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Proton Transfer Steps (proton + transfer_step)
Selected AbstractsFactor analysis of spectroelectrochemical reduction of FAD reveals the pKa of the reduced state and the reduction pathwayJOURNAL OF CHEMOMETRICS, Issue 12 2007Edmund R. Malinowski Abstract The free flavin adenine dinucleotide (FAD) cofactor is known to exhibit a pH-dependent midpoint potential involving a simultaneous two-electron transfer step (n,=,2). Uv-vis spectroelectrochemical reductions of FAD at constant pH, ranging from 5 to 9, were recorded and analyzed by factor analysis. Principal factor analysis was used to determine the number of species present at each pH. The results indicate that only two composite forms of FAD are present: the oxidized and the reduced forms. Window factor analysis was used to extract the concentration profiles of the controlling species. The oxidized form was found to be a single pH-independent species, whereas the reduced form consists of two species. The pH-dependent spectroscopic changes of reduced FAD were best modeled by a single proton transfer step involving two different ionization states with an apparent pKa,=,6.3. This value compares favorably with those obtained from NMR and from midpoint potential measurements. At pH 6, the reduction of FAD was found to be first order, whereas at pH 9 the reduction is zero order; these observations are explained in terms of the reaction pathway involving xanthine oxidase, its substrate, and the pH. Copyright © 2007 John Wiley & Sons, Ltd. [source] An extended dead-end elimination algorithm to determine gap-free lists of low energy statesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2007Edda Kloppmann Abstract Proteins are flexible systems and commonly populate several functionally important states. To understand protein function, these states and their energies have to be identified. We introduce an algorithm that allows the determination of a gap-free list of the low energy states. This algorithm is based on the dead-end elimination (DEE) theorem and is termed X-DEE (extended DEE). X-DEE is applicable to discrete systems whose state energy can be formulated as pairwise interaction between sites and their intrinsic energies. In this article, the computational performance of X-DEE is analyzed and discussed. X-DEE is implemented to determine the lowest energy protonation states of proteins, a problem to which DEE has not been applied so far. We use X-DEE to calculate a list of low energy protonation states for two bacteriorhodopsin structures that represent the first proton transfer step of the bacteriorhodopsin photocycle. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] New Pentadentate Carboxylate-Derivatized Sulfur Ligands Affording Water Soluble Iron Complexes with [Fe(NS4)] Cores that Bind Small Molecules (CO, NO, PMe3) as Co-LigandsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 3 2004Dieter Sellmann Abstract In the search for polydentate sulfur ligands that are able to form water-soluble iron complexes which can bind nitrogenase relevant molecules, the new pentadentate ligands pyCO2MeS4,H2 [2,6-bis[2-mercapto-3-(methoxycarbonyl)phenylthio]dimethylpyridine] (1) and pyCO2HS4,H2 [2,6-bis(2-mercapto-3-carboxyphenylthio)dimethylpyridine] (2) having NS4 donor atom sets and terminal thiolate donors have been synthesized. The starting material was CO2MeS2,H2 (2,3-dimercapto benzoic acid methyl ester) which was alkylated with 2,6-bis[(tosyloxy)methyl]pyridine. The problem of specifically achieving regioselective mono-alkylation of this 1,2-benzene-dithiol derivative was solved by carrying out the alkylation of CO2MeS2,H2 at ,78 °C in the presence of stoichiometric amounts of a base. Saponification of 1 afforded the carboxylic acid derivative. Coordination of pyCO2MeS42, to FeII in the presence of co-ligands (L = CO, PMe3) yielded the complexes [Fe(L)(pyCO2MeS4)] where L = CO (5) or PMe3 (4). Upon treatment with NOBF4, complex 5 afforded [Fe(NO)(pyCO2MeS4)]BF4 (7) which could be subsequently converted to the isolable 19 valence electron species [Fe(NO)(pyCO2MeS4)] (8) upon reduction with N2H4. In the absence of