There are various methods that have been developed over these years to study protein-protein interactions (PPIs). PPI plays a big role in the cell-signalling cascade; for instance, dephosphorylation of glycogen synthase by protein phosphatase-1 results in glycogen synthesis. To know whether a specific protein binds to its partner, for example, whether TFIIH interacts with TFIIE or TFIIF to complete the pre-initiation complex in transcription, different methods such as co-immunoprecipitation (co-IP), glutathione-S-transferase (GST) pull down assays, yeast-two-hybrid (Y2H) assays, isothermal titration calorimetry (ITC), surface plasmon resonance (SPR), nuclear magnetic resonance (NMR) spectroscopy and etc. can be use to validate PPIs. Yet, doing one experiment using one method is not enough to validate the PPI between two or more proteins. Factors such as overexpression of proteins and manipulation of the agents used in the experiment could result in a bias data. Thus, the results should be unbiased by incorporating different methods in the experiment to validate the PPI. In this essay, the different methods will be described and the factors that cause the different methods giving rise to different results will be discussed. Co-IP is the most commonly used methods to verify protein-protein interactions (Berggård et al., 2007). Antibodies that are specific to the bait complexes are used to capture the bait complexes in a cell lysate shown in Fig. 1. The antibody is immobilized on Protein A/G, which is covalently bound to the agarose beads. Since the antibody is specific to only the bait complex, the antibody will not bind to other proteins found in the cell lysate, and hence, these proteins will be wash off. The antibody-bait compl... ... middle of paper ... ...nflammatory Arthritis in Mice. Science. 332 (6028), pp. 478-484. Wissmueller S., Font J., Liew C.W., Cram E., Schroeder T., Turner J., Crossley M., Mackay J.P. and Matthews J.M. (2011). Protein-protein interactions: analysis of a false positive GST pulldown result. Proteins. 79 (8), pp. 2365-2371. Yu H. (1999). Extending the size limit of protein nuclear magnetic resonance. Proceedings of the National Academy of Sciences. 96 (2), pp. 332-334. Zhang X., Tang H., Ye C. and Liu M. (2006). Structure-based drug design: NMR-based approach for ligand-protein interactions. Drug Discovery Today: Technologies. 3 (3), pp. 241-245. Zhou YL., Liao JM., Du F. and Liang Yi. (2005). Thermodynamics of the interaction of xanthine oxidase with superoxide dismutase studied by isothermal titration calorimetry and fluorescence spectroscopy. Thermochimica Acta. 426 (1-2), pp. 173-178.
CP consists of a single domain with high α-helical content [4]. The N-terminal part this domain is surface exposed whereas the C-terminal region buried in the virion. Several experiments indicate the CP is an O-glycoprotein. Equal amounts of galactose and fructose residues are O-linked to an acetylated serine residue at the N-terminal region [2]. This mediates the formation of a structured...
Phosphorylation and dephosphorylation can activate or deactivate a protein but changing in 3-D conformation and as a result changing the ability to interact with other proteins. Just like in Arabidopsis and other an...
Tymoczko, J. L., Berg, J. M., & Stryer, L. (2013). Biochemistry: A Short Course, 2nd Edition. New York, NY: W. H. Freeman and Co.
M proteins: M proteins are found on the surface of the organism and protect it against phagocytosis. The M proteins prevent the attachment of complement proteins to the cell. Complement proteins which are attached to the bacterium “tag” it for destruction by phagocytic cells, such as neutrophils and macrophages, in a process called opsonisation. By inhibiting this process, the M protein allows the group A streptococcus to survive longer...
“This knowledge will help us design drugs that mimic the viral effects on these proteins to either activate a host’s immune response or shut it down,” said Dr. Michael Gale, associate ...
In summary, this excerpt went over how proteins are a linear polymer of amino acids linked together by peptide bonds. There are various interactions between the amino acids, which are mostly non-covalent, that stabilize the structure of a folded protein. There are 20 unique amino acids found naturally and can be grouped into three categories based off the nature of their R groups located on the side of the amino acids. Hydrophilic, hydrophobic or amino acids with a special R group which are composed of cysteine, glycine and proline. The Alpha helix and beta sheet are the most abundant structures of protein secondary structures. These stabilize hydr...
Protein can be derived from two different food sources, these are animal proteins (meat) and plant proteins (vegetables, fruits, beans and nuts.) What a lot of people don’t know is that these proteins are not creates equal or share the same beneficial properties. Here I will discuss them both...
NMR experiments can provide useful structural information and probe different aspects of the molecule’s nuclear environment. Suggest two NMR experiments that may illustrate how a globular protein could respond to the changes of pH, temperature, and
In the hierarchial organisation of proteins, domains are found at the highest level of tertiary structure. Since the term was first used by Wetlaufer (1973) a number of definitions exist reflecting author bias, however all of the definitions agree that domains are independently folding compact units. Domains are frequently coded by exons and therefore have specific functionality. Among the many descriptions of protein domains the two most striking and simple are " Protein evolutionary units" and "Basic currency of Proteins".
Many proteins are the most prominent structural motif of the functional protein in its native conformation known as the alpha helix (Pauling et al. 1951). When a protein follows the wrong folding pathway, the protein misfolds and becomes a toxic configuration. When a protein becomes toxic, it obtains a motif known as the beta sheet. Although the beta sheet conformation also exists in many functional native proteins, the abnormal conformational change from alpha helix to beta sheet exposes
The noncovalent interactions that maintain the three-dimensional structure of proteins are weak. Considering this, they are easily disrupted. The unfolding of protein is called denaturation. [1] Denaturation happens because the bonding interactions which are responsible for the secondary structure (hydrogen bonds to amides) and tertiary structure undergo disruption. There are different types of bonding interactions between “side chains” in tertiary structure. This includes hydrogen bonding, salt bridges, disulfide bonds, and non-polar hydrophobic interactions which may be disrupted. Therefore a variety of physical and chemical agents can cause denaturation.
There are four main levels of a protein, which make up its native conformation. The first level, primary structure, is just the basic order of all the amino acids. The amino acids are held together by strong peptide bonds. The next level of protein organization is the secondary structure. This is where the primary structure is repeated folded so that it takes up less space. There are two types of folding, the first of which is beta-pleated sheets, where the primary structure would resemble continuous spikes forming a horizontal strip. The seco...
...–called JANUS protein). Remote connections that are imperceptible by arrangement correlations may be caught by sequence–to–structure–fitness (or threading) methodologies: the hunt grouping is efficiently contrasted with all known protein structures. An initio forecasts of protein 3d structure remains the significant provoke; a few advancement has been made as of late by joining together factual with force–field based.
Proteins carry out various biological functions by their interactions between another protein and other molecules. Consequently, they also regulate the signaling pathways and many biochemical processes of living organisms. Mutations involved in these interactions can cause many diseases in human being. Protein visualization will help us know about the molecular mechanisms of these diseases (Gonzalez & Kann., 2012).
Proteins are polymers of amino acids. A typical protein may be composed of hundreds of amino acids. Denaturation of a protein means loss of the protein's function due to its three dimensional structural which are held by a combination of forces which are hydrogen bonds, salt bridges also known as ionic interactions, disulphide bridges, and the hydrophobic interactions are altered in the protein. Denaturation of proteins occurred due to the hydrogen bonding in the peptide linkage are disrupted when there is an applying external stress such as by applying heat, treatment with organic compounds such as alcohols, heavy metals, or acids and bases. As a result, causing the folded three-dimensional protein to become unfold and unravel.