Task 8 (MSUD)

Results

Lab journal

Visualization of mutations

• Original residues and mutations in BCKDHA (1U5B chain A)
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  Original residues of BCKDHA are marked in red.

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  Mutant residues are marged in orange.

Selected mutations

Following are the selected mutations from HGMD and dbSNP. Changes in physicochemical properties, secondary structures, amino acid substitution scores, conservation and prediction results of different programs are also shown in the table:

mutation	physicochemical changes	secondary structure	BLOSUM62 score	PAM250 score	PSSM conservation WT	PSSM conservation mutant	MSA conservation WT	MSA conservation mutant	SIFT	Polyphen2	MutationTaster	SNAP	DB
P38H	small/fixed conformation/apolar to large/aromatic/polar	-	-2	0	31	0	0.29	0	tolerated	benign	polymorphism	NA	dbSNP
M82L	sulfur-containing to aliphatic/branched	E	2	4	12	59	0.36	0.01	tolerated	benign	disease causing	NA	dbSNP
T151M	small/polar to apolar/sulfur-containing	-	-1	-1	8	0	0.8	0	tolerated	probably/possibly damaging	disease causing	NA	HGMD
A222T	apolar to polar	H	0	1	64	4	0.38	0	affect protein function	probably damaging	disease causing	NA	dbSNP
C264W	small/sulfur-containing to large/aromatic	E	-2	-8	52	0	0.91	0	affect protein function	probably/possibly damaging	disease causing	NA	HGMD
R265W	positively-charged to aromatic/larger	E	-3	2	12	0	0.36	0.38	affect protein function	probably damaging	disease causing	NA	HGMD
R314Q	guanidin/large/positively-charged to amin	H	1	1	23	0	0.35	0	affect protein function	probably damaging	disease causing	NA	dbSNP
R346H	hydrophilic to hydrophobic/aromatic	-	0	2	92	0	0.9	0	affect protein function	probably damaging	disease causing	NA	HGMD
I361V	smaller	H	3	4	64	10	0.89	0.01	tolerated	benign/possibly damaging	disease causing	NA	dbSNP
Y413H	uncharged to positively-charged	-	2	0	74	1	0.9	0	affect protein function	probably damaging	disease causing	NA	HGMD

SIFT

The following table shows the prediction of mutation effects by SIFT. 6 out of 10 mutations are predicted to affect protein function.

mutation	prediction	score	median sequence conservation	sequences represented at position
P38H	tolerated	0.16	3.16	17
M82L	tolerated	0.56	3.03	43
T151M	tolerated	0.05	3.03	46
A222T	affect protein function	0.04	3.03	46
C264W	affect protein function	0.00	3.03	46
R265W	affect protein function	0.00	3.03	46
R314Q	affect protein function	0.01	3.03	46
R346H	affect protein function	0.00	3.03	46
I361V	tolerated	0.12	3.03	46
Y413H	affect protein function	0.00	3.03	46

Polyphen2

The prediction resuls of Polyphen2 are shown in the following table. 7 out of 10 mutations are predicted to be probably damaging (at least for the trained set HumDiv). For the mutation T151M, this does not agree with the results of SIFT. But for this mutations the Polyphen scores are also the lowest of all mutations that are predicted to be damaging. So Polyphen sees an uncertainty for this mutation too, if it is damaging.

	HumDiv				HumVar
mutation	prediction	score	sensitivity	specificity	prediction	score	sensitivity	specificity
P38H	benign	0.118	0.93	0.96	benign	0.042	0.93	0.62
M82L	benign	0.002	0.99	0.30	benign	0.006	0.97	0.45
T151M	probably damaging	0.963	0.78	0.95	possibly damaging	0.622	0.80	0.85
A222T	probably damaging	1.000	0.00	1.00	probably damaging	0.943	0.65	0.91
C264W	probably damaging	0.989	0.72	0.97	possibly damaging	0.887	0.71	0.89
R265W	probably damaging	1.000	0.00	1.00	probably damaging	1.000	0.00	1.00
R314Q	probably damaging	1.000	0.00	1.00	probably damaging	0.998	0.18	0.98
R346H	probably damaging	1.000	0.00	1.00	probably damaging	0.993	0.47	0.96
I361V	benign	0.386	0.90	0.89	possibly damaging	0.610	0.80	0.83
Y413H	probably damaging	1.000	0.00	1.0	probably damaging	0.999	0.09	0.99