university of jyväskylä, finland august 2012 university of
TRANSCRIPT
Sh
ort C
ou
rse:
So
lutio
n S
tructu
re Determ
inatio
n
In O
rgan
ic Ch
emistry an
d C
hem
ical Bio
log
y
Sam
uel H
. Gellm
anU
niversity o
f Wisco
nsin
– Mad
ison
, US
A
Au
gu
st 2012U
niversity o
f Jyväskylä, Fin
land
V. Fo
ldam
ers
FO
LDA
ME
RS
-- Oligom
ers that adopt compact,
predictable and well-defined conform
ations
A
new strategy for controlling
molecular shape and function
Proteins: W
orkhorse Molecules in B
iology
Proteins: W
orkhorse Molecules in B
iologyS
equence (1D)
Shape (3D
) F
unction…
Tyr – His – A
la – Leu – Phe – Leu – G
ly – Lys…Pepsin (P
DB
6AP
R)
NH
HNNH
O
O
OR
R
NH
+ H3 N
NH
O
O
OR
R
O -
H2 O
Martick, S
cott C
ell 126:309 (2006)
Proteins vs. R
NA
: Backbone V
ariation is Possible
OO
Base
OPO
OO - H
O
HNNH
O
O
R
van d
en B
erg et al. E
mb
o J 14:4123 (1995)
Biopolym
er Folding S
imulated
with S
imple Lattice m
odels
22
= h
ydro
ph
ob
ic
= p
olar
Dill et al. P
rotein
Scien
ce 4:561 (1995)
Foldam
er Exam
ples: Extended P
eptidic Backbones
-Pep
tides:
Gervay, F
leetO
AcO
OA
c
HN
OO
AcO
OA
c
HNHN
OO
-Pep
tides:
-Pep
tides: NH
NHNH
OO
OS
eebach
, Gellm
an, G
un
g,
Died
erichsen
, DeG
rado
, Fleet,
Fü
löp
, Win
kler, Berkessel,
Sch
epartz,...
NH
HN
OS
chreib
er ("vinylo
go
us p
eptid
es"), S
eebach
, Han
essian, G
ellman
, S
mith
...
RR
O
NH
OR
R
-Pep
tides:
Gervay, F
leetO
AcO
OA
c
HN
OO
AcO
OA
c
HNHN
OO
-Pep
tides:
-Pep
tides: NH
NHNH
OO
OS
eebach
, Gellm
an, G
un
g,
Died
erichsen
, DeG
rado
, Fleet,
Fü
löp
, Win
kler, Berkessel,
Sch
epartz,...
NH
HN
OS
chreib
er ("vinylo
go
us p
eptid
es"), S
eebach
, Han
essian, G
ellman
, S
mith
...
RR
O
NH
OR
R
Foldam
er Exam
ples: Extended P
eptidic Backbones
Foldam
er Exam
ples: Nucleotide A
nalogues
Nielsen
, Acc. C
hem
. Res.
32:624 (1999)
Pep
tide-N
ucleic A
cids (P
NA
s):
NNH
O
Base
Ph
osp
ho
roth
ioates:
Millig
an, M
atteucci &
Martin
J. Med
. Ch
em. 36:1923 (1993)
O
NNH
O
Base
O
OO
Base
OPO
S -
OO
Base
OPO
S -
O
OO
Base
OPO
O -
OO
Base
OPO
O -
O
DN
A:
Foldam
er Exam
ples
Helical P
epto
ids:
Dill, Z
uckerm
ann
, Co
hen
, Barro
n, K
irshen
bau
m,
Blackw
ell, Ko
dad
ek, Ap
pella...
NN
O
OR
R
HN O
O
O
N
OO
H
O
R
R
RR
Aro
matic O
ligo
amid
es
Ham
ilton
, Go
ng
, Hu
c,...
NN
HH
N
OO
HN
NH
OO
MeO
2 CC
O2 M
e
Arom
atic Foldam
er Design: H
uc et al.
Huc et al. J. A
m. C
hem. S
oc. 2007, 129, 11348.
Foldam
er Exam
ples: Beyond C
arboxamides
-Am
ino
xy Acid
Olig
om
ers:
Su
lfon
amid
e Olig
om
ers:
Urea O
ligo
mers:
Gen
nari, L
iskamp
Yan
g
SNH
SNH
SNH
OO
OR
R'
NH
ONH
ONH
OO
O
OO
RR
'
NHNH
HNHN
NHNH
OR
OR
'
OG
uich
ard
O
Foldam
er Exam
ples: Purely H
ydrocarbon Backbones
Mo
ore
m-P
hen
ylene-eth
ynylen
e Olig
om
ers:
J. S. M
oo
re et al., Ch
em. R
ev. 101:3893 (2001)A
Field
Gu
ide to
Fo
ldam
ers
NHNH
NHNH
NHNH
OO
OO
OO
NH
HNNH
HNNH
HN
O
O
O
O
O
O
-Peptides
Seebach et al.; G
ung et al.; Fleet et al.; D
eGrado et al.; D
iederichsen et al.; Ichikawa et al.;
Winkler, K
lein et al.; Martinek, F
ülöp et al.; Kessler et al.; S
chepartz et al.; Berkessel et al.;
Sharm
a, Kunw
ar et al., Chandrasekhar, Jagadeesh, Jagannadh et al.; H
ofmann et al.;
Wu et al.; V
an Gunsteren et al.; Jorgensen et al.; B
runsveld et al., Ortuño et al.;…
Extrapolation from
-P
eptides: -P
eptides
-Peptides w
ith Acyclic R
esidues (3)
H2 N
NHNH
NHNH
NHOH
OO
OO
OO
D. S
eebach et al. Helv. C
him. A
cta 1996, 79, 913 and 2043.D
. Seebach and J. L. M
atthews C
hem. C
omm
un. 1997, 2015.
14-helix in organic solvents
NH
O
NH
O
NH
O
NH
OR
R'
NH
R'''
HH
OR
''H
14-atom
H-b
on
ded
ring
s
-Peptides w
ith Acyclic R
esidues (3)
H2 N
NHNH
NHNH
NHOH
OO
OO
OO
D. S
eebach et al. Helv. C
him. A
cta 1996, 79, 913 and 2043.D
. Seebach and J. L. M
atthews C
hem. C
omm
un. 1997, 2015.
NH
O
NH
O
NH
O
NH
OR
R'
NH
R'''
HH
OR
''H
CH
(i) -- CH
(i+3) NO
E
14-helix in organic solvents
-Peptide S
econdary Structure: S
tabilize Helix w
ithC
yclic -A
mino A
cid Residues?
14-Helix
(Crystal stru
cture)
Appella, C
hristianson et al.JACS
1996, 118, 13071.
tBuO
NH
O
NH
NH
O
NHNH
O
NH
OCH2 Ph
O
O
O
O
14-atom
ring
H-b
on
d
NO
E P
atterns for the -P
eptide 14-Helix
NH
NH
OO
O
NHNH
OO
O
O
H
H
H
H
H
H
H
H
NO
ES
Y d
ata (CD
3 OH
, 5˚C, tm
ix = 400 ms)
(Joe B
archi an
d X
iaolin
Hu
ang
, NIH
)
sequ
ence
con
form
ation
Barch
i et al., J. Am
. Ch
em. S
oc. 122:2711 (2000)
Qualitative Indication of 14-H
elix Stability from
S
low H
/D E
xchange ( 1H N
MR
)
tBuO
NH
O
NHNH
O
NHNH
ONH
OBn
OO
OO
Appella, C
hristianson et al.JACS
1996, 118, 13071.
CD
3 OD
tBuO
OBn
O
NHNH
OO
No
n-fo
lded
con
trol (*):
-Peptide S
econdary Structure: C
ontrol over Helix
Shape via C
hoice of Cyclic C
onstraint
12-Helix
Appella,
Christianson et al.,
Nature 1997, 387, 381.
HN
O
HN
O
HN
O
HN
O
HN
O
BocNH
HN
O
HN
O
OCH2 Ph
O
12-atom
ring
H-b
on
d
HN
O
HN
O
HN
O
HN
O
HN
O
HN
O
OC
H2 P
h
OO
H
H
H
H
HH
HH
HH
HH
RO
ES
Y D
ata (pyrid
ine-d
5 and
CD
3 OH
)
(Joe B
archi an
d X
iaolin
Hu
ang
, NIH
)
Ap
pella et al., N
ature 387:381 (1997)
Barch
i et al., J. Am
. Ch
em. S
oc. 122:2711 (2000)
NO
E P
atterns for the -P
eptide 12-Helix
-Peptide vs.
-Peptide H
elices
-helix
310 -helix
12-helix14-helix
NHNH
NHNH
NHNH
NH
OO
OO
OO
O
NH2
CO2 H
NH2
CO2 H
NH
HNNH
HNNH
HN
O
O
O
O
O
O
RR
R
RR
Sheet S
econdary Structure in
-Peptides?
Krauthäuser et al. JA
CS
1997, 119, 11719.C
hung et al. JAC
S 1998, 120, 10555.
See also:
Seebach et al. A
ngew. C
hem. Int. E
d. 1999, 38, 1595.M
artinek et al. Angew
. Chem
. Int. Ed. 2002, 41, 1718.
NH2
CO2 H
H
CO2 H
NH2
H
CO2 H
HR H
R*
NH2
H2 N
CO2 H
R*R
Fo
r helices…
Fo
r sheets…
C-C
~ gau
che
C-C
~ anti
A
-Peptide R
everse Turn
N
N
OO
HN
O
N
N
OO
HN
O
L. C
hristian
son
, Y. Ch
un
g
IR D
ata in C
H2 C
l2 (N-H
Stretch
Reg
ion
)
A M
inimal
-Peptide H
airpin: O
ne Residue in E
ach Strand and a R
everse Turn
Ph
H
O
O
N
O
N
NH
OO
N
NH
OSPh
Chung, C
hristianson, Stanger, P
owell, G
ellman J. A
m. C
hem. S
oc. 1998, 120, 10555.
Minim
al -P
eptide Hairpin: N
OE
Data (C
D2 C
l2 )
Ph
OH
OH
N
ON
NSPh
H
O
N
N
O
HH
Alternative
-Peptide R
everse Turns
Seeb
ach et al., A
ng
ew. C
hem
. In
t. Ed
. En
gl. 1999, 38, 1595.
Ph
OH
OH
N
ON
NS
Ph
H
O
N
N
O
Stran
d resid
ues: K
rauth
äuser et al.,
J. Am
. Ch
em. S
oc. 1997, 119, 11719.
Reverse tu
rn: C
hu
ng
et al., J. A
m. C
hem
. So
c. 1998, 120, 10555.
OH
NCO
2 HN
H3 +
O
O
NH
HN
O
NH
O
NH
NH
3 +
14-Helix F
ormation by a
-Peptide H
examer in W
ater(T
he Ultim
ate Challenge in P
eptide Folding…
)
+ H3 N
+ H3 N
O
O
O
NH
3 +
NH
O
BnO
NH
NH
O
Ph
NH
O
NH
NH
OC
H3
O
vs.
(crystal)
(2D N
MR
)
Backbone overlay: rm
sd = 0.27 Å
Appella, B
archi, Durell, G
ellman J. A
m. C
hem. S
oc. 1999, 121, 2309.
tBuO
NH
O
NH
NH
O
NHNH
O
NH
OCH2 Ph
O
O
O
O
Synthesis R
equired…
OM
e
OO
OM
e
OH
OO
OM
e
NH
Cbz
OO
IN
HC
bz
O
OM
eH
O
NH
Cb
z
O
OM
eB
ocHN
NH
Cb
z
O
OM
eB
ocH
N
CH
2 Cl2
NaH
CO
3
NH
Cbz
O
OHN
HC
bz
O
OM
eB
ocHN
1. DB
U, P
hH
, R
eflux
2. NaO
Me, 0 °C
1. MsC
l, NE
t32. B
u4 + N
3 -
I2 , KI
3. PB
u3 , H
2 O
4. Bo
c2 O
Pig
Liver
Esterase
pH
8.0
1. EtO
CO
Cl
2. NaN
3
3. Ph
H, R
eflux
4. Bn
OH
, Reflu
x5. N
aOH
, MeO
H
1. H2 , P
d-C
2. Cb
z-Cl, N
Et3
NaO
Me,
MeO
H, R
eflux
Appella et al. J. O
rg. Chem
. 2000, 65, 4766
Cyclic vs. A
cyclic Residues:
Dram
atic Conform
ational Effects in W
ater(C
ircular Dichroism
)
+ H3 N
+ H3 N
O
O
O
NH
3 +
NH
O
BnO
NH
NH
O
Ph
NH
O
NH
NH
OC
H3
O
O
O
O
NH
3 +
NH
O
BnO
NH
NH
3 +
NH
ONH
O
NH
3 +
NH
NH
OC
H3
O
+ H3 N
+ H3 N
+ H3 N
O
O
O
NH
O
BnO
NH
NH
ONH
O
NH
NH
OC
H3
O
O
O
O
NH
3 +
NH
O
BnO
NH
3 +
NH
Ph
NH
3 +
NH
ONH
O
NH
NH
OC
H3
O
Appella, B
archi, Durell, G
ellman J. A
m. C
hem. S
oc. 1999, 121, 2309.
A P
reorganized 14-Helix S
hows H
igh Therm
al Stability
OO
O+ H
3 N
+ H3 N
+ H
3 N
NH
O
BnO
NHNH
O
NH
O
NHNH
OC
H3
O
O+ H
3 N
NH
O
BnO
NH
O
OC
H3
25oC
45oC
65oC
80oC
25oC
Ion Pairing A
llows 14-H
elix Form
ation in Water
Without C
yclic Residues
i-Pr
+
+ H3 N
NHNH
OO
O
CO
2 -
-
i-Pr
2
Seebach et al. J. C
hem. S
oc., Chem
. Com
mun., 2001, 649.
+
i-Pr
NHNH
NH
OO
O
-
-+
NHO
-
O
-
+
+ H3 N
-
CO
2 -
+ H3 N
+-C
heng & D
eGrado J. A
m. C
hem. S
oc., 2001, 123, 5162.+
NHNH
OO
O
NHNH
NH*
OO
O
NH
O
CO
2 -
NHC
O2 -
NH
3 +N
H3 +
CO
2 -
+ H3 N
NH
OC
O2 -
HO
CH
3
CH
3
CH
3
CH
3
CH
3
Circular D
ichroism: C
yclic Residues D
iminish
Environm
ental Effects on F
olding
-25
-20
-15
-10 -5 0 5
10
15
19
02
00
21
02
20
23
02
40
25
02
60
Wa
ve
len
gth
(nm
)
[ ] (103 deg cm2 decimol-1)
MeO
H
pH
7
pH
2
pH
12
H2 N
NHNH
NHNH
OO
OO
O
NHNH
NH
2
OO
- O2 C
+ H3 N
+ H3 N
- O2 C
T. R. R
aguse / Seebach sequence
Circular D
ichroism: C
yclic Residues D
iminish
Environm
ental Effects on F
olding
-25
-20
-15
-10 -5 0 5
10
15
19
02
00
21
02
20
23
02
40
25
02
60
Wa
ve
len
gth
(nm
)
[ ] (103 deg cm2 decimol-1)
MeO
H
pH
7
pH
2
pH
12
-25
-20
-15
-10 -5 0 5
10
15
19
02
00
21
02
20
23
02
40
25
02
60
Wa
ve
len
gth
(nm
)
[ ] (103 deg cm2 decimol-1)
MeO
H
pH
7
pH
2
pH
12
H2 N
NHNH
NHNH
OO
OO
O
NHNH
NH
2
OO
- O2 C
+ H3 N
+ H3 N
- O2 C
H2 N
O
NHNH
OO
NH
O
NHNH
OO
NH
O
NH
2
- O2 C
- O2 C
+ H3 N
+ H3 N
T. R. R
aguse
NO
Es D
emonstrate 14-H
elix Form
ation in Solution
H2 N
O
NHNH
OO
NH
O
NHNH
OO
NH
O
NH
2
- O2 C
- O2 C
+ H3 N
+ H3 N
H
H
H
H
H
H
HH
HH
H2 N
O
NHNH
OO
NH
O
NHNH
OO
NH
O
NH
2
- O2 C
- O2 C
+ H3 N
+ H3 N
H
H
H
H
H
H
HH
HH
Meth
ano
l
Water, p
H 7R
aguse, Lai, Gellm
an J. Am
. Chem
. Soc. 2003, 125, 5592.
i,i+3 NO
Es
12-Helix F
ormation in W
ater by Hexam
ers (RO
ES
Y)
OS
O
OS
O
OS
O
OCH3
NN
HN
ON
HN
ON
N
HN
O
HN
O
N
HN
O
NH2
O
HN
OH2
H2
H2
++
+
Lee, Syud, W
ang, Gellm
an J. Am
. Chem
. Soc. 2001, 123, 7721.
H
H
H
H
HH
HH
HH
HH
N
HN
ON
HN
ON
HN
O
HN
O
HN
O
NH2
O
HN
OH2
H2
H2
++
+
Wang, E
spinosa, Gellm
an J. Am
. Chem
. Soc. 2000, 122, 4821.
i,i+2 NO
Es
Will the 12-H
elix Tolerate A
cyclic Residues?
HN
O
HN
O
HNHN
O
HN
OO
NH2
ON
HN
O
R
NH3
HN
O
NH3
++
+ H2
Will the 12-H
elix Tolerate A
cyclic Residues?
Yes.
LePlae, F
isk, Porter, W
eisblum, G
ellman J. A
m. C
hem. S
oc. 2002, 124, 6820
HN
O
HN
O
HNHN
O
HN
OO
NH2
O
H
H
H
H
NH
HH
H
HHN
OH
HR
NH3
HN
O
H
NH3
HH
++
+H2
Num
erous NO
Es betw
een sequentially non-adjacent residues (C
D3 O
H), all characteristic of the 12-helix
New
Foldam
ers:H
omogeneous vs. H
eterogeneous Backbones
Hom
ogeneous Backbones: A
ll residues in the same class
(e.g., conventional peptides, DN
A, R
NA
, -peptides,
-peptides)
Heterogeneous B
ackbones: Residues of different classes
(e.g., …?)
/-P
eptide Foldam
ers?
