Self-Assembled Peptide Nano-Superstructure towards Enzyme Mimicking Hydrolysis

Article abstract of DOI:10.1002/anie.202105830

The structural arrangement of amino acid residues in native enzymes underlies their remarkable catalytic properties, thus providing a notable point of reference for designing potent yet simple biomimetic catalysts. Herein, we describe a minimalistic appro

Full text of DOI:10.1002/anie.202105830

A Journal of the Gesellschaft Deutscher Chemiker
Angewandte
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Accepted Article
Title: Self-assembled peptide nano-superstructure towards enzyme
mimicking hydrolysis
Authors: Ehud Gazit, Yu Chen, Yuqin Yang, Asuka A. Orr, Pandeeswar
Makam, Boris Redko, Elvira Haimov, Yannan Wang, Linda
J. W. Shimon, Sigal Rencus-Lazar, Meiting Ju, Phanourios
Tamamis, and Hao Dong
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10.1002/anie.202105830
Angewandte Chemie International Edition
RESEARCH ARTICLE
Self-assembled peptide nano-superstructure towards enzyme
mimicking hydrolysis
Yu Chen† [a], Yuqin Yang† [b], Asuka A. Orr† [c], Pandeeswar Makam[d], Boris Redko[e], Elvira Haimov[e],
Yannan Wang[f], Linda J. W. Shimon[g], Sigal Rencus-Lazar[a], Meiting Ju[f], Phanourios Tamamis*[c],
Hao Dong*[b], Ehud Gazit*[a][h]
[a]
[b]
[c]
Dr. Y. Chen, Dr. S. Rencus-Lazar, Prof. E. Gazit
The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Israel
E-mail: ehudga@tauex.tau.ac.il
Y. Yang, Prof. Hao Dong
Kuang Yaming Honors School & Institute for Brain Sciences, Nanjing University, China
E-mail: donghao@nju.edu.cn
A. A. Orr, Prof. P. Tamamis
Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States
E-mail: tamamis@tamu.edu
[d]
[e]
[f]
Dr. P. Makam
Department Applied Chemistry, IIT(BHU), Varanasi, India
Dr. B. Redko, Dr. E. Haimov
BLAVATNIK CENTER for Drug Discovery, Tel Aviv University, Israel
Y. Wang, Prof. M. Ju
National & Local Joint Engineering Research Center on Biomass Resource Utilization, Nankai University, China
Dr. L. J. W. Shimon
Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
Prof. E. Gazit
[g]
[h]
Department of Materials Science and Engineering, Tel Aviv University, Israel
Supporting information for this article is given via a link at the end of the document.
enzymes, the "bottom-up" approach for the fabrication of complex
nanomaterials has also spawned new developments in this direction
and provided scientists with an ever-evolving toolbox of artificial
enzymes[4]. Enzyme-inspired supramolecular catalysts hold great
promise in medical and industrial biotransformation applications[5]. In
particular, peptides and peptide derivatives are predominantly
attractive components for constructing supramolecular catalysts, as
evidenced by the fact that complex enzymes in biological systems
comprise mainly of the 20 genetically-encoded amino acids. The
development of such an enzyme-inspired peptide supramolecular
catalyst is expected to offer a more robust and efficacious alternative
to industrial and academic enzymatic catalysis and more in-depth
insight into the origin of the native enzyme[6].
Abstract: The structural arrangement of amino acid residues in native
enzymes underlies their remarkable catalytic properties, thus
providing a notable point of reference for designing potent yet simple
biomimetic catalysts. Herein, we describe a minimalistic approach to
construct a dipeptide-based nano-superstructure with enzyme-like
activity. The self-assembled biocatalyst comprises one peptide as a
single building block, readily synthesized from histidine. Through
coordination with zinc ion, the peptide self-assembly procedure allows
the formation of supramolecular β-sheet ordered nanocrystals, which
can be used as basic units to further construct higher-order
superstructure. As a result, remarkable hydrolysis activity and
enduring stability are demonstrated. Our work exemplifies the use of
a bioinspired supramolecular assembly approach to develop next-
generation biocatalysts for biotechnological applications.
