Editing Coiled coil

{{Short description|Structural motif in proteins}}
{{other uses|Coiled coil (disambiguation)}}
[[Image:GCN4 coiled coil dimer 1zik rainbow.png|thumb|200px|right|Figure 1: The classic example of a coiled coil is the GCN4 [[leucine zipper]] (PDB accession code 1zik), which is a parallel, left-handed [[homodimer]]. However, many other types of coiled coil exist.]]

A '''coiled coil''' is a [[structural motif]] in [[Protein|proteins]] in which two to seven<ref name="Liu20062">{{cite journal |vauthors=Liu J, Zheng Q, Deng Y, Cheng CS, Kallenbach NR, Lu M |date=Oct 2006 |title=A seven-helix coiled coil |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=103 |issue=42 |pages=15457–62 |bibcode=2006PNAS..10315457L |doi=10.1073/pnas.0604871103 |pmc=1622844 |pmid=17030805 |doi-access=free}}</ref> [[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.) They have been found in roughly 5-10% of proteins and have a variety of functions.<ref>{{Cite journal |last1=Szczepaniak |first1=Krzysztof |last2=Bukala |first2=Adriana |last3=da Silva Neto |first3=Antonio Marinho |last4=Ludwiczak |first4=Jan |last5=Dunin-Horkawicz |first5=Stanislaw |date=2021-04-01 |editor-last=Elofsson |editor-first=Arne |title=A library of coiled-coil domains: from regular bundles to peculiar twists |url=https://academic.oup.com/bioinformatics/article/36/22-23/5368/6039120 |journal=Bioinformatics |language=en |volume=36 |issue=22–23 |pages=5368–5376 |doi=10.1093/bioinformatics/btaa1041 |issn=1367-4803 |pmc=8016460 |pmid=33325494}}</ref> They are one of the most widespread motifs found in protein-protein interactions. To aid protein study, several tools have been developed to predict coiled-coils in protein structures.<ref>{{Cite journal |last1=Walshaw |first1=John |last2=Woolfson |first2=Derek N |date=2001-04-13 |title=SOCKET: a program for identifying and analysing coiled-coil motifs within protein structures11Edited by J. Thornton |url=https://www.sciencedirect.com/science/article/pii/S0022283601945450 |journal=Journal of Molecular Biology |volume=307 |issue=5 |pages=1427–1450 |doi=10.1006/jmbi.2001.4545 |pmid=11292353 |issn=0022-2836|url-access=subscription }}</ref> Many coiled coil-type proteins are involved in important biological functions, such as the regulation of [[gene expression]] — e.g., [[Transcription factor|transcription factors]]. Notable examples are the [[Oncoprotein|oncoproteins]] [[c-Fos]] and [[c-Jun]], as well as the muscle protein [[tropomyosin]]. 

==Discovery==

The possibility of coiled coils for α-[[keratin]] was initially somewhat controversial. [[Linus Pauling]] and [[Francis Crick]] independently came to the conclusion that this was possible at about the same time. In the summer of 1952, Pauling visited the laboratory in [[England]] where Crick worked. Pauling and Crick met and spoke about various topics; at one point, Crick asked whether Pauling had considered ''coiled coils'' (a term Crick came up with), to which Pauling said he had. Upon returning to the United States, Pauling resumed research on the topic. He concluded that coiled coils exist, and submitted a lengthy manuscript to the journal ''[[Nature (journal)|Nature]]'' in October. Pauling's son Peter Pauling worked at the same lab as Crick, and mentioned the report to him. Crick believed that Pauling had stolen his idea, and submitted a shorter note to ''Nature'' a few days after Pauling's manuscript arrived. Eventually, after some controversy and frequent correspondences, Crick's lab declared that the idea had been reached independently by both researchers, and that no intellectual theft had occurred.<ref>{{cite web| vauthors = Hager T |title=Narrative 43, Coils Upon Coils|url=http://scarc.library.oregonstate.edu/coll/pauling/proteins/narrative/page43.html|work=Linus Pauling and the Structure of Proteins|publisher=Oregon State University Special Collections and Archives Research Center|access-date=May 15, 2013}}</ref>  In his note (which was published first due to its shorter length), Crick proposed the ''coiled coil'' and as well as mathematical methods for determining their structure.<ref name="crick52">
{{cite journal | vauthors = Crick FH | title = Is alpha-keratin a coiled coil? | journal = Nature | volume = 170 | issue = 4334 | pages = 882–883 | date = November 1952 | pmid = 13013241 | doi = 10.1038/170882b0 | s2cid = 4147931 | bibcode = 1952Natur.170..882C }}</ref> Remarkably, this was soon after the structure of the [[alpha helix]] was suggested in 1951 by [[Linus Pauling]] and coworkers.<ref name="pauling51">
{{cite journal | vauthors = Pauling L, Corey RB, Branson HR | title = The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 37 | issue = 4 | pages = 205–211 | date = April 1951 | pmid = 14816373 | pmc = 1063337 | doi = 10.1073/pnas.37.4.205 | doi-access = free | bibcode = 1951PNAS...37..205P }}</ref> These studies were published in the absence of knowledge of a keratin sequence. The first keratin sequences were determined by Hanukoglu and Fuchs in 1982.<ref name="pages = –-1982">{{cite journal | vauthors = Hanukoglu I, Fuchs E | title = The cDNA sequence of a human epidermal keratin: divergence of sequence but conservation of structure among intermediate filament proteins | journal = Cell | volume = 31 | issue = 1 | pages = 243–252 | date = November 1982 | pmid = 6186381 | doi = 10.1016/0092-8674(82)90424-X | s2cid = 35796315 | url = https://zenodo.org/record/890743 }}</ref><ref name="pages = –-1983">{{cite journal | vauthors = Hanukoglu I, Fuchs E | title = The cDNA sequence of a Type II cytoskeletal keratin reveals constant and variable structural domains among keratins | journal = Cell | volume = 33 | issue = 3 | pages = 915–924 | date = July 1983 | pmid = 6191871 | doi = 10.1016/0092-8674(83)90034-X | s2cid = 21490380 | url = https://zenodo.org/record/890739 }}</ref>

