Structure of a cyclic peptide with a catalytic triad, determined by computer simulation and NMR spectroscopy

Björn Walse, Magnus Ullner, Christer Lindbladh, Leif Bülow, Torbjörn Drakenberg, Olle Teleman

Research output: Contribution to journalArticleScientificpeer-review

6 Citations (Scopus)

Abstract

We report the design of a cyclic, eight-residue peptide that possesses the catalytic triad residues of the serine proteases. A manually built model has been relaxed by 0.3 ns of molecular dynamics simulation at room temperature, during which no major changes occurred in the peptide. The molecule has been synthesised and purified. Two-dimensional NMR spectroscopy provided 35 distance and 7 torsion angle constraints, which were used to determine the three-dimensional structure. The experimental conformation agrees with the predicted one at the β-turn, but deviates in the arrangement of the disulphide bridge that closes the backbone to a ring. A 1.2 ns simulation at 600 K provided extended sampling of conformation space. The disulphide bridge reoriented into the experimental arrangement, producing a minimum backbone rmsd from the experimental conformation of 0.8 Å. At a later stage in the simulation, a transition at Ser3 produced more pronounced high-temperature behaviour. The peptide hydrolyses p-nitrophenyl acetate about nine times faster than free histidine.
Original languageEnglish
Pages (from-to)11-22
JournalJournal of Computer-Aided Molecular Design
Volume10
Issue number1
DOIs
Publication statusPublished - 1996
MoE publication typeA1 Journal article-refereed

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