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Ferredoxin-dependent glutamate synthase (FdGltS), 2-oxoglutarate (2-OG) and L-glutamine (L-Glu) contribute to the activation of the glutaminase site and to ammonia transfer through the tunnel in a two step process. This process requires partial activation upon binding of 2-OG at the synthase site, followed by full activation brought about by glutamine binding.

A study is conducted in which the effects of ethylene glycol and methanol on the structural changes of the ammonia-specific site of the oxygen-evolving complex (OEC) during the S1 to S2 transition is described. The possible interactions of ethylene glycol and methanol with the OEC are also discussed.

Experiments have shown that hydroxylamine oxidoreductase (HAO) is thermodynamically poised to catalyze reduction of N[O.sub.2.sup.-] to N[H.sub.4.sup.-]. HAO has not catalyzed the disproportionation of N[H.sub.2]OH, despite the thermodynamically favorability of such a process, and the opportunity presented by the HAO structure.

Kinetic isotope effects for both phases (rapid burst phase and slow plateau phase) of the urease-catalyzed hydrolysis of hydroxyurea were measured at pH 6.0 and 25 degree [Celsius] to understand the observed nitrogen isotope effects for the ammonia leaving group and hydroxylamine leaving group. The observed similarity of the magnitude of the carbon isotope effects argues for formation of a common intermediate during both phases.

A locally enhanced sampling (LES) strategy for modeling ammonia transfer between the active sites of Escherichia coli glutamine 5'-phosphoribosylpyrophosphate amidotransferase (GPATase) in its active conformation is presented. The combined LES/PMF approach provides new insights into the molecular basis of the reduced ammonia transfer efficiency exhibited by the L415A GPATase mutant.

Multiple independent molecular dynamics simulations of membrane-bound and membrane-free forms were performed to analyze the dynamics of rat (monoamine oxidase membrane A) MAOA and clarify the relationship between the mechanics of the enzyme and its function. The results obtained confirmed with mutational analysis and suggested that modifications of interdomain hinge residues decreased the activity of rat MAOA in solution and the presence of the lipid environment is found to assist in the decoupling of the interdomain motions.

Two forms of formyl glycinamide ribonucleotide (FGAR) amidotransferase (PurL), large and small, are characterized. The flexibility of the PurS dimer has played a major role in the activation of the complex and the formation of the ammonia channel.

The mechanism for the transport of N[H.sub.3] through the small subunit of carbamoyl phosphate synthetase (CPS) is demonstrated by using molecular dynamic simulations. The calculation results for high overall free-energy barrier for the transport of ammonium suggest that the tunnel in the small subunit of CPS is not an ammonium (N[H.sub.4.sup.+]), but an ammonia (N[H.sub.3]) channel.

The 2-fluoroethylamine (FE) permeability in intact human red blood cells (RBCs) under equilibrium exchange conditions on the sub-second time scale is studied using [.sup.19.F] magnetization transfer NMR spectroscopy. The apparent rate constant for the exchange of Fe was higher than for water but significantly lower than that for ammonia.

The effects of ammonia on the S2Q(sub A)(super -)/S(sub 1)Q(sub A) Fourier transform infrared (FTIR)difference spectrum of photosystem II (PSII) are examined in order to obtain structural information about ammonia coordination to the catalytic site of the oxygen-evolving complex (OEC) during S(sub 1) to S(sub 2) transition. The results suggest that the structural difference of the OEC between the normal g = 2 multiline form and the NH3-stabilized g = 4.1 form is small.