Hydroxyl radical probe of the calmodulin-melittin complex interface by electrospray ionization mass spectrometry

The calcium-dependent interaction of calmodulin and melittin is studied through the application of a radical probe approach in which solutions of the protein and peptide and protein alone are subjected to high fluxes of hydroxyl and other oxygen radicals on millisecond timescales. These radicals are generated by an electrical discharge within an electrospray ion source of a mass spectrometer. Condensation of the electrosprayed droplets followed by proteolytic digestion of both calmodulin and melittin has identified residues in both which participate in the interaction and/or are shielded from solvent within the protein complex. Consistent with other theoretical models and available experimental data, the tryptophan residue of melittin at position 19 is shown to be critical to the formation of the complex with the C-terminal domain of peptide enveloped by and protected from oxidation upon binding to the protein. Furthermore, the N-terminal domain (to residue 36) and tyrosine at position 99 in calmodulin are significantly protected from limited oxidation upon the binding of melittin while exposing the phenylalanine residue at position 92 of the flexible loop domain. The N-terminus (through residue 36) of calmodulin is shown to lie in closer proximity to the melittin helix than its C-terminal counterpart (residues 127-148) based upon the protection levels measured at reactive residues within these segments of the protein.     

Electrospray-assisted modification of proteins: a radical probe of protein structure

A new approach is described to probe the structure of proteins through their reactivity with oxygen-containing radicals. Radical-induced oxidative modification of proteins is achieved within an electrospray ion source using oxygen as a reactive nebulizer gas at high needle voltages. This method facilitates the rapid oxidation of proteins as the molecules emerge from the electrospray needle tip. Electrospray mass spectra of both ubiquitin and lysozyme reveal that over 50% of the protein can be modified under these conditions. The radical-induced oxidative modification of amino acid side chains is correlated with their solvent accessibility to obtain information on a protein's higher-order structure. The oxidation sites in hen lysozyme have been identified by proteolysis of the condensed protein solution and tandem mass spectrometry (MS/MS). Oxidation of tryptophan at positions 62 and 123 occurs exclusively over all other tryptophan residues, consistent with the relative solvent accessibilities of the residue side chains based on the NMR structure of the protein. Radical-induced oxidative modification of cysteine (Cys), methionine (Met), tryptophan (Trp), phenylalanine (Phe), tyrosine (Tyr), proline (Pro), histidine (His), and leucine (Leu) residues is also reported, providing sufficient reactive markers to span a protein sequence. This facile oxidation process could be applied to investigate the molecular mechanism by which reactive oxygen species interact with a particular protein domain as a means to investigate the onset of certain diseases.     

High energy collision-induced dissociation of alkali-metal ion adducts of crown ethers and acyclic analogs.

High energy collision-induced dissociation (CID) techniques were applied for structural elucidation of alkali-metal ion adducts of crown ethers. The CID of alkali-metal adducts of tetraglyme and hexaethylene glycol were also evaluated to contrast the fragmentation pathways of the cyclic ethers with those of acyclic analogs. A common fragmentation channel for alkali-metal ion adducts of all the ethers, which results in distonic radical cations, is the homolytic cleavage of carbon-carbon bonds. Additionally, dissociation by carbon-oxygen bond cleavages occurs, and these processes are analogous to the fragmentation pathways observed for simple protonated ethers. The proposed fragmentation pathways for alkali-metal ion adducts of crown ethers result mostly in odd-electron, acyclic product ions. Dissociation of the alkali-metal ion adducts of the acyclic ethers is dominated by losses of various neutral species after an initial hydride or proton transfer. The CID processes for all ethers are independent of the alkali-metal ion sizes; however, the extent of dissociation of the complexes to bare alkali-metal ions increases with the size of the metal.     

