[System] polypeptide self-assembly literature information extraction

[User]
Supramolecular self-assembly offers an efficient pathway for creating
macroscopically chiral structures in biology and materials science. Here, a new
peptide consisting of an N-(9-fluorenylmethoxycarbonyl) headgroup connected to
an aromatic phenylalanine-tryptophan dipeptide and terminated with zwitterionic
lysine (Fmoc-FWK) and its cationic form (Fmoc-FWK-NH2) were designed for
self-assembly into chiral structures. It was found that the Fmoc-FWK peptide
self-assembled into left-handed helical nanoribbons at pH 11.2-11.8, whereas it
formed nanofibers at pH 5 and 12 and large flat ribbons composed of many
nanofibers in the pH range of 6-11. However, only nanofibers were observed in
the cases of Fmoc-FWK-NH2 at different values. A series of structural
characterizations based on CD, FTIR, UV-vis and fluorescence spectroscopy reveal
that the electrostatic and aromatic interactions and the associated hydrogen
bonding direct the self-assembly into various structures. The enhanced π-π
stacking and hydrogen bonding were found in the helical nanoribbons. This
difference in intermolecular interactions should be derived from the ionization
of carboxyl and amino groups from lysine residues at different pH values.
Furthermore, we performed molecular dynamics simulations to gain insight into
the assembly mechanisms. The results imply that a relatively rigid molecular
conformation and the strong intramolecular aromatic interaction between Trp and
Fmoc groups favor chiral self-assembly. This study is the first attempt to
design a Fmoc-tripeptide for the fabrication of helical structures with
macroscopic chirality, which provides a successful example and allows us to
create new peptide-based chiral assembly systems.

Materials. N-(9-Fluorenylmethoxycarbonyl)-phenylalanine-trypto-
phan-lysine (Fmoc-Phe-Trp-Lys-OH, Fmoc-FWK, 98%), N-(9-ﬂuo-
renyl methoxycarbonyl)-phenylalanine-tryptophan-lysine-NH2 (Fmoc-
FWK-NH2, 98%), and phenylalanine-tryptophan-lysine (FWK, 98%)
were synthesized by GL Biochem Ltd. (China). All other chemicals
were of analytical grade and were obtained from commercial sources.
Preparation of Fmoc-FWK Helical Nanoribbons. In a typical
experiment, the lyophilized Fmoc-FWK peptide was dissolved in a
mixed solvent of acetonitrile−H2O (v/v = 1) at a concentration of 35
mg mL−1 at 60 °C. The resulting peptide solution was then diluted to
a ﬁnal concentration of 7 mg mL−1 in an aqueous solution at pH 11.5.
Within several seconds, a peptide hydrogel was formed and then aged
at room temperature for 1 day without disturbance to ensure complete
self-assembly. For Fmoc-FWK-NH2 peptides, the peptide assemblies
were obtained following the same procedure as described before. To
investigate the eﬀect of pH on self-assembly, aqueous solutions with
diﬀerent pH values ranging from 5 to 12 were used.
Compositional Analysis. The chemical compositions of
hydrogels formed at pH 7, 9, 10 and 11.5, respectively, were measured
by high-performance liquid chromatography (HPLC) and liquid
chromatography−mass spectrometry (LC−MS). Speciﬁcally,
formed hydrogels were directly freeze dried and then dissolved in
acetonitrile solvent. The concentrations of Fmoc-FWK and its
hydrolysate (FWK) were determined using an Agilent HPLC 1200
system (Agilent Technologies, USA) equipped with a UV−vis detector
operated at 220 nm on a Venusil MP-C18 column (5 μm, 4.6 mm ×
250 mm, Tianjin Bonna-Agela Technologies Ltd., China). The mobile
phase was composed of acetonitrile and water with increasing
acetonitrile content from 20 to 70% over 25 min at a total ﬂow rate
of 1 mL min−1. The pure Fmoc-FWK and FWK were used as
standards to produce the calibration curve for
the quantitative
calculation. Both chemicals were further conﬁrmed by LC−MS
analysis, which was performed on a Agilent 1200 HPLC system
coupled to an Agilent 6310 ion-trap mass spectrometer (Agilent
Technologies, USA) with an ESI source, operated in positive-ion
Rheological Measurement. Rheological measurements were
carried out using a Stress Tech rheological instrument (Rheological
Instruments AB CO., Sweden). The stock peptide solution (35 mg
mL−1) was poured onto the plate of the instrument, which was held at
25 °C by using an integrated temperature controller. Then, an aqueous
solution at pH 5, 7, or 11.5 was added immediately. The storage
modulus G′ and loss modulus G″ were measured as a function of time
at a constant frequency of 1 rad s−1. After 30 min, a frequency sweep
(0.1−50 Hz) test was conducted to measure the frequency-dependent
storage and loss shear moduli.
Morphological Characterization. The hydrogels were frozen at
−45 °C and subsequently dried under vacuum. All samples were
sputter-coated with platinum using an E1045 Pt-coater (Hitachi High-
technologies CO., Japan) and then imaged with an S-4800 ﬁeld
emission scanning electron microscope (SEM, Hitachi High-
technologies CO., Japan) at an acceleration voltage of 3 keV. The
morphology of the peptide assemblies was further assessed using a
JEOL 100CX-II transmission electron microscope (TEM, JEOL Ltd.,
Japan) operated at 80 keV. To prepare samples, the hydrogel was
dispersed in ddH2O, and a 10 μL aliquot of aqueous dispersion was
placed onto a 300 mesh carbon-coated copper grid, air dried, and then
negatively stained with 1 wt % phosphotungstic acid solution for 2 min
before imaging. The samples for atomic force microscopy (AFM)
measurement were prepared as follows: the hydrogel was dispersed in
ddH2O, and a 100 μL aliquot of the aqueous dispersion was spread on
a mica surface and air dried before observation. AFM images were
recorded using an Agilent 5500 atomic force microscope (Agilent,
USA) equipped with N9797 AU-1FP Pico software in tapping mode.
Structural Characterization. Circular dichroism (CD) analysis
was performed on a Jasco J-810 CD spectropolarimeter (Jasco Inc.,
Japan) over a wavelength range of 185−350 nm with a resolution of 1
nm. Spectra were recorded three times using a scanning speed of 100
nm min−1 with a bandwidth of 1 nm. Fourier transform infrared
spectroscopy (FTIR) spectra of xerogels were recorded on a Nicolet-
560 FTIR spectrometer (Nicolet Co., USA) with a KBr pellet method
across the range of 400−4000 cm−1. A total of 16 scans were
accumulated with a resolution of 4 cm−1 for each spectrum. UV−vis
spectra were monitored on a TU-1810 UV−vis spectrophotometer
(Persee Instruments Ltd., China) with a wavelength range of 200−700
nm. Fluorescence spectra were recorded on a Cary Eclipse
spectroﬂuorometer (Agilent CO., USA) with excitation at 280 nm.
All ﬂuorescence spectra were recorded at 25 °C. The excitation and
emission slit widths were ﬁxed at 5 and 5 nm, respectively.
Figure 1. (a) Molecular structure of the Fmoc-FWK peptide. (b) SEM, (c, d) AFM, and (e, f) TEM images of the Fmoc-FWK helical nanoribbons
formed at pH 11.5.
prepare the peptide solutions, 1 mg of Fmoc-FWK peptide was
dissolved in 1 mL of ddH2O. The pH of the resulting solution was
adjusted with 0.5 M NaOH or 0.1 M HCl. A pH meter was used to
measure the pH values of all of the solutions. For peptide assemblies,
the peptide hydrogel was synthesized as mentioned before and then
dispersed in ddH2O to a ﬁnal concentration of 0.07 mg mL−1.
pH Titration. Fmoc-FWK-OH or Fmoc-FWK-NH2 peptides were
dissolved in ddH2O at a concentration of 10 mmol L−1 at pH 2.5 by
adding 0.1 M HCl. The titration curves were recorded by monitoring
the pH values during the stepwise addition of small volumes of 0.5 M
NaOH. The samples were stirred to ensure complete mixing during
the titration process. No signiﬁcant diﬀerence (0.3 pH unit) was
observed between the two pH measurements. The pH measurements
were performed using a TitroLine Alpha Plus AutomaticTitrator
(Scott CO., Germany).
Molecular Dynamics Simulations. Hydrogen atoms of
Fmoc-tripeptide residues were added using Discovery Studio (version
2.5.5, Accelrys). The system was centered in a cubic box of TIP3P
water molecules, and a suﬃcient number of Na+ ions and HPO4
H2PO4− were added to neutralize the negative charges. A CHARMm
force ﬁeld was used to assign molecules, and classical molecular
dynamics (MD) simulations were performed using Discovery Studio
(version 2.5.5, Accelrys). The system energy was ﬁrst minimized by
performing 5000 steps using the steepest descent algorithm, followed
by an additional 2000 steps of minimization using the conjugate
gradient method. Then,
the system was heated to the target
temperature of 300 K for a period of 2 ps under constant-pressure
periodic boundary conditions (NPT). Subsequently, the system was
allowed to equilibrate for 1 ps at constant pressure and temperature
(NPT) with a time step of 1 fs, followed by 1 ns of production
simulation performed under the same conditions. A cutoﬀ of 14 Å was
used for nonbonded interactions, and long-range electrostatic
interactions were treated by means of
the particle mesh Ewald
(PME) method. The MD simulation results were further analyzed
using Discovery Studio software (version 2.5.5, Accelrys).

