In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a common three-dimensional structure that appears in a variety of different, evolutionarily unrelated molecules.[1] 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.
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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 intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA.[2] 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 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.[3] Two classes of cruciform DNA have been described; folded and unfolded.
G-quadruplexsecondary structures (G4) are formed in nucleic acids by sequences that are rich in guanine.[4] They are helical in shape and contain guanine tetrads that can form from one,[5] two[6] or four strands.[7]
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.[8] An R-loop is similar to a D-loop, but in this case the third strand is RNA rather than DNA.[9] The third strand has a base sequence which is complementary to one of the main strands and 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".[10]
In proteinsEdit
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 tandem repeats.
^Johansson, M.U. (23 July 2012). "Defining and searching for structural motifs using DeepView/Swiss-PdbViewer". BMC Bioinformatics. 13 (173): 173. doi:10.1186/1471-2105-13-173. PMC3436773. PMID 22823337.
^Bolshoy, Alexander (2010). Genome Clustering: From Linguistic Models to Classification of Genetic Texts. Springer. p. 47. ISBN9783642129513. Retrieved 24 March 2021.
^Shlyakhtenko LS, Potaman VN, Sinden RR, Lyubchenko YL (July 1998). "Structure and dynamics of supercoil-stabilized DNA cruciforms". J. Mol. Biol. 280 (1): 61–72. CiteSeerX10.1.1.555.4352. doi:10.1006/jmbi.1998.1855. PMID 9653031.
^Routh ED, Creacy SD, Beerbower PE, Akman SA, Vaughn JP, Smaldino PJ (March 2017). "A G-quadruplex DNA-affinity Approach for Purification of Enzymaticacvly Active G4 Resolvase1". Journal of Visualized Experiments. 121 (121). doi:10.3791/55496. PMC5409278. PMID 28362374.
^Largy E, Mergny J, Gabelica V (2016). "Chapter 7. Role of Alkali Metal Ions in G-Quadruplex Nucleic Acid Structure and Stability". In Astrid S, Helmut S, Roland KO S (eds.). The Alkali Metal Ions: Their Role in Life(PDF). Metal Ions in Life Sciences. Vol. 16. Springer. pp. 203–258. doi:10.1007/978-3-319-21756-7_7. PMID 26860303.
^Sundquist WI, Klug A (December 1989). "Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops". Nature. 342 (6251): 825–9. Bibcode:1989Natur.342..825S. doi:10.1038/342825a0. PMID 2601741. S2CID 4357161.
^Sen D, Gilbert W (July 1988). "Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis". Nature. 334 (6180): 364–6. Bibcode:1988Natur.334..364S. doi:10.1038/334364a0. PMID 3393228. S2CID 4351855.
^DePamphilis, Melvin (2011). Genome Duplication. Garland Science, Taylor & Francis Group, LLC. p. 419. ISBN9780415442060. Retrieved 24 March 2021.
^Al-Hadid, Qais (July 1, 2016). "R-loop: an emerging regulator of chromatin dynamics". Acta Biochim Biophys Sin (Shanghai). 48 (7): 623–31. doi:10.1093/abbs/gmw052. PMC6259673. PMID 27252122.
^Kasamatsu, H.; Robberson, D. L.; Vinograd, J. (1971). "A novel closed-circular mitochondrial DNA with properties of a replicating intermediate". Proceedings of the National Academy of Sciences of the United States of America. 68 (9): 2252–2257. Bibcode:1971PNAS...68.2252K. doi:10.1073/pnas.68.9.2252. PMC389395. PMID 5289384.
^Hettiarachchy, Navam S (2012). Food Proteins and Peptides: Chemistry, Functionality, Interactions, and Commercialization. CRC Press Taylor & Francis Group. p. 16. ISBN9781420093421. Retrieved 24 March 2021.
^Dubey, R C (2014). Advanced Biotechnology. S Chand Publishing. p. 505. ISBN978-8121942904. Retrieved 24 March 2021.
^Milner-White, E. James (September 26, 2011). "Functional Capabilities of the Earliest Peptides and the Emergence of Life". Genes. 2 (4): 674. doi:10.3390/genes2040671. PMC3927598. PMID 24710286.
^Milner-White, E. James (September 26, 2011). "Functional Capabilities of the Earliest Peptides and the Emergence of Life". Genes. 2 (4): 678. doi:10.3390/genes2040671. PMC3927598. PMID 24710286.
SMoS SMoS - Database of Structural Motifs of Superfamily
S4
Further readingEdit
Chiang YS, Gelfand TI, Kister AE, Gelfand IM (2007). "New classification of supersecondary structures of sandwich-like proteins uncovers strict patterns of strand assemblage". Proteins. 68 (4): 915–921. doi:10.1002/prot.21473. PMID 17557333. S2CID 29904865.
