Multifaceted folding in a foldamer featuring highly cooperative folds

Article abstract of DOI:10.1039/c2cc35649j

Herein, we report on the folding pattern observed in a synthetic peptide featuring two highly mutually dependent, yet strikingly dissimilar, closed networks of hydrogen-bonded rings that work in a cumulative fashion to stabilize the entire folded architec

Full text of DOI:10.1039/c2cc35649j

View Article Online / Journal Homepage / Table of Contents for this issue
Dynamic Article Links
ChemComm
Cite this: Chem. Commun., 2012, 48, 11205–11207
www.rsc.org/chemcomm
COMMUNICATION
Multifaceted folding in a foldamer featuring highly cooperative foldsw
Veera V. E. Ramesh,a Gowri Priya,a Amol S. Kotmale,b Rajesh G. Gonnade,c
Pattuparambil R. Rajamohananb and Gangadhar J. Sanjayan*a
Received 3rd August 2012, Accepted 25th September 2012
DOI: 10.1039/c2cc35649j
Herein, we report on the folding pattern observed in a synthetic
peptide featuring two highly mutually dependent, yet strikingly
dissimilar, closed networks of hydrogen-bonded rings that work
in a cumulative fashion to stabilize the entire folded architecture
of the peptide. Structural studies unequivocally suggest that
disruption of any one of these mutually-dependent hydrogen-
bonded networks is deleterious to the stability of the fully folded
conformation of the peptide.
It is noteworthy that 6-membered hydrogen-bonding is
predominantly observed in aromatic oligoamides. The Hamilton
group first described in detail the conformational preferences of
Ant (anthranilic acid), a constrained aromatic amino acid.11 In its
homo-oligomers 1 (Fig. 1), Ant promotes sheet-like secondary
structures featuring robust six-membered-ring intramolecular
hydrogen-bonding (C6-type H-bonding), as evident from
extensive structural investigations.11 While investigating the
conformational propensities of aromatic–aliphatic mixed
oligomers,8b,12 we obtained 2, which is a close analog of 1
having a proline (Pro) residue at the C-terminus.11
Against all the odds, the crystallographic studies13 of 2 had
something startling in the offing. The crystal structures of 2
showed not only the absence of the anticipated 6-membered
ring hydrogen-bonding (C6), but also the emergence of a fully
folded conformation featuring two unusual folds – neither of
them was observed alone in the fragments or oligomers.11,12
Much more intriguing is the fact that both the dissimilar folds
are highly symbiotically associated, and destruction of any one
of them has been shown to be highly detrimental to the
stability of the other, causing collapse of the entire folded
structural architecture. It is noteworthy that although 2
possesses all the required hydrogen-bonding codes which are
essential to help the molecule adopt the ‘‘C6’’ hydrogen-
bonding pattern as shown in Fig. 1, the molecule surprisingly
adopts the doubly folded conformation featuring two distinctly
Folding is a fundamental physical phenomenon by which
biopolymers fold into their characteristic three-dimensional
compact structures – quite often mediated by a collection of
non-covalent forces.1,2 In order to carry out specific biochemical
reactions, and effect biological responses, proteins adopt precise
three-dimensional conformations through folding – a process if
turned erroneous (protein misfolding) can have deleterious effects
on the biological processes.3 During the folding process, a protein
picks out the right conformation, out of billions of other possible
conformations. However, owing to their sheer size and intricacy,
proteins pose considerable challenges in investigation and
understanding of their folding patterns and preferences. Thus,
the first step towards unraveling the mystery behind protein
folding is to understand closely how its smaller counterpart – a
peptide – folds.4
Discrete non-natural oligomers, called foldamers, with
predictable and well-characterized folding patterns offer
considerable advantages in this context owing to their simplified
backbone and less intricate structural architectures, when compared
to proteins.5 Indeed, since the inception of the foldamer concept, a
wealth of knowledge has been generated pertaining to the folding
characteristics of both natural and unnatural oligomers, which has
culminated in the successful development of synthetic oligomers
offering diverse biomedical6 and material science applications.7
Aromatic oligoamide foldamers display well-characterized folding
patterns when compared to their aliphatic counterparts.8–11
a Division of Organic Synthesis, National Chemical Laboratory,
Dr. Homi Bhabha Road, Pune 411 008, India.
E-mail: gj.sanjayan@ncl.res.in; Fax: +91 020-25902629;
Tel: +91 020-25902629
b Central NMR Facility, National Chemical Laboratory, Pune, India
c Centre for Material Characterization, National Chemical
Laboratory, Pune, India
w Electronic supplementary information (ESI) available: Experimental
procedures and spectra. CCDC 858579–858584. For ESI and crystallo-
graphic data in CIF or other electronic format see DOI: 10.1039/
c2cc35649j
Fig. 1 Extended sheet conformation displayed by Ant-Ant-Ant 1
with repeating C6 H-bonding 1 (left)11 and its analogous structure
Ant-Ant-Pro 2 (right) that does not possess any 6-membered H-bonding
(this work).
c
This journal is The Royal Society of Chemistry 2012
Chem. Commun., 2012, 48, 11205–11207 11205

