Anomalous diffusion of water in biological tissues.

This article deals with the characterization of biological tissues and their pathological alterations. For this purpose, diffusion is measured by NMR in the fringe field of a large superconductor with a field gradient of 50 T/m, which is rather homogenous and stable. It is due to the unprecedented properties of the gradient that we are able not only to determine the usual diffusion coefficient, but also to observe the pronounced Non-Debye feature of the relaxation function due to cellular structure. The dynamics of the probability density follow a stretched exponential or Kohlrausch-Williams-Watts function. In the long time limit the Fourier transform of the probability density follows a long-tail Lévy function, whose asymptotic is related to the fractal dimension of the underlying cellular structure. Some of the properties of Lévy walk statistics are discussed and its potential importance in understanding certain biophysical phenomena like diffusion processes in biological tissues are pointed out. We present and discuss for the first time NMR data giving evidence for Lévy processes that capture the essential features of the observed power law (scaling) dynamics of water diffusion in fresh tissue specimens: carcinomas, fibrous mastopathies, adipose and liver tissues.     

Hydrodynamic properties of macromolecular complexes. I. Translation

We have developed an improved theory for calculating the translational frictional coefficients of rigid macromolecular complexes composed of unequal spherical subunits. The Yamakawa hydrodynamic interaction tensor, which improves on the Oseen tensor by taking account of the finite sizes of the frictional subunits, has been generalized to accomodate nonidentical subunits. Iterative numerical methods are described for solving the set of simultaneous hydrodynamic interaction equations, thus avoiding preaveraging. The theory is applied to prolate ellipsoids of revolution, to lollipops, and to dumbbells, and comparison is made with earlier, more approximate theories.     

Anomalous electrophoresis of deoxyribonucleic acid restriction fragments on polyacrylamide gels

A detailed study has been made of the polyacrylamide gel electrophoresis of DNA restriction fragments obtained from two plasmids, pBR322 and p82-6B. Variables studied were molecular weight, gel concentration, temperature, and electric field strength. The retardation coefficients of the larger fragments (greater than 800 base pairs) were independent of molecular weight. The retardation coefficients of the smallest fragments (less than or equal to 300 base pairs) were proportional to Mr1/3, and therefore to the mean geometric radii of the fragments. The logarithm of the relative mobility of all fragments was also proportional to Mr1/3. The anomalous migration of certain fragments on polyacrylamide gels was found to be "transportable" into fragments generated by different restriction enzymes. Anomalous migration was enhanced at lower temperatures and disappeared upon increasing the temperature. A fragment which migrated anomalously slowly migrated even more anomalously when dimerized; dimerizing a normally migrating fragment resulted in the normal migration of the dimerized fragment. Anomalously migrating fragments were found to be localized in distinct regions of the pBR322 circle.     

Anthracycline gels. Preparation and some physico-chemical properties

Gels have been prepared from aqueous solutions of anthracyclines by addition of salts. The gels are thixotropic and thermally reversible. They are stable for several months in the refrigerator and for long times even at room temperature. The gel-solution transition (melting) temperature depends on the concentration of the anthracycline and on the concentration and nature of the added salt. The melting has been followed by 1H-NMR. Only weak intermolecular interactions (stacking and hydrogen bonds) originate the drug network, within which the solvent is entrapped. 1H-NMR and polarimetric data suggest a stacked helical arrangement of the anthracycline molecules. The gelation process is cooperative.     

The macromolecular properties of peanut agglutinin

The dependence upon solution conditions of the quaternary structure and gross conformation of peanut agglutinin was examined by sedimentation equilibrium, sedimentation velocity, gel chromatography, and circular dichroism. At pH 8, the protein exists as a compactly folded tetramer of molecular weight 98,000. Between pH 4.75 and pH 3.0, the molecular reversibly dissociates to a (still globular) dimer. In the presence of denaturants such as SDS or guanidinium chloride, the protein dissociates to its four equal-sized constituents polypeptide chains. The circular dichroic spectrum of peanut lectin exhibits changes in the near ultraviolet upon binding of lactose, whereas the far ultraviolet spectrum remains unchanged. Dissociation to the dimeric state produces subtle changes in both the near and far ultraviolet circular dichroic spectrum.     

