Letizia Tavagnacco1, Ester Chiessi2, Marco Zanatta3, Andrea Orecchini4,5, Emanuela Zaccarelli1. 1. CNR-ISC and Department of Physics , Sapienza University of Rome , Piazzale A. Moro 2 , 00185 Rome , Italy. 2. Department of Chemical Sciences and Technologies , University of Rome Tor Vergata , Via della Ricerca Scientica I , 00133 Rome , Italy. 3. Department of Computer Science , University of Verona , Strada Le Grazie 15 , 37138 Verona , Italy. 4. Department of Physics and Geology , University of Perugia , Via A. Pascoli , 06123 Perugia , Italy. 5. CNR-IOM c/o Department of Physics and Geology , University of Perugia , Via A. Pascoli , 06123 Perugia , Italy.
Abstract
The long debated protein dynamical transition was recently found also in nonbiological macromolecules, such as poly- N-isopropylacrylamide (PNIPAM) microgels. Here, by using atomistic molecular dynamics simulations, we report a description of the molecular origin of the dynamical transition in these systems. We show that PNIPAM and water dynamics below the dynamical transition temperature T d are dominated by methyl group rotations and hydrogen bonding, respectively. By comparing with bulk water, we unambiguously identify PNIPAM-water hydrogen bonding as mainly responsible for the occurrence of the transition. The observed phenomenology thus crucially depends on the water-macromolecule coupling, being relevant to a wide class of hydrated systems, independently from the biological function.
The long debated protein dynamical transition was recently found also in nonbiological macromolecules, such as poly- N-isopropylacrylamide (PNIPAM) microgels. Here, by using atomistic molecular dynamics simulations, we report a description of the molecular origin of the dynamical transition in these systems. We show that PNIPAM and water dynamics below the dynamical transition temperature T d are dominated by methyl group rotations and hydrogen bonding, respectively. By comparing with bulk water, we unambiguously identify PNIPAM-water hydrogen bonding as mainly responsible for the occurrence of the transition. The observed phenomenology thus crucially depends on the water-macromolecule coupling, being relevant to a wide class of hydrated systems, independently from the biological function.
The well-known
protein dynamical
transition takes place in hydrated protein suspensions at a relatively
low temperature, usually called T, typically between 220 and 240 K, but depending on the specific
system. After the first observation in 1989 for myoglobin,[1] the transition has been reported in several kinds
of proteins, including ribonuclease A,[2] cytochrome c,[3] lysozyme,[4] and other biomacromolecules such as RNA,[5] DNA,[6] and lipid bilayers,[7] irrespective of secondary structure, folding,
and degree of polymerization.[8−10] The transition consists of a
steep enhancement of the atomic mobility that, below T, is limited to harmonic vibrations
and methyl rotations. At T, anharmonic motions and local diffusion of groups of atoms
are triggered, which, for proteins, is a prerequisite to the onset
of activity.[11−13] It is important to remark that T does not coincide with the calorimetric
glass transition temperature, which is found to occur at even lower
temperatures. While the dynamical transition always occurs in aqueous
environments, with a water content that is kept to a minimum to avoid
the onset of ice crystallization, the role of water is still a debated
issue. Evidence was reported in favor of a concomitant activation
of the water dynamics at the transition, as shown for folded and intrinsically
disordered proteins.[10,14,15] These studies suggest a strong interplay between protein and water,
but different interpretations have also been proposed in the literature
going from a water-slaved to a water-driven protein dynamics.[16−18]Very recently, elastic incoherent neutron scattering experiments
reported the occurrence of a dynamical transition at T ∼ 250 K also for a nonbiological
system, i.e., poly(N-isopropylacrylamide), PNIPAM,
microgels.[19] Like proteins, PNIPAM microgels
have an extended covalent connectivity and an amphipilic character.