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"Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "50/50 Acetonitrile/H2O", "peptide_concentration(mg/ml)": "7.0", "PH": "8.0", "temperature(celsius)": "25.0", "heating_cooling": "Yes", "incubation_period(min)": "1440.0"}, {"peptide_sequence": "FWK", "self-assembly_phase": "ribbon", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "50/50 Acetonitrile/H2O", "peptide_concentration(mg/ml)": "7.0", "PH": "9.0", "temperature(celsius)": "25.0", "heating_cooling": "Yes", "incubation_period(min)": "1440.0"}, {"peptide_sequence": "FWK", "self-assembly_phase": "ribbon", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "50/50 Acetonitrile/H2O", "peptide_concentration(mg/ml)": "7.0", "PH": "10.0", "temperature(celsius)": "25.0", "heating_cooling": "Yes", "incubation_period(min)": "1440.0"}, {"peptide_sequence": "FWK", "self-assembly_phase": "ribbon", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "50/50 Acetonitrile/H2O", "peptide_concentration(mg/ml)": "7.0", "PH": "11.0", "temperature(celsius)": "25.0", "heating_cooling": "Yes", "incubation_period(min)": "1440.0"}, {"peptide_sequence": "FWK", "self-assembly_phase": "fiber", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "50/50 Acetonitrile/H2O", "peptide_concentration(mg/ml)": "7.0", "PH": "5.0", "temperature(celsius)": "25.0", "heating_cooling": "Yes", "incubation_period(min)": "1440.0"}, {"peptide_sequence": "FWK", "self-assembly_phase": "fiber", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "50/50 Acetonitrile/H2O", "peptide_concentration(mg/ml)": "7.0", "PH": "12.0", "temperature(celsius)": "25.0", "heating_cooling": "Yes", "incubation_period(min)": "1440.0"}, {"peptide_sequence": "FWK", "self-assembly_phase": "fiber", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Amidation", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "50/50 Acetonitrile/H2O", "peptide_concentration(mg/ml)": "7.0", "PH": "4.0", "temperature(celsius)": "25.0", "heating_cooling": "Yes", "incubation_period(min)": "1440.0"}, {"peptide_sequence": "FWK", "self-assembly_phase": "fiber", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Amidation", 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[System] polypeptide self-assembly literature information extraction

[User]
Copyright © 2013 Elsevier Inc. All rights reserved.

