Conserved moiety

There is a rich literature for the determination of these symmetry families [31], and this might be of use in the back-translation problem. In any case, for structural unidentifiability caused by conserved moieties the back-translation may be formulated by simple linear combinations [3, 6]. Another special case where improved solutions of the back-translation problem are possible is term elimination and lumping [6] examples of both these cases in the model for insulin signaling are provided in the next section. First, however, we must consider the back-translation problem in the example introduced above. 

Anguelova, M Cedersund, G., Johansson, M Franzen, C.-J., Wennberg, B., Conserved moieties may lead to unidentifiable rate expressions in biochemical models, IETSyst. Biol. 2006,1(4) 230-237. 

Kholodenko, B.N., Sauro, H.M. and Westerhoff, H.V. (1994b) Control by enzymes, coenzymes and conserved moieties. A generalisation of the connectivity theorem of metabolic control analysis. Eur. J. Biochem. 225, 179-186. 

We conclude that P-oxidation flux can be controlled by the [NAD ]/[NADH] and [acyl-CoA]/[CoA] ratios in intact mitochondrion. The gross intramitochondrial [NAD ]/[NADH] ratio may not exert control directly over P-oxidation because of the channelling of NAD(H) between 3-hydroxyacyl-CoA dehydrogenases and complex I. Although control of P-oxidation, by CoA acylation or acetylation and feedback inhibition via the 3-ketoacyl-CoA thiolases, is possible it appears to be unlikely to have much impact in intact mitochondrion because (i) 3-ketoacyl-CoA esters are not observed as intermediates of mitochondrial P-oxidation (ii) the K for CoASH of the 3-ketoacyl-CoA thiolases is comparable to that of mitochondrial CoASH-dependent dehydrogenases and much lower than that of CPT II. However, further work characterising the dependence of mitochondrial P-oxidation on these conserved-moiety cycles is necessary. 

The presence of conserved elements and conserved moieties cause linear dependence between the rows of the stoichiometric matrix p and decrease the rank of the stoichiometric matrix. In most cases, the number of species Ns is much less than the number of reaction steps N, that is, Ns < Wr. If the stoichiometric matrix p has N rows and Ns columns, and conserved properties are not present, then the rank of the stoichiometric matrix is usually Ns - If Nq conserved properties are present, then the rank of the stoichiometric matrix isN = Ns— Nq- In this case, the original system of ODEs can be replaced by a system of ODEs having N variables, since the other concentrations can be calculated from the computed concentrations using algebraic relations related to the conserved properties. 

The palladium-catalyzed cyclization of compound 138 amply demonstrates the utility of the Stille reaction as a macrocyclization method (see Scheme 37). This efficient ring closure is just one of many examples disclosed by J.E. Baldwin and his group at Oxford.58 Interestingly, compound 138 can be employed as a stereoisomeric mixture of vinylstannanes because both stereoisomers converge on the same cyclized product. To rationalize this result, it was suggested that the configuration of the vinylstannane moiety is conserved in the cyclization, but that the macrocycle resulting from the (Z)-vinylstannane stereoisomer isomerizes to the thermodynamically favored trans product under the reaction condi-... 

With chiral auxiliaries1,41 a remote chiral moiety is temporarily introduced into the substrate in order to direct the nucleophilic addition diastereoselectively. The chiral auxiliary can be removed from the initial addition product with complete conservation of the chirality of the desired product and also of the chiral auxiliary. The recovered chiral auxiliary can then be reused in further reactions. Therefore, chiral auxiliaries are used to chiralize an a priori achiral carbonyl substrate by the introduction of a covalently bound, but nevertheless easily removable, chiral source. 

Many GPCRs contain one or more conserved cysteine residues within their C-terminal tails, which are modified by covalent attachment of palmitoyl or isoprenyl residues. The palmitoyl moiety is anchored in the lipid bilayer forming a fourth intracellular loop. There is evidence that palmitoylation of a GPCR is a dynamic process and may affect receptor desensitization. 

Phenylphosphate synthase consists of three subunits with molecular masses of 70, 40, and 24kDa. Subunit 1 resembles the central part of classical phospho-enolpyruvate synthase which contains a conserved histidine residue. It catalyzes the exchange of free [ C] phenol and the phenol moiety of phenylphosphate but not the phosphorylation of phenol. Phosphorylation of phenol requires subunit 1, MgATP, and another protein, subunit 2 (40kDa), which resembles the N-terminal part of phosphoenolpyruvate synthase. Subunit 1 and 2 catalyze the following reaction ... 

The abundance of structural information has led to a significant increase in the use of structure-based methods both to identify and to optimise inhibitors of protein kinases. The focus to date has centred upon small molecule ATP-competitive inhibitors and there are numerous examples of protein-ligand complexes available to guide design strategies. ATP binds in the cleft formed between the N- and C-terminal lobes of the protein kinase, forming several key interactions conserved across the protein kinase family. The adenine moiety lies in a hydrophobic region between the jS-sheet structure of subdomains I and II and residues from subdomains V and VIb. A... 

If a four-membered ring peroxide (1.2-dioxetane) is involved in a reaction, its concerted bond cleavage into two carbonyl moieties should yield one of these in its excited electronic state on the basis of the orbital symmetry conservation rules of R. B. Woodward and R. Hoffmann ... 

Material balances can be written for moieties which are conserved during the reaction, such as the atoms of a particular element or the total charge, or for reactant or product species if the stoichiometry is unambiguous. Oxidation-reduction reactions may be particularly troublesome. In the following situation, for example, one cannot write a material balance relating protons to water molecules. Consider the oxidation of O2 to H2O and the equilibrium dissociation of I O. 

In writing balance equations for the partial equilibrium model, two quantities are absolutely conserved. These are the total number of sulfate moieties and the net charge in solution. The resulting equations are ... 

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