[System] polypeptide self-assembly literature information extraction

[User]
The self-assembly of peptides into ordered supramolecular structures, such as
fibrils and crystals, is of relevance in such diverse areas as molecular
medicine and materials science. However, little information is available about
the fundamental thermodynamic driving forces of these types of self-assembly
processes. Here, we investigate in detail the thermodynamics of assembly of
diphenylalanine (FF). This dipeptide forms the central motif of the Aβ peptides,
which are associated with Alzheimer's disease through their presence in amyloid
plaques in the nervous systems of affected individuals. We identify the
molecular origins of the self-assembly of FF in aqueous solution, and we
evaluate these findings in the context of the aggregation free energies of
longer peptides that are able to form amyloid fibrils. We find that the
thermodynamics of FF assembly displays the typical characteristics of
hydrophobic desolvation processes, and detailed analysis of the temperature
dependence of the kinetics of assembly within the framework of crystallization
theories reveals that the transition state from solution to crystalline
aggregates is enthalpically unfavorable and entropically favorable,
qualitatively similar to what has been found for longer sequences. This
quantitative comparison of aggregating peptides of very different lengths is the
basis of an in-depth understanding of the relationship between sequence and
assembly behavior.

Reagents and Solutions. Solutions of FF were prepared by the
suspension of diphenylalanine (Bachem, Basel, Switzerland) in
distilled water (18.2 Ω/m) followed by ultrasonication in a sonic
bath until the suspension was homogeneous and heating to 80−100
°C. Following 30 min at ∼100 °C, no visible aggregates were
observable for concentrations up to and including 4.5 g/L (14.5 mM).
Seed solutions
for growth experiments were prepared by the
sonication (via ultrasonic bath) at room temperature of 2 g/L water
solutions that had been allowed to aggregate and left standing for at
least 1 day.
FF was used as received without further puriﬁcation, while the
sample of GF as obtained required further puriﬁcation. A solution of
crude GF was prepared from 692 mg GF (PeptaNova, Sandhausen,
Germany) and 13 mL of distilled water at 100 °C. On cooling, GF
precipitated as ﬁne, needle-like crystals with a habit similar to FF (yield
312 mg). These crystals were removed from the mother liquor by
Concentration Measurements. The dipeptide concentrations
were determined by UV spectrophotometry using a Cary 400
instrument version 8.01. Spectra were recorded
spectrophotometer,
between 300 and 230 nanometres with a reading every 0.4 nm.
Spectral bandwidth was 2 nm. The spectrophotometer was ﬁtted with
a variable temperature stage (Peltier thermocouple system). Glass
cuvettes of path length 2 mm or 4 mm were used depending on the
volume of solution available for the test. Concentration was taken to
be proportional to the absorption value at 258 nm, using a molar
absorption coeﬃcient of 390 M−1 cm−1, calculated from the molar
absorption coeﬃcient of phenylalanine. The change in peak
absorbance with temperature was found by heating a solution of 0.5
g/L concentration from 4 to 70 °C, and this was used to correct
readings at each temperature.
From repeated preparations of FF solutions from as-received
lysophilized peptide of diﬀerent batches, we found that FF
concentrations (as determined from the absorption at 258 nm) were
reproducibly ca. 25% lower than predicted from weighing the peptide.6
The majority, but not all, of this diﬀerence can be attributed to the
water content of the received peptide, as determined by thermogravi-
metric analysis (data not shown). Therefore, unlike previous studies,6
in the present study we relied entirely on the UV absorption
measurements.
To investigate potential subcritical association in water and hence
the validity of the crystallization model (which assumes no long-lived
association below the critical concentration, and nucleation-dependent
association thereafter), solutions at concentrations 0.10−1.00 g/L
were prepared by dilution of 1.00 g/L stock. These were allowed to
stand for 1 h, and then ultracentrifuged for 1 h at 62 000g. The
absorption above zero (set at 300 nm) at 258 nm was plotted against
concentration.
To ascertain critical concentrations (solubility) as a function of
temperature, quantities of FF at a range of concentrations were
prepared and allowed to equilibrate slowly in quiescent conditions to
room temperature and then held at 4 °C overnight in the presence of a
number of macroscopic crystals. The temperature controlled stage of
the spectrophotometer was set to the starting temperature (either 4 or
8 °C) and the program “Wavelength Scans at Temperature
Increments”, from the Agilent Web site, was used to record a series
of spectra between 230 and 300 nm following stirring for 80 min at a
number of temperatures between 8 and 68 °C. The uncertainty in the
FF concentrations, Δcs, was determined from repeated measurements.
From the uncertainties in the concentration measurements at diﬀerent
temperatures, we determined the uncertainty in the enthalpy of
crystallization, ΔΔH, by using the van’t Hoﬀ equation, according to
. The error in the entropy of crystallization was
the growth
kinetics of the FF crystals were carried out as described previously,14
that here the measurements were performed at diﬀerent
temperatures. The ﬂow reactors were microﬂuidic devices constructed
from polydimethylsiloxane (PDMS):58,59 a 25 μm thick layer of SU-8
3025 photoresist was spin-coated onto a silicon wafer, exposed to UV-
light through a mask in which the device design was printed, then
manufactured in 1-methoxy-2-propyl acetate (PGMEA). The micro-
ﬂuidic device was fabricated from Sylgard 184 PDMS elastomer
(DowCorning, Midland, MI), using 1 h curing at 65 °C. After cutting
the device, punching the holes for inlets and outlets, and activation via
plasma treatment with a Femto plasma bonder (Diener Electronic,
Ebhausen, Germany), the microﬂuidic device was bonded to a 3 × 1
in. microscope slide. A suspension of seed crystals was passed through
the device, and once suﬃcient crystals had settled in the central
chamber, a ﬂow of FF solution was initiated at a rate of 800 μL/h,
corresponding to velocities on the order of millimeters per second in
the channel center, by means of a NemeSys syringe pump (Cetoni,
Korbussen, Germany). Temperature was controlled using a micro-
scope heating stage. Measurements of lengths of growing microcrystals
were made every 5 s using time lapse photography, using a Zeiss Axio
Observer A1 microscope (Carl Zeiss,
Jena, Germany) and a
CoolSNAP-MYO camera (Photometrics, Tucson, AZ). The axial
growth rates were computed as the mean ± standard deviation of the
ﬁve fastest growing structures.14 We measured the axial growth rates at
a FF concentration of 1.2 g/L at diﬀerent temperatures (22, 28, 38, 44,
and 48 °C), and used the data on the temperature dependence of the
critical concentration to correct for the fact that the driving force for
aggregate growth decreases at higher temperatures (see the Supporting
Information for details of the analysis).
Dynamic Light Scattering. DLS experiments were performed
with a Zetasizer ZSP Instrument (Malvern, UK), using a scattering
angle of 173° (forward scattering). Concentrated stock solutions were
prepared at elevated temperatures, and then the solutions were passed
through a 220 nm pore size syringe ﬁlter and measured in disposable
small volume sizing cuvettes at diﬀerent temperatures and dilution
factors. The data were plotted as size distributions weighted by
scattering intensity.

