| Damped-Dynamics Flexible Fitting Biophysical Journal, Volume 95, Issue 7, 1 October 2008, Pages 3192-3207 Julio A. Kovacs, Mark Yeager and Ruben Abagyan Abstract In fitting atomic structures into EM maps, it often happens that the map corresponds to a different conformation of the structure. We have developed a new methodology to handle these situations that preserves the covalent geometry of the structure and allows the modeling of large deformations. The first goal is achieved by working in generalized coordinates (positional and internal coordinates), and the second by avoiding harmonic potentials. Instead, we use dampers (shock absorbers) between every pair of atoms, combined with a force field that attracts the atomic structure toward incompletely occupied regions of the EM map. The trajectory obtained by integrating the resulting equations of motion converges to a conformation that, in our validation cases, was very close to the target atomic structure. Compared to current methods, our approach is more efficient and robust against wrong solutions and to overfitting, and does not require user intervention or subjective decisions. Applications to the computation of transition pathways between known conformers, homology and loop modeling, as well as protein docking, are also discussed. Abstract | Full Text | PDF (1732 kb) |
| Translational Diffusion of Fluorescent Proteins by Molecular Fourier Imaging Correlation Spectroscopy Biophysical Journal, Volume 91, Issue 9, 1 November 2006, Pages 3482-3498 Michael C. Fink, Kenneth V. Adair, Marina G. Guenza and Andrew H. Marcus Abstract The ability to noninvasively observe translational diffusion of proteins and protein complexes is important to many biophysical problems. We report high signal/noise (≥250) measurements of the translational diffusion in viscous solution of the fluorescent protein, DsRed. This is carried out using a new technique: molecular Fourier imaging correlation spectroscopy (M-FICS). M-FICS is an interferometric method that detects a collective Fourier component of the fluctuating density of a small population of fluorescent molecules, and provides information about the distribution of molecular diffusivities. A theoretical analysis is presented that expresses the detected signal fluctuations in terms of the relevant time-correlation functions for molecular translational diffusion. Furthermore, the role played by optical orientational degrees of freedom is established. We report Fickian self-diffusion of the DsRed tetramer at short timescales. The long-time deviation of our data from Fickian behavior is used to determine the variance of the distribution of the protein self-diffusion coefficient. We compare our results to the expected outcomes for 1), a bi-disperse distribution of protein species, and 2), dynamic disorder of the host solvent. Abstract | Full Text | PDF (983 kb) |
| Modeling the Role of Incisures in Vertebrate Phototransduction Biophysical Journal, Volume 91, Issue 4, 15 August 2006, Pages 1192-1212 Giovanni Caruso, Paolo Bisegna, Lixin Shen, Daniele Andreucci, Heidi E. Hamm and Emmanuele DiBenedetto Abstract Phototransduction is mediated by a G-protein-coupled receptor-mediated cascade, activated by light and localized to rod outer segment (ROS) disk membranes, which, in turn, drives a diffusion process of the second messengers cGMP and Ca in the ROS cytosol. This process is hindered by disks—which, however, bear physical cracks, known as incisures, believed to favor the longitudinal diffusion of cGMP and Ca. This article is aimed at highlighting the biophysical functional role and significance of incisures, and their effect on the local and global response of the photocurrent. Previous work on this topic regarded the ROS as well stirred in the radial variables, lumped the diffusion mechanism on the longitudinal axis of the ROS, and replaced the cytosolic diffusion coefficients by effective ones, accounting for incisures through their total patent area only. The fully spatially resolved model recently published by our group is a natural tool to take into account other significant details of incisures, including their geometry and distribution. Using mathematical theories of homogenization and concentrated capacity, it is shown here that the complex diffusion process undergone by the second messengers cGMP and Ca in the ROS bearing incisures can be modeled by a family of two-dimensional diffusion processes on the ROS cross sections, glued together by other two-dimensional diffusion processes, accounting for diffusion in the ROS outer shell and in the bladelike regions comprised by the stack of incisures. Based on this mathematical model, a code has been written, capable of incorporating an arbitrary number of incisures and activation sites, with any given arbitrary distribution within the ROS. The code is aimed at being an operational tool to perform numerical experiments of phototransduction, in rods with incisures of different geometry and structure, under a wide spectrum of operating conditions. The simulation results show that incisures have a dual biophysical function. On the one hand, since incisures line up from disk to disk, they create vertical cytoplasmic channels crossing the disks, thus facilitating diffusion of second messengers; on the other hand, at least in those species bearing multiple incisures, they divide the disks into lobes like the petals of a flower, thus confining the diffusion of activated phosphodiesterase and localizing the photon response. Accordingly, not only the total area of incisures, but their geometrical shape and distribution as well, significantly influence the global photoresponse. Abstract | Full Text | PDF (558 kb) |
Copyright © 2005 The Biophysical Society. All rights reserved.
