A helix bundle is a small
protein fold
Fold, folding or foldable may refer to:
Arts, entertainment, and media
* ''Fold'' (album), the debut release by Australian rock band Epicure
*Fold (poker), in the game of poker, to discard one's hand and forfeit interest in the current pot
*Above ...
composed of several
alpha helices that are usually nearly parallel or antiparallel to each other.
Three-helix bundles
Three-helix bundles are among the smallest and fastest known cooperatively folding structural domains. The three-helix bundle in the
villin
Villin-1 is a 92.5 kDa tissue-specific actin-binding protein associated with the actin core bundle of the brush border. Villin-1 is encoded by the ''VIL1'' gene. Villin-1 contains multiple gelsolin-like domains capped by a small (8.5 kDa) "headp ...
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. The 40-residue
HIV
The human immunodeficiency viruses (HIV) are two species of '' Lentivirus'' (a subgroup of retrovirus) that infect humans. Over time, they cause acquired immunodeficiency syndrome (AIDS), a condition in which progressive failure of the immu ...
accessory protein has a very similar fold and has also been the subject of extensive study.
There is no general
sequence motif
In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an ''N''-glycosylation site motif can be defined as ''As ...
associated with three-helix bundles, so they cannot necessarily be
predicted
A prediction (Latin ''præ-'', "before," and ''dicere'', "to say"), or forecast, is a statement about a future event or data. They are often, but not always, based upon experience or knowledge. There is no universal agreement about the exact ...
from sequence alone. Three-helix bundles often occur in
actin-binding protein Actin-binding proteins (also known as ABPs) are proteins that bind to actin. This may mean ability to bind actin monomers, or polymers, or both.
Many actin-binding proteins, including α-actinin, β-spectrin, dystrophin, utrophin and fimbrin, do t ...
s and in
DNA-binding proteins.
Four-helix bundles
Four-helix bundles typically consist of four helices packed in a
coiled-coil
A coiled coil is a structural motif in proteins in which 2–7
alpha helix, alpha-helices are coiled together like the strands of a rope. (Protein dimer, Dimers and Protein trimer, trimers are the most common types.) Many coiled coil-type protei ...
arrangement with a
steric
Steric effects arise from the spatial arrangement of atoms. When atoms come close together there is a rise in the energy of the molecule. Steric effects are nonbonding interactions that influence the shape ( conformation) and reactivity of ions ...
ally 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.
[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, 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. Four-helix bundle can have thermal stability more than 100 °C. Other examples of four-helix bundles include
cytochrome,
ferritin,
human growth hormone
Growth hormone (GH) or somatotropin, also known as human growth hormone (hGH or HGH) in its human form, is a peptide hormone that stimulates growth, cell reproduction, and cell regeneration in humans and other animals. It is thus important in h ...
,
cytokine,
and
Lac repressor C-terminal. The four-helix bundle fold has proven an attractive target for de novo
protein design, with numerous de novo four-helix bundle proteins having been successfully designed by rational
and by combinatorial
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
A coiled coil is a structural motif in proteins in which 2–7
alpha helix, alpha-helices are coiled together like the strands of a rope. (Protein dimer, Dimers and Protein trimer, trimers are the most common types.) Many coiled coil-type protei ...
References
External links
SCOP cytochrome c fold
{{Protein tertiary structure
Protein folds