 8-nucleotide RNA and six different ligands, all of which have a guanidinium moiety, by using electrospray ionization (ESI) and collisionally activated dissociation (CAD) mass spectrometry (MS). The order of complex stability correlated almost linearly with the number of ligand atoms that can potentially be involved in hydrogen-bond or salt-bridge interactions with the RNA, but not with the proton affinity of the ligands. However, ligand dissociation of the complex ions in CAD was generally accompanied by proton transfer from ligand to RNA, which indicated conversion of salt-bridge into hydrogen-bond interactions. The relative stabilities and dissociation pathways of [RNA+m L-n H] n- complexes with different stoichiometries (m=1-5) and net charge (n= 2-5) revealed both specific and unspecific ligand binding to the RNA.

Mass spectrometric analysis of in vitro nuclear aggregates of polyamines

RATIONALE

In the nuclei of eukaryotic cells, polyamines and phosphate ions self-assemble via ionic interactions and hydrogen bonding, generating three families of supramolecular compounds that have been named large (l-), medium (m-) and small (s-) nuclear aggregates of polyamines (NAPs). In a simulated nuclear environment, polyamines and phosphate ions generate the in vitro NAPs (ivNAPs) that share strict structural and functional analogies with their cellular cognates. Mass spectrometric data are expected to provide important structural details of NAPs/ivNAPs.

METHODS

We used both electrospray ionization (ESI) and nitrocellulose (NC) matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) to support a variety of analytical techniques previously addressed to structurally characterize NAPs/ivNAPs.

RESULTS

The dominant m/z values of s-ivNAP (m/z 735, 749, 761) are compatible with a defined set of cyclic or linear aggregates. On the basis of the experimental molecular mass (a cluster centred at m/z 2980), the m-ivNAP corresponds to the supramolecular assembly of four modules of s-ivNAPs. No informative mass spectra were obtained for the l-ivNAP.

CONCLUSIONS

MS data support the models of NAPs that have been inferred by using an array of analytical techniques. NC MALDI-MS contributed much more effectively than ESI-MS to the structural characterization of ivNAPs.

ETD and sequential ETD localize the residues involved in D2-A2A heteromerization

ETD²to identify binding site in NCX.

Excursions in polynuclear platinum DNA binding

Polynuclear platinum agents are a structurally unique class of anti-cancer drugs, distinct from the cisplatin family. To describe the chemistry and biology of this class, it was necessary to challenge the accepted paradigms for the structure-activity relationships; design new chemotypes and delineate the structures and consequences of their DNA binding modes. This article summarizes the structural changes induced in DNA by both covalent (bond-forming) and non-covalent (ligand recognition) adducts. Solution (Nuclear Magnetic Resonance), solid state (crystallography) and gas-phase (Electrospray Ionization Mass Spectrometry) techniques have all been used to describe the new DNA structures along with molecular biological techniques. The combined approaches allow molecular description of hitherto unobserved adducts such as long-range major-groove interstrand crosslinks; directional isomers on DNA and a third class of ligand-DNA binding, the phosphate clamp. The phosphate recognition is distinct from ''classic'' minor-groove recognition or intercalation.

Gas-phase behavior of noncovalent transmembrane segment complexes

Specific helix oligomerization between transmembrane segments (TMSs) is often promoted by motifs like GxxxG. Disruption of this motif in the transmembrane segments of vesicular stomatitis virus G-protein and of glycophorin A results in a reduced dimerization level studied by in vivo systems like ToxR. This paper reports the influence of sequence motifs like GxxxG in solution and the gas phase.The transmembrane segments may behave differently in the gas and liquid phase, because of the absence of surrounding solvent molecules in the gas phase. Comparison of experiments depending on peptide properties performed in the gas and liquid phase discloses that the peptides retain 'some memory' of their liquid-phase structure in the gas phase. A direct correlation has been found between helicity in solution as determined by circular dichroism and dimerization in the gas phase monitored by electrospray mass spectrometry. These results show that a proper folding in solution is required for oligomerization.On the other hand, sequence-specific oligomerization depending on the GxxxG motif was not observed with the mass spectrometric detection. Further on, neither concentration-dependent complex studies nor studies regarding complex stability in the gas phase - via collision-induced dissociation (CID) - led to sequence-specific differences.Finally, the findings show that in mass spectrometric measurements noncovalent interactions of studied TMSs is rather more dependent on the secondary structure and proper folding than on their primary structure.