Biophysical Journal, Volume 89, Issue 4, 2258-2276, 1 October 2005
doi:10.1529/biophysj.104.057331
Biophysical Theory and Modeling
J. Michael Schurr*,
,
, David P. Rangel* and Sergio R. Aragon†
* Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
† Department of Chemistry/Biochemistry, San Francisco State University, San Francisco, California 94132
Address reprint requests to J. Michael Schurr, Tel.: 206-543-6681; Fax: 206-685-8665.
exceeds in magnitude the contribution of the exchange reactions. Under the assumption that the exchange contribution is dominated by sites in the first surface-contiguous layer, the ratio of the average exchange constant to its neutral random value is determined for each osmolyte. These ratios all lie in the range 1.0±0.15, which indicates rather slight deviations from random occupation near the macromolecular surface. Finally, a mechanism is proposed whereby the chemical identity of an osmolyte might be concealed from partially ordered multilayers of water in clefts, grooves, and pits, and its consequences are noted.The effects of weakly interacting osmolytes on the conformational equilibria and ligand binding reactions of biological macromolecules have been studied intensively over the past two decades 1,2,3,4. A major objective in many cases was to ascertain the difference between the number of water molecules “associated” with the products of a particular reaction on one hand and the corresponding number “associated” with its reactants on the other. The precise meaning, or interpretation, of the numbers of “associated” waters and the differences therein remains a subject of discussion and some debate 5,6,7,8,9. This general approach to studying changes in “associated” waters has come to be known as the osmotic stress method. In the case of a solution, consisting of water (solvent, component 1), dilute macromolecules (components 2J, J=1, … M), and neutral osmolyte (cosolvent, component 3), the osmotic stress method yields the slope
where K is the equilibrium constant for the reaction when written so as to take no account of either water or osmolyte, a1 is the activity of the water, and
denotes the concentrations of each kind of macromolecule. This slope is extrapolated to the limit of infinite dilution,
The difference in “associated” waters between products and reactants is sometimes taken to be the aforementioned slope,
![]() | (1) |
and
denote the respective standard state chemical potentials,
and
denote the respective stoichiometric coefficients of the reaction under consideration, and![]() | (2) |
and the symmetrically defined
are concentration-based “preferential interaction coefficients”, which characterize the variation of that part of
that does not depend upon
with either
respectively.Alternative preferential interaction coefficients are defined in connection with equilibrium dialysis experiments and are usually molality based. The molalities of species 1, 2, and 3 are denoted by, respectively,
and
Two common molality-based preferential interaction coefficients are:
and
where the index J denoting the macromolecular conformation has been suppressed. Although relations between these and other molality-based preferential interaction coefficients have been intensively investigated, the connections between molality-based and concentration-based preferential interaction coefficients, like
have received less attention. Clever and intuitive thermodynamic approaches indicate that for any given macromolecular species 2,
![]() | (3) |
can be regarded as the excess number of osmolyte molecules in the vicinity of the macromolecule above the quantity that would be expected from the number of water molecules in that region and the bulk concentration ratio, 
Although the analysis below indicates that Eq. (3) is correct, the rigor of the thermodynamic approaches used to derive it is debatable. For example, the neglect of the osmotic pressure due to the macromolecule within its local domain is justifiable only for a domain of very great size, yet in many cases that domain was assumed to extend no more than one or two hydration layers beyond the macromolecule. The likely resolution of this paradoxical circumstance is noted briefly below.
