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Frontiers in Biology

ISSN 1674-7984

ISSN 1674-7992(Online)

CN 11-5892/Q

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Front. Biol.    2015, Vol. 10 Issue (5) : 448-457    https://doi.org/10.1007/s11515-015-1370-2
RESEARCH ARTICLE
Reckoning the SIX1 mutation’s effects in branchio-oto-renal syndrome — A bioinformatics approach
B. Preethi,V. Shanthi,K. Ramanathan()
Industrial Biotechnology Division, School of Bio Sciences and Technology, VIT University, Vellore − 632014, Tamil Nadu, India
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Abstract

Branchio-oto-renal syndrome (BOR) is autosomal dominant disorder which generates hearing impairment and kidney failures in affected individuals. The disease genomic maps were drawn back in recent years, demonstrating, missense mutations responsible in disease were located in SIX1, EYA1 and EYA2 genes. We try to uncover molecular biology of the syndrome with bioinformatics perspective, taking SIX1 and EYA2 protein interaction at center point. The study initiated with 23 natural mutations of SIX1 gene. They were first analyzed with prediction servers like SIFT, PolyPhen2, I Mutant, SNPs&GO, PHD-SNP and Panther, to identify their impact on their structural stability and function. Subsequently it narrowed down to seven consistent with our quest. They were analyzed on IUPred disorder prediction server. Later SIX1 and its all mutant proteins were docked with EYA2 protein using GRAMM-X server. The binding affinity of docked structures was analyzed using DFIRE2 algorithm. The results justify the earlier wet laboratory studies and indicate the reason behind them. Finally we summarize that the proven inactivity of all other mutants is due to the structural disorder created by mutations, hence usual molecular interaction is hindered; strangely protein interaction takes place at DNA binding site of SIX1 mutants.
Keywords branchio-oto-renal syndrome (BOR)      hearing loss      damaging mutations      SIX1      EYA2      protein-protein interactions     
Corresponding Author(s): K. Ramanathan   
Just Accepted Date: 21 August 2015   Online First Date: 30 September 2015    Issue Date: 30 October 2015
 Cite this article:   
B. Preethi,V. Shanthi,K. Ramanathan. Reckoning the SIX1 mutation’s effects in branchio-oto-renal syndrome — A bioinformatics approach[J]. Front. Biol., 2015, 10(5): 448-457.
 URL:  
https://academic.hep.com.cn/fib/EN/10.1007/s11515-015-1370-2
https://academic.hep.com.cn/fib/EN/Y2015/V10/I5/448
Fig.1  Docked complexes of the native and mutant SIX1 with EYA2 protein.
S.No Uniprot ID and rs ID Amino acid change Tolerance index Predictions PSIC Predictions I Mutant 2.0 Predictions
1 Q15475 V17E 0 Deleterious 0.999 Probably damaging −0.03 Destabilizing
2 Q15475 H73P 0.01 Deleterious 0.621 Possibly damaging 0.36 Stabilizing
3 Q15475 V106G 0 Deleterious 1 Probably damaging −4.2 Destabilizing
4 Q15475 R112C 0 Deleterious 1 Probably damaging −1.31 Destabilizing
5 Q15475 P249L 0.69 Non-deleterious 0.001 Benign −0.95 Destabilizing
6 Q15475 R99C 0 Deleterious 1 Probably damaging −1.07 Destabilizing
7 Q15475 R110Q 0 Deleterious 1 Probably damaging −0.97 Destabilizing
8 Q15475 R110W 0 Deleterious 1 Probably Damaging −0.37 Destabilizing
9 Q15475 W122R 0 Deleterious 0.97 Probably damaging −1.85 Destabilizing
10 Q15475 Y129C 0 Deleterious 1 Probably damaging 0.13 Stabilizing
11 rs374638294 P211L 0.28 Non-deleterious 0 Benign 0.72 Stabilizing
12 rs371998997 V168I 0.07 Non-deleterious 0.987 Probably damaging −0.26 Destabilizing
13 rs370259896 L260Q 0.09 Non-deleterious 0.025 Benign 0.24 Stabilizing
