| Life with a Svedberg ultracentrifuge Trends in Biochemical Sciences, Volume 2, Issue 10, 1 October 1977, Pages N219-N220 A.G. Ogston Abstract In his final article on the Svedberg Ultracentrifuge A. G. Ogston looks back on some of the problems and accidents that beset the machine and its operators and also talks about life in Oxford's Biochemistry Department during the machine's heyday. Abstract | PDF (390 kb) |
| Artificial molecular sieves and filters: a new paradigm for biomolecule separation Trends in Biotechnology, Volume 26, Issue 6, 1 June 2008, Pages 311-320 Jianping Fu, Pan Mao and Jongyoon Han Abstract Patterned regular sieves and filters with comparable molecular dimensions hold great promise as an alternative to conventional polymeric gels and fibrous membranes to improve biomolecule separation. Recent developments of microfabricated nanofluidic sieves and filters have demonstrated superior performance for both analytical and preparative separation of various physiologically relevant macromolecules, including proteins. The insights gained from designing these artificial molecular sieves and filters, along with the promising results gathered from their first applications, serve to illustrate the impact that they can have on improving future separation of complex biological samples. Further development of artificial sieves and filters with more elaborate geometrical constraints and tailored surface functionality is believed to provide more promising ideals and results for biomolecule separation, which has great implications for proteomic research and biomarker discovery. Abstract | Full Text | PDF (2566 kb) |
| Models for Excluded Volume Interaction between an Unfolded Protein and Rigid Macromolecular Cosolutes: Macromolecular Crowding and Protein Stability Revisited Biophysical Journal, Volume 88, Issue 2, 1 February 2005, Pages 971-985 Allen P. Minton Abstract Statistical-thermodynamic models for the excluded volume interaction between an unfolded polypeptide chain and a hard sphere or hard rod cosolute are presented, permitting estimation of the free energy of transfer of a polypeptide chain with fixed radius of gyration from a dilute (ideal) solution to a solution containing volume fraction of either cosolute. Also presented is a general thermodynamic description of the equilibrium between a unique native state and a manifold of unfolded or partially unfolded states of a protein distinguished by their respective radii of gyration. Together with results of a Monte Carlo calculation of the distribution of radii of gyration of four different unfolded proteins published by Goldenberg in 2003, these models are used to estimate the effect of intermolecular excluded volume upon an experimentally measurable apparent two-state constant for equilibrium between native and nonnative conformations of each of the four proteins, and upon the experimentally measurable root mean-square radius of gyration of the unfolded protein. Model calculations predict that addition of inert cosolutes at volume fractions exceeding 0.1 stabilizes the native state relative to unfolded states by an amount that increases strongly with and with the size of the native protein relative to the size of inert cosolute, and results in significant compaction of the manifold of unfolded states. Predicted effects are in qualitative and/or semiquantitative accord with the results of several published experimental studies. Abstract | Full Text | PDF (312 kb) |
Copyright © 2000 The Biophysical Society. All rights reserved.
Biophysical Journal, Volume 79, Issue 5, 2314-2321, 1 November 2000
doi:10.1016/S0006-3495(00)76477-0
Biophysical Theory and Modeling
Address reprint requests to Theo Odijk, Mosterdsteeg 13, Theory of Complex Fluids, 2301 EA Leiden, P.O. Box 11036, The Netherlands, Tel.: +31-71-5145-346; Fax: +31-71-5145-346.The transport of particles through concentrated polymer solutions and gels is still incompletely understood despite many investigations over several decades. In particular, major unsolved problems are the diffusion and electrophoresis of proteins in congested solutions. These are important both with regard to the characterization of the proteins themselves and the mechanism of their transport through biopolymer suspensions (synthetic and in tissues). Here, the effects of polymer depletion on these transport problems will be addressed, for they appear not to have been dealt with before. I concentrate especially on the practical case of small proteins migrating through a semi-dilute solution of flexible polymer chains. The protein radius may then be substantially smaller than the correlation length of the suspension leading to a considerable simplification of the depletion theory.
