# Helix bundle > Mediated Wiki article. Canonical URL: https://mediated.wiki/source/Helix_bundle > Markdown URL: https://mediated.wiki/source/Helix_bundle.md > Source: https://en.wikipedia.org/wiki/Helix_bundle > Source revision: 1314009828 > License: Creative Commons Attribution-ShareAlike 4.0 International (https://creativecommons.org/licenses/by-sa/4.0/) A '''helix bundle''' is a small [protein](/source/protein) [fold](/source/tertiary_structure) composed of several [alpha helices](/source/alpha_helix) that are usually nearly parallel or antiparallel to each other. ==Three-helix bundles== [[Image:Villin-1qqv.png|thumb|300px|An example of the three-helix bundle fold, the headpiece [domain](/source/structural_domain) from the protein [villin](/source/villin) as expressed in [chicken](/source/chicken)s (PDB ID 1QQV).]] Three-helix bundles are among the smallest and fastest known cooperatively folding structural domains.{{cite journal | last1 = Wickstrom | first1 = L | last2 = Okur | first2 = A | last3 = Song | first3 = K | last4 = Hornak | first4 = V | last5 = Raleigh | first5 = DP | last6 = Simmerling | first6 = CL. | year = 2006 | title = The unfolded state of the villin headpiece helical subdomain: computational studies of the role of locally stabilized structure | journal = J Mol Biol | volume = 360| issue = 5| pages = 1094–107 | pmid = 16797585 | doi=10.1016/j.jmb.2006.04.070| pmc = 4805113 }} The three-helix bundle in the [villin](/source/villin) headpiece domain is only 36 [amino acid](/source/amino_acid)s long and is a common subject of study in [molecular dynamics](/source/molecular_dynamics) simulations because its [microsecond](/source/microsecond)-scale folding time is within the timescales accessible to simulation.{{cite journal | last1 = Duan | first1 = Y | last2 = Kollman | first2 = PA. | year = 1998 | title = Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution | journal = Science | volume = 282 | issue = 5389| pages = 740–4 | pmid = 9784131 | doi = 10.1126/science.282.5389.740 |bibcode = 1998Sci...282..740D }}{{cite journal | last1 = Jayachandran | first1 = G | last2 = Vishal | first2 = V | last3 = Pande | first3 = VS. | year = 2006 | title = Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece | journal = J Chem Phys | volume = 124 | issue = 16| page = 164902 | pmid = 16674165 | doi=10.1063/1.2186317|bibcode = 2006JChPh.124p4902J | doi-access = free }} The 40-residue [HIV](/source/HIV) accessory protein has a very similar fold and has also been the subject of extensive study.{{cite journal | last1 = Herges | first1 = T | last2 = Wenzel | first2 = W. | year = 2005 | title = In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field | journal = Phys Rev Lett | volume = 94 | issue = 1| article-number = 018101 | doi = 10.1103/PhysRevLett.94.018101 | pmid = 15698135 | bibcode=2005PhRvL..94a8101H| arxiv = physics/0310146 | s2cid = 1477100 }} There is no general [sequence motif](/source/sequence_motif) associated with three-helix bundles, so they cannot necessarily be [predicted](/source/protein_structure_prediction) from sequence alone. Three-helix bundles often occur in [actin-binding protein](/source/actin-binding_protein)s and in [DNA-binding protein](/source/DNA-binding_protein)s. ==Four-helix bundles== Four-helix bundles typically consist of four helices packed in a [coiled-coil](/source/coiled-coil) arrangement with a [steric](/source/steric)ally close-packed [hydrophobic core](/source/hydrophobic_core) in the center. Pairs of adjacent helices are often additionally stabilized by [salt bridges](/source/salt_bridge_(protein)) 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](/source/globin_fold).Branden C, Tooze J. (1999). ''Introduction to Protein Structure'' 2nd ed. Garland Publishing: New York, NY. The specific topology of the helices is dependent on the protein – helices that are adjacent in sequence are often [antiparallel](/source/Antiparallel_(biochemistry)), although it is also possible to arrange antiparallel links between two pairs of parallel helices. Because [dimeric](/source/protein_dimer) coiled-coils are themselves relatively stable, four-helix bundles can be [dimer](/source/protein_dimer)s of coiled-coil pairs, as in the [Rop protein](/source/Rop_protein). Four-helix bundle can have thermal stability more than 100 °C. Other important examples of four-helix bundles include [cytochrome](/source/cytochrome), [ferritin](/source/ferritin), [human growth hormone](/source/human_growth_hormone), [cytokine](/source/cytokine), and [Lac repressor](/source/Lac_repressor) C-terminal. The four-helix bundle fold has proven an attractive target for de novo [protein design](/source/protein_design), with numerous de novo four-helix bundle proteins having been successfully designed by rational{{cite journal | last1 = Regan | first1 = L. | last2 = DeGrado | first2 = W. F. | year = 1988 | title = Characterization of a helical protein designed from first principles | journal = Science | volume = 241 | issue = 4868| pages = 976–978 | pmid = 3043666 | doi = 10.1126/science.3043666 |bibcode = 1988Sci...241..976R }} and by combinatorial{{cite journal | last1 = Hecht | first1 = MH | last2 = Das | first2 = A | last3 = Go | first3 = A | last4 = Bradley | first4 = LH | last5 = Wei | first5 = Y | year = 2004 | title = De novo proteins from designed combinatorial libraries | journal = Protein Science | volume = 13 | issue = 7| pages = 1711–1723 | pmid = 15215517 | doi=10.1110/ps.04690804 | pmc = 2279937}} methods. 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. ==See also== *[Knobs into holes packing](/source/Knobs_into_holes_packing) ==References== {{Reflist}} ==External links== * [https://web.archive.org/web/20110516101013/http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.b.g.A.html SCOP cytochrome c fold] * [https://web.archive.org/web/20110516101018/http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.b.h.html SCOP nucleic acid-binding three-helix bundles] * [https://web.archive.org/web/20071209035938/http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.b.db.html SCOP four-helix bundles] * [https://web.archive.org/web/20071116012846/http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.b.di.html SCOP Rop-like proteins] * [https://web.archive.org/web/20070306164042/http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.b.html SCOP all-alpha proteins] {{Protein tertiary structure}} Category:Protein folds --- Adapted from the Wikipedia article [Helix bundle](https://en.wikipedia.org/wiki/Helix_bundle) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/Helix_bundle?action=history)). 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