Phosphorylation

A phosphorylated serine residue

Phosphorylation is the addition of a phosphoryl group (PO₃²⁻) to a molecule. Phosphorylation and its counterpart, dephosphorylation, turn many protein enzymes on and off, thereby altering their function and activity. Protein phosphorylation is one type of post-translational modification.

Protein phosphorylation in particular plays a significant role in a wide range of cellular processes. Its prominent role in biochemistry is the subject of a very large body of research (as of March 2015, the MEDLINE database returns over 240,000 articles on the subject, largely on protein phosphorylation).

Protein phosphorylation

History

In 1906, Phoebus Levene at the Rockefeller Institute for Medical Research identified phosphate in the protein vitellin (phosvitin),^[1] and by 1933 had detected phosphoserine in casein, with Fritz Lipmann.^[2] However, it took another 20 years before Eugene P. Kennedy described the first ‘enzymatic phosphorylation of proteins’.^[3]

Function

Reversible phosphorylation of proteins is an important regulatory mechanism that occurs in both prokaryotic and eukaryotic organisms.^[4][5][6][7] Kinases phosphorylate proteins and phosphatases dephosphorylate proteins. Many enzymes and receptors are switched "on" or "off" by phosphorylation and dephosphorylation. Reversible phosphorylation results in a conformational change in the structure in many enzymes and receptors, causing them to become activated or deactivated. Phosphorylation usually occurs on serine, threonine, tyrosine and histidine residues in eukaryotic proteins. Histidine phosphorylation of eukaryotic proteins appears to be much more frequent than tyrosine phosphorylation.^[8] In prokaryotic proteins phosphorylation occurs on the serine, threonine, tyrosine, histidine or arginine or lysine residues.^[4][5][8][9] The addition of a phosphate (PO₄) molecule to a polar R group of an amino acid residue can turn a hydrophobic portion of a protein into a polar and extremely hydrophilic portion of molecule. In this way protein dynamics can induce a conformational change in the structure of the protein via long-range allostery with other hydrophobic and hydrophilic residues in the protein.

One such example of the regulatory role that phosphorylation plays is the p53 tumor suppressor protein. The p53 protein is heavily regulated^[10] and contains more than 18 different phosphorylation sites. Activation of p53 can lead to cell cycle arrest, which can be reversed under some circumstances, or apoptotic cell death.^[11] This activity occurs only in situations wherein the cell is damaged or physiology is disturbed in normal healthy individuals.

Upon the deactivating signal, the protein becomes dephosphorylated again and stops working. This is the mechanism in many forms of signal transduction, for example the way in which incoming light is processed in the light-sensitive cells of the retina.

Regulatory roles of phosphorylation include

• Biological thermodynamics of energy-requiring reactions
  • Phosphorylation of Na⁺/K⁺-ATPase during the transport of sodium (Na⁺) and potassium (K⁺) ions across the cell membrane in osmoregulation to maintain homeostasis of the body's water content.
• Mediates enzyme inhibition
  • Phosphorylation of the enzyme GSK-3 by AKT (Protein kinase B) as part of the insulin signaling pathway.^[12]
  • Phosphorylation of src tyrosine kinase (pronounced "sarc") by C-terminal Src kinase (Csk) induces a conformational change in the enzyme, resulting in a fold in the structure, which masks its kinase domain, and is thus shut "off".^[13]
• Important for protein-protein interaction via "recognition domains."
  • Phosphorylation of the cytosolic components of NADPH oxidase, a large membrane-bound, multi-protein enzyme present in phagocytic cells, plays an important role in the regulation of protein-protein interactions in the enzyme.^[14]
• Important in protein degradation.
  • In the late 1990s, it was recognized that phosphorylation of some proteins causes them to be degraded by the ATP-dependent ubiquitin/proteasome pathway. These target proteins become substrates for particular E3 ubiquitin ligases only when they are phosphorylated.

