Structure Of Mcfabz Protein

The shape and magnitude of the UV spectra depends on the composition of amino acid in each protein. Due to the aromatic amino acid residues in the protein, the observed UV absorbance was mainly in the 240 nm to 340 nm region. In Figure 1 to 3, the maximal absorbance of each protein was approximately at 280 nm. The difference in magnitudes of the peak observed was linked to the differences in the amino acid contents in each of the proteins. The peak of lysozyme was greater than those of BSA and gelatin, because lysozyme has a greater number of tryptophan residues. Lysozyme has six tryptophan residues, whereas BSA and gelatin has two and zero, respectively (Department of Chemistry, 2014). Lysozyme has three times more tryptophan residues

Non-competitive inhibitors bind to the enzyme away from the active site but change the tertiary stricture of the protein and so the shape of the active sit. This means that the

Green Fluorescent Protein, produced by the bioluminescent jellyfish Aequorea victoria, is a protein that fluoresces green under ultraviolet light. Since its discovery, properties of the protein have been improved by mutations in the gene resulting in the expansion of its spectrum, which now contains brighter variants and multiple different colors. GFP is used in a wide variety of applications and technologies. Its many different applications have contributed greatly, and continue to do so, in numerous fields of study including, but not limited to, cellular and molecular biology, microbiology, biotechnology, and medicine.

Tsien, Roger Y. "THE GREEN FLUORESCENT PROTEIN." Annual Review of Biochemistry 67 (1998). Howard Hughes Medical Institute. Web. 7 Nov. 2016.

It is predicted that 0° C will measure the least amount of activity, while the most activity at 37°C. This is because the enzyme’s natural state is already at 37° C in the body, where it is known to be very active

When it’s complete the complex separates into enzymes and product(s). Chemicals that are activators that bind the enzyme to be active. Enzyme activity that shut off because of chemicals are known as inhibitors and the results can also be noted as competitive or noncompetitive inhibition. In this experiment we will be exploring

The effects of temperature, pH, specificity and cofactors of enzyme activity were tested. An enzyme is an organic catalyst that speeds up metabolic reactions by lowering the activation energy in cells. Activation energy is the minimum amount of energy needed for the chemical reaction to occur and can be affected by altering the enzyme’s environment as shown during the experiments. When the enzyme is not at the optimal temperature or pH, then the enzyme may become denatured, inactive and lose its normal shape. The enzyme used was Lactase, which binds to the substrate lactose. A substrate is the reactant in the enzymatic reaction and binds to the contact region on the enzyme called the active site. Enzymes have three dimensional shapes

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.

First classical methods are described. The CHARMM force field, which we have used in this thesis is also briefly described. Then the quantum mechanical methods such as ab initio and semiempirical methods are briefly described. The SCC-DFTB method is described more elaborately since we have used SCC-DFTB as the quantum mechanical method to study the reaction mechanism in this thesis. Then QM/MM methods are described with available methods to study enzymatic reaction mechanisms.

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

For this experiment we determine the Michaelis constant (Km) and the maximum velocity (Vmax) and inhibition of alkaline phosphate. Using the different graph created and different methods of calculation I was able to determine the Km and Vmax for the different mixtures, and also what type of inhibitor it was. For mixtures 1-5, the Vmax was 4.04 and the Km was 0.019. For mixtures 6-10, the Vmax was 3.82 and the Km was 0.023. Using the slope from the graph of Lineweaver-Burk for reactions 6-10 I was able to determine Ki, which was 171.53, by calculating the [I] using C1V1=C2V2 scheme, which was 0.012. By plotting in the same graph the Lineweaver-Burk graph for reaction 1-5 and 6-10, I was able to determine that it was competitive inhibitor and

Zinc coordinates proteins with four different surroundings with different roles: catalytic, co-catalytic, structural and interface. In many proteins Zn2+ ions also serve to correct polypeptide folding. Furthermore, zinc is a cofactor in all six enzyme classes.

In vitro: Metiamide was found to be competitive with aldehyde substrates and noncompetitive with the coenzyme, binding to both the free E3 isozyme and the enzymezcoenzyme binary complex. The structure moiety of metiamide accounting for E3 isozyme inhibition was identified to be the side-chain polar group [1].

RAF harbors a structurally typical kinase domain, with the C terminal lobe (C lobe) and N terminal lobe (N lobe) being connected by a short flexible hinge. The active sites of RAF lie in the interface of the two lobes, including the nucleotide (ADP or ATP) binding site, the magnesium binding site (DFG motif) and the phospho-acceptor site (activation segment) (Fig. 1A). The elastic hinge controls the movements between two lobes, which facilitates substrate recruitment as well as product release [21]. A closed conformation between two lobes is necessary for catalytic activity of the kinase domain [22]. Specifically, the fixation of the αC helix of the N lobe and an unfolded activation segment into the “IN” position could place the catalytic residues into a productive orientation and distance (Fig. 1B). What’s more, dimerization of RAF potentiates its independent activation and limits the response of conventional RAF inhibitors. Although the visualization of the dimeric RAF by some crystal structures has provided insightful information on the structural basis and conformational transitions of dimerization-dependent RAF activation (Fig. 1C) [23].

Researchers have taken a closer look at the structure of the active site that facilitates the bioluminescent reaction; they found the Arg218 residue plays a heavy role in the secure binding of luciferin. The guanidinium side chain of Arg218 is particularly responsible for binding with the benzothiazole ring of the luciferin substrate. Moreover, Arg218 establishes electrostatic interactions with the ground state product of the phenol group ionization of luciferin, yet Arg218 also stabilizes the final excited state phenolate ion of oxyluciferin (Branchini, B.R., Magyar, R.A., Murtiashaw, M.H., and Portier, N.C, 2001, 2415-2416). The proper binding of luciferin determines the color of the light emission and is dependent on the amount of rotation of the excited oxyluciferin molecule. To further understand the role of Arg218, researchers created a mutant enzyme without the Arg218 residue to determine its impact on substrate production. When researchers converted the Arg residue to Lys, there was a 15-fold increase in Km for luciferin; the Km value suggests the substrate binding affinity of the enzyme. The increase in Km shows that luciferase has a lowered affinity to bind with substrates. This shows that a manipulation of the Arg218 residue can affect the catalytic activity of the enzyme. Usually, the enzyme loses its high binding affinity with luciferin.