Peptoid helicity modulation: Precise control of peptoid secondary structures via position-specific placement of chiral monomers

Article abstract of DOI:10.1039/c3cc49373c

The degree of peptoid helicity can be effectively modulated by position-specific incorporation of α-chiral aromatic monomers. In this study, we report the structural role of each monomer position collected from 30 comprehensive model peptoid oligomers demonstrating a meticulous manner to fine-tune peptoid secondary structures. This journal is the Partner Organisations 2014.

Full text of DOI:10.1039/c3cc49373c

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Peptoid helicity modulation: precise control of
peptoid secondary structures via position-specific
placement of chiral monomers†
Cite this: Chem. Commun., 2014,
50, 4465
Received 10th December 2013,
Accepted 7th March 2014
Hye-Min Shin,a Chang-Muk Kang,b Myung-Han Yoon*a and Jiwon Seo*bc
DOI: 10.1039/c3cc49373c
www.rsc.org/chemcomm
The degree of peptoid helicity can be effectively modulated by binding peptoids,11 antifreeze protein mimics,12 and artificial light-
position-specific incorporation of a-chiral aromatic monomers. In this harvesting complexes.13
study, we report the structural role of each monomer position collected
To further emulate the elegant 3-D structures of natural proteins
from 30 comprehensive model peptoid oligomers demonstrating a and expand the functional applications of peptoids, it is desirable to
meticulous manner to fine-tune peptoid secondary structures.
access more precisely controlled peptoid conformations (or partially
unfolded peptoids) and thereby to understand further the underlying
Inspired by exquisite natural systems, scientists have sought to principles of sequence–structure relationship in peptoid foldamers.
generate protein-like structures and functions from non-natural While early peptoid research mainly focused on the construction of
heteropolymers.1 A prerequisite for successful mimicry would be stable helical peptoid structures, a wide range of other conformational
to understand how a heteropolymer sequence determines its possibilities between fully helical and non-helical still remains
folded structure and consequently function.
unexplored. The conformational space is exploited by natural
Peptoids are a class of bioinspired heteropolymers based on proteins extensively, and the partially unfolded structure plays
oligo-N-substituted glycine backbones, which are often used as pivotal roles in signaling and regulatory pathways.18 In this
a versatile platform to mimic the functions of natural peptides and study, we employed an approach inspired by the ‘sergeant-and-
proteins.2 A central theme in the peptoid research community has soldier effect’ in the seminal polyisocyanate research14 and
been discovering the factors that influence the three-dimensional investigated the effect of position-specific placement of a-chiral
(3-D) peptoid conformation.3–7 Unlike natural peptides, each side monomer(s) on the 3-D peptoid conformation.
chain of peptoid monomers is appended to the amide nitrogen
Our hypothesis is that there exist multiple specific positions in a
rather than to the a-carbon, eliminating the possibility of backbone peptoid sequence where structure-inducing a-chiral aromatic
hydrogen-bonding driven secondary structure formation. However, monomers (i.e., sergeants) can effectively regulate the conforma-
peptoids fully modified with bulky a-chiral side chains have been tions of a multitude of achiral monomers (i.e., soldiers) in the same
demonstrated to adopt stable and well-defined ‘fully helical’ folds chain; therefore, the extent of peptoid helicity can be effectively
in solution by mainly employing local steric and electronic inter- manipulated by regio-specific incorporation of a few structure-
actions.3 Thereafter, the dependence of such a peptoid helical inducing monomers. Such a fine adjustability of peptoid helicity
conformation on oligomer sequence,4 chain length,5 monomer serves as a rational design strategy to generate moderately helical
identity,6 and solvent composition7 has been elucidated. Based peptoids that fill the gap between fully helical and non-helical
on this information, a variety of functional peptoid foldamers have structures (Fig. 1(A)) and provide an insight into fine-tuning
been successfully developed including antimicrobial peptoids,8 peptoid functions.
pulmonary surfactant protein mimics,9 asymmetric catalysts,10 zinc
Initially, we posed three major questions as follows: (1) Do
there exist ‘lynchpin’ monomer positions that predominantly
regulate the overall peptoid structure? Conversely, do there exist
trivial positions that minimally affect the given peptoid structure?;
(2) If two a-chiral aromatic monomers are incorporated, is the
level of each contribution simply additive or synergistic?; and
(3) If two a-chiral aromatic monomers with opposite senses
(i.e., monomer with (R) or (S) chirality) are incorporated into the
same sequence, which one will govern the overall handedness?
