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Megan Fellows Molecular Modeling Assignment III: Part A (1) Describe the secondary structure within the subunit in full detail. How many beta strands are there? Are they parallel or antiparallel? The amino acid coil winds throughout the protein subunit connecting the alpha helices and the beta strands.There are 6 beta strands in antiparallel sets. (2) Approximately what percent of the subunit is helical? What does the coil represent? The coil represents amino acids in primary structure. It looks as though about half of the protein subunit is helical. There are 31 alpha helices present ranging from 3 to 24 amino acids. The subunit (3) Do most of the hydrogen bonds form between the backbones or the side chains? What is the range of hydrogen bond distances? It can be seen from the image that most of the H­bonds form between the backbones. However, there are a few H­bonds between sidechains. There are 23 hydrogen bonds total in the selected portion of the subunit. The h­bond distances range from LYS342.B, NZ and GLU346.B, OE2 with an h­bond of 3.266 angstroms to GLN330.B, N and GLU326.B, O and the H­bond distance is 2.654 angstroms. (4) Describe the atoms (including which residues they are on) that are forming hydrogen bonds to support the secondary structure. Are these atoms part of the backbone or the side chains? The two beta strands are composed of amino acids in the following order: 1. GLN, MET, LEU 2. TYR, VAL, GLU. The atoms that are forming the hydrogen bonds are the oxygen of the carboxylic acid on one strand and the hydrogen bound to the nitrogen on the N­terminus on the other strand. N­H of Q255.B with O of Y 262.B N­ Hof Y262.B with O of Q255.B N­H of L257.B with O of E260.B N­H of E260.B with O of L257.B These atoms are part of the backbone. In the image you can also see one H­bond off of the amide of Q255.B and the orange coil. (5) What are the h­bond pattern differences between alpha helices and beta sheets? Between antiparallel and parallel beta sheets? Draw diagrams on a piece of paper representing the h­bond pattern of each secondary structure motif. An alpha helix is stabilized by h­bonds that form between the N­H of an amino acid and the C=O of a residue 4 amino acids away from it. These bonds form between the backbone of the helix. Beta sheets hydrogen bond with residues on the opposite sheet. The h­bonding varies depending on if the beta sheet is antiparallel or parallel. If the beta sheet is parallel the N­H from one residue will bond with the C=O of the residue on the opposite sheet and diagonal. The residues in a parallel sheet are h­bonded in a 1:2 ratio. If the beta sheet is in the antiparallel configuration the N­H of one residue will h­bond to the C=O of the residue directly across from it. In antiparallel beta sheets the h­bonds occur in a 1:1 ratio. (6) How does a 310 helix differ from an alpha helix? Each amino acid in this type of helix corresponds to a 120 degree turn in the helix. There are 10 atoms in the ring. The N­H of an amino acid group forms and h­bond with the C=O of the amino acid three residues earlier. The type of H bonding can be seen in the image below. In a typical alpha helix the N­H of an amino acid group forms and h­bond with the C=O of the amino acid 4 residues earlier. (7) Describe the tertiary structure of the subunit. The tertiary structure of the subunit consists of 31 alpha helices and 6 beta strands. These secondary structures are connected by a long coil of single amino acids which is called the protein’s backbone. As a whole prostaglandin H2 synthase consists of two different tertiary subunits, A and B. (8) What types of intermolecular forces are known to stabilize tertiary structure? Do these stabilizing interactions occur between the side chains or the back bone? The tertiary structure can be stabilized by hydrogen bonds, van der waals interactions, ionic bonds hydrophobic interactions and disulfide linkages. Hydrogen bonds can form between side chains and in the back bone. Hydrophobic interactions are generally seen in the secondary structures of alpha helices and beta sheets where the hydrophobic amino acids are positioned towards each other so that weak interactions can occur between them. Disulfide linkages occur between cysteine groups. (9) Think about where you might find such an interaction. Find an example in subunit B of prostaglandin H2 synthase. Include an image. There is a disulfide linkage between C36.B and C47.B that helps to stabilize the tertiary structure of subunit B. This disulfide linkage helps to stabilize the tertiary structure of the B subunit. (10) Describe the quaternary structure of prostaglandin H2 synthase. The quaternary structure is made up of two subunits A and B. The subunits are both composed of an extensive network of alpha helices, beta sheets, and coil. The subunits are connected by interactions between the tertiary structures of the subunits. (11)​
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What types of intermolecular forces are known to stabilize quaternary structure? Do these involve the side chains or backbones? The quaternary structure of a protein is usually stabilized by weak interactions between the exposed surfaces of the protein’s subunits. For example, a residue buried in the middle of a subunit will usually not interact with another subunit. (12) ​
In the image below you can see an h­bond between the N­H of G51.B and the C=O of the E319.A. The A and B indicate that the the glycine is on the B subunit and the glutamate of subunit A. The H­bond between subunit A and subunit B helps to stabilize the quaternary structure. Part B. (1)​
I would expect to find the non­polar aliphatic groups in the area of the enzyme that is partially submerged in the plasma membrane. The interior of the plasma membrane is hyrophobic as are the non­polar amino acids alanine, glycine, isoleucine, valine, leucine, and methionine so I would expect the enzyme “anchor” to be composed of these amino acids. (2) Light blue is the most hydrophilic, white is neutral, and orange is the most hydrophobic. Image 1 shows the ‘underside’ of the prostaglandin H2 synthase. There are two hydrophobic regions/bands that protrude from the underside that seem as though they would find a way to nest into the hydrophobic inner of the phospholipid bilayer. Image 2 shows the 3D structure of these protrusions better. Image 3 shows the ‘top’ portion of the synthase. As you can see from the image there really isn’t a concentrated grouping of hydrophobic amino acids leading me to assume that image 1 corresponds to the hydrophobic region that “anchors” the synthase. Image 1: Image 2: Image 3: