Protein Dynamics Quiz | Biology

Quiz Answer Key and Fun Facts

1. In the beginning, it was believed that proteins were rigid entities which bound substrates that fitted perfectly into their binding pockets. This idea of shape complementarity is called the Lock and Key Hypothesis. Which person is credited with developing this theory?

Answer: Emil Fischer

Prior to a good understanding of protein dynamics, the function of proteins was thought to be entirely (if not primarily) based on shape complementarity. The best example to illustrate this point is the enzymes. These proteins specifically bind to substrate and catalyse reactions that would be many orders of magnitude slower without the enzyme.

The Lock and Key Hypothesis took something we knew (that protein shape was important to function) and stated that this explained enzyme efficiency.

2. Weaknesses in the Lock and Key Hypothesis began to emerge as more work was done. For example, it fails to explain the ability of molecules to bind to proteins and influence the protein's ability to bind other substrates. What name is given to this phenomenon?

Answer: Allosteric regulation

Allosteric literally means "different shape". It soon emerged that proteins were not rigid entities, but could change their shape. For example, some proteins can bind small regulator molecules which either increase or decrease the ability of the protein to bind to its target substrate.

This offers a level of regulation in the cell. For example, a small molecule which decreases a protein's binding ability may be produced when the protein is overactive, and so prevents unnecessary expenditure of energy and/or the build-up of potentially toxic compounds.

3. Improved understanding of protein mechanisms showed that proteins are not rigid, and that large domain movements can be seen in some proteins. One example is a protein known to be activated by calcium. Upon binding calcium ions, this 148 amino acid protein undergoes a large conformational change to reveal two hydrophobic protein binding sites. Which protein is this?

Answer: Calmodulin

Calmodulin can be seen as a stalk with a lobe at either end. Calcium binding causes the lobes to move, revealing hydrophobic patches that bind to target proteins. Calmodulin influences the activity of several proteins in the cell, and this is believed to be facilitated by the flexibility of the stalk. Calmodulin activates many kinases and phosphatases, as well as activating the SERCA pump, which decreases the amount of calcium in the cell and is thus an example of negative feedback.

4. Koshland's Induced Fit Hypothesis came to replace the Lock and Key Hypothesis as the favoured theory of protein binding. Which of the following best describes the Induced Fit Hypothesis?

Answer: Substrate binding causes a conformational change in the protein, allowing it to adopt its active form

Enzymes often require binding of a separate entity before it can begin to catalyse biochemical reactions. The binding energy released upon the formation of this interaction is used to change the conformation of the protein, changing it from an inactive state to an active state.

5. As analytical methods became more advanced, it became clear that proteins were more dynamic than anyone had first thought. These protein motions occur over a wide range of timescales. Which of the following protein motions is incorrectly matched with the timescale over which it usually occurs?

Answer: Protein folding - picoseconds

Nuclear Magnetic Resonance (NMR) demonstrated that proteins in solution are heterogeneous (i.e. they exist as several structural forms). Importantly, protein dynamics occur at several levels, and at a range of time that spans several orders of magnitude. Dynamics can be speedy bond rotations, as well as slower and more cumbersome movements of whole domains. Protein folding tends to occur anywhere from the order of milliseconds to hours.

6. Dynamics are essential to protein function, and it is therefore important to ensure that proteins are not too stable. To do this, proteins have to finely balance which two thermodynamic quantities?

Answer: Enthalpy and Entropy

To remain in their native, folded state, proteins must have a negative value for their Gibb's free energy (G). This is achieved by reducing enthalpy (H) and/or increasing entropy (S). This is demonstrated in the equation G = H - (T x S) (where T = temperature).

However, if the protein is too stable, it is less dynamic and will be less able to carry out its function. The stabilising interactions (such as ionic bonds and hydrogen bonds) are therefore finely tuned to give a compromise between protein stability and protein dynamics.

7. The most dynamic areas of proteins are usually those involved in binding other components. Upon binding, however, the binding region becomes less dynamic. Which of these is least likely to contribute to the stability of the protein-substrate interaction?

Answer: Entropy decreases massively

If entropy were to decrease massively the interaction would not be energetically favourable. However, as stated in the question, there is a local decrease in entropy upon substrate binding, as protein dynamics at this site are reduced. Proteins often redistribute their dynamics upon substrate binding, and therefore compensate for this local decrease in entropy by making other areas of the protein more entropic. Shape complementarity and non-covalent interactions both stabilise the interaction between the protein and the substrate.

The statement that binding sites tend to be the most dynamic can be verified by limited proteolysis, which preferably cleaves dynamic regions.

8. In opposition to the Induced Fit hypothesis, some believe that the active conformation already exists in solution, and that substrate molecules merely select this conformation. Upon binding, there is a shift in the equilibrium of the protein dynamics to favour this active conformation. What is this rival theory of protein binding known as?

Answer: The Conformation Selection Model

While the Induced Fit Hypothesis says that substrate binding activates the protein, the Conformation Selection Model says that the active state of the protein pre-exists. This latter theory states that proteins are in thermal equilibrium, and that upon substrate binding to the active state of the protein, there will be an equilibrium shift for other proteins towards this active conformation, thus allowing them to bind the substrate also.

9. If it is true that active protein conformations can exist in solution in the absence of other molecules, it should be possible to observe these active conformations in a solution of just the protein. Does this happen?

Answer: Sometimes

If the Conformation Selection Model is true, then active proteins should be present regardless of whether or not allosteric regulators are present. NtrC, a bacterial enzyme involved in the regulation of nitrogen levels, has been shown to exist in its phosphorylated conformation (its active form) even when not phosphorylated. Conversely, SpeB (a protease) does not seem to be capable of adopting its active conformation spontaneously, but instead requires the binding of regulatory molecules first, as is consistent with the Induced Fit Hypothesis.

10. Considering examples such as immunoglobulin E, dihydrofolate reductase, and even haemoglobin, protein binding can often be seen as a combination of there being pre-existing active conformers, while still obeying the Induced Fit Hypothesis.

Answer: True

Much remains unclear in concern to protein dynamics. As we saw in the interesting information for question 9, NtrC appears to support the Conformation Selection Model, whereas SpeB seems to disprove it. It seems likely therefore, that this model is a valid one, but one that is not universal.

Interestingly, there are several examples which unify the Induced Fit Hypothesis and the Conformation Selection Model. For example, dihydrofolate reductase exists in thermal equilibrium in a number of states, one of which is most capable of binding to a particular factor. Once this factor binds, there is a shift in equilibrium (consistent with the Conformation Selection Model) and a conformational change to a new set of conformations (consistent with the Induced Fit Hypothesis).

This new set of conformations is also in thermal equilibrium and, again, one of these conformations is more capable than the others of binding the next required factor.

Source: Author doublemm

This quiz was reviewed by FunTrivia editor WesleyCrusher before going online.
Any errors found in FunTrivia content are routinely corrected through our feedback system.

Protein Dynamics Trivia Quiz

This quiz provides an overview of how our knowledge of protein dynamics has improved over the years and how this has helped us understand protein interactions and behaviour.

NEXT>

NEXT>

NEXT>

NEXT>

NEXT>

NEXT>

NEXT>

NEXT>

NEXT>