Small protein
{{Short description|Protein fold class, typically <100 amino acids long}}
Small proteins are a diverse fold class of proteins (usually <100 amino acids long).{{cite journal | vauthors = Kihara D, Skolnick J | title = The PDB is a covering set of small protein structures | journal = Journal of Molecular Biology | volume = 334 | issue = 4 | pages = 793–802 | date = December 2003 | pmid = 14636603 | doi = 10.1016/j.jmb.2003.10.027 | citeseerx = 10.1.1.333.477 }}{{cite journal | vauthors = Su M, Ling Y, Yu J, Wu J, Xiao J | title = Small proteins: untapped area of potential biological importance | journal = Frontiers in Genetics | volume = 4 | pages = 286 | date = December 2013 | pmid = 24379829 | pmc = 3864261 | doi = 10.3389/fgene.2013.00286 | doi-access = free }}{{cite journal | vauthors = Storz G, Wolf YI, Ramamurthi KS | title = Small proteins can no longer be ignored | journal = Annual Review of Biochemistry | volume = 83 | issue = 1 | pages = 753–77 | date = 2014-06-02 | pmid = 24606146 | doi = 10.1146/annurev-biochem-070611-102400 | pmc = 4166647 }} Their tertiary structure is usually maintained by disulphide bridges,{{cite journal | vauthors = Cheek S, Krishna SS, Grishin NV | title = Structural classification of small, disulfide-rich protein domains | journal = Journal of Molecular Biology | volume = 359 | issue = 1 | pages = 215–37 | date = May 2006 | pmid = 16618491 | doi = 10.1016/j.jmb.2006.03.017 }} metal ligands,{{cite journal|last1=Berg|first1=J. M.|url=https://www.jbc.org/article/S0021-9258(19)39172-0/pdf|url-status=live|archive-url=https://web.archive.org/web/20220508064711/https://www.jbc.org/article/S0021-9258%2819%2939172-0/pdf|archive-date=8 May 2022|title = Zinc fingers and other metal-binding domains. Elements for interactions between macromolecules | journal = The Journal of Biological Chemistry | volume = 265 | issue = 12 | pages = 6513–6 | date = April 1990 |doi=10.1016/S0021-9258(19)39172-0 | pmid = 2108957 |doi-access=free }} 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. {{cite journal | vauthors = Brandenburg F, Klähn S | title = Small but smart: On the diverse role of small proteins in the regulation of cyanobacterial metabolism | journal = Life | volume = 10 | issue = 12 | date = 2020 | page = 322 | doi = 10.3390/life10120322 | pmid = 33271798 |pmc=7760959 | doi-access = free | bibcode = 2020Life...10..322B }}
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. {{Cite journal |last1=Richardson |first1=E. J. |last2=Watson |first2=M. |date=2012-03-09 |title=The automatic annotation of bacterial genomes |url=https://doi.org/10.1093/bib/bbs007 |journal=Briefings in Bioinformatics |volume=14 |issue=1 |pages=1–12 |doi=10.1093/bib/bbs007 |issn=1467-5463 |pmc=3548604 |pmid=22408191}} RNA sequencing or mass spectrometric data sets available are also incorporated into computational predictions. {{Cite journal |last1=Sberro |first1=Hila |last2=Fremin |first2=Brayon J. |last3=Zlitni |first3=Soumaya |last4=Edfors |first4=Fredrik |last5=Greenfield |first5=Nicholas |last6=Snyder |first6=Michael P. |last7=Pavlopoulos |first7=Georgios A. |last8=Kyrpides |first8=Nikos C. |last9=Bhatt |first9=Ami S. |date=2019-08-22 |title=Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes |journal=Cell |language=English |volume=178 |issue=5 |pages=1245–1259.e14 |doi=10.1016/j.cell.2019.07.016 |issn=0092-8674 |pmc=6764417 |pmid=31402174}}{{Cite journal |last1=Miravet-Verde |first1=Samuel |last2=Ferrar |first2=Tony |last3=Espadas-García |first3=Guadalupe |last4=Mazzolini |first4=Rocco |last5=Gharrab |first5=Anas |last6=Sabido |first6=Eduard |last7=Serrano |first7=Luis |last8=Lluch-Senar |first8=Maria |title=Unraveling the hidden universe of small proteins in bacterial genomes |journal=Molecular Systems Biology |year=2019 |language=en |volume=15 |issue=2 |pages=e8290 |doi=10.15252/msb.20188290 |issn=1744-4292 |pmc=6385055 |pmid=30796087}}
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.{{Cite journal |last1=Ingolia |first1=Nicholas T. |last2=Brar |first2=Gloria A. |last3=Rouskin |first3=Silvia |last4=McGeachy |first4=Anna M. |last5=Weissman |first5=Jonathan S. |title=The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments |journal=Nature Protocols |year=2012 |language=en |volume=7 |issue=8 |pages=1534–1550 |doi=10.1038/nprot.2012.086 |pmid=22836135 |pmc=3535016 |issn=1750-2799}}
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.{{Cite journal |last1=Ahrens |first1=Christian H. |last2=Wade |first2=Joseph T. |last3=Champion |first3=Matthew M. |last4=Langer |first4=Julian D. |date=2022-01-18 |editor-last=Henkin |editor-first=Tina M. |title=A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry |journal=Journal of Bacteriology |language=en |volume=204 |issue=1 |pages=e00353–21 |doi=10.1128/jb.00353-21 |issn=0021-9193 |pmc=8765459 |pmid=34748388}}