Signaling networks

Elucidating complex signaling pathway phosphorylation events can be difficult. In cellular signaling pathways, protein A phosphorylates protein B, and B phosphorylates C. However, in another signaling pathway, protein D phosphorylates A, or phosphorylates protein C. Global approaches such as phosphoproteomics, the study of phosphorylated proteins, which is a sub-branch of proteomics, combined with mass spectrometry-based proteomics, have been utilised to identify and quantify dynamic changes in phosphorylated proteins over time. These techniques are becoming increasingly important for the systematic analysis of complex phosphorylation networks.^[15] They have been successfully used to identify dynamic changes in the phosphorylation status of more than 6000 sites after stimulation with epidermal growth factor.^[16] Another approach for understanding Phosphorylation Network, is by measuring the genetic interactions between multiple phosphorylating proteins and their targets. This reveals interesting recurring patterns of interactions – network motifs.^[17] Computational methods have been developed to model phosphorylation networks ^[18][19] and predict their responses under different perturbations.^[20]

Protein phosphorylation sites

There are thousands of distinct phosphorylation sites in a given cell since: 1) There are thousands of different kinds of proteins in any particular cell (such as a lymphocyte). 2) It is estimated that 1/10 to 1/2 of proteins are phosphorylated (in some cellular state). 3) One study indicates that 30% of proteins in the human genome can be phosphorylated, and abnormal phosphorylation is now recognized as a cause of human disease.^[21] 4) Phosphorylation often occurs on multiple distinct sites on a given protein.

Since phosphorylation of any site on a given protein can change the function or localization of that protein, understanding the "state" of a cell requires knowing the phosphorylation state of its proteins. For example, if amino acid Serine-473 ("S473") in the protein AKT is phosphorylated, AKT is, in general, functionally active as a kinase. If not, it is an inactive kinase.

Types of phosphorylation

See also kinases for more details on the different types of phosphorylation

Within a protein, phosphorylation can occur on several amino acids. Phosphorylation on serine is the most common, followed by threonine. Tyrosine phosphorylation is relatively rare but is at the origin of protein phosphorylation signaling pathways in most of the eukaryotes. However, since tyrosine phosphorylated proteins are relatively easy to purify using antibodies, tyrosine phosphorylation sites are relatively well understood. Histidine and aspartate phosphorylation occurs in prokaryotes as part of two-component signaling and in some cases in eukaryotes in some signal transduction pathways.^[22] In prokaryotes, histidine's nitrogen act as nucleophine and it binds to phosphate group. Once it is phosphorylated, aspertate, hydroxyll group bind to the nucleophile just like normal phorphorylation process.Presence of histidine causes phosphorylation to be chemically different for bacteria than Eukaryotes. Phosphorylation can enable to binding site and also cause to prevent binding by blocking the active site by causing confrontational change. Example, EGF and insuline receptors.

Phosphorylation of Glucose

• D-glucose + ATP -> D-glucose-6-phosphate + ATP ΔG° = -16.7
• The liver plays a crucial role in controlling blood sugar concentrations, and breaks down glucose into carbon dioxide and glycogen.
• Research D. G. Walker of the University of Birmingham determined the presence of two specific enzymes in adult guinea pig liver, both of which catalyze the phosphorylation of glucose to glucose 6 phosphate. The two enzymes have been identified as a specific glucokinase ^[23] (ATP-D-glucose 6-phosphotransferase) and non-specific hexokinase (ATP-D-hexose 6-phosphotransferase).

Detection and characterization

Antibodies can be used as powerful tool to detect whether a protein is phosphorylated at a particular site. Antibodies bind to and detect phosphorylation-induced conformational changes in the protein. Such antibodies are called phospho-specific antibodies; hundreds of such antibodies are now available.^[24] They are becoming critical reagents both for basic research and for clinical diagnosis.