September 02, 2023
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For other uses see Motif disambiguation This article includes a list of general references but it lacks sufficient corresponding inline citations Please help to improve this article by introducing more precise citations August 2016 Learn how and when to remove this template message In a chain like biological molecule such as a protein or nucleic acid a structural motif is a common three dimensional structure that appears in a variety of different evolutionarily unrelated molecules 1 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 Contents 1 In nucleic acids 2 In proteins 3 See also 4 References 5 Further readingIn nucleic acids EditSee also Non B database This section needs expansion You can help by adding to it 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 2 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 3 Two classes of cruciform DNA have been described folded and unfolded G quadruplex G quadruplex secondary structures G4 are formed in nucleic acids by sequences that are rich in guanine 4 They are helical in shape and contain guanine tetrads that can form from one 5 two 6 or four strands 7 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 8 An R loop is similar to a D loop but in this case the third strand is RNA rather than DNA 9 The third strand has a base sequence which is complementary to one of the main strands and 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 10 In proteins EditIn 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 tandem repeats Beta hairpin Extremely common Two antiparallel beta strands connected by a tight turn of a few amino acids between them 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 11 Helix loop helix Consists of 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 a helices joined by a short strand of amino acids and found in many proteins that regulate gene expression 12 Nest Extremely common Three consecutive amino acid residues form an anion binding concavity 13 Niche Extremely common Three or four consecutive amino acid residues form a cation binding feature 14 See also EditSequence motif Short linear motif Protein tandem repeatsReferences Edit Johansson M U 23 July 2012 Defining and searching for structural motifs using DeepView Swiss PdbViewer BMC Bioinformatics 13 173 173 doi 10 1186 1471 2105 13 173 PMC 3436773 PMID 22823337 Bolshoy Alexander 2010 Genome Clustering From Linguistic Models to Classification of Genetic Texts Springer p 47 ISBN 9783642129513 Retrieved 24 March 2021 Shlyakhtenko LS Potaman VN Sinden RR Lyubchenko YL July 1998 Structure and dynamics of supercoil stabilized DNA cruciforms J Mol Biol 280 1 61 72 CiteSeerX 10 1 1 555 4352 doi 10 1006 jmbi 1998 1855 PMID 9653031 Routh ED Creacy SD Beerbower PE Akman SA Vaughn JP Smaldino PJ March 2017 A G quadruplex DNA affinity Approach for Purification of Enzymaticacvly Active G4 Resolvase1 Journal of Visualized Experiments 121 121 doi 10 3791 55496 PMC 5409278 PMID 28362374 Largy E Mergny J Gabelica V 2016 Chapter 7 Role of Alkali Metal Ions in G Quadruplex Nucleic Acid Structure and Stability In Astrid S Helmut S Roland KO S eds The Alkali Metal Ions Their Role in Life PDF Metal Ions in Life Sciences Vol 16 Springer pp 203 258 doi 10 1007 978 3 319 21756 7 7 PMID 26860303 Sundquist WI Klug A December 1989 Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops Nature 342 6251 825 9 Bibcode 1989Natur 342 825S doi 10 1038 342825a0 PMID 2601741 S2CID 4357161 Sen D Gilbert W July 1988 Formation of parallel four stranded complexes by guanine rich motifs in DNA and its implications for meiosis Nature 334 6180 364 6 Bibcode 1988Natur 334 364S doi 10 1038 334364a0 PMID 3393228 S2CID 4351855 DePamphilis Melvin 2011 Genome Duplication Garland Science Taylor amp Francis Group LLC p 419 ISBN 9780415442060 Retrieved 24 March 2021 Al Hadid Qais July 1 2016 R loop an emerging regulator of chromatin dynamics Acta Biochim Biophys Sin Shanghai 48 7 623 31 doi 10 1093 abbs gmw052 PMC 6259673 PMID 27252122 Kasamatsu H Robberson D L Vinograd J 1971 A novel closed circular mitochondrial DNA with properties of a replicating intermediate Proceedings of the National Academy of Sciences of the United States of America 68 9 2252 2257 Bibcode 1971PNAS 68 2252K doi 10 1073 pnas 68 9 2252 PMC 389395 PMID 5289384 Hettiarachchy Navam S 2012 Food Proteins and Peptides Chemistry Functionality Interactions and Commercialization CRC Press Taylor amp Francis Group p 16 ISBN 9781420093421 Retrieved 24 March 2021 Dubey R C 2014 Advanced Biotechnology S Chand Publishing p 505 ISBN 978 8121942904 Retrieved 24 March 2021 Milner White E James September 26 2011 Functional Capabilities of the Earliest Peptides and the Emergence of Life Genes 2 4 674 doi 10 3390 genes2040671 PMC 3927598 PMID 24710286 Milner White E James September 26 2011 Functional Capabilities of the Earliest Peptides and the Emergence of Life Genes 2 4 678 doi 10 3390 genes2040671 PMC 3927598 PMID 24710286 PROSITE Database of protein families and domains SCOP Structural classification of Proteins CATH Class Architecture Topology Homology FSSP FSSP PASS2 PASS2 Protein Alignments as Structural Superfamilies SMoS SMoS Database of Structural Motifs of Superfamily S4 S4 Server for Super Secondary Structure Motif MiningFurther reading EditChiang YS Gelfand TI Kister AE Gelfand IM 2007 New classification of supersecondary structures of sandwich like proteins uncovers strict patterns of strand assemblage Proteins 68 4 915 921 doi 10 1002 prot 21473 PMID 17557333 S2CID 29904865 Retrieved from https en wikipedia org w index php title Structural motif amp oldid 1140249516, wikipedia, wiki, book, books, library,