Based on sequence and secondary structure prediction analyses identified the coiled-coil domains of keratins.<ref name="pages = –-1983" /> These models have been confirmed by structural analyses of coiled-coil domains of keratins.<ref name="pmid24265184">{{cite journal | vauthors = Hanukoglu I, Ezra L | title = Proteopedia entry: coiled-coil structure of keratins | journal = Biochemistry and Molecular Biology Education | volume = 42 | issue = 1 | pages = 93–94 | date = Jan 2014 | pmid = 24265184 | doi = 10.1002/bmb.20746 | s2cid = 30720797 | doi-access = free }}</ref>

==Molecular structure==

Coiled coils usually contain a repeated pattern, ''hxxhcxc'', of hydrophobic (''h'') and charged (''c'') [[amino-acid]] residues, referred to as a [[heptad repeat]].<ref name="mason2004">
{{cite journal | vauthors = Mason JM, Arndt KM | title = Coiled coil domains: stability, specificity, and biological implications | journal = ChemBioChem | volume = 5 | issue = 2 | pages = 170–176 | date = February 2004 | pmid = 14760737 | doi = 10.1002/cbic.200300781 | s2cid = 39252601 }}</ref>
The positions in the heptad repeat are usually labeled ''abcdefg'', where ''a'' and ''d'' are the hydrophobic positions, often being occupied by [[isoleucine]], [[leucine]], or [[valine]]. Folding a sequence with this repeating pattern into an [[alpha-helix|alpha-helical]] [[secondary structure]] causes the hydrophobic residues to be presented as a 'stripe' that coils gently around the helix in left-handed fashion, forming an [[amphiphile|amphipathic]] structure. The most favorable way for two such helices to arrange themselves in the water-filled environment of the [[cytoplasm]] is to wrap the hydrophobic strands against each other sandwiched between the [[hydrophilic]] amino acids. Thus, it is the burial of hydrophobic surfaces that provides the [[thermodynamic]] driving force for the oligomerization. The packing in a coiled-coil interface is exceptionally tight, with almost complete [[van der Waals force|van der Waals]] contact between the [[Substituent|side-chains]] of the ''a'' and ''d'' residues. This tight packing was originally predicted by [[Francis Crick]] in 1952<ref name="crick52"/> and is referred to as [[knobs into holes packing]].

The [[alpha-helix|α-helices]] may be parallel or anti-parallel, and usually adopt a ''left-handed'' super-coil (Figure 1).  Although disfavored, a few ''right-handed'' coiled coils have also been observed in nature and in designed proteins.<ref name="harbury1998">{{cite journal | vauthors = Harbury PB, Plecs JJ, Tidor B, Alber T, Kim PS | title = High-resolution protein design with backbone freedom | journal = Science | volume = 282 | issue = 5393 | pages = 1462–1467 | date = November 1998 | pmid = 9822371 | doi = 10.1126/science.282.5393.1462 }}</ref>

