Side chain Side chain Interactions in Interactions in α α -helices -helices Ph.D. Dissertation Defense 04/23/08 Prashant Girinath Dept. of Chemistry SUNY- University at Buffalo
Welcome message from author
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Side chainSide chain Interactions in Interactions in αα-helices-helices
Ph.D. Dissertation Defense04/23/08
Prashant GirinathDept. of Chemistry
SUNY- University at Buffalo
H: Alpha HelixS: SheetT: TurnR: Random Coil
-40
-20
0
20
40
60
80
103
·
θ (d
eg·c
m2 ·d
mol
-1 )
180 260220λ (nm)
H
R
S
T
The α-Helix
Pauling, L. et. al. Proc. Natl. Acad. Sci. U. S. A. 1951, 37, 205-207Barlow, D. J.; Thornton, J. M. J. Mol. Biol. 1988, 168, 601-619.
www.aveda.comwww.time.com
(i, i+4)
(i, i+3)
top viewside view
Strop, P.; Mayo, S. L. Biochemistry 2000, 39, 1251-1255.
Lysine (Lys, K)
OH3N
O
NH3
+
+
Arginine (Arg, R)
OH3N
O
HN
+
HN
NH3
+
Aspartic acid (Asp, D)
OH3N
O
+
O-
O
Glutamic acid (Glu, E)
OH3N
O
+
O O
- - - -
-
Charged amino acids
Does Side chain Length Matter?
n=1, Dap, S-2,3-diamonipropionic acid 2, Dab, S-2,4-diaminobutyric acid 3, Orn, L-ornithine 4, Lys, L-lysine
NH
O
H3N
n
+
Peptide Sequence
EXaa3: Ac-YGG A EAAX A EAAX A EAAX A-NH2
EXaa4: Ac-YGG A EAAAX EAAAX EAAAX A-NH2
EXaa5: Ac- YGG EAAAAX EAAAAX EAAAAX -NH2
Xaa (X): Dap, Dab, Orn, Lys
w Lys = 0.93w Orn = 0.63w Dab = 0.32w Dap = 0.14
Baldwin, R. L. et. al J. Mol. Biol. 1996, 257, 726-734Marqusee, S.; Baldwin, R. L. Proc. Natl. Acad. Sci. U. S. A. 1987, 84, 8898-8902
ELys5EOrn5EDab5EDap5
-30
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[!]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
EXaa5 CD at pH 7
EXaa5 CD pH 2 - pH 12
ELys5EOrn5EDab5EDap5
-30
-25
-20
-15
-10
-5
0
2 4 6 8 10 12
[!] 2
22 (
10
3·d
eg·c
m2·d
mol-1
)
pH
H: Alpha HelixS: SheetT: TurnR: Random Coil
-40-20
020406080
103
·θ
(deg
·cm2 ·d
mol
-1 )
180 260220λ (nm)
H
R
S
T
EXaa5 CD at pH 2
ELys5EOrn5EDab5EDap5
-40
-20
0
20
40
60
80
200 210 220 230 240 250
[!]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
ELys4EOrn4EDab4EDap4
-40
-20
0
20
40
60
80
190 200 210 220 230 240 250
[ !] (1
03·d
eg·c
m2·d
mol-1
)
" (nm)
EXaa4 CD at pH 7
EXaa4 CD pH 2 - pH 12
ELys4EOrn4EDab4EDap4
-30
-25
-20
-15
-10
-5
0
2 4 6 8 10 12
[!] 2
22 (
10
3·d
eg
·cm
2·d
mo
l-1)
pH
ELys4EOrn4EDab4EDap4
-40
-20
0
20
40
60
80
190 200 210 220 230 240 250
[ !] (1
03·d
eg·c
m2·d
mol-1
)
" (nm)
EXaa4 CD at pH 2
Scholtz, J. M et.al. Biochemistry 1993, 32, 9668-9676
Lys = robust interaction
Lys - 1 methylene ≠ robustness
ELys3EOrn3EDab3EDap3
-20
-10
0
10
20
30
40
190 200 210 220 230 240 250
[!]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
EXaa3 CD at pH 7
EXaa3 CD pH 2 - pH 12
ELys3EOrn3EDab3EDap3
-30
-25
-20
-15
-10
-5
0
2 4 6 8 10 12
[ !] 2
22 (
10
3·d
eg
·cm
2·d
mo
l-1)
pH
ELys3EOrn3EDab3EDap3
-20
-10
0
10
20
30
190 200 210 220 230 240 250
[!]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
EXaa3 CD at pH 2
Lys = interaction
Lys - 1 methylene ≠ interaction
Molecular Modeling
Dunbrack, R. L.; Karplus, M. J. Mol. Biol. 1993, 230, 543-574.
