Working with Enzymes: Part I -The Simple Kinetic Spectrophotometric Assay

About Christopher Dieni
Chris is an alumnus of Concordia University in Montreal, Quebec, Canada, where he completed his undergraduate degree and researched peroxisome biogenesis mutations in yeast. He has a Ph.D. in Chemistry from Carleton University in Ottawa, Ontario, Canada, where he studied the comparative biochemistry and physiology of frogs that could freeze solid and thaw back to life, as naturally as we go to sleep and wake up. Chris then moved to a postdoc at Penn State, studying the regulation of protein complexes in cancer biochemistry. He is currently back in Montreal, working in the biotech industry of probiotics. His interests lie in metabolic adaptation to stress, with a focus on enzymology, reversible protein phosphorylation and signal transduction.

At the end of my last article, I began providing some of the tips and tricks of practical work with enzymes at the bench. Now we’ll start to cover one of the cornerstone techniques of enzymology work: the enzyme assay.

Starting with the simple and eventually working our way to the more complex, this article introduces the principles of assaying enzymes spectrophotometrically. It relies on a friendly and relatively well-known piece of lab equipment used by biologists and chemists – the UV-Visible spectrophotometer (let’s just use the short-form “spec” for simplicity).

Assay principle

A spec assay works by following a reaction as it progresses from substrates to products. For this to be meaningful there must be a shift in the absorbance spectrum (or a spectral shift) of the biochemicals present indicating that a change has taken place. By setting the spec to monitor a certain wavelength range, you can track the progress of the reaction by the disappearance of substrates or the appearance of products. Monitoring a reaction in real-time is a kinetic assay. An end-point assay is when you run the reaction for a pre-determined length of time but then treat the sample in some way before returning to the spec experiment.

As an example, I’m going to use something I studied from back in my own graduate days – glucose-6-phosphate dehydrogenase. In this G6PDH reaction, glucose-6-phosphate (G6P) and oxidized nicotinamide adenine dinucleotide phosphate (NADP+) react to form 6-phosphoglucono-?-lactone (6PG?L) and reduced nicotinamide adenine dinucleotide phosphate (NADPH). NADP+ absorbs negligibly at a wavelength of 340 nm, whereas NADPH absorbs strongly at this same wavelength (see diagram 1).

Diagram 1: The reaction: G6P + NADP+? 6PG?L + NADPH
Tracking the appearance of NADPH at 340 nm

Assay components

For a simple spec enzyme assay, certain components need to be present:

• Chromophore/chromogenic substrate: The substrate, which is the chromophore, or will become the chromophore after reacting. In my G6PDH study, the chromogenic substrate was NADP+, which reacted to form NADPH, the chromophore.
• Other substrate(s): If they are part of the reaction, other substrates need to be there; otherwise, the biochemical reaction simply will not take place. With G6PDH, this was G6P; NADP+ would not have reacted to form NADPH had G6P not been present.
• Cofactors, activators, ions: Ions or compounds which are not directly used up within the reaction, but without which the reaction will not proceed at an appreciable rate. Some Mg2+ needed to be added to my G6PDH reaction in the form of MgCl2.
• Your enzyme of interest: Either derived from animal tissue, plant extract, cell lysates, or any other source; crude and full of contaminant proteins, partially purified, or purified to >98% homogeneity. Whatever the case, you will need to find the best method for obtaining your enzyme of interest, and what level of purity you need to work with.
• Buffer: For consistency, you will want a final assay volume made of a pH-specific buffer, so that 1) there is enough “room” (volume) for all the assay components to be added at the highest expected concentrations of each, and 2) your enzyme is kept at the optimum pH and ionic strength for the reaction you are monitoring. For my G6PDH assay, this was always a 200 µL final volume in a 96-well microplate.

Notice that I have not even attempted to suggest any concentrations of substrates or other assay components, or the assay pH. This is all part of your individual optimization process. Looking through the literature at previous studies involving your enzyme will give you a starting point, but from there it is a process of scientific trial and error – or optimization, as it is commonly referred to – to determine what conditions work best for you.