Introduction
Guided by the minimalistic principle originally described by
DeGrado[7], various catalytic self-assembling peptide structural units
A considerable number of enzymes with fascinating activity
have naturally evolved to control complex chemical processes with
extraordinary efficiency and selectivity[1]. As one of the most
ubiquitous metalloenzymes, carbonic anhydrases (CA) are found in
most organisms in all kingdoms of life and are involved in diverse
physiological functions, including respiration and cellular pH
maintenance[2]. Specifically, as an effective hydrolase, CAII is of great
significance in industrial "small molecule" chemical conversion. With
the insights obtained from the X-ray crystallographic structure of CAII,
significant progress has been successfully made in the de novo
design of protein scaffolds to catalyze biological reactions[3]. In
addition to the evolution of these large molecules based artificial
8]
derived from amyloid sequences have been discovered[6a,
.
Korendovych and coworkers designed a series of amyloid-like fibril
heptapeptide-based supramolecular esterase with alternating
hydrophobic and hydrophilic residues[9]. The resulting peptide library
was screened for catalyzing the hydrolysis of acyl esters in the
presence of zinc. Although catalytic peptide assemblies discovered in
these pioneering studies are very promising, several intrinsic
drawbacks, including high costs of preparation and purification, low
operational stability, and inefficient recycling and reuse, severely
hamper their widespread applications[8a, 10]
.
1
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Cyclic dipeptides, as the smallest cyclic peptides, have complex
side-chain substituents, which can be used as a model to mimic a
catalytic active site[11]. The versatile hydrogen bonding capabilities of
mechanism of cyclo-HH and zinc iodide (cyclo-HH-ZnI2) was
investigated using all-atom molecular dynamics (MD) simulations and
X-ray crystallography analysis. The cyclo-HH-ZnI2 nanowires
displayed hydrolytic activity, with exceptional stability and recyclability.
The activity of the catalyst was retained after five cycles, making it
more robust and durable than other biomolecular artificial hydrolase
complexes. Moreover, using hydrolytic catalysis as a model reaction,
theoretical calculations and experimental studies unambiguously
identified that the rate-determining step of the entire reaction was the
nucleophilic attack process, and the confined local environment was
critical for hydrolysis.
the diketopiperazine motif form
a unique and stable packing
arrangement, which can be used as a robust scaffold to overcome the
problem of enzymatic degradation[12]. Here, inspired by the structure
of the active site of CAII, we aimed to incorporate histidine residues
into one short peptide segment, which will serve as the basic building
block of a supramolecular catalyst. For this purpose, we used cyclic-
dihistidine (cyclo-HH) as a building block to prepare a supramolecular
assembly-based nano-superstructure with hydrolytic activity through
a simple and general method (Scheme 1). The self-assembly
Scheme 1. Design of a cyclic dipeptide supramolecular assembly-based nano-superstructure for mimicking the molecular structure of the active
site of CAII.
(FLIM) studies of the photodynamic properties of the cyclo-HH-ZnI2
nanowires[15]. Upon excitation at 400 nm, the cyclo-HH-ZnI2 nanowires
Results and Discussion
Cyclic dipeptides represent
a large class of secondary
exhibited bright fluorescence emission centered at 500 nm (Figure
S4). The lifetime image and phasor approach analysis revealed the
high homogeneity of the cyclo-HH-ZnI2 nanowire superstructure with
a uniform fluorescence lifetime of approximately 2.3 ns[16] ((Figure 1f,
Figure S5-S7). The porosity of the cyclo-HH-ZnI2 nanowire
superstructure was investigated by measuring the N2 adsorption at 77
K. The Brunner-Emmet-Teller (BET) surface area and pore volume
were calculated to be as high as 257.36 m2/g and 0.45 cm3/g,
respectively. An extensive N2 uptake below 0.1 P/P0 indicating
extensive microporosity and a distinct capillary condensation step at
higher relative pressures (P/P0 = 0.7 to 1) were also recorded,
demonstrating the formation of mesoporosity (Figure 1g, Figure S8).
The observed mesopores were attributed to the void space between
cyclo-HH-ZnI2 nanocrystals, enforced by their hierarchical
arrangement in the microstructure, as observed in Figure 1d. These
cyclo-HH-ZnI2 multiporous structures may host abundant catalytic
active sites and provide flexible transport pathways to diffuse
reactants during the hydrolytic process, and therefore could be
metabolites containing 2,5-diketopiperazine heterocycles, which are
ubiquitous and evolutionarily conserved in various organisms[13]. They
were also identified as chemical degradation products in roasted
coffee, which contributes to the perceived bitterness. Inspired by this
thermal treatment process, cyclo-HH was first synthesized using an
eco-friendly microwave-assisted solid-phase peptide method[14]
(Figure 1a, Figure S1-S3). To allow self-assembly, cyclo-HH was
mixed with ZnI2 under controlled hydrothermal conditions, resulting in
nanostructure formation. The one-dimensional nanowire morphology
of the resulting cyclo-HH-ZnI2 assemblies was observed by scanning
electron microscopy (SEM) and transmission electron microscopy
(TEM) (Figure 1b-d). Interestingly, the large-scale, well-dispersed
nanoparticles with an average size of 10 nm could be detected in high-
resolution images, indicating that the nanowire superstructures were
indeed composed of numerous nanoparticles. The powder X-ray
diffraction (PXRD) pattern (Figure 1e) of the cyclo-HH-ZnI2 nanowires
exhibited high crystallinity.
