Does a Charge Tag Really Provide a Fixed Charge?

Analysis of Fragmentation Pathways of Peptide Modified with Quaternary Ammonium and Phosphonium Group as Ionization Enhancers

Peptide modification by a quaternary ammonium group containing a permanent positive charge is a promising method of increasing the ionization efficiency of the analyzed compounds, making ultra-sensitive detection even at the attomolar level possible. Charge-derivatized peptides may undergo both charge remote (ChR) and charge-directed (ChD) fragmentation. A series of model peptide conjugates derivatized with N,N,N-triethyloammonium (TEA), 1-azoniabicyclo[2.2.2]octane (ABCO), 2,4,6-triphenylopyridinium (TPP) and tris(2,4,6-trimetoxyphenylo)phosphonium (TMPP) groups were analyzed by their fragmentation pathways both in collision-induced dissociation (CID) and electron-capture dissociation (ECD) mode. The effect of the fixed-charge tag type and peptide sequence on the fragmentation pathways was investigated. We found that the aspartic acid effect plays a crucial role in the CID fragmentation of TPP and TEA peptide conjugates whereas it was not resolved for the peptides derivatized with the phosphonium group. ECD spectra are mostly dominated by c_n ions. ECD fragmentation of TMPP-modified peptides results in the formation of intense fragments derived from this fixed-charge tag, which may serve as reporter ion.

A Quantitative Study of the Effects of Guest Flexibility on Binding Inside a Coordination Cage Host

We have performed a systematic investigation of the effects of guest flexibility on their ability to bind in the cavity of a coordination cage host in water, using two sets of isomeric aliphatic ketones that differ only in the branching patterns of their alkyl chains. Apart from the expected increase in binding strength for C9 over C7 ketones associated with their greater hydrophobic surface area, within each isomeric set there is a clear inverse correlation between binding free energy and guest flexibility, associated with loss of conformational entropy. This can be parameterized by the number of rotatable C-C bonds in the guest, with each additional rotatable bond resulting in a penalty of around 2 kJ mol-1 in the binding free energy, in good agreement with values obtained from protein/ligand binding studies. We used the binding data for the new flexible guests to improve the scoring function that we had previously developed that allowed us to predict binding constants of relatively rigid guests in the cage cavity using the molecular docking programme GOLD (Genetic Optimisation of Ligand Docking). This improved scoring function resulted in a significant improvement in the ability of GOLD to predict binding constants for flexible guests, without any detriment to its ability to predict binding for more rigid guests.

Suppression of peptide ion dissociation under electron capture: role of backbone amide hydrogen

RATIONALE

The electron capture dissociation (ECD) of proteins/peptides is affected by the nature and sequence of amino acid residues. Electron capture/transfer with no dissociation is an intriguing phenomenon that has occasionally been observed. We have previously identified that diarginated peptides enriched with glutamic acid residues were found to show suppression of backbone fragmentation. In this paper, we report the effect of geometrical parameters of a peptide, including chain length, conformation and amide hydrogen, on the suppression of ECD fragmentation using synthetic model peptides.

METHODS

Glycine containing model polypeptides were used to probe the mechanism. Molecular-mechanics was used to obtain the conformation of the precursor ions. The ECD experiments were performed on a Bruker APEX III 4.7 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer.

RESULTS

Significant decreases in the intensities of the fragment ions were observed for the 23-mer polypeptide with only one E residue. This implied that the E:R ratio was no longer the sole determining factor for the occurrence of suppression effects. Results of conformational searches showed that there was a hydrogen-bonding 'ladder' formed in the 23-mer polypeptide, which was not found in the 15-mer peptide. Substituting the normal amino acid residues by the corresponding N-methylated amino acid residues in the model peptide, the suppression effect disappeared.

CONCLUSIONS

Our results indicate that survival of the intact reduced peptide ion after electron capture depends also on the length of the peptide. The amide hydrogen was critical in forming the resonance structure that suppressed the ECD fragmentation.

Electrospray ionization tandem mass spectrometry study of six isomeric cationic amphiphiles with ester/amide linker

RATIONALE

Isomeric cationic amphiphiles differing only in the orientation of the linker group have been demonstrated to possess dramatically changed gene transfer efficacies. Studies aimed at understanding structure-stability correlations of such isomeric cationic amphiphiles at the molecular level are yet to be undertaken. Such studies may throw significant new insights into the mechanistic origin on their contrasting bioactivities.

METHODS

Electrospray ionization mass spectrometry (ESI-MS) and multi-stage tandem mass spectrometric (MS(n)) experiments were performed on a LCQ ion trap mass spectrometer. The decomposition pathway was confirmed by high-resolution mass spectrometry data from a quadrupole time-of-flight (Q-TOF) mass spectrometer. Dissociation curves were drawn based on the intensities of precursor and product ions.

RESULTS

The collision-induced dissociation (CID) spectra of the M(+) ion of each isomeric pair showed distinct product ions (3 pairs). Normal esters (1 and 3) showed abundant product ions with a neighboring group participation (NGP) reaction and reverse esters (lipid 2 and 4) showed McLafferty rearrangement product ions. The spectra of a normal amide (5) and a reverse amide (6) are similar to that found in the corresponding ester, except for the absence of the McLafferty rearrangement in 6. Dissociation curves revealed that normal esters/amide decompose at lower energy than those of corresponding reverse esters/amide.

CONCLUSIONS

The lipids which easily decompose (flexible) show dramatically enhanced gene delivery capabilities and the lipids which decompose at higher collision energy (CE) values (rigid) are transfection incompetent.