I first summarize the transport properties of various protein and other small probes determined experimentally. An attempt will be made to stick to the requirements: 1) a ≪ ξ i.e., the protein radius (or its equivalent when the protein is not exactly spherical in shape) is much smaller than the correlation length of the polymer solution (or gel for illustrative purposes). It is recalled that the static correlation length ξ has several interpretations in polymer scaling theory (de Gennes, 1979b). In the context of this paper, it is well to realize that ξ determines the screening of the excluded-volume effect: the average interaction between two segments is effectively zero when their separation is greater than ξ. (ξ ∼ c0−3/4 for a polymer of concentration c0 in a good solvent). 2) The solutions are really semi-dilute, i.e., the molar mass of the flexible polymer must be high enough and the concentration well beyond that of the overlap concentration c*, although the volume fraction must remain smaller than unity. 3) The probe particle ought to be mesoscopic in size, i.e., a ≫ A, the protein should be larger than A, the length of a Kuhn segment of the polymer. 4) Ideally, the interaction between the protein and the polymer should be hard or purely entropic. It is, of course, difficult to judge how well these conditions have been met. Diffusion, sedimentation and electrophoresis coefficients have all been measured, but I will simply group these in terms of a retardation factor R. A local Stokes–Einstein relation may or may not hold. In some experiments, the concentration dependence of the respective retardation factors for sedimentation and diffusion have turned out to be identical (see Ogston et al, who investigated the proteins ovalbumin, serum albumin, and γ-globulin in sulphated proteoglycan). The general form of R has often been found to be a stretched exponential in the polymer concentration c0.
![]() | (1) |
I have collected the exponents μ and ν from a variety of experiments in Table 1. There is no pretense to completeness; the data are representative, although I have included especially those measurements where the authors are concerned with defining the semi-dilute regime. It is obvious that there is no clear consensus with regard to the values for μ and ν. Unfortunately, the complete data concerning the range of polymer concentrations are not always presented; incorporating any data within the dilute regime will markedly affect the exponent ν. The scatter in the data also implies the necessity for more theoretical work on the complicated phenomena involved in the hindered transport of probe particles. Also included in Table 1 are several gel experiments for the sake of comparison. If the cross-linking density of the gel is relatively low, the restricted transport of proteins ought to be similar to that in a polymer solution.
| Table 1 The exponents from Eq. (1) measured for various probe particles in semi-dilute polymer solutions and gels |
| Experimental Technique | Nanoparticle | Radius (nm) | Polymer | μ | ν | ||
|---|---|---|---|---|---|---|---|
| Capillary electrophoresis | Human serum albumin | 2.7 | Polyacrylamide solution | 1.0 | 1.0 | ||
| Radko and Chrambach, 1996 | Polystyrene carboxylate | 7.0 | |||||
| Polystyrene sulfate | 9.5 | ||||||
| Electrophoresis | a-Lactalbumin | 1.4 | Polyethylene glycol solution | 1.0 | |||
| Radko and Chrambach, 1997 | Carbonicanhydrase | 1.85 | 1.1 | ||||
| Various proteins | >2.2 | 0.69 | 0.69 | ||||
| Diffusion by holographic interferometry | Bovine serum albumin (BSA) | 3.55 | Dextran solution | 0.5–1.0 | |||
| Kosar and Phillips, 1995* | |||||||
| Tracer diffusion | BSA | 3.55 | DNA solution | 1.0 | |||
| Wattenberger et al | |||||||
| Diffusion by light scattering | BSA | 3.55 | Polyethylene oxide (PEO) solution | 0.6–0.76 | |||
| Phillies et al | |||||||
| Sedimentation | BSA | 3.55 | PEO solution | 0.70 | |||
| Langevin and Rondelez, 1978 | BSA | 3.55 | PEO solution | 0.70 | |||
| Diffusion and sedimentation | Ovalbumin | 2.8 | Sulphated proteoglycan solution | 0.5 | |||
| Ogston et al | BSA | 3.55 | |||||
| γ-Globulin | 5.6 | ||||||
| Diffusion | γ-Crystallin | 2.35 | Hyaluronic acid solution | 1.0 | |||
| Laurent et al† | |||||||
| Sedimentation | BSA | 3.55 | Hyaluronic acid solution | 1.0 | |||
| Laurent and Pietruszkiewics, 1961† | |||||||
| Electrophoresis | Various proteins and dyes | 0.51–5.81 | Polyacrylamide gel | 1.0 | |||
| Rodbard and Chrambach, 1971a | |||||||
| Electrophoresis | BSA | 3.55 | Polyacrylamide gel | 1.0 | |||
| Rodbard and Chrambach, 1971b | |||||||
| Diffusion | Various small molecules | Average one nm | Polyacrylamide gel | 1.0 | 0.75 | ||
| Tokita et al | |||||||
| * My estimates for ν from their Fig. 7. † My estimates for ν for their data in the semi-dilute regime. |