Furthermore, we performed fluorescence excitation-emission
matrix contour profile and confocal fluorescence lifetime microscopy
extremely useful in hydrolysis[10h, 17]
.
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Figure 1. Characterization of the cyclo-HH-ZnI2 nanowires. (a) One-step synthesis of cyclo-HH via a simple microwave-assisted solid-phase
peptide method. (b) SEM and (c, d) TEM images of as-synthesized cyclo-HH-ZnI2 nanowires. The yellow dashed frame in (c) indicates the area
selected for high-magnification imaging shown in (d). Scale bars, 200 nm, 500 nm, and 50 nm (b to d, respectively). (e) Fitting of the experimental
PXRD of cyclo-HH-ZnI2 nanowires (blue) and calculated diffractogram of cyclo-HH-ZnI2 single crystal (red). The grey line represents the
difference between the diffractograms. (f) Two-dimensional histogram phasor plots generated from FLIM images of cyclo-HH-ZnI2 nanowires.
The colors correspond to the occurrence frequency. (g) N2 adsorption isotherms of cyclo-HH-ZnI2 nanowires (filled circles: adsorption, empty:
desorption).
MD simulations can be powerful tools in providing insights into
molecular self-assembly by analyzing the initial nucleation of
molecules in different environments[18]. Here, we performed multiple
multi-ns explicit solvent MD simulations in CHARMM[19] to investigate
the initial stages of cyclo-HH self-assembly in the presence of Zn2+
and iodide ions. Across all simulations, visual inspection confirmed
that highly disordered aggregates of cyclo-HH molecules broke apart
and reformed, indicating that the cyclo-HH molecules were not
trapped in a local energetic minimum in a given simulation and
facilitated higher-order structures. Within the simulations, ordered
antiparallel and parallel configurations of cyclo-HH dimers were
observed, with the former being the predominant configuration (Figure
S9, Table S1), in line with the crystallographic data (Table S2).
According to the time-evolution structural analysis of the antiparallel
configurations (Figure S9, Table S1), the elementary unit formation
began from coordinating the two histidine side chains of two cyclo-HH
molecules with a Zn2+ ion (Figure 2a i-ii). Subsequently, two cyclo-
HH molecules coordinating with Zn2+ began forming hydrogen bond
interactions between their backbone atoms to eventually form
antiparallel β-bridge configurations. (Figure 2a iii-iv). These β-sheet-
like dimeric conformations could constitute the elementary units that
comprise the self-assembled clusters and subsequently the larger
crystals.
To validate our hypothesis and further characterize the specific
self-assembly mechanism, we extended the solvothermal reaction
time to crystalize the micrometer-sized cyclo-HH-ZnI2 single crystals
(Figure S10, S11) and analyzed the resulting structures via X-ray
crystallography (Table S2). The simulated diffractogram from the
single-crystal was vastly consistent with the pattern of the cyclo-HH-
ZnI2 nanowire, indicating a similar molecular organization (Figure 1e,
S12). Cyclo-HH-ZnI2 crystallized in the orthorhombic space group
Pbcn, with one cyclo-HH molecule, one neutral [Zn(L)2I2] unit per
asymmetric unit (Figure 2b). The Zn(II) ion was attached with two
iodine ligands and further coordinated with two nitrogen atoms from
the imidazole groups on two different cyclo-HH molecules, providing
a central coordination site geometric tetrahedron (Figure 2c). The
diketopiperazine rings on two adjacent cyclic dipeptides were linked
through β-sheets hydrogen bonding with N － H···O ＝ C
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(donor···acceptor) distances of 2.86 Å and 2.83 Å (Figure 2d). It is
worth noting that the antiparallel configurations of cyclo-HH dimers
observed within the simulations (Figure 2a iv) were in line with the X-
ray crystal structure (Figure 2b-d). Upon structural alignment of all the
antiparallel dimer configurations derived from the simulations to the
X-ray crystal structure, the root-mean-square deviation of the cyclo-
HH dimer heavy atoms was found to be only 1.93 ± 0.66 Å.
