Editing Structural motif

{{Short description|Type of common three-dimensional structure in chain-like biological molecules}}
{{other uses|Motif (disambiguation)}}
{{more footnotes|date=August 2016}}

In a [[polymer|chain-like]] biological [[molecule]], such as a [[protein]] or  [[nucleic acid]], a '''structural motif''' is a common [[Biomolecular structure#Tertiary structure|three-dimensional structure]] that  appears in a variety of different, evolutionarily unrelated molecules.<ref>{{cite journal |last1=Johansson |first1=M.U. |title=Defining and searching for structural motifs using DeepView/Swiss-PdbViewer |journal=BMC Bioinformatics |date=23 July 2012 |volume=13 |issue=173 |page=173 |doi=10.1186/1471-2105-13-173 |pmid=22823337 |pmc=3436773 |doi-access=free }}</ref> A structural motif does not have to be associated with a [[sequence motif]]; it can be represented by different and completely unrelated sequences in different proteins or RNA.

==In nucleic acids==
{{See also|Non-B database}}

{{Expand section|date=August 2020}}

Depending upon the sequence and other conditions, nucleic acids can form a variety of structural motifs which is  thought to have biological significance.

;[[Stem-loop]]:  Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA.<ref>{{cite book |last1=Bolshoy |first1=Alexander |title=Genome Clustering: From Linguistic Models to Classification of Genetic Texts |date=2010 |publisher=Springer |isbn=9783642129513 |page=47 |url=https://books.google.com/books?id=CwBEn59owdoC&pg=PA47 |access-date=24 March 2021}}</ref> The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop. The resulting structure is a key building block of many RNA secondary structures.

;[[Cruciform DNA]]: '''Cruciform DNA''' is a form of non-B DNA that requires at least a 6 [[nucleotide]] sequence of [[inverted repeats]] to form a structure consisting of a stem, branch point and loop in the shape of a cruciform, stabilized by negative [[DNA supercoiling]].<ref name="pmid9653031">{{cite journal |vauthors=Shlyakhtenko LS, Potaman VN, Sinden RR, Lyubchenko YL |title=Structure and dynamics of supercoil-stabilized DNA cruciforms |journal=J. Mol. Biol. |volume=280 |issue=1 |pages=61–72 |date=July 1998 |pmid=9653031 |doi=10.1006/jmbi.1998.1855 |citeseerx=10.1.1.555.4352 }}</ref> Two classes of cruciform DNA have been described; folded and unfolded. 
 
;[[G-quadruplex]]: ''G-quadruplex'' [[Nucleic acid secondary structure|secondary structures]] (G4) are formed in nucleic acids by sequences that are rich in [[guanine]].<ref>{{cite journal | vauthors = Routh ED, Creacy SD, Beerbower PE, Akman SA, Vaughn JP, Smaldino PJ | title = A G-quadruplex DNA-affinity Approach for Purification of Enzymaticacvly Active G4 Resolvase1 | journal = Journal of Visualized Experiments | volume = 121 | issue = 121 | date = March 2017 | pmid = 28362374 | pmc = 5409278 | doi = 10.3791/55496 }}</ref>  They are helical in shape and contain guanine tetrads that can form from one,<ref name="Springer">{{cite book | first1 = Eric | last1 = Largy | first2 = Jean-Louis | last2 = Mergny | first3 = Valérie | last3 = Gabelica | name-list-style = vanc | publisher = Springer | date = 2016 | series = Metal Ions in Life Sciences | volume = 16 | title = The Alkali Metal Ions: Their Role in Life | editor1-last = Astrid | editor1-first = Sigel | editor2-last = Helmut | editor2-first = Sigel | editor3-last = Roland K.O. | editor3-first = Sigel | chapter = Chapter 7. Role of Alkali Metal Ions in G-Quadruplex Nucleic Acid Structure and Stability | pages = 203–258 | doi = 10.1007/978-3-319-21756-7_7 | pmid = 26860303 | isbn = 978-3-319-21755-0 | url = https://hal.archives-ouvertes.fr/hal-01524114/file/article.pdf }}</ref> two<ref name="ReferenceC">{{cite journal | vauthors = Sundquist WI, Klug A | title = Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops | journal = Nature | volume = 342 | issue = 6251 | pages = 825–9 | date = December 1989 | pmid = 2601741 | doi = 10.1038/342825a0 | bibcode = 1989Natur.342..825S | s2cid = 4357161 }}</ref> or four strands.<ref name="ReferenceB">{{cite journal | vauthors = Sen D, Gilbert W | title = Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis | journal = Nature | volume = 334 | issue = 6180 | pages = 364–6 | date = July 1988 | pmid = 3393228 | doi = 10.1038/334364a0 | bibcode = 1988Natur.334..364S | s2cid = 4351855 }}</ref>

