Evaluation of ?-Amino Acid Replacements in Protein Loops: Effects on Conformational Stability and Structure.

ABSTRACT: ?-Amino acids have a backbone that is expanded by one carbon atom relative to ?-amino acids, and ? residues have been investigated as subunits in protein-like molecules that adopt discrete and predictable conformations. Two classes of ? residue have been widely explored in the context of generating ?-helix-like conformations: ?3 -amino acids, which are homologous to ?-amino acids and bear a side chain on the backbone carbon adjacent to nitrogen, and residues constrained by a five-membered ring, such the one derived from trans-2-aminocyclopentanecarboxylic acid (ACPC). Substitution of ? residues with their ?3 ?homologues within an ?-helix-forming sequence generally causes a decrease in conformational stability. Use of a ring-constrained ? residue, however, can offset the destabilizing effect of ??? substitution. Here we extend the study of ??? substitutions, involving both ?3 and ACPC residues, to short loops within a small tertiary motif. We start from previously reported variants of the Pin1 WW domain that contain a two-, three-, or four-residue ?-hairpin loop, and we evaluate ??? replacements at each loop position for each variant. By referral to the ?,? angles of the native structure, one can choose a stereochemically appropriate ACPC residue. Use of such logically chosen ACPC residues enhances conformational stability in several cases. Crystal structures of three ?-containing Pin1 WW domain variants show that a native-like tertiary structure is maintained in each case.

SUBMITTER: Mortenson DE 

PROVIDER: S-EPMC5944345 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature