I'm curious about how protein structures are defined in general, but in particular, I'm wondering how a target structure can be specified without knowing the amino acid sequence.

For example, in protein design (or from what I gather on the wikipedia page http://en.wikipedia.org/wiki/Protein_designs), scientists design a 3D structure that will perform a particular function. They then try to come up with an amino acid sequence that will fold properly into that structure.

How can a 3D structure be defined if no amino acid sequence (and hence no molecular geometry) has been determined?

  • $\begingroup$ You don't create some structure and then try to find the amino acids that will create it; the residues themselves are important. Generally modelling is based on known motifs. The basic steps are: model in silico, test in vitro, fail, repeat. $\endgroup$ – canadianer Feb 12 '15 at 21:12
  • $\begingroup$ Hmm, how is de novo protein design done? From the article: "In de novo design the entire sequence is designed anew, based on no previous sequence" $\endgroup$ – ZenPylon Feb 12 '15 at 21:25
  • $\begingroup$ Right, the sequence is designed anew. I also said generally. $\endgroup$ – canadianer Feb 12 '15 at 21:27
  • $\begingroup$ I think that's what I was going for in my question - how can a sequence be designed anew? I understand the idea of protein prediction - design an amino acid sequence, try to predict how it folds. But protein design is the reverse. Am I misunderstanding the meaning of "target structure"? $\endgroup$ – ZenPylon Feb 12 '15 at 21:33
  • $\begingroup$ Afaik. they use quantum-mechanical models to calculate the active site and probably the whole enzyme structure. Enzyme designing is a very new topic and you'll need a lot of math to understand it. $\endgroup$ – inf3rno Feb 14 '15 at 1:25

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