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出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2016/08/02 20:24:50」(JST)

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This example of a naturally occurring pseudoknot is found in the RNA component of human telomerase. Sequence from.^[1]

Threedimensional structure of a pseudoknot from a human telomerase RNA. (A) sticks (B) backbone. The pdb-file is based on PDB: 1YMO.

A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982.^[2] Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots.

Prediction and identification

The structural configuration of pseudoknots does not lend itself well to bio-computational detection due to its context-sensitivity or “overlapping” nature. The base pairing in pseudoknots is not well nested; that is, base pairs occur that "overlap" one another in sequence position. This makes the presence of pseudoknots in RNA sequences more difficult to predict by the standard method of dynamic programming, which use a recursive scoring system to identify paired stems and consequently, most cannot detect non-nested base pairs. The newer method of stochastic context-free grammars suffers from the same problem. Thus, popular secondary structure prediction methods like Mfold and Pfold will not predict pseudoknot structures present in a query sequence; they will only identify the more stable of the two pseudoknot stems.

It is possible to identify a limited class of pseudoknots using dynamic programming, but these methods are not exhaustive and scale worse as a function of sequence length than non-pseudoknotted algorithms.^[3]^[4] The general problem of predicting lowest free energy structures with pseudoknots has been shown to be NP-complete.^[5]^[6]

Biological significance

Several important biological processes rely on RNA molecules that form pseudoknots, which are often RNAs with extensive tertiary structure. For example, the pseudoknot region of RNase P is one of the most conserved elements in all of evolution. The telomerase RNA component contains a pseudoknot that is critical for activity,^[1] and several viruses use a pseudoknot structure to form a tRNA-like motif to infiltrate the host cell.^[7]

References

^ ^a ^b Chen JL, Greider CW. (2005). "Functional analysis of the pseudoknot structure in human telomerase RNA". Proc Natl Acad Sci USA 102(23): 8080–5.
^ Staple DW, Butcher SE (June 2005). "Pseudoknots: RNA structures with diverse functions". PLoS Biol. 3 (6): e213. doi:10.1371/journal.pbio.0030213. PMC 1149493. PMID 15941360. Retrieved 2010-07-15.
^ Rivas E, Eddy S. (1999). "A dynamic programming algorithm for RNA structure prediction including pseudoknots". J Mol Biol 285(5): 2053–2068.
^ Dirks, R.M. Pierce N.A. (2004) An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. "J Computation Chemistry". 25:1295-1304, 2004.
^ Lyngsø RB, Pedersen CN. (2000). "RNA pseudoknot prediction in energy-based models". J Comput Biol 7(3–4): 409–427.
^ Lyngsø, R. B. (2004). Complexity of pseudoknot prediction in simple models. Paper presented at the ICALP.
^ Pleij CW, Rietveld K, Bosch L (1985). "A new principle of RNA folding based on pseudoknotting.". Nucleic Acids Res 13 (5): 1717–31. doi:10.1093/nar/13.5.1717. PMC 341107. PMID 4000943.

External links

Rfam entry for Pseudoknots

English Journal

A novel cis-acting element within the capsid-coding region enhances flavivirus vRNA replication by regulating genome cyclization.

Liu ZY, Li XF, Jiang T, Deng YQ, Zhao H, Wang HJ, Ye Q, Zhu SY, Qiu Y, Zhou X, Qin ED, Qin CF.SourceDepartment of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
Journal of virology.J Virol.2013 Apr 10. [Epub ahead of print]
Cis-acting elements in the viral genome RNA (vRNA) are essential for the translation, replication and/or encapsidation of RNA viruses. In this study, a novel conserved cis-acting element was identified in the capsid-coding region of mosquito-borne flavivirus. The downstream of 5' cyclization sequenc
PMID 23576500

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.

Hajdin CE, Bellaousov S, Huggins W, Leonard CW, Mathews DH, Weeks KM.SourceDepartment of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290.
Proceedings of the National Academy of Sciences of the United States of America.Proc Natl Acad Sci U S A.2013 Apr 2;110(14):5498-503. doi: 10.1073/pnas.1219988110. Epub 2013 Mar 15.
A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruse
PMID 23503844

Specific contacts between protein S4 and ribosomal RNA are required at multiple stages of ribosome assembly.