NNH
NH
HN
O
O
HN
O
O
NNH
NH
NH2
O
O
HN
O
O
HN
OH
H
H2 N
OH
CO2 H
2D N
MR
An
alysis (CD
3 OH
)
Nu
mero
us i --> i+2 an
d i --> i+3 N
OE
s
Hayen
, Sch
mitt, N
gassa, T
ho
masso
n, G
ellman
A
ng
ew. C
hem
. Int. E
d. 43:505 (2004)
NO
E D
ata Suggest T
wo C
onformations
Populated in S
olution
11-Helix
[C=O
(i) -- H-N
(i+3)]
14/15-Helix
[C=O
(i) -- H-N
(i+4)]
NH
NH
HN
O
O
HN
O
O
NH
NH
NH2
O
O
HN
O
O
HN
O
1111
NH
NH
HN
O
O
HN
O
O
NH
NH
NH2
O
O
HN
O
O
HN
O
15
14
/-P
eptide Helix
Modeling
11-Helix
14/15-Helix
(Molecular M
echanics: S
YB
YL / M
MF
F94s;
continuum M
eOH
model;
12 residues)M. S
chmitt
11-Helix
14/15-Helix
M. S
chmitt
??
Neither
/-P
eptide Helix A
ccounts for All N
OE
s
Am
phiphilic /
-Peptide 15-m
ers: Insight into H
elix Preference from
Physical P
roperties?
NH
NH
HNO
O
HNO
O
NN
NH
NH
HNO
O
HNO
O
HN
O
H2
NH
NH
HNO
O
HNO
O
NH
NH2
OHN
O
O
NH2
H2
+
+
+H3 N
+
H3 N
+
NH
NH
HNO
O
HNO
O
NNH
NH
HNO
O
HNO
O
NHN
O
NH
NH
HNO
O
HNO
O
NNH
NH2
OHN
O
OH2
H2
H2
+
++
H3 N
H3 N
++
NNH
NH
HNO
O
HNO
O
NH
NH
HNO
O
HNO
O
NHN
O
NH
NH
HNO
O
HNO
O
NNH
NH2
OHN
O
O
H2
H2
H2
+
++
H3 N
H3 N
++
Am
phiphilic as 11-helix
Am
phiphilic as 14/15-helix
Not am
phiphilic as either helix2 x Lys (+
)5 x Leu3 x A
PC
(+)
5 x AC
PC
M. S
chmitt
Am
phiphilic /
-Peptide 15-m
er isomers:
Axial P
rojections
11-helix14/15-helix
Am
phiphilic 11-Helix
Design
Am
phiphilic 14/15-Helix
Design
Neither H
elix Am
phiphilicD
esign
Purple =
cationicB
lack = hydrophobic
Am
phiphilic /
-Peptide 15-m
er isomers:
Reverse-P
hase HP
LC R
etention
Min
ute
s
16
18
20
22
24
26
28
30
32
34
36
38
40
42
44
mVolts
-100
-50 0
50
100
150
200
250
300
350
SP
D-1
0A
vp C
h1-2
20nm
cat1
1h-p
ure
3: 2
20 n
m, 8
nm
cat1
415h
SP
D-1
0A
vp C
h1-2
20nm
catn
eith
er-p
ure
mV
Retention Tim
e (min)
11-Helix
Design
No H
elixD
esign14/15-H
elixD
esign
Conditions: C
8 column; linear gradient 20-->
60% B
over 40 min;
A =
water, B
= C
H3 C
N (both 0.1%
CF
3 CO
2 H)
Sch
mitt, W
eisblu
m, G
ellman
J. A
m. C
hem
. So
c. 126:6848 (2004)
Stro
ng
HP
LC
reten
tion
su
gg
ests that
14/15-helix is
Preferred
?
/-P
eptide 15-mers: N
OE
Analysis
HN
O
NH
NH
HNO
O
HN
O
O
R
R
NH
HN
O
OR
NO
E p
attern exp
ected fo
r 11-helix b
ut n
ot 14/15-h
elix [no
ne o
bserved
]
NO
E p
attern exp
ected fo
r 14/15-helix b
ut n
ot 11-h
elix [4 or 5 o
f 7 ob
served]
Sch
mitt, W
eisblu
m, G
ellman
J. A
m. C
hem
. So
c. 129:417 (2007)
HN
O
HN
O
OH3 C
CH3 NH
NH
HN
O
O
H3 C
CH3
Ch
oi, G
uzei, S
pen
ce, Gellm
an
J. Am
. Ch
em. S
oc. 130 :6544 (2008)
14/15-Helix
11-Helix
/-P
eptide Crystal S
tructures Reveal Tw
o Helical C
onformations
Cyclically C
onstrained -R
esidues Strongly P
romote
/
-Peptide H
elix Form
ation
NNH
NH
HN
O
O
HN
O
O
NNH
NH
NH2
O
O
HN
O
O
HN
OH
H
H2 N
OH
CO2 H
NNH
NH
HN
O
O
HN
O
O
NNH
NH
NH2
O
O
HN
O
O
HN
OH
H
H2 N
OH
CO2 H
NH
NH
HN
O
O
HN
O
O
NH
NH
NH2
O
O
HN
O
O
HN
O
H2 N
OH
CO2 H
H2 N
H2 N
Medium
-rangeN
OE
s in CD
3 OH
Many
Many
None
Sch
mitt, C
ho
i, Gu
zei, Gellm
an J. A
m. C
hem
. So
c. 127:13130 (2005)
Cyclically C
onstrained -R
esidues Strongly P
romote
/
-Peptide H
elix Form
ation
Can w
e quantify this effect?
