Difference between revisions of "Task 9 Lab Journal (MSUD)"
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==Selection of structure model== |
==Selection of structure model== |
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| − | As a tradeoff between resolution and sequence completeness, we have chose the PDB structure 2BFF as model structure for BCKDHA. |
+ | As a tradeoff between resolution and sequence completeness of the structure model, we have chose the PDB structure 2BFF as model structure for BCKDHA. |
==Visualizatin of mutant structures== |
==Visualizatin of mutant structures== |
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Revision as of 15:10, 12 July 2013
Contents
Selection of structure model
As a tradeoff between resolution and sequence completeness of the structure model, we have chose the PDB structure 2BFF as model structure for BCKDHA.
Visualizatin of mutant structures
In order to get the position of mutations in PDB structure 2BFF, we have aligned the SEQRES sequence of 2BFF to reference sequence of BCKDHA using Needleman Wunsch algorithm. The position of mutations should be shifted 45 residues back. Alignment is shown below:
NP_000700.1 1 MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDD 50
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SEQUENCE 1 ---------------------------------------------SSLDD 5
NP_000700.1 51 KPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKE 100
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SEQUENCE 6 KPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKE 55
NP_000700.1 101 KVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALDN 150
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SEQUENCE 56 KVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALDN 105
NP_000700.1 151 TDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKER 200
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SEQUENCE 106 TDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKER 155
NP_000700.1 201 HFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGF 250
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SEQUENCE 156 HFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGF 205
NP_000700.1 251 NFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG 300
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SEQUENCE 206 NFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG 255
NP_000700.1 301 NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDE 350
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SEQUENCE 256 NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDE 305
NP_000700.1 351 VNYWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERK 400
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SEQUENCE 306 VGYWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERK 355
NP_000700.1 401 PKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK 445
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SEQUENCE 356 PKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK 400
Energy comparisons
FoldX
We have adopted the example files from FoldX to perform a batched evaluation of the energy of mutant structures. Because, in our case, we are interested in the effect of single point mutations on protein structure and function, we simply assigned the 5 chosen mutations into 5 rows with tailing semicolon.