==Biological roles==
As coiled-coil domains are common among a significant amount of proteins in a wide variety of protein families, they help proteins fulfill various functions in the cell. Their primary feature is to facilitate protein-protein interaction and keep proteins or domains interlocked. This feature corresponds to several subfunctions, including membrane fusion, molecular spacing, oligomerization tags, vesicle movement, aid in movement proteins, cell structure, and more.<ref>{{Cite journal |last1=Rose |first1=Annkatrin |last2=Schraegle |first2=Shannon J. |last3=Stahlberg |first3=Eric A. |last4=Meier |first4=Iris |date=2005-11-16 |title=Coiled-coil protein composition of 22 proteomes – differences and common themes in subcellular infrastructure and traffic control |journal=BMC Evolutionary Biology |volume=5 |issue=1 |pages=66 |doi=10.1186/1471-2148-5-66 |issn=1471-2148 |pmc=1322226 |pmid=16288662 |bibcode=2005BMCEE...5...66R |doi-access=free }}</ref>

===Membrane fusion===
[[Image:gp41 coiled coil hexamer 1aik sideview.png|thumb|200px|right|Side view of the gp41 hexamer that initiates the entry of HIV into its target cell.]]

A coiled coil domain plays a role in [[human immunodeficiency virus type 1]] (HIV-1) infection. Viral entry into CD4-positive cells commences when three subunits of a glycoprotein 120 ([[gp120]]) bind to CD4 receptor and a coreceptor.<ref>{{cite journal |vauthors=Shaik MM, Peng H, Lu J, Rits-Volloch S, Xu C, Liao M, Chen B |date=January 2019 |title=Structural basis of coreceptor recognition by HIV-1 envelope spike |journal=Nature |volume=565 |issue=7739 |pages=318–323 |doi=10.1038/s41586-018-0804-9 |pmc=6391877 |pmid=30542158}}</ref>  Glycoprotein gp120 is closely associated with a trimer of [[gp41]] via van der Waals interactions. Eventually, the gp41 N-terminal fusion peptide sequence anchors into the host cell. A [[spring-loaded]] mechanism is responsible for bringing the viral and cell membranes in close enough proximity that they will fuse. The origin of the spring-loaded mechanism lies within the exposed gp41, which contains two consecutive heptad repeats (HR1 and HR2) following the fusion peptide at the N terminus of the protein. HR1 forms a parallel, trimeric coiled coil onto which HR2 region coils, forming the trimer-of-hairpins (or six-helix bundle) structure, thereby facilitating membrane fusion through bringing the membranes close to each other.<ref>{{cite journal |vauthors=Wilen CB, Tilton JC, Doms RW |date=August 2012 |title=HIV: cell binding and entry |journal=Cold Spring Harbor Perspectives in Medicine |volume=2 |issue=8 |pages=a006866 |doi=10.1101/cshperspect.a006866 |pmc=3405824 |pmid=22908191}}</ref> The virus then enters the cell and begins its replication.  Recently, inhibitors derived from HR2 such as [[Enfuvirtide|Fuzeon]] (DP178, T-20) that bind to the HR1 region on gp41 have been developed.<ref name="pmid152317622">{{cite journal |vauthors=Greenberg ML, Cammack N |date=August 2004 |title=Resistance to enfuvirtide, the first HIV fusion inhibitor |journal=The Journal of Antimicrobial Chemotherapy |volume=54 |issue=2 |pages=333–40 |doi=10.1093/jac/dkh330 |pmid=15231762|doi-access=free }}</ref> However, peptides derived from HR1 have little viral inhibition efficacy due to the propensity for these peptides to aggregate in solution. Chimeras of these HR1-derived peptides with GCN4 [[Leucine zipper|leucine zippers]] have been developed and have shown to be more active than [[Enfuvirtide|Fuzeon]].<ref>{{cite journal |vauthors=Eckert DM, Kim PS |date=September 2001 |title=Design of potent inhibitors of HIV-1 entry from the gp41 N-peptide region |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=98 |issue=20 |pages=11187–11192 |bibcode=2001PNAS...9811187E |doi=10.1073/pnas.201392898 |pmc=58705 |pmid=11572974 |doi-access=free}}</ref>  [[Human immunodeficiency virus type 2]] has a membrane envelope glycoprotein with similar structure to HIV-1 gp41, but containing substitutions for a glycine amino acid residue in the coiled coil domain that may impact trimer stability.<ref>{{cite journal|vauthors=Chen B, Chou JJ|title=Structure of the transmembrane domain of HIV-1 envelope glycoprotein|journal=The FEBS Journal|volume=284|pages=1171-1177|doi=10.1111/febs.13954|pmid=27868386|pmc=5448286|year=2017|doi-access=free}}</ref>