Cyclically C
onstrained -R
esidues Strongly P
romote
/
-Peptide H
elix Form
ation
Can w
e quantify this effect?
1. Po
pu
lation
analysis is ch
alleng
ing
for
-pep
tide seco
nd
ary structu
res.
2.N
o exam
ples o
f reliable p
op
ulatio
n an
alysis for fo
ldam
er seco
nd
ary structu
res to d
ate.
Cyclically C
onstrained -R
esidues Strongly P
romote
/
-Peptide H
elix Form
ation
Can w
e quantify this effect?
1. Po
pu
lation
analysis is ch
alleng
ing
for
-pep
tide seco
nd
ary structu
res.
2.N
o exam
ples o
f reliable p
op
ulatio
n an
alysis for fo
ldam
er seco
nd
ary structu
res to d
ate.
3.U
se thio
ester exchan
ge to
add
ress the ro
le of cyclic resid
ue co
nstrain
ts?
+
KT
EK
Fo
ld+
Thioester E
xchange Design:
Packing of an
-Helix against an
/-P
eptide Helix
Price, H
adley, S
teinkru
ger, G
ellman
An
gew
. Ch
em. In
t. Ed
. 49:368 (2010)
Thioester E
xchange Design:
Packing of an
-Helix against an
/-P
eptide Helix
-Helix
/-P
eptid
e14/15-H
elix
Exam
ine site o
n
solven
t-expo
sed
side.
Hyd
rop
ho
bic C
ore
So
lvent-E
xpo
sed p
ositio
n
Thioester E
xchange Design:
Packing of an
-Helix against an
/-P
eptide Helix
Quantitative E
valuation of Residue P
reorganization to
/-P
eptide Helix S
tability (1 Site)
vs.
Quantitative E
valuation of Residue P
reorganization to
/-P
eptide Helix S
tability (5 Sites)
Tow
ard Helix B
undle Foldam
er Tertiary S
tructure?
+++
+++
+++
Pro
tein p
receden
t: DeG
rado
et al., Scien
ce 270:935 (1995)
Self-asso
ciation
to
discrete ag
greg
ate(h
ydro
ph
ob
ic drive)
(Dim
er - hexam
er)
CO
2 -
+ H3 N
Am
ph
iph
ilic helix
hyd
rop
ho
bic
hyd
rop
hilic
En
gin
eer loo
ps,
diversify seq
uen
ce, etc.
Am
phiphilic 14-Helix: A
nalytical Ultracentrifugation
(Sedim
entation Equilibrium
; 60 krpm, 10 m
M T
ris, pH 8.0)
0.3 mM
1.7 mM
NH
2
O
NHNH
O
NH+ H
3 N
OO
HO
+ H3 N
3cyclo
hexyl
cycloh
exyl
+
Detection of
-Peptide S
elf-Association by N
MR
(100 mM
acetate, pH 3.8)
0.2 mM
0.4 mM
0.8 mM
1.4 mM
1.8 mM
4.0 mM
8.0 mM
NH
2
O
NHNH
O
NH+ H
3 N
OO
HO
+ H3 N
3cyclo
hexyl
cycloh
exyl
+
Non-A
ggregating Control C
ompound
+
Ch
x
3
+
NH
2
O
NHNH
O
NH+ H
3 N
OO
+H
O
Ch
x
+ H3 N
3C
hx
Ch
xC
hx
Ch
x
NO
N-A
MP
HIP
HIL
ICO
NHNH
O
NH+ H
3 N
OO
HO
+ H3 N
AM
PH
IPH
ILIC
Ch
x
NHN
H2
O
NH
O
Ch
x+
+
Ch
x
Ch
xC
hx
Ch
x+
VS
.
Monom
er-Hexam
er Equilibrium
?
Sed
imen
tation
equ
ilibriu
m resu
lts:0.3 m
M0.6 m
M
0.8 mM
1.3 mM
1.8 mM
Raguse, Lai, LeP
lae, Gellm
an Org. Lett. 2001, 3, 3963.
Mo
no
mer
(10 mM
Tris, p
H 8, 60,000 rp
m) M
on
om
er + Hexam
er
Unim
olecular -P
eptide Folding?
