Exploring Protein Structure With The Molecular Visualization Firstglance

Figure 3. Protein expression and purification protocol is shown in the schematic in (A). To confirm expression of the P278L mutant, a western blot was performed. Note the presence of Kif5A in all fractions, and enriched in the E1 and E2 eluate.

Proteins are biological macromolecules made from smaller building units called amino acids. There are 20 natural occurring amino acids which can combine in various ways to form a polypeptide. There are four distinctive levels of protein structure: primary, secondary, tertiary and quaternary. The primary structure of a protein is important in determining the final three dimensional structure and hence the role and function of a particular protein, both in the human body and in life around us. The secondary structure of a protein can fall into two major categories; α-helices or β-sheets, other variants also exist such as β-turns {{20 Brändén, Carl-Ivar, 1934- 1991}}. The precise folding or these secondary structures into a three dimensional shape is known as the tertiary structure of a protein and multiple polypeptides bound together via covalent and non-covalent bonds forms the complex quaternary structure of a protein.

B. Original diagram of the different levels of protein structure (i.e., primary, secondary, tertiary, and quaternary).

Sophisticated software compared these parts using existing proteins of the human genome to determine the actual proteins in the samples. They found that the Maiden's profile of

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

This assignment will outline the function of proteins in living organisms and the important roles of different types of protein. “Protein composes 10-30% of cell mass and is the basic structural material of the body” (Marieb E.N.M et al, 2004). Protein is a nutrient that living organisms need to exist and grow, as well as water being a key feature. “All protein contains carbon, oxygen, hydrogen and nitrogen” (Marieb E.N.M et al, 2004). Amino acids form links of 20, “The sequences at which they are bound together produces proteins that vary widely in both structure and function” (Marieb E.N.M et al, 2004).

4a). This protein had the characteristics of two interactions and a 544 amino acid residue. To further support the claim of the TPP1 interaction with POT1, TPP1 antibody was pulled down with flag tagging POT1 (Fig. 4b). Hence, these data validate the claim of the POT1, and TPP1 form one complex [17].

It is of great interest to see how far the scientific community has come across with identifying the genes and functions of each encoding protein. The science brought different interventions, as each gene has the possibility of interaction and the whole cellular environment has a type of role to engage in the complex day to day regulation of our eukaryotic cells.

We know that proteins are basically just amino acids bonded by peptide bonds which form a chain. However the function of protein is determined by the structure of that protein itself, we can determine the structure of an amino acid by observing what sequence the amino are in, each protein or polypeptide as its own unique sequence of amino acids, we refer

The structure of a protein is a complex and dense arrangement, consisting of four levels of understanding. Firstly, the primary structure is simply the sequence of amino acids in the polypeptide chain. This determines the rest of the protein structure. After this, the primary structure can fold into an alpha helix and a Beta pleated sheet. Many hydrogen bonds between the chain make it a stable and strong structure. Next is the tertiary structure, which is the most important in terms of specificity, as every protein has a unique tertiary structure, which is responsible for its properties and function. Weak hydrogen bonds, ionic bonds and disulphide bridges hold this structure together. Finally, the quaternary structure

The primary protein structure can be likened to a human chain in which each person is assumed to be an amino acid and their hands viewed as the carboxyl and amino groups. The person on one end of the chain, who has a free left hand, is assumed to be the free carboxyl group. The person on the other end, who has a free right hand, is assumed to be the free amino group. Everyone in this chain has a left hand linked to somebody’s right hand and a right hand linked to somebody else’s left hand forming peptide bonds. The heads and legs just like the side chains and hydrogens, do not take part in the linking.

He designated this protein, Protein X. Though attempts have been made to isolate the elusive Protein X, no success has occurred and is thus a continued focus in recent research (Prusiner, 1998).

The overall objective of the project is to identify the proteins that interact with EccA1 using a yeast two-hybrid assay test and to characterize the particular regions of the proteins that interact. The TB DNA was isolated from a PCR colony to be used as a template for a PCR reaction. An agarose gel was created and used for electrophoresis of the DNA. A UV illuminator displayed the image of the agarose gel. Use of the analytic software such as 4Peaks, the NCBI tools BLAST and CDD, TUBERCULIST, and CLUSTAL Omega. As a result, the identity of the unknown protein was discovered. Information about the protein, such as the protein’s genes that interacted with EccA1, particular structure and function, and protein alignment, were gathered from these softwares as well. The outcome of the experiment is expected to result in the

What can studies of serine proteases tell us about the relationship between protein structure, function and evolution?