In addition, their network structure maximizes the ability of water
confinement. For the same macromolecular concentration, water accessible
surface area in PNIPAM microgels is about 30% larger as compared to
a globular protein, thus magnifying the matrix-induced effect on water
properties.[20] This results in the observation
of the dynamical transition in PNIPAM–water suspensions with
a very large water content, up to roughly 60% of water (w/w). These
findings thus extend the dynamical transition concept beyond the world
of biological function, encompassing the much wider context of hydrated
complex macromolecular entities.To unveil the molecular mechanisms
involved in the dynamical transition,
in this work we perform atomistic molecular dynamics simulations using
a nanoscale model of the microgel in water (Figure A) that quantitatively reproduces the experimental
results.[19] By varying PNIPAM concentration
and exploring a wide range of temperatures, we probe PNIPAM and water
dynamics in detail. We find that below T both PNIPAM and water motions are characterized
by an Arrhenius behavior, controlled by methyl rotations and hydrogen
bonds, respectively. By monitoring the hydrogen bonding pattern, we
find that long-lived PNIPAM–water bonds are primarily responsible
for the observed water behavior at low temperatures. This is confirmed
by the comparison with bulk water, which does not display the same
features.[21] Our results clearly highlight
the fact that the dynamical transition is a feature genuinely associated
with water–macromolecule coupling.
Figure 1
(A) Microgel network
model. Backbone and side chain atoms are displayed
in magenta and yellow, respectively; water molecules and periodic
images of backbone atoms are represented in blue and gray, respectively.
Polymer hydrogen atoms are omitted for clarity. The two side
frames report the chemical structure of the repeating unit (top) and
of the cross-link (bottom). (B) Temperature dependence of MSD calculated
for PNIPAM hydrogen atoms at 1 ns (main figure) and 150 ps (inset).
Results are displayed for PNIPAM mass fractions of 30% (purple diamonds),
40% (green circles), and 60% (blue triangles). The dashed lines are
guides to the eye suggesting a linear behavior corresponding to the
dry sample, for which the dynamical transition is suppressed.[19]
(A) Microgel network
model. Backbone and side chain atoms are displayed
in magenta and yellow, respectively; water molecules and periodic
images of backbone atoms are represented in blue and gray, respectively.
Polymer hydrogen atoms are omitted for clarity. The two side
frames report the chemical structure of the repeating unit (top) and
of the cross-link (bottom). (B) Temperature dependence of MSD calculated
for PNIPAM hydrogen atoms at 1 ns (main figure) and 150 ps (inset).
Results are displayed for PNIPAM mass fractions of 30% (purple diamonds),
40% (green circles), and 60% (blue triangles). The dashed lines are
guides to the eye suggesting a linear behavior corresponding to the
dry sample, for which the dynamical transition is suppressed.[19]In biological macromolecules, the protein dynamical transition
is usually detected by monitoring the atomic mean squared displacements
(MSD) through several experimental techniques.[1,22,23] The MSD can also be easily calculated as
a function of time by molecular dynamics simulations. Its value at
a given time, equal to that of a given experimental resolution, can
then be monitored as a function of T. This is done
in Figure B where
the MSD of PNIPAM hydrogen atoms of a portion of microgel is reported
for both long (1 ns) and short (150 ps) times. On increasing temperature,
a sudden promotion of large amplitude motions is visible in both cases,
thus excluding the possibility that the observation of a transition
is an artifact induced by the resolution limit of the accessible time
or frequency window.[24] In addition, the
concentration dependence of the MSD reveals that the transition is
more pronounced in more hydrated systems, in agreement with what has
been found for proteins.[14] This overall
qualitative description of the molecular process does not allow full
understanding of the microscopic interplay between water and the macromolecule
originating this effect. Therefore, in the following, we analyze in
detail the dynamical behavior of both PNIPAM and water.First
of all, it is important to exclude that the transition is
due to an underlying structural change in the system. To this aim,
we analyzed the structural alterations of the polymer matrix in the
200–290 K interval. Similarly to what is observed in proteins,[1] no structural variations of the polymer network
were found at T, neither
as a whole, as shown by the temperature dependence of PNIPAM radius
of gyration reported in Figure A, nor locally, as visible from the distributions of dihedral
angles of the backbone and the temperature dependence of intramolecular hydrophilic
and hydrophobic interactions reported in Figures S1 and S2, thus confirming the kinetic character of the transition.
