Sequence-based mutation analysis of ARSA

Intro

Description of Mutations

We randomly picked 10 missense mutations from dbSNP and HGMD. The mutations are listed below, together with a pymol mutagenesis image and a description of the properties of the mutations.

Nr.	mutation	position	reference	mutation	both
1	Asp-Asn	29
			Description of Asp-Asn Aspartic acid (Asp) Asparagine (Asn) BLOSUM62 PAM1 PAM250 1 (worst: -4) 36 (worst: 0) 7 (worst: 0) Aspartic acid is an acidic amino acid while Asparagine is a hydrophilic amino acid. So the mutation changes the behaviour towards water as well as the pH.
2	Pro - Ala	136
			Description of Pro-Ala Proline (Pro) Alanine (Ala) BLOSUM62 PAM1 PAM250 -1 (worst: -4) 22 (worst: 0) 11 (worst: 0) Proline and Alanine are both hydrophobic amino acids. So the behaviour towards water does not change. As Proline is a cyclic amino acid, it can "break" alpha-helices and is structural very important. Alanine is one the the smallest amino acids and so the mutation from Pro to Ala should have a big influence on the structure of ARSA.
3	Gln-His	153
			Description of Gln-His Glutamine (Gln) Histidine (His) BLOSUM62 PAM1 PAM250 0 (worst: -3) 20 (worst: 0) 7 (worst: 0) Glutamine is a hydrophilic amino acid while Histidine is a basic amino acid. So the behaviour towards water changes as well as the charge of the amino acid. Also Gln and His are very different in structure, so His needs much more space than Gln, which should have a big influence on the structure of ARSA.
4	Trp-Cys	193
			Description of Trp-Cys Tryptophan (Trp) Cysteine (Cys) BLOSUM62 PAM1 PAM250 -2 (worst: -4) 0 (worst: 0) 1 (worst: 1) Tryptophan is a hydrophobic, aromatic amino acid while Cysteine is a hydrophilic amino acid. So the behaviour towards water changes dramatically. Also, Trp is the largest amino acid while Cys is a rather small amino acid. So the space needed for the amino acid changes also. This should have a huge influence on the structure of ARSA.
5	Thr-Met	274
			Description of Thr-Met Threonine (Thr) Methionine (Met) BLOSUM62 PAM1 PAM250 -1 (worst: -3) 2 (worst: 0) 1 (worst: 0) Threonine is a hydrophilic amino acid while Methionine is a hydrophobic amino acid. So the behaviour towards water changes. Also, Methionine has a very long sidechain while Threonine does not. So the structure of ARSA should be altered by this mutation.
6	Phe -Val	356
			Description of Phe-Val Phenylalanine (Phe) Valine (Val) BLOSUM62 PAM1 PAM250 -1 (worst: -4) 1 (worst: 0) 10 (worst: 1) Phenylalanine and Valine are both hydrophobic amino acids. So the only impact on structure could come frome the structural differences between Phe and Val. Phe has a aromatic ring and due to that needs more space than Val.
7	Thr-Ile	409
			Description of Thr-Ile Threonine (Thr) Isoleucine (Ile) BLOSUM62 PAM1 PAM250 -2 (worst: -3) 7 (worst: 0) 4 (worst: 0) Threonine is a hydrophilic amino acid while Isoleucine is a hydrophobic amino acid. So the behaviour towards water changes.
8	Asn-Ser	440
			Description of Asn-Ser Asparagine (Asn) Serine (Ser) BLOSUM62 PAM1 PAM250 1 (worst: -4) 34 (worst: 0) 8 (worst: 0) Asparagine and Serine are both hydrophilic amino acids. Also they are almost of the same size. So the mutation should not have a very dramatic effect.
9	Cys-Gly	489
			Description of Cys-Gly Cystein (Cys) Glycine (Gly) BLOSUM62 PAM1 PAM250 -3 (worst: -4) 1 (worst: 0) 4 (worst: 0) Cystein and Glycine are both hydrophilic amino acids. The only difference is the size: Gly is the smallest of the amino acids while Cys is a little bigger. The effect should not be that dramatically.
10	Arg-His	496
			Description of Arg-His Arginine (Arg) Histidine (His) BLOSUM62 PAM1 PAM250 0 (worst: -3) 8 (worst: 0) 5 (worst: 1) Arginine and Histidine are both basic amino acids so the only effect could come from the difference in size of the two.