To address the aforementioned questions, we chose a family of
a School of Materials Science and Engineering, Gwangju Institute of Science and
Technology, Gwangju, 500-712, Republic of Korea. E-mail: mhyoon@gist.ac.kr
b Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju,
500-712, Republic of Korea
c Division of Liberal Art and Sciences, Gwangju Institute of Science and Technology,
Gwangju, 500-712, Republic of Korea. E-mail: jseo@gist.ac.kr
† Electronic supplementary information (ESI) available: Detailed procedures for
the synthesis, characterization, and purification of all new compounds. See DOI:
10.1039/c3cc49373c
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Table 1 Sequences of the peptoids synthesized herein
Fig. 1 (A) CD plots of representative peptoid heptamers showing helicity
modulation. The term ‘fully helical’ was used to indicate the highest helicity
reached by a heptameric peptoid composed of Nspe and Npm monomers,
as a comparative term in conjunction with non-helical and moderately
helical. (B) Schematics of effective control over peptoid folding via
position-specific placement of an a-chiral monomer.
peptoid heptamers composed of an a-chiral aromatic monomer
(Nspe or (S)-(À)-1-phenylethylamine) as a structure-inducer and
achiral monomers (Npm or benzylamine) as structural followers.
Firstly, peptoid heptamers 1–9 were synthesized using microwave-
assisted15 solid-phase peptoid submonomer synthesis methods16
by varying the position of the a-chiral aromatic monomer from the
C-terminus (Table 1). Peptoids 1 and 2 were prepared as non-helical
and fully helical sequence controls, respectively.4a Peptoids 3–9
were designed to evaluate the contribution of a single Nspe to the
helical fold at a series of positions from the C-terminus. The degree
of helical fold was measured by the circular dichroism (CD)
intensity at 220 nm, which has been assigned as a relevant signal
to the helical conformation of Nspe-based peptoids.5,6j,7
Incorporation of a single Nspe monomer at different positions
showed distinct CD spectra (Fig. 2(A) and (B)). The CD spectra of
peptoids 5, 7 and 8 indicate a typical signature of a right-handed
polyproline type-I (PPI) peptoid helix, with two CD minima at 202 and
220 nm (Fig. 2(A)). Among these three peptoids, the placement of
Nspe at the second position from the N-terminus (peptoid 8) provided
the largest CD signal at 220 nm. The degree of helical fold gradually
decreased as the Nspe position shifted from the second (8) to the third
(7) and then to the fifth (5) positions from the N-terminus. On the
other hand, peptoids 6 and 9, where Nspe was located at the middle
of the heptamer sequence and at the first from the N-terminus,
respectively, showed CD spectra similar to that of non-helical peptoid
1 with virtually flat ellipticity over the 190 to 260 nm region (Fig. 2(B)).
Peptoid 4 revealed the moderate signal at the short-wavelength
(B195 nm) p - p* transition region, however, no apparent CD
signal was observed at longer wavelength (Fig. 2(B)). Notably,
peptoid 3 with Nspe at the first position from the C-terminus
showed a helix-like CD signature with strong p - p* transition
Fig. 2 CD spectra of peptoid heptamers 3–14 (50 mM in acetonitrile) were
recorded as per-residue molar ellipticity, or [y]. Data were acquired at
20 1C. Each spectral plot shows distinct effects of position-specific
incorporation of a single Nspe (A, B) and two Nspe’s (C). Additional plots
are displayed for demonstration of helicity inversion (D), synergistic (E), and
at 198 nm (Fig. 2(A)). This position was previously pointed out additive contribution (F) with two Nspe monomers incorporated.
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by Barron and coworkers as crucial for stabilizing the helical
conformation of peptoid oligomers.4a Based on the CD spectra
of peptoids 3–9, peptoids 10–21 were synthesized to investigate
the cooperative effects of multiple a-chiral monomer positions
on regulating the resultant heptamer conformation.
Firstly, peptoids 10–13, which contain two Nspe monomers
at the helix-inducing positions, were synthesized. As shown in
Fig. 2(C), peptoids 10–13 showed characteristic CD spectra of a
peptoid helix. A moderate but well-established helical fold was
observed in peptoids 10, 12, and 13, confirming the importance of
the second position from the N-terminus and the first position
from the C-terminus. Peptoid 11, however, showed a relatively
weaker degree of helicity probably due to the incorporation of
Nspe monomers at the less critical positions. It is also noteworthy
that the level of contribution of the two a-chiral aromatic side
chains was either synergistic (10 and 11, Fig. 2(E)) or additive
(12 and 13, Fig. 2(F)); for instance, the CD intensity of 13 was
similar to the sum of those of 3 and 8 (additive, Fig. 2(F)) while 10
Fig. 4 Comparison of the magnitude of the ellipticity measured by CD at
220 nm for selected peptoids studied herein.
calculated to be 57% in the heptamer (i.e., four out of seven),
showed stronger intensity at 198 nm and at 220 nm compared to the but the CD intensity of 21 at 220 nm was obtained as 76% of the
added intensity of 3 and 4 (synergistic, Fig. 2(E)). When two identical intensity of the fully helical peptoid 2 (Fig. 4). Interestingly, as the
monomers with opposite chirality (i.e., Nrpe) were incorporated at number of incorporated Nspe’s is increased (13 o 20 o 21 o 2),
the helix-inducing sites, the opposite CD signature showing helicity we observed more pronounced synergistic effects among the
inversion was observed (Fig. 2(D)).3a,5 Moreover, when both Nspe
influential sites (Fig. 4 and Fig. S8, see ESI†).
