Bacteriorhodopsin is the smallest autonomous light-driven proton pump. Proposals as to how it achieves the directionality of its trans-membrane proton transport fall into two categories: accessibility-switch models in which proton transfer pathways in different parts of the molecule are opened and closed during the photocycle, and affinity-switch models, which focus on changes in proton affinit...

Experimental protein-protein interaction (PPI) networks are increasingly being exploited in diverse ways for biological discovery. Accordingly, it is vital to discern their underlying natures by identifying and classifying the various types of deterministic (specific) and probabilistic (nonspecific) interactions detected. To this end, we have analyzed PPI networks determined using a range of hi...

Twelve 3-cyano-4-(substituted phenyl)-6-phenyl-2(1H)-pyridinones were investigated by tandem mass spectrometry using positive as well as negative electrospray ionization. The influence of the electron affinity of the substituent and the steric effect on the fragmentation is discussed. Pyridinones with a substituent of low proton affinity show loss of water, HCN or benzene from the pyridinone ri...

Seven water-soluble, tetradentate bis(3-hydroxy-N-methyl-pyridin-2-one) (bis-Me-3,2-HOPO) ligands were synthesized that vary only in linker geometry and rigidity. Solution-phase thermodynamic measurements were conducted between pH 1.6 and pH 9.0 to determine the effects of these variations on proton and uranyl cation affinity. Proton affinity decreases by introduction of the solubilizing trieth...

The absorption spectra of a series of inhibitors bound at the active site of Delta(5)-3-ketosteroid isomerase from Pseudomonas putida were found to exhibit substantial variations in the contributions of the protonated and deprotonated forms. Systematic variation of the inhibitor solution pK(a) combined with a method of quantifying the contributions of each protonation state showed the oxyanion ...

The gas-phase structures of alkali-metal cationized glutamine are investigated by using both infrared multiple photon dissociation (IRMPD) action spectroscopy, utilizing light generated by a free electron laser, and theory. The IRMPD spectra contain many similarities that are most consistent with glutamine adopting nonzwitterionic forms in all ions, but differences in the spectra indicate that ...

The acid-sensing ion channels (ASICs) open in response to extracellular acidic pH, and individual subunits display differential sensitivity to protons and calcium. ASIC1a acts as a high affinity proton sensor, whereas ASIC2a requires substantially greater proton concentrations to activate. Using chimeras composed of ASIC1a and ASIC2a, we determined that two regions of the extracellular domain (...