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"C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "100 H2O", "peptide_concentration(mg/ml)": "0.828", "PH": "7.0", "temperature(celsius)": "44.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FF", "self-assembly_phase": "none", "N-terminal_modification": "Free", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "100 H2O", "peptide_concentration(mg/ml)": "0.736", "PH": "7.0", "temperature(celsius)": "44.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FF", "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 H2O", "peptide_concentration(mg/ml)": "1.122", "PH": "7.0", "temperature(celsius)": "48.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FF", "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 H2O", "peptide_concentration(mg/ml)": "1.224", "PH": "7.0", "temperature(celsius)": "48.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FF", "self-assembly_phase": "none", "N-terminal_modification": "Free", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "100 H2O", "peptide_concentration(mg/ml)": "0.918", "PH": "7.0", "temperature(celsius)": "48.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FF", "self-assembly_phase": "none", "N-terminal_modification": "Free", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "100 H2O", "peptide_concentration(mg/ml)": "0.816", "PH": "7.0", "temperature(celsius)": "48.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FF", "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 H2O", "peptide_concentration(mg/ml)": "1.232", "PH": "7.0", "temperature(celsius)": "52.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FF", "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 H2O", "peptide_concentration(mg/ml)": "1.344", "PH": "7.0", "temperature(celsius)": "52.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FF", "self-assembly_phase": "none", "N-terminal_modification": "Free", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "100 H2O", "peptide_concentration(mg/ml)": "1.008", "PH": "7.0", "temperature(celsius)": "52.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FF", "self-assembly_phase": "none", "N-terminal_modification": "Free", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "100 H2O", "peptide_concentration(mg/ml)": "0.896", "PH": "7.0", "temperature(celsius)": "52.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FF", "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 H2O", "peptide_concentration(mg/ml)": "1.375", "PH": "7.0", "temperature(celsius)": "56.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FF", "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 H2O", "peptide_concentration(mg/ml)": "1.5", "PH": "7.0", "temperature(celsius)": "56.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FF", "self-assembly_phase": "none", "N-terminal_modification": "Free", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "100 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"tube", "N-terminal_modification": "Free", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "100 H2O", "peptide_concentration(mg/ml)": "1.68", "PH": "7.0", "temperature(celsius)": "60.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FF", "self-assembly_phase": "none", "N-terminal_modification": "Free", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "100 H2O", "peptide_concentration(mg/ml)": "1.26", "PH": "7.0", "temperature(celsius)": "60.0", "heating_cooling": "No", "incubation_period(min)": "nan"}, {"peptide_sequence": "FF", "self-assembly_phase": "none", "N-terminal_modification": "Free", "C-terminal_modification": "Free", "Non-terminal_modification": "nan", "peptide_conjugate_mixture": "Peptide", "conjugate_partner": "nan", "solution": "100 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[System] polypeptide self-assembly literature information extraction