Interestingly, the cis- and trans-conformational cyclic dipeptides
bridged zinc ions to form unusual meso-helix motifs in one single
strand along the b-axis, giving rise to an infinite one-dimensional chain
(Figure S13). Furthermore, these discrete meso-helical chains were
interconnected by π-π stacking interactions of imidazole rings (Figure
S14), thereby further stabilizing the crystal structure (Figure 2e).
Figure 2. Structural analysis of the cyclo-HH-ZnI2 assemblies. (a) The number of instances of interactions for molecules eventually forming
antiparallel configurations within the simulations. The tracked interactions are: (i) one imidazole ring of a cyclo-HH molecule coordinating with
one ZnI2 (red), (ii) two imidazole rings belonging to opposing cyclo-HH molecules coordinating with a single ZnI2 (blue), (iii) two cyclo-HH
molecules forming one hydrogen bond between their backbones while coordinating with a single ZnI2 (green), and (iv) two cyclo-HH molecules
forming an antiparallel configuration while coordinated with ZnI2 (purple). Representative illustration of the cyclo-HH and ZnI2 self-assembly
process into a β-sheet-like elementary structure, as detected by MD simulations and structural analysis software, is shown. (b) Single-crystal
structure of cyclo-HH-ZnI2 in Pbcn space group. Color code: green, C; red, O; blue, N; purple, Zn; and cyan, Iodine. (c) Zn(II)-centered geometric
tetrahedron: a Zn(II) atom coordinated with two ligands and two N-donor atoms from the imidazole groups of two different cyclo-HH molecules.
(d) β-sheets hydrogen bonding connecting two adjacent cyclic-dipeptides. (e) 3D supramolecular structure packed between the imidazole rings
of adjacent 1D chains.
Next, we sought to examine the hydrolytic activity of the cyclo-
HH-ZnI2 nanowires [20]. For this purpose, p-nitrophenyl acetate (pNPA)
hydrolysis was used as a probe reaction (Figure 3a). Figure 3b
shows the most energetically favored binding mode of the pNPA
imidazole ring NH group (Figure 3b). Additionally, the ester group
was in close proximity to the bound Zn2+ ion (Figure 3b). Overall, as
the hydrolysis of pNPA occurs at the ester group, the resulting
structures could be indicative of cyclo-HH-ZnI2 potential biocatalytic
activity.
substrate according to molecular docking using AutoDock4Zn[21] (with
[21]
an affinity of -5.8 kcal mol-1 based on the AutoDock4Zn
scoring
The hydrolysis activity of cyclo-HH-ZnI2 nanowires towards
pNPA was investigated by monitoring the time-dependent
absorbance changes of the reaction product, p-nitrophenol (pNP), at
405 nm. Interestingly, cyclo-HH-ZnI2 nanowires were found to be
capable of ester hydrolysis, as in the presence of the cyclo-HH-ZnI2
nanowire catalyst, the colorless pNPA solution turned yellow,
indicating the formation of the reaction product pNP. Moreover,
increasing concentrations of cyclo-HH-ZnI2 nanowires resulted in an
evident enhancement of the reaction rate (Figure 3c, Figure S16). In
function). Owing to the confined spatial environment formed between
the discrete meso-helical chains, it appears that the pNPA substrate
molecules can be aligned between cyclo-HH-ZnI2 β-sheet-like
grooves (Figure S15), where each substrate is sufficiently proximal
for nucleophile attacks. In the most energetically favored binding
mode, pNPA was stabilized through a hydrogen bond between its
ester carbonyl group and a cyclo-HH imidazole ring NH group, as well
as a hydrogen bond between its nitro group and a separate cyclo-HH
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contrast, under similar conditions, the control substrate solution
without the catalyst did not show any visible color change. The
enzymatic kinetics of the cyclo-HH-ZnI2 nanowires was further studied
to characterize the enzyme-like properties. By changing the
concentration of the pNPA substrate while keeping the catalyst
concentration constant (Figure 3d), the reactant adsorption
equilibrium constant (Kα) could be calculated as 0.232 mM, with a
maximum initial velocity (Vmax) of 1.32×10-3 mM s−1. Notably, the
calculated catalytic efficiency[22] (kcat/Kα, where kcat is the turnover
number) was 93.21 M−1 s−1. With the same absolute molarity (0.063
