The scatter diagram (<i>w</i>, <i>v</i>).

<p><i>X</i>-axis indicates <i>w</i> and <i>y</i>-axis indicates <i>v</i>.</p

Equilibrium of free energy.

<p>Equilibrium of free energy.</p

Reaction names (RM) and their corresponding related genes.

<p>Reaction names (RM) and their corresponding related genes.</p

<i>w</i> scopes, number of reactions (NR) and their percentages.

<p><i>w</i> scopes, number of reactions (NR) and their percentages.</p

Construction and Analysis of the Model of Energy Metabolism in <em>E. coli</em>

<div><p>Genome-scale models of metabolism have only been analyzed with the constraint-based modelling philosophy and there have been several genome-scale gene-protein-reaction models. But research on the modelling for energy metabolism of organisms just began in recent years and research on metabolic weighted complex network are rare in literature. We have made three research based on the complete model of <em>E. coli</em>’s energy metabolism. We first constructed a metabolic weighted network using the rates of free energy consumption within metabolic reactions as the weights. We then analyzed some structural characters of the metabolic weighted network that we constructed. We found that the distribution of the weight values was uneven, that most of the weight values were zero while reactions with abstract large weight values were rare and that the relationship between <em>w</em> (weight values) and <em>v</em> (flux values) was not of linear correlation. At last, we have done some research on the equilibrium of free energy for the energy metabolism system of <em>E. coli</em>. We found that (free energy rate input from the environment) can meet the demand of (free energy rate dissipated by chemical process) and that chemical process plays a great role in the dissipation of free energy in cells. By these research and to a certain extend, we can understand more about the energy metabolism of <em>E. coli</em>.</p> </div

Flux distribution of <i>E. coli</i>_iAF1260.

<p><i>X</i>-axis indicating every reaction in <b>rxns</b> (the order is as the same as in <b>rxns</b>, total 2382) and <i>y</i>-axis indicating the value of its corresponding flux (unit is mmol gDW⁻¹h⁻¹). <b>Rxns</b> is the reaction set in the model.</p

Our computation result comparing with Ref. [5].

<p>Note: Row A – Number in <i>E. coli</i>_iAF1260; Row B – Our computation result comparing with Ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055137#pone.0055137-Feist1" target="_blank">[5]</a>.</p><p>Column A – reactions with unknown ; .</p><p>Column B – reactions with known but involving compounds with unknown ; .</p><p>Column C – reactions with known but not involving compounds with unknown ; .</p><p>Column D – total reactions with known.</p

<i>w</i> scopes, number of reactions (NR) and reaction names (RM).

<p><i>w</i> scopes, number of reactions (NR) and reaction names (RM).</p

Weight value distribution of the metabolic network of <i>E. coli</i>_iAF1260.

<p><i>X</i>-axis indicates every reaction in the reconstructed reactions (the order is as the same as in <b>rxns</b>, total 2077) and <i>y</i>-axis indicates the value of its corresponding weight. <b>rxns</b> is the reaction set in the model.</p

Sulfur Ligand Substitution at the Nickel(II) Sites of Cubane-Type and Cubanoid NiFe₃S₄ Clusters Relevant to the C-Clusters of Carbon Monoxide Dehydrogenase

Substitution reactions at the nickel site of the cubane-type cluster [(Ph3P)NiFe3S4(LS3)]2- (2) have been investigated in the course of a synthetic approach to the C-clusters of CODH. Reaction of 2 with RS- or toluene-3,4-dithiolate affords [(RS)NiFe3S4(LS3)]3- (R = Et (5), H (6)) or [(tdt)NiFe3S4(LS3)]3- (7), demonstrating that anionic sulfur ligands can be bound at the NiII site. Clusters 5 and 6 contain tetrahedral Ni(μ3-S)3(SR) sites. Cluster 7 is of particular interest because it includes a cubanoid NiFe3(μ2-S)(μ3-S)3 core and an approximately planar Ni(tdt)(μ3-S)2 unit. The cubanoid structure is found in all C-clusters, and an NiS4-type unit has been reported in C. hydrogenoformans CODH. Clusters 5/6 are formulated to contain the core [NiFe3S4]1+ ≡ Ni2+ (S = 1) + [Fe3S4]1- (S = 5/2) and 7 the core [NiFe3S4]2+ ≡ Ni2+ (S = 0) + [Fe3S4]0 (S = 2) on the basis of structure, 57Fe isomer shifts, and 1H NMR isotropic shifts. Also reported are [(EtS)CuFe3S4(LS3)]3- (9) and [Fe4S4(LS3)(tdt)]3- (11). The structures of 5−7, 9, and 11 are presented. Cluster 11, with a five-coordinate Fe(tdt)(μ3-S)3 site, provides a clear structural contrast with 7, which is currently the closest approach to a C-cluster but lacks the exo iron atom found in the NiFe4S4,5 cores of the native clusters. (CODH = carbon monoxide dehydrogenase, LS3 = 1,3,5-tris((4,6-dimethyl-3-mercaptophenyl)thio)-2,4,6-tris(p-tolylthio)benzene(3−), tdt = toluene-3,4-dithiolate