Does a backwardly read protein sequence have a unique native state?

Abstract

Amino acid sequences of native proteins are generally not palindromic. Nevertheless, the protein molecule obtained as a result of reading the sequence backwards, i.e. a retro-protein, obviously has the same amino acid composition and the same hydrophobicity profile as the native sequence. The important questions which arise in the context of retro-proteins are: does a retro-protein fold to a well defined native-like structure as natural proteins do and, if the answer is positive, does a retro-protein fold to a structure similar to the native conformation of the original protein? In this work, the fold of retro-protein A, originated from the retro-sequence of the B domain of Staphylococcal protein A, was studied. As a result of lattice model simulations, it is conjectured that the retro-protein A also forms a three-helix bundle structure in solution. It is also predicted that the topology of the retro-protein A three-helix bundle is that of the native protein A, rather than that corresponding to the mirror image of native protein A. Secondary structure elements in the retro-protein do not exactly match their counterparts in the original protein structure; however, the amino acid side chain contract pattern of the hydrophobic core is partly conserved.

MONSSTER: a method for folding globular proteins with a small number of distance restraints

“…In contrast to sec(k,j ), it is defined with respect to the six conformational bins, left and right-handed extend/b states, left and right-handed wide turns, and left and right-handed helices/tight turns. It depends on both r 2* i − 2, i + 1 and r 2* i − 1, i + 2 (see equation (1)) and acts to propagate secondary structural elements (Olszewski et al, 1996a).…”

Differential Transit Peptide Recognition during Preprotein Binding and Translocation into Flowering Plant Plastids

“…This inherent property has attracted considerable interest in using retro-peptides to study various structure function relationships of peptides/proteins, including antimicrobial peptides (Pellegrini and von Fellenberg, 1999) and Leu zippers (Holtzer et al, 2000). They have also been used to examine protein folding (Olszewski et al, 1996;Lacroix et al, 1998) and antibody recognition (Guichard et al, 1994;Benkirane et al, 1995).…”

The retro -GCN4 leucine zipper sequence forms a stable three-dimensional structure

“…Physicochemical properties that are related to the amino acid composition or the hydrophobicity profile should not be affected by the inversion of the sequence, supporting the idea that retro-sequences might fold into a native-like conformation. Modeling experiments suggested that reversal of the backbone direction may result in a topological mirror image of the native structure of the protein (2) or may produce the same topology as that of the parent protein (3,4). Thus far, no structure elucidation of a retro-Lpeptide at atomic resolution has been reported.…”