The proteins [[SNAP25|SNAP-25]], [[synaptobrevin]], and [[STX1A|syntaxin-1]] have alpha-helices which interact with each other to form a coiled-coil [[SNARE protein|SNARE complex]]. Zippering the domains together provides the necessary energy for vesicle fusion to occur.<ref>{{Cite journal |last1=Chen |first1=Yu A. |last2=Scheller |first2=Richard H. |date=February 2001 |title=SNARE-mediated membrane fusion |url=https://www.nature.com/articles/35052017 |journal=Nature Reviews Molecular Cell Biology |language=en |volume=2 |issue=2 |pages=98–106 |doi=10.1038/35052017 |pmid=11252968 |s2cid=205012830 |issn=1471-0072|url-access=subscription }}</ref>

=== Molecular spacers ===
The coiled-coil motif may also act as a spacer between two objects within a cell.  The lengths of these molecular spacer coiled-coil domains are highly conserved. The purpose of these molecular spacers may be to separate protein domains, thus keeping them from interacting, or to separate vesicles within the cell to mediate vesicle transport. An example of this first purpose is Omp‐α found in ''[[Thermotoga maritima|T. maritima]]''.<ref>{{Cite journal |last1=Truebestein |first1=Linda |last2=Leonard |first2=Thomas A. |date=September 2016 |title=Coiled-coils: The long and short of it |journal=BioEssays |language=en |volume=38 |issue=9 |pages=903–916 |doi=10.1002/bies.201600062 |issn=0265-9247 |pmc=5082667 |pmid=27492088}}</ref> Other proteins keep vesicles apart, such as p115, [[giantin]], and [[GM130]] which interact with each other via coiled-coil motifs and act as a tether between the [[Golgi apparatus|Golgi]] and a nearby vesicle.<ref>{{Cite journal |last1=Linstedt |first1=Adam D. |last2=Jesch |first2=Stephen A. |last3=Mehta |first3=Amy |last4=Lee |first4=Tina H. |last5=Garcia-Mata |first5=Rafael |last6=Nelson |first6=David S. |last7=Sztul |first7=Elizabeth |date=April 2000 |title=Binding Relationships of Membrane Tethering Components |journal=Journal of Biological Chemistry |volume=275 |issue=14 |pages=10196–10201 |doi=10.1074/jbc.275.14.10196 |pmid=10744704 |issn=0021-9258 |doi-access=free }}</ref> The family of proteins related to this activity of tethering vesicles to the Golgi are known as golgins.<ref>{{Cite journal |last1=Witkos |first1=Tomasz M. |last2=Lowe |first2=Martin |date=2016-01-11 |title=The Golgin Family of Coiled-Coil Tethering Proteins |journal=Frontiers in Cell and Developmental Biology |volume=3 |page=86 |doi=10.3389/fcell.2015.00086 |issn=2296-634X |pmc=4707255 |pmid=26793708 |doi-access=free }}</ref> Finally, there are several proteins with coiled-coil domains involved in the [[kinetochore]], which keeps [[Chromosome|chromosomes]] separated during [[cell division]]. These proteins include [[NDC80|Ndc-80]], and [[NUF2|Nuf2p]]. Related proteins interact with [[Microtubule|microtubules]] during cell division, of which mutation leads to cell death.<ref>{{Cite journal |last1=Jeyaprakash |first1=A. Arockia |last2=Santamaria |first2=Anna |last3=Jayachandran |first3=Uma |last4=Chan |first4=Ying Wai |last5=Benda |first5=Christian |last6=Nigg |first6=Erich A. |last7=Conti |first7=Elena |date=May 2012 |title=Structural and Functional Organization of the Ska Complex, a Key Component of the Kinetochore-Microtubule Interface |journal=Molecular Cell |volume=46 |issue=3 |pages=274–286 |doi=10.1016/j.molcel.2012.03.005 |pmid=22483620 |issn=1097-2765|doi-access=free }}</ref>

