The internal oligopeptide sequences missing in crystals are isordered domains

Abstract

Prior to their maturation as a biological structure or function, nascent polypeptides fold to form three dimensional structures composed of α helices, β sheets and disordered regions. The amino acid sequence of the processed polypeptide is stored in FASTA format (www.rcsb.org) and it is almost always longer than that in the crystal structure, retrievable in PyMol stored in pdb format, wherein the absence of residues has been noted at the C-terminal, N-terminal and at intra-polypeptide locations of crystals. Indeed, a large number of protein crystals in the data base exhibit internal missing string.1 Crystallographers generally consider that the missing residues are due to low electron density undetectable in low resolution crystallography. Since some of the gaps at the N and C termini can be attributed to posttranslational processing, the presence of missing internal oligopeptides may lead to misinterpretation of the secondary structure domains in the immediate vicinity of the gaps as well as in the flanking segments. While studying the phylogeny of proteins2 we considered the possibility that the extent of evolutionary conservation of residues defining individual secondary structure domains may be one of the determinants. As we came across the cases of internal missing intra-molecular residues here we analyze their structure and significance.