Top view of a triosephosphateisomerase (TIM) barrel (PDB accession code 8TIM), colored from blue (N-terminus) to red (C-terminus).

The TIM barrel is an extremely common protein fold consisting of eight α-helices and eight parallel β-strands that alternate along the peptide backbone. The structure is named after triosephosphateisomerase, the first protein discovered with this topology. Triose-phosphate isomerase (TIM), is an enzyme (EC 5. ... A diagram of the alpha helix structure of amino acids In proteins, the α helix is a major structural motif in secondary structure. ... Diagram of Î’-Pleated sheet and bond structure of protein The β sheet (also β-pleated sheet) is a commonly occurring form of regular secondary structure in proteins, first proposed by Linus Pauling and Robert Corey in 1951. ... In biochemistry, the tertiary structure of a protein is its overall shape. ... Triose-phosphate isomerase (TIM), is an enzyme (EC 5. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ...

Structure and composition

TIM barrels are considered α/β protein folds because they include both helices and sheets in a single domain. The α-helices and β-strands form a solenoid that curves around to close on itself in a doughnut shape, topologically known as a toroid. The parallel β-strands form the inner wall of the doughnut (hence, a β-barrel), whereas the α-helices form the outer wall of the doughnut. A toroid is a doughnut-shaped object whose surface is a torus. ...

Side view of the same TIM barrel (PDB code 8TIM).

It should be emphasized that, although the ribbon diagram shows a hole in the protein's central core, the amino acid side chains are not shown in this representation. The protein's core is actually tightly packed with bulky hydrophobic amino acid residues. The packing interactions between the sheets and helices are also dominated by hydrophobicity and the branched aliphatic residues valine, leucine, and isoleucine comprise about 40% of the total residues in the β-strands^[1]. An amino acid residue is what is left of an amino acid once a molecule of water has been lost (an H+ from the nitrogenous side and an OH- from the carboxylic side) in the formation of a peptide bond. ... The term Side chain can have different meanings depending on the context: In chemistry and biochemistry a side chain is a part of a molecule attached to a core structure. ... In chemistry, hydrophobic or lipophilic species, or hydrophobes, tend to be electrically neutral and nonpolar, and thus prefer other neutral and nonpolar solvents or molecular environments. ... In chemistry, non-aromatic and non-cyclic (acyclic) organic compounds are called aliphatic. ... Valine is one of the 20 natural amino acids, and is coded for in DNA. Nutritionally, valine is also an essential amino acid. ... Leucine is one of the 20 most common amino acids and coded for by DNA. It is isomeric with isoleucine. ... Isoleucine is one of the 20 natural amino acids, and is coded for in DNA. Its chemical composition is identical to that of leucine, but the arrangement of its atoms is slightly different, resulting in different properties. ...

Loop regions

Of the approximately 200 residues required to fully form a TIM barrel, about 160 are considered structurally equivalent between different proteins sharing this fold. The remaining residues are located on the loop regions that link the helices and sheets; the loops at the C-terminal end of the sheets tend to contain the active site, which is one reason this fold is so common: the residues required to maintain the structure and the residues that effect enzymatic catalysis are for the most part distinct subsets. The linking loops can, in fact, be so long that they contain other protein domains. The C-terminal end refers to the extremity of a protein or polypeptide terminated by an amino acid with a free carboxyl group (COOH). ... The active site of an enzyme is the binding site where catalysis occurs. ... Ribbon diagram of the enzyme TIM. TIM is catalytically perfect, meaning its conversion rate is limited, or nearly limited to its substrate diffusion rate. ...

References

1. ↑  Carl Branden and John Tooze. 1999. Introduction to Protein Structure 2nd ed. Garland Publishing: New York, NY. pp 47-50.

See also

• triosephosphateisomerase
• protein folding

Triose-phosphate isomerase (TIM), is an enzyme (EC 5. ... Protein folding is the process by which a protein structure assumes its functional shape or conformation. ...

External links

• SCOP list of proteins adopting the TIM barrel fold

Further reading

• R. K. Wierenga (2001). "The TIM-barrel fold: a versatile framework for efficient enzymes". FEBS Lett. 492 (3): 192–198. DOI:10.1016/S0014-5793(01)02236-0.