Predicting the conformations of peptides and proteins in early evolution

Biology Direct

Table 1 The major categories of protein conformations:

Conformation	Conf. type	Native folded	Native unfolded	Native unfolded and denatured.	Early peptides.
α-helix	Reg.rep.	+++			+
β-sheet (as in native proteins)	Reg.rep.	+++			++
PPII (polyproline type II)	Reg rep	++	+++	+	+
nests	Enant	++	++	+	+++
amyloid (multi-layer) β-sheet	Reg.rep.			+++	+++
(multi-layer)α-sheet	Enant.		+	++	+++
metal-peptide	Reg.rep.	+	+	+	++

Notes: The distributions of conformations in folded, unfolded and denatured native proteins are indicated and also their expected distributions in early peptides assuming they consist randomly of L and D amino acids and a high proportion of glycines. Enant. indicates enantiomeric peptides, where main chain atoms of successive amino acids are enantiomers. Reg. rep. indicates conformations where main chain atoms of successive amino acids are the same (the α-helix is right-handed in proteins; PPII is a left-handed helix in proteins; β-sheet has two forms with opposite handedness, one of which predominates in proteins, and, unlike the helices, intermediate or mixed forms are possible). In peptides with random proportions of L and D amino acids the two chiral forms are equally likely. Beta-sheet in native proteins has at most four layers of sheet and less than 300 amino acid residues, while amyloid and α-sheet have multiple layers and typically thousands of residues or more.

ISSN: 1745-6150