Recently several articles appeared in which
or the equivalent
was expressed in terms of the so-called Kirkwood-Buff integrals 10,
and
where g12(r) and g32(r) are the pair correlation functions, which are described in greater detail below 11,12,13,14. The derivation of the main relation followed an unusually circuitous, piecewise, and technically demanding route that took place over three different articles and a book that collectively spanned 26 years 11,15,16,17. Chitra and Smith combined two relations that appeared earlier in Ben-Naim’s book 17, namely his Eq. 6.7.49 for
and Eq. 6.17.16 for
to obtain the final expression for
The Eq. 6.7.49 was explicitly derived in Ben-Naim’s book, but the derivation of the much more difficult Eq. 6.17.16 was simply described as quite lengthy and omitted entirely. In fact, the first stage of that proof was presented in his 1975 article 15, and the second stage was presented in his 1988 article 16. Unfortunately, neither Chitra and Smith 11 nor Ben-Naim 17 referenced directly those earlier articles, from which the entire proof could be assembled. Chitra and Smith 11 demonstrated the approximate validity of their expression for
by molecular dynamics simulations of both the pair correlation functions and the free energies of insertion of different small species 2 into aqueous solutions over a wide range of concentrations of various cosolvents. Shimizu 13 suggested a way to obtain the separate G12 and G32 from the measured
and
where
is the partial molecular volume. He employed a relation between
and G12 and G32 that was also first presented in Ben-Naim’s book 17 (Eq. 6.17.22), but the derivation, described as quite lengthy, was also omitted entirely. Again, a two-stage proof of the relevant relation can be found in the same two earlier articles 15,16. Shimizu 12 also extended his idea to determine the changes, ΔG32 and ΔG12, accompanying a reaction of species 2 from the measured
and
which was assumed to be the entire ΔV associated with the reaction. Shimizu and Smith 14 examined the differences between the effects of crowders, such as polyethylene glycol, and small osmolytes, such as glycerol, that stabilize native protein structures, on the separate G12 and G23. Schellman 18 undertook a related analysis in terms of the cross-second virial coefficients (
).
The initial objective of this study is to provide a complete and much simpler derivation of the relevant expression for
directly from the results of Kirkwood and Buff 10, as well as some important details that are missing from their original treatment of multicomponent thermodynamics. Such details include the choice of origin of the coordinate frame in a highly deformable macromolecule, its manifestation in the pair correlation functions, the invariance of the integrals of
to that choice, a complete definition of the pair correlation function in the classical grand ensemble, and a derivation of the partial molecular volume. This derivation of
follows a considerably more direct line than the Ben-Naim-Chitra-Smith development, and is technically much simpler. All of the results of Kirkwood and Buff that are needed to derive
were rederived and found to be correct. In addition, a short proof of Ben-Naim’s expression for
is provided in Appendix D .
Connections between this concentration-based
and the molality-based
and
are derived via thermodynamic arguments that make use of certain expressions of Anderson et al. 19,20, which were also verified by rederivation.
The main objective of this study is to clarify the meaning(s) of the
and
and especially to relate them to more familiar quantities such as excluded volumes and equilibrium constants for osmolyte-solvent exchange in the region surrounding the macromolecule 21,22,23,24,25,26. Although this development is more heuristic than rigorous, useful predictions and significant insights emerge. As an example, the experimental
data for seven different osmolytes interacting with bovine serum albumin (BSA) are analyzed using this formulation in conjunction with geometrical parameters reckoned from the crystal structure of human serum albumin (HSA). The separate excluded volume and exchange contributions are evaluated. Under the assumption that only the surface-contiguous layer of osmolyte sites is important, the ratio of the average exchange constant to its neutral random value is obtained in each case.
Finally, a mechanism is proposed whereby the chemical identity of the osmolyte may be concealed from partially ordered hydration multilayers in clefts, grooves, and pits, and its consequences are briefly noted.
