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Biophys J, June 2002, p. 2876-2891, Vol. 82, No. 6
Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Saint Paul, Minnesota 55108-1022 USA
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ABSTRACT |
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Biological macromolecules are often studied in mixed
solvents. To understand cosolvent-macromolecule interactions, the
preferential interaction coefficient,
3, may help
determine surface solvent compositions.
3 measures the
amounts of water, B1, and cosolvent, B3, within the "local domain," the (possibly
far-reaching) region surrounding the macromolecule where the solvent is
nonbulk-like. The local domain's boundary is, however, vague and it is
unclear which molecules are counted in Bi. It is
useful to explore a simple model system to make
Bi more concrete and to understand which aspects
of the surface solvent distribution,
(x), are sampled by
3. We performed computer simulations on a
two-dimensional (2D) system consisting of a hard-wall solute (the
macromolecule) in a mixed solvent (hard disks of different radii). We
simultaneously calculated
3 and
(x). We
found that 1) in practice, the local domain's boundary is demarked by
the outer limit of the first cosolvent (not water) layer;
Bi mainly counts the solvent near the
macromolecule; 2) assuming B1 to count only the
waters within the first water layer is a poor approximation; 3) when
determining B1 and B3,
water and cosolvent molecules must be counted from the same region of
space. We speculate that these 2D results may serve as a first-order
approximation for the dominant contributions to
3 even
in three dimensions, so long as the cosolvent is not strongly excluded
from the macromolecular surface and there is no significant long-ranged
solvent structure.
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INTRODUCTION |
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Mixed solvent systems are important to the
understanding of the structure and stabilities of macromolecules. For
example, the cosolvents urea and guanidine hydrochloride have long been used to study protein denaturation, sucrose is added to stabilize proteins, and alcohols are condensing agents for DNA. (Technically, molecules such as urea, guanidine hydrochloride, and sucrose are cosolutes. However, at typical concentrations, they make up a significant fraction of the solution
8M urea is 43 wt % urea and 2 M
sucrose is 55 wt % sucrose. These cosolute molecules bathe and solvate
the macromolecular solute as water does. To emphasize the cosolvents'
role in solvation and to treat them on an equal footing with water, we
refer to both cosolvents and cosolutes as "cosolvent" molecules.)
To understand cosolvent-macromolecule interactions, it is necessary to
determine where the cosolvent molecules are; do they tend to lie within
the bulk solvent or do they prefer to associate with the macromolecule?
In particular, what is the distribution (or the composition) of solvent
at the macromolecular surface? Currently, there is little information
on this. The primary experimental means of obtaining atomic-resolution
data on solvent structure are x-ray diffraction and nuclear magnetic
resonance (NMR) experiments (Wiithrich et al., 1996
).
Both types of experiments are fairly complex and require specialized
equipment. Also, they tend not to see all solvent
molecules equally. Crystallography detects the more ordered waters
(Levitt and Park, 1993
) whereas NMR more easily sees
those with longer residence times and those that are closer to the
surface (Otting et al., 1991
; Otting,
1997
). (In several NMR studies of proteins in mixed solvents,
only a few cosolvent molecules could be unambiguously identified
(Liepinsh and Otting, 1997
; Ponstingl and Otting,
1997
; Liepinsh et al., 1999
).) Other techniques,
such as hydrodynamic, small-angle x-ray and neutron scattering,
calorimetric, dielectric, and vapor-pressure absorption isotherm
experiments, provide only low-resolution data on surface-associated
solvent (see, e.g., Kuntz and Kauzmann, 1974
;
Pessen and Kumosinsky, 1985
; Rupley and Careri,
1991
; Svergun et al., 1998
). Atomic-resolution
molecular mechanics simulations pose as an alternative to experiment;
in practice, however, equilibrating the mixed solvent in the presence
of a macromolecule is time-consuming and, to date, only two works
(Tirado-Rives et al., 1997
; Sprous et al.,
1998
) have published the distributions of neutral cosolvents at
a macromolecular surface.
Measurement of the preferential interaction coefficient,
3,
|
(1) |
3 are
straightforward (although tedious) and can be done by a variety of
methods (see, e.g., Casassa and Eisenberg, 1964
3
data have already been gathered on proteins and DNA in the presence of
many cosolvents as discussed in several review articles (Kuntz
and Kauzmann, 1974To understand what
3 tells us about the water and
cosolvent distributions (or compositions) at a solute surface, let us
first describe in molecular terms what
3 measures by
using the "local-bulk domain" (AKA "two-domain") model (see
Record et al., 1998
and references therein), depicted in
Fig. 1. The "bulk domain" consists of
the region where the solvent displays the same properties as the mixed
solvent in the absence of macromolecular solutes. That region is
sufficiently far away from any solute so that the solvent doesn't
"know" anything about the presence of solutes. In the "local
domain" the solvent properties have in some way been affected by the
solute. When all species are uncharged and when
3 is
measured at dilute concentration of solute,
3 can be
interpreted as (Record and Anderson, 1995
; Inoue
and Timasheff, 1972
; Reisler et al., 1977
)
|
(2) |