A weight-function approach for determining watershed initial conditions for combustion waves

In many generic combustion models, one finds that a combustionwave will develop with a specific wave speed. However, thereare possible initial temperature profiles which do not evolveinto such waves, but rather die out to the ambient temperature.There can exist, in some models, a clear distinction betweenthose initial conditions that do evolve into combustion wavesand those that do not; this is sometimes referred to as thewatershed initial condition. When fuel consumption is consideredto be negligible, analytical methods can be used to obtain theexact watershed. In this paper, we consider the problem of determiningpseudo-watersheds and ascertaining the relationship betweenthese pseudo-watersheds and the exact watersheds. In the processa novel weight-function approach for infinite spatial domainsis developed.     

Collision-activated dissociation mass spectra of crown ethers,perfluorinated crown ethers and related macrocycles

The collision-activated dissociation (CAD) mass spectra for a series of crown ethers, perfluoro crown ethers, cryptands and several dicyclohexano substituted crown ethers are reported. The CAD spectra were acquired with a triple quadrupole mass spectrometer, and in some cases spectra were recorded as a function of collision energy. In general, the protonated crown ethers dissociate via a series of losses of C₂H₄O units. The perfluoro crown ethers dissociate predominantly via losses of C₂F₄O units. The dicyclohexano ethers fragment in analogous ways in conjunction with cleavage of the cyclohexano rings. CAD spectra are also reported for acyclic ether systems.     

Synthesis of cytotoxic cyanobactin,Wewakazole B

We report herein the synthesis of cytotoxic cyanobactin, Wewakazole B through an efficient solution-phase approach. The key steps of the synthesis are the macrocyclic lactamization of linear dodecapeptide and construction of two hexapeptides with three different substituted oxazole rings.     

Impact of limited oxidation on protein ion mobility and structure of importance to footprinting by radical probe mass spectrometry

The effect of hydroxyl radical induced oxidation on the collision cross-sections of hen egg lysozyme and bovine ubiquitin was investigated by travelling wave ion mobility mass spectrometry for the first time. The oxidized ions of lysozyme and ubiquitin share common collision cross-sections with their unoxidized counterparts suggesting that they share common structures that were unaffected by limited oxidation. In the case of bovine ubiquitin, two distinct conformers were detected for the protein in its unoxidized and oxidized states though no change in the levels of each was observed upon oxidation. This supports the validity of Radical Probe Mass Spectrometry (RP-MS) using an electrical discharge source for protein footprinting experiments. Travelling wave ion mobility mass spectrometry has been used for the first time to confirm that limited oxidation does not have an impact on the global structure of proteins.     

Vibrational relaxation of the C-X stretching mode in halobenzenes

The Raman linewidths of the carbon-halogen stretching mode in several halobenzenes were measured as a function of temperature and in dilute cyclohexane solution. It was found that, as in an earlier investigation on haloalkanes, the vibrational relaxation efficiencies, τ^?1_iso, vary in the order Cl > Br > I. The temperature dependence of τ_iso, together with the results in dilute solution, provide evidence that dipolar interactions play a significant role in vibrational relaxation in these systems.     

On‐plate deposition of oxidized proteins to facilitate protein footprinting studies by radical probe mass spectrometry

The on‐plate deposition of oxidized proteins is described to advance footprinting applications by radical probe mass spectrometry (RP‐MS). An electrospray ionization (ESI) needle assembly mounted vertically over a 384‐target matrix‐assisted laser desorption/ionization (MALDI) plate enabled the limited oxidation of proteins as they were released in the charged droplets ahead of their deposition on the plate. This method combined with on‐plate proteolytic digestion protocols expedites the analysis of proteins oxidized by RP‐MS, and avoids the need to collect and reconstitute samples prior to analysis by MALDI mass spectrometry. Oxidation of peptides from solutions in water as well as an ammonium bicarbonate solution was investigated to test the optimal conditions required for on‐plate oxidation of proteins. These comprised of peptides with a wide range of reactive amino acids including Phe, Tyr, Pro, His, Leu, Met and Lys that were previously shown to oxidize in both electrospray discharge and synchrotron radiolysis based footprinting experiments. The on‐plate deposition of lysozyme oxidized at electrospray needle voltages of 6 and 9 kV were carried out to demonstrate conditions suitable for footprinting experiments as well as those that induce the onset of protein damage. Copyright © 2012 John Wiley & Sons, Ltd.