Lab Journal Hemochromatosis Task9

3D mutations with SCWRL4

First, the wild type sequence was extracted from the FASTA entry of 1A6Z on rcsb.org. Then, using mut_seq.py, all mutant sequences were generated. The mutated structures were then generated with SCWRL4 using the following command

Scwrl4 -i <1a6z chain A pdb file> -o <mutated pdb> -s <mutated sequence file>

To check, whether only the right residue was mutated, the sequence of the PDB files containing the mutations were extracted and compared:

RSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVFYDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQVILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNRAYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTYQVEHPGLDQPLIVIW
RSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVFYDDESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQVILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNRAYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIW
RSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVFYDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHIFTVDFWTIMENHNHSKESHTLQVILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNRAYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIW
RSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVFYDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQVILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNRAYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVISSVTTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIW
RSHSLHYLFMGASEQDLGLSLFEALGYMDDQLFVFYDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQVILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNRAYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIW

mut_seq.py

<source lang="python"> import copy seq="rllrshslhylfmgaseqdlglslfealgyvddqlfvfydhesrrveprtpwvssrissqmwlqlsqslkgwdhmftvdfwtimenhnhskeshtlqvilgcemqednstegywkygydgqdhlefcpdtldwraaeprawptklewerhkirarqnraylerdcpaqlqqllelgrgvldqqvpplvkvthhvtssvttlrcralnyypqnitmkwlkdkqpmdakefepkdvlpngdgtyqgwitlavppgeeqrytcqvehpgldqpliviw" seq= list(seq)

mut = {53:"M",63:"D",97:"I",217:"I",282:"Y"}

for key in mut.iterkeys(): mut_seq = copy.deepcopy(seq) mut_seq[key-23] = mut[key] ## -(22+1) 22 for PDB - seq offset and 1 for indexing starting at 0 fName= str(key) + mut[key] + ".seq" with open(fName,"w+") as f: f.write("".join(mut_seq[3:])) #leave out first three residues because they are missing in the PDB structure

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