mM), the peptide building block cyclo-HH showed an approximately
6-fold reduced activity compared to cyclo-HH-ZnI2 nanowire,
revealing the fact that the differences in the microenvironment at the
catalytic rate is greatly affected by the size of the biocatalyst, which
was attributed to the increased catalytic surface area with abundant
catalytic active sites[10h, 23]. To assess the substrate specificity, cyclo-
HH-ZnI2 nanowires were mixed with various nitrophenyl esters
comprising different side-chain lengths, and the catalytic activity was
assayed (Figure S18). Cyclo-HH-ZnI2 nanowires showed excellent
catalytic activity towards two other ester substrates, namely 4-
nitrophenyl butyrate (pNPB) and 4-nitrophenyl valerate (pNPV). The
catalytic stability of the cyclo-HH-ZnI2 nanowire catalyst was also
assessed. As shown in Figure S19, when the ZnI2 nanowires were
stored in the air at room temperature for 30 days, the original catalytic
activity was still retained, and no significant decrease in the activity
was observed. Moreover, the cyclo-HH-ZnI2 nanowires could be
easily separated from the product compound for recycling purposes,
and retaining more than 80% of the initial activity even after five cycles
of use (Figure 3e). The decreased activity may be due to the
redispersion and agglomeration of the nanoparticles during washing
and centrifuging (Figure S20).
active sites of the Zn(II) coordination tetrahedron may account for the
10d, 10f]
major difference in catalytic activity[5b,
(Figure S17).
Furthermore, a control experiment using cyclo-HH-ZnI2 single crystal
as a catalyst showed that its activity was approximately 3-fold lower
than that of cyclo-HH-ZnI2 nanowires (Figure 3d), indicating the
Figure 3. The ester hydrolysis activity of cyclo-HH-ZnI2 nanowires. (a) Schematic illustration of ester hydrolysis catalyzed by cyclo-HH-ZnI2
nanowires. (b) Docked structure of p-nitrophenyl acetate (pNPA) bound to the cyclo-HH-ZnI2 slab based on the crystal structure. (c) Time-
dependent absorbance at 405 nm during pNPA hydrolysis in the presence of different doses of cyclo-HH-ZnI2 nanowires. The blank sample
represents a buffer-only control (PBS, pH=7.4). (d) Steady-state kinetic assay of pNPA hydrolysis reaction in the presence of cyclo-HH-ZnI2
nanowires, cyclo-HH-ZnI2 single crystal, and cyclo-HH and Zn(II). (e) Relative activity of cyclo-HH-ZnI2 nanowires in pNPA hydrolysis reaction
during recycling and reuse. (f) Catalytic reaction mechanism and the optimized structures along the reaction pathway. A cluster containing key
groups around the catalytic center is shown. Only the hydrogen atoms bonded to nitrogen or oxygen in the catalytic center are shown for clarity.
The zinc and iodide atoms are represented as gray and pink balls, respectively.
5
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Following the experimental characterization of the catalytic
esterase activity of the cyclo-HH-ZnI2 nanowires, we carried out first-
principle density functional theory calculations to study the catalytic
reaction path starting from a possible binding mode of pNPA to cyclo-
HH-ZnI2, as shown in Figure 3f. Particularly in this structure, the ester
group of pNPA was located near the active site, defined as a
coordinated Zn2+ ion with the neighboring groups: the Zn2+ ion was
bound to two imidazole rings of histidine residues and coordinated by
two iodine ions, as revealed by the X-ray structure. Then, one iodine
ion of the active site was replaced by a hydroxyl group, which was
expected to exert a nucleophilic attack of the ester bond in the
following reaction path, as we previously shown in a relevant
system[10e]. We added three water molecules around the hydroxyl
group in the model to stabilize the system. The chemical environment
around the active site was also reserved to mimic the restricted
environment of the reaction. The initial structure of complex1 was
based on the docking structure representing a possible binding mode
of pNPA towards the cyclo-HH-ZnI2 cluster. The reaction took place
in the chemically confined environment, and the steric hindrance
restricted the orientation of the substrate during the reaction pathway.
