Gaucher Disease: Task 09 - Structure-based mutation analysis

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Revision as of 16:48, 30 August 2013 by Kalemanovm (talk | contribs) (3. Creation of mutated structures)

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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)
rs368786234 AGC ⇒ AGA 77 38 Ser ⇒ Arg (S ⇒ R) polar ⇒ polar neutral ⇒ positive
rs374003673 AAT ⇒ AGT 141 102 Asn ⇒ Ser (N ⇒ S) polar ⇒ polar neutral ⇒ neutral
CM992894 GGA ⇒ GAA 241 202 Gly ⇒ Glu (G ⇒ E) nonpolar ⇒ polar neutral ⇒ negative
CM880036 AAC ⇒ AGC 409 370 Asn ⇒ Ser (N ⇒ S) polar ⇒ polar neutral ⇒ neutral
CM870010 CTG ⇒ CCG 483 444 Leu ⇒ Pro (L ⇒ P) nonpolar ⇒ nonpolar neutral ⇒ neutral
Selected mutations of GBA sequence P04062. Mapping of the UniProt positions onto the PDB ATOM sequence is given.

</figtable>

The following figures visualize the residues we are going to mutate on the reference structure, 2V3E, chain B.

As can be seen on the first subfigure, none of the residues to be mutated lies in the proximity of one of the three binding sites. 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 SQWRL 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.


Energy comparisons

Lab journal

foldX

Minimise

Gromacs (optional task for those who love MD!)