Cheng, D
eGrado J. A
m. C
hem. S
oc. 2002, 124, 11564
Crystal S
tructure of a -P
eptide Helix B
undle
Schepartz et al. J. A
m. C
hem. S
oc. 2007, 129, 1532.
-Peptide H
elices: Pioneering S
tudies of Helix
Form
ation in Organic S
olvents
Seeb
ach et al.
Helv. C
him
. Acta 1998, 81, 983.
Han
essian et al.
J. Am
. Ch
em. S
oc. 1998, 120, 8569.
HNH
O
HNO
Bn
O
4
HNH
O
Seeb
ach et al.
Ch
em. C
om
mu
n. 2001, 207.
HNO
H
O
3
NHO
HN
O
NHO
HN
O
14-Helix
Improved H
elix Stability w
ith Constrained
-Am
ino Acids?
HN
O
-Resid
ue w
ithcyclic co
nstrain
t
NO
2
+
H
O
NH
PhP
h
OT
MS
(20 mo
l %)N
O2
(10 mo
l %)
HO
2 C
NaB
H4
dr 16:1:1
majo
r diastereo
mer:
87% yield
, 99% ee
Jon
esO
x.
NO
2
CO
2 HH
NO
2
CH
2 OH
H
HN
O
-Resid
ue w
ithcyclic co
nstrain
t
Synthesis
Precedents:
List, Pojarliev, M
artin Org. Lett. 3:2423 (2001)
Betancort, B
arbas Org. Lett. 3 :3737 (2001)
Santanu et al. C
hem. R
ev. 107 :5471 (2007)(m
ostly nitrostyrenes)
Guo, C
hi, Alm
eida, Guzei, P
arker, Gellm
an J. A
m. C
hem. S
oc. 131:16018 (2009).
Improved H
elix Stability w
ith Constrained
-Am
ino Acids?
HN
O
Seeb
ach et al.
Helv. C
him
. Acta 1998, 81, 983.
Han
essian et al.
J. Am
. Ch
em. S
oc. 1998, 120, 8569.
HNH
O
HNO
Bn
O
4
Hom
o-oligomers of the C
onstrained -A
mino A
cid R
etain 14-Helix P
ropensity
Guo, Z
hang, Reidenbach,
Giuliano, G
uzei, Spencer, G
ellman
Angew
. Chem
. Int. Ed. 50 :5843 (2011)
New
Foldam
ers: /
-Peptide H
elix
i,i+3 H-b
on
ds
HNNH
HN
O
O
NHO
O
O
NH
O
OBn
HN
OO
HNNH
HN
O
O
O
NH
OH
H
Stru
cture-d
efin
ing
NO
Es (C
DC
l3 ):
Guo, C
hi, Alm
eida, Guzei, P
arker, Gellm
an J. A
m. C
hem. S
oc. 131 :16018 (2009).12-H
elix(C
rystal Stru
cture)
Stru
cture-d
efin
ing
NO
Es in
CD
Cl3
(no
t sho
wn
)
Guo, A
lmeida, Z
hang, Reidenbach,
Choi, G
uzei, Gellm
an J. A
m. C
hem. S
oc. 132 :7868 (2010)
i,i+3 H-b
on
ds
New
Foldam
ers: /
-Peptide H
elix
13-Helix
(Crystal S
tructu
re)
-Helix M
imicry from
//
-Peptides?
NH
HNNH
O
O
OR
R
HNNH
HN
O
O
O
RR
R
NH
OHN
O
R
R
Seven
resid
ues =
Two
turn
s of
-helix
-helix w
heel”
-Helix M
imicry from
//
-Peptides?
NH
HNNH
O
O
OR
R
HNNH
HN
O
O
O
RR
R
NH
OHN
O
R
R
NH
HN
O
O
RNH
HNNH
NH
HN
O
O
OO
O
R
R
R
Sam
e nu
mb
er of
backb
on
e atom
s as seven
resid
ues
-Helix M
imicry from
//
-Peptides?
NH
HNNH
O
O
OR
R
HNNH
HN
O
O
O
RR
R
NH
OHN
O
R
R
NH
HN
O
O
RNH
HNNH
NH
HN
O
O
OO
O
R
R
R
//
-Pep
tide
Helix w
heel?
Sam
e nu
mb
er of
backb
on
e atom
s as seven
resid
ues
-Helix M
imicry from
//
-Peptides?