===As oligomerization tags===
Because of their specific interaction coiled coils can be used as "tags" to stabilize or enforce a specific oligomerization state.<ref name="Deiss_20142">{{cite journal |vauthors=Deiss S, Hernandez Alvarez B, Bär K, Ewers CP, Coles M, Albrecht R, Hartmann MD |date=June 2014 |title=Your personalized protein structure: Andrei N. Lupas fused to GCN4 adaptors |journal=Journal of Structural Biology |volume=186 |issue=3 |pages=380–5 |doi=10.1016/j.jsb.2014.01.013 |pmid=24486584 |doi-access=free}}</ref> A coiled coil interaction has been observed to drive the oligomerization of the [[BBS2]] and [[BBS7]] subunits of the [[BBSome]]. <ref>{{cite journal |last1=Chou |first1=Hui-Ting |last2=Apelt |first2=Luise |last3=Farrell |first3=Daniel P. |last4=White |first4=Susan Roehl |last5=Woodsmith |first5=Jonathan |last6=Svetlov |first6=Vladimir |last7=Goldstein |first7=Jaclyn S. |last8=Nager |first8=Andrew R. |last9=Li |first9=Zixuan |last10=Muller |first10=Jean |last11=Dollfus |first11=Helene |last12=Nudler |first12=Evgeny |last13=Stelzl |first13=Ulrich |last14=DiMaio |first14=Frank |last15=Nachury |first15=Maxance V. |date=3 September 2019 |title=The Molecular Architecture of Native BBSome Obtained by an Integrated Structural Approach |journal=Structure |volume=27 |issue=9 |pages=1384–1394 |doi=10.1016/j.str.2019.06.006 |pmc=6726506 |pmid=31303482 |last16=Walz |first16=Thomas}}</ref><ref>{{cite journal |last1=Ludlam |first1=WG |last2=Aoba |first2=T |last3=Cuéllar |first3=J |last4=Bueno-Carrasco |first4=MT |last5=Makaju |first5=A |last6=Moody |first6=JD |last7=Franklin |first7=S |last8=Valpuesta |first8=JM |last9=Willardson |first9=BM |date=17 September 2019 |title=Molecular architecture of the Bardet-Biedl syndrome protein 2-7-9 subcomplex. |journal=The Journal of Biological Chemistry |volume=294 |issue=44 |pages=16385–16399 |doi=10.1074/jbc.RA119.010150 |pmc=6827290 |pmid=31530639 |doi-access=free}}</ref> Because coiled-coils generally interact with other coiled coils, they are found in proteins which are required to form dimers or tetramers with more copies of themselves.<ref>{{Cite journal |last1=Cabezon |first1=Elena |last2=Butler |first2=P. Jonathan G. |last3=Runswick |first3=Michael J. |last4=Walker |first4=John E. |date=August 2000 |title=Modulation of the Oligomerization State of the Bovine F1-ATPase Inhibitor Protein, IF1, by pH |journal=Journal of Biological Chemistry |language=en |volume=275 |issue=33 |pages=25460–25464 |doi=10.1074/jbc.M003859200 |pmid=10831597 |doi-access=free }}</ref>  Because of their ability in driving [[Protein oligomer|protein oligomerization]], they have also been studied in their use in forming synthetic nanostructures.<ref>{{Cite journal |last=Park |first=Won Min |date=2020-05-19 |title=Coiled-Coils: The Molecular Zippers that Self-Assemble Protein Nanostructures |journal=International Journal of Molecular Sciences |language=en |volume=21 |issue=10 |pages=3584 |doi=10.3390/ijms21103584 |issn=1422-0067 |pmc=7278914 |pmid=32438665 |doi-access=free }}</ref>