The subsequent bond formation between the carbon atom of the
carbonyl group of pNPA and the oxygen atom of the hydroxide ion
(bound to the Zn atom) led to an intermediate complex2. This
nucleophilic attack of the hydroxyl ligand occurred through the
transition state (TS1/2), where the carbonyl group's carbon atom was
close to the hydroxide ion's oxygen atom. Importantly, this was
calculated to be the rate-determining step along the reaction path,
with a Gibbs free energy barrier ΔG≠ = 12.1 kcal/mol. Consequently,
the C1-O5 bond cleaved through TS2/3 to convert the hydrolysis
products, an acetic acid moiety and a p-nitrophenoxide anion, as
shown in complex3. The conversion of complex 2 to 3 is exceedingly
exothermic, with ΔG0 = -12.2 kcal/mol. Finally, one proton transferred
from the acetic acid moiety to the p-nitrophenoxide anion through a
water molecule, as shown in TS3/4, leading to the single hydrolysis
product (pNP) (in complex 4). Furthermore, the proton transferred
from the distal imidazole moiety to the acetoxyl group, where the other
acetic acid product was formed, and the original complex was
restored[10e]. The release of the acetic acid molecule from the active
site and the subsequent binding of a new water molecule to the active
site re-initiated the entire process.
Conclusion
In summary, inspired by the structure of the active site of CAII,
we successfully constructed a simple cyclo-dipeptidyl supramolecular
nano-superstructure and implemented an effective hydrolysis
biocatalyst according to the concept of minimalistic de novo design.
Unlike natural enzymes composed of hundreds of amino acid
sequences, the newly-designed cyclo-HH-ZnI2 biocatalyst utilizes
only a cyclo-dipeptide as the single building block, and can be easily
synthesized using the environmentally friendly microwave-assisted
solid-phase peptide method. Through coordination with zinc ions, the
cyclo-HH self-assembly process can be well controlled to produce
zero-dimensional, homogeneous nanostructures, which can then be
used as basic units to form a higher-order nanoarchitecture. The
superstructure nano-assembly contains abundant catalytic active
sites and can provide a flexible transportation route for the diffusion of
reactants in the hydrolysis process. As a result, an effective hydrolytic
activity of 93.21 M−1 s−1 can be achieved.
Additionally, the cyclo-HH-ZnI2 biocatalyst is strikingly stable
under long storage and markedly reusable, which is of great
significance in the field of industrial "small molecule" chemical
conversion. Moreover, quantum mechanics calculations were used to
probe the catalytic effect, indicating that the reaction rate-determining
step is the nucleophilic attack process. Moreover, the steric hindrance
of the local environment of the cyclo-HH-ZnI2 biocatalyst restricts the
orientation of the substrate during the reaction, which is essential for
efficient hydrolysis. This simple supramolecular strategy provides an
attractive new alternative to state-of-the-art biocatalysts, and can be
further extended to fabricate other artificial biocatalysts toward robust
and efficient chemical transformations.
Acknowledgements
Y. Chen, Y.Q. Yang and A.A. Orr, contributed equally to this work. This work was supported in part by the European Research Council under
the European Union Horizon 2020 research and innovation program (No. 694426) (E.G.), Joint NSFC-ISF Grant (no. 3145/19) (E.G.), National
Natural Science Foundation of China (No. 21833002) (H.D.), and Natural Science Foundation of Jiangsu Province (No. BK20190056) (H.D.).
Y. Chen acknowledges the Center for Nanoscience and Nanotechnology at Tel Aviv University for financial support. A.A. Orr acknowledges
Texas A&M University Graduate Diversity Fellowship from the TAMU Office of Graduate and Professional Studies. MD simulations and
associated calculations were conducted using the Ada supercomputing cluster at the Texas A&M High Performance Research Computing
Facility, and additional computational resources available to P.T. at Texas A&M University. Parts of the calculations were performed using
computational resources on an IBM Blade cluster system from the High-Performance Computing Center (HPCC) of Nanjing University. The
authors thank Mariana Hildebrand, Leeor Kronik and the members of the Dong, Tamamis and Gazit laboratories for helpful discussions.
Competing Interests
The authors declare no competing interests.
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Keywords: biocatalysis • peptide • self-assembly • nano-superstructure • supramolecular chemistry
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Entry for the Table of Contents
The peptide nano-superstructure employs a cyclic dipeptide as a building block, is inspired by the coffee roasting process, and can be easily
synthesized. The self-assembled biocatalyst displays enzyme-like hydrolysis activity, with exceptional stability and recyclability. This catalytic
peptide assembly provides a potent complement for minimalistic biocatalysts and offers an attractive alternative to the current arsenal of natural
metalloenzymes.
7
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