Is “fragment-based” still the way forward in template-free protein structure prediction?

Out of the many questions surrounding the notion that you can predict a protein’s structure from its sequence, there is one in particular that I decided to tackle during last group meeting.

Protein structure prediction is a hard problem (do I sound repetitive?). One of the many cop outs employed by the structure prediction community is the idea that you can break down known structures into fragments and use these protein pieces to perform predictions. This is known as fragment-assembly or fragment-based template-free protein structure prediction.

As absurd as the idea may seem, there is robust evidence that suggests that this is actually a viable strategy. There is a notion that the fragment space is complete; you can reconstruct the backbone of any known structure based on the torsion angles of fragments from other structures. In less technical jargon, you can effectively use fragments and combine them to re-create any of the protein structures that we know and to a fairly acceptable level of precision.

So, technically, it is possible to predict a protein structure using fragments from other structures. In practice, you are still left with the problem of choosing the right fragments to model your sequence of interest. How easy do you think that is?

We can look at this question in light of observations that were made back in the early 80s. Kabsch and Sander reported that two protein fragments having exactly the same sequence can present completely different structures [1]. This complies with the notion that global properties can affect and even define local structure, which in turn suggests that selecting the right fragments to assemble a structure is not necessarily a straightforward process.

The starting point for protein structure prediction is a sequence. Since we are talking about template-free protein structure prediction, it is safe to assume that there is no good global sequence match to your target with a known structure (otherwise you would use that match/structure as a template). Hence, fragment selection is restricted to local sequence similarity, which, as suggested in the previous paragraph, is not necessarily ideal.

On the other hand, we are becoming increasingly more accurate in inferring one-dimensional properties from a protein’s sequence. These properties can and often are used to enhance our fragment-selection capabilities. Yet, even using the state-of-the-art in secondary structure and torsion angle prediction, fragment selection is still fairly imprecise.

During group meeting I highlighted a possible contrast between practical fragment space and general (or possible) fragment space. My premise is simple.  I define practical fragment space as the fragments that we can accurately select from the possible fragment space to model protein structures. In my opinion, it would be extremely interesting to quantify the difference between the two. This would answer the fundamental question of how useful fragment-assembly actually is. More importantly, it would help the community make an educated decision in regards to whether template-free structure prediction strategies should shift from fragment-based to ones based on distance constraints, an approach that is gaining popularity due to the success of contact predictions.

I am very keen to investigate this further. Maybe for my next blog post, we will have an answer! Stay tuned.

[1] Kabsch, Wolfgang, and Christian Sander. “On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations.” Proceedings of the National Academy of Sciences  81.4 (1984): 1075­1078.