Figure 2
(A) Temperature
dependence of PNIPAM radius of gyration. (B) Arrhenius
plot of the average lifetime (in ps) of a rotational state, τ, of a methyl group. (C) Fraction of backbone
mobile dihedrals as a function of the temperature. In (A), (B), and
(C) systems with PNIPAM mass fractions of 30, 40, and 60% (w/w) are
displayed with purple diamonds, green circles, and blue triangles,
respectively. (D) Temperature dependence of the MSD of backbone tertiary
carbon atoms Cα that are directly
connected to the side chain. Here, n is the index
of residue, varying from 1 to 180, the total number of repeating units
in our network model. Circles indicate the 12 carbon atoms belonging
to cross-links. The MSD is calculated at 150 ps for a PNIPAM mass
fraction of 30% (left panel), 40% (central panel), and 60% (right
panel). Errors within the symbol size.
(A) Temperature
dependence of PNIPAM radius of gyration. (B) Arrhenius
plot of the average lifetime (in ps) of a rotational state, τ, of a methyl group. (C) Fraction of backbone
mobile dihedrals as a function of the temperature. In (A), (B), and
(C) systems with PNIPAM mass fractions of 30, 40, and 60% (w/w) are
displayed with purple diamonds, green circles, and blue triangles,
respectively. (D) Temperature dependence of the MSD of backbone tertiary
carbon atoms Cα that are directly
connected to the side chain. Here, n is the index
of residue, varying from 1 to 180, the total number of repeating units
in our network model. Circles indicate the 12 carbon atoms belonging
to cross-links. The MSD is calculated at 150 ps for a PNIPAM mass
fraction of 30% (left panel), 40% (central panel), and 60% (right
panel). Errors within the symbol size.The homogeneity of chemical composition in PNIPAM microgels
allows
us to identify a hierarchy of motion modes. The expected fastest motion
is the torsion of side chain methyl groups, which is active at all
the explored temperatures (Figure S3 and Table S1). Indeed by extending the explored temperature
range down to 63 K, an onset of anharmonicity consistent with the
activation of methyl group rotation is detected at about 150 K (see Figure S4), in agreement with the behavior observed
in biomacromolecules.[8,25−27] We find that
the average lifetime of a methyl rotational state is independent of
the degree of hydration and follows an Arrhenius behavior (Figure B) for all investigated
temperatures with an activation energy, E, of about 13.5 kJ mol–1 (Table S3). This value is similar to that reported
for methyl groups in the hydrophobic core of proteins, in homomeric
polypeptides and in bulk polymers.[25,28,29]Another class of motions in the polymer network
can be ascribed
to the rotation of the backbone dihedral angles. Figure C shows the evolution of the
fraction of mobile backbone dihedral angles x with T. Its behavior closely
resembles that of the MSD behavior of PNIPAM (Figure B): the mobile backbone dihedral angles are
very scarce below T,
and an abrupt increase of their number occurs at and above T. The details of the backbone
torsional dynamics are reported in the SI text (see Table S2). A further analysis of atomic motions has been carried
out by calculating the MSD of the tertiary carbon atoms of the backbone. Figure D shows that the
segmental dynamics of the polymer scaffold is quenched up to ∼250
K but is switched on at higher temperatures. In addition, while the
dynamical behavior of PNIPAM is overall homogeneous below T, above this temperature we
observe the onset of dynamical heterogeneities. Namely, the carbon
atoms belonging to the junctions of the network (solid points in Figure D) develop lower
local diffusivities, evidencing the role of the topological constraints
on the dynamics. The comparison between different PNIPAM concentrations
highlights the plasticizing effect of water, which results in a larger
mobility for a higher degree of hydration. These results focus the
principal role played by the backbone dynamics in the dynamical transition,
in agreement with what observed in experimental studies on polypeptides.[25,26] Moreover, the enhancement of anharmonic fluctuations at increasing
water content (Figures B and 2D) is similar to what observed for
polypeptides in the presence of side chains.[26]To monitor the PNIPAM dynamics as a function of T, we consider the self-intermediate scattering function (SISF) of
PNIPAM hydrogen atoms (Table S4 and SI text), which is well described, at long times,
by a stretched exponential with characteristic time τ. The SISF is sensitive to the single particle dynamics
at a specific wavevector Q. We focus on the value Q = 2.25 Å–1, corresponding, in real
space, to the position of the first maximum of the oxygen–oxygen
structure factor in bulk water.[30] In Figure A an Arrhenius plot
of τ is reported for three different
PNIPAM concentrations, indicating a slowing down at the highest PNIPAM
concentration, while the systems at 30% and 40% (w/w) of polymer display
similar values of τ (Table S3). We also report in Figure A the water translational self-diffusion
coefficient D as a function
of T. The direct comparison between PNIPAM and water
dynamics allows us to highlight several important features. First
of all, we notice that both τ and D display a change of behavior
around ∼250 K, that we identify as the dynamical transition.
