Prochiral relationship quotes

Carbon-fate maps for metabolic reactions | Bioinformatics | Oxford Academic

quotes have been tagged as relationships: Jess C. Scott: 'When someone loves you, the way they talk about you is different. You feel safe and comfor. Thus, when prochiral carbon atoms are present in a metabolite, we need to . where sA and sB are quote-delimited InChI™ strings for metabolites A and B, c ∈ {c .. In silico atomic tracing by substrate-product relationships in Escherichia coli . synthesis, biological activities and functions, symbiotic relationships, medical applications thesis, biosynthesis, and bioactivities (chiral recognition in vivo) of natural prod- ucts that appear in In this context we quote from the abstract of.

We also eliminated a reaction if structural information i. C or C in R or if the reaction was annotated as missing information e. We ultimately assigned carbon-fate maps for reactions.

Relationships Quotes ( quotes)

Thus, the carbon atoms in a metabolite are referenced by integer indices 1 to n, where n is the number of carbon atoms.

This software tool implements graph comparison methods to identify the maximum common substructures of two chemical compounds. With this tool, we identified the common substructures of all possible substrate-product pairs for each reaction of interest.

Because enzymes are chiral catalysts, prochiral atoms, even though they are constitutionally equivalent, can be selectively transformed in enzyme-catalyzed reactions Eliel, An example is conversion of citrate to isocitrate. For this reaction, a partial mapping of carbon atoms from citrate to isocitrate is shown in Figure 1 between panels 1C and D. Thus, when prochiral carbon atoms are present in a metabolite, we need to identify which of these atoms are reactive to define a correct mapping of atom fates.

To determine if constitutionally equivalent carbon atoms are homotopic or prochiral, we use substitution and addition criteria Eliel, The structures of the different isotopomers are identical if the substituted atoms are homotopic, whereas they are different e.

This structural information, which is required to determine the relative positions of prochiral carbon atoms, is considered in the manual specification of fate maps see below. View large Download slide Chemical structures of metabolites with homotopic and prochiral pairs of carbon atoms. A 2D structure of succinate, which contains homotopic carbon atoms 1 and 2; 3 and 4.

B 2D structure of citrate, which contains prochiral carbon atoms 1 and 2; 3 and 4. C 3D structure of citrate, in which the relative positions of the prochiral carbon atoms can be seen.

D 2D structure of isocitrate. In the enzymatic conversion of citrate to isocitrate, atoms 2 and 6 of citrate map to atoms 4 and 2 of isocitrate, respectively, as indicated by the lines connecting the corresponding atoms.

Prochirality

Atom 1 in citrate is constitutionally equivalent to atom 2 but is not reactive because of its distinct local environment. Maps were refined manually through text editing at the level of BNGL as needed. Information about reaction mechanisms was obtained primarily from textbooks Berg et al.

The primary literature was consulted as needed. In this language, in general, text-encoded graphs are used to represent structured objects and graph-rewriting rules, which are called reaction rules, are used to represent biochemical transformations of objects.

In BNGL, an object has a name and a collection of named component parts, each of which can be associated with a set of attributes. Identifiers are delimited by quotation marks. As usual in BNGL, component names are placed immediately after a metabolite object name and enclosed in parentheses. In the database, to identify reaction centers without using color, we use lower case letters to represent carbon atoms inside reaction centers, and we use upper case letters to represent carbon atoms outside reaction centers.

Use of component attributes is not needed to define carbon-fate maps; however, attribute labels, which are prefixed by tilde characters, can be added as needed for a specific application to indicate mass numbers, which is important for distinguishing between 12C and 13C. In BNGL, a reaction rule represents a generalized reaction that permits multiple reactants e.

It is comprised of lists of text-encoded sub graphs, each representing a collection of objects e. In the rules considered here, each subgraph is identical to a graph for a metabolite up to attribute labels for mass numbers. Note that if, in a 'thought experiment', we were to change either one of the prochiral hydrogens on a prochiral carbon center to a deuterium the 2H isotope of hydrogenthe carbon would now have four different substituents and thus would be a chiral center.

Consider the isomerization reaction below, which is part of the biosynthesis of isoprenoid compounds. We do not need to understand the reaction itself it will be covered in chapter 14 ; all we need to recognize at this point is that the isomerase enzyme is able to distinguish between the prochiral 'red' and the 'blue' hydrogens on the isopentenyl diphosphate IPP substrate. For the sake of clarity, we'll look at a very simple molecule, ethanol, to explain this system.

To name the 'red' and 'blue' prochiral hydrogens on ethanol, we need to engage in a thought experiment. If we, in our imagination, were to arbitrarily change red H to a deuterium, the molecule would now be chiral and the chiral carbon would have the R configuration D has a higher priority than H. For this reason, we can refer to the red H as the pro-R hydrogen of ethanol, and label it HR. Conversely, if we change the blue H to D and leave red H as a hydrogen, the configuration of the molecule would be S, so we can refer to blue H as the pro-S hydrogen of ethanol, and label it HS.

Looking back at our isoprenoid biosynthesis example, we see that it is specifically the pro-R hydrogen that the isopentenyl diphosphate substrate loses in the reaction.

Determining Re and Si Faces of a Prochiral Molecule 005

Prochiral hydrogens can be designated either enantiotopic or diastereotopic. If either HR or HS on ethanol were replaced by a deuterium, the two resulting isomers would be enantiomers because there are no other stereocenters anywhere on the molecule. Thus, these two hydrogens are referred to as enantiotopic.

R -GAP already has one chiral center. If either of the prochiral hydrogens HR or HS is replaced by a deuterium, a second chiral center is created, and the two resulting molecules will be diastereomers one is S,R, one is R,R. Thus, in this molecule, HR and HS are referred to as diastereotopic hydrogens.

Relationships Quotes

Finally, hydrogens that can be designated neither enantiotopic nor diastereotopic are called homotopic. If a homotopic hydrogen is replaced by deuterium, a chiral center is not created. The three hydrogen atoms on the methyl CH3 group of ethanol and on any methyl group are homotopic. An enzyme cannot distinguish among homotopic hydrogens.

When appropriate, label prochiral hydrogens as HR or HS.