Let us consider a system comprising ν different molecular species, α, β, … η, at constant T, V. In this case, when each species j undergoes a change of 
![]() | (4) |
![]() | (5) |
Thus, the column vector containing the ν different dμk is related to the ν different dNj by the matrix relation dμ=M dN, where the elements of M are given by Eq. (5). Inversion of this matrix relation gives dN=M−1dμ, or
![]() | (6) |
![]() | (7) |
Kirkwood and Buff 10 established that the
in Eq. (7) are directly related to integrals of the relevant pair correlation functions,
![]() | (8) |
is the αβ-pair correlation function, or radial distribution function, and r=|r1-r2| is the distance between the arbitrarily chosen central atom of an α-molecule at r1 and that of a β-molecule at r2, as indicated in Appendix A . A complete definition of gαβ(r12) in the grand ensemble 27 is given in Eq. (A1) in Appendix A . It must be emphasized that gαβ(r12) pertains to no atoms other than the arbitrarily chosen central atom of each molecule, and will in general depend upon that choice. Because the relations presented here derive ultimately from fluctuations in the numbers of molecules in a volume V that is large enough to contain on average a great many molecules of each kind, those relations must be independent of the choice of central atom. It may be concluded from Eq. (8) that integrals of the gαβ(r)-1 over the volume V, or at least from 0 out to a distance where gαβ(r) has converged to 1.0, are independent of the choice of central atom. The grand ensemble used to derive Eq. (8) can itself be derived by considering that the volume V is a tiny fraction of an enormously larger supersystem with a fixed number of molecules 27.The pair correlation function has the following physical meaning. If the chosen central atom of a molecule of kind α is located at r1, then cβgαβ(r) is the probability per unit volume of finding the chosen central atom of a molecule of kind β at r2, such that r=|r1-r2|. A completely random disposition of β-molecules in the vicinity of α corresponds to gαβ(r)=1.0. In general, gαβ(r) is the factor by which the purely random probability per unit volume (i.e., cβ) must be multiplied to reckon the actual probability per unit volume of finding a β-molecule at distance r from an α-molecule. The pair correlation functions are by definition symmetric, so gαβ(r)=gβα (r), and also Bαβ=Bβα. We shall later regard cβgαβ(r) as the rotationally averaged mean density of centers of β-molecules at a distance r from the center of an α-molecule.
The matrix relation in Eq. (8) can be written as B=(kT/V)M−1, which can be inverted to give M=(kT/V)B−1, and
![]() | (9) |
For the particular case of a three-component system held at constant T and V, the chemical potential μ2(T,c1,c2,c3) depends on all three concentrations, so
![]() | (10) |
is held constant, then
and it follows from Eq. (10) that![]() | (11) |
An equation analogous to Eq. (10) holds for dμ1, from which it follows that
![]() | (12) |
![]() | (13) |
It is shown in Appendix B that
where
denotes the partial molecular volume (m3/molecule). Then Eq. (13) yields
![]() | (14) |
After substituting Eq. (14) into Eq. (12) and rearranging one finds
![]() | (15) |
After substituting Eqs. (14) into Eq. (11), and Eq. (11) into Eq. (2), there results
![]() | (16) |
The
must be evaluated in the same limit.The right-hand side of Eq. (16) is partially evaluated by leaving the
factors in place, but expanding the
in terms of elements of the three-component B-matrix,
where
![]() | (17) |
Every term in both the numerator and denominator of the right-hand side of Eq. (16) contains at least one factor of c2, which can be divided out. Any remaining terms that still contain a factor of c2 will vanish in the limit
and are therefore omitted. After effecting some factorization and cancellation, the result can be expressed as
![]() | (18) |
It remains to evaluate the factor in parentheses on the right-hand side of Eq. (18). An expression for
was presented by Kirkwood and Buff 10 without explicit derivation. That derivation is sketched briefly in Appendix C and the result is given in Eq. (C6). Note that the denominator of Eq. (C6) is independent of α, and cancels out of the ratio,
An important simplification is that
applies in the limit
which leaves just a two-component (2×2), rather than a three-component (3×3) B-matrix, so the indicated cofactors become just elements of the two-component B-matrix. In fact, Eq. (C6) gives the simple expressions,
and
where D is the denominator, which cancels out of
After performing straightforward algebra, invoking the symmetry, Bαβ=Bβα, and omitting any canceling terms, the entire factor in parentheses reduces to c1/c3, and Eq. (18) becomes simply
![]() | (19) |
From the definition of G12 in Eq. (17), it is clear that c1G12 is the excess number of 1-molecules in the vicinity of a 2-molecule beyond what would be expected from a random disposition of 1-molecules. An analogous meaning holds for c3G32. Although the c1G12 and c3G32 in Eq. (19) are explicitly excess numbers, rather than the total numbers of molecules in a domain surrounding the 2-molecule, Eq. (19) for
can be written in a form that is completely analogous to Eq. (3) for
as will be seen.