==Design==
[[File:Coiled coil structure.gif|thumb|Secondary and tertiary structure of the coiled-coil motif. The heptad repeat often consists of specific amino acids, seen in the figure. Knobs into holes packing is also shown.<ref name="Lapenta-2018">{{Cite journal |last1=Lapenta |first1=Fabio |last2=Aupič |first2=Jana |last3=Strmšek |first3=Žiga |last4=Jerala |first4=Roman |date=2018 |title=Coiled coil protein origami: from modular design principles towards biotechnological applications |url=http://xlink.rsc.org/?DOI=C7CS00822H |journal=Chemical Society Reviews |language=en |volume=47 |issue=10 |pages=3530–3542 |doi=10.1039/C7CS00822H |issn=0306-0012|doi-access=free |pmid=29400389 }}</ref>]]
The general problem of deciding on the folded structure of a protein when given the amino acid sequence (the so-called [[protein structure prediction|protein folding problem]]) has only been solved partially.  However, the coiled coil is one of a relatively small number of folding motifs for which the relationships between the sequence and the final folded structure are comparatively well understood.<ref name="Bromely2008">
{{cite journal | vauthors = Bromley EH, Channon K, Moutevelis E, Woolfson DN | title = Peptide and protein building blocks for synthetic biology: from programming biomolecules to self-organized biomolecular systems | journal = ACS Chemical Biology | volume = 3 | issue = 1 | pages = 38–50 | date = January 2008 | pmid = 18205291 | doi = 10.1021/cb700249v }}</ref><ref name="mahrenholz2011">
{{cite journal | vauthors = Mahrenholz CC, Abfalter IG, Bodenhofer U, Volkmer R, Hochreiter S | title = Complex networks govern coiled-coil oligomerization--predicting and profiling by means of a machine learning approach | journal = Molecular & Cellular Proteomics | volume = 10 | issue = 5 | pages = M110.004994 | date = May 2011 | pmid = 21311038 | pmc = 3098589 | doi = 10.1074/mcp.M110.004994 | doi-access = free }}</ref> Harbury ''et al.'' performed a landmark study using an archetypal coiled coil, GCN4, in which rules that govern the way that peptide sequence affects the oligomeric state (that is, the number of [[alpha-helix|alpha-helices]] in the final assembly) were established.<ref name="Harbury1993">
{{cite journal | vauthors = Harbury PB, Zhang T, Kim PS, Alber T | title = A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants | journal = Science | volume = 262 | issue = 5138 | pages = 1401–1407 | date = November 1993 | pmid = 8248779 | doi = 10.1126/science.8248779 | s2cid = 45833675 | bibcode = 1993Sci...262.1401H }}</ref><ref name="Harbury1994">
{{cite journal | vauthors = Harbury PB, Kim PS, Alber T | title = Crystal structure of an isoleucine-zipper trimer | journal = Nature | volume = 371 | issue = 6492 | pages = 80–83 | date = September 1994 | pmid = 8072533 | doi = 10.1038/371080a0 | s2cid = 4319206 | bibcode = 1994Natur.371...80H }}</ref> The GCN4 coiled coil is a 31-amino-acid (which equates to just over four ''heptads'') parallel, dimeric (i.e., consisting of two [[alpha-helix|alpha-helices]]) coiled coil and has a repeated [[isoleucine]] (or I, in [[Amino acid#Table of standard amino acid abbreviations and properties|single-letter code]]) and [[leucine]] (L) at the ''a'' and ''d'' positions, respectively, and forms a dimeric coiled coil. When the amino acids in the ''a'' and ''d'' positions were changed from I at ''a'' and L at ''d'' to I at ''a'' and I at ''d'', a trimeric (three alpha-helices) coiled coil was formed. Furthermore, switching the positions of L to ''a'' and I to ''d'' resulted in the formation of a tetrameric (four [[alpha-helix|alpha-helices]]) coiled coil. These represent a set of rules for the determination of coiled coil oligomeric states and allows scientists to effectively "dial-in" the oligomerization behavior. Another aspect of coiled coil assembly that is relatively well understood, at least in the case of dimeric coiled coils, is that placing a polar residue (in particular [[asparagine]], N) at opposing ''a'' positions forces parallel assembly of the coiled coil. This effect is due to a self-complementary [[hydrogen bond]]ing between these residues, which would go unsatisfied if an N were paired with, for instance, an L on the opposing helix.<ref name="Woolfson2005">
{{cite book | vauthors = Woolfson DN | title = Fibrous Proteins: Coiled-Coils, Collagen and Elastomers | chapter = The design of coiled-coil structures and assemblies | volume = 70 | issue = 4 | pages = 79–112 | year = 2005 | pmid = 15837514 | doi = 10.1016/S0065-3233(05)70004-8 | isbn = 9780120342709 | series = Advances in Protein Chemistry }}</ref>

It was recently demonstrated by Peacock, [[Zoe Pikramenou|Pikramenou]] and co-workers that coiled coils may be self-assembled using lanthanide(III) ions as a template, thus producing novel imaging agents.<ref>{{cite journal | vauthors = Berwick MR, Lewis DJ, Jones AW, Parslow RA, Dafforn TR, Cooper HJ, Wilkie J, Pikramenou Z, Britton MM, Peacock AF | display-authors = 6 | title = De novo design of Ln(III) coiled coils for imaging applications | journal = Journal of the American Chemical Society | volume = 136 | issue = 4 | pages = 1166–1169 | date = January 2014 | pmid = 24405157 | pmc = 3950886 | doi = 10.1021/ja408741h }}</ref>

