Structural Biochemistry/Proteins/Posttranslational Modification of Proteins

Posttranslation modification is the process by which proteome complexity (the global collection of proteins) is built by diversification at both the mRNA level and after translation ofmRNAs into proteins by covalent modification of specific proteins. There are two broad categories of posttranslational modifications. The first is the covalent addition of one of more groups, such as phosphoryl, acetyl, or glycosyl, to one or more of the amino acid side chains in a particular protein. The second is the hydrolytic cleavage of one or more peptide bonds in a protein by protein called proteases (protein hydolases). There are more the 200 kinds of posttranslational modifications and almost all of them occur by covalent addition of groups to side chains in thousands of proteins carried out by enzymes. These enzymes are proteins with catalytic activity dedicated to effecting the posttranslational modifications. There are many types of catalytic posttranslations, with about 500 proteases encoded in the human genome and over 500 protein kinases for covalent phosphorylations of proteins. Also, there are nearly 150 protein phosphates opposing and balancing the action of protein kinases. Furthermore, there is a small subset of proteins which undergo automodifications- modifications without the help of ancillary catalysts to effect covalent change.

Scope of Posttranslational Modifications

The diversity of posttranslational modifications by the proteome can be plotted on multiple axis. One scope is the number of proteins modified and thus the number of modified proteins produced. These numbers can differ for a given protein. A second and third axis of scope of posttranslational modification is by the type of amino acid side chain modified and also the type of covalent chemical modification introduced by the posttranslational modification enzymes. In posttranslational modification, the chemical reaction is of enzyme catalyzed transfer of an electrophilic fragment of a co-substrate molecule onto a nucleophilic side chain of the protein undergoing modification. The chemical modification occurs when the attacking nucleophilic side chain of the protein transfers the electrophile. Therefore, common sites for posttranslational modifications are side chains of proteins that can potentially act as nucleophiles.

Reversible vs. Irreversible Posttranslational Modifications of Proteins

Some posttranslational modifications of proteins are irreversible, due to the nature of the biological function enabled by the modification. The most irreversible modifications are the proteolytic cleavages undergone by all proteins during their life cycles. The removal of N-terminal signal sequences of all proteins passing into the endoplasmic reticulum during the first stage of eukaryotic cell pathways is also irreversible. Also note that some posttranslational modifications are freely reversible in vivo but not in vitro.

Post-Translational Modifications in Circadian Rhythms

Circadian rhythms are the biological clocks that exist in living organisms. These clocks are produced by oscillations in gene expression. Transcriptions factors and negatively acting transcription factors control the expressions of certain genes in an organisms genome.

An example of a circadian rhythm in humans based on day and night.

These factors are proteins in themselves, and are thus subject to modifications after they have been folded (post-translational modifications). Modifications made to these transcription factors effect the rhythms of the genes on which they act. The effects of post-translation modifications can be studied on the positive transcription factors as well as on the negative factors. As reported by Dunlap et al., modification by phosphorylation, either by kinases or phosphatases, on the positively acting transcription factors result in its degradation. The same can be said about the negatively acting transcription factors, except that there are possibly non-degradative effects as well. For example, the negatively acting transcription factors can be phosphorylated by kinases and transported by these negatively acting factors in order to phosphorylate the positively acting transcription factors. The positively acting transcription factors, in turn, become inactivated.

Non-transcriptional Oscillator (NTO)

Theoretical evidences and recent discoveries have proven that there is a possible connection between non-transcriptional oscillator (NTO) and transcriptional/translational feedback loops (TTFLs). TTFL regulates translational modifications and engages in many important cellular programming relative to the circadian rhythm. However, studies have shown that the TFFL is challenged by the emergence of NTO circadian rhythms in cyanobacteria. NTO in eukaryotes produce a a very influential rhythmic output that is present in all organisms. As a result, NTO and TTFL elements are paired cooperatively in circadian science.

NTO and TTFL oscillators have history in operating separately, but evidence suggest that the coupling of the oscillators to function as a whole will be an evolutionary advantage. Linking NTO and TTFL enhances overall circadian performance. Mathematical and experimental data proved that the oscillators feed back to each other under habitual physiological conditions. 

---

Reference: Walsh, Christopher. "Posttranslational Modification of Proteins: Expanding Nature's Inventory." Roberts and Co. (2006): 7-24.

Inteins

An intein is a segment of protein that is able of excising itself and rejoining the remaining portions that do code for information, exteins, through a peptide bond. Splicing of inteins occur after translation, so inteins are present in the DNA template and mRNA strand, but are cut out from the final protein product. The precursor of the intein may from one gene, or from two genes. In split inteins, the inteins come from two genes. An example of split inteins is in cyanobacteria where DNA E is coded by two genes, dnaE-n and dnaE-c. The dnaE-n has an N intein, while the dnaE-c has a C intein. The two inteins will both be spliced and the two extein regions, dnaE-n and dnaE-c, will be joined.

Slonczewski, Joan L. Foster, John W. Microbiology: An Evolving Science, Second Edition, W.W. Norton & Company. 2009.