The pair correlation functions g12(r) and g32(r) must converge to the value 1.0 at large distances. Typically, for small osmolytes in a solution of dilute macromolecules, this occurs within, at most, a few nanometers beyond the maximum extension of the macromolecule (species 2). Thus, the upper limit of the integral in G12 or G32 can be reduced from ∞ to R, where R is any value sufficiently great that both g12(r) and g32(r) have converged to 1.0. Then Eq. (19) can be written as
![]() | (20) |
is the number of α-molecules within a sphere of radius R around the 2-molecule. The relevant criterion for the minimum size, Rmin, of the domain surrounding the macromolecule is clearly the convergence of the relevant pair correlation functions to 1.0 at all
Because standard osmolytes are typically at least a few times larger than water, species 3 is typically excluded by the macromolecule from a larger volume than is species 1. Consequently, g32(r) cannot possibly converge to 1.0 within the volume defined by the centers of 1-molecules in the first hydration shell, and the minimum domain size generally must involve more water molecules than those in the first hydration shell in order for Eq. (20) to be valid.Equation (20) is rigorously valid for a finite domain size of radius
even though no account was taken of the osmotic pressure due to the macromolecule. This is likely a consequence of allowing the domain boundary to move with the macromolecule, so that it can never be contacted by the macromolecule and never experience its contribution to the osmotic pressure inside the macromolecular domain.
The preferential interaction coefficient can also be written in the simple form
![]() | (21) |
can also be obtained simply by replacing the index 1 by 3 and vice versa in Eqs. (2), which is permitted by the evident symmetry of the theory in regard to 1↔3 interchange. It follows from Eqs. (19) that![]() | (22) |
The right-hand side of Eq. (22) is just
which matches the right-hand side of Eq. (3). Furthermore, it is shown by thermodynamic arguments in Appendix E that in the limit, 
![]() | (23) |
(c.f. Eqs. (E16) and (E19)). The relations in Eq. (23) were obtained by assuming that
and
remain constant, independent of
and
This should be a rather good approximation, when
and
which correspond to prevailing conditions in many studies.
is obtained via vapor pressure osmometry, and
is measured by equilibrium dialysis. At typically low osmolyte volume fractions
is quite close to
but
is rather different 5,19,20. In any case, most experimental work has reported
or
or both. Equation (23) thus provides the principal connections between these theoretical expressions for
(or
) in terms of pair correlation functions and the experimentally measured quantities.We note that this
cannot be simply expressed as
because there is no Maxwell relation equating
to
Moreover,
is also not equivalent to
because direct evaluation of the latter in terms of
and
9 yielded a result that is not equivalent to the right-hand side of Eq. (22).
Radial distribution functions of multicomponent systems have not yet been treated rigorously and analytically, and no suitable approximate formulation in terms of basic quantities, such as excluded volumes and exchange constants for specific sites, was presented previously. Heuristic approximate evaluations of various contributions to c1g12(r), c3g32(r),
and
are presented in the following section.
In general, both repulsive exclusion forces and attractive binding forces contribute simultaneously to
and
These contributions are evaluated approximately below. Comparisons with the models adopted by other workers will be discussed after this model is developed.
To simplify the discussion, let us first consider the effects of repulsive hard-core exclusion forces between the water (species 1) and the macromolecule (species 2). The superscript “ex” is used to indicate a contribution arising from such forces. A substantial void region, where
is expected around r=0, as illustrated in Fig. 1. If both species 1 and 2 were perfectly spherical, then this void region would be followed at larger r by the region of the first coordination shell, where
11,17,28. This is true even in the case of hard spheres with no attractive interactions whatsoever. The first coordination shell would then be followed by a dip of g12(r) below 1.0, which in turn would be followed by a weaker second coordination shell, a second shallower dip, and so on, finally leveling off to g12(r)=1.0. In the case of a nonspherical macromolecule, the dips and peaks associated with the void volumes and coordination shells arising from different parts of the surface are superposed with a distribution of relative “phases”, so that
likely exhibits simply a more or less smooth rise to a plateau at 1.0, as indicated in Fig. 1. Because typical neutral osmolytes (species 3) are larger than water, the void regions of
would extend outward somewhat farther than in the case of
as indicated also in Fig. 1. The volumes excluded to the centers of species 3 and 1 can be expressed as
and
respectively. The difference between the volumes accessible to the centers of species 1 and 3 within the macromolecular domain is defined by,
which is also the difference between the volumes excluded to species 3 and 1.