Physical properties of polyethyleneimine-alginate gels

Summary The procedure for preparation of polyethyleneimine (PEI)-alginate gel and some of its physical properties are presented. The rigidity modulus (G) of the gel appears to increase to the second power of PEI concentration. Shrinkage is linearly related to pH up to pH 6.0. G increases as the pH is lowered, and decreases after freezing. The gels does not dissolve on heating and are strong, but fairly brittle. They are resistant to proteolytic enzymes.     

The macromolecular properties of blood-group substances. Sedimentation-velocity and viscosity measurements

1. Sedimentation-velocity, intrinsic-viscosity and partial-specific-volume measurements on a typical blood-group-specific glycoprotein are reported for a range of environmental conditions. 2. The sedimentation coefficients, S, are strongly concentration-dependent, and follow the reciprocal law; the limiting values at 2°, 25° and 45°, after correction to 25°, show slight dependence on temperature. 3. The intrinsic viscosities, [η], at 25° and 45° show more marked temperature-dependence, and correspond to a very asymmetric or very expanded molecular conformation. 4. From the value of the ratio K/[η], where K=S⁰.d(1/S)/dc, it is concluded that the molecular conformation is roughly spherical; application of the Einstein viscosity equation then suggests an expansion factor of about 60, compatible with a flexible configuration approaching that of a random coil. 5. The sedimentation coefficient is not affected by variation of ionic strength in the range 0·01–0·50, nor by pH in the range 3–10. 6. Sodium dodecyl sulphate at 1·5% produces a small decrease in S; the effect is greater than would be expected from the observed extent of binding, but is too small to correspond to a significant change in secondary structure; the serological activity is unaffected by sodium dodecyl sulphate. 7. All the properties observed indicate the absence of any secondary structure in blood-group substances.     

Compressed representations of macromolecular structures and properties

We introduce a new and unified, compressed volumetric representation for macromolecular structures at varying feature resolutions, as well as for many computed associated properties. Important caveats of this compressed representation are fast random data access and decompression operations. Many computational tasks for manipulating large structures, including those requiring interactivity such as real-time visualization, are greatly enhanced by utilizing this compact representation. The compression scheme is obtained by using a custom designed hierarchical wavelet basis construction. Due to the continuity offered by these wavelets, we retain very good accuracy of molecular surfaces, at very high compression ratios, for macromolecular structures at multiple resolutions.     

The effect of macromolecular polyanions on the functional properties of human hemoglobin.

The binding of dextran sulphate and heparin to human hemoglobin and their effect on the properties of gas transport have been investigated. Both dextran sulphate and heparin are strongly bound by oxy-hemoglobin as well as deoxyhemoglobin and the stoichiometry of the binding (polyanion/tetrameric hemoglobin) is less than unity; sedimentation analysis gives indication for the existence of octomers. The oxygen affinity of hemoglobin is decreased, to the same extent, by both dextran sulphate and heparin. This effect is pH-dependent. In addition the polyanions affect the position and the magnitude of the Bohr effect. In the presence of dextran sulphate the recombination of hemoglobin with carbon monoxide after flash photolysis is biphasic and the fraction of quickly reacting material increases with dilution of the protein.     

Mechanical properties of globular proteins gels: 1. Incipient gelation behaviour

It has long been known that globular protein molecules in concentrated aqueous solution can be converted into a different form by heating or use of denaturing agents. Under certain conditions of pH and ionic strength, elastic gels are formed. This work describes kinetic measurements of viscosity and elasticity close to the gel point (sol-gel transition) in bovine serum albumin solutions. These studies and optical rotation measurements near the gel point lend support to the conclusions of earlier structural studies on this system, that the gel is fibrillar in nature.     

Red cell aging. II. Anomalous electrophoretic properties of neuraminidase treated human erythrocytes.

Desialylation of human red blood cells (RBC) by Vibrio cholerae neuraminidase (VCN) was found to produce cells with electrophoretic properties which were inconsistent with the view of simple loss of N-acetylneuraminic acid (NANA) as the sole effect of VCN treatment. Modification of human RBC with 50--350 U VCN/10(10) RBC for one hour at 37 degrees C releases 90-100% of the NANA and produces a progressive decrease towards zero in their electrophoretic mobilities when measured in 0.15 M NaCl (pH 7.2) at 25 degrees C. The appearance of positive groups on the desialylated cells was indicated by the VCN-treated cells displaying positive mobilities below approximately pH 5.5 and increased negative mobilities at approximately pH 9 as well as substantial increases in their mobility at neutral pH following treatment with formaldehyde. Adsorption of about 95% of the VCN activity at 0 degrees C to the RBC did not produce any significant change in their electrophoretic mobilities thus indicating that the observed changes in the electrophoretic properties of the RBC following VCN treatment could not be attributable to adsorption of VCN. These studies indicate that the cationic charge groups which appear at the electrophoretic surface of the RBC after VCN treatment are probably of endogenous origin. It is suggested that this alteration rather than simple NANA release may operate to shorten the in vivo survival time of desialylated red cells.     

