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

From Bioinformatikpedia
(S77R)
(N141S)
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<gallery widths=300px heights=200px caption="PyMol visualization of the mutation '''N141S''' (PDB 102) of the structure 2V3E, chain B, created with SCWRL." perrow="3">
 
<gallery widths=300px heights=200px caption="PyMol visualization of the mutation '''N141S''' (PDB 102) of the structure 2V3E, chain B, created with SCWRL." perrow="3">
 
File:2V3E_B_mutation_N102S_sticks.png| Comparison of wild type (wt) Asparagine 141 (magenta) and mutant Serine (orange). The mutated side chain is a little shorter and points towards another direction.
 
File:2V3E_B_mutation_N102S_sticks.png| Comparison of wild type (wt) Asparagine 141 (magenta) and mutant Serine (orange). The mutated side chain is a little shorter and points towards another direction.
File:2V3E_B_N102_hb.png| '''Asparagine 141''' (PDB 102)is located in a helix and forms four hydrogen contacts: two with the main-chain carboxyl- and amino-groups with two helix amino acids (one in each direction) and two with the side chain. One of the contacts of the Asparagine side chain also binds to the same residue in the helix as the Asparagine amino-group binds. The second hydrogen bond of the Asparagine side chain is formed with the side chain of a residue in the neighboring helix, fixing the two helices to each other in this way.
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File:2V3E_B_N102_hb.png| '''Asparagine 141''' (PDB 102)is located in a helix and forms four hydrogen contacts: two with the main-chain carboxyl- and amino-groups with two helix amino acids (one in each direction) and two with the side chain. One of the contacts of the Asparagine side chain also binds to the same residue in the helix as the Asparagine amino-group binds. The second hydrogen bond of the Asparagine side chain is formed with the side chain of a residue in the neighboring helix. Maybe this bond plays a stabilizing role between the two helices.
 
File:2V3E_B_mutant_102S_hb_2diff.png| Hydrogen bonds formed by the mutant Serine 141. A contact that was formed between the native Asparagine side chain and a side chain pointing from a neighboring helix (showed in sticks) is missing, as well as a second contact with a residue in the same helix. Instead, the mutated Serine side chain forms a contact with another residue in the same helix.
 
File:2V3E_B_mutant_102S_hb_2diff.png| Hydrogen bonds formed by the mutant Serine 141. A contact that was formed between the native Asparagine side chain and a side chain pointing from a neighboring helix (showed in sticks) is missing, as well as a second contact with a residue in the same helix. Instead, the mutated Serine side chain forms a contact with another residue in the same helix.
 
File:2V3E_B_mutant_102S_hb_spheres_missing_contact.png| Spheres representation of the mutant Serine and the missing contact with the neighboring helix.
 
File:2V3E_B_mutant_102S_hb_spheres_missing_contact.png| Spheres representation of the mutant Serine and the missing contact with the neighboring helix.
 
File:2V3E_B_mutant_102S_hb_spheres_no_loop_clash.png| Spheres representation of the mutant Serine and a proximate loop (gray spheres) - there is no clash.
 
File:2V3E_B_mutant_102S_hb_spheres_no_loop_clash.png| Spheres representation of the mutant Serine and a proximate loop (gray spheres) - there is no clash.
 
</gallery>
 
</gallery>
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The mutation N141S is benign, therefore the missing stabilizing contact between the two helices is probably not so important.
We would predict the mutation N141S as having an effect.
 
   
 
====G241E====
 
====G241E====

Revision as of 22:19, 30 August 2013

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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

N141S

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

G241E

We would predict the mutation G241E as benign.

N409S

We would predict the mutation N409S as non-effect.

L483P

We would predict the mutation L483P as having an effect.


Energy comparisons

Lab journal

foldX

Minimise

Gromacs (optional task for those who love MD!)