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Updated: Aug 18, 2026

From Constructs to Crystals – Towards Structure Determination of β-barrel Outer Membrane Proteins
Published on: July 4, 2016
Closed loops of TIM barrel protein fold
Zakhar M Frenkel1, Edward N Trifonov
1Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel. zfrenkel@yahoo.com
Abstract:
The closed loops within the proteins of the TIM-barrel fold family are analyzed and compared sequence- and structure-wise. The size distribution of the closed loops of the TIM-barrels confirms universal preference to the standard size of 25-30 residues. 3D structural RMSD comparisons of the closed loops and presentation of their sequences in binary form suggest that the TIM-barrel proteins are built from descendants of several types of basic closed loop prototypes. Comparison of these prototypes points to a likely common ancestor--the alpha helix containing closed loops of 28 amino acids. The presumed ancestor is characterized by specific binary consensus sequence.
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