Errors in the MHCII pathway are usually associated with immune-deficiency and disease. The alternative cross regulation pathway requires MHCI molecules to copy MHCII molecules and present exogenous antigen and depends on the trafficking facilitated by adapter proteins [2, 4]. These proteins recognize and bind to conserved sorting sequences in the cytoplasmic domain acting as signals [2, 3]. Di-leucine-based and tyrosine-based signal sequences are the main signals seen for endosome trafficking. In humans both these signals are involved in MHCI cross presentation.
For the protozoan parasite Entamoeba histolytica, the causative agent of human amebiasis, the accurate formation of disulfide bonds is an important biochemical modification required for the correct folding of some proteins, including proteins involved in the adhesion and destruction of human tissues. Amebic proteins such as the Gal/GalNAc-inhibitable lectin and the pore-forming peptides have disulfide bonds which are crucial for the acquisition of their active conformation [4, 5]. Thus, the identification and characterization of amebic enzymes that play key roles in protein folding is essential to understand this biochemical process and gain insight knowledge of the cell biology of this parasite. An entamoebal PDI enzyme (EhPDI) that exhibits oxidative refolding activity in vivo as well as oxidative and reductive activities in vitro has been identified [6, 7]. Structurally, EhPDI shares domain architecture with the Dictyostelium discoideum homologue, DdPDI , featuring two active thioredoxin domains and a D-domain (also known as Erp29c domain).
While in nature amino acids may possess either the D or L configuration, amino acids within proteins almost exclusively possess the latter, as this allows proteins to have binding sites with three-dimensional properties matching those of their ligands. From an evolutionary standpoint, the existence of D-amino acids in certain proteins and peptides is highly beneficial since many D-amino acid-containing peptides participate in defense roles. This group includes antibiotic activities of secreted peptides against neighboring bacteria as well as toxic effects of psycho-active peptides on larger predators. The mode of action for these peptides involves their insertion into another organism that often possesses defense mechanisms based on stereo-specific recognition, like in the case of proteolytic enzymes and antibodies. The presence of D-amino acids prevents the host’s defense system from recognizing and degrading the peptide (Kesssel,A.
RNAi involves complementary base-pairing with the target RNA to bring about repression, while DNA and chromatin modification requires bromodomains, chromodomains, specific amino-acid residues and chemical groups for protein- DNA and -histone interaction. RNAi, DNA and chromatin modification are involved in heterochromatin formation and gene regulation and genome stability.
The antigen binding site is constructed from VL and VH domains of the antibody molecule whereby sequence in this region is highly variable (Watson et al., 2008)). There is also domain of the antibody where the regions do not differ among different antibody molecules and is called “C” or constant. In developing B cells, DNA sequences of immunoglobulin unable to express directly from germ line so the individual gene segments must be rearrange to assemble a functional gene. During the development of B cells the V and J light-chain segments are spliced and join random by somatic recombination process. These segments are then brought together with CL-coding region by RNA splicing.
2) Similarities and differences of the family of Ubiquitin; Structure The ubiquitin family is large, but shares a few characteristics. Some of these characteristics includes; the ubiquitin folding and the biochemical mechanism they use to bind to the target protein. The ubiquitin structure was analyzed as part of a larger NMR study to understand new techniques including H/D exchange. This technique contributed mostly on the information of the protein folding.
This is researched in detail by examining the physical form of USP7 and finding the domains that interact with theses viral proteins and assessing the competition between p53 and EBNA1 for these sites of contact. The cDNA of the de-ubiquinating enzyme under study (USP7) was cut usin... ... middle of paper ... ...tant pathway for p53 stabilization and methods” by Li et al. which shed a light upon the stabilizing effect of USP7 binding to p53, and expanded on the USP7 structure and function. The results and findings were supported by experimental data, which were appropriate and resourceful for the study. The data was shown with clarity through an array of tables, graphs, and figures.
Mechanism of Tyrosine Kinase The mechanism of tyrosine kinase involves the transfer of phosphate group from ATP involved in phoshporylation to a substrate, which in turn releases ADP and phosphotyrosine. Figure 1: Mechanism of Tyrosine kinase.4 Tyrosine kinase receptors belong to a large family of receptors that share similar molecular structures, which consists of a ligand binding region, a sing... ... middle of paper ... ...r chemotherapy has been useful so far, but more experiments and clinical trials can still be created to perfect it. References 1. Hubbard, Stevan. R., Handbook of Cell Signaling; Stuctures of Serine/Threonine and Tyrosine Kinases.
Protein glycosylation is one of the most common post-translational modifications, conferring a diverse set of functional properties. O-linked glycans can have important roles for immune-associated molecules; however the prominent glycans found on the MHC family are N-linked. Like other post-translational protein modifications, N-linked glycans are preferentially attached to a consensus protei... ... middle of paper ... ...ion. The repertoire of N-glycans found on MHC molecules and different antigen presenting cell types is a reflection of the differential usage of numerous glycosyltransferase and glycosidase enzymes, from which there are in excess of 200 in the mammalian genome (1). In addition, conditions of chronic inflammation such as cancer, rheumatoid arthritis, and inflammatory bowel disease can further influence glycan structure by modifying enzyme expression, availability of carbohydrate building blocks, and increased protein expression over the limits of the N-glycosylation secretory pathway.
Moreover, they specifically interact with nucleosome particles and are released from chromatin by limited nuclease digestion, suggesting preferential binding to transcriptionally active chromatin (Arwood and Spiker, 1990; Lichota and ... ... middle of paper ... ...odology is established in the Grasser-lab (Launholt et al., 2006; Pedersen et al., 2010; Pedersen et al., 2011). WP4. Another approach to learn about the function of HMGA is the identification of protein interactors. Therefore, recombinant HMGA fused to gluthatione S transferase (GST) is immobilised (in parallel GST alone serves as control) and is incubated with nuclear protein extracts. Proteins that specifically bind GST-HMGA (but not GST) are identified by MALDI-TOF mass spectrometry that is perfomed at the Biochemistry Department at Regensburg University.