Protein quinary structure
Protein quinary structure refers to the features of
In order to perform their functions, proteins often need to find a specific counterpart to which they will bind in a relatively long encounter. In a very crowded cytosol, in which proteins engage in a vast and complex network of attracting and repelling interactions, such search becomes challenging, because it involves sampling a huge space of possible partners, of which very few will be productive. A solution to this challenge requires that proteins spend as little time as possible on each encounter, so that they can explore a larger number of surfaces, while simultaneously making this interaction as intimate as possible, so if they do come across the right partner, they will not miss it.[6] In this sense, quinary structure is the result of a series of adaptations present in protein surfaces, which allow proteins to navigate the complexity of the cellular environment.
Early observations
With the sense with which it is used today, the term quinary structure first appeared in the work of McConkey, in 1989.
Protein interactions and quinary structure
Despite the crudeness of McConkey's experiment, his interpretation of the results have proved to be accurate. Rather than simply being hydrophilic, protein surfaces must have carefully been modulated by evolution and adapted to this network of weak interactions, often called quinary interactions. It is important to note that protein-protein interactions responsible for the emergence of quinary structure are fundamentally different from specific protein encounters. The latter are the result of relatively high-stability binding, often linked to functionally meaningful events –many of which have already been described [8]– while the former are often interpreted as some background noise of physiologically unproductive misinteractions that complicate the interpretation of protein networks and need to be avoided, so that normal cellular functions can proceed.[9][10][11]
The transient nature of these protein encounters complicates the study of quinary structure. Indeed, the interactions responsible for this upper level of protein organisation are weak and short-lived, and hence would not produce protein-protein complexes that could be isolated by conventional biochemical methods. Therefore, quinary structure can only be understood in vivo.[12]
In-cell NMR and quinary structure
In-cell NMR is an experimental technique prominent in the research field of protein quinary structure. The physical principle of in-cell NMR measurements is identical to that of conventional protein NMR, but the experiments rely on expressing high concentrations of the probe protein, which should remain soluble and contained in the cellular space; which introduces additional difficulties and limitations. However, these experiments provide critical insights about the cross-talk between a probe protein and the intracellular environment.
Early attempts at using in-cell NMR to study protein quinary structure were hindered by a limitation caused by the very phenomenon they were trying to understand. Many probe proteins tested in these experiments turned out to produce broad signals, near the detection limit of the method, when measured inside cells of Escherichia coli. In particular, these proteins seemed to tumble as if they had molecular weights much larger than those corresponding to their size. These observations seemed to indicate that the proteins were sticking to other macromolecules, which would have led to poor relaxation properties [13]
Other in-cell NMR experiments showed that single amino acid changes of surface residues could be used to consistently modulate the tumbling of three different proteins inside bacterial cells.
References
- PMID 27676610.
- PMID 7248453.
- ^ "Probing Protein Quinary Interactions by in-cell NMR". ResearchGate. Retrieved 2019-09-02.
- PMID 29266932. Retrieved 2019-09-02.
- PMID 28126529.
- PMID 20952181.
- ^ PMID 6954476.
- PMID 19887638.
- S2CID 25318867.
- PMID 16384916.
- PMID 22416125.
- S2CID 33478753.
- S2CID 44250541.
- PMID 28536196.