Comparative Modeling Tutorial
Part 2 - Intermolecular interactions between the R-HPC and R-HPCDH
Background
In Part 1, you assigned the stereochemical configuration of HPC with a few simple rules. We saw that there were four different chemical groups or moieties bonded to the chiral carbon. Ignoring the hydrogen for now, the three other moieties were a methyl (-CH3), a hydroxyl (-OH) and a sulfonate (-RSO3-) where R=CH2CH3SCH2. In order for the enzyme to oxidize HPC, it must first place residues in a conformation that will bind these different chemical moieties. The methyl group would be expected to bind to a hydrophobic surface that could be provided by alanine (Ala), Methionine (Met), leucine(Leu), isoleucine(Ile), or phenylalanine (Phe). The hydroxyl moiety is polar and could be expected to hydrogen bond with polar and negatively charged residues. The negatively charged sulfonate moiety can be expected to bind to positively charged residues like arginine (Arg) and lysine (Lys) as well as residues that can provide a hydrogen bond. The sulfonate moiety is a bit more complicated since it is attached to a relatively large hydrophobic group. Therefore we will divide this moiety up into the thioethane part and the sulfonate part.
We could imagine how we might engineer an enzyme to bind R-HPC by creating a binding pocket that has residues placed in such an arrangement as to bind the different moieties of HPC. In this step, we will identify these residues.
In the JMol window, one chain of the R-HPCDH structure is displayed in a ribbon representation.
First, complete the following steps to make visualization easier.
Show substrate Zoom in to take a closer look Hide the protein
Next we will turn on the protein sidechains that interact with the substrate molecule. One way to do this is just turn on the residues that are within 5.0 or 7.0 Angstroms of the substrate. Mousing over the residues will show their identity (this part can be a little unresponsive but should ultimately work).
A better way to think about the binding/intermolecular interactions that will help in understanding the structural basis for stereoselectivity in R- and S-HPCDHs is to divide up the interactions by what binds the 3 different moieties attached to the chiral carbon in R-HPC.
These residues bind the substrate through intermolecular interactions. These particular ones can be classified as hydrophobic (water-repelling), electrostatic (opposite charges attract) or hydrogen-bonded (dipole-dipole interactions to be exact).
Sulfonate binding pocket: As mentioned in the Background, residues that bind the sulfonate moiety can be divided up into those that binds the SO3- moeity and the residues that bind the thioethane moiety.
Turn on residues that bind to thioethane moiety and enter their identity in the text fields below. Turn on residues that bind to sulfonate moiety and enter their identity in the text fields below.
Show sulfonate binding residues Hide sulfonate binding residues
Hydroxyl binding pocket:
Turn on residues that bind to hydroxyl moiety and enter their identity in the boxes above.
You will see that in our model, Tyr155 is missing a proton attached to the oxygen atom (the phenolic proton). This residue is postulated to be negatively charged in the enzyme’s active site and thus can act as a proton acceptor in the chemical mechanism that we discuss later. It is often the case that residues critical for catalyzing reactions have shifted pKa's (i.e. their protonation state differs by what it would be in an aqueous environment)
Show hydroxyl binding residues
Hide hydroxyl binding residues
Methyl binding pocket:
Turn on residues that bind to methyl group and enter their identity in the text fields below.
Show methyl binding resiudes
Hide methyl binding resiudes
Fill in the residues you've identified using the form below.