3 by dialysis equilibrium
even when m2 is not negligibly small. (They also
proposed functional forms for how B3 and
B1 depend on m

|
(3) |
1 is merely a different way of presenting the
information in
3. In this work we consider only
uncharged species. The equations for
3 and
1 are modified when charges are present (see, e.g., Record et al., 1998
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(Note that in the literature there is another valid interpretation of
Eqs. 2 and 3, in which the Bi values are
heuristically thought of as "effective total numbers of [cosolvent]
and water molecules in contact with sites on the [solute] surface"
(Timasheff, 1998
). The exact interpretation used here
and by others (Arakawa and Timasheff, 1982b
;
Record and Anderson, 1995
; Hammou et al., 1998
) is different in that the Bi values
count the number of real solvent molecules in the entire local domain,
not solvent molecules effectively contacting the solute surface.)
The sign of
3 tells us about the local solvent
composition as compared to that of the bulk solvent. Dividing Eq. 2 by
B1 (which is positive by definition), we see
that the sign of
3 is determined by the quantity
B3/B1
m

3 < 0 (
1 > 0), the solvent composition (but not necessarily
the solvent density) of the local domain is depleted in cosolvent
and/or enriched in water relative to that of the bulk binary solvent.
This is what is meant by the term "preferential hydration."
Likewise, when
3 > 0 (
1 < 0) the
solvent composition of the local domain is depleted in water and/or
enriched in cosolvent relative to bulk, and is described by the term
"preferential binding" (although there may be no actual binding
going on) or "preferential accumulation" of cosolvent.
"Preferential solvation" by water/cosolvent is another commonly
used term.
Unfortunately, it is not yet clear how to interpret the magnitude of
3. Because solvent interactions are relatively weak, there is unlikely to be a sharp physical boundary between the local and
bulk domains (Kuntz and Kauzmann, 1974
). Hence, one cannot say definitively which solvent molecules are counted in Bi and contributing to
3. Also,
for the purpose of understanding solute-solvent interactions,
information on the solvent population right next to the solute is
desired. However, experimental evidence indicates that the local domain
can extend over quite a large territory, even when the interactions are
short-ranged. For example, changes in water structure due to solid
hydrophobic surfaces can be sensed tens of nanometers away (see, e.g.,
Blokzijl and Engberts, 1993
; Vogler,
1998
). Even the water distribution around proteins (Komeiji et al., 1993
; Lounnas et al.,
1994
; Makarov et al., 1998
), peptides
(Gerstein and Lynden-Bell, 1993
), and small solutes
(e.g., argon (Blokzijl and Engberts, 1993
) and
N-methylacetamide (Beglov and Roux, 1996
)) as
well as the distributions of urea and trifluoroethanol around a methane
solute (Smith, 1999
) display two or more peaks, corresponding to two or more layers of structured solvent.
Thermodynamic experiments suggest that the protein perturbs solvent
beyond the first water shell (see Lounnas et al., 1994
and references therein). In summary, not only is it not clear which
solvent molecules are counted in Bi, but also
the counted solvent molecules may not be contacting, nor binding, nor
necessarily even close to the solute. Because of these two issues, it
is not yet clear how to turn
3 data into quantitative
information on the solvent population near the solute.
The broad goal of our research is to get quantitative information on
the solvent distribution (or composition) at the solute surface from
3. In particular, we would like to obtain the number of
cosolvent (water) molecules within the first cosolvent (water) shell at
the solute surface. We call this quantity
B



