Protein quinary structure

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Protein quinary structure refers to the features of protein surfaces that are shaped by evolutionary adaptation to the physiological context of living cells. [1] [2] [3] [4] Quinary structure is thus the fifth level of protein complexity, additional to protein primary, secondary, tertiary and quaternary structures. As opposed to the first four levels of protein structure, which are relevant to isolated proteins in dilute conditions, quinary structure emerges from the crowdedness of the cellular context, [5] in which transient encounters among macromolecules are constantly occurring.

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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. [7] In his work, McConkey runs 2D electrophoresis gels on the total protein content of hamster (CHO) and human (HeLa) cells. In a 2D electrophoresis gel experiment, the coordinates of a protein depend on its molecular weight and its isoelectric point. Given the evolutionary distance between humans and hamsters, and considering evolutionary rates typical of mammals, one would expect a large number of substitutions to have occurred between hamsters and humans, a fraction of which would involve acidic (aspartate and glutamate) and basic (arginine and lysine) residues, resulting in changes in the isoelectric point of many proteins. Strikingly, hamster and human cells yielded almost identical fingerprints in the experiment, implying that many fewer of those substitutions actually took place. McConkey suggested in that paper [7] that the reason why the proteins of humans and hamsters had not diverged as much he anticipated was that an additional selective pressure must have been related to the many non-specific “interactions that are inherently transient” experienced by proteins in the cytoplasm and which “constitute the fifth level of protein organization”.

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. [14] Charged and hydrophobic residues were shown to have the largest impact in protein intracellular mobility. In particular, more negatively charged proteins would tumble faster in comparison with near-null or positively charged proteins. In contrast, the presence of many hydrophobic residues in the protein surface would slow down protein intracellular tumbling. Protein dipole moment, a measure of charge separation across the protein, was shown to have a significant contribution to protein mobility, where high dipole moments would correlate with slower tumbling.

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References

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  2. ↑ Edelstein, S. J. (October 1980). "Patterns in the quinary structures of proteins. Plasticity and inequivalence of individual molecules in helical arrays of sickle cell hemoglobin and tubulin". Biophysical Journal. 32 (1): 347–360. Bibcode:1980BpJ....32..347E. doi:10.1016/S0006-3495(80)84961-7. PMC   1327314 . PMID   7248453.
  3. ↑ "Probing Protein Quinary Interactions by in-cell NMR". ResearchGate. Retrieved 2019-09-02.
  4. ↑ Shekhtman, Alexander; Burz, David S.; DeMott, Christopher; Breindel, Leonard (2018). "Real-Time In-Cell Nuclear Magnetic Resonance: Ribosome-Targeted Antibiotics Modulate Quinary Protein Interactions". Biochemistry. 57 (5). U.S.: United States Department of Agriculture: 540–546. doi:10.1021/acs.biochem.7b00938. PMC   5801172 . PMID   29266932 . Retrieved 2019-09-02.
  5. ↑ Danielsson, J.; Oliveberg, M. (2017). "Comparing protein behaviour in vitro and in vivo, what does the data really tell us?". Current Opinion in Structural Biology. 42: 129–135. doi:10.1016/j.sbi.2017.01.002. PMID   28126529.
  6. ↑ Jacek T. Mika; Bert Poolman (2011). "Macromolecule diffusion and confinement in prokaryotic cells". Current Opinion in Biotechnology. 22 (1): 117–126. doi:10.1016/j.copbio.2010.09.009. PMID   20952181.
  7. 1 2 McConkey, E. H. (1989). "Molecular evolution, intracellular organization, and the quinary structure of proteins". Proceedings of the National Academy of Sciences of the United States of America. 79 (10): 3236–3240. doi: 10.1073/pnas.79.10.3236 . PMC   346390 . PMID   6954476.
  8. ↑ Wlodarski, T.; Zagrovic, B. (2009). "Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin". Proceedings of the National Academy of Sciences of the United States of America. 106 (46): 3236–3240. Bibcode:2009PNAS..10619346W. doi: 10.1073/pnas.0906966106 . PMC   2780739 . PMID   19887638.
  9. ↑ Schreiber, G.; Fersht, A. R. (1996). "Rapid, electrostatically assisted association of proteins". Nature Structural Biology. 3 (5): 427–431. doi:10.1038/nsb0596-427. PMID   8612072. S2CID   25318867.
  10. ↑ Deeds, E. J.; Ashenberg, O.; Shakhnovich, E. I. (2006). "From The Cover: A simple physical model for scaling in protein-protein interaction networks". Proceedings of the National Academy of Sciences of the United States of America. 103 (2): 311–316. arXiv: q-bio/0509001 . Bibcode:2006PNAS..103..311D. doi: 10.1073/pnas.0509715102 . PMC   1326177 . PMID   16384916.
  11. ↑ Jian-Rong Yang; Ben-Yang Liao; Shi-Mei Zhuang; Jianzhi Zhang (2012). "Protein misinteraction avoidance causes highly expressed proteins to evolve slowly". Proceedings of the National Academy of Sciences of the United States of America. 109 (14): E831–E840. doi: 10.1073/pnas.1117408109 . PMC   3325723 . PMID   22416125.
  12. ↑ Wirth, A. J.; Gruebele, M. (2013). "Quinary protein structure and the consequences of crowding in living cells: Leaving the test-tube behind". BioEssays. 35 (11): 984–993. doi:10.1002/bies.201300080. PMID   23943406. S2CID   33478753.
  13. ↑ Peter B. Crowley; Elysian Chow; Tatiana Papkovskaia (2011). "Protein Interactions in the Escherichia coli Cytosol: An Impediment to In-Cell NMR Spectroscopy". ChemBioChem. 12 (7): 1043–1048. doi:10.1002/cbic.201100063. PMID   21448871. S2CID   44250541.
  14. ↑ Xin Mu; Seongil Choi; Lisa Lang; David Mowray; Nikolay V. Dokholyan; Jens Danielsson; Mikael Oliveberg (2017). "Physicochemical code for quinary protein interactions in Escherichia coli". Proceedings of the National Academy of Sciences of the United States of America. 114 (23): E4556–E4563. Bibcode:2017PNAS..114E4556M. doi: 10.1073/pnas.1621227114 . PMC   5468600 . PMID   28536196.
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