N terminal-protected L-style amino acids (Fmoc-L-Lys(Boc)-OH,
Fmoc-L-Phe-OH,
Fmoc-L-Tyr-OH, Rink amide MBHA resin,
N-hydroxybenzotriazole anhydrous(HOBt), N,N0-diisopropyl ethyl-
amine (DIEA), O-(1H-benzotriazole-1-yl)-N,N,N0,N0-tetramethyl-
uronium hexaﬂuorophosphate (HBTU), and triﬂuoroacetic acid
(TFA) were purchased from GL Biochem (Shanghai) Ltd and used
as received. Solvents such as dichloromethane (DCM), N,N-di-
methyl formamide (DMF) with purity of P99% were purchased
from BMJ Tech (Beijing) Ltd and used without further redistillation.
1,1,1,3,3,3-hexaﬂuoro-2-propanol (HFIP) was from Sigma Aldrich.
Water used was processed from a Millipore water puriﬁcation
system with a minimum resistivity of 18 MO cm.
were performed concurrently with the mixture of TFA, triisopro-
pylsilane, and H2O at the volume ratio of 95:2.5:2.5.
The cleavage mixture was ﬁltered into a round-bottomed ﬂask
and rotary evaporated to concentrated solution, which was subse-
quently dropped into ice-cold ethyl ether for precipitation. The
suspension was centrifuged for 5 min at 4 (cid:3)C with a speed of
8000–10,000 rpm. The bottom solid product was collected and
rinsed with abundant amount of ice-cold ether. Repeating the
ether washing and centrifuging until the pH of the supernatant
ﬂuid remained constant at pH 5–6. The ﬁnal products were lyoph-
ilized for 2 days and then subjected to mass spectrometry and high
performance liquid chromatography (HPLC) analyses (Supporting
information, Fig. S1), which revealed high purity (>95%) of the four
peptides.
The four peptides exhibited quite different solubilities due to
their different structural characteristics. FFK was quite hydropho-
bic and only partially soluble in water at ambient temperature.
For preparation of FFK solution, the mixture of water and HFIP
(9.5:0.5, v/v) was used to dissolve the peptide at 1.0 mg/mL with
sonication for 30 min. The less hydrophobic peptides FYK, YFK,
and YYK were well soluble in water, but were also dissolved in
the same ratio of water/HFIP mixture for consistency between pep-
tides, while the concentration was higher to be 5.0 mg/mL. The ﬁ-
nal solution pH was around 5–6 for each peptide due to presence of
adventitious TFA leaving from the deprotection process. The pep-
tide solutions were incubated for at least one week before charac-
terization for the systems to be well equilibrated.
TEM samples were prepared from the peptide solutions using a
negative staining method. A drop of the solution was ﬁrstly placed
onto a carbon Formvar-coated copper grid. After 8–10 min, excess
ﬂuid was removed, and the grid was negatively stained with 2% (w/v)
uranyl acetate solution. The samples were then viewed using JEOL
JEM-2100UHR electron microscope operated at 200 kV.
A Nicolet 6700 FT-IR spectrometer equipped with a deuterated
triglycine sulfate (DTGS) detector was used for infrared measure-
ments. For recording the infrared spectra of the peptides in solu-
tion, the ATR-FTIR was performed on an ARK HATR accessory
equipped (Thermal Electron) with a ZnSe crystal and a trough sam-
pling plate. The peptide solutions (dissolved in D2O) were pipetted
onto the ZnSe crystal plate, spreading evenly across the surface.
Then, the spectra were recorded at room temperature by averaging
of 256 scans with resolution of 4 cm(cid:3)1. Reference spectrum was re-
corded with a 5% (volume fraction) HFIP solution in D2O and sub-
tracted from the sample spectra.
The ﬂuorescence measurements were conducted using a Fluoro
Max-P spectrophotometer (JOBIN YVON) at room temperature. For
measuring the intrinsic ﬂuorescence spectra of each peptide, the
solution was excited at 257 nm, and the emission spectra were re-
corded from 260 nm to 500 nm. Fluorescence probe technique was
used to determine the critical aggregation concentration (CAC) of
each peptide from measurement of the pyrene polarity index
I1/I3. I1/I3 is the ratio between the ﬂuorescence intensities of peaks
I and III of pyrene emission spectrum. A quartz cuvette with path-
length of 0.5 cm was used. Pyrene was excited at 335 nm, and the
emission spectra were scanned from 350 to 500 nm. For ThT ﬂuo-
rescence measurements, the emission spectra were recorded by
setting excitation at 442 nm, with the excitation and emission slits
at 5.0 and 2.0 nm, respectively.

[Assistant] [{"peptide_sequence": "FFK", "self-assembly_phase": "tube", "N-terminal_modification": "Acetylation", "C-terminal_modification": "Amidation", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "5/95 HFP/H2O", "peptide_concentration(mg/ml)": "1.0", "PH": "5.5", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "20160.0"}, {"peptide_sequence": "FYK", "self-assembly_phase": "fiber", "N-terminal_modification": "Acetylation", "C-terminal_modification": "Amidation", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "5/95 HFP/H2O", "peptide_concentration(mg/ml)": "5.0", "PH": "5.5", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "20160.0"}, {"peptide_sequence": "YFK", "self-assembly_phase": "fiber", "N-terminal_modification": "Acetylation", "C-terminal_modification": "Amidation", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "5/95 HFP/H2O", "peptide_concentration(mg/ml)": "5.0", "PH": "5.5", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "20160.0"}]


