3NI3

54-Membered ring macrocyclic beta-sheet peptide

Summary for 3NI3

• Entry DOI: 10.2210/pdb3ni3/pdb
• Descriptor: 54-membered ring macrocyclic beta-sheet peptide, ISOPROPYL ALCOHOL (3 entities in total)
• Functional Keywords: artificial beta sheet dimer, unknown function
• Total number of polymer chains: 12
• Total formula weight: 22377.63

Authors

Sawaya, M.R.,Eisenberg, D.,Nowick, J.S.,Korman, T.P.,Khakshoor, O. (deposition date: 2010-06-15, release date: 2010-09-15, Last modification date: 2023-11-15)

Primary citation

Khakshoor, O.,Lin, A.J.,Korman, T.P.,Sawaya, M.R.,Tsai, S.C.,Eisenberg, D.,Nowick, J.S.
X-ray crystallographic structure of an artificial beta-sheet dimer.
J.Am.Chem.Soc., 132:11622-11628, 2010

PubMed Abstract: This paper describes the X-ray crystallographic structure of a designed cyclic beta-sheet peptide that forms a well-defined hydrogen-bonded dimer that mimics beta-sheet dimers formed by proteins. The 54-membered ring macrocyclic peptide (1a) contains molecular template and turn units that induce beta-sheet structure in a heptapeptide strand that forms the dimerization interface. The X-ray crystallographic structure reveals the structures of the two "Hao" amino acids that help template the beta-sheet structure and the two delta-linked ornithine turn units that link the Hao-containing template to the heptapeptide beta-strand. The Hao amino acids adopt a conformation that resembles a tripeptide in a beta-strand conformation, with one edge of the Hao unit presenting an alternating array of hydrogen-bond donor and acceptor groups in the same pattern as that of a tripeptide beta-strand. The delta-linked ornithines adopt a conformation that resembles a hydrogen-bonded beta-turn, in which the ornithine takes the place of the i+1 and i+2 residues. The dimers formed by macrocyclic beta-sheet 1a resemble the dimers of many proteins, such as defensin HNP-3, the lambda-Cro repressor, interleukin 8, and the ribonuclease H domain of HIV-1 reverse transcriptase. The dimers of 1a self-assemble in the solid state into a barrel-shaped trimer of dimers in which the three dimers are arranged in a triangular fashion. Molecular modeling in which one of the three dimers is removed and the remaining two dimers are aligned face-to-face provides a model of the dimers of dimers of closely related macrocyclic beta-sheet peptides that were observed in solution.

PubMed: 20669960
DOI: 10.1021/ja103438w

Experimental method

X-RAY DIFFRACTION (1.34 Å)