3 and Bi data two hurdles
need to be overcome.
The first hurdle is that the relationship between
B
B
3 should be
due to the first-shell solvent molecules. If
3 is mostly
a function of the B


3? If so, then we can get a sense of
how
3 samples the properties of the nearby solvent distribution.
Second, a validated method of obtaining B1 and
B3 from
3 is needed. With one
experimental quantity (
3) and two desired unknowns (B1 and B3), some
assumptions on the Bi values or on the solvent distributions must be made. For example, 1) it has been suggested that
B1 be obtained from (or compared to) independent
experiments on the macromolecular solute in the absence of cosolvent
(Inoue and Timasheff, 1972
; Lee and Timasheff,
1974
, 1981
;
Lee and Lee, 1981
; Na and Timasheff,
1981
; Arakawa and Timasheff, 1982a
,
b
, 1985
;
Timasheff, 1998
; Courtenay et al.,
2000a
), e.g., by the NMR method of Kuntz (1971)
or by the vapor pressure measurements of Bull and Breese
(1968)
, or that B1 be obtained using a
different cosolvent (e.g., a "completely excluded" one
(Courtenay et al., 2000a
)). The assumption here is that
B1 is unchanged by the addition of (or a change
in the) cosolvent. 2) Various researchers have made comparisons of
B1 values to the amount of water in a monolayer (Zhang et al., 1996
; Hammou et al., 1998
;
Courtenay et al., 2000a
) suggesting that
B1 ~ B
). 4) A steric-exclusion model
(Arakawa and Timasheff, 1985
; Bhat and Timasheff,
1992
) attributes preferential hydration to the cosolvent
molecules' larger-than-water size. The cosolvent molecules cannot
closely approach the solute, and the region right up against the solute
is assumed to be filled only with pure bulk water. 5) In the analysis
of osmotic stress experiments, which often aim to measure the number of
water molecules "bound" or "released" in a reaction like the
binding of a ligand to a protein (Parsegian et al.,
1995
), it is assumed that
B3 = 0 (see
Parsegian et al., 1995
; Timasheff, 1998
,
references therein, and below). Parsegian et al. (1995)
discuss under what conditions this approximation is valid, but not all
works have followed their careful guidelines. (To translate the
language of osmotic stress to that of preferential interactions, see
Table 1 of Parsegian et al.,
2000
; also, what is called New, the
"excess number of waters," is equivalent to
1;
similarly, Nes, the "excess number of
[cosolvent molecules]," is
3. By equating
New with a difference in number of waters associated with the product versus with the reactant, the implicit assumption is that
B3 = 0.) 6) By assuming
that B1 and B3 values are
constant, independent of solvent composition, the
Bi values can be readily obtained from the slope
and intercept of linear
3 versus
m
1 versus
1/m
; Lee and Lee, 1979
,
1981
; Na and Timasheff, 1981
; Lee and Timasheff, 1981
; Eisenberg,
1994
).
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Clearly, various assumptions have been used to understand
3 (or
1) data or to extract
B1 and B3 values from
these data; to date, none of these assumptions has been validated
against surface solvent distributions.
To overcome these two hurdles, what is needed is a way to
measure, on the same solute-mixed solvent system, both
3
and the water and cosolvent distributions around the solute. From the latter, Bi and B
3. We chose to model a 2D system because the lower
dimensionality lets us simulate a system with many fewer molecules (a
ratio of ~N
1/3 fewer than in three
dimensions) with a considerable savings in computational time. This is
critical because it is difficult to gather sufficient statistics to
precisely determine
3 (which is a measure of
fluctuations). The time savings allows us to examine many different
water:cosolvent compositions
including those fairly dilute in
cosolvent
and several different cosolvent sizes. Equilibration was not
a serious issue (as it is for more realistic simulations) except in
cases of very dilute cosolvent and/or large cosolvent molecules.
Because our conclusions are qualitative, originating from a sound
physical basis, extending our results to three dimensions and to
complex-shaped molecules is straightforward.
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For each of the many solvent compositions and cosolvents we studied, we
analyzed the surface solvent distributions and made comparisons to
3. We found the following: 1) although the local domain
in principle can extend quite far from the solute surface, in practice,
its boundary can be demarked by a cosolvent (not water) monolayer, if
solvent structure is short-ranged. (The cosolvent monolayer is thicker
than the water monolayer because cosolvent molecules are larger than
water molecules.) 2) The solvent structure associated with the second
and further layers of solvent can mostly be ignored (if solvent
structure is short-ranged). 3) Combining 1) and 2) yields a recipe for
Bi (see also Fig. 3
B):
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(4) |
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(5) |



