Task 9 Lab Journal (MSUD)

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
                                                                  |||||
SEQUENCE           1 ---------------------------------------------SSLDD      5

NP_000700.1       51 KPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKE    100
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE           6 KPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKE     55

NP_000700.1      101 KVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALDN    150
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE          56 KVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALDN    105

NP_000700.1      151 TDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKER    200
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE         106 TDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKER    155

NP_000700.1      201 HFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGF    250
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE         156 HFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGF    205

NP_000700.1      251 NFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG    300
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE         206 NFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG    255

NP_000700.1      301 NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDE    350
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE         256 NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDE    305

NP_000700.1      351 VNYWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERK    400
                     |.||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE         306 VGYWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERK    355

NP_000700.1      401 PKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK    445
                     |||||||||||||||||||||||||||||||||||||||||||||
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.