Substitution Matrices

To compare the different mutations here the scores for the three matrices in one table:

• BLOSUM62
• PAM1
• PAM250

Nr.	Substitution	BLOSUM62	PAM1	PAM250
1	Asp(D) -> Asn(N)	1 (worst: -4)	36 (worst: 0)	7 (worst: 0)
2	Pro(P) -> Ala(A)	-1 (worst: -4)	22 (worst: 0)	11 (worst: 0)
3	Gln(Q) -> His(H)	0 (worst: -3)	20 (worst: 0)	7 (worst: 0)
4	Trp(W) -> Cys(C)	-2 (worst: -4)	0 (worst: 0)	1 (worst: 1)
5	Thr((T) -> Met(M)	-1 (worst: -3)	2 (worst: 0)	1 (worst: 0)
6	Phe(F) -> Val(V)	-1 (worst: -4)	1 (worst: 0)	10 (worst: 1)
7	Thr(T) -> Ile(I)	-2 (worst: -3)	7 (worst: 0)	4 (worst: 0)
8	Asn(N) -> Ser(S)	1 (worst: -4)	34 (worst: 0)	8 (worst: 0)
9	Cys(C) -> Gly(G)	-3 (worst: -4)	1 (worst: 0)	4 (worst: 0)
10	Arg(R) -> His(H)	0 (worst: -3)	8 (worst: 0)	5 (worst: 1)

Secondary Structure

As one can see in the picture above, none of the mutations is in the middle of a secondary structure element. Only the mutations 1,2,4 and 5 are close to or - depending on the prediction method - at the border of secondary structure elements.

SNAP

We ran snap using the following command:

snapfun -i ARSA.fasta -m mutants.txt -o snap.out

output:

nsSNP	Prediction	Reliability Index	Expected Accuracy
-----	------------	-------------------	-------------------
D29N	Non-neutral		7			96%
Q153H	 Neutral 		0			53%
T274M	Non-neutral		6			93%
T409I	Non-neutral		1			63%
C489G	Non-neutral		5			87%
W193C	Non-neutral		3			78%
F356V	 Neutral 		1			60%
N440S	Non-neutral		2			70%
R496H	 Neutral 		1			60%
P136A	Non-neutral		4			82%

In order to analyze all possible combinations of amino acid substitutions from the above mutated positions, we used the Generate Mutants tool on http://rostlab.org/services/snap/submit to create all possible exchanges from the following pattern: referenceAminoAcidPosition* . Then we again executed snap:

snapfun -i ARSA.fasta -m all_mutants.txt -o snap_all.out

Next, we wrote a perl script to parse and summarize the SNAP output in the following table, which shows which amino acid substitutions are Non-neutral or Neutral:

ref\mutation	A	R	N	D	C	Q	E	G	H	I	L	K	M	F	P	S	T	W	Y	V
D29	Non-neutral	Non-neutral	Non-neutral		Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral
Q153	Non-neutral	Non-neutral	Neutral	Non-neutral	Non-neutral		Non-neutral	Non-neutral	Neutral	Non-neutral	Non-neutral	Non-neutral	Neutral	Non-neutral	Neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral
T274	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral		Non-neutral	Non-neutral	Non-neutral
T409	Neutral	Non-neutral	Neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral		Non-neutral	Non-neutral	Non-neutral
C489	Non-neutral	Non-neutral	Non-neutral	Non-neutral		Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral
W193	Non-neutral	Non-neutral	Neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral		Non-neutral	Non-neutral
F356	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Neutral	Non-neutral	Non-neutral	Neutral	Neutral	Neutral	Non-neutral	Neutral		Non-neutral	Non-neutral	Non-neutral	Non-neutral	Neutral	Neutral
N440	Non-neutral	Non-neutral		Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral
R496	Non-neutral		Non-neutral	Non-neutral	Non-neutral	Neutral	Non-neutral	Non-neutral	Neutral	Non-neutral	Non-neutral	Neutral	Non-neutral	Neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Neutral	Non-neutral
P136	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral		Non-neutral	Non-neutral	Non-neutral	Non-neutral	Non-neutral

