Nucleic acid quaternary structure

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Nucleic acid primary structureNucleic acid secondary structureNucleic acid tertiary structureNucleic acid quaternary structure
The image above contains clickable links
The image above contains clickable links
Interactive image of nucleic acid structure (primary, secondary, tertiary, and quaternary) using DNA helices and examples from the VS ribozyme and telomerase and nucleosome. (PDB: ADNA, 1BNA, 4OCB, 4R4V, 1YMO, 1EQZ​)
DNA coils and winds around histone proteins to condense into chromatin.

Nucleic acid quaternary structure refers to the interactions between separate nucleic acid molecules, or

gene transcription
will be inhibited.

DNA

DNA quaternary structure is used to refer to the binding of DNA to histones to form nucleosomes, and then their organisation into higher-order chromatin fibres.[2] The quaternary structure of DNA strongly affects how accessible the DNA sequence is to the transcription machinery for expression of genes. DNA quaternary structure varies over time, as regions of DNA are condensed or exposed for transcription. The term has also been used to describe the hierarchical assembly of artificial nucleic acid building blocks used in DNA nanotechnology.[3]

The quaternary structure of DNA refers to the formation of chromatin. Because the

histones. The nucleosome core usually contains around 146 DNA base pairs wrapped around a histone octamer.[4]  The histone octamer is made of eight total histone proteins, two of each of the following proteins: H2A, H2B, H3, and H4.[5]  Histones are primarily responsible for shaping the nucleosomes, therefore drastically contributing to chromatin structure.[4]  Histone proteins are positively-charged and therefore can interact with the negatively-charged phosphate backbone of DNA.[5]  One portion of core histone proteins, known as histone tail domains, are extremely important for keeping the nucleosome tightly wrapped and giving the nucleosome secondary and tertiary structure. This is because the histone tail domains are involved in interactions between nucleosomes. The linker histone, or H1 protein, is also involved maintaining nucleosome structure. The H1 protein has the special role of ensuring that DNA stays tightly wound.[4]

Modifications to histone proteins and their DNA are classified as quaternary structure. Condensed chromatin,

Enzymes, known as epigenetic writers and epigenetic erasers, catalyze either the addition or removal of several modifications to the histone tail domains. For instance, an enzyme writer can methylate Lysine-9 of the H3 core protein, which is found in the H3 histone tail domain. This can lead to gene repression as the chromatin gets remodeled and resembles heterochromatin. However, dozens of modifications can be made to histone tail domains. Therefore, it is the sum of all those modifications that determine whether chromatin will resemble heterochromatin or euchromatin.[7]

The three-dimensional folding motif known as the kissing loop. In this diagram, two kissing loop models are overlaid to show structural similarities. The white backbone and pink bases are from B. subtilis, and the gray backbone and blue bases are from V. vulnificus.[8]
A Minor Motif interaction

RNA

RNA is subdivided into many categories, including messenger RNA (

lncRNA), and several other small functional RNAs. Whereas many proteins have quaternary structure, the majority of RNA molecules have only primary through tertiary structure and function as individual molecules rather than as multi-subunit structures.[1] Some types of RNA show clear quaternary structure that is essential for function, whereas other types of RNA function as single molecules and do not associate with other molecules to form quaternary structures. Symmetrical complexes of RNA molecules are extremely uncommon compared to protein oligomers.[1] One example of an RNA homodimer is the VS ribozyme from Neurospora, with its two active sites consisting of nucleotides from both monomers.[9] The best known example of RNA forming quaternary structures with proteins is the ribosome, which consists of multiple rRNAs, supported by rProteins.[10][11] Similar RNA-Protein complexes are also found in the spliceosome
.

Riboswitches

ligands. Riboswitches determine how gene expression responds to varying concentrations of small molecules in the cell[12] This motif has been observed in flavin mononucleotide (FMN), cyclic di-AMP (c-di-AMP), and glycine. Riboswitches are said to show pseudoquaternary structure. Several structurally similar regions of a single RNA molecule fold together symmetrically. Because this structure arises from a single molecule and not from multiple separate molecules, it cannot be referred to as true quaternary structure.[1] Depending on where a riboswitch binds and how it is arranged, it can suppress or allow a gene to be expressed[12] Symmetry is an important part of biomolecular three-dimensional configurations. Many proteins are sy.mmetrical on the level of quaternary structure, but RNAs rarely have symmetrical quaternary structures. Even though tertiary structure is variant and essential for all types of RNAs, RNA oligimerization is relatively rare.[1]

rRNA

polypeptide
to be formed, proper association of the mRNA and both of the ribosome subunits must occur. At left, the secondary structure of rRNA in the peptidyltransferase center of the ribosome in yeast. The peptidyltransferase center is where the formation of the peptide bond is catalyzed during translation. At right, the three-dimensional structure of the peptidyltransferase center. The helical rRNA is associated with globular ribosomal proteins. Incoming codons arrive at the A site and move to the P site, where peptide bond formation is catalyzed. One specific three dimensional structure that is commonly observed in rRNA is the A-minor motif. There are four types of A-minor motifs, all of which include many unpaired
minor groove.[1]

tRNA

While consensus secondary and tertiary structures have been observed in tRNAs, there has not been evidence of tRNAs creating a quaternary structure thus far.

70S ribosome and other proteins.[13][12]

Other small RNAs

pRNA

cryo-EM structures suggest pRNA may also form pentameric rings.[14]

Kissing loop Motif

In this model, based on Dengue Virus Methyltransferase, four monomers of methyltransferase surround two octamers of RNA. The nucleic acid associations demonstrate the kissing loop motif. The three-dimensional folding motif known as the kissing loop. In this diagram, two kissing loop models are overlaid to show structural similarities. The white backbone and pink bases are from B. subtilis, and the gray backbone and blue bases are from V. vulnificus.

The kissing loop motif has been observed in

retroviruses and RNAs that are encoded by plasmids.[12]
The determination of the number of kissing loops to form the capsid varies between 5 and 6. Five kissing loops have been shown to have a stronger stability due to the particular symmetry that the 5 kissing loop structure provides.

Small nuclear RNA

Small nuclear RNA (

macromolecularcomplex. Quaternary structure allows snRNA to detect mRNA sequences that need to be excised.[15]

References

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  3. ISBN 978-3-527-31563-5
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  4. ^
    PMID 25980611
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  5. ^ a b Annunziato A (2008). "DNA Packaging: Nucleosomes and Chromatin". Nature Education. 1 (1): 26.
  6. ^ Duggan NM, Tang ZI (2010). "The Formation of Heterochromatin and RNA interference". Nature Education. 3 (9): 5.
  7. ISBN 978-1464109485
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  8. PMID 24040136
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  9. PMID 26414446
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  10. S2CID 36722002
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  11. PMID 11296253
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  12. ^
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  14. PMID 21471452
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  15. PMID 21441581
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