Saw
ada, G
ellman
J. Am
. Ch
em. S
oc. 133:7336 (2011)
NH
HN
O
O
RNH
HNNH
NH
HN
O
O
OO
O
R
R
R
//
-Pep
tide h
elical con
form
ation
in H
2 O(N
OE
-restrained
dyn
amics; 12-m
er)
CD
Data S
uggest High
//
-Peptide H
elix Stability
(H2 O
vs. 1:1 H2 O
:CH
3 OH
)
//
Structure
Function
Ho
st-Defen
se Pep
tide M
imicry
NH2
OO
HN
N
HN
O
N
HN
O
HN
O
HN
O
HN
O
HN
OH2
H2
++
n
++++++++
++
++
++++
Nan
ofi
ber A
ssemb
ly
CatalysisA
ldo
lase-like activity
NH
2
O
NHNH
O
NHNH
OO
HO
+ H3 N
3
O
Lyotro
pic
liqu
id crystallin
ep
hases
(Cryo
-TE
M; H
artgerin
k, Rice)
Po
rter et al. Natu
re 404:565 (2000)M
ow
ery et al. JAC
S 129:15474 (2007)
Po
meran
tz, Ab
bo
tt, Gellm
an JA
CS
128 :8730 (2006)
OH
O
O
O
O
O
O
H
O
NHNH
O
HO
O
NH
O
NHNH2
O
NH3
O
3
Fo
ldin
g an
d
assemb
ly req
uired
An
tibacterial ran
do
m co
po
lymers
Mü
ller, Win
dso
r, Po
meran
tz, Gellm
an, H
ilvert A
ng
ew C
hem
Int E
d 48:922 (2009)
++
++
ST
RU
CT
UR
E
FU
NC
TIO
N
General P
latform for M
imicry of P
rotein-Recognition S
urfaces?
(Goal =
inhibitors of deleterious protein-protein interactions)
small
mo
lecule
fold
amer
vs.
Pro
tein A
Pro
tein B
Pro
tein A
Pro
tein B
Pro
tein B
Pro
tein B
Pro
tein A
Pro
tein A
An
/-P
eptide that Mim
ics an -helix from
HIV
Protein
gp41 and Inhibits Viral E
ntry
Ho
rne, Jo
hn
son
, Ketas, K
lasse, Lu
, Mo
ore, G
ellman
PNAS
106:14751 (2009)
HN
CH3
O
HN
NH
H2 N
NH2
+
O
ZX
N
HNC
H2
O+
HNC O
Conclusions:
Conform
ational mim
icry of proteins with foldam
ers offers m
any opportunities for solution structure determination.
Establishing
folding rules for new
backbones enables function-based engineering.
New
Shapes?
Polyproline H
elices: No H
ydrogen Bonds!
Polyproline I
3.3 residues/turn1.9 Å
rise/residue
Polyproline II
3.0 residues/turn3.1 Å
rise/residue
N
O
HN
O
N
O
HN
Ocis am
idetrans
amide
(Helix-form
ing peptoids, Arm
and et al.P
roc. Natl. A
cad. Sci. 1998, 95, 4309)
(collagen)
A
-Peptide A
nalogue of a Polyproline H
elix?
NH
CO2 H
pyrrolidine-3-carboxylic acid
The rotam
er problem:
O
N
CO2 CH3
O
N
CO2 CH3
O
N
CO2 CH3
O
O
N
CO2 CH3
O
O
N
CO2 CH3
OB
. Huck
H. C
arlson et al., Univ. M
ichigan
NO
E A
nalysis of Monom
er Consistent w
ith Expected
Rotam
er Preference
N
O
O
NO(C
DC
l3 , rm tem
p)
B. H
uck
Counting A
mide R
otamer S
tates by 13C N
MR
(C
arbonyl Region)
B. H
uck
O
N
O
OCH3
4
O
O
N
O
OCH3
4
Synthesis: 5,5
-Disubstituted M
onomers
N
1) NaB
H4
2) CH
3 I, Ag
2 OM
eO2 C
63%
OT
BS
1) TB
AF
2) TsC
l
3) NaC
NN
1) con
c. HC
l2) B
oc
2 O
3) TM
SC
HN
2
OT
BS
HO
90%
Bo
c
N
73%
CN
CH
3 O
Bo
cN
CH
3 O
Bo
c
O
OC
H3
Bo
c
Startin
g m
aterial: Oh
take et al., Bu
ll. Ch
em. S
oc. Jap
an 1999, 72, 2737.
Limited T
orsional Options
N
CH3 O
O
OO
N
OCH3O
HO
NR
O
R'
N R''
O
R'''
Sim
ulations suggest two
minim
a, -80o and -160
o
ca. -80o
N. F
isk, B. H
uck
NO
ES
Y A
nalysis of a Heterotetram
er (CD
Cl3 ):
NO
Es B
etween N
on-Adjacent R
esidues
N
O
ON
OCH3 O
OO
O
N
ON
O
F
O
1
23
4
Residue 1
Residue 3
Residue 2
Residue 4
N. F
isk, B. H
uck
Tetram
er Structures: S
imulation vs. N
MR
: -80o, -80
o, -80o
: -160o, -160
o, -160o
: -160o, -160
o, -80o
(Major, by N
MR
)