;[[D-loop]]: A '''displacement loop''' or '''D-loop''' is a [[DNA]] structure where the two strands of a double-stranded DNA molecule are separated for a stretch and held apart by a third strand of DNA.<ref>{{cite book |last1=DePamphilis |first1=Melvin |title=Genome Duplication |date=2011 |publisher=Garland Science, Taylor & Francis Group, LLC |isbn=9780415442060 |page=419 |url=https://books.google.com/books?id=uSoWBAAAQBAJ&q=A+displacement+loop+or+D-loop+is+a+DNA+structure+where+the+two+strands+of+a+double-stranded+DNA+molecule+are+separated+for+a+stretch+and+held+apart+by+a+third+strand+of+DNA&pg=PA419 |access-date=24 March 2021}}</ref>  An [[R-loop]] is similar to a D-loop, but in this case the third strand is RNA rather than DNA.<ref>{{cite journal |last1=Al-Hadid |first1=Qais |title=R-loop: an emerging regulator of chromatin dynamics |journal=Acta Biochim Biophys Sin (Shanghai) |date=July 1, 2016 |volume=48 |issue=7 |pages=623–31 |doi=10.1093/abbs/gmw052 |pmid=27252122 |pmc=6259673 |doi-access=free }}</ref>  The third strand has a [[nucleobase|base]] sequence which is [[Complementarity (molecular biology)|complementary]] to one of the main strands and [[base pair|pairs]] with it, thus displacing the other complementary main strand in the region.  Within that region the structure is thus a form of [[triple-stranded DNA]]. A diagram in the paper introducing the term illustrated the D-loop with a shape resembling a capital "D", where the displaced strand formed the loop of the "D".<ref name=Kasamatsu>{{Cite journal
 | last1 = Kasamatsu | first1 = H.
 | last2 = Robberson | first2 = D. L.
 | last3 = Vinograd | first3 = J.
 | title = A novel closed-circular mitochondrial DNA with properties of a replicating intermediate
 | journal = Proceedings of the National Academy of Sciences of the United States of America
 | volume = 68
 | issue = 9
 | pages = 2252–2257
 | year = 1971
 | pmid = 5289384
 | pmc = 389395
 | doi=10.1073/pnas.68.9.2252
| bibcode = 1971PNAS...68.2252K
 | doi-access = free
 }}</ref>

==In proteins==

In proteins, a structural motif describes the connectivity between secondary structural elements. An individual motif usually consists of only a few elements, e.g., the 'helix-turn-helix' motif which has just three. Note that, while the ''spatial sequence'' of elements may be identical in all instances of a motif, they may be encoded in any order within the underlying [[gene]]. In addition to secondary structural elements, protein structural motifs often include loops of variable length and unspecified structure. Structural motifs may also appear as [[Protein tandem repeats|tandem repeats]].