[System] polypeptide self-assembly literature information extraction

[User]
Hydrogels formed by ultrashort peptides are emerging as cost-effective materials
for cell culture. However, L-peptides are labile to proteases, while their
D-isomers are thought to not support cell growth as well. In contrast, the
self-assembly behaviour and biological performance of heterochiral peptides
(i.e., made of both d and l amino acids) are largely unknown. In this study, we
evaluate the effects of amino acid chirality on tripeptide self-assembly and
hydrogelation at physiological pH, and cytocompatibility in fibroblast cell
culture. A series of uncapped hydrophobic tripeptides with all combinations of
d, l amino acids was prepared, tested for self-assembly under physiological
conditions, and analysed by circular dichroism, FT-IR, cryo-TEM, AFM, and
Thioflavin T fluorescence imaging. Amino acid chirality has a profound effect on
the peptides' supramolecular behaviour. Only selected isomers form hydrogels,
and of amyloid structure, as confirmed by rheology and XRD. Importantly, they
are able to maintain the viability and proliferation of fibroblasts in vitro.
This study identifies two heterochiral gels that perform well in cell culture
and will assist in the design of innovative and cost-effective peptide gel
biomaterials.

onto the grid. Aer 30 seconds adsorption time the grid was
blotted manually using a Whatman 541 lter paper,
approximately 6–10 seconds. The blotting time was optimised
for each sample. The grid was then plunged into liquid ethane
cooled by liquid nitrogen. Frozen grids were stored in liquid
nitrogen until required. The samples were examined using a
Gatan 626 cryoholder (Gatan, Pleasanton, CA, USA) and Tecnai
12 TEM (FEI, Eindhoven, The Netherlands) at an operating
voltage of 120 kV. At all times low dose procedures were fol-
lowed, using an electron dose of 8–10 electrons ˚A
(cid:3)2 for all
imaging. Images were recorded using either a Megaview III CCD
camera and AnalySIS camera control soware (Olympus.) using
magnications in the range 40 000(cid:4) to 110 000(cid:4), or a FEI Eagle
4k (cid:4) 4k CCD camera (FEI, Eindhoven, The Netherlands) at
magnications in the range 15 000–30 000(cid:4).
The secondary structure of peptides was analysed using a 0.1 cm
quartz cell on a Jasco J815 Spectropolarimeter, with 1 s inte-
grations and a step size of 1 nm with a bandwidth of 1 nm over a
range of wavelengths from 200 to 280 nm. Peptide samples were
freshly prepared by mixing the two precursor solutions directly
in the CD cell, thus, without the second round of sonication, to
preserve the quartz cell. Spectra were recorded aer 15 min.
Measurements were repeated at least 5 times, and to reduce the
noise near 200 nm, their average is plotted.
FT-IR spectra were collected on a Nicolet 6700 FT-IR spec-
trometer in ATR mode. A portion of the gel was transferred onto
a clean piece of silicon wafer (1 cm (cid:4) 1 cm), then gently spread
over the surface by pressing a coverslip on top; the coverslip was
immediately removed and samples were dried under vacuum
for 24 h. Dried samples on the silicon wafers were placed
directly onto the ATR crystal. Scans were between 1800 and 1500
Dynamic time sweep rheological analysis was conducted on an
Ares rheometer
(TA Instruments, USA) with a 25 mm
aluminium parallel plate geometry. A Peltier temperature
controller was connected to the rheometer to maintain a
temperature of 25 (cid:5)C. Peptide samples were freshly prepared by
mixing the two precursor solutions directly on the rheometer to
register early stages of gelation, thus without the second round
of sonication. Samples were immediately analysed with a gap of
(cid:3)1. Aer 60
300 mm, a strain of 0.3% and a frequency of 10 rad s
minutes of gelation, strain sweeps were recorded with a
(cid:3)1 and frequency sweeps with a strain of
frequency of 10 rad s
0.3%. Data acquisition was repeated in triplicate, and average
values were plotted.
Gel precursor solutions were prepared as indicated above and
12.5 ml of each were immediately placed on wells of a “m-Slide
Angiogenesis” uncoated (Ibidi, Germany, through DKSH Aus-
tralia). 25 ml of a solution of ThT (200 mM in 50 mM glycine–
NaOH pH 7.5, 0.2 mm ltered) were placed on top. Aer 15
minutes, the slides were imaged on a Leica SP5 microscope
(63(cid:4) water immersion objective, NA 1.2, ex. 458 nm, em. 468–
600 nm). Samples treated and stained with an identical protocol
but without the peptide were used as a control and did not
reveal any of the uorescent structures described in the text
(data not shown).
X-ray ber diﬀraction (XRD)
A Bruker D8 Advance X-ray Diﬀractometer with CuKa radiation
(40 kV, 40 mA) equipped with a LynxEye silicon strip detector
was employed to determine the X-ray diﬀraction (XRD) patterns.
Each sample was scanned over the 2-theta range from 1(cid:5) to 60(cid:5)
with a step size of 0.02(cid:5) and a count time of 1.6 seconds per step.
An air scatter slit was used to reduce the beam intensity at low
angles. Analyses were performed on the collected XRD data for
each sample using the Bruker XRD search match program
EVA™. Samples were mounted on zero background plates
consisting of a silicon wafer located in a standard Bruker
specimen holder, and were dried overnight in air.
Tripeptides in solution were assessed for cytotoxicity in accor-
dance with ISO 10993, and tripeptide gels were also probed for
their ability to support cell viability and proliferation. For
cytotoxicity studies, L929 mouse broblast cells were seeded at
10 000 cells per well of a 96-well tissue culture plate in 100 ml of
media (MEM + GlutaMAX™-I (GIBCO)), supplemented with 1
vol% NEAA (non-essential amino acids, GIBCO), 2 vol% Anti–
Anti (Antimycotic–Antibiotic, GIBCO), and 10 vol% FBS (fetal
bovine serum, SAFC Biosciences) and cultured at 37 (cid:5)C, 5% CO2
overnight. Tripeptides were dissolved in the media at the
highest concentration possible without occurrence of precipi-
(cid:3)1) and 1 : 1 serial dilutions
tation or gelation (i.e., 1 mg ml
(cid:3)1 were prepared. The tripeptide solutions
down to <8 mg ml
were sterile-ltered and 100 ml were applied to monolayers that
were then cultured for a further 24 hours. Cells were imaged on
an inverted microscope (Olympus IX71) before quantitation by
reduction of resazurin (120 ml of a 1 : 9 solution of PrestoBlue®
in media for 1.5 hours) and 100 ml assayed for uorescence on a
Pherastar uorometer (ex. 540–20 nm, em. 590–20 nm). Media
without tripeptide as a negative control, and 5 vol% dime-
thylsulphoxide (DMSO) in media as a positive control, were
included. Monolayers remained subconuent throughout. For
gel studies, gel precursor solutions were prepared as indicated
previously and 15 ml of each were mixed directly in triplicate
wells of a “m-Slide Angiogenesis” uncoated (Ibidi, Germany,
through DKSH Australia), thus without the second round of
sonication. Aer 24 h, gels were pre-treated with 30 ml of media
for 1 h. L929s were added to the gels (10 000 cells per cm2 in 30
ml media), and cultured at 37 (cid:5)C, 5% CO2 for up to 72 h, by
handling the slides according to the manufacturers' instruc-
tions, including the addition of a few drops of deionised water
in the empty space between the wells to minimise sample