Investigation of double-stranded DNA/drug interaction by ESI/FT ICR: orientation of dissociations relates to stabilizing salt bridges

Noncovalent complexes of DNA and Hoechst 33258 were investigated by ESI-FT/ICR MS in various activation modes (collision-induced dissociation (CID), sustained off-resonance irradiation collision-induced dissociation (SORI-CID), infrared multiphoton dissociation (IRMPD) and electron detachment dissociation (EDD)). The binding selectivity of Hoechst 33258 was confirmed by the comparative study of its noncovalent association with different DNA sequences. The CID spectra of [ds + HO - 5H](5-) obtained with a linear hexapole ion trap resulted in unzipping of the strands. This outcome is a clue to the drug-binding mode, shading light on the localization of the binding sites of Hoechst 33258 to the DNA sequence. The IRMPD and SORI-CID experiments mainly gave DNA backbone cleavages and internal fragment ions. From this result, information on the localization of the binding sites of Hoechst 33258 in the DNA sequence was obtained. No sodium cationization was observed on the DNA sequence ions although they were present on fragmentation of the duplex, indicating that the backbone cleavages were generated from the single strand associated with the Hoechst 33258 where the number of alkali cation is restricted. Under electron detachment (ED) conditions, multiple EDs were achieved for the [ds + HO - 5H](5-) ion without any significant dissociation. The presence of drug appears to enhance the stability of the multiply charged system. It was proposed that the studied noncovalent complex involved the formation of zwitterions and consequently strong salt-bridge interactions between DNA and drug.

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.

Mass spectrometry of protein-ligand complexes: enhanced gas-phase stability of ribonuclease-nucleotide complexes

Noncovalent protein-ligand complexes are readily detected by electrospray ionization mass spectrometry (ESI-MS). Ligand binding stoichiometry can be determined easily by the ESI-MS method. The ability to detect noncovalent protein-ligand complexes depends, however, on the stability of the complexes in the gas-phase environment. Solution binding affinities may or may not be accurate predictors of their stability in vacuo. Complexes composed of cytidine nucleotides bound to ribonuclease A (RNase A) and ribonuclease S (RNase S) were detected by ESI-MS and were further analyzed by MS/MS. RNase A and RNase S share similar structures and biological activity. Subtilisin-cleavage of RNase A yields an S-peptide and an S-protein; the S-peptide and S-protein interact through hydrophobic interactions with a solution binding constant in the nanomolar range to generate an active RNase S. Cytidine nucleotides bind to the ribonucleases through electrostatic interactions with a solution binding constant in the micromolar range. Collisionally activated dissociation (CAD) of the 1:1 RNase A-CDP and CTP complexes yields cleavage of the covalent phosphate bonds of the nucleotide ligands, releasing CMP from the complex. CAD of the RNase S-CDP and CTP complexes dissociates the S-peptide from the remaining S-protein/nucleotide complex; further dissociation of the S-protein/nucleotide complex fragments a covalent phosphate bond of the nucleotide with subsequent release of CMP. Despite a solution binding constant favoring the S-protein/S-peptide complex, CDP/CTP remains electrostatically bound to the S-protein in the gas-phase dissociation experiment. This study highlights the intrinsic stability of electrostatic interactions in the gas phase and the significant differences in solution and gas-phase stabilities of noncovalent complexes that can result.

