Describing Pathways

Biochemical pathways are representative of the kind of complex data that are generally best handled in an object-oriented manner. They are ideally modeled as object graphs and typical access patterns involve traversals through the graph. In addition, many-to-many relationships are common between participating objects. 

A key issne concerns the treatment of roles a molecular entity can adopt. Rather than performing multiple inheritance from a protein and catalyst class (static multiple inheritance), for example, to derive an enzyme subclass, we instead combine the role object catalysis with the metabolic entity protein through aggregation (dynamic mnltiple inheritance). Thus, the metabolic entity maintains a list of the roles it can assnme along with the context for each role for instance, a protein may assume the role of catalyst for a given instance of a reaction class. In this way, the protein object can adopt differing roles (e.g., catalyst, transporter) in different scenarios. Also, an object can acqnire additional roles easily as they are discovered without having to modify or rebuild its class definition. 

In particular, the benefits of the approach are becoming apparent through its application to regulation of metabolism. The model is extensible to the representation of less well-defined regulatory networks and is flexible enough to handle the problem of incomplete or missing data. 

For example, not all the steps in a cascade leading to the eventual phosphorylation by a protein kinase may be known, but the process as a whole can be treated as an object that is a composite of those individual steps — some or all of which might be unspecified. 

Connectors are a generic form of connectivity information that can be assigned to a pair of structures. Connectors may be shifted the start and end points may be attached to other objects, and open connectors are explicitly allowed for intermediate results. 

---

The systematic work carried out by Fetzner group with enzymatic catalysis resulted in the identification of four pathways of aerobic degradation of quinoline (and its derivatives) [326], shown in Fig. 23. The four pathways are named on the basis of the metabolic intermediates identified in the respective pathways, some steps and reactions have been considered in previously described pathways, but are included here to show the comprehensive nature of this work. 

At present, all availabale data and evidences taken together allow us to postulate the following biosynthetic pathway for the APRs (Figure 2.26) In a first branch 2DOS is formed by the already described pathway elucidated earlier (see Figure 2.10) by use of the conserved gene products of C -, S -, and E -type... 

The word amphibolic is often applied to those metabolic sequences that are part of a catabolic cycle and at the same time are involved in a biosynthetic (anabolic) pathway. Another term, anaplerotic, is sometimes used to describe pathways for the synthesis of regenerating substrates. This word, which was suggested by H. L. Komberg, comes from a Greek root meaning "filling up."80... 

It is well established that oxygen in the presence of platinum (Adams catalyst) can achieve specific oxidation of secondary alcohols by a preferential attack upon hydrogen in an equatorial position (25). Catalytic oxidation of methyl a- and /3-D-galactopyranoside (26), fallowed by catalytic reduction with hydrogen, led to the formation of methyl a- and /3-6-deoxy-D-galactopyranoside (D-fuco-pyranoside) in 15% and 35% yield, respectively. This oxidation-reduction sequence with selective oxidation at carbon 4 as the initial step is structurally closely related to the above described pathway for TDPG-oxidoreductase. 

Figure 7.10 summarizes both described pathways as the proposed reaction mechanism. 

A fundamental question remains whether MMEJ is a distinct mechanism of DNA repair or simply a dEferent manEestation of previously described pathways. Yeast MMEJ is markedly inefficient and largely irrelevant to basal DNA repaE (40, 43),... 

Both xanthylium salts shown in Figure 5 have been detected in wine stored with no care to avoid oxidation, supporting the occurrence of the above described pathways (33, SO, 51), This constitutes an in5)ortant support to the occurrence of the above described pathways, since the xanthylium salts is expected to result from anthocyanin-tannin condensation have never been detected. 

Regarding evidence, it is important to realize that evidence against the D model is not necessarily evidence for the A model. Much of what can be cited as evidence against the D model could be a consequence of pathway X and therefore cannot be construed as evidence against the D model, which describes pathway R. 

Since from the beginning two electrophiles (carbonyl compound and alkyl chloroformate) and two nucleophiles (HMDS and allyltrimethylsilane) are present in the media, the challenge of this reaction is to drive it for the previously described pathway. Side reactions such as allylation of the carbonyl compound and reaction between electrophihc alkyl chloroformate and nucleophilic allyltrimethylsilane were efficiently avoided using the proper Lewis acid as catalyst, being in this case the inexpensive FeSO -TH O. 

In 2007, Jitaru [7] described pathways to methane, ethylene and formic acid on copper electrodes. Thus, the anion radical C02 formed according to Equation 1.6 may undergo a reaction with another CO2 molecule to yield carbon monoxide and a carbonate anion radical, according to Equation 1.15. 

---