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DOI: 10.1038/ncomms10335
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The sequence of a peptide programs its self-assembly and hence the expression of specic
properties through non-covalent interactions. A large variety of peptide nanostructures has
been designed employing different aspects of these non-covalent interactions, such as
dispersive interactions, hydrogen bonding or ionic interactions. Here we demonstrate the
sequence-controlled fabrication of molecular nanostructures using peptides as bio-organic
building blocks for two-dimensional (2D) self-assembly. Scanning tunnelling microscopy
reveals changes from compact or linear assemblies (angiotensin I) to long-range ordered,
chiral honeycomb networks (angiotensin II) as a result of removal of steric hindrance by
sequence modication. Guided by our observations, molecular dynamic simulations yield
atomistic models for the elucidation of interpeptide-binding motifs. This new approach
to 2D self-assembly on surfaces grants insight at the atomic level that will enable the use of
oligo- and polypeptides as large, multi-functional bio-organic building blocks, and opens a
new route towards rationally designed, bio-inspired surfaces.
1 Max Planck Institute for Solid State Research, Heisenbergstrae 1, 70569 Stuttgart, Germany. 2 Bernha
userstrae 75, 70771 Leinfelden-Echterdingen,
Germany. 3 Institut de Physique de la Matie`re Condensee, Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne, Switzerland. Correspondence and
requests for materials should be addressed to S.A. (email: s.abb@fkf.mpg.de) or to S.R. (email: s.rauschenbach@fkf.mpg.de).
ARTICLE
ARTICLE
Leu
Tyr
Arg
N
Asp
Val
Ile
His
Pro
C
His
Phe
8
9
1
2
10
10
C terminal
interface
N terminal
interface
C terminal
interface
N terminal
interface
Figure 1 | Decapeptide angiotensin I on Au(111). (a) MD-optimized molecular structure of adsorbed At-I. (b) Scheme of the molecular structure of At-I
with the residues highlighted in orange (polar) and green (nonpolar). (c) STM image (1.5 V, 29 pA; scale bar, 4 nm) of structure A with schematic model of
the staggered chains assembly. (d) Atomistic MD model of structure A with highlighted regions (magenta and blue) indicating important binding motifs.
On the left side, the simulated STM image of that MD structure is overlaid. On the right side, a schematic model can be found. (e) STM image (1.5 V, 29 pA;
scale bar, 4 nm) of structure B with schematic model of the stacked assembly and indication of rows of alternating contrast at the C and N terminal
interface. (f) Atomistic MD model of structure B with highlighted regions (blue rectangle and magenta oval) indicating important binding motifs and the
region of the C and N terminal interface. On the left side, the simulated STM image of that MD structure is overlaid. On the right side, a schematic model
can be found.
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Angiotensin II
Asp
Arg
Asp
Asp
Tyr
Arg
Ile
Pro
o
Val
Val
Hiss
Leu
u
Tyr
Phe
e
H
is
His
Ile
Pro
Val
Arg
Leu
His
Ile
Pro
His
Phe
Tyr
His
Phe
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3
5
7
8
1
2
2.3 nm
Figure 3 | Network of angiotensin II on Au(111). (a) STM image (1.3 V, 35.5 pA; scale bar, 15 nm) of a large, well-ordered honeycomb network. The
diamond indicates the unit cell, the hexagon demonstrates the chirality of the network as the hexagonal pore (red) is tilted anticlockwise by 6 with respect
to the hexagonal superstructure (blue). In the upper right corner, a linear arrangement is encircled in white. (b) The schematic arrangement of the At-II
molecules according to MD simulations demonstrates the nonpolar (green) decoration of the pore with the polar residues (orange) in the inside of the
nanostructure. A circular arrow indicates the chiral vertex. The polarnonpolarpolar-binding motif at the short edge of the dimer is indicated by a green/
orange background at the lower right corner. (c) High-resolution STM image (1.3 V, 35.5 pA; scale bar, 2 nm; left) overlapped with the MD-simulated model
(middle) and the calculated electron density (right) for comparison with the STM image. DFT was performed on the optimized structure of a dimer and
subsequently overlaid with the MD structure.
