FAQs
Here you can find explanatory answers to questions concerning the project. If you still find some objection, please feel free to contact.
Is the Mosaic Q simply a consequence of the hydrophobic core?
This is the most common objection to the project. The answer is NO, and for different reasons. First, analysis show that the value Q is determined by the number of amino acids (n) in the structure. That is, any two proteins, or actually any set of two or more proteins with the same number of amino acids will have a similar value of Q. It does not matter whether the proteins in question are globular (bigger hydrophobic core) or elongated (smaller hydrophobic core), as long as they have the same number of amino acids, the value Q will be similar. Second, it has been demonstrated that deviation from the empirical law is not correlated to protein compactness nor protein surface area (see the project at Github), reinforcing the idea that the value Q is not a direct consequence of the hydrophobic core. Third, multiple visualizations show that, apart from the hydrophobic core (where most hydrophobic amino acids reside) the rest of amino acids (polar, acidic, basic, special) group together according to their type in clusters of similar size and shape, this is what the Mosaic Q model consist of.
Are the observed clusters of non-hydrophobic amino acids a consequence of the existence of the hydrophobic core? In other words, if hydrophobic residues group together, it's logical that the remaining residues group together, right?
This is another common objection. The important point here is that, there is not one, but actually several types of non-hydrophobic amino acids (namely polar, acidic, basic and special). And there are clusters for each one of those non-hydrophobic types. Besides, some of these types (acidic and basic) are charged types, so energetically one would expect that amino acids of these types would not group together in clusters, but apparently they do, as analysis and multiple visualizations demonstrate.
OK, but maybe the existence of clusters is a consequence of the organization of amino acids into different elements of secondary structure (beta-sheets, alpha helices, etc), isn't it?
We must remember that the Mosaic Q pattern is a pattern in the 3D space, meaning that any two elements of secondary structure distant in the polypeptidic chain maybe together in the tertiary structure, or vice versa, but in all or at least most cases the mosaic appears in the 3D structure. Also, multiple structures are composed of different subunits (multimeric proteins) and still the mosaic is present in those cases too.
Does the Mosaic Q pattern appear in ALL proteins?
The project suggests a very strong signal of a recurring pattern in protein structure. But of course, the experimental law is not perfect. Also, the deviations from the mosaic pattern maybe related to the biological properties of the protein in question. Particulary, it is clear that the mosaic pattern must affect interactions of proteins with other proteins and biomolecules, which gives an opportunity for the scientific community to explore applications in biomedicine. That's why we want to raise attention to this property.
Given the definition of Q (or Q_alt), isn't it already expected a growing relation between Q and the number of amino acids (n)?
Yes, but it is not expected that the relation follows such a precise equation. Also, why that specific shape of the relation (curve) and no other? In fact, the stochastic simulations show that actually the shape of the curve depends on the nature of the clusters in the mosaic. In other words, the analysis demonstrate that only one mosaic configuration seems to appear in nature.
The stochastic simulations could be more realistic.
Yes, that's true, and we encourage the community to generate more sophisticated simulations and models to comprenhend better the mosaic. The hydrophobic core + 8-residue Shape I configuration for polar, acidic, basic and special residues is just an approximation to the mosaic. But again, the big point is that the results demonstrate that the experimental law can only be explained by a specific morphology and size of the clusters, which we call the Mosaic Q pattern.
Hmm still, give me more arguments in favor of this apparent pattern.
Well, you don't have to believe anything. We invite newcomers to check the presence of the mosaic on proteins chosen by themselves. In the Participate section you can see how to visualize the pattern in Jmol with specific commands (analogous results are rendered with other visualization tools). Also, the source code of the project is available online for anyone to check and examine. Even more, if you become enthusiastic with the project you can contribute by sharing your own example of rendered image evidence to the collaborative project repository, or even better, developing research in this field. Check out also the Community page, which contains different platforms and tools in which the project has been already accepted or listed.