Hypervalent Ammonium Radicals. Effects of Alkyl Groups and Aromatic Substituents

Neutralization by collisional electron transfer of gaseous benzylalkylammonium ions produces transient hypervalent radicals whose dissociations depend on the substituents in the aromatic ring and at the amine nitrogen atom. Benzylammonium radical, C6H5CH2NH3•, dissociates mainly by N−H bond cleavage to give benzylamine. Dissociation of the CH2−N bond to benzyl radical and ammonia is less abundant. Benzylmethylammonium, C6H5CH2NH2CH3•, dissociates by CH2−N, N−CH3, and N−H bond cleavages to give methylamine, benzyl radical, benzylamine, and N-methylbenzylamine. Benzyldimethylammonium, C6H5CH2NH(CH3)2•, undergoes loss of dimethylamine and hydrogen, while the loss of methyl is less important. (2,3,4,5,6-Pentafluorobenzyl)dimethylammonium radical, C6F5CH2NH(CH3)2•, dissociates mainly by fission of the pentafluorophenyl ring to give CnFm fragments with CF• as the dominating product, while bond dissociations at the hypervalent nitrogen atom are less important. The relative stabilities of pentafluorobenzyl and tropyl cations and radicals are assessed by ab initio calculations. (3,5-Dinitrobenzyl)dimethylammonium radical, (NO2)2C6H3CH2NH(CH3)2•, undergoes competitive losses of hydrogen and NO and intramolecular proton transfer onto the dinitrophenyl ring. Mechanisms for these reactions are suggested involving dissociative electron attachment at the aromatic ring and formation of hypervalent ammonium radicals and zwitterionic intermediates

Statistical results of the three multiple regressions models.

<p>Statistical results of the three multiple regressions models.</p

The three aspects of egg orientation (roll, pitch, and yaw) in a single Forster’s tern egg. White areas indicate daytime, while gray areas indicate nighttime.

<p>The red line represents roll, the black line indicates pitch, and the green line indicates yaw. Note the large change in yaw angle relative to roll and pitch, as well as the difference in egg turning activity between night and day.</p

Five days of egg temperature and egg turn rate from a single tern nest.

<p>The blue line represents egg temperature, and the orange bars represent the number of egg turns in each hour. White areas indicate daytime, while gray areas indicate nighttime.</p

The hourly number of turns and egg temperature during the night and during the day in terns.

<p>(A) Hourly number of turns. (B) Egg temperature. The boxes denote the median, 25 & 75% quartiles, the range of data, and outliers.</p

Proximity-Dependent Labeling of Cysteines

Mapping protein–protein interactions is crucial for understanding various signaling pathways in living cells, and developing new techniques for this purpose has attracted significant interest. Classic methods (e.g., the yeast two-hybrid) have been supplanted by more sophisticated chemical approaches that label proximal proteins (e.g., BioID, APEX). Herein we describe a proximity-based approach that uniquely labels cysteines. Our approach exploits the nicotinamide N-methyltransferase (NNMT)-catalyzed methylation of an alkyne-substituted 4-chloropyridine (SS6). Upon methylation of the pyridinium nitrogen, this latent electrophile diffuses out of the active site and labels proximal proteins on short time scales (≤5 min). We validated this approach by identifying known (and novel) interacting partners of protein arginine deiminase 2 (PAD2) and pyruvate dehydrogenase kinase 1 (PDK1). To our knowledge, this technology uniquely exploits a suicide substrate to label proximal cysteines in live cells

Proximity-Dependent Labeling of Cysteines

Mapping protein–protein interactions is crucial for understanding various signaling pathways in living cells, and developing new techniques for this purpose has attracted significant interest. Classic methods (e.g., the yeast two-hybrid) have been supplanted by more sophisticated chemical approaches that label proximal proteins (e.g., BioID, APEX). Herein we describe a proximity-based approach that uniquely labels cysteines. Our approach exploits the nicotinamide N-methyltransferase (NNMT)-catalyzed methylation of an alkyne-substituted 4-chloropyridine (SS6). Upon methylation of the pyridinium nitrogen, this latent electrophile diffuses out of the active site and labels proximal proteins on short time scales (≤5 min). We validated this approach by identifying known (and novel) interacting partners of protein arginine deiminase 2 (PAD2) and pyruvate dehydrogenase kinase 1 (PDK1). To our knowledge, this technology uniquely exploits a suicide substrate to label proximal cysteines in live cells

xComb: A Cross-Linked Peptide Database Approach to Protein−Protein Interaction Analysis

We developed an informatic method to identify tandem mass spectra composed of chemically cross-linked peptides from those of linear peptides and to assign sequence to each of the two unique peptide sequences. For a given set of proteins the key software tool, xComb, combs through all theoretically feasible cross-linked peptides to create a database consisting of a subset of all combinations represented as peptide FASTA files. The xComb library of select theoretical cross-linked peptides may then be used as a database that is examined by a standard proteomic search engine to match tandem mass spectral data sets to identify cross-linked peptides. The database search may be conducted against as many as 50 proteins with a number of common proteomic search engines, e.g. Phenyx, Sequest, OMSSA, Mascot and X!Tandem. By searching against a peptide library of linearized, cross-linked peptides, rather than a linearized protein library, search times are decreased and the process is decoupled from any specific search engine. A further benefit of decoupling from the search engine is that protein cross-linking studies may be conducted with readily available informatics tools for which scoring routines already exist within the proteomic community

Surface Acoustic Wave Nebulization of Peptides As a Microfluidic Interface for Mass Spectrometry

We describe the fabrication of a surface acoustic wave (SAW) device on a LiNbO3 piezoelectric transducer for the transfer of nonvolatile analytes to the gas phase at atmospheric pressure (a process referred to as nebulization or atomization). We subsequently show how such a device can be used in the field of mass spectrometry (MS) detection, demonstrating that SAW nebulization (SAWN) can be performed either in a discontinuous or pulsed mode, similar to that for matrix assisted laser desorption ionization (MALDI) or in a continuous mode like electrospray ionization (ESI). We present data showing the transfer of peptides to the gas phase, where ions are detected by MS. These peptide ions were subsequently fragmented by collision-induced dissociation, from which the sequence was assigned. Unlike MALDI mass spectra, which are typically contaminated with matrix ions at low m/z, the SAWN generated spectra had no such interference. In continuous mode, the SAWN plume was sampled on a microsecond time scale by a linear ion trap mass spectrometer and produced multiply charged peptide precursor ions with a charge state distribution shifted to higher m/z compared to an identical sample analyzed by ESI. The SAWN technology also provides the opportunity to re-examine a sample from a flat surface, repeatedly. The process can be performed without the need for capillaries, which can clog, reservoirs, which dilute the sample, and electrodes, which when in direct contact with sample, cause unwanted electrochemical oxidation. In both continuous and pulsed sampling modes, the quality of precursor ion scans and tandem mass spectra of peptides was consistent across the plume’s lifetime

Overlap of kernel density estimates for Laysan albatross foraging from Kure and Oahu during phases of the reproductive cycle.

<p>Red tones represent Kure Atoll, blue represent Oahu and contour lines represent the 95%, 75%, 50%, and 25% kernel estimates during the a) incubation b) chick guard c) post-guard and d) non-breeding stages. Kure colony location is indicated by a triangle, and Oahu colony location is indicated by an asterisk.</p