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[System] polypeptide self-assembly literature information extraction

[User]
Hydrogels are of great interest as a class of materials for tissue engineering,
axonal regeneration, and controlled drug delivery, as they offer 3D interwoven
scaffolds to support the growth of cells. Herein, we extend the family of the
aromatic Fmoc-dipeptides with a library of new Fmoc-peptides, which include
natural and synthetic amino acids with an aromatic nature. We describe the
self-assembly of these Fmoc-peptides into various structures and characterize
their distinctive molecular and physical properties. Moreover, we describe the
fabrication of the bioactive RGD sequence into a hydrogel. This unique material
offers new opportunities for developing cell-adhesive biomedical hydrogel
scaffolds, as well as for establishing strategies to modify surfaces with
bioactive materials.

Hydrogels and Solution Preparation. Lyophilized Fmoc-FF, Fmoc-
(cid:1)-(2-naphthyl)-L-alanine (Fmoc-2-Nal), Fmoc-phenylalanine-proline
(Fmoc-FP), Fmoc-phenylalanine-serine(tBu) (Fmoc-FS(tBu)), Fmoc-
phenylalanine-glycine (Fmoc-FG), Fmoc-glycine-phenylalanine (Fmoc-
GF) (Bachem, Bubendorf, Switzerland), Fmoc-arginine-glycine-aspartic
acid (Fmoc-RGD), Fmoc-phenylalanine-arginine-glycine-aspartic acid
(Fmoc-FRGD), and Fmoc-arginine-glycine-aspartic acid-phenylalanine
(Fmoc-RGDF) (Peptron, Daejeon, South Korea) were dissolved in
dimethyl sulfoxide (DMSO) at concentrations of 100 or 25 mg mL-1.
The hydrogels were prepared by diluting the stock solution in ultra
pure water (Biological Industries, Beit Haemeck, Israel) at a ﬁnal
peptide concentration of 5 mg mL-1. Different hydrogel concentrations
were prepared by using different peptide-solution-to-water ratios. To
avoid any preaggregation and premature assembly, the stock solutions
were prepared fresh for each experiment.
Congo Red Staining and Birefringence. A 20 µL aliquot was
allowed to dry on a glass microscope slide. Staining was performed
by the addition of a solution of 80% ethanol saturated with congo red
and NaCl. Birefrigence was determined with a SZX-12 Stereoscope
(Olympus, Hamburg, Germany) equipped with a polarizing stage.
Rheological Analysis. The in situ hydrogel formation, mechanical
properties, and cross-linking kinetics were characterized by an AR-G2
rheometer (TA Instruments). Time-sweep oscillatory tests in parallel-
plate geometry were performed on 210 µL of fresh solution (resulting
in a gap size of 0.6 mm), 1 min after its preparation, at room
temperature. Each Fmoc-peptide was tested six times and their average
is shown. Oscillatory strain (0.01-100%) and frequency sweeps
(0.01-100 Hz) were conducted to ﬁnd the linear viscoelastic region,
wherein the time sweep oscillatory tests were performed.
Fourier Transform Infrared (FTIR) Spectroscopy. FTIR spectra
were collected using a Nicolet Nexus 470 FTIR spectrometer with a
DTGS (deuterated triglycine sulfate) detector. Hydrogel samples were
formed directly on a CaF2 plate, resuspended with D2O, and vacuum-
dried. Measurements were taken using a 4 cm-1 resolution and by
averaging 2000 scans. The absorbance maxima values were determined
using an OMNIC analysis program (Nicolet). The obtained absorption
spectra were smoothed by applying the Savitzky-Golay function to
eliminate noise and operating the second derivative transformation on
the spectra using the Peakﬁt software version 4.12 (SYSTAT Software
Inc., Richmond, CA).
Transmission Electron Microscopy (TEM) Analysis. A total of
100 µL of hydrogel was prepared and a part of it was placed on a
400-mesh copper grid. After 1 min, the piece of gel and excess ﬂuid
were removed. Negative staining was obtained by covering the grid
with 10 µL of 2% uranyl acetate in water. After 2 min, excess uranyl
acetate solution was removed. Samples were viewed using a JEOL
1200EX TEM operating at 80 kV.
Scanning Electron Microscopy (SEM) Analysis. A piece of freshly
formed gel was placed on a microscope glass coverslip, dried at room
temperature, and then spattered with gold. Images were obtained with
a JSM JEOL 6300 SEM operating at 5.0 kV.
Atomic Force Microscopy (AFM) Analysis. For AFM analysis,
an aliquot of low concentration hydrogel was deposited on freshly
cleaved mica surface. The samples were probed by a Digital Instrument
(DI) MultiModeTM NanoScope IV AFM, using Mikromasch NSC15/
Si3N4 cantilever (resonant frequency f ) 325 kHz, spring constant k
) 40 N/m) in a tapping mode.
Viability Analysis. For cell growth in vitro experiments, Chinese
hamster ovary (CHO) cells were grown in Dulbecco’s Modiﬁed Eagle
Medium (DMEM) supplemented with 10% fetal calf serum, 100 U
mL-1 penicillin, 100 U mL-1 streptomycin, and 2 mmol L-1 L-glutamine
(all from Beit Haemeck, Israel). Cells were maintained at 37 °C in a
humidiﬁed atmosphere containing 5% CO2. Subconﬂuent cells were
harvested by trypsinization, counted, and diluted in the culture medium
to 2 × 105 cells mL-1. The hydrogels were swelled overnight with 0.1
mL DMEM. The next day, DMEM was removed and 100 µL of the
Figure 1. (a) Molecular structure of the nine Fmoc-peptides. (b) A
macroscopic image of the hydrogels: (1) Fmoc-FRGD; (2) Fmoc-
RGDF; (3) Fmoc-2-Nal; (4) Fmoc-FG; (5) Fmoc-FF.
CHO cells (2 × 104 cells) were placed overtop the hydrogel. After a
24 h incubation period at 37 °C, the viability of the cells was determined
using a 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide
(MTT) assay.41