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a
7
5
6 - domain
6 - distorted
Figure 4 | Defects of the honeycomb network. (a) STM image (1.8 V, 32.6 pA; scale bar, 10 nm) showing distance defects within the dimer (white
rectangle) and rotational defects at the vertex (white circle). (b) STM image (1.3 V, 35.5 pA; scale bar, 10 nm) of a linear grain boundary running horizontally
in the central part of the image. The domains are tilted by B1 indicated by the white lines. (c) STM image (2.4 V, 38.7 pA; scale bar, 10 nm) of grain
boundaries with larger rotational offset (B1625) resulting in grain boundaries with seven-membered (green) and ve-membered (red) rings to reduce
stress.
Due to the bulky residues, the strong peptide bonds and the
restriction in two dimensions, the molecule on the surface is
relatively rigid. Therefore, the different afnities of individual
amino acids level out and the binding of the peptide must be
considered as a compound effect involving entire molecules
rather than the binding of the individual amino acids.
Discussion
The amino-acid sequence in naturally occurring proteins controls
the conformation, as well as the specic interactions of the
proteins. Here we demonstrate a remarkably similar scheme, by
which oligopeptides form long-range ordered nanostructures in
two dimensions at a surface despite the apparent complexity and
exibility of the molecular building block. On the basis of the
submolecular STM resolution that validates the atomistic MD
simulations, we are able to obtain detailed models that allow for
the identication of basic design principles and binding motifs.
By comparing the self-assembly of At-I and At-II, which only
differ by two amino acids, we learned that using sterically
demanding amino acids avoids backfolding and self-passivation
of the single peptides on the surfaces resulting in a rigid building
block of predictable behaviour. In addition, a balanced distribution of polar and nonpolar moieties is essential to provide specic
binding sites, as well as passivation of the assembly, respectively,
which is crucial for the long-range order assembly of oligopeptides on surfaces.
Our approach of obtaining a microscopic understanding from
highly resolved STM measurements requires the feedback with
MD and DFT modelling, and achieves for the rst time the
sequence-programmed assembly of oligopeptides on surfaces at
the amino-acid level. The detailed experimental mapping of
peptides and peptide assemblies on surfaces will serve as a model
system to validate the emerging theoretical approaches in this
eld30,34,36. Together, high-resolution STM data and atomistic
simulations allow for the exploration of promising binding motifs
and their rational optimization.
To ensure high-quality samples, the species was mass selected before deposition
(Supplementary Fig. 10). For deposition, the ions were decelerated to 10 eV to
ensure soft landing of the biomolecules. In this energy range, fragmentation of the
molecular ions upon deposition can be neglected. During the deposition, the
sample was held at room temperature and the ion current was measured on the
sample to estimate the coverage (At-II, z 2, 43 pAh; At-I, z 3, 60 pAh;
pAh picoampere hours).
Before the deposition, a Au(111) single crystal was cleaned by subsequent cycles
of sputtering (1 kV, 30 min) and annealing (930 K, 10 min) and then transferred
into the deposition chamber without breaking the vacuum. After deposition, the
sample was transferred to the STM chamber into a variable temperature STM
(Omicron VT-STM). STM measurements were conducted at 40 K to immobilize
the adsorbents on the surface. Measurement parameters are given with respect to
the grounded sample. STM images were processed with WSxM 5.0 (ref. 37).
References
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formic acid to result in a concentration of 10 4 M. These solutions were used with
our home-build ES-IBD (Supplementary Fig. 9; Supplementary Methods) to bring
the molecules into the gas phase.
6
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Author contributions
S.A., S.R. and K.K. designed the research. S.A. and S.R. carried out the experiments. S.A.,
S.R. and L.H. analysed the data. L.H. performed MD simulations. R.G. performed DFT
calculations on the optimized MD structures. All authors contributed to and discussed
the manuscript.
Additional information
Supplementary Information accompanies this paper at http://www.nature.com/
naturecommunications
Competing nancial interests: The authors declare no competing nancial interests.
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How to cite this article: Abb, S. et al. Two-dimensional honeycomb network through
sequence-controlled self-assembly of oligopeptides. Nat. Commun. 7:10335
doi: 10.1038/ncomms10335 (2016).
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