Stability : t > g+ > g-
ELys4:ELys4: (t, g+)(t, g+)((g-, g+g-, g+))
Others: ((t, g+t, g+))(i)
(i+4)
Interacting Species
Lowest Energy Conformations
Cheng, R. P. et. al. Biochemistry 2007, 46, 10528-10537
(i)
(i+3)
Stability : t > g+ > g-
ELys3:ELys3: ((t, tt, t))((g+, g+g+, g+))
Others: ((t, t, g-g-))
Interacting Species
Lowest Energy Conformations
Cheng, R. P. et. al. Biochemistry 2007, 46, 10528-10537
Cheng, R. P. et. al. Biochemistry 2007, 46, 10528-10537
What about Asp?What about Asp?
Lysine (Lys, K)
OH3N
O
NH3
+
+
Arginine (Arg, R)
OH3N
O
HN
+
HN
NH3
+
Aspartic acid (Asp, D)
OH3N
O
+
O-
O
Glutamic acid (Glu, E)
OH3N
O
+
O O
- - - -
-
Glu Glu - One - One methylene methylene = Asp= Asp
NH
O
O-
On
n=1, Asp (D), L-aspartic acid 2, Glu (E), L-glutamic acid 3, Aad (J), S-2-aminoadipic acid
n=1, Dap, S-2,3-diamonipropionic acid 2, Dab, S-2,4-diaminobutyric acid 3, Orn, L-ornithine 4, Lys, L-lysine
NH
O
H3N
n
+
Peptide Sequence
ZXaa3: Ac-YGG A ZAAX A ZAAX A ZAAX A-NH2
ZXaa4: Ac-YGG A ZAAAX ZAAAX ZAAAX A-NH2
ZXaa5: Ac- YGG ZAAAAX ZAAAAX ZAAAAX -NH2
Z: D(Asp), E(Glu), J(Aad)
Xaa (X): Dap, Dab, Orn, Lys
w Aad = 1.19w Glu = 0.45w Asp = 0.31
DXaa4 CD at pH 7
DLys4DOrn4DDab4DDap4
-40
-20
0
20
40
60
200 210 220 230 240 250
[!] (1
03·d
eg·c
m2·d
mol-1
)
" (nm)
DXaa4 CD pH 2 - pH 12
-35
-30
-25
-20
-15
-10
-5
0
2 4 6 8 10 12
DLys4DOrn4DDab4DDap4
[!] 2
22 (1
03.d
eg
.cm
2.d
mol-1
)
pH
DXaa4 CD at pH 2
DLys4DOrn4DDab4DDap4
-30
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[!]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
For environment sensitive (i, i+4)interactions
NatureNature uses Asp!uses Asp!
DXaa3 CD at pH 7
DLys3DOrn3DDab3DDap3
-30
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[!] (1
03·d
eg·c
m2·d
mol-1
)
" (nm)
DXaa3 CD pH 2 - pH 12
-35
-30
-25
-20
-15
-10
-5
0
2 4 6 8 10 12
DLys3DOrn3DDab3DDap3
[ !] 2
22 (1
03.d
eg.c
m2.d
mol-1
)
pH
DXaa3 CD at pH 2
DLys3DOrn3DDab3DDap3
-30
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[ !] (1
03·d
eg·c
m2·d
mol-1
)
" (nm)
Asp = (Glu - 1 methylene)
Asp ≠ robust interaction
For robust interactions
Nature needs Nature needs GluGlu!!
Glu + 1 methylene = Aad = ?
AadLys4AadOrn4AadDab4AadDap4
-40
-20
0
20
40
60
80
200 210 220 230 240 250
[!]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
AadXaa4 CD at pH 7
AadXaa4 CD pH 2 - pH 12
-35
-30
-25
-20
-15
-10
-5
0
2 4 6 8 10 12
AadLys4AadOrn4AadDab4AadDap4
[!] 2
22 (1
03.d
eg
.cm
2.d
mo
l-1)
pH
AadLys4AadOrn4AadDab4AadDap4
-40
-20
0
20
40
60
200 210 220 230 240 250
[!] (1
03·d
eg·c
m2·d
mol-1
)
" (nm)
AadXaa4 CD at pH 2
AadXaa3 CD at pH 7
AadLys3AadOrn3AadDab3AadDap3
-30
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[ !]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
AadXaa3 CD pH 2 - pH 12
-35
-30
-25
-20
-15
-10
-5
0
2 4 6 8 10 12
AadLys3AadOrn3AadDab3AadDap3
[!] 2
22 (1
03.d
eg.c
m2.d
mol-1
)
pH
AadXaa3 CD at pH 2
AadLys3AadOrn3AadDab3AadDap3
-30
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[!]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
Nature does not need Aad!