V





V


1 values are not accurate.
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METHODS |
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Model of the solvent and solute
In our simplified model, the water and cosolvent are small and large hard circular 2D disks of radii R1 and R3, respectively. The macromolecular solute's surface is modeled as a flat hard 2D "wall" of effectively infinite length. The only interactions are excluded-volume in nature. The solvent molecule disks cannot overlap with each other or with the solute hard wall. Fig 2 A displays a sample configuration.
We chose to model this simple system primarily for the savings in
computational time, as mentioned in the Introduction. Representing the
solvent and solute as low-resolution hard circular disks and as a hard
flat surface, respectively, also speeds computation and allows us to
examine excluded-volume effects on
3 without the
complication of shape effects. Future work would involve simulations of
the hard sphere model in three dimensions to make direct comparisons with experiment, and might also add soft interactions (see, e.g., Silverstein et al., 1998
) and examining differently
shaped solutes and solvent.
In this work we performed simulations with several different cosolvent
radii: R3/R1 = 1.3 (which is approximately the cosolvent:water hard-sphere-radius ratio
for methanol); 1.6 (ethanol, ethylene glycol, trifluoroethanol, urea);
2.0, 2.3 (glucose); 3.0 (sucrose); and 4.0 (which is the ratio of the
radius of gyration of PEG 200 to the water radius). To obtain the
values of R3/R1, the
hard-sphere radii are averages from values tabulated in Tang and
Bloomfield, 2000
, except that of trifluoroethanol is an average
from the values calculated using the methods described in
Edward, 1970
and Ben-Amotz and Willis,
1993
, and the radius of gyration of PEG 200 is from Bhat
and Timasheff, 1992
.
Monte Carlo simulations
We mimic a dialysis equilibrium by simulating two different boxes, one (denoted the "ms" box) containing the hard-wall macromolecular solute surface plus binary solvent; and the other box ("bulk"), containing only the binary solvent. Fig. 2, A and B show sample configurations of the ms and bulk boxes, respectively. Each box, separately, is simulated under the grand canonical ensemble with the parameters (µ1, µ3, V). This means that the water and the cosolvent in the ms box are in chemical equilibrium with the water and the cosolvent of an infinite bath of mixed solvent with parameters (µ1, µ3); the bulk box's solvent is also in exchange equilibrium with an infinite bath of mixed solvent with the same parameters (µ1, µ3). Because the solvent of both the ms and bulk boxes are in chemical equilibrium with the same infinite mixed-solvent bath, the ms and bulk boxes are, in effect, in chemical equilibrium with each other. This is how we mimicked a dialysis equilibrium.
Because both boxes (separately) were simulated under the grand
canonical ensemble, the numbers of water and cosolvent molecules (N1 and N3, respectively)
in each box fluctuate, but their equilibrium averages
N1
and
N3
are
well defined. Because of the constraint of not allowing overlap of
solvent with the hard walls, there is a very small net reduction of
particles from the ms box relative to the bulk box
(
Nmsi
<
Nbulki
), which is what
3 detects.
In this paper we examine many different binary solvents, each specified
by the variables (R3/R1,
r
), where
r

