Biology:Small protein

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Short description: Protein fold class, typically <100 amino acids long

Small proteins are a diverse fold class of proteins (usually <100 amino acids long).[1][2][3] Their tertiary structure is usually maintained by disulphide bridges,[4] metal ligands,[5] and or cofactors such as heme. Some small proteins serve important regulatory functions by direct interaction with certain enzymes and are therefore also an interesting tool for biotechnological applications in microorganisms. [6]

Identification of small proteins

The size of small proteins has limited their identification and characterization for a long time. However, the various examples of functionality have led to the development of methods for their identification.

For larger ORFs, computational identification is based solely on their long uninterrupted coding potential. Computational searches for small proteins take into account multiple parameters, such as the presence of a ribosome binding site and amino acid conservation. [7] RNA sequencing or mass spectrometric data sets available are also incorporated into computational predictions. [8][9]

A method extensively used for the identification of small proteins is ribosome profiling (Ribo-seq or ribosome footprinting). Ribosome profiling uses next generation sequencing and targets only mRNA sequences protected by the ribosomes. Binding of a ribosome on an mRNA suggests that the transcript is being actively translated, allowing for the identification even of very small ORFs.[10]

Mass spectrometry is the best method thus far for identifying small proteins, but their sizes again pose a barrier. However, several adjustments are possible to perform to improve detection and data quality.[11]

See also

References

  1. ↑ "The PDB is a covering set of small protein structures". Journal of Molecular Biology 334 (4): 793–802. December 2003. doi:10.1016/j.jmb.2003.10.027. PMID 14636603. 
  2. ↑ "Small proteins: untapped area of potential biological importance". Frontiers in Genetics 4: 286. December 2013. doi:10.3389/fgene.2013.00286. PMID 24379829. 
  3. ↑ "Small proteins can no longer be ignored". Annual Review of Biochemistry 83 (1): 753–77. 2014-06-02. doi:10.1146/annurev-biochem-070611-102400. PMID 24606146. 
  4. ↑ "Structural classification of small, disulfide-rich protein domains". Journal of Molecular Biology 359 (1): 215–37. May 2006. doi:10.1016/j.jmb.2006.03.017. PMID 16618491. 
  5. ↑ Berg, J. M. (April 1990). "Zinc fingers and other metal-binding domains. Elements for interactions between macromolecules". The Journal of Biological Chemistry 265 (12): 6513–6. doi:10.1016/S0021-9258(19)39172-0. PMID 2108957. https://www.jbc.org/article/S0021-9258(19)39172-0/pdf. 
  6. ↑ "Small but smart: On the diverse role of small proteins in the regulation of cyanobacterial metabolism". Life 10 (12): 322. 2020. doi:10.3390/life10120322. PMID 33271798. 
  7. ↑ Richardson, E. J.; Watson, M. (2012-03-09). "The automatic annotation of bacterial genomes". Briefings in Bioinformatics 14 (1): 1–12. doi:10.1093/bib/bbs007. ISSN 1467-5463. PMID 22408191. PMC 3548604. https://doi.org/10.1093/bib/bbs007. 
  8. ↑ Sberro, Hila; Fremin, Brayon J.; Zlitni, Soumaya; Edfors, Fredrik; Greenfield, Nicholas; Snyder, Michael P.; Pavlopoulos, Georgios A.; Kyrpides, Nikos C. et al. (2019-08-22). "Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes" (in English). Cell 178 (5): 1245–1259.e14. doi:10.1016/j.cell.2019.07.016. ISSN 0092-8674. PMID 31402174. 
  9. ↑ Miravet‐Verde, Samuel; Ferrar, Tony; Espadas‐García, Guadalupe; Mazzolini, Rocco; Gharrab, Anas; Sabido, Eduard; Serrano, Luis; Lluch‐Senar, Maria (2019). "Unraveling the hidden universe of small proteins in bacterial genomes" (in en). Molecular Systems Biology 15 (2): e8290. doi:10.15252/msb.20188290. ISSN 1744-4292. PMID 30796087. 
  10. ↑ Ingolia, Nicholas T.; Brar, Gloria A.; Rouskin, Silvia; McGeachy, Anna M.; Weissman, Jonathan S. (2012). "The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments" (in en). Nature Protocols 7 (8): 1534–1550. doi:10.1038/nprot.2012.086. ISSN 1750-2799. PMID 22836135. 
  11. ↑ Ahrens, Christian H.; Wade, Joseph T.; Champion, Matthew M.; Langer, Julian D. (2022-01-18). Henkin, Tina M.. ed. "A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry" (in en). Journal of Bacteriology 204 (1): e00353–21. doi:10.1128/jb.00353-21. ISSN 0021-9193. PMID 34748388. 




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