Analyzing the behaviors of τ and D in detail, we notice that
they are compatible with an Arrhenius dependence both below and above T.[19] However, we will discuss later that only the low-temperature regime
can be attributed to a true activation process. Instead, the high
temperature data show a remarkably similar T-dependence
for both τ and D at all explored concentrations with
a common apparent Arrhenius slope. We further notice that an inversion
of the (putative) Arrhenius slope is detected between PNIPAM and water
across T. In particular,
for PNIPAM there is a crossover between a lower and a higher slope
regime when temperature is increased above T, while water shows the opposite trend.
Figure 3
Arrhenius
plots of (A) water diffusion coefficient D (circles, in cm2/s ×
105) and SISF relaxation times for PNIPAM hydrogen atoms
τ (diamonds, in ps) calculated
for PNIPAM mass fraction of 30% (left panel), 40% (central panel),
and 60% (right panel). (B) Water diffusion coefficient (in cm2/s × 105) calculated for bulk water and hydration
water for different PNIPAM concentrations. In all panels, solid lines
are Arrhenius fits to the data and dotted lines are guides to the
eye.
Arrhenius
plots of (A) water diffusion coefficient D (circles, in cm2/s ×
105) and SISF relaxation times for PNIPAM hydrogen atoms
τ (diamonds, in ps) calculated
for PNIPAM mass fraction of 30% (left panel), 40% (central panel),
and 60% (right panel). (B) Water diffusion coefficient (in cm2/s × 105) calculated for bulk water and hydration
water for different PNIPAM concentrations. In all panels, solid lines
are Arrhenius fits to the data and dotted lines are guides to the
eye.We recall that the number of hydration
water molecules for PNIPAM
is experimentally estimated to be ∼12 ± 1 per residue
below the lower critical solution temperature.[31,32] Therefore, for the three concentration values considered in this
work, the water molecules can be entirely classified as hydration
water (see also Experimental Section). Hence,
it is instructive to compare the T-dependence of D between hydration water and
bulk water, as shown in Figure B. No clearly identifiable change at T occurs for bulk water, suggesting the central
role of PNIPAM–water coupling in the occurrence of the dynamical
transition. Having identified the presence of a dynamical coupling
between PNIPAM and water, we now ask the question whether a change
of connectivity for the water molecules occurs at the transition.
To this aim, we report in Figure A,B the temperature behavior of the number of PNIPAM–water
and water–water hydrogen bonds (HBs), respectively. None of
these observables display a sharp variation at T. We find an increasing number of PNIPAM–water
HBs as a function of PNIPAM concentration and concomitantly a decrease
of the number of water–water HBs, with no discontinuity with
respect to the behavior of bulk water. This suggests that no increase
of water structuring is originated in the surroundings of the hydrophobic
groups. It is important to stress that the overall water structuring
in microgel suspensions is always larger than for bulk water, with
the total number of HBs (water–water and water–PNIPAM)
increasing with polymer concentration (Figure S5). Thus, we can discard a structural origin of the transition
in terms of HB connectivity.