N
/
N
= m
is the average packing fraction (fractional volume occupancy) of the
bulk solution (
(
N

R32 +
N

R12)/V).
Except where indicated, all studies were performed with
= 0.39-0.40. We chose this value because, at this density, the amount of
surface solvent structure is as much as or more than that seen by
experiment and high-resolution simulations (see, e.g., Burling
et al., 1996
; Tirado-Rives et al., 1997
;
Sprous et al., 1998
; Pettitt et al.,
1998
). In any case, changing the overall packing fraction does
not greatly affect the
3 values. For the solvent system
of (R3/R1 = 2, r
3 by 14%; increasing
to 0.5 increases |
3| by 17%. For the solvent
sytem of (R3/R1 = 2, r
3| are
11% and +7%, respectively.
Below, we describe the details of the boxes and the simulations. Table 1 lists the simulation parameters for each of the mixed solvents. The ms box has two opposing hard walls at left and right, and periodic boundary conditions at top and bottom. The opposing hard walls are sufficiently far apart that they are separated by a large region of solvent that is bulk-like (i.e., whose density is uniform at the same value as in the bulk box). The opposing hard walls are thus not interacting with each other and the limit of dilute solute is maintained. In the bulk box we have implemented periodic boundary conditions in all directions. Starting configurations were created by one by one, placing each solvent molecule at a random location; if there was an overlap, a new random location was selected repeatedly until a nonoverlapping location for the molecule was found. The starting values of Ni were the same for both the ms and bulk boxes.
The Monte Carlo moves for each solvent species, i, consisted
of 1) displace steps, in which a random molecule of species
i is displaced to a new location; the new location is random
within a square with sides of length 2R1
centered at the molecule's original location; 2) create moves, in
which a molecule of species i is created at a random
location in the box; and 3) destroy moves, in which a random molecule
of species i is removed from the box. The sequence of events
during the Monte Carlo sequence is 1) a species (water or cosolvent) is
chosen randomly; 2) a type of move (displace, create, or destroy) is
chosen randomly; 3) the move is accepted or rejected based on a
Metropolis criterion (see, e.g., Allen and Tildesley,
1987
). In practice, because there are only hard interactions,
the displace move is accepted as long as there is no overlap. The
acceptance probability for the create move is min[1,
ziV/(N

exp(µi/(kT))/

i is the thermal de Broglie wavelength
i = (h2/2
mikT)1/2).
The acceptance probability for the destroy move is min[1,
N






), zi = 

). To increase the computational speed, we used the cell
method of neighbor lists (see Allen and Tildesley, 1987
)
for the waters. For each binary solution
(R3/R1,
r
), we performed at least six
simulations with different random seeds to obtain statistics and error
bars. Error bars were calculated as the standard error.
Calculation of
3 and Bfs
During each simulation run, for each box (ms or bulk), we
gathered
N1
and
N3
data. For the ms box, we also
calculated
1(x) and
3
(x), the average densities of water and cosolvent molecule
centers, respectively, at a distance x from the hard wall.
Fig. 3 A, shows an example of such a distribution.
We calculated
3 based on its definition. If we divide
Eq. 1 by the molecular weight of water, we see that
3
can be recast in terms of the cosolvent(solute):water number ratios,
ri
(
Ni
/
N1
):
3 =
r3/
r2. Because the
ms box is essentially the bulk box with two solutes (two hard walls,
far apart) added to it, we can directly calculate
3 by
approximating the derivative by a difference:
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(6) |
indicates the difference between the ms and bulk boxes
(e.g.,
r
rms
rbulk). Let us now determine
r3 and
r2:
|
(7) |
|
(8) |