; [[Beta hairpin]]: Extremely common. Two [[antiparallel (biochemistry)|antiparallel]] beta strands connected by a tight turn of a few amino acids between them.
; [[Beta sheet#Greek key motif|Greek key]]: Four beta strands, three connected by hairpins, the fourth folded over the top.
; [[Omega loop]]: A loop in which the residues that make up the beginning and end of the loop are very close together.<ref>{{cite book |last1=Hettiarachchy |first1=Navam S |title=Food Proteins and Peptides: Chemistry, Functionality, Interactions, and Commercialization |date=2012 |publisher=CRC Press Taylor & Francis Group |isbn=9781420093421 |page=16 |url=https://books.google.com/books?id=WWfMBQAAQBAJ&q=omega+loop+A+loop+in+which+the+residues+that+make+up+the+beginning+and+end+of+the+loop+are+very+close+together&pg=PA16 |access-date=24 March 2021}}</ref>
; [[Basic-helix-loop-helix|Helix-loop-helix]]: Consists of [[Alpha helix|alpha helices]] bound by a looping stretch of amino acids. This motif is seen in transcription factors.
; [[Zinc finger]]: Two beta strands with an alpha helix end folded over to bind a zinc [[ion]]. Important in DNA binding proteins.
; [[Helix-turn-helix]]: Two α helices joined by a short strand of amino acids and found in many proteins that regulate gene expression.<ref>{{cite book |last1=Dubey |first1=R C |title=Advanced Biotechnology |date=2014 |publisher=S Chand Publishing |isbn=978-8121942904 |page=505 |url=https://books.google.com/books?id=SKgrDAAAQBAJ&q=Helix-turn-helix+Two+%CE%B1+helices+joined+by+a+short+strand+of+amino+acids+and+found+in+many+proteins+that+regulate+gene+expression&pg=PA505 |access-date=24 March 2021}}</ref>
; [[Nest (protein structural motif)|Nest]]: Extremely common. Three consecutive amino acid residues form an anion-binding concavity.<ref>{{cite journal |last1=Milner-White |first1=E. James |title=Functional Capabilities of the Earliest Peptides and the Emergence of Life |journal=Genes |date=September 26, 2011 |volume=2 |issue=4 |page=674 |doi=10.3390/genes2040671 |pmid=24710286 |pmc=3927598 |doi-access=free }}</ref>
; [[Niche (protein structural motif)|Niche]]: Extremely common. Three or four consecutive amino acid residues form a cation-binding feature.<ref>{{cite journal |last1=Milner-White |first1=E. James |title=Functional Capabilities of the Earliest Peptides and the Emergence of Life |journal=Genes |date=September 26, 2011 |volume=2 |issue=4 |page=678 |doi=10.3390/genes2040671 |pmid=24710286 |pmc=3927598 |doi-access=free }}</ref>

==See also==
* [[Sequence motif]]
* [[Short linear motif]]
* [[Protein tandem repeats]]

==References==
{{Reflist}}
*[[PROSITE]] [http://www.expasy.org/prosite Database of protein families and domains]
*[[Structural Classification of Proteins|SCOP]] [https://web.archive.org/web/20070911012207/http://scop.mrc-lmb.cam.ac.uk/scop/ Structural classification of Proteins]
*[[CATH]] [http://www.cathdb.info/ Class Architecture Topology Homology]
*[[Families of structurally similar proteins|FSSP]] [https://web.archive.org/web/20030925185235/http://www.bioinfo.biocenter.helsinki.fi:8080/dali/index.html FSSP]
*[[PASS2]] [https://web.archive.org/web/20060831195006/http://caps.ncbs.res.in/campass/pass.html PASS2 - Protein Alignments as Structural Superfamilies]
*[[SMoS]] [http://caps.ncbs.res.in/SMoS SMoS - Database of Structural Motifs of Superfamily] {{Webarchive|url=https://web.archive.org/web/20070126135233/http://caps.ncbs.res.in/SMoS/ |date=2007-01-26 }}
*S4 [https://web.archive.org/web/20081121033341/http://www1.i2r.a-star.edu.sg/~azeyar/SuperSSE/ S4: Server for Super-Secondary Structure Motif Mining]

==Further reading==
* {{cite journal |vauthors=Chiang YS, Gelfand TI, Kister AE, Gelfand IM |title=New classification of supersecondary structures of sandwich-like proteins uncovers strict patterns of strand assemblage. |journal=Proteins |volume=68 |issue=4 |pages=915–921 |year=2007 |pmid=17557333 |doi=10.1002/prot.21473|s2cid=29904865 }}

{{DEFAULTSORT:Structural Motif}}
[[Category:Protein structural motifs]]
[[Category:Protein structure]]