Example of posttranslational modification detected on a 2D gel (spot boundaries delimited by analysis software, identification by mass spectrometry, P46462 is the protein ID in Expasy)

PTM (Posttranslational Modification) isoforms are easily detected on 2D gels. Indeed, phosphorylation replaces neutral hydroxyl groups on serines, threonines, or tyrosines with negatively charged phosphates with pKs near 1.2 and 6.5. Thus, below pH 5.5, phosphates add a single negative charge; near pH 6.5, they add 1.5 negative charges; above pH 7.5, they add 2 negative charges. The relative amount of each isoform can also easily and rapidly be determined from staining intensity on 2D gels.

In some very specific cases, the detection of the phosphorylation as a shift in the protein's electrophoretic mobility is possible on simple 1-dimensional SDS-PAGE gels, as it's described for instance for a transcriptional coactivator by Kovacs et al.^[25] Strong phosphorylation-related conformational changes (that persist in detergent-containing solutions) are thought to underlie this phenomenon. Most of the phosphorylation sites for which such a mobility shift has been described fall in the category of SP and TP sites (i.e. a proline residue follows the phosphorylated serine or threonine residue).

More recently large-scale mass spectrometry analyses have been used to determine sites of protein phosphorylation. Over the last 4 years, dozens of studies have been published, each identifying thousands of sites, many of which were previously undescribed.^[26][27] Mass spectrometry is ideally suited for such analyses using HCD or ETD fragmentation, as the addition of phosphorylation results in an increase in the mass of the protein and the phosphorylated residue. Advanced, highly accurate mass spectrometers are needed for these studies, limiting the technology to labs with high-end mass spectrometers. However, the analysis of phosphorylated peptides by mass spectrometry is still not as straightforward as for “regular”, unmodified peptides. Recently EThcD has been developed combining electron-transfer and higher-energy collision dissociation. Compared to the usual fragmentation methods, EThcD scheme provides more informative MS/MS spectra for unambiguous phosphosite localization.^[28]

A detailed characterization of the sites of phosphorylation is very difficult, and the quantitation of protein phosphorylation by mass spectrometry requires isotopic internal standard approaches.^[29] A relative quantitation can be obtained with a variety of differential isotope labeling technologies.^[30] There are also several quantitative protein phosphorylation methods, including fluorescence immunoassays, Microscale Thermophoresis, FRET, TRF, fluorescence polarization, fluorescence-quenching, mobility shift, bead-based detection, and cell-based formats.^[31][32]

Other kinds

ATP, the "high-energy" exchange medium in the cell, is synthesized in the mitochondrion by addition of a third phosphate group to ADP in a process referred to as oxidative phosphorylation. ATP is also synthesized by substrate-level phosphorylation during glycolysis. ATP is synthesized at the expense of solar energy by photophosphorylation in the chloroplasts of plant cells.

Phosphorylation of sugars is often the first stage of their catabolism. It allows cells to accumulate sugars because the phosphate group prevents the molecules from diffusing back across their transporter.

See also

• Moiety conservation
• Phosida
• RegPhos

References

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2. Lipmann FA, Levene PA (October 1932). "Serinephosphoric acid obtained on hydrolysis of vitellinic acid" (PDF). J. Biol. Chem. 98 (1): 109–114.
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22. Thomason P, Kay R (September 2000). "Eukaryotic signal transduction via histidine-aspartate phosphorelay" (PDF). J. Cell. Sci. 113 (18): 3141–50. PMID 10954413.
23. Walker DG, Rao S (1964). "The role of glucokinase in the phosphorylation of glucose by rat liver". Biochemical Journal 90 (2): 360–368.
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28. Frese, Christian; Houjiang Zhou; Thomas Taus; A. F. Maarten Altelaar; Karl Mechtler; Albert J. R. Heck; Shabaz Mohammed (March 1, 2013). "Unambiguous Phosphosite Localization using Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)". J Proteome Res. 12 (3): 1520–1525. doi:10.1021/pr301130k. PMC 3588588. PMID 23347405.
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External links

• Functional analyses for site-specific phosphorylation of a target protein in cells (A Protocol)