Saponaria Officinalis

Thiol groups are important to protein folding and forming disulphide bonds that are essential to protein structure. Determining the number of thiol groups in a protein is important in determining the tertiary structure of the protein. The ovalbumin is the experiment was purified from egg white using centrifugation and ammonium sulphate precipitation and then the thiol groups identified using DTNB and spectroscopy. The ovalbumin was found to have one thiol group; from this we were also to infer that DNTB alkylates thiolgroups; whereas SDS keeps proteins denatured.

Having removed the detergent, the protein will refold. As shown by the Anfinsen experiment the polypeptide sequence determines the folding and therefore the three dimensional structure. As the polypeptide sequence is unaltered refolding can occur through the process of nucleation aggregation and compaction. In order to test that the protein was no longer denatured, the absorbency of the solution at 412nm could be measured and compared with the graph in figure 1 above, it should match the plot of standard ovalbumin in the absence of SDS.

sHSPs are a ubiquitous class of chaperones found across all kingdoms of life. sHSP range in size from 12-42 kilo Daltons in large oligomers of 12 to >32 subunits and the structure is homologous across all species. The sHSP monomer consists of three domains: a disordered N-terminal arm, a beta-sandwich α-crystallin domain, and a flexible C-terminal extension. The N-terminal domain is the most variable region with little conservation between species. Experimental evidence also suggests N-terminal involvement in substrate binding and protection. The α-crystallin domain is the most highly conserved region and adopts a β-sandwich conformation composed of 7 to 8 anti-parallel β-strands (Basha et al, 2012). The C-terminus contains an I-X-I motif, which helps to satblizie the oligomeric form of the sHSP (Basha et al, 2012).

A protein has multiple existing structures, these are the primary, secondary, tertiary and quaternary structures which occur progressively. A protein is essentially a sequence of amino acids which are bonded adjacently, and interact with one another in various ways depending on the R group that the amino acid contains. There are 20 different amino acids which are able to be arranged in any given order, thus giving rise to a potential 2.433x1018 (4.s.f) different combinations, and therefore interactions between the various amino acids.

"The three-dimensional crystal structure of cholera toxin". J Mol Biol. 251 (4): 563–73. doi:10.1006/jmbi.1995.0456. PMID

Proteins are polymeric chains that are built from monomers called amino acids. All structural and functional properties of proteins derive from the chemical properties of the polypeptide chain. There are four levels of protein structural organization: primary, secondary, tertiary, and quaternary. Primary structure is defined as the linear sequence of amino acids in a polypeptide chain. The secondary structure refers to certain regular geometric figures of the chain. Tertiary structure results from long-range contacts within the chain. The quaternary structure is the organization of protein subunits, or two or more independent polypeptide chains.

. The 3-D tertiary structure of polypeptide proteins globular and is the result of interactions that occur between R groups. Tertiary structure is a result of the bonds between sidechains of amino acids, the R groups. The structure and bonds involve alpha helices, beta pleated sheets, and also regions unique to each protein. Tertiary proteins are held together by four different types of forces; hydrogen bonds, hydrophobic interactions (including Van der Waals interactions), ionic bonding (electrostatic interactions), and disulfide bridges (strong covalent bonds). Hydrogen bonds occur within and between polypeptide chains and the aqueous environment. Hydrogen bonding forms between a highly electronegative oxygen atom or a nitrogen atom and a hydrogen atom attached to another oxygen atom or a nitrogen atom. This links the amino acid

addition, there seem to be several hydrogen bonds between the protein and the phosphate backbone of the DNA such as the oxygen in the phosphate group at position 33.

When studying medicine it is important to know how the pharmaceutical drug will affect the body, how quickly the drug will work, and what are the short term and long term effects of the drug on the disease. It is important to know the structure of the molecules, to see exactly where the inhibitor will bind, or if it will even bind at all. In the experiment, Structure Based Approach to the Development of Potent and Selective Inhibitors of Dihydrofolate Reductase from Cryptosporidium, they studied the crystal structures of the inhibitors and used computational analysis to determine which in inhibitor would bind the best. The overall goal is to make sure that the inhibitor binds to the correct active site, and that it is the only site.

Some proteins are made up of amino acids that contain sulphur. There are only two amino acids that contain sulphur, Methionine and Cysteine. Methionine has a thioether side chain, -(CH2)2-S-CH3, whereas, cysteine has a thiol group side chain, -CH2-SH. In proteins, the cysteine side chains form covalent bonds between each other to produce disulphide bonds, as a result of oxidation. The process of oxidation produces stable

For the second part of the experiment, one had to use the knowledge learn from viewing protein molecules in FirstGlance in Jmol to analyze the protein PDB ID: 4EEY. The analysis of this protein was done using the RSCB protein data bank (PDB) at (http://www.rcsb.org/pdb/home/home.do).2

Protein molecules are made soluble in buffered liquid and isotopically labeled. Therefore, allows thermodynamics, studies of the kinetics aspects of structures and interactions with other components.

Crystal structure allows researchers to understand the functions of any compound. In biochemistry, structure dictates function. With the use of crystal structure analysis, scientists have a better way of analyzing specific proteins or enzymes and their function in our body. Observation of the human mitochondrial chaperonin is important because it assists in folding of mitochondrial proteins that allow for the production of energy in the cell. It also participates in specific process like apoptosis, inflammation and carcinogenesis. The study presents the structure of these human mitochondrial chaperonin to have an “American football”-shaped intermediate. It consists of two 7-membered chaperoning rings that are capped at each end. The symmetric and asymmetric bindings between the rings of the chaperonin suggest a mechanism that is distinct from the mechanism of E. Coli.

Bettelheim, Brown, Campbell and Farrell assert that polypeptide chains do not extend in straight lines but rather they fold in various ways and give rise to a large number of three-dimensional structures (594). This folding or conformation of amino acids in the localized regions of the polypeptide chains defines the secondary structure of proteins. The main force responsible for the secondary structure is the non-covalent

Meanwhile, if temperature is increased denatures the proteins. Proteins then unfold and the non-polar groups which were previously in the interior of the molecule become exposed. This leads to a decrease in the solubility of the protein in aqueous environment. Addition of ethanol, methanol, acetone and the like decreases the dielectric constant and thus decreases protein’s solubility. (Boyer, 2000)