potential co-ligands, coordination of pyCO2MeS42, to FeII afforded the dinuclear complex [Fe(pyCO2MeS4)]2 (6) whilst coordination to NiII gave [Ni(pyCO2MeS4)]x (3). Solubility of these complexes in water could be achieved by replacing the CO2Me groups with CO2H substituents. The ligand pyCO2HS42, afforded the iron complexes [Fe(L)(pyCO2HS4)] [L = CO (10) and PMe3 (12)] and [Fe(NO)(pyCO2HS4)]BF4 (11). Both 10 and 12 could be reversibly deprotonated to give the corresponding water-soluble salts (NMe4)2[Fe(L)(pyCO2S4)] with L = CO {(NMe4)2 [9]} and PMe3 {(NMe4)2 [13]}. The complexes were characterized by elemental analysis, spectroscopic methods and X-ray structural determinations. The molecular structure of [Fe(PMe3)(pyCO2HS4)] (12) was found to exhibit inter- and intramolecular O,H···O and O,H···S hydrogen bonds which serve as models for proton transfer steps from external sources to the active sites of metal sulfur enzymes. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] A Role for Internal Water Molecules in Proton Affinity Changes in the Schiff Base and Asp85 for One-way Proton Transfer in Bacteriorhodopsin,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Joel E. Morgan Light-induced proton pumping in bacteriorhodospin is carried out through five proton transfer steps. We propose that the proton transfer to Asp85 from the Schiff base in the L-to-M transition is accompanied by the relocation of a water cluster on the cytoplasmic side of the Schiff base from a site close to the Schiff base in L to the Phe219-Thr46 region in M. The water cluster present in L, formed at 170 K, is more rigid than that at room temperature. This may be responsible for blocking the conversion of L to M at 170 K. In the photocycle at room temperature, this water cluster returns to the site close to the Schiff base in N, with a rigid structure similar to that of L at 170 K. The increase in the proton affinity of Asp85, which is a prerequisite for the one-way proton transfer in the M-to-N transition, is suggested to be facilitated by a structural change which disrupts interactions between Asp212 and the Schiff base, and between Asp212 and Arg82. We propose that this liberation of Asp212 is accompanied by a rearrangement of the structure of water molecules between Asp85 and Asp212, stabilizing the protonated Asp85 in M. [source] Collision-induced dissociation of protonated tetrapeptides containing , -alanine, , -aminobutyric acid, , -aminocaproic acid or 4-aminomethylbenzoic acid residues,RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 22 2006Erach R. Talaty The influence of the presence and position of a single , -alanine, , -aminobutyric acid, , -aminocaproic acid or 4-aminomethylbenzoic acid residue on the tendency to form b - and y -type product ions was determined using a group of protonated tetrapeptides with general sequence XAAG, AXAG and AAXG (where X refers to the position of amino acid substitution). The hypothesis tested was that the ,alternative' amino acids would influence product ion signal intensities by inhibiting or suppressing either the nucleophilic attack or key proton transfer steps by forcing the adoption of large cyclic intermediates or blocking cyclization altogether. We found that specific b ions are diminished or eliminated completely when ,A, ,Abu, Cap or 4AMBz residues are positioned such that they should interfere with the intramolecular nucleophilic attack step. In addition, differences in the relative proton affinities of the alternative amino acids influence the competition between complementary bn and yn ions. For both the AXAG and the XAAG series of peptides, collision-induced dissociation (CID) generated prominent b ions despite potential inhibition or suppression of intramolecular proton migration by the ,A, ,Abu, Cap or 4AMBz residues. The prominent appearance of b ions from the AXAG and XAAG peptide is noteworthy, and suggests either that proton migration occurs through larger, ,whole' peptide cyclic intermediates or that fragmentation proceeds through a population of [M+H]+ isomers that are initially protonated at amide O atoms. Copyright © 2006 John Wiley & Sons, Ltd. [source] | ||||||||||