Small proteins are a diverse
fold class of
proteins
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respondi ...
(usually <100
amino acids long). Their tertiary structure is usually maintained by
disulphide bridges
In biochemistry, a disulfide (or disulphide in British English) refers to a functional group with the structure . The linkage is also called an SS-bond or sometimes a disulfide bridge and is usually derived by the coupling of two thiol groups. In ...
,
metal ligands,
and or
cofactors
Cofactor may also refer to:
* Cofactor (biochemistry), a substance that needs to be present in addition to an enzyme for a certain reaction to be catalysed
* A domain parameter in elliptic curve cryptography, defined as the ratio between the orde ...
such as
heme
Heme, or haem (pronounced / hi:m/ ), is a precursor to hemoglobin, which is necessary to bind oxygen in the bloodstream. Heme is biosynthesized in both the bone marrow and the liver.
In biochemical terms, heme is a coordination complex "consis ...
. 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.
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 multiple parameters, such as the presence of a ribosome binding site and amino acid conservation.
RNA sequencing
RNA-Seq (named as an abbreviation of RNA sequencing) is a sequencing technique which uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment, analyzing the continuously changing c ...
or
mass spectrometric data sets available are also incorporated into computational predictions.
A method extensively used for the identification of small proteins is
ribosome profiling
Ribosome profiling, or Ribo-Seq (also named ribosome footprinting), is an adaptation of a technique developed by Joan Steitz and Marilyn Kozak almost 50 years ago that Nicholas Ingolia and Jonathan Weissman adapted to work with next generation s ...
(Ribo-seq or ribosome footprinting). Ribosome profiling uses
next generation sequencing
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The ...
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.
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.
See also
*
Cysteine-rich protein Cysteine-rich proteins (also cysteine-rich peptide, CRP, disulphide-rich peptide) are small proteins that contain a large number of cysteines. These cysteines either cross-link to form disulphide bonds, or bind metal ions by chelation, stabilisi ...
*
Intrinsically disordered proteins
In molecular biology, an intrinsically disordered protein (IDP) is a protein that lacks a fixed or ordered three-dimensional structure, typically in the absence of its macromolecular interaction partners, such as other proteins or RNA. IDPs ran ...
*
Metal-binding protein
Metal-binding proteins are proteins or protein domains that chelate a metal ion.
Binding of metal ions via chelation is usually achieved via histidines or cysteines. In some cases this is a necessary part of their folding and maintenance of a ...
*
Micropeptide
Micropeptides (also referred to as microproteins) are polypeptides with a length of less than 100-150 amino acids that are encoded by short open reading frames (sORFs). In this respect, they differ from many other active small polypeptides, which ...
References
Proteins
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