and
versus the distance r between the central atoms of species 2 and either 1 or 3, respectively. The
and
are those parts of the pair correlation functions that arise solely from repulsive exclusion forces between species 2 and either 1 or 3, respectively.The
contribution to
can be understood heuristically in terms of the osmotic pressure-volume work required to introduce a 2-molecule into the solution. The 2-molecule must effectively extrude the centers of the osmolytes (species 3) from a region occupied by the centers of the waters (species 1), which requires the input of work equal to
where π is the osmotic pressure of species 1 in the bulk solution. This work appears as a term in
which is the increase in solution free energy upon adding a 2-molecule to the solution. The variation of the osmotic pressure of species 1 with its activity is given by
Thus, the osmotic work contribution to
is
when
is sufficiently dilute that
This simple analysis breaks down, when
becomes comparable to 
In the void regions, where
and
vanish,
and
are practically independent of either
or
The contribution of repulsive exclusion forces to
is obtained from Eq. (21) as
![]() | (24) |
Any variation of
with c1 or c3 should be rather slight, due to the constancy of the void volumes, so
should remain nearly constant, so long as
doesn’t change much from the value,
which will be the case, provided that
Due to the generally larger void volume of g32(r) in comparison to g12(r), both
and
should be generally positive. In view of Eqs. (22), it is also expected that
![]() | (25) |
denotes the contribution of purely repulsive exclusion forces. Hence,
is expected to be proportional to c3 and negative.Let us now consider generic attractive forces, long-range van der Waals forces in particular, that may affect the densities of (centers of) species 1 and 3 in the region immediately beyond the void volume. Such mean densities are denoted by
and
where the superscript “ga” denotes generic attractions. For simplicity it will be assumed here that such generic attractions do not discriminate significantly between species 1 or 3, so that the ratio of their densities at any r beyond the void volume matches that of the bulk solution, that is
which implies that
even though both may differ significantly from 1.0. In that case, the net contributions to
and
reckoned from Eqs. (21), respectively, are
Thus, generic, but nondiscriminating, attractions may alter the local densities of species 1 and 3, but make no net contribution to the preferential interaction coefficients. Nonvanishing contributions of attractive interactions presumably arise from discriminatory exchange reactions, as indicated in the following section.
Schellman 21,22,23,24,25,26 introduced the notion that the relevant reactions in solution were exchange reactions at sites or regions near the surface of the macromolecule (species 2). The objective here is to incorporate such exchanges within this formulation of the preferential interaction coefficients in terms of integrals over particular pair correlation functions.
