Difference between revisions of "Gaucher Disease: Task 09 - Structure-based mutation analysis"

From Bioinformatikpedia
(N409S)
(L483P)
Line 122: Line 122:
 
<gallery widths=300px heights=200px caption="PyMol visualization of the mutation '''L483P''' (PDB 444) of the structure 2V3E, chain B, created with SCWRL." perrow="3">
 
<gallery widths=300px heights=200px caption="PyMol visualization of the mutation '''L483P''' (PDB 444) of the structure 2V3E, chain B, created with SCWRL." perrow="3">
 
File:2V3E_B_mutation_L444P_sticks.png| Comparison of wild type (wt) Leucine 483 (magenta) and mutant Proline (orange). The mutant Proline is a circle amino acid, which has very different properties than the hydrophobic Leucine. Is leads to a shift in the main chain conformation "backwards", so that the beginning of the neighboring strand is shifted.
 
File:2V3E_B_mutation_L444P_sticks.png| Comparison of wild type (wt) Leucine 483 (magenta) and mutant Proline (orange). The mutant Proline is a circle amino acid, which has very different properties than the hydrophobic Leucine. Is leads to a shift in the main chain conformation "backwards", so that the beginning of the neighboring strand is shifted.
File:2V3E_B_L444_hb.png| '''Leucine 483''' (PDB 444) lies at the very beginning of a beta strand. There is another beta strand in the proximity on the right, which is followed by three others, forming a beta sheet. However, the Leucine does not form any contact with the neighboring strand, as its side chain is hydrophobic and point in another direction. The Leucine forms an interesting hydrogen bond with its amino-group to the side chain of a residue located in the neighboring turn. After this loop another beta-strand follows.
+
File:2V3E_B_L444_hb.png| Leucine 483 (PDB 444) lies at the very beginning of a beta strand. There is another beta strand in the proximity on the right, which is followed by three others, forming a beta sheet. However, the Leucine does not form any contact with the neighboring strand, as its side chain is hydrophobic and point in another direction. The Leucine forms an interesting hydrogen bond with its amino-group to the side chain of a residue located in the neighboring turn. After this loop another beta-strand follows.
 
File:2V3E_B_mutant_444P_hb_sticks_missing_contact.png| The mutant Proline 483 does not form a hydrogen bond with the residue in the loop, like the Leucine main chain amino-group does (see the corresponding figure), because Proline lacks a free amino-group because of the loop formation.
 
File:2V3E_B_mutant_444P_hb_sticks_missing_contact.png| The mutant Proline 483 does not form a hydrogen bond with the residue in the loop, like the Leucine main chain amino-group does (see the corresponding figure), because Proline lacks a free amino-group because of the loop formation.
 
</gallery>
 
</gallery>

Revision as of 22:35, 30 August 2013

<css>

table.colBasic2 { margin-left: auto; margin-right: auto; border: 1px solid black; border-collapse:collapse; }

.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>

This page is under construction.

Preparation

1. Choice of a structure to work with

We chose the structure 2V3E, chain B, which has the following properties:

<figtable id="2V3E">

PDB-ID Resolution (Å) Chain Covered residues (UniProt seq.) Missing residues (ATOM seq.) Covered residues (ATOM seq.) R-Value(obs.) R-Free pH Temperature (K)
2V3E 2.0 A/B 40-536 (92.7%) A: 31, (498-503), B: (-1), (498-503) A: -1-30, 32-497, B: 0-497 0.163 0.220 7.5 100
2V3E, chain B, the chosen reference structure of GBA sequence P04062.

</figtable>

For more information about other candidates and the missing residues, see the lab journal.

2. Visualization of the mutations to work with

We selected the following five mutation from the mutations selected in for this task:

<figtable id="mutations">

Reference Codon change Codon Number (UniProt) Codon Number (PDB) Amino Acid change Polarity Charge (pH) Disease causing?
rs368786234 AGC ⇒ AGA 77 38 Ser ⇒ Arg (S77R) polar ⇒ polar neutral ⇒ positive FALSE
rs374003673 AAT ⇒ AGT 141 102 Asn ⇒ Ser (N141S) polar ⇒ polar neutral ⇒ neutral FALSE
CM992894 GGA ⇒ GAA 241 202 Gly ⇒ Glu (G241E) nonpolar ⇒ polar neutral ⇒ negative TRUE
CM880036 AAC ⇒ AGC 409 370 Asn ⇒ Ser (N409S) polar ⇒ polar neutral ⇒ neutral TRUE
CM870010 CTG ⇒ CCG 483 444 Leu ⇒ Pro (L483P) nonpolar ⇒ nonpolar neutral ⇒ neutral TRUE
Selected mutations of GBA sequence P04062. Mapping of the UniProt positions onto the PDB ATOM sequence is given.

</figtable>

The following figure visualizes the five residues we are going to mutate on the reference structure, 2V3E, chain B.

As can be seen on the image, none of the residues to be mutated lies in the proximity of one of the three binding sites. (See also the second subfigures of the figure galleries in the next subsection for close up on the residues and their hydrogen bonds.) However, four of the residues lie within a secondary structure element (beta sheet or helix) and one - Glycine 241 - in a turn near a helix. This implies that exchange of these residues with others with different functional groups, polarity and charge could lead to destruction of some hydrogen bonds within or between the secondary structures (e.g. Asparagine 141). This might lead to structural changes and even to destruction of the secondary structures or important blocks of secondary structure elements. Moreover, an exchange with a side chain of a bigger size might lead to clashed with proximate residues (e.g. with the loop near the Serine 77).

3. Creation of mutated structures

We used SQWRL4 to create the five mutated structures. (See lab journal.) The mutated residues in comparison to the native residues, the hydrogen of the mutants and possible clashes are shown in the following figures.

S77R

According to this images, we would also predict the mutation S77R as not disease causing.

N141S

The mutation N141S is benign, therefore the missing stabilizing contact between the two helices is probably not so important.

G241E

As no changes in the hydrogen bonds or clashes etc. can be noticed, we would predict the mutation G241E as benign. However, it is a disease causing mutation. Maybe the effect is caused by the polarity and negative charge of the mutant Glutamate, instead of the nonpolar and neutral Glycine.

N409S

We would predict the mutation N409S as non-effect. Due to the fact that all hydrogen bonds remain conserved in the mutant and that no clashes etc. could be detected, we would predict the mutation G241E as benign. Moreover, the both amino acids, Asparagine and Serine, are both polar and neutral. Nevertheless, if is disease causing. TODO: try to find again what we oversee!

L483P

We would predict the mutation L483P as having an effect - and so it is.


Energy comparisons

Lab journal

foldX

Minimise

Gromacs (optional task for those who love MD!)