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"solution": "5/95 DMSO/H2O", "peptide_concentration(mg/ml)": "5.0", "PH": "8.4", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FF", "self-assembly_phase": "hydrogel", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "5/95 DMSO/H2O", "peptide_concentration(mg/ml)": "5.0", "PH": "10.2", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FF", "self-assembly_phase": "hydrogel", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "5/95 DMSO/H2O", "peptide_concentration(mg/ml)": "5.0", "PH": "12.0", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FP", "self-assembly_phase": "none", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "20/80 DMSO/H2O", "peptide_concentration(mg/ml)": "5.0", "PH": "3.0", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FP", "self-assembly_phase": "none", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "20/80 DMSO/H2O", "peptide_concentration(mg/ml)": "5.0", "PH": "4.8", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FP", "self-assembly_phase": "none", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "20/80 DMSO/H2O", "peptide_concentration(mg/ml)": "5.0", "PH": "6.6", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FP", "self-assembly_phase": "none", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "20/80 DMSO/H2O", "peptide_concentration(mg/ml)": "5.0", "PH": "8.4", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FP", "self-assembly_phase": "none", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "20/80 DMSO/H2O", "peptide_concentration(mg/ml)": "5.0", "PH": "10.2", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FP", "self-assembly_phase": "none", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "20/80 DMSO/H2O", "peptide_concentration(mg/ml)": "5.0", "PH": "12.0", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FP", "self-assembly_phase": "none", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "5/95 DMSO/H2O", "peptide_concentration(mg/ml)": "5.0", "PH": "3.0", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FP", "self-assembly_phase": "none", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "5/95 DMSO/H2O", "peptide_concentration(mg/ml)": "5.0", "PH": "4.8", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FP", "self-assembly_phase": "none", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "5/95 DMSO/H2O", "peptide_concentration(mg/ml)": "5.0", "PH": "6.6", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FP", "self-assembly_phase": "none", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "5/95 DMSO/H2O", "peptide_concentration(mg/ml)": "5.0", "PH": "8.4", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FP", "self-assembly_phase": "none", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "5/95 DMSO/H2O", "peptide_concentration(mg/ml)": "5.0", "PH": "10.2", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FP", "self-assembly_phase": "none", "N-terminal_modification": "Fmoc", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "5/95 DMSO/H2O", "peptide_concentration(mg/ml)": "5.0", "PH": "12.0", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "nan"}]


[System] polypeptide self-assembly literature information extraction

[User]
Change of chirality is a useful tool to manipulate the aqueous self-assembly
behaviour of uncapped, hydrophobic tripeptides. In contrast with other short
peptides, these tripeptides form hydrogels at a physiological pH without the aid
of organic solvents or end-capping groups (e.g. Fmoc). The novel hydrogel
forming peptide (D)Leu-Phe-Phe ((D)LFF) and its epimer Leu-Phe-Phe (LFF)
exemplify dramatic supramolecular effects induced by subtle changes to
stereochemistry. Only the d-amino acid-containing peptide instantly forms a
hydrogel in aqueous solution following a pH switch, generating long fibres (>100
μm) that entangle into a 3D network. However, unexpected nanostructures are
observed for both peptides and they are particularly heterogeneous for LFF.
Structural analyses using CD, FT-IR and fluorescent amyloid staining reveal
anti-parallel beta-sheets for both peptides. XRD analysis also identifies key
distances consistent with beta-sheet formation in both peptides, but suggests
additional high molecular order and extended molecular length for (D)LFF only.
Molecular modelling of the two peptides highlights the key interactions
responsible for self-assembly; in particular, rapid self-assembly of (D)LFF is
promoted by a phenylalanine zipper, which is not possible because of steric
factors for LFF. In conclusion, this study elucidates for the first time the
molecular basis for how chirality can dramatically influence supramolecular
organisation in very short peptide sequences.