Noticeable observations with peptoid heptamers are as
follows: (1) the second position from the N-terminus was the most
influential in helical structure formation; and (2) the first position
and Nrpe were incorporated into the same chain, uncharacter-
istic CD spectra were obtained, indicating the counteractive
effect of two opposite chirality (15 and 16, see ESI,† Fig. S6).17
Next, a series of peptoid heptamers 17–20 with three Nspe from the N-terminus and the middle position in the oligomer were
monomers at different positions were synthesized. Based on the minimally effective in the secondary structure formation. To con-
two chiral monomer results, peptoids 17 and 20 were synthesized to firm the validity of these arguments in the even longer oligomer
have three Nspe monomers at minimally influential positions (i.e., sequences, peptoids 22–30 were synthesized. Peptoid heptamer,
octamer, and decamer (8, 28, and 30, respectively), which all have
one Nspe at the influential second position from N-terminus, clearly
exhibited helical signature as denoted by almost identical CD
features of these oligomers (Fig. S7(A), see ESI†). However, non-
the first, fourth, and sixth positions from N-terminus) and at most
influential positions (i.e., the second, third, and seventh positions
from N-terminus), respectively. As expected, the CD spectra of 17
and 20 showed a dramatic contrast (Fig. 3(A)). Peptoid 20 showed
a typical helix CD signature, whereas peptoid 17 exhibited an amer (29) showed an unusually enhanced negative CD signal at
almost non-helical CD signature despite the same percentage of around 203 nm, reminiscent of that of a threaded loop conforma-
helix-inducing chiral monomer contents (Nspe 43%). Therefore, tion of the Nspe nonamer.7 In the case of longer peptoid sequences
we confirmed that the above-mentioned uninfluential positions with a single Nspe incorporated at the uninfluential middle
position, undecamer (23) and tridecamer (24) showed almost
non-helical CD signatures (Fig. S7(B), ESI†).
show almost-zero synergetic contribution to helix formation even
with three chiral monomers present.
In the context of the questions we posed at the beginning, the
above-mentioned results suggest the following: even a single a-chiral
A slightly weaker negative Cotton effect was observed with
peptoids 18 and 19 which have one Nspe site variation from 20
(Fig. 3(A)). When four Nspe’s were positioned at the most influential aromatic monomer at one of the influential sites of oligopeptoids
sites (peptoid 21 in Fig. 3(B)), an even larger magnitude of the provided a moderately helical signature in CD spectra. The particular
ellipticity at 220 nm was observed. The percentage of Nspe was role of this specific position is conserved in the longer peptoid
oligomers. When multiple numbers of helix-inducing monomers
are incorporated into these influential positions, the cooperative
structure-inducing effect is more pronounced as exemplified by
peptoids 13, 20, and 21 in striking contrast to 17 (Fig. 4). In other
words, the position-specific placement as well as the numerical
percentage of a-chiral aromatic monomers4a in a given peptoid
chain is crucial in terms of determining the 3-D conformation
of a peptoid. It is noteworthy that the less influential positions
can be used as the sites to introduce various functional groups
appended to achiral monomers without hampering the overall
structural integrity of peptoids.
Fig. 3 CD spectra of peptoid heptamers (50 mM in acetonitrile) with (A)
three (17–20) and (B) four chiral monomers (21). In (B), CD spectra of 1 and
2 were drawn for comparison.
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5 C. W. Wu, T. J. Sanborn, R. N. Zuckermann and A. E. Barron, J. Am.
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In summary, we investigated the effect of position-specific place-
ment of a-chiral aromatic monomer(s) on the peptoid secondary
structure. The structural role of each position in a peptoid heptamer
is now well understood; in particular, the existence of lynchpin-like
structure-inducing positions and virtually uninfluential positions in
an oligopeptoid sequence was confirmed. The judicious placement
of a-chiral aromatic monomers can effectively modulate the overall
peptoid helicity, and the helicity modulation can be used as a way
to fine-tune peptoid functions. Both theoretical modeling and
structural analysis, which can provide a deeper understanding on
our experimental observations, are currently underway, and we
anticipate this study can offer a useful insight toward a rational
design of various functional peptoid oligomers.
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