[User]
© 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Figure 7. Photocatalytic degradation of MO by TiO2 synthesized under differ-
ent conditions. (a) Pure TiO2 synthesized without peptide template.
(b–e) TiO2 nanofibers or nanoparticles synthesized by using the Fmoc-FFD
template at (b) pH 5, (c) pH 6, (d) pH 7, and (e) pH 8. C0 is the initial concen-
tration and Ci is the residual concentration of MO. The error bars represent
the standard deviations.
N-(9-Fluorenylmethoxycarbonyl)-protected phenylalanine–phenyl–
alanine–aspartic acid tripeptide (Fmoc-Phe–Phe–Asp-OH, Fmoc-
FFD) was synthesized by GL Biochem Ltd. (Shanghai, China). Titani-
um diisopropoxide bis(acetyl-acetonate) (TDA, 75 % in isopropanol)
was purchased from Tokyo Chemicals Industry. Tris(hydroxymethyl)
aminomethane was purchased from Alfa Aesar. (Beijing, China).
The TiO2 nanofibers can be synthesized by using Fmoc-FFD as the
template. Typically, lyophilized Fmoc-FFD powder (25.988 mg) was
dissolved in ultra-pure H2O (5 mL) at a concentration of 8 mm. The
pH of the peptide solution was adjusted by the addition of appro-
priate amounts of 0.5 m Tris buffer or 0.5 m HCl with stirring at
room temperature (25 8C). After the mixture had been stirred for
30 min, TDA (75 % in isopropanol, 145.75 mL) was added to the
mixture with stirring at 55 8C. Then, the mixture was allowed to
react at 55 8C with stirring for 2 h. The products were dried by
freeze drying. All organics were then removed by calcination at
550 8C for 6 h.
The pure TiO2 was synthesized without using the peptide as tem-
plate. The TDA (75 % in isopropanol, 145.75 mL) was added to ultra-
pure H2O (5 mL) with stirring at 55 8C. The mixture was allowed to
react at 55 8C with stirring for 2 h. The products were dried by
freeze drying. Then, the dried products were calcined at 550 8C for
Photocatalytic degradation of MO by the TiO2 nanofibers
synthesized by using Fmoc-FFD peptide as a template
Methyl orange (MO) was selected to investigate the photocatalytic
activity of the as-synthesized TiO2 nanofibers. First, TiO2 nanofiber
photocatalyst (10 mg) was suspended in MO solution (10 mL of
10 mg L@1). In the dark, the solution was sonicated for 5 min and
stirred for 30 min to establish the adsorption and desorption equi-
librium. Then, a 16.7 A lamp was used to irradiate the solutions. A
UV/Vis spectrophotometer (TV-1810, Beijing PERSEE) was used to
measure the content of the remaining MO by taking out a small
amount of sample every hour. The degradation rate of MO was cal-
culated from the absorption peak at 464 nm. As a control experi-
ment, pure TiO2 was used to degrade MO under the same condi-
tions. The experiments were repeated three times for each synthe-
sized TiO2 catalyst in the photocatalytic degradation.
The morphologies of the TiO2 nanofibers were examined by SEM
(Hitachi High-Technologies Co., Japan) with an acceleration voltage
of 3 kV. The TEM images were recorded with a JEOL 1200EX elec-
tron microscope operating at 80 kV. Powder X-ray diffraction
(PXRD) patterns were recorded with a PANalytical/X’Pert PRO MPD
system with CuKa radiation (l = 1.5406 a). The CD measurements
were collected by using a J-810 circular dichroism spectrophotom-
eter (JASCO, Japan) with 0.1 mm path length quartz cuvettes.
Molecular dynamics simulations (MDs) were performed by using
the Gromacs program[23] under the Amber99SB-ILDN force field.[24]
The initial structure of Fmoc-FFD was constructed by using Accel-
rys Materials Studio 2.5 software. Models were placed in an ortho-
rhombic periodic boundary condition (PBC) box with a margin of
2 nm, filled with TIP3P water molecules. The system was electrically
neutralized by adding extra Na + ions. The 5000 steepest descent
steps and 5000 conjugate gradient minimization steps were per-
formed to minimize the energy of system. Then, a 1 ns restraint
simulation at a time step of 1 fs was performed in the NPT ensem-
ble to make water molecules relax, followed by production simula-
tion of 40 ns in the NPT ensemble at a temperature of 300 K. The
Particle Mesh Ewald (PME) method[25] was used to calculate non-
bonded and long-range electrostatic interactions with a cut-off
value of 1.0 nm. The MD trace was further analyzed by using

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