1) How robust is robust?
2) Nature + Innovation = ?
NH
O
O-
On
n=1, Asp (D), L-aspartic acid 2, Glu (E), L-glutamic acid 3, Aad (J), S-2-aminoadipic acid
n=1, Dap, S-2,3-diamonipropionic acid 2, Dab, S-2,4-diaminobutyric acid 3, Orn, L-ornithine 4, Lys, L-lysine
NH
O
H3N
n
+
Peptide Sequence
XaaZ3: Ac-YGG A XAAZ A XAAZ A XAAZ A-NH2
XaaZ4: Ac-YGG A XAAAZ XAAAZ XAAAZ A-NH2
XaaZ5: Ac- YGG XAAAAZ XAAAAZ XAAAAZ -NH2
Z: D(Asp), E(Glu), J(Aad)
Xaa (X): Dap, Dab, Orn, Lys
XaaZ4 CD at pH 7
LysAad4OrnAad4DabAad4DapAad4
-30
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[!]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
LysAsp4OrnAsp4DabAsp4DapAsp4
-30
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[!]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
LysGlu4OrnGlu4DabGlu4DapGlu4
-30
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[!] (1
03·d
eg·c
m2·d
mol-1
)
" (nm)
XaaZ4 CD at pH 2
LysGlu4OrnGlu4DabGlu4DapGlu4
-30
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[!]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
LysAsp4OrnAsp4DabAsp4DapAsp4
-30
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[ !]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
LysAad4OrnAad4DabAad4DapAad4
-30
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[!]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
XaaZ3 CD at pH 7
LysGlu3OrnGlu3DabGlu3DapGlu3
-30
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[!]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
LysAad3OrnAad3DabAad3DapAad3
-30
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[ !]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
LysAsp3OrnAsp3DabAsp3DapAsp3
-30
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[ !]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
XaaZ3 CD at pH 2
LysGlu3OrnGlu3DabGlu3DapGlu3
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[!]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
LysAad3OrnAad3DabAad3DapAad3
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[ !]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
LysAsp3OrnAsp3DabAsp3DapAsp3
-20
-10
0
10
20
30
40
200 210 220 230 240 250
[ !]
(10
3·d
eg
·cm
2·d
mo
l-1)
" (nm)
Nature + Human Innovation =
NH
O
Aib
10θ
(deg
·cm
·dm
ol
λ (nm)
2
The 310 helix
Therapeutically relevantfolding intermediate to α-helix
EKEK
EK KE
AA
A
A
E A E K A K E A E K A K
(i,i+3) E-K, K-E stabilizes310 helix
(i,i+4) E-E, K-K destabilizesαHelix
(i,i+2) E-E, K-K destabilizesrandom coil
Ln: Ac-YGG-(EAEKAK)n-NH2
310-Helix Design
-0.01
0
0.01
0.02
0.03
0.04
0.05
0.06
0.07
161016201630164016501660167016801690
A
U
! cm-1
L1
L2
VaLd-A
L4
L5
L6
L3
1655Random coil
1650α-Helix
16351635331010-Helix-Helix
Amide I band νcm-1
Structure
IR Spectra
-3 104
-2.5 104
-2 104
-1.5 104
-1 104
-5000
0
200 210 220 230 240 250
[!]
(deg
cm
2 d
mo
l-1)
" (nm)
L1
L2
L3
L4
L5
L6
CD Spectra
NMR
Ac Y1 G2 G3 E4 E6 E10 E12 K15 E16
d!N(i,i+1)
NH2
d!N(i,i+3)
d!"(i,i+3)
d#N(i,i+1)
A5 K7 A8 K9 A11 K13 A14 A17 E18 K19 K21A20
d#N(i,i+2)
d#N(i,i+3)
d!N(i,i+2)
d!"(i,i+1)
d!"(i,i+2)
NMR inconclusive due to sequence degeneracy
CD and IR indicate presence of 310-helix
Thanks
Hsien-Po Chiu
Raheel Ahmad
Marc Koyack
Yuta Suzuki
Casey Kilpatrick
Olivia Barrett
Donald Gullickson
Todd Doran
Dr. William DeGrado (U. Penn)
Dr. Donald Engel (U. Penn)
Teng Kai Yang (Nvidia)
Dr. Dinesh Sukumaran
Dr. Hanudatta Atreya
Dr. William Koehn
Dr. Khalid Ahsan
Dr. Matthew Disney
Thanks
Dr. Bing Gong
Dr. James Garvey
Dr. Michael Detty
Dr. Richard Cheng
Related Documents
