Essay On Protein Structure Assurance

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.

An NMR spectrum was also taken for our product sample which was close to the ideal but was a little off. Ideally there should be five peaks for the five chemical shifts from the five hydrogen groups on the product structure. The first peak should occur in the mid six ppm and can be described as a quartet. The second peak should occur at a ppm in the high 6s and should be another quartet. The third peak should be a triplet occurring at a low 7ppm. The fourth peak should be close by to the third, being another triplet. Finally, the fifth peak should be a doublet occurring at a mid 7ppm. The ppms for the ideal and the actual differ greatly in the fact that they span from approximately 5.3-6.25 instead of the ideal 6.5-7.5. It is fact that chemical shifts caused by benzene rings occur in the 6 to 8 ppm range, thus the nmr we received as a result can be somewhat doubted.. Ideally the first and second peaks should be a result of the hydrogens furthest away from the rings and the

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.

It was evident that the three dimensional structure of Saporin-S6 was highly occupied with α helices based on the percentage of the peak ratios. It is important to look at the intensity of the peak or broadness of the peak to identify the bonding strength of two molecules. By observing the peaks of the different bond possibilities, its structure can be determined. Once the structure is fully determined, peaks that would show a major change were chosen to observe how the structure of the protein changed. It is the disappearance of the peaks in a spectrum that would indicate the defolding of Saporin-S6. If there are new peaks that occur in the final results, it indicated the aggregation of the unbroken strands of the protein. Saporin-S6 is a protein that is made up of 253 amino acids. To simplify the data analysis, these scientist

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.

Most proteins have a primary, secondary and tertiary structure, but some of them, like hemoglobin, also have a quaternary structure. The primary structure of a protein is represented by the ordered succession of its amino acids held together by covalent bonds. While in nature amino acids may possess either the D or L configuration, amino acids within

A key property is the spin of the proton. The spin of a proton is expressed in ± k (1/2), where k is a coefficient. During the NMR process, an external magnetic field is applied on the protons, partially polarizing them. This will cause them to all align in the same orientation, around the magnetic field direction, as it is the easiest to maintain that position. This is called the Minimum Magnetic Potential Energy. Its other spin state is its high energy spin state, where it spins in the opposite direction around the magnetic field.

Introduction: The goal of this experiment was to practice using the FirstGlance in Jmol molecular visualization to examine key structural features of proteins. This work is important because protein structure can be related to function, multiple-sequence alignments and evolutionary preservation, and designing drug. FirstGlance in Jmol makes it fairly easy to perceive structure-function relationships in the protein you chose. Using FirstGlance, it is easy to visualize and distinguish chains, and disulfide bonds are obvious. Alpha helices and beta strands are evident due to the "cartoon" secondary structural schematic.

NMR spectroscopy was initially created to help chemists who had made odd compounds that they couldn't distinguish. In the method (and similarly as in MRI), an obscure specimen is put in a static amagnetic field, quickly energized with radio-recurrence photons (light), and after that permitted to re-radiate those photons. NMR works in light of the fact that the trademark recurrence of the re-transmitted photons fluctuates marginally in light of the structure of the particle. A proton independent from anyone else may retain and reemit 900 MHz photons, yet when it gets close different charges, (for example, in an expansive hydrocarbon chain), the attractive field around it is gets curved and twisted thus its full recurrence may move to something like 906 MHz. This implies NMR might be utilized to produce "spectra" comparing to the measure of reverberation at different frequencies, which thus uncovers points of interest of the structure of atoms. So if a scientific expert takes a gander at the NMR range of her obscure example and sees a colossal crest close to 906 MHz, then she realizes that her specimen likely has no less than one hydrocarbon chain some place on

Therefore, if we had many copies of two different proteins that were both 298 amino acids long, they would travel together through the gel in a mixed band. As a result, we would not be able to use SDS-PAGE to separate these two proteins of the same molecular weight from each other. Some possible errors that occurred during this lab include poorly executing inserting the MW marker solution into the well of the gel. This caused not so clear bands as shown in figure 1. Incorrect measurements of the migration could also lead to errors in the data. The molecular weight of the protein was determined by plotting a graph of the Log MW vs migration (cm) and generating a standard curve. The unknown sample molecular weight was calculated as 79.43 kD. Experimental errors in this lab could be minimized by carefully loading the wells on the

since all unbounded protein removed and only bounded protein (PTEN and other protein that has affinity toward the ligand) left. Note that, some samples diluted to fall in the standard range and there are samples excluded for not being in the range. The eluted sample should include a purified PTEN and the SDS-PAGE in figure 4 confirm these expectations. The red arrow refer to PTEN and it has the same Mw 63.1 as the pervious gel, which indicated that this band is PTEN band. The eluted samples present in the SDS-PAGE shows other bands with PTEN, which represents other proteins that have affinity toward the ligand. Other purifying technique can be add to this protocol such as size exclusion chromatography to obtain more purified sample. In addition, mass spectrometry can be used to obtain the sequence and the Mw of the band (after digestion the protein from the gel) to confirm that band represent PTEN

Atomic charges were assigned to the receptor using AMBER7 FF99 force field. The protein complex was minimized using AMBER7 FF99 force field. Finally the 3D structure of the prepared protein was saved as PDB file.

Campbell and Farrell define proteins as polymers of amino acids that have been covalently joined through peptide bonds to form amino acid chains (61). A short amino acid chain comprising of thirty amino acids forms a peptide, and a longer chain of amino acids forms a polypeptide or a protein. Each of the amino acids making up a protein, has a fundamental design that comprises of a central carbon or alpha carbon that is bonded to a hydrogen element, an amino grouping, a carboxyl grouping, and a unique side chain or the R-group (Campbell and Farrell 61).

Quantification of proteins is needed to determine the progress of protein purification. As the protein becomes more purified, its specific activity will increase as well. In Experiment 4.1, dilutions of PNP are prepared, and the Bradford Method was used to measure protein concentration.

According to the model evaluation program Verify3D, 80.00% of the amino acid residues in this homology model had an average 3D-1D score greater than 0.2, which qualifies it as a passing model (Lüthy et al., 1992). However, between residues 44-66 on the Verify3D plot, the score dips below the 0.2 threshold, falling as low as -0.04. This can be explained by the fact that when aligned against each other, the query sequence and template sequence consist of different types of amino acid residues in this range (Table 1). The query sequence consists of the residues YTAEADGNTIFTKTIPSGITISA, while the template sequence 4IPU_A consists of the residues KDWGKGLSIGVLASGSIAAPLRK. After analyzing these two aligned sequences, some stark differences