Phe-Wang resin, O-benzotriazole-N,N,N,N0-tetramethyl-uro-
nium-hexaﬂuoro-phosphate (HBTU), and Fmoc protected L-
leucine were purchased from GL Biochem Ltd. Fmoc-protected
D-leucine was purchased from Mimotopes. All
purchased were of analytical grade from Merck. Piperidine, tri-
ﬂuoroacetic acid (TFA), diisopropyl ethyl amine (DIPEA), trii-
sopropyl silane (TIPS) were from Acros. Sodium dihydrogen
phosphate and disodium hydrogen phosphate were from BDH
AnalaR. High purity Milli-Q-water (MQ water) with a resistivity
greater than 18 MU cm was obtained from an in-line Millipore
RiOs/Origin system. Silicon wafers (M.M.R.C Pty Ltd.) were
cleaned by ultrasonication (1 h) in a surfactant solution of 2%
ethanol with 2% RBS 35 (Pierce) followed by rinsing with
copious amounts of MQ water and dried with nitrogen, then
cleaned for 1 h in a UV/ozone Procleaner(cid:2) (Bioforce Nano-
sciences). 1H-NMR spectra were recorded at 400 MHz, and 13C-
NMR spectra were recorded at 100 MHz on a Bruker Instrument
Biospin Av400H. Chemical shifts are reported in ppm relative to
TMS. Low resolution ESI-MS spectra were acquired with a
Shimadzu LCMS-2010EV mass spectrometer using a cone
voltage of 50 V and the source was maintained at 80 (cid:4)C. The
solvent used was methanol containing 0.1% formic acid with a
ﬂow rate of 0.1 ml min(cid:3)1.
The secondary structure of the peptides was analysed using a
0.1 cm quartz cell on a Jasco J815 Spectropolarimeter, with 1s
integrations, 1 accumulation and a step size of 1 nm with a band
width of 1 nm over a range of wavelengths from 200 to 280 nm.
Peptide samples freshly prepared in buffer A were diluted with
buffer B directly in the CD cell, and the spectra were recorded
after 15 min. Measurements were repeated at least 5 times, and to
reduce the noise near 200 nm, their average was plotted.
FT-IR spectra were collected on a Nicolet 6700 FT-IR spec-
trometer in ATR mode. Freshly prepared sonicated peptide
samples were analysed. Alternatively, they were left to settle and
gel for 24 h in a glass vial. As no signiﬁcant difference was seen in
the signal identity between the two time points, spectra at 24 h
are reported. A portion of the gel was then transferred on a clean
piece of silicon wafer (1 cm (cid:5) 1 cm), then gently spread by
pressing a coverslip on top, and dried under vacuum for 24 h.
Dried samples on the silicon wafers were placed directly to the
ATR crystal, facing down. Scans were between 1800 and
1500 cm(cid:3)1 with 80 accumulations at a resolution of 4 cm(cid:3)1.
Both peptides were synthesised using standard Fmoc solid phase
peptide synthesis with HBTU activation, following the same
procedure described previously.26 Crude peptides were too
hydrophobic to be precipitated in cold ether, thus the majority of
TFA was evaporated under nitrogen ﬂow, and the remaining oil
was redissolved in a mixture of acetonitrile–water, and then
Dynamic time sweep rheological analysis was conducted on an
(TA Instruments, USA) with a 25 mm
aluminium parallel plate geometry. A Peltier temperature
controller was connected to the rheometer to maintain a
temperature of 25 (cid:4)C. Freshly prepared and sonicated peptide
sample solutions were either immediately analysed, or left to
settle for 24 h. A gap of 300 mm was set. Strain sweeps were
Gel precursor solutions were prepared as indicated above and
25 ml were immediately placed on wells of a ‘‘m-Slide Angiogen-
esis’’ uncoated (Ibidi, Germany, through DKSH Australia). 25 ml
of a solution of Thioﬂavin T (200 mM in 50 mM glycine–NaOH
pH 7.5, 0.2 mm ﬁltered) were placed on top. After 15 minutes, the
slides were imaged on a Leica SP5 microscope (63(cid:5) water
immersion objective, NA 1.2, excitation 458 nm, emission 468–
600 nm). Alternatively, gels prepared in glass vials as described
above were left to settle, and at later time points (24 h, or up to 7
days) were transferred onto the slides, stained and imaged as
described above. Samples treated and stained with an identical
protocol but without the peptide, were used as control and did
not reveal any of the ﬂuorescent structures described in the text
(data not shown).
An Asylum Research MFP-3D atomic force microscope (Santa
Barbara, CA, USA) was used to measure surface topography in
tapping mode with ultrasharp silicon nitride tips (NSC15 non-
contact silicon cantilevers, MikroMasch, Spain). The tips used in
this study had a typical force constant of 40 N m(cid:3)1 and a reso-
nant frequency of 320 kHz. Typical scan settings involved the use
of an applied piezo deﬂection voltage of 0.6–0.7 V at a scan rate
of 0.7 Hz. All images were processed (1st order ﬂattening algo-
rithm) and linescans were generated using Igor Pro software.
Freshly prepared and sonicated peptide samples were spread
onto a clean square of silicon wafer (1 cm (cid:5) 1 cm) by gently
pressing a glass coverslip on top. Samples were then dried in a
vacuum oven at room temperature for 24 h. Alternatively, freshly
prepared peptide samples were left to settle and gel for 24 h, or up
to 3 days, after which a small part of the gel was transferred onto
a clean square piece of silicon wafer and dried as described
A laboratory-built humidity-controlled vitriﬁcation system was
used to prepare the hydrogels for imaging in a thin layer of
vitriﬁed ice using cryo-TEM. Humidity was kept close to 80% for
all experiments, and the ambient temperature was 22 (cid:4)C. 200-
mesh copper grids coated with a perforated carbon ﬁlm (Lacey
carbon ﬁlm: ProSciTech, Qld, Australia) were used for all
experiments. Grids were glow discharged in nitrogen for 5
seconds immediately before use. Hydrogels were prepared as
described above with or without sonication, showing no signiﬁ-
cant difference in their structure. They were either analysed
immediately after preparation, or at different time points (after
24 h, or up to 3 days). At the time of analysis, the hydrogels were
disrupted by tapping against the glass vial, and samples were
agitated with the pipette tip in order to liquefy them if possible.
Approximately 4 ml aliquots of sample were pipetted onto each
grid prior to plunging. In the case of samples which could not be
liqueﬁed adequately, the gel was smeared gently onto the grid.
After 30 seconds adsorption time the grid was blotted manually
using Whatman 541 ﬁlter paper, for approximately 6–10 seconds.
Blotting time was optimised for each sample. The grid was then
plunged into liquid ethane cooled by liquid nitrogen. Frozen
grids were stored in liquid nitrogen until required. The samples
were examined using a Gatan 626 cryoholder (Gatan, Pleas-
anton, CA, USA) and a Tecnai 12 Transmission Electron
Microscope (FEI, Eindhoven, The Netherlands) at an operating
voltage of 120 kV. At all times low dose procedures were fol-
lowed, using an electron dose of 8–10 electrons per (cid:1)A2 for all
imaging. Images were recorded using a Megaview III CCD
camera and AnalySIS camera control software (Olympus) using
magniﬁcations in the range 40 000(cid:5) to 110 000(cid:5).
Carbon-coated 300-mesh copper grids were glow-discharged in
nitrogen to render the carbon ﬁlm hydrophilic. A 4 ml aliquot of
the sample was pipetted onto each grid. After 30 seconds
adsorption time the excess was drawn off using Whatman 541
ﬁlter paper, followed by staining with 2% aqueous potassium
phosphotungstate at pH 7.2, for 10 seconds. Grids were air-dried
until needed. Samples were examined using a Tecnai 12 Trans-
mission Electron Microscope (FEI, Eindhoven, The Nether-
lands) at an operating voltage of 120 kV. Images were recorded
using a Megaview III CCD camera and AnalySIS camera control
software (Olympus). Each grid was systematically examined and
imaged to reﬂect a representative view of the sample. This was
important as samples of this type can be very non-homogeneous
on the grid; they tend not to disperse evenly and the structures
occur in distinct patches.
A Bruker D8 Advance X-ray Diffractometer with CuKa radia-
tion (40 kV, 40 mA) equipped with a LynxEye silicon strip
detector was employed to determine the X-ray diffraction (XRD)
patterns. Each sample was scanned over the 2-theta range from
1(cid:4) to 60(cid:4) with a step size of 0.02(cid:4) and a count time of 1.6 seconds
per step. An air scatter slit was used to reduce the beam intensity
at low angles. Analyses were performed on the collected XRD
data for each sample using the Bruker XRD search match
program EVA(cid:2). The samples were mounted on zero back-
ground plates consisting of a silicon wafer located in a standard
Bruker specimen holder, and were dried in air prior to analysis.
Tripeptide structures were constructed in SybylX1.1 and model
structures minimised using the AMBER force ﬁeld, Kollman all
atom charges, and implicit water (dielectric constant of 80). The
minimisations were carried out by aligning copies of the tripep-
tides in an anti-parallel alignment with the distances between
backbone amides being set to the optimum hydrogen bonding
distance (2.7 (cid:1)A). Steric clashes between the terminal Phe and Leu
moieties were relieved by rotating the Phe rings away from the
Leu (L-isomer) or leaving them in an extended conformation (D-
isomer) with the backbones being set to a beta-sheet conforma-
tion. The centre Phe rings were aligned parallel to each other to
maximise any p–p stacking interactions. The structures gener-
ated this way were then subjected to energy minimisation also

