________________
Phys Biol. 2004 Jun;1(1-2):42-52.
The
influence of geometry, surface character, and flexibility on the
permeation
of ions and water through biological pores.
Beckstein O, Sansom
MS.
Department of Biochemistry, University of Oxford, South Parks
Road,
Oxford OX1 3QU, UK.
oliver@biop.ox.ac.ukA
hydrophobic constriction site can act as an efficient barrier to
ion and
water permeation if its diameter is less than the diameter of
an ion's first
hydration shell. This hydrophobic gating mechanism is
thought to operate in a
number of ion channels, e.g. the nicotinic
receptor, bacterial
mechanosensitive channels (MscL and MscS) and
perhaps in some potassium
channels (e.g. KcsA, MthK and KvAP).
Simplified pore models allow one to
investigate the primary
characteristics of a conduction pathway, namely its
geometry (shape,
pore length, and radius), the chemical character of the pore
wall
surface, and its local flexibility and surface roughness.
Our
extended (about 0.1 micros) molecular dynamic simulations show that
a
short hydrophobic pore is closed to water for radii smaller than
0.45
nm. By increasing the polarity of the pore wall (and thus
reducing
its hydrophobicity) the transition radius can be decreased until
for
hydrophilic pores liquid water is stable down to a radius
comparable
to a water molecule's radius. Ions behave similarly but
the
transition from conducting to non-conducting pores is even steeper
and
occurs at a radius of 0.65 nm for hydrophobic pores. The presence
of water
vapour in a constriction zone indicates a barrier for ion
permeation. A
thermodynamic model can explain the behaviour of water
in nanopores in terms
of the surface tensions, which leads to a
simple measure of 'hydrophobicity'
in this context. Furthermore,
increased local flexibility decreases the
permeability of polar
species. An increase in temperature has the same
effect, and we
hypothesize that both effects can be explained by a decrease
in the
effective solvent-surface attraction which in turn leads to
an
increase in the solvent-wall surface free
energy.
__________________________
Proc Natl Acad Sci U S A.
2003 Jun 10;100(12):7063-8. Epub 2003 May
9.
Liquid-vapor oscillations
of water in hydrophobic nanopores.
Beckstein O, Sansom
MS.
Department of Biochemistry, University of Oxford, South Parks
Road,
Oxford OX1 3QU, United Kingdom.
Water plays a key role in
biological membrane transport. In ion
channels and water-conducting pores
(aquaporins), one-dimensional
confinement in conjunction with strong surface
effects changes the
physical behavior of water. In molecular dynamics
simulations of
water in short (0.8 nm) hydrophobic pores the water density in
the
pore fluctuates on a nanosecond time scale. In long simulations
(460
ns in total) at pore radii ranging from 0.35 to 1.0 nm we
quantify
the kinetics of oscillations between a liquid-filled and
a
vapor-filled pore. This behavior can be explained as
capillary
evaporation alternating with capillary condensation, driven
by
pressure fluctuations in the water outside the pore. The
free-energy
difference between the two states depends linearly on the radius.
The
free-energy landscape shows how a metastable liquid state
gradually
develops with increasing radius. For radii > approximately 0.55
nm it
becomes the globally stable state and the vapor state
vanishes.
One-dimensional confinement affects the dynamic behavior of the
water
molecules and increases the self diffusion by a factor of
2-3
compared with bulk water. Permeabilities for the narrow pores are
of
the same order of magnitude as for biological water pores. Water
flow
is not continuous but occurs in bursts. Our results suggest
that
simulations aimed at collective phenomena such as hydrophobic
effects
may require simulation times >50 ns. For water in
confined
geometries, it is not possible to extrapolate from bulk or short
time
behavior to longer time
scales.
______________________________
J Chem Phys. 2005 Nov
15;123(19):194502.
Links
Effect of flexibility on hydrophobic
behavior of nanotube water
channels.
Andreev S, Reichman D, Hummer
G.
Department of Chemistry and Chemical Biology, Harvard
University,
Cambridge, MA 02138, USA.
