Task 9: Structure-based mutation analysis

<css> table.colBasic2 { margin-left: auto; margin-right: auto; border: 1px solid black; border-collapse:collapse; width: 40%; }

.colBasic2 th,td { padding: 3px; border: 1px solid black; }

.colBasic2 td { text-align:left; }

/* for orange try #ff7f00 and #ffaa56 for blue try #005fbf and #aad4ff

maria's style blue: #adceff grey: #efefef

/

.colBasic2 tr th { background-color:#efefef; color: black;} .colBasic2 tr:first-child th { background-color:#adceff; color:black;} </css>

Lab_Journal_Hemochromatosis_Task9

Structure Selection

PDB ID	Res [A]	R-value (obs)	pH	missing residues	coverage
1A6Z	2.60	2.33	6.5	1-3	83.4%
1DE4	2.80	2.31	8.0	1-3	83.4%

From the two available structures, we chose 1A6Z, because it has a slightly higher resolution and a nearly identical resolution compared to 1DE4. On the downside, 1A6Z was resolved at a pH value of 6.5, which is more distant to the physiological pH than the resolution pH of 1DE4. 1A6Z was chosen nevertheless, because it was used in all previous tasks, in order to keep consistency.

Mutations

Mutation	Disease causing ?
Val53Met	Yes
His63Asp	Yes
Met97Ile	No
Thr217Ile	No
Cys282Tyr	Yes

</figtable>

Structure Mutation using SCWRL

Val53Met

**Figure 2:** Wild type(grey) and mutant(red) residues for position 53.

</figtable> Figure 2 shows that the mutation to Methionin does not change the polar contacts of the residue. But Methionin extends further into the binding pocket than Valin, which might disturb the structure of the binding pocket and inhibit the binding process.

His63Asp

**Figure 3:** Wild type (grey) and mutant (red) residues for position 63.

Regarding the polar contacts of residue 63, there is no change, because both variants do not exhibit polar interactions (Figure 3). Also, the mutation lies in a loop region and does not disturb an ordered secondary structure. But nevertheless, the mutation is disease causing, which might be due to the fact that the loop where it is located is still part of the binding interface to ferritin and that the change from an aromatic, mainly uncharged residue to a negatively charged residue disturbs this interface.

Met97Ile

**Figure 4:** Wild type(grey) and mutant(red) residues for position 97.

Both variants show the same polar contacts, which are only the intra-backbone hydrogen bonds that stabilize the alpha helix (Figure 4). The isoleucin is slightly smaller than methione, but the residue stays uncharged and nonpolar and thus, although it is located directly at the binding interface to ferritin, the mutatiion is neutral.

T217I

**Figure 5:** Wild type(grey) and mutant(red) residues for position 217.

C282Y

**Figure 6:** Wild type(grey) and mutant(red) residues for position 282. The disulfide bridge binding partner of C282 is shown in white.

Structure Mutation using foldX

**Figure 7:** Comparison between mutations performed by SCWRL(green) and foldx(cyan).