View Article Online
different folds – one towards the N-terminus with a C10-hydrogen-
bonded network, and the other one at the C-terminus displaying a
C11-hydrogen-bonded network (Fig. 2A and E).
mutual dependency of the H-bonded networks, resulted in the
formation of the following analogs (Fig. 3). The three molecules
3, 4 and 5 feature a similar backbone structure to that of 2,
except that they are devoid of the H-bond donor at the
N-terminus. In place of the crucial N-acetyl group that would
have otherwise contributed to establish the C10 H-bonding as in
2, the oligoamides 3, 4 and 5 possess a nitro group – devoid of
H-bond donor ability. The substituents at the C-terminus were
different (N-Me in 3, N-tBu in 4 and p-Br-anilide in 5), keeping
the N-terminus nitro group constant, in order to gauge the
substituent effects. Comparison of the crystal structures of 3, 4
and 5 (Fig. 3B, D and F, respectively) unequivocally reveals
that the C10 H-bonding observed in 2 is clearly absent in these
cases due to the lack of an H-bonding donor at the N-terminus.
Surprisingly, deletion of the H-bonding donor at the N-terminus
not only caused vanishing of the C10 structure, but also the C11
structure. In the absence of these folds, the emergence of the
C9 structure (avN–HÁÁÁO = 2.05 A, avNÁÁ ÁO = 2.87 A and
avH-bond angle = 1681) was clearly evident, which is also observed
in the solution-state, as could be deduced from NMR studies
(ESIw, S74). The involvement of strong intra-molecular hydrogen
bonding interactions was also substantiated by [D6]-DMSO
titration of 2a (Dd o 0.57 ppm) (ESIw, S55) and variable
A closer look at the C10-hydrogen-bonded network in the
crystal structure of 2a (Fig. 2C) reveals that it involves two
consecutive Ant residues, predisposed in an anti-periplanar
arrangement, featuring strong hydrogen-bonding (N–HÁ Á ÁO =
2.11 A, NÁ Á ÁO = 2.97 A and H-bond angle = 1611) (Fig. 2B).
The C11-hydrogen-bonded network (Fig. 2D), in contrast,
involves the C-terminal Ant and Pro residues, aligned in an
anti-periplanar arrangement, with strong hydrogen-bonding
(N–HÁ Á ÁO = 2.11 A, NÁ Á ÁO = 2.94 A and H-bond angle =
1641). An exactly similar hydrogen-bonding arrangement is
noted in the opposite enantiomer 2b (Fig. 2E–H), and a
crystal of 2a grown in DMSO (ESIw, S12 and Fig. 1), which
unequivocally precluded any crystal packing effects and/or
crystal–solvent competitive interactions which could have interfered
in the hydrogen-bonding interactions.
The unusual hydrogen-bonded networks and their symbiotic
relationship in effectively toppling the strong 6-membered
H-bonding observed herein suggest that it is, presumably, their
enhanced stability in such an arrangement which reinforces the
entire folded architecture of 2. This conjecture is clearly vetted
by the following observation that alteration of any of these
hydrogen-bonded networks, however dissimilar they are, causes
collapse of the entire doubly folded architecture. It is note-
worthy that 2a retains similar conformational features in the
solution-state as well, as could be deduced from conformational
investigations by NMR studies (ESIw, S73). Intense efforts to
crystallize the modified analogs featuring altered N- and
C-terminal H-bond donors, which would throw light on the
temperature studies of 2a (263–323 K; Dd/DT o À3 ppb KÀ1
)
(ESIw, S58). The characteristic IR NH stretching frequencies
at B3300 cmÀ1 (ESIw, S26–S31) are also suggestive of
H-bonding interactions in the solution-state.
In an attempt to verify the individual contribution of the
C-terminus H-bond donor in the stabilization of the entire fold
as observed in 2, the analog 6 (Fig. 3G) was made that lacks an
amide group. Extensive efforts culminated in the formation of
Fig. 2 Molecular structure of AcNH-Ant-Ant-LPro-NHMe 2a with its observed H-bonding pattern (A), crystal structure of 2a (B) and its
excerpts (C, D), molecular structure of AcNH-Ant-Ant-DPro-NHMe 2b with its observed H-bonding pattern (E), crystal structure of 2b (F) and its
excerpts (G, H). Note: all hydrogens, except the polar ones, have been deleted for clarity in the crystal structures.
c
11206 Chem. Commun., 2012, 48, 11205–11207
This journal is The Royal Society of Chemistry 2012