== Biomedical applications ==
[[File:Coiled coil protein origami.gif|thumb|Some examples of protein nanostructures made using coiled-coil motifs. The top three pictures shown in the figure more accurately models the nanostructure, while the pictures underneath describe their basic shape. These may be used as building blocks to create further nanostructures.<ref name="Lapenta-2018" />]]
Coiled-coil motifs have been experimented on as possible building block for [[Nanostructure|nanostructures]], in part because of their simple design and wide range of function based primarily on facilitating protein-protein interaction. Simple guidelines for [[de novo synthesis]] of new proteins containing coiled-coil domains have led to many applications being hypothesized, including drug delivery, regenerating tissue, protein origami, and much more.<ref name="Jorgensen-2022">{{Cite journal |last1=Jorgensen |first1=Michael D. |last2=Chmielewski |first2=Jean |date=2022 |title=Recent advances in coiled-coil peptide materials and their biomedical applications |url=http://dx.doi.org/10.1039/d2cc04434j |journal=Chemical Communications |volume=58 |issue=83 |pages=11625–11636 |doi=10.1039/d2cc04434j |pmid=36172799 |s2cid=252514360 |issn=1359-7345|url-access=subscription }}</ref> In regards to drug delivery, coiled-coil domains would help overcome some of the hazards of chemotherapeutic drugs, by keeping them from leaking into healthy tissue as they are transported to their target. Coiled-coil domains can be made to bind to specific proteins or cell surface markers, allowing for more precise targeting in drug delivery.<ref>{{Cite journal |last1=McFarlane |first1=Ainsley A. |last2=Orriss |first2=George L. |last3=Stetefeld |first3=Jörg |date=December 2009 |title=The use of coiled-coil proteins in drug delivery systems |journal=European Journal of Pharmacology |language=en |volume=625 |issue=1–3 |pages=101–107 |doi=10.1016/j.ejphar.2009.05.034 |pmc=7094320 |pmid=19835864}}</ref>  Other functions would be to help store and transport drugs within the body that would otherwise degrade rapidly, by creating nanotubes and other structure svia the interlocking of coiled-coil motifs.<ref name="Jorgensen-2022" /> By utilizing the function of oligomerization of proteins via coiled-coil domains, antigen display can be amplified in vaccines, increasing their effectiveness.<ref>{{Cite journal |last1=Schroeder |first1=Ulrich |last2=Graff |first2=Alexandra |last3=Buchmeier |first3=Sabine |last4=Rigler |first4=Per |last5=Silvan |first5=Unai |last6=Tropel |first6=David |last7=Jockusch |first7=Brigitte M. |last8=Aebi |first8=Ueli |last9=Burkhard |first9=Peter |last10=Schoenenberger |first10=Cora-Ann |date=March 2009 |title=Peptide Nanoparticles Serve as a Powerful Platform for the Immunogenic Display of Poorly Antigenic Actin Determinants |url=http://dx.doi.org/10.1016/j.jmb.2008.11.023 |journal=Journal of Molecular Biology |volume=386 |issue=5 |pages=1368–1381 |doi=10.1016/j.jmb.2008.11.023 |pmid=19063898 |issn=0022-2836|url-access=subscription }}</ref>

The oligomerization of coiled-coil motifs allows for the creation of protein origami and protein building blocks. Metal-ligand interactions, covalent bonds, and ionic interactions have been studied to manipulate possible coiled-coil interactions in this field of study.<ref name="Jorgensen-2022" /> Several different nanostructures can be made by combining coiled-coil motifs such that they are self-assembling building blocks. However, several difficulties remain with stability.<ref>{{Cite journal |last=Park |first=Won Min |date=January 2020 |title=Coiled-Coils: The Molecular Zippers that Self-Assemble Protein Nanostructures |journal=International Journal of Molecular Sciences |language=en |volume=21 |issue=10 |pages=3584 |doi=10.3390/ijms21103584 |issn=1422-0067 |pmc=7278914 |pmid=32438665 |doi-access=free }}</ref> Using peptides with coiled-coil motifs for scaffolding has made it easier to create 3D structures for cell culturing. 3D hydrogels can be made with these peptides, and then cells may be loaded into the matrix.<ref>{{Cite journal |last1=Dexter |first1=A. F. |last2=Fletcher |first2=N. L. |last3=Creasey |first3=R. G. |last4=Filardo |first4=F. |last5=Boehm |first5=M. W. |last6=Jack |first6=K. S. |date=2017 |title=Fabrication and characterization of hydrogels formed from designer coiled-coil fibril-forming peptides |url=http://xlink.rsc.org/?DOI=C7RA02811C |journal=RSC Advances |language=en |volume=7 |issue=44 |pages=27260–27271 |doi=10.1039/C7RA02811C |bibcode=2017RSCAd...727260D |s2cid=98941102 |issn=2046-2069|doi-access=free }}</ref> This has applications in the study of tissue, tissue engineering, and more.<ref name="Jorgensen-2022" />

