Can We Determine a Protein Structure Quickly?

Abstract

Can we determine a high resolution protein structure quickly, say, in a week? I will show this is possible by the current technologies together with new computational tools discussed in this article. We have three potential paths to explore:• X-ray crystallography. While this method has produced the most protein structures in the PDB (Protein Data Bank), the nasty trial-and-error crystallization step remains to be an inhibitive obstacle.• NMR (Nuclear Magnetic Resonance) spectroscopy. While the NMR experiments are relatively easy to do, the interpretation of the NMR data for structure calculation takes several months on average.• In silico protein structure prediction. Can we actually predict high resolution structures consistently? If the predicted models remain to be labeled as "predicted", and these structures still need to be experimentally verified by the wet lab methods, then this method at best can serve only as a screening tool. I investigate the question of "quick protein structure determination" from a computer scientist point of view and actually answer the more relevant question "what can a computer scientist effectively contribute to this goal".

A Medical Informatics View of Quantum Computation

“…As of December 2008, 47,132 protein structures had been solved by X-ray crystallography, 7,627 by Nuclear Magnetic Resonance (NMR), and none by computation alone. Currently, computed structures of average-to-large molecular weight proteins are not credible unless there is additional wet-structure information (X-ray or NMR) (Li, 2010).…”

Recent Advances in Computational Methods for Nuclear Magnetic Resonance Data Processing

“…, the chemical shift coordinates of the coupling nuclei, in any given spectrum. This is the key step in the entire NMR protein structure determination process because the following steps are all built upon this step [8,9] . The automated peak picking problem was first studied two decades ago [10] .…”