Mayerle M, Woodson SA.AbstractAssembly of bacterial 30S ribosomal subunits requires structural rearrangements to both its 16S rRNA and ribosomal protein components. Ribosomal protein S4 nucleates 30S assembly and associates rapidly with the 5' domain of the 16S rRNA. In vitro, transformation of initial S4-rRNA complexes to long-lived, mature complexes involves refolding of 16S helix 18, which forms part of the decoding center. Here we use targeted mutagenesis of Geobacillus stearothermophilus S4 to show that remodeling of S4-rRNA complexes is perturbed by ram alleles associated with reduced translational accuracy. Gel mobility shift assays, SHAPE chemical probing, and in vivo complementation show that the S4 N-terminal extension is required for RNA binding and viability. Alanine substitutions in Y47 and L51 that interact with 16S helix 18 decrease S4 affinity and destabilize the helix 18 pseudoknot. These changes to the protein-RNA interface correlate with no growth (L51A) or cold-sensitive growth, 30S assembly defects, and accumulation of 17S pre-rRNA (Y47A). A third mutation, R200A, over-stabilizes the helix 18 pseudoknot yet results in temperature-sensitive growth, indicating that complex stability is finely tuned by natural selection. Our results show that early S4-RNA interactions guide rRNA folding and impact late steps of 30S assembly.
RNA (New York, N.Y.).RNA.2013 Apr;19(4):574-85. doi: 10.1261/rna.037028.112. Epub 2013 Feb 21.
Assembly of bacterial 30S ribosomal subunits requires structural rearrangements to both its 16S rRNA and ribosomal protein components. Ribosomal protein S4 nucleates 30S assembly and associates rapidly with the 5' domain of the 16S rRNA. In vitro, transformation of initial S4-rRNA complexes to long-
PMID 23431409

Japanese Journal

期待精度最大化に基づくRNAシュードノット予測

佐藤健吾,加藤有己,阿久津達也,浅井潔
情報処理学会研究報告. BIO, バイオ情報学 2010-BIO-22(6), 1-6, 2010-07-21
RNA に観測されるシュードノットと呼ばれる部分構造は,多くの場合 3 次元空間上での折り畳みを補助する役割を担うことが知られており,シュードノットを含めた RNA 2 次構造予測はその立体構造決定への手がかりを与えるものと期待される.本稿では,期待精度最大化に基づくシュードノット構造予測法 IPknot を提案する.IPknot では,シュードノットを考慮した事後塩基対確率分布を,シュードノット …
NAID 110007990853

整数計画法によるシュードノットつきRNA2次構造予測

プンサップアンヤーニー,加藤有己,阿久津達也
情報処理学会研究報告. MPS, 数理モデル化と問題解決研究報告 2007(128), 137-142, 2007-12-20
生体高分子の機能の解明にはその折り畳み構造を理解する必要があるとされている.特に,機能的非コードRNAが注目を集めている.RNAの立体構造を予測することは困難であるため,シュードノットを含む,または含まない2次構造を予測する研究が行われてきた.本稿では,整数計画法を2次構造予測に適用する手法を提案する.ここで,シュードノットを含まない構造と,任意の平面的シュードノット構造を予測するための2つの定式 …
NAID 110006595413

整数計画法によるシュードノットつきRNA2次構造予測

プンサップアンヤーニー,加藤有己,阿久津達也
情報処理学会研究報告. BIO, バイオ情報学 2007(128), 137-142, 2007-12-20
生体高分子の機能の解明にはその折り畳み構造を理解する必要があるとされている.特に,機能的非コードRNAが注目を集めている.RNAの立体構造を予測することは困難であるため,シュードノットを含む,または含まない2次構造を予測する研究が行われてきた.本稿では,整数計画法を2次構造予測に適用する手法を提案する.ここで,シュードノットを含まない構造と,任意の平面的シュードノット構造を予測するための2つの定式 …
NAID 110006594837

Related Pictures

★リンクテーブル★

リンク元	「偽結節」「偽結び目構造」「シュードノット」

「偽結節」

　　[★]

英: pseudotubercle, false tubercle, false knot, pseudoknot

「偽結び目構造」

　　[★]

英: pseudoknot
関: シュードノット

「シュードノット」

　　[★]

英: pseudoknot
関: 偽結び目構造

[Chen-1] Chen JL, Greider CW. (2005). "Functional analysis of the pseudoknot structure in human telomerase RNA". Proc Natl Acad Sci USA 102(23): 8080–5.

[Staple-2] Staple DW, Butcher SE (June 2005). "Pseudoknots: RNA structures with diverse functions". PLoS Biol. 3 (6): e213. doi:10.1371/journal.pbio.0030213. PMC 1149493. PMID 15941360. Retrieved 2010-07-15.

[Rivas-3] Rivas E, Eddy S. (1999). "A dynamic programming algorithm for RNA structure prediction including pseudoknots". J Mol Biol 285(5): 2053–2068.

[Dirks-4] Dirks, R.M. Pierce N.A. (2004) An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. "J Computation Chemistry". 25:1295-1304, 2004.

[Lyngso-5] Lyngsø RB, Pedersen CN. (2000). "RNA pseudoknot prediction in energy-based models". J Comput Biol 7(3–4): 409–427.

[Lyngso_04-6] Lyngsø, R. B. (2004). Complexity of pseudoknot prediction in simple models. Paper presented at the ICALP.

[pmid4000943-7] Pleij CW, Rietveld K, Bosch L (1985). "A new principle of RNA folding based on pseudoknotting.". Nucleic Acids Res 13 (5): 1717–31. doi:10.1093/nar/13.5.1717. PMC 341107. PMID 4000943.

v t e Biomolecular structure

Protein structure	Primary Secondary Tertiary Quaternary Determination Prediction Design Thermodynamics

Nucleic acid structure	Primary Secondary Tertiary Quaternary Determination Prediction Design Thermodynamics

See also	Protein Protein domain Protein engineering Nucleic acid DNA RNA Nucleic acid double helix

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pseudoknot