A variety of theories has been put forward to explain Eq. (1). Ogston introduced the notion of relating the volume accessible to a probe within a fibrous network to the diffusion of the particle (Ogston, 1958,Ogston et al). (Note that this idea was also used independently in percolative transport theories of electrons in disordered media [see Balberg, 1987,Isichenko, 1992]). If the volume excluded to a probe by one fiber is v the pertinent accessible probability is 1−(v/V) where V is the volume of the system. For n fibers interacting with the probe independently, the total accessible volume must be
![]() |
Ogston's assumption in its simplest form (diffusion proportional to accessible volume) then implies ν=1 for the exponent in Eq. (1). This line of reasoning has been corroborated by computer simulations (Johansson and Löfroth, 1993) on the diffusion of spheres in networks of slender fibers. The Ogston ansatz has also been tested by others (Slater and Guo, 1995,Slater and Guo, 1996), though on porous media that are not necessarily always semi-dilute. For concentrated systems, the assumption of independent probabilities must clearly break down. Ogston et al also tried to explain why the exponent ν in Eq. (1) might deviate from unity.
A second class of theories deals with the screening of the hydrodynamic flow induced by the diffusing probe. The surrounding fibrous or polymeric network forms an obstruction because the fluid sticks to its convoluted surface. Such argumentation leads to a form given by Eq. (1) in view of Brinkman screening (Brinkman, 1947,Cukier, 1984). The concentration dependence of the diffusion is then given in terms of the hydrodynamic screening length ξH
![]() | (2) |
The segment distribution surrounding a protein in a semi-dilute polymer is depleted. The density tends to zero at the surface of the probe (de Gennes, 1979b). There are thus two types of effects missing from the theories quoted above. First is the rearrangement of the depletion layer as the probe diffuses through the polymeric network. Second, the segment density fluctuates strongly so the particle is hindered by an inhomogeneous medium. As we shall see, these difficulties become manageable theoretically when the probe is small compared with the polymer correlation length. It is first well to recall the equilibrium depletion theory in this precise limit. A small sphere immersed in a semi-dilute polymer has a depletion layer surrounding it of volume φ (a3) where a is the radius of the sphere (de Gennes, 1979a,Odijk, 1996). Hence, the number of depleted segments should be proportional to c0a3 and so the work wd of inserting the sphere into the solution must also be proportional to c0. Accordingly, we have (de Gennes, 1979a).
![]() | (3) |
![]() | (4) |
) is the segment density at position
. For depletion around a small sphere situated at the origin, we have c(
)=c0[1−(a/r)]2 (Odijk, 1996,Odijk, 1997b). The fact that wd should be proportional to the polymer concentration has been recently verified in experiments concerning the phase separation of protein–polymer solutions (S. Wang, J. van Dijk, J. Smit, T. Odijk, manuscript in preparation).Small proteins are several nanometers in diameter. At volume fractions of aqueous polymer <∼0.1, the correlation length ξ is generally greater than ∼10nm, so the asymptotic limit α ≪ ξ is perfectly realizable. The semi-dilute solution may be viewed as a strongly fluctuating background (de Gennes, 1979b) in which a protein is diffusing. The typical length scale of the polymer inhomogeneity is ξ, and the cooperative diffusion coefficient of the polymeric gel is kBT/6π η ξ, where η is the viscosity of water, (de Gennes, 1976,de Gennes, 1979b). Hence, in this, effectively nondraining, approximation, the characteristic time of decay of the polymeric background inhomogeneities is about τb≈ η ξ3/kBT. In contrast, within the depletion layer surrounding the translating protein, the polymer segments must reorganize themselves on a much faster time scale. In effect, the number of segments associated with the depletion layer is of order a3co: a very small number, because we require ξ ≫ a. A section of depleted polymer contains (a/A)2 segments (Odijk, 1996,Odijk, 2000), so the time scale associated with such a section diffusing out of the depletion layer should be of order τs≈ η a5/A2kBT, which is considerably shorter than τb. In summary, the diffusive transport of the protein may be split into two parts. One involves the very local friction exerted by the probe on the polymer, an effect that may be termed dynamic depletion. Second, this “dressed” particle (protein together with dynamic depletion layer) diffuses through the inhomogeneous polymer solution on much longer time scales. In the next section, I compute the local effect of dynamic depletion in a free-draining approximation. Few segments are involved in this process and most of the polymeric stress turns out to be restricted to a region close to the moving protein. The diffusion of the dressed probe will be dealt with by extending Ogston's argumentation to semi-dilute polymers.
