Sequence-Based Mutation Analysis Hemochromatosis

Hemochromatosis>>Task 6: Sequence-based mutation analysis

Riddle of the Task

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Short task description

Detailed description: Sequence-based mutation analysis

Protocol

A protocol with a description of the data acquisition and other scripts used for this task is available here.

SNPs

From MSUD: M35T V53M G93R Q127H A162S L183P T217I R224W E277K C282S

Amino acid features

<figtable id="TODO_ID">

TODO: description.

Mutation	Hydrophobicity (wt)	Hydrophobicity (mt)	Polarity (wt)	Polarity (mt)	pI (wt)	pI (mt)	v.d.W. volume (wt)	v.d.W. volume (mt)
M35T	1.9	-0.7	nonpolar	polar	5.74	5.60	124	93
V53M	4.2	1.9	nonpolar	nonpolar	6.00	5.74	105	124
G93R	-0.4	-4.5	nonpolar	polar	6.06	10.76	48	148
Q127H	-3.5	-3.2	polar	polar	5.65	7.60	114	118
A162S	1.8	-0.8	nonpolar	polar	6.01	5.68	67	73
L183P	3.8	-1.6	nonpolar	nonpolar	6.01	6.30	124	90
T217I	-0.7	4.5	polar	nonpolar	5.60	6.05	93	124
R224W	-4.5	-0.9	polar	nonpolar	10.76	5.89	148	163
E277K	-3.5	-3.9	polar	polar	3.15	9.60	109	135
C282S	2.5	-0.8	polar	polar	5.05	5.68	86	73

</figtable>

Evolutionary analysis

BLOSUM62/PAM1/PAM250

<figtable id="TODO_ID">

TODO: description.

Mutation	BLOSUM62	PAM1	PAM250
M35T	-1	6	500
V53M	1	4	200
G93R	-2	0	200
Q127H	0	20	700
A162S	1	28	900
L183P	-3	2	300
T217I	-1	7	400
R224W	-3	2	200
E277K	1	7	800
C282S	-1	11	700

</figtable>

PSSM

Tables for the mutations can be found here.

M35T

• Secondary structure assignment: sheet

SEQ (mt):     LRSHSLHYLFTGASEQDLGLS
DSSP (wt):     CCEEEEEEEEEEECCCCCCE
PsiPred (wt): CCCCCCCEEEEEEECCCCCCC
PsiPred (mt): CCCCCCCEEEEEEECCCCCCC

<figtable id="m35t_pymol">

Table TODO: ...

	Wildtype.	Mutant.

</figtable>

V53M

• Secondary structure assignment: sheet

SEQ (mt):     GLSLFEALGYMDDQLFVFYDH
DSSP (wt):    CCECCEEEEEECCEEEEEEEC
PsiPred (wt): CCCEEEEEEEECCEEEEEEEC
PsiPred (mt): CCCEEEEEEEECCEEEEEEEC

<figtable id="v53m_pymol">

Table TODO: ...

	Wildtype.	Mutant.

</figtable>

G93R

• Secondary structure assignment: helix

SEQ (mt):     MWLQLSQSLKRWDHMFTVDFW
DSSP (wt):    HHHHHHHHHHHHHHHHHHHHH
PsiPred (wt): HHHHHHHHHHHHHHHHHHHHH
PsiPred (mt): HHHHHHHHHHHHHHHHHHHHH

<figtable id="G93R_pymol">

Table TODO: ...

	Wildtype.	Mutant.

</figtable>

Q127H

• Secondary structure assignment: coil

SEQ (mt):     TLQVILGCEMHEDNSTEGYWK
DSSP (wt):    EEEEEEEEEECCCCCEEEEEE
PsiPred (wt): EEEEECCCCCCCCCCCCCEEE
PsiPred (mt): CEEEECCCEECCCCCCCCCCE

A162S

• Secondary structure assignment: helix

SEQ (mt):     TLDWRAAEPRSWPTKLEWERH
DSSP (wt):    HCEEEECCHHHHHHHHHHHCC
PsiPred (wt): CCCEECCCCCHHHHHHHHHHH
PsiPred (mt): CCCEECCCCCHHHHHHHHHHH

L183P

• Secondary structure assignment: helix (trusting DSSP)

SEQ (mt):     KIRARQNRAYPERDCPAQLQQ
DSSP (wt):    CHHHHHHHHHHHHHHHHHHHH
PsiPred (wt): HHHHHHHHCCCCCCHHHHHHH
PsiPred (mt): HHHHHHHHCCCCCCHHHHHHH

T217I

• Secondary structure assignment: coil

SEQ (mt):     PPLVKVTHHVISSVTTLRCRA
DSSP (wt):    CCEEEEEEEECCCCEEEEEEE
PsiPred (wt): CCCEEEECCCCCCCCEEEEEE
PsiPred (mt): CCCEEEECCCCCCCCEEEEEE

R224W

• Secondary structure assignment: sheet

SEQ (mt):     HHVTSSVTTLWCRALNYYPQN
DSSP (wt):    EEECCCCEEEEEEEEEEECCC
PsiPred (wt): CCCCCCCCEEEEEECCCCCCC
PsiPred (mt): CCCCCCCCEEEEEECCCCCCC

E277K

• Secondary structure assignment: helix (trusting DSSP)

SEQ (mt):     WITLAVPPGEKQRYTCQVEHP
DSSP (wt):    EEEEEECCCHHHHEEEEEECC
PsiPred (wt): EEEEEECCCCCCCEEEEEECC
PsiPred (mt): EEEEEECCCCCCCEEEEEECC

C282S

• Secondary structure assignment: sheet

SEQ (mt):     VPPGEEQRYTSQVEHPGLDQP
DSSP (wt):    ECCCHHHHEEEEEECCCCCCC
PsiPred (wt): ECCCCCCCEEEEEECCCCCCC
PsiPred (mt): ECCCCCCCCEEEEECCCCCCC

References

<references/>