Figure 4
Temperature dependence of the average number
of hydrogen bonds
between PNIPAM and water (A) and between water molecules (B) per water
molecule; Arrhenius plot of the average lifetime (in ps) of PNIPAM-water
hydrogen bonds τ (C) and of water–water
hydrogen bond τ (D). Results referring
to PNIPAM mass fraction of 30%, 40%, and 60 wt % are displayed in
purple, green, and blue, respectively. Bulk water data are shown in
pink. The pink frames highlight the region where the dynamical transition
occurs. Errors within the symbol size.
Temperature dependence of the average number
of hydrogen bonds
between PNIPAM and water (A) and between water molecules (B) per water
molecule; Arrhenius plot of the average lifetime (in ps) of PNIPAM-water
hydrogen bonds τ (C) and of water–water
hydrogen bond τ (D). Results referring
to PNIPAM mass fraction of 30%, 40%, and 60 wt % are displayed in
purple, green, and blue, respectively. Bulk water data are shown in
pink. The pink frames highlight the region where the dynamical transition
occurs. Errors within the symbol size.We further monitor the characteristic lifetime of PNIPAM–water
τ and water–water τ HB interactions. As shown in Figure C and 4D, τ and τ both follow an Arrhenius behavior with similar
values of activation energies of about 55 kJ mol–1 (Table S3), irrespective of hydration
level. We also note that the lifetime of PNIPAM–water HB is
considerably longer than the lifetime of water–water HB and
cannot be estimated below T due to the finite simulation time. This finding is in agreement
with previous results on the protein dynamical transition,[33] which suggested that the lifetime of protein–water
HB interactions diverges at T. The activation energy of HB is equal to that estimated from
the Arrhenius dependence of D for T < T (see Table S3). Instead,
the PNIPAM relaxation time τ has
an activation energy of ∼16 kJ mol–1 for T < T which
is independent of the concentration and is comparable to that calculated
for the rotation of the methyl groups (see Figure B). These findings suggest that below T PNIPAM dynamics is dominated
by methyl rotations, while the translational dynamics of water is
controlled by its hydrogen bonding within the microgel environment.For T > T, both observables τ and D show a similar temperature
dependence, that could be interpreted as an Arrhenius regime,[19] providing activation energies very close to
each other, i.e., ∼30 ± 2 kJ mol–1 for
τ and ∼36 ± 2 kJ mol–1 for D. However, these values cannot be attributed to any specific structural
rearrangement, indicating that this apparent Arrhenius behavior[34] may result from the superposition of different
contributions. The fact that the apparent activation energy is higher
than the methyl rotation one and lower than the one corresponding
to HB lifetime gives rise to a “slope” inversion of
PNIPAM and water dynamics, as observed in the data of Figure , similarly to hydrated lysozyme
results.[35] Hence, above the dynamical transition
temperature, we cannot distinguish a dominant specific molecular motion,
but rather we only detect a correlation between polymer segmental
dynamics and diffusive motion of bound water. This dynamical interplay
can only be active when the PNIPAM–water HB lifetime is sufficiently
short that the exchange of hydrogen bonded water molecules is still
effective[33] and was recently confirmed
in the water-soluble states of a PNIPAM linear chain.[36]Differently, the dynamical transition clearly marks
the onset,
below T, of distinct
dominant motions, respectively, for PNIPAM and water. The comparison
with bulk water further allows us to identify that it is primarily
the hydrogen bond pattern of water within the microgel, dictated by
the slowest PNIPAM–water HB, that dominates the low-T water dynamics. The T-dependence of D for bulk water is further
analyzed in the Supporting Information,
where it is shown that at high temperatures the data are well described
by a power-law decay (see Figure S6 Supporting
Information) in agreement with previous studies.[21,35] For low T, also bulk water follows an Arrhenius
dependence but with a much higher activation energy (∼80 kJ
mol–1), indicating a different mechanism than hydrogen
bonding controlling its dynamics, even if the number of water–water
HB increases as T decreases. This leads us to exclude
a direct influence of water–water hydrogen bonding on the dynamical
transition. Instead, we can clearly isolate the contribution of PNIPAM–water
hydrogen bonding, which is slower than water–water HB by roughly
2 orders of magnitude at each T for the same PNIPAM
concentration (see Figure C,D). Therefore, PNIPAM–water hydrogen bonding must
be the trigger of the Arrhenius dependence below T and thus the microscopic mechanism
responsible for the occurrence of the dynamical transition.It is also interesting to discuss the relatively large value of T for PNIPAM microgels with
respect to protein systems. The average number of macromolecule–water
hydrogen bonds formed was found to be 1.2 and 1.1 for lysozyme and
plastocyanin per protein residue, respectively,[18,37] while for PNIPAM–water hydrogen bonds we find ∼2.[38] Thus, the different macromolecule–water
interaction may play a primary role in determining the value of T. We also note that the value
of T was also found
to depend on the hydration level h(4,39,40) (h = g water/g protein),
with lower values found for higher water content. However, such a
variation appears to be significant at low h,[39] tending to saturate at large water content.