== References ==
{{reflist|33em}}

== Further reading ==
{{refbegin|33em}}
* {{cite journal | doi = 10.1107/S0365110X53001964 | vauthors = Crick FH | year = 1953 | title = The Packing of α-Helices: Simple Coiled-Coils | journal = Acta Crystallogr | volume = 6 | issue = 8| pages = 689–697 | bibcode = 1953AcCry...6..689C | doi-access = free }}
* {{cite journal | vauthors = Nishikawa K, Scheraga HA | title = Geometrical criteria for formation of coiled-coil structures of polypeptide chains | journal = Macromolecules | volume = 9 | issue = 3 | pages = 395–407 | year = 1976 | pmid = 940353 | doi = 10.1021/ma60051a004 | bibcode = 1976MaMol...9..395N }}
* {{cite journal | vauthors = Harbury PB, Zhang T, Kim PS, Alber T | title = A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants | journal = Science | volume = 262 | issue = 5138 | pages = 1401–1407 | date = November 1993 | pmid = 8248779 | doi = 10.1126/science.8248779 | s2cid = 45833675 | bibcode = 1993Sci...262.1401H }}
* {{cite journal | vauthors = Gonzalez L, Plecs JJ, Alber T | title = An engineered allosteric switch in leucine-zipper oligomerization | journal = Nature Structural Biology | volume = 3 | issue = 6 | pages = 510–515 | date = June 1996 | pmid = 8646536 | doi = 10.1038/nsb0696-510 | s2cid = 30381026 }}
* {{cite journal | vauthors = Harbury PB, Plecs JJ, Tidor B, Alber T, Kim PS | title = High-resolution protein design with backbone freedom | journal = Science | volume = 282 | issue = 5393 | pages = 1462–1467 | date = November 1998 | pmid = 9822371 | doi = 10.1126/science.282.5393.1462 }}
* {{cite journal | vauthors = Yu YB | title = Coiled-coils: stability, specificity, and drug delivery potential | journal = Advanced Drug Delivery Reviews | volume = 54 | issue = 8 | pages = 1113–1129 | date = October 2002 | pmid = 12384310 | doi = 10.1016/S0169-409X(02)00058-3 }}
* {{cite journal | vauthors = Burkhard P, Ivaninskii S, Lustig A | title = Improving coiled-coil stability by optimizing ionic interactions | journal = Journal of Molecular Biology | volume = 318 | issue = 3 | pages = 901–910 | date = May 2002 | pmid = 12054832 | doi = 10.1016/S0022-2836(02)00114-6 }}
* {{cite journal | vauthors = Gillingham AK, Munro S | title = Long coiled-coil proteins and membrane traffic | journal = Biochimica et Biophysica Acta (BBA) - Molecular Cell Research | volume = 1641 | issue = 2–3 | pages = 71–85 | date = August 2003 | pmid = 12914949 | doi = 10.1016/S0167-4889(03)00088-0 | doi-access = free }}
* {{cite journal | vauthors = Mason JM, Arndt KM | title = Coiled coil domains: stability, specificity, and biological implications | journal = ChemBioChem | volume = 5 | issue = 2 | pages = 170–176 | date = February 2004 | pmid = 14760737 | doi = 10.1002/cbic.200300781 | s2cid = 39252601 }}
{{refend}}

== External links ==
* [http://www.proteopedia.org/wiki/index.php/Keratins Coiled-coil domains of keratins]

=== Coiled-coil related software ===

==== Prediction, detection, and visualization ====
* {{Webarchive |url=https://archive.today/20121223004906/http://supfam2.cs.bris.ac.uk/SUPERFAMILY/spiricoil |title=Spiricoil predict Coiled Coil and Oligormeric state from a protein sequences}}
* {{Webarchive |url=https://archive.today/20020111053708/http://www.russell.embl-heidelberg.de/cgi-bin/coils-svr.pl |title=NCOILS}}
* [http://groups.csail.mit.edu/cb/paircoil2 Paircoil2] / [http://groups.csail.mit.edu/cb/paircoil Paircoil]
* [http://www.syntbio.net/bCIPA/ bCIPA] Estimates Tm values for coiled coil pairs
* [https://people.bath.ac.uk/jm2219/biology/bcipa-library.php bCIPA library screen] Screens a library of sequences against a single defined target and estimates Tm values for all coiled coils pairs.
* [http://people.bath.ac.uk/jm2219/biology/bcipa-interactome.php bCIPA Interactome Screen] Screens all interactions between a selection of defined sequences and estimates Tm values for all coiled coil pairs.
* [http://3d-alignment.eu/ STRAP] contains an algorithm to predict coiled-coils from AA-sequences.
* [http://www.bioinf.jku.at/software/procoil/ PrOCoil] predicts the oligomerization of coiled coil proteins and visualizes the contribution of each individual amino acid to the overall oligomeric tendency.
* [http://www.grigoryanlab.org/drawcoil/ DrawCoil] creates helical wheel diagrams for coiled coils of any oligomerization state and orientation.

==== Databases ====
* [http://supfam.org/SUPERFAMILY/spiricoil Spiricoil] uses protein domain annotation to predict coiled coil presence and oligormeric state for all completely sequenced organisms
* [http://coiledcoils.chm.bris.ac.uk/ccplus/search/ CC+] {{Webarchive|url=https://web.archive.org/web/20111108092907/http://coiledcoils.chm.bris.ac.uk/ccplus/search/ |date=2011-11-08 }} is a [[relational database]] of coiled coils found in the [[protein data bank|PDB]]
* [http://supfam.org/SUPERFAMILY SUPERFAMILY] protein domain annotation for all completely sequenced organisms based on the expertly curated [[Structural Classification of Proteins|SCOP]] coiled coil class

{{Protein tandem repeats}}
{{Protein secondary structure}}

[[Category:Protein folds]]