14 rs368974927 P249Q 0.32 Non-deleterious 0.242 Benign −1.93 Destabilizing
15 rs200835641 A95V 0 Deleterious 0.984 Probably damaging 0.98 Stabilizing
16 rs200205240 T252A 0.95 Non-deleterious 0 Benign −0.37 Destabilizing
17 rs149265761 D227E 0.61 Non-deleterious 0 Benign 0.64 Stabilizing
18 rs149166341 H44Q 0.87 Non-deleterious 0.006 Benign −0.12 Destabilizing
19 rs146357380 E28D 0.84 Non-deleterious 0.022 Benign 0.54 Stabilizing
20 rs146129487 E217K 0.91 Non-deleterious 0.704 Possibly damaging −0.49 Destabilizing
21 rs144481204 D227Y 0.01 Deleterious 0.874 Possibly damaging 0.44 Stabilizing
22 rs143516729 T165I 0.45 Non-deleterious 0.155 Benign −0.35 Destabilizing
23 rs142301715 N193I 0.24 Non-deleterious 0.138 Benign 0.73 Stabilizing
Tab.1  List of variants predicted to be functionally significant by SIFT, PolyPhen 2.0 and I Mutant 2.0
S.No Amino acid change PHD-SNP probability PANTHER probability SNP&GO probability Prediction
1 V17E 0.98 0.962 0.991 Disease
2 R99C 0.984 0.987 0.991 Disease
3 V106G 0.939 0.972 0.989 Disease
4 R110Q 0.965 0.976 0.99 Disease
5 R110W 0.978 0.995 0.992 Disease
6 R112C 0.986 0.993 0.993 Disease
7 W122R 0.989 0.985 0.993 Disease
Tab.2  List of variants that were predicted to be functionally significant by SNP&Go, PHD-SNP and PANTHER, mutants in bold letter are significantly deleterious and highly damaging
Fig.2  Order and disorder prediction from protein sequence, based on IUPred and ANCHOR algorithm. (A) SIX1 wild type, (B) V17E and (C) R99C.
Fig.3  Order and disorder prediction from protein sequence, based on IUPred and ANCHOR algorithm. (A) V106G (B) R110Q and (C) R110W.
Fig.4  Order and disorder prediction from protein sequence, based on IUPred and ANCHOR algorithm. (A) R112C and (B) W122R.
S.No Docked protein complexes Main chain-main chain interactions Main chain-side chain interactions Side chain-side chain interactions Total number of interactions
1 SIX1-EYA2 2 5 2 9
2 V17E-EYA2 2 4 0 6
3 R99C-EYA2 0 10 7 17
4 V106G-EYA2 0 10 7 17
5 R110Q-EYA2 0 10 7 17
6 R110W-EYA2 1 2 7 10
7 R112C-EYA2 1 10 7 18
8 W122R-EYA2 0 10 11 21
Tab.3  List of intermolecular hydrogen bonds essential for the stability of SIX1-EYA2 docked complex.
S.No Docked protein complexes Number of ionic interactions Total number of interactions Free energy of binding (kcal/mol)
1 SIX1-EYA2 1 9 −843.913
2 V17E-EYA2 1 6 −841.117
3 R99C-EYA2 5 17 −854.855
4 V106G-EYA2 5 17 −854.141
5 R110Q-EYA2 5 17 −854.932
6 R110W-EYA2 1 10 −640.758
7 R112C-EYA2 6 18 −855.918
8 W122R-EYA2 6 21 −852.954
Tab.4  Details of number of ionic interactions, total interactions and binding energy of docked complex
Fig.5  Showing the similarity pattern between normalized free energy, number of total interactions and number of ionic interactions in corresponding docked files.
Fig.6  Visualization of ionic interactions between Native and Mutant SIX1 protein and EYA2.
S.No Docked protein complexes Number of ionic interactions POS (SIX1) RES POS (EYA2) RES
1 SIX1-EYA2 1 41 ASP 210 LYS
2 V17E-EYA2 1 41 ASP 210 LYS
3 R99C-EYA2 5 12 GLU 210 LYS
153 GLU 223 ARG
183 GLU 111 ARG
42 HIS 108 ASP
152 ARG 1 GLU
4 V106G-EYA2 5 12 GLU 210 LYS
153 GLU 223 ARG
183 GLU 111 ARG
42 HIS 108 ASP
152 ARG 1 GLU
5 R110Q-EYA2 5 12 GLU 210 LYS
153 GLU 223 ARG
183 GLU 111 ARG
42 HIS 108 ASP
152 ARG 1 GLU
6 R110W-EYA2 1 185 LYS 125 GLU
7 R112C-EYA2 6 12 GLU 210 LYS
47 GLU 111 ARG
153 GLU 223 ARG
183 GLU 111 ARG
42 HIS 108 ASP
152 ARG 1 GLU
8 W122R-EYA2 6 12 GLU 210 LYS
47 GLU 111 ARG
153 GLU 223 ARG
183 GLU 111 ARG
42 HIS 108 ASP
152 ARG 1 GLU
Tab.5  Elaborated Ionic interactions in the docked protein complexes
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