We stress that the PNIPAM mass fractions that we have explored correspond
to water content h = 2.33, 1.5, and 0.67 for 30%,
40%, and 60%, respectively, thus to a completely different water content
region with respect to all previous studies.In conclusion,
the present results provide a microscopic description
of the origin of the “protein-like” dynamical transition
observed in microgels. The correlation between the information extracted
from the analysis of PNIPAM relaxations times, water self-diffusion
coefficients, and hydrogen bonding interactions allowed us to identify
the molecular processes which control the dynamics of both PNIPAM
and water below the dynamical transition temperature. In particular,
we found that below T PNIPAM dynamics is governed by the rotation of the methyl groups
belonging to the side chains and that a sudden increase of the polymer
segmental dynamics occurs at T. On the other hand, hydrogen bonding interactions determine
water dynamics below T. By comparing the low temperature behavior of water in the microgels
suspensions to that of bulk water, we also found that the hydrogen
bonding interactions between PNIPAM and water play the primary role
in determining water dynamics below T. Altogether these findings support the idea that
the macromolecule–water coupling is the driving ingredient
of the dynamical transition. Thus, such phenomenology should be rather
general, taking place in all hydrated macromolecular systems which
are able, at the same time, to efficiently confine water in order
to avoid ice formation and to couple it via hydrogen bonding. These
findings also rule out the possibility to observe a dynamical transition
in dry systems, where similar findings[41] must then be ascribed to a different molecular mechanism.
Experimental
Section
PNIPAM microgel is modeled as an isotropic network
composed of
12 atactic chains connected by 6 bis(acrylamide) cross-links. Periodic
images of the network are covalently bonded to mimic the 3-D percolation
of the microgel. This model has a monomer/cross-linker ratio that,
given the heterogeneous structure of PNIPAM microgels, describes a
region of the particle close to the core–shell boundary, and
it quantitatively reproduces neutron scattering results.[19] Three PNIPAM mass fractions of 30, 40, and 60%
(w/w), corresponding to hydration levels of 14, 9, and 4 water molecules
per PNIPAM residue, respectively, were investigated. All-atom MD simulations
are performed in the range between 293 and 223 K. At each T, trajectory data are collected for ∼0.5 μs.
We adopt the OPLS-AA force field[42] with
the implementation by Siu et al.[43] for
PNIPAM and the Tip4p/ICE model[44] for water.
MD simulations are also carried out for a cubic box containing 1782
Tip4p/ICE water molecules following a similar procedure. Additional
details are reported in Sections S7–S9 of the SI Text.
Authors: J H Roh; J E Curtis; S Azzam; V N Novikov; I Peral; Z Chowdhuri; R B Gregory; A P Sokolov Journal: Biophys J Date: 2006-07-14 Impact factor: 4.033
Authors: Gokhan Caliskan; Robert M Briber; D Thirumalai; Victoria Garcia-Sakai; Sarah A Woodson; Alexei P Sokolov Journal: J Am Chem Soc Date: 2006-01-11 Impact factor: 15.419
Authors: Aziz Ben-Miled; Afshin Nabiyan; Katrin Wondraczek; Felix H Schacher; Lothar Wondraczek Journal: Polymers (Basel) Date: 2021-05-18 Impact factor: 4.329