The velocity of a segment in the polymer surrounding the protein is given by a balance of forces exerted on the segment (Yamakawa, 1971)
![]() | (5) |
(
) is the velocity of the solvent, m is the mobility of a segment, and f=−∂ μ/∂
is the force on the particular segment by the surrounding swarm of segments in terms of the chemical potential μ. Because the Stokesian approximation to the hydrodynamics applies, the velocity of the solvent is a superposition of a background velocity
0, the original velocity of the fluid in the absence of the polymer, and the velocity
in, induced by the force f, exerted by the polymer on the fluid. The latter velocity would involve a screened Oseen tensor in a Freed–Edwards description (Freed, 1978) with a screening length ξH as introduced above, but it is neglected in the free-draining approximation used here. In fact, the velocity
o leading to convective diffusion may also be disregarded, a supposition proven below.Next, we need the segment chemical potential. Assuming the nonequilibrium-free energy is now given by Eq. (4), we compute the potential as a functional derivative in terms of the more convenient variable Ψ(Ψ2≡c/c0)
![]() | (6) |
, t); t =time; Δ=Laplacian. Accordingly, the continuity equation for the segment density leads to a nonlinear diffusion equation![]() | (7) |
in the z direction and a uniform density Ψ2=1. At the surface of the spherical probe (r=a), we have Ψ=0, the segment density must tend to zero. Moreover, the segments cannot penetrate the protein, so the radial flux must also vanish at the surface.![]() | (8) |
At low velocities of the probe, it is possible to solve Eq. (7) perturbatively. We seek a stationary solution: ∂c/∂t=0. We introduce Ψ=Ψ0+ϵ into Eq. (7), letting ϵ(
) be a relatively small variable. The zeroth-order distribution, Ψ0, is the solution to a Laplace equation (Odijk, 1997b,Odijk, 2000)
![]() | (9) |
)≡Δϵ, satisfying a Laplace equation,![]() | (10) |
![]() | (11) |
We next rewrite the segment velocity in terms of α and Ψ0 using Eqs. (5).
![]() | (12) |
![]() | (13) |
![]() | (14) |
![]() | (15) |
![]() | (16) |
. Upon positioning the fixed probe at the origin, the velocity of the segments changes by virtue of the impenetrability of its surface. The difference between the two forces in the respective cases gives us the polymer contribution to the drag,![]() |
![]() |
![]() |
![]() |
![]() |
Next, we still have to ascertain whether or not the effect of convective diffusion is negligible. Because the fluid is incompressible, we express the convective term missing from Eq. (7) as
![]() | (18) |
![]() | (19) |
On time scales considerably longer than the reorganization time τs of segments within the dynamically evolving depletion layer, the protein diffuses as one dressed particle (protein+depletion layer) through the polymer network. The latter is quite inhomogeneous because it fluctuates strongly as discussed earlier. We would now like to compute the volume Va accessible to the protein in a manner similar to Ogston's analysis of the same quantity for a sphere in a fibrous network (Ogston, 1958). His straight rigid fibers are, however, fixed entities, whereas the semi-dilute polymer is not, an issue we deal with in what follows.
The polymer solution is enclosed in a container of volume V, which is hypothetically split up into cubic boxes each of size λ3. The scale λ is chosen such that a ≪ λ ≪ ξ. Thus, a protein in a certain box i sees an essentially homogeneous polymer solution on the scale of the box given one particular realization out of an ensemble of polymer configurations. On a scale λ, we may neglect details concerning the dressed particle (protein+depletion layer) and fluctuations of the semi-dilute network on scales of order ξ.