View Article Online
Fig. 3 Molecular and crystal structures of 3 (A, B), 4 (C, D), 5 (E, F) and 6 (G, H), respectively. Note: H-bonding pattern has been highlighted in
the molecular structures. Structural changes, as compared to 2a, have been highlighted in the molecular structures of 3–6.
crystals of 6 whose crystal structure (Fig. 3H) astonishingly
revealed the absence of not only the C11 but also the C10 H-bonded
networks – with the consequence of complete breakdown of
the entire folded architecture of the peptide. The only H-bonding
observed in this case was the Hamilton-type C6 bonding –
characteristic of consecutive Ant rings.11 This observation
unambiguously establishes the role of the C-terminus amide group
in stabilizing the doubly folded conformation observed in 2.
In summary, this work illustrates how multiple folds of
dissimilar structural features can ‘‘symbiotically’’ cause and
stabilize peptide folding. The individual contribution of each
H-bonded network in the stability of the entire folded architecture
of the peptide has been investigated, which clearly suggests that
they work in a cumulative and mutually accommodative manner
to help the peptide adopt a preferred folded conformation.
Intriguingly, the twin-fold observed in 2 is not only devoid of
the robust C6 H-bonding observed in oligo Ants,11 but also the
C9 H-bonding, when Ant precedes Pro residue.12 The unusual
observation with the folding characteristics seen in peptides
containing Ant and Pro residues in 2 : 1 ratios suggests that these
residues of constitutional ratios other than 1 : 1 and 2 : 1 might
give further insight into the folding characteristics of these
synthetic oligomers – a study which is in progress.
4 (a) C. Toniolo, M. Crisma, F. Formaggio and C. Peggion, Biopolymers,
2001, 60, 396; (b) D. Seebach, A. K. Beck and D. J. Bierbaum,
Chem. Biodiversity, 2004, 1, 1111; (c) P. G. Vasudev, S. Chatterjee,
N. Shamala and P. Balaram, Chem. Rev., 2011, 111, 657;
(d) J. S. Nowick, Acc. Chem. Res., 2008, 41, 1319; (e) H. Wennemers,
Chem. Commun., 2011, 47, 12036; (f) A. B. Smith, A. K. Charnley and
R. Hirschmann, Acc. Chem. Res., 2011, 44, 180.
5 (a) S. H. Gellman, Acc. Chem. Res., 1998, 31, 173; (b) D. J. Hill,
M. J. Mio, R. B. Prince, T. S. Hughes and J. S. Moore, Chem. Rev.,
2001, 101, 3893; (c) G. Guichard and I. Huc, Chem. Commun.,
2011, 47, 5933; (d) T. A. Martinek and F. Fulop, Chem. Soc. Rev.,
2011, 41, 687; (e) X. Li, Y. D. Wu and D. Yang, Acc. Chem. Res.,
2008, 41, 1428; (f) P. I. Saraogi and A. D. Hamilton, Chem. Soc.
Rev., 2009, 38, 1726; (g) Z. T. Li, J. L. Hou and C. Li, Acc. Chem.
Res., 2008, 41, 343; (h) C. E. Schafmeister, Z. Z. Brown and
S. Gupta, Acc. Chem. Res., 2008, 41, 1387; (i) C. Tomasini,
G. Angelici and N. Castellucci, Eur. J. Org. Chem., 2011, 3648.
6 (a) C. M. Goodman, S. Choi, S. Shandler and W. DeGrado, Nat.
Chem. Biol., 2007, 3, 252; (b) A. D. Bautista, J. S. Appelbaum,
C. J. Craig, J. Michel and A. Schepartz, J. Am. Chem. Soc., 2010,
132, 2904; (c) E. A. Porter, X. Wang, H. S. Lee, B. Weisblum and
S. H. Gellman, Nature, 2000, 404, 565; (d) W. S. Horne, Expert
Opin. Drug Discovery, 2011, 6, 1247.
7 (a) Q. Gan, Y. Ferrand, C. Bao, B. Kauffmann, A. Grelard,
H. Jiang and I. Huc, Science, 2011, 331, 1172; (b) P. Prabhakaran,
G. Priya and G. J. Sanjayan, Angew. Chem., Int. Ed., 2012,
51, 4006.
8 (a) B. Gong, Acc. Chem. Res., 2008, 41, 1376; (b) A. Roy,
P. Prabhakaran, P. K. Baruah and G. J. Sanjayan, Chem. Commun.,
2011, 47, 11593, and references cited therein.
9 K. Ghosh and J. S. Moore, J. Am. Chem. Soc., 2011, 133, 19650.
10 J. J. V. Gorp, J. A. J. M. Vekemans and E. W. Meijer, Chem.
Commun., 2004, 60.
VVER, GP and ASK thank CSIR, New Delhi, for research
fellowships. This work was funded by NCL-IGIB-JRI.
11 Y. Hamuro, S. J. Geib and A. D. Hamilton, J. Am. Chem. Soc.,
1996, 118, 7529.
Notes and references
1 C. B. Anfinsen, Science, 1973, 181, 223.
12 P. Prabhakaran, S. S. Kale, V. G. Puranik, P. R. Rajamohanan,
O. Chetina, J. A. K. Howard, H. J. Hofmann and G. J. Sanjayan,
J. Am. Chem. Soc., 2008, 130, 17743.
2 L. M. Salonen, M. Ellermann and F. Diederich, Angew. Chem.,
Int. Ed., 2011, 50, 4808.
3 R. L. Wiseman and J. W. Kelly, Science, 2011, 332, 44.
13 CCDC 858579–858584 (2–6)w.
c
This journal is The Royal Society of Chemistry 2012
Chem. Commun., 2012, 48, 11205–11207 11207