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Helix bundle
From Wikipedia, the free encyclopedia
A helix bundle is a small protein fold composed of three or four alpha helices and held together by nonlocal hydrophobic interactions.
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Three-helix bundles are among the smallest and fastest known cooperatively folding structural domains.[1] The three-helix bundle in the villin headpiece domain is only 36 amino acids long and is a common subject of study in molecular dynamics simulations because its microsecond-scale folding time is within the timescales accessible to simulation. Although a famous early simulation[2] approached but did not converge to the native state, more extensive sampling using distributed computing methods has been used to observe successful folding events.[3] The 40-residue HIV accessory protein has a very similar fold and has also been the subject of extensive study.[4] There is no general sequence motif associated with three-helix bundles, so they cannot necessarily be predicted from sequence alone. Three-helix bundles often occur in actin-binding proteins and in DNA-binding proteins.
Four-helix bundles typically consist of four helices packed in a coiled-coil arrangement with a sterically close-packed hydrophobic core in the center. Pairs of adjacent helices are often additionally stabilized by salt bridges between charged amino acids. The helix axes typically are oriented about 20 degrees from their neighboring helices, a much shallower incline than in the larger helical structure of the globin fold.[5]
The specific topology of the helices is dependent on the protein - helices that are adjacent in sequence are often antiparallel, although it is also possible to arrange antiparallel links between two pairs of parallel helices. Because dimeric coiled-coils are themselves relatively stable, four-helix bundles can be dimers of coiled-coil pairs, as in the Rop protein. Other examples of four-helix bundles include cytochrome, ferritin, human growth hormone, and cytokines.[5] Although sequence is not conserved among four-helix bundles, sequence patterns tend to mirror those of coiled-coil structures in which every fourth and seventh residue is hydrophobic.
- ^ Wickstrom L, Okur A, Song K, Hornak V, Raleigh DP, Simmerling CL. (2006). The unfolded state of the villin headpiece helical subdomain: computational studies of the role of locally stabilized structure. J Mol Biol 60(5):1094-107. PMID 16797585
- ^ Duan Y, Kollman PA. (1998). Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282(5389):740-4. PMID 9784131
- ^ Jayachandran G, Vishal V, Pande VS. (2006). Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece. J Chem Phys 124(16):164902. PMID 16674165
- ^ Herges T, Wenzel W. (2005). In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field. Phys Rev Lett 94(1):018101. PMID 15698135
- ^ a b Branden C, Tooze J. (1999). Introduction to Protein Structure 2nd ed. Garland Publishing: New York, NY.
- SCOP cytochrome c fold
- SCOP nucleic acid-binding three-helix bundles
- SCOP four-helix bundles
- SCOP Rop-like proteins
- SCOP all-alpha proteins
| Protein tertiary structure | ||
|---|---|---|
| General: | Structural domain | Protein folding | |
| All-α folds: | Helix bundle | Globin fold | Homeodomain fold | Alpha solenoid | |
| All-β folds: | Immunoglobulin fold | Beta barrel | Beta-propeller domain | |
| α/β folds: | TIM barrel | Leucine-rich repeat | Flavodoxin fold | Thioredoxin fold | Trefoil knot fold | |
| α+β folds: | Ferredoxin fold | Ribonuclease A | SH2-like fold | |
| Irregular folds: | Conotoxin | |
| ←Secondary structure | Structure determination methods | Quaternary structure→ |
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