Let us consider first the jth site, which may contain either a single osmolyte (species 3) or
water molecules (species 1). For osmolytes that do not bear charged groups, it is expected that
but that assumption need not be invoked at this point. The exchange reaction for this site is written as
![]() | (26) |
denotes a complex with
bound waters on average in the jth site and M·L denotes a complex with a single bound osmolyte at the jth site. It is not required that
be an integer. When the macromolecule M (species 2) is sufficiently dilute, the equilibrium constant for Eq. (26) is![]() | (27) |
is the osmolyte activity for its hypothetical Henry’s Law mol fraction 1.0 standard state, wherein each osmolyte experiences only the environment of its infinitely dilute solution (in water). The fraction of occupied (by osmolyte) j-sites is![]() | (28) |
The instantaneous density of the central atom of a 3-molecule in the jth site for any fixed configuration of the 2-molecule is a three-dimensional δ-function, δ(r-rj), where rj is the variable position of the central atom of the 3-molecule in the jth site in a coordinate frame originating on the central atom of the 2-molecule. When this density is averaged (with appropriate statistical weights) over the rj for all allowed positions and configurations of the 3-molecule in the site and over all configurations of the 2-molecule, and that result is in turn rotationally averaged about the chosen central atom of the 2-molecule, there results a distributed or smeared density function,
which depends only on the distance r from that central atom and should be peaked near the average distance
The preceding averages are taken only over those configurations, wherein rj lies within the somewhat arbitrarily defined boundaries of the jth exchange site for each configuration of species 2. This density function is still normalized, so 
The density function for those 1-molecules that occupy the jth site, when the 3-molecule is absent, is defined in the following way. First the center of a 3-molecule with a fixed configuration is placed at rj in the jth site of a 2-molecule with a fixed configuration. The surrounding solution is assumed to consist entirely of 1-molecules. The density of all the η1 1-molecules in the solution,
is then averaged over all positions and configurations of those same 1-molecules. The resulting mean density of 1-molecules will practically vanish over an excluded volume,
that depends upon the particular rj and fixed configurations ξ and ζ of the 2- and 3-molecules, respectively. The quantities ξ and ζ should be regarded as generalized vectors, or lists, of the coordinates of all the atoms in the 2-molecule and 3-molecule, respectively. Now, the 3-molecule is removed, but the configuration of the 2-molecule is held fixed at ξ. The 1-molecules are allowed to equilibrate with the 2-molecule in that same configuration ξ. The mean density of those 1-molecules, whose centers lie within the particular excluded volume,
is defined by
where the sum runs only over the
(variable) 1-molecules in each configuration, whose centers at
lie within V(rj,ξ,ζ), and the average is taken over all configurations of 1-molecules. This mean density of 1-molecules in V(rj,ξ,ζ) is further averaged over the rj (within the jth site), ξ, and ζ by repeating this initial averaging process for various rj, ξ, and ζ, and then averaging the results over rj, ξ, and ζ. One obtains
where the subscripts denote the final averages over rj, ξ, and ζ. By definition, the average value of
for the jth site is
When species 3 has no charged groups, so electrostriction effects are negligible, it is expected that the average number of 1-molecules that occupy an empty exchange site is
Finally, rotational averaging of
around the central atom of the 2-molecule yields
which depends only upon the scalar distance r from the central atom of the 2-molecule. The normalization integral remains unchanged, so
It is expected that the final smeared density,
will normally be peaked near
and exhibit a slightly greater width than
because the centers of multiple 1-molecules are involved.
In light of the preceding remarks, the contribution of the jth site to the mean density of 1-molecules in the vicinity of the 2-molecule is
![]() | (29) |
![]() | (30) |
and
:![]() | (31) |
![]() | (32) |
The total contributions of exchange reactions at all such sites are
and
where the sums run over all sites (j), which lie beyond the macromolecular void volume.
Let us now consider a model system that exhibits simultaneously all of the aforementioned repulsive exclusion forces, generic attractions, and discriminatory interactions that are responsible for exchange. For simplicity, we shall assume that the contributions of the various interactions to the total mean densities, c1g12(r) and c3g32(r), are additive. This important assumption is not generally valid and merits some discussion. For any given fixed configuration of species 2, the repulsive hard-core exclusion forces between 2 and either 1 or 3 affect the densities of species 1 and 3 in one region of space, whereas attractions or repulsions of longer range act on 1 and 3 in a different region (outside the hard core, but still inside the macromolecular domain of radius R). Hence, the effects of the short-range and longer-range interactions are largely spatially complementary, and would be expected to be nearly additive, even after configurational and rotational averaging of species 2. Nondiscriminatory generic attractions make no net contribution to
or
and are not considered further here. In regard to exchange reactions, some interaction between exchanging sites is generally expected. The neglect of such interactions renders this discussion oversimplified in an important regard, whenever
is not small compared to
Nevertheless, useful insights may emerge, and quantitatively useful accuracy may be obtained whenever 
Under this additivity assumption
![]() | (33) |
![]() | (34) |
Equations (24) give the
in terms of c1, c3 and
and Eqs. (31) express the
in terms of νj, Kj, a3, and a1.
