Molecular modeling MoFe-protein

Many researchers have considered models for possible intermediates in the nitrogenase reaction. Two possible dinitrogen attachments to the FeMoco factor of MoFe-protein have been put forward. Symmetric, edge- or side-on modes discussed by Dance48 would lead to a reaction sequence such as is shown in reaction 6.11. In contrast, the asymmetric end-on terminal mode discussed in the work of Nicolai Lehnert50 may be favored thermodynamically and by molecular orbital calculations. Reaction sequence 6.13 below illustrates one scenario for the asymmetric model. 

Finally, we must consider how protons are delivered to complete the reaction. Without definitive evidence, molecular modeling has identified three likely proton-transfer routes (71). One is the interstitial channel, filled with water molecules, that nms between the a- and )3-subunits from the surface of the MoFe protein to the pool of water molecules around the homocitrate of the FeMo-cofactor. This channel could deliver protons rapidly to boimd substrate and might also provide a pathway for N2 and NH4+ to enter and leave the reduction site (see also the section Substrate-Binding Site). Extensive theoretical studies of the hydrogen-related chemistry of the FeMo-cofactor use this same interstitial channel to deliver protons (75). These studies indicate that the delivery of electrons to the FeMo-cofactor causes its sulfur atoms to become more basic which, in turn, makes them attractive sites for protonation by water molecules in the interstitial pool. Once transferred, these protons become reduced to hydrogen atoms that can then migrate across the FeMo-cofactor structure to other Fe and S atoms and become involved in substrate reduction (76). 

The Mo enzyme consists of two components (1) the Fe protein (molecular weight 57,000 daltons), which contains iron and sulfur (4 atoms of each per protein) and (2) the MoFe protein (220,000 daltons, Uz subunits), which contains both metals (1 atom Mo, 32 atoms Fe). Each also contains S ions (ca. one per iron), which act as bridging ligands for the metals. The protein contains special Fe—S clusters called P clusters that have EPR resonances like those of no other Fe—S cluster. A soluble protein-fiee molybdenum and iron-containing cluster can be separated from the enzyme. This iron-molybdenum cofactor, or FeMo-co, was known to have approximately 1 Mo, 7-8 Fe, 4-6 S ", and one molecule of homocitrate ion. As for the P cluster, there was no agreement on the structure of FeMo-co for many years. In purified form FeMo-co does crystallize, and it can restore N2 reducing activity to samples of mutant N2ase that are inactive because they lack FeMo-co. On the other hand, no crystal structure of FeMo-co proved possible, and no synthetic model complex was found that could activate the mutant enzyme. 

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