Temperature

Just as it is up to you to optimize your substrate concentrations, so too is it necessary for other aspects of your assay, such as temperature. Last time, I indicated the importance of keeping your enzyme on ice until you were ready to assay it. You probably won’t run your assay at ice-cold temperature unless such a temperature has physiological relevance for your organism (as was the case with my freeze-tolerant frogs). In most cases, higher temperatures are desirable. “Room temperature” may suffice, but if your lab is in a building where this fluctuates wildly due to a poor HVAC system, then even a precisely duplicated enzyme assay can have strikingly different activities due to that temperature variation. Thankfully, this is the 21st century, and almost all kinetic assays are performed on temperature-controlled specs, such that you can set to 25 °C, 30 °C, 37 °C, or whatever your temperature of interest may be. However, in order to get consistent results, remember to equilibrate the bulk of the reaction volume to the reaction temperature (usually in the spec) before the last, critical component is added to start the reaction.

Another word on assay temperature: your temperature of interest may or may not be the same at which your host organism normally lives. For a human enzyme, the automatic assumption may be 37 °C, but bear in mind that the dynamics of an enzyme in vitro are far different than they are in a living cell at physiological conditions. Yes – at some point you may want, or need, to assay your enzyme at your organism’s living temperature for the purposes of physiological relevance, but that may not be your primary goal.

Starting the assay and assessing how much enzyme you need

The vessel in which the enzymatic reaction is mixed and monitored could be anything from the small well of a transparent 96-well microplate, to a 1 mL or 2 mL cuvette, depending on the equipment at your disposal. In this vessel, mix all the components except for one – the enzyme (or one of the substrates critical to the reaction). This will depend on any specialized kinetic measurements you might be interested in. But realize that upon addition of that final component, your enzyme reaction begins immediately! As such, you need to have a measure of speed and dexterity.

Whether you are using modern software or an old-fashioned chart recorder, begin recording immediately after you have mixed your vessel and placed it back into the spec. At this point, you will also need to learn another important lesson: the concentration of your enzyme matters! Here’s why…

The more enzymes you have, the more binding sites of the enzyme are available to bind substrates. The more substrates that can be bound at any given time, the greater the turnover of your substrate into product. And so, high enzyme levels = high reaction rate.

The fewer enzymes you have, the less binding sites of those enzymes are available to bind substrates. Even if you cram all the substrate possible into your reaction vessel, less substrate can be bound at any given time because the few enzyme binding sites present will already be occupied by high levels of substrate. Less capacity to bind substrate leads to lower turnover of your substrate into product. And so, low enzyme levels = low reaction rate.

Overall, you want an enzyme assay where your reaction can be measured in an appreciable amount of time. If it progresses so quickly that it is over by the time you mix your reaction vessel and begin recording, this is of no use to you. If it progresses so slowly that it takes longer than a few minutes, this is also of no use to you- not to mention incredibly impractical (see diagram 2).

  Diagram 2

Beyond the running of the assay

What we have covered here are the most basic principles of making a simple spec enzyme assay work for you. Now that you have an assay up and running, how will you use it?

• Will you examine the basic kinetic parameters of your enzyme? How it binds its substrates and what affinity it has for them? What is the maximal rate of catalysis, (Vmax)?
• Will you vary your assay pH or temperature and determine the effect on your enzyme? The presence of increasing concentrations of ions and ionic strength? The effect of suspected activators and inhibitors?
• Will you throw denaturants like urea and guanidinium chloride at your enzyme and see how well (or poorly) its activity holds up against them?

Those decisions are up to you…

Next time

It is very easy when your enzyme assay involves a reaction with a measureable spectral shift (G6PDH and NADPH). But what happens when your reaction of interest does not cause a spectral shift? In that case, the formation of a product must then be coupled to a secondary reaction (or more) which will produce the desired spectral shift. More to come!

Reference (my G6PDH study)
Dieni, C.A. and Storey, K.B. 2010. Regulation of glucose-6-phosphate dehydrogenase by reversible phosphorylation in liver of a freeze-tolerant frog. J. Comp. Physiol. B 180: 1133-1142.

Speak Your Mind

Protein Analysis, Detection & Assay