A helix bundle is a small

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...

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 The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues earli ...

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 acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha ...

s long and is a common subject of study in

molecular dynamics Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of th ...

simulations because its

microsecond A microsecond is a unit of time in the International System of Units (SI) equal to one millionth (0.000001 or 10−6 or ) of a second. Its symbol is μs, sometimes simplified to us when Unicode is not available. A microsecond is equal to 100 ...

-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 '' ...

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 protein DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or double-stranded DNA. Sequence-specific DNA-binding proteins generally interact with the major groove of B-DNA, becau ...

Four-helix bundles

Four-helix bundles typically consist of four helices packed in a coiled-coil 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 The hydrophobic effect is the observed tendency of nonpolar substances to aggregate in an aqueous solution and exclude water molecules. The word hydrophobic literally means "water-fearing", and it describes the segregation of water and nonpola ...

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 Cytochromes are redox-active proteins containing a heme, with a central Fe atom at its core, as a cofactor. They are involved in electron transport chain and redox catalysis. They are classified according to the type of heme and its mode of bin ...

ferritin Ferritin is a universal intracellular protein that stores iron and releases it in a controlled fashion. The protein is produced by almost all living organisms, including archaea, bacteria, algae, higher plants, and animals. It is the primary ...

, human growth hormone,

cytokine Cytokines are a broad and loose category of small proteins (~5–25 kDa) important in cell signaling. Cytokines are peptides and cannot cross the lipid bilayer of cells to enter the cytoplasm. Cytokines have been shown to be involved in a ...

, and

Lac repressor The ''lac'' repressor (LacI) is a DNA-binding protein that inhibits the expression of genes coding for proteins involved in the metabolism of lactose in bacteria. These genes are repressed when lactose is not available to the cell, ensuring tha ...

C-terminal. The four-helix bundle fold has proven an attractive target for de novo

protein design Protein design is the rational design of new protein molecules to design novel activity, behavior, or purpose, and to advance basic understanding of protein function. Proteins can be designed from scratch (''de novo'' design) or by making calcul ...

, 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.

References

External links

SCOP cytochrome c fold

{{Protein tertiary structure Protein folds

Three-helix bundles

Four-helix bundles

See also

References

External links