Investigation of non-covalent complexes of glutathione with common amino acids by electrospray ionization mass spectrometry

AIM

To study the non-covalent interaction between glutathione and common amino acids.

METHODS

A stoichiometry of glutathione and common amino acids were mixed to reach the equilibrium, and then the mixed solution was investigated by electrospray ionization mass spectrometry (ESI-MS). The binding of the complexes was further examined by collision-induced dissociation (CID) in a tandem mass spectrometer as well as UV spectroscopy. To avoid distinct ionization efficiency discrepancy and signal suppression in the ESI-MS measurements, the interaction between glutathione (GSH) and glutamate (Glu) was quantitatively evaluated. The total concentrations and series of m/z of peak intensities for glutathione and amino acids could be achieved, respectively. Due to the existence of some oligomeric species arising from glutathione or amino acids, an improved calculation formula was proposed to calculate the dissociation constants of glutathione binding to amino acids.

RESULTS

The ESI mass spectra revealed that glutathione could interact easily with Met, Phe, Tyr, Ser, or Ile to form non-covalent complexes. The binding of the complexes was further confirmed by CID experiments in a tandem mass spectrometer as well as UV spectroscopy. Moreover, an improved calculation formula was successfully applied to determine the dissociation constants of glutathione binding to Glu, His, or Gln. Finally, a possible formation mechanism for the complexes of glutathione with amino acids was proposed.

CONCLUSION

The reduced polypeptide gamma-glutathione can interact with each of 8 common amino acids, including Glu, His, and Gln to form non-covalent complexes with different affinity.

Chiral discrimination of alpha-amino acids by DNA tetranucleotides under electrospray ionization conditions

A set of DNA tetranucleotides, which are 3'- or 5'-end extended versions of GCA, was used as chiral selectors for the discrimination of enantiomers of alpha-amino acids. The [X+Y-2H](2-) ions of the 1:1 complexes were generated by electrospraying a mixture of tetranucleotide (X) and amino acid (Y) solution. Chiral discrimination was achieved by studying the collision-induced dissociation spectra of the [X+Y-2H](2-) ion and the ratio of relative abundance of precursor ion to that of the product ion was used to measure the extent of discrimination. Among the tetranucleotides used, GCAA and GGCA exhibited better discrimination, in which GCAA showed D-selectivity and GGCA showed L-selectivity for the studied amino acids. In addition, binding constants were measured for the 1:1 complexes of phenylalanine enantiomers with GCAA and GGCA. Ltd.

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.

Noncovalent complexes between DNA and basic polypeptides or polyamines by MALDI-TOF

MALDI-MS was evaluated as a method for the study of noncovalent complexes involving DNA oligonucleotides and various polybasic compounds (basic polypeptides and polyamines). Complexes involving single-stranded DNA were successfully detected using DHAP matrix in the presence of an ammonium salt. Control experiments confirmed that the interactions involved basic sites of the polybasic compounds and that the complexes were not formed in the gas phase but were pre-existing in the matrix crystals. Moreover, the pre-existence in solution was probed by isothermal titration calorimetry at concentration and ionic strength similar to those used for mass spectrometry. Spectra showed no important difference between negative and positive ion modes. The influence of nature and size of DNA and polybasic compound on the relative intensities and stoichiometries of the complexes was investigated. Despite the fact that relative intensities can be affected by ionization yields and the gas-phase stabilities of the different species, numerous trends observed in the MALDI study were consistent with the expected in-solution behaviors. Experimental conditions related to sample preparation were investigated also. Complex abundance generally decreased when increasing the ammonium acetate concentration. It was dramatically decreased when using ATT instead of DHAP. Penta-L-arginine is an exception to these observations. Lastly, in the case of complexes involving DNA duplex, the ATT matrix was shown to favor the observation of specific DNA duplex but not that of its complex with polybasic compounds. Inversely, DHAP was appropriate for the conservation of DNA-polybasic compound interaction but not for the transfer of intact duplex.