Saponaria Officinalis

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.

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.

The bonds that link the amino acids are strong covalent bonds that endure the heat but the bonds that stabilize the 3D structure (like ovomucin and ovalbumin) are weak hydrogen bonds. When the hydrogen bonds break, the proteins are resolved. When two spread out proteins are in contact,

. 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

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 the metabolic workhorses of the cell; they engage in a variety of essential activities ranging from enzymatically catabolizing macromolecular food sources to serving as structural components that maintain cell stability. Maximizing protein function relies on intricate non-covalent interactions occurring on the secondary, tertiary, and quaternary levels that help determine the overall shape of the protein. In their native states, proteins will assume the most energetically favorable configuration. Occasionally however, cells are exposed to exogenous disruptions such as heat stress. Heat Stress can compromise protein three-dimensional structure. Hydrophobic residues tend to be buried in the interior of the protein but when

SDS (sodium dodecyl sulphate) is a chemical agent that is used to denature protein molecules by straightening the polypeptide chain. Disulphide bonds are found in the tertiary structure of proteins and would not react if the protein remained folded. Without SDS, there would not be any thiol groups

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

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.

Heat shock proteins are chaperone proteins with many functions. Some known functions of heat shock proteins are of assisting the folding of nonnative proteins, stabilizing cellular proteins under stressful conditions such as heat, and aiding in the degradation of proteins. Hsp90 is a particular heat shock protein with a specific role. Hsp90 not only assists proteins undergoing stress but it also helps unstressed cells with intracellular transport and cell signaling. It is a required protein for the activation of certain growth factor and steroid hormone receptors, protein kinases and other signaling molecules which are protooncogenic. As Hsp90 stabilizes certain oncogenes in tumor growth, Hsp90 inhibitors are of interest for investigation for anti-cancer drugs as inhibition of Hsp90 may induce apoptosis for the cancerous cells. The particular structure of this protein gives this protein its identity and ability to function the way that it does. The structure of Hsp90 will be explored, particularly 1YET with geldanamycin as a ligand viewed from X-ray diffraction.

Chaperonins are one our of the two types of chaperones that assist in protein folding. It does not actually participate in protein folding, but isolates aggregated protein from other compounds to be able to interact with its individual strand. It provides a stable environment that ensures proper folding. The protein comes in contact with the Gro-EL-GroES complex that has a bullet or a symmetrical football shaped complex. Here, the intermediate folding of protein is activated.

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

The A chain of ricin exhibits a large amount of secondary structure. This structure consists of seven α helices; these α helices are comprised of 80 amino acid residues, which equals to 30% of the protein is helical. A chain contains a five stranded β sheet composed of amino acid residues 67-116, and comprising 15% of the protein. These residues, however, aren’t directly involved in the sheet. The A chain folds into three random domains. The first domain forms the bottom of the A chain. This domain contains the amino-terminal through 117 residues, which is dominated by the β sheet, making it appear as a flat domain. Five α helices dominate the second domain, but is comprised of amino acid residues 118-210. The only free sulfhydoxyl group on the second α helix resides in this domain, and is bonded to the single methyl mercury of the isomorphous derivative. The second domain sits over and to left of the first domain. The third domain exhibited by the A-chain forms a circular domain that strongly interacts with the B-chain as mentioned earlier. The third domain contains the 211-267 amino acid residues, and is quite distinct from the second domain. This dis-similarity is due to the amino acid residues in the third domain are

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)