Posttranslational modification types

Other structural features that anchor a protein to a lipid bilayer may occur by posttranslational modification. Types of posttranslational modifications that have been recognized are (1) attachment of lipid [3] (2) fatty acid acylation of... 

The transcriptional activity of NRs is also modulated by various posttranslational modifications of the receptors themselves or of their coregulatory proteins. Phosphorylation, as well as several other types of modification, such as acetylation, SUMOylation, ubiquitinylation, and methylation, has been reported to modulate the functions of NRs, potentially constituting an important cellular integration mechanism. In addition to the modifications of the receptors themselves, such modifications have been reported for their coactivators and corepressors. Therefore, these different modes of regulation reveal an unexpected complexity of the dynamics of NR-mediated transcription. 

The human HS cycle can be considered broadly as a period which leads to the dramatic shift in activities of the transcriptional and translational machinery followed by eventual recovery and resumption of original activities preceding stress. Figure 1 depicts many of the key events in the HS cycle for a typical human cell line such as cervical carcinoma-derived HeLa cells. Most cells respond in an identical fashion, but some cell types that have distinctive HS responses. These differences are manifested by shifts in the relative concentrations of accumulated HS proteins and possibly in the pattern of posttranslational modifications. In all cases, however, the cellular stress response is heralded by induction of a specific transcription factor whose DNA binding activity facilitates increased expression of one or more of the stress-inducible genes. 

Size-based analysis of SDS-protein complexes in polyacrylamide gels (SDS-PAGE) is the most common type of slab gel electrophoresis for the characterization of polypeptides, and SDS-PAGE is one of the most commonly used methods for the determination of protein molecular masses.117 The uses for size-based techniques include purity determination, molecular size estimation, and identification of posttranslational modifications.118119 Some native protein studies also benefit from size-based separation, e.g., detection of physically interacting oligomers. 

Figure 6 Cartoon of histone posttranslational modifications. Histone proteins are known for having multiple numbers of the same posttranslational modification and multiple types of posttranslational modifications on their lysine tails responsible for binding DMA. The histone code as it is called relies on the dynamic nature of phosphorylation, acetylation, and mono-, di-, and trimethylation.

Phosphopantetheine tethering is a posttranslational modification that takes place on the active site serine of carrier proteins - acyl carrier proteins (ACPs) and peptidyl carrier proteins (PCPs), also termed thiolation (T) domains - during the biosynthesis of fatty acids (FAs) (use ACPs) (Scheme 23), polyketides (PKs) (use ACPs) (Scheme 24), and nonribosomal peptides (NRPs) (use T domain) (Scheme 25). It is only after the covalent attachment of the 20-A Ppant arm, required for facile transfer of the various building block constituents of the molecules to be formed, that the carrier proteins can interact with the other components of the different multi-modular assembly lines (fatty acid synthases (FASs), polyketide synthases (PKSs), and nonribosomal peptide synthetases (NRPSs)) on which the compounds of interest are assembled. The structural organizations of FASs, PKSs, and NRPSs are analogous and can be divided into three broad classes the types I, II, and III systems. Even though the role of the carrier proteins is the same in all systems, their mode of action differs from one system to another. In the type I systems the carrier proteins usually only interact in cis with domains to which they are physically attached, with the exception of the PPTases and external type II thioesterase (TEII) domains that act in trans. In the type II systems the carrier proteins selectively interact... 

In mammals a single PPTase is used for the posttranslational modification of three different apo-proteins the carrier proteins of mitochondrial and cytosolic FASs and the aminoadipate semialdehyde reductase implicated in lysine degradation. The crystal structure of human PPT ase has been determined and found to be most closely related to the class II Sfp-like enzymes. Architectural and mechanistic differences between the type II human PPTase and the type I bacterial PPTases include a divalent cation coordinated by the a-phosphate of CoA, a Glu and an Asp residue, and three water ligands in type I PPTases versus a divalent cation coordinated by a- and /3-phosphates of CoA, two to three protein side chains, and a water molecule in the human PPT ase. 

Prolyl 4-hydroxylation is the most abundant posttranslational modification of collagens. 4-Hydroxylation of proline residues increases the stability of the triple helix and is a key element in the folding of the collagen triple helix. " In vertebrates, almost all the Yaa position prolines of the Gly-Xaa-Yaa repeat are modified to 4(I( )-hydroxylproline by the enzyme P4H (EC 1.14.11.2), a member of Fe(II)- and 2-oxoglutarate-dependent dioxygenases. This enzyme is an 0 2/ b2-type heterotetramer in which the / subunit is PDI (EC 5.3.4.1), which is a ubiquitous disulfide bond catalyst. The P4H a subunit needs the 13 subunit for solubility however, the 13 subunit, PDI, is soluble by itself and is present in excess in the ER. Three isoforms of the a subunit have been identified and shown to combine with PDI to form [a(I)]2/ 2) [< (II)]2/32> or [a(III)]2/32 tetramers, called the type... 

How do we then envision the protein microarray as a proteomics tool We now estimate the human genome to comprise around 30,000 genes. For gene expression analysis using DNA microarrays, 1000 to 10,000 gene elements are often used. Since proteins undergo posttranslational modification (>200 different types see McDonald and Yates, 2000, Reference 40) and can occur as isoforms and multiprotein complexes, the number of protein expression elements needs to be much larger. 

The N-terminal tails of histone proteins are rich in arginine and lysine residues and undergo various types of posttranslational modifications. There are small modifications such as acetylation, methylation, phosphorylation but also the attachment of larger peptide groups such as ubiquitinylation and sumoylation [1]. This has an impact on chromatin structure and subsequently on gene transcription and the epigenetic maintenance of altered transcription after cell division [2],... 

Many polypeptide chains are covalently modified, either while they ae still attached to the ribosome or after their synthesis has been completed. Because the modifications occur after translation is initiated they are called posttranslational modifications. These modifications maj include removal of part of the translated sequence, or the covalent add-tion of one or more chemical groups required for protein activity. Som< types of posttranslational modifications are listed below. 

Tropoelastin molecules are crosslinked in the extracellular space through the action of the copper-dependent amine oxidase, lysyl oxidase. Specific members of the lysyl oxidase-like family of enzymes are implicated in this process (Liu etal, 2004 Noblesse etal, 2004), although their direct roles are yet to be demonstrated enzymatically. Lysyl oxidase catalyzes the oxidative deamination of e-amino groups on lysine residues (Kagan and Sullivan, 1982) within tropoelastin to form the o-aminoadipic-6-semialdehyde, allysine (Kagan and Cai, 1995). The oxidation of lysine residues by lysyl oxidase is the only known posttranslational modification of tropoelastin. Allysine is the reactive precursor to a variety of inter- and intramolecular crosslinks found in elastin. These crosslinks are formed by nonenzymatic, spontaneous condensation of allysine with another allysine or unmodified lysyl residues. Crosslinking is essential for the structural integrity and function of elastin. Various crosslink types include the bifunctional crosslinks allysine-aldol and lysinonorleucine, the trifunctional crosslink merodes-mosine, and the tetrafunctional crosslinks desmosine and isodesmosine (Umeda etal, 2001). 

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