[Assistant] [{"peptide_sequence": "LFF", "self-assembly_phase": "nanosphere", "N-terminal_modification": "Free", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "100 PBS", "peptide_concentration(mg/ml)": "10.0", "PH": "7.4", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "5.0"}, {"peptide_sequence": "lFF", "self-assembly_phase": "hydrogel", "N-terminal_modification": "Free", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "100 PBS", "peptide_concentration(mg/ml)": "10.0", "PH": "7.4", "temperature(celsius)": "25.0", "heating_cooling": "No", "incubation_period(min)": "5.0"}]


[System] polypeptide self-assembly literature information extraction

[User]
DOI: 10.1038/s41467-018-05568-9
PMCID: PMC6089888
PMID: 30104564 [Indexed for MEDLINE]

Accumulating studies demonstrate that aromatic linear-
dipeptides, with the representative model of diphenylalanine
(FF)11, can self-assemble into nanostructures with remarkable
physiochemical features12,13, such as optic14,15, electrical16, fer-
roelectric17 (including piezoelectric18 and pyroelectric19) prop-
erties20–23. Especially,
the supramolecular morphologies and
properties can be easily modiﬁed by amino acids substitutions24,
covalent conjugation25 or co-assembly with external moieties26,27.
For example, upon substitution of one F with tryptophan (W),
self-assembling FW nanostructures present a smaller bandgap of
2.25 eV, compared to 3.25 eV of FF nanotubes28, thus showing
improved conductive29
and photoluminescent properties24.
Moreover, recent studies revealed that cyclo-dipeptides with
backbones of 2,5-diketopiperazine conﬁgurations, derived from
dehydration condensation of linear dipeptides16,30, self-assemble
into photoluminescent nanostructures different from their linear
counterparts31,32.

[Assistant] [{"peptide_sequence": "FW", "self-assembly_phase": "fiber", "N-terminal_modification": "Free", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "100 Methanol", "peptide_concentration(mg/ml)": "1.665", "PH": "7.0", "temperature(celsius)": "70.0", "heating_cooling": "No", "incubation_period(min)": "5.0"}, {"peptide_sequence": "WW", "self-assembly_phase": "nanosphere", "N-terminal_modification": "Free", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "100 Methanol", "peptide_concentration(mg/ml)": "1.855", "PH": "7.0", "temperature(celsius)": "70.0", "heating_cooling": "No", "incubation_period(min)": "5.0"}, {"peptide_sequence": "YY", "self-assembly_phase": "tube", "N-terminal_modification": "Free", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "100 DMSO", "peptide_concentration(mg/ml)": "1.632", "PH": "7.0", "temperature(celsius)": "70.0", "heating_cooling": "No", "incubation_period(min)": "5.0"}, {"peptide_sequence": "FF", "self-assembly_phase": "nanosphere", "N-terminal_modification": "Free", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "100 DMSO", "peptide_concentration(mg/ml)": "1.472", "PH": "7.0", "temperature(celsius)": "70.0", "heating_cooling": "No", "incubation_period(min)": "5.0"}, {"peptide_sequence": "HH", "self-assembly_phase": "fiber", "N-terminal_modification": "Free", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "100 Methanol", "peptide_concentration(mg/ml)": "1.372", "PH": "7.0", "temperature(celsius)": "70.0", "heating_cooling": "No", "incubation_period(min)": "5.0"}]