N3
N
and

N1
N
. Inserting Eqs. 7 and 8 into
Eq. 6, and performing a Taylor's expansion keeping only first-order
terms in

N3
/
N
and 
N1
/
N
,
we obtain
|
(9) |
Note that this method of obtaining
3 from a grand
canonical simulation is different than that of Record and co-workers
(Mills et al., 1986
; Olmsted et al.,
1989
, 1991
,
1995
) who simulated without
explicit water. Because our simulations contain explicit water, they
are more useful for examining effects where the interactions with water
are comparable in magnitude with interactions with cosolvent.
B
i(x):
|
(10) |

i(x) distribution (see,
e.g., Fig. 3 A) and demarks the "end" of the first shell
of species i; x


In this paper, all lengths are reported in units of the water radius
(i.e., a water radius is "1"). In the limit of dilute solute, the
amount of solvent accumulated at a surface depends linearly on the
surface area if the surface is uniform. Therefore,
3,
1, Bi, and
B
3,
1,
Bi, and B
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RESULTS |
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How Bi depends on the solvent near the solute
In practice, the local domain is demarked by the outer edge of a
cosolvent monolayer; Bi depends mostly on
B
(x) curves then look like Fig. 3 B. The local domain in this
approximation has a well-defined outer boundary at the end of the
cosolvent first shell (at x









i(x) out to
x
B


3 for all solvent compositions and cosolvent sizes.
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3
(data not shown).
3 is indeed dominated by the first shells of water and
cosolvent. The solvent structure associated with the second and higher shells can be mostly ignored for the purposes of determining
3 and for understanding from where the dominant
contributions to
3 arise. Also, because the solvent
beyond the first shells can be assumed to be bulk-like in density, the
local domain in practice extends only to the end of the cosolvent monolayer.
A recipe for relating Bi to
B



V



V

x

V
[(R2 + x
(R2 + x
Assuming that B1 counts only the water in a
monolayer leads to the prediction of the wrong sign for
3


V



r

3 to B
r


r

3 < 0. (When there are only
excluded-volume interactions, the smaller species is always
preferentially accumulated relative to the larger because the smaller
molecules can better fit in the cavities and crevices between the
larger ones and the solute surface. That's why potato chip crumbs are
at the bottom of the bag.)
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3 is
then too positive.
Even though we can ignore water's nonbulk properties beyond its first
shell (and assume bulk behavior in these farther regions), we cannot
ignore the actual water molecules beyond the water's first shell. Some
of them still need to be counted in B1. The region from which one counts water molecules to obtain
B1 must be the same as that from which one
counts cosolvent molecules for B3 (more below).
How thick is a cosolvent monolayer?
We've established earlier that, for practical purposes, the local domain extends only to the end of the cosolvent first shell. How far from the surface is that? Let us describe in physical terms approximately where the peaks and troughs in the
3(x) distribution should lie.
(The argument is based on that by Ben-Naim (1974)
3(x) is considered. The light gray
molecule, which is usually a water because most molecules are waters,
fills the space between the observed cosolvent and the wall. We see that in the cosolvent distribution, the first and second peaks lie
approximately distances R3 (plus a little for
thermal motion) and 2R1 + R3 (plus a little) from the wall, respectively.
The first minimum (the end of the first cosolvent peak) should lie somewhere in between, ~R1 + R3 (plus some) from the wall.
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When determining B1, count waters from the same region of space as when determining B3
We wish to emphasize, at this point, that when counting water molecules for B1, one needs to count molecules from the same region of space as when counting cosolvent molecules. Above, we showed that when B<