As was discussed above, the number of segments depleted by a small protein is proportional to the concentration, so the depletion energy also scales with the concentration. A particular realization of the polymer is defined by the function c (
i), which denotes the (effectively constant) polymer density in each box situated at
i and labeled i. Hence, the work of depletion may be written as
![]() | (20) |
We next need the excluded volume between the protein and the polymer enclosed solely within box i. This is simply the cross virial coefficient
![]() | (21) |
i). The protein interacts with a “blob” of polymer of size a; this contains a2/A2 segments in the quasi-ideal case (this number would be different were the solvent to be very good; for a full discussion, see Odijk, 1996). There are pi blobs in box i interacting independently with the probe. This work of depletion wb is smaller than kBT, which allows the Boltzmann factor to be linearized (wi=piwb). Note that Eq. (21) is asymptotically exact in the limit a ≪ ξ.The fraction of volume accessible to the protein owing to the polymer in box i is simply (1−(Bi/V)). Accordingly, the total accessible volume is
![]() | (22) |
![]() |
i) is the number of segments within box Ni divided by the volume λ3, the summation may be carried out independent of the distribution of polymer into the respective boxes. We finally end up with an expression for the accessible volume in terms of the depletion energy, wd=kc0kBT (where c0 is the bulk concentration),![]() | (23) |
![]() | (24) |
We have focused on two effects that have been analyzed independently here: local dynamic depletion and diffusion of the probe at long time scales. They should be compared with the retardation by hydrodynamic screening (see Eq. (2)). An ideally consistent theory would include all three effects at the same time but is a formidable undertaking for the following reasons. In the hydrodynamic screening theories, all polymeric detail is smeared out on scales less than the screening length ξH (Freed, 1978,de Gennes, 1976). Such a smoothing would be incompatible with the existence of a dynamic depletion layer of size a of the protein. Next, inhomogeneity of the polymeric network is an essential phenomenon in trying to understand the diffusion of the probe. Hence, even within a self-consistent field scheme, hydrodynamic screening and the fluctuating polymeric drag on the protein must be dealt with and derived on the same level. If the solvent is very good, fluctuations in the polymer density are so great that we should turn to renormalization theory. Setting up dynamic versions of current renormalization analyses of equilibrium depletion about small particles (Eisenriegler et al,Eisenriegler, 1997,Hanke et al) is clearly no mean task.
The polymeric drag on the protein has been estimated within a free-draining approximation. It is difficult to assign a definite value to the segment mobility because it depends on the chemical detail of a segment. If one were to insist on the segments interacting with each other in a fully nondraining limit, one would have a local drag (i.e., for a dressed probe=protein+its depletion layer, in the absence of long-range hydrodynamic screening),
![]() |
If the three effects discussed above contribute in principle to the impediment of a diffusing protein, it may explain the variety of (effective) values for the exponents μ and ν compiled in Table 1. One difficulty of interpretation is the lack of quantitative precision in the hydrodynamics as stressed above. Recent electrophoresis experiments on small probes (Radko and Chrambach, 1996,Radko and Chrambach, 1997) in well-defined semi-dilute polymer solutions suggest that μ and ν should be equal to unity. It is thus of interest to test the prediction, Eq. (24) as such, quantitatively. Radko and Chrambach, 1996,Radko and Chrambach, 1997 used Ferguson plots in which the logarithm (base 10) of the electrophoretic mobility of the protein was plotted against the concentration c0 of the polymer in g/ml. The depletion theory (Eqs. (4)) predicts a retardation coefficient K10 (ml/g) (see Eq. (1))
![]() | (25) |
Given the variety of retardation exponents measured in the past (Table 1), the discussion of the previous paragraph must be regarded as preliminary. One conclusion of the present work is that several regimes for probe transport may exist depending on the probe size and the properties of the polymer. The particular exponents (unity) found by Radko and Chrambach, 1996,Radko and Chrambach, 1997 may well stem from the fact that 1) the protein radii a are actually considerably smaller that the polymer correlation lengths ξ; 2) care has been exercised in establishing the concentration regimes are really semi-dilute; 3) the interaction between probe and polymer is quasi-ideal (see Eq. (4)). Their retardation exponents deviated from unity for larger proteins. We have recently determined the partitioning of small proteins between the two isotropic phases resulting from the phase separation of protein–polysaccharide solutions (S. Wang, J. van Dijk, J. Smit and T. Odijk, manuscript in preparation). Eqs. (4) are well satisfied when the polymer solutions are semidilute. There is therefore strong evidence for the empirical validity of an Ogston-like argument leading to Eq. (24). A rigorous analytical proof for the proportionality of the diffusion coefficient of a probe in a semidilute system to its accessible volume is lacking.
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