To examine the regime of small c3 in more detail, additional approximations are invoked. First, it is assumed that
and
are independent of c3 (which has units of molecules/m3) up to a molar concentration of 1.0. To lowest order in c3, that gives
and
where γ3 is the activity coefficient of species 3. With these approximations, and the exact relation,
Eqs. (33) become,
![]() | (35) |
![]() | (36) |
We imagine that a lattice of exchanging sites (or cells) with initial volume
fills the entire osmolyte-accessible region of the macromolecular domain of radius R
An osmolyte is regarded as bound to a particular site, when its central atom lies within that cell. The initial cell volume is taken as
so the cell size matches the partial molecular volume of the osmolyte. Thus, if all of the initial sites were filled, species 3 would just fill the entire volume. The average number of 1-molecules that occupy a cell, when the osmolyte is absent, is assumed to be
which is exact far from the macromolecular surface, and is almost certainly a fairly good approximation even near the macromolecular surface, except when electrostriction effects are large. Thus, the species 1 would just fill the lattice volume in the absence of species 3. While holding the overall lattice volume constant, one could now choose a smaller uniform cell size for the lattice of exchange sites, namely
where
is an integer, provided that the contributions of each site to
are reduced by the same factor,
and that the j-sums in Eqs. (35) are extended from the original L sites of volume
to the mL smaller sites of volume
For some sufficiently large value of m, when
should become entirely independent of m or
A lattice cell size in that range is adopted here. The center of the jth cell is taken at position q(j), and its exchange constant, Kq(j), may vary from one cell to the next in a limited way, so as to create a gradient of the Kq(j) along any reasonably smooth path in the discrete q(j) space. Both
and the exchange constant, Kq(j), for each smaller cell of volume,
are taken as the values typical of a site with the initial volume,
whose center lies within that smaller cell, with the understanding that m-1 adjacent sites are closed, whenever an osmolyte binds to the smaller cell in question. In this way, any region of volume
will bind one and only one osmolyte in approximately the same way as a function of a3 or a1, regardless of the number of cells into which is it subdivided, and the maximum densities of species 1 and 3 will remain unchanged. The smaller lattice cell volumes are employed simply to represent the spatial variation of the exchange constants at higher resolution than is afforded by cells of volume
By suitable adjustment of the Kj associated with the various sites in the lattice, it is possible to create any conceivable mean densities c1g12(r) and c3g32(r) at a level of resolution set by the lattice cell size, subject to the implicit volume conservation rule invoked here (i.e.,
). The approximate validity of this model is limited to the regime of small volume fraction of species 3, so that events in any one region of volume
do not affect events in neighboring regions of the same size. The large anticooperativity associated with the closure of m-1 binding sites surrounding a given site, when it becomes occupied, generally has a very strong influence on the system, except when the volume fraction of species 3 is small. In that special case, for a cell volume
Eqs. (35) become
![]() | (37) |
![]() | (38) |
When the standard free energy change for an exchange reaction vanishes, Kj=1.0. First, let us consider the limit of small c3, where, γ3→1.0 and
→1.0, so the numerator of each term in the j-sums of Eqs. (37) becomes
For typical small neutral osmolytes, excluding molecules the size of trehalose and sucrose, one expects that
Note that, if
as was assumed in early treatments of exchange by Schellman 21,22,23,24,25,26, then
and the entire exchange contribution of the jth site would vanish. Although the condition, Kj=1.0, is the point of neutrality in terms of vanishing standard state free energy change, it is not generally the point of neutrality in regard to purely random binding in the neighborhood of a 2-molecule, because ν 1-molecules are released for every 3-molecule bound. The point of neutrality in regard to random binding of 1- and 3-molecules at the jth site, when γ3=1.0 and
is clearly Kj=ν.
In general, sites that lie out in the bulk solution sufficiently far from the surface of the 2-molecule can make no net contribution to
or
so for such sites it is absolutely required that
which can be taken as the general condition for neutrality of any site in regard to random binding of 1’s and 3’s. Smaller values of Kj yield a positive contribution of the jth site to 
We consider next the limit, wherein
so the second terms in the denominators of Eqs. (37) can be ignored. The product,
is unitless, and has the same value in any units, so one can take c3 in mol/L and
in L/mol. For small neutral osmolytes, one typically has
and
up to c3=1.0M. Thus, for
the inequality,
will be satisfied, when
Hence, Kj could be as large as 10, and still satisfy this inequality for c3=1.0M. In other words, K could be up to 2–3 times greater than the neutral random binding value,
and still the second terms in the denominators of Eqs.