Carbon nanotubes can serve as
simple nonpolar water channels. Here we
report computer simulations exploring
the relationship between the
mechanical properties of such channels and their
interaction with
water. We show that on one hand, increasing the flexibility
of the
carbon nanotubes increases their apparent hydrophobic
character,
while on the other hand the presence of water inside the
channel
makes them more resistant to radial collapse. We quantify the
effect
of increasing flexibility on the hydrophobicity of the nanotube
water
channel. We also show that flexibility impedes water transport
across
the nanotube channel by increasing the free-energy barriers to
such
motion. Conversely, the presence of water inside the nanotube
is
shown to affect the energetics of radial collapse in a water
nanotube,
an ostensibly mechanical property. We quantify the
magnitude of the effect
and show that it arises from the formation of
energetically favorable
low-dimensional water structures inside the
nanotube such as one-dimensional
wires and two-dimensional
sheets.
_______________________________
Phys Rev Lett. 2005 Sep
23;95(13):130603. Epub 2005 Sep 21.
Coarse nonlinear dynamics and
metastability of filling-emptying
transitions: water in carbon
nanotubes.
Sriraman S, Kevrekidis IG, Hummer G.
Department of Chemical
Engineering and PACM, Princeton University,
Princeton, New Jersey 08544, USA.
rudram@princeton.eduUsing a coarse-grained molecular
dynamics (CMD) approach we study the
apparent nonlinear dynamics of water
molecules filling or emptying
carbon nanotubes as a function of system
parameters. Different levels
of the pore hydrophobicity give rise to tubes
that are empty,
water-filled, or fluctuate between these two long-lived
metastable
states. The corresponding coarse-grained free-energy surfaces
and
their hysteretic parameter dependence are explored by linking MD
to
continuum fixed point and bifurcation algorithms. The results
are
validated through equilibrium MD
simulations.
_______________________________
J Chem Phys.
2004 Oct 22;121(16):7955-65.
Links
Electric field and temperature
effects on water in the narrow
nonpolar pores of carbon
nanotubes.
Vaitheeswaran S, Rasaiah JC, Hummer G.
Laboratory of
Chemical Physics, National Institute of Diabetes and
Digestive and Kidney
Diseases, National Institutes of Health,
Building 5, Bethesda, MD 20892-0520,
USA.
Water molecules in the narrow cylindrical pore of a (6,6)
carbon
nanotube form single-file chains with their dipoles
collectively
oriented either up or down along the tube axis. We study
the
interaction of such water chains with homogeneous electric fields
for
finite closed and infinite periodically replicated tubes.
By
evaluating the grand-canonical partition function term-by-term, we
show
that homogeneous electric fields favor the filling of previously
empty
nanotubes with water from the bulk phase. A two-state
description of the
collective water dipole orientation in the
nanotube provides an excellent
approximation for the dependence of
the water-chain polarization and the
filling equilibrium on the
electric field. The energy and entropy
contributions to the free
energy of filling the nanotube were determined from
the temperature
dependence of the occupancy probabilities. We find that the
energy of
transfer depends sensitively on the water-tube interaction
potential,
and that the entropy of one-dimensionally ordered water chains
is
comparable to that of bulk water. We also discuss implications
for
proton transfer reactions in
biology.
______________________________
__
Nature. 2001 Nov
8;414(6860):188-90.
Water conduction through the hydrophobic channel of a
carbon
nanotube.
Hummer G, Rasaiah JC, Noworyta JP.
Laboratory of
Chemical Physics, National Institute of Diabetes and
Digestive and Kidney
Diseases, National Institutes of Health,
Bethesda, Maryland 20892-0520, USA.
hummer@helix.nih.gov
Confinement of matter on the
nanometre scale can induce phase
transitions not seen in bulk systems. In the
case of water, so-called
drying transitions occur on this scale as a result
of strong
hydrogen-bonding between water molecules, which can cause the
liquid
to recede from nonpolar surfaces to form a vapour layer
separating
the bulk phase from the surface. Here we report molecular
dynamics
simulations showing spontaneous and continuous filling of a
nonpolar
carbon nanotube with a one-dimensionally ordered chain of
water
molecules. Although the molecules forming the chain are in
chemical
and thermal equilibrium with the surrounding bath, we
observe
pulse-like transmission of water through the nanotube.
These
transmission bursts result from the tight hydrogen-bonding
network
inside the tube, which ensures that density fluctuations in
the
surrounding bath lead to concerted and rapid motion along the
tube
axis. We also find that a minute reduction in the attraction
between
the tube wall and water dramatically affects pore hydration,
leading
to sharp, two-state transitions between empty and filled states on
a
nanosecond timescale. These observations suggest that carbon
nanotubes,
with their rigid nonpolar structures, might be exploited
as unique molecular
channels for water and protons, with the channel
occupancy and conductivity
tunable by changes in the local channel
polarity and solvent
conditions.