Multiple sequence alignments

First, we downloaded the HSSP file for ARSA to get all proteins, which are homologuous to it. Then we downloaded all mammalian protein sequences from Uniprot. This was achieved by searching for the term taxonomy:40674, which codes for all mammalian protein sequences. We saved all sequences in one multiple fasta file. Then we extracted all homologuous mammalian proteins to human ARSA by mapping the ids from the HSSP file to sequence ids in the multi fasta file. This yielded 75 homologuous mammalian sequences to human ARSA.
Next, we calculated a multiple sequence alignments of these proteins (including ARSA) with Muscle. The Jalview image of the alignment is shown below.

Multiple sequence alignments of all 75 homologuous sequences using muscle

The following table shows the conservation of the original amino acid in the reference sequence and their mutations at the respective positions.

pos	conservation - reference	conservation - mutant
29	0.86	0
153	0.14	0
274	0.87	0
409	0.35	0.16
489	0.80	0.05
193	0.13	0
356	0.15	0
440	0.15	0
496	0.14	0.01
136	0.93	0

PSI-BLAST

blastpgp -i ARSA.fasta -d /data/blast/nr/nr -e 10E-6 -j 5 -Q psiblast.mat -o psiblast_eval10E_6.it.5.new.txt

Last position-specific scoring matrix computed, weighted observed percentages rounded down, information per position, and relative weight of gapless real matches to pseudocounts
          A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V   A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V
  29 D   -5 -5 -2  8 -7 -3 -1 -4 -4 -6 -7 -4 -6 -7 -5 -3 -4 -7 -6 -6    0   0   0 100   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  2.49 1.56
 153 Q    3  2 -1  4 -4 -1 -1 -2  0 -2 -3 -3  4 -2 -3 -1 -2 -3 -2 -2   26  10   3  23   0   3   3   3   2   2   1   1  13   2   1   3   2   0   1   2  0.53 1.48
 274 T   -3 -4 -3 -4 -2 -4 -4 -5 -5 -4 -4 -4 -3 -5 -4  1  8 -6 -5 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   7  92   0   0   0  1.94 1.62
 409 T   -1  0  0 -1 -2 -1 -1  0 -1 -1 -1  0 -1 -1  3  0  1  6  0 -1    5   5   5   4   1   3   4   8   1   3   6   5   1   2  13   6   8  11   3   4  0.26 0.95
 489 C    2 -1  1 -4  8 -4 -4 -2 -1 -1 -2 -3 -1 -4 -4  0  0  5 -1 -3   15   4   8   0  36   0   0   2   1   3   3   1   1   0   0   6   5   9   2   0  0.99 1.22
 440 N   -5 -3  6  5 -6 -2 -1 -4 -3 -6 -6 -3 -6 -6  2 -2 -3 -6 -6 -5    0   1  46  36   0   1   2   0   0   0   0   1   0   0  10   1   1   0   0   0  1.48 1.67
 356 F   -3 -1 -5 -5 -3  0 -1 -6  1  3  0 -1  0  2 -6 -3 -2 -3  5  3    1   4   0   0   1   5   4   0   3  18   8   5   2   8   0   1   2   0  20  20  0.59 1.62
 193 W   -2  4  2  3 -5  0  0 -2  0 -3 -4  1 -3 -1 -2 -1 -2  1  1 -3    3  25  11  16   0   4   5   3   2   2   1   7   0   2   2   4   2   2   5   2  0.46 1.45
 136 P   -3 -5 -5 -5 -6 -4 -4 -5 -5 -6 -6 -4 -6 -7  9 -4 -4 -7 -6 -5    1   0   0   0   0   0   0   0   0   0   0   0   0   0  98   0   0   0   0   0  3.03 1.61
 496 R   -3  1  0 -3 -4  1  1 -1  1 -3  1  1 -2  2  4  0 -3 -1 -1 -3    1   7   4   1   0   5  10   4   3   1  16   9   0   9  20   8   1   1   1   1  0.34 0.96