Role of solvent properties of aqueous media in macromolecular crowding effects

Analysis of the macromolecular crowding effects in polymer solutions show that the excluded volume effect is not the only factor affecting the behavior of biomolecules in a crowded environment. The observed inconsistencies are commonly explained by the so-called soft interactions, such as electrostatic, hydrophobic, and van der Waals interactions, between the crowding agent and the protein, in addition to the hard nonspecific steric interactions. We suggest that the changes in the solvent properties of aqueous media induced by the crowding agents may be the root of these “soft” interactions. To check this hypothesis, the solvatochromic comparison method was used to determine the solvent dipolarity/polarizability, hydrogen-bond donor acidity, and hydrogen-bond acceptor basicity of aqueous solutions of different polymers (dextran, poly(ethylene glycol), Ficoll, Ucon, and polyvinylpyrrolidone) with the polymer concentration up to 40% typically used as crowding agents. Polymer-induced changes in these features were found to be polymer type and concentration specific, and, in case of polyethylene glycol (PEG), molecular mass specific. Similarly sized polymers PEG and Ucon producing different changes in the solvent properties of water in their solutions induced morphologically different α-synuclein aggregates. It is shown that the crowding effects of some polymers on protein refolding and stability reported in the literature can be quantitatively described in terms of the established solvent features of the media in these polymers solutions. These results indicate that the crowding agents do induce changes in solvent properties of aqueous media in crowded environment. Therefore, these changes should be taken into account for crowding effect analysis.     

Teaching macromolecular modeling.

Training newcomers to the field of macromolecular modeling is as difficult as is training beginners in x-ray crystallography, nuclear magnetic resonance, or other methods in structural biology. In one or two lectures, the most that can be conveyed is a general sense of the relationship between modeling and other structural methods. If a full semester is available, then students can be taught how molecular structures are built, manipulated, refined, and analyzed on a computer. Here we describe a one-semester modeling course that combines lectures, discussions, and a laboratory using a commercial modeling package. In the laboratory, students carry out prescribed exercises that are coordinated to the lectures, and they complete a term project on a modeling problem of their choice. The goal is to give students an understanding of what kinds of problems can be attacked by molecular modeling methods and which problems are beyond the current capabilities of those methods.     

Immunogenic properties of neomycin conjugates with macromolecular carriers]

To obtain diagnostic antibodies to neomycin, immunogenic properties of the neomycin conjugates with macromolecular carriers were studied. Bovine serum albumin and copolymers of N-vinylpyrrolidone with crotonic acid and N-hydroxyphthalimide ether of crotonic acid were used as carriers. It was shown that immunization of mice by the conjugates in combination with Freund's adjuvant resulted in production of neomycin antibodies, the titer being 1/80 to 1/130. When the antibiotic conjugates with the copolymers of N-vinylpyrrolidone were used and not the neomycin conjugates with the carrier of the protein nature, the neomycin antibodies were produced in the absence of Freund's full adjuvant. With the use of the isolated antibodies to neomycin a method for indirect solid phase enzyme immunoassay of neomycin was developed at the minimum detectable level of 25 ng/ml.     

Electrophoretic mobility of DNA in gels. II. Systematic experimental study in agarose gels

A systematic study has been undertaken to prove or disprove the predictions of a revised reptation model, biased reptation with fluctuations (BRF). Our data, which scan about two orders of magnitude of DNA sizes and of electric fields, and a fourfold range of gel concentrations, are in qualitative and quantitative agreement with the model and support the applicability of this theory to DNA gel electrophoresis. In particular, we show that the mobility in the compression zone scales as the first power of the electric field, and that the limit of separation scales as the inverse first power of the electric field, for low enough fields. © 1994 John Wiley & Sons, Inc.     

Effects of sterilization treatments on some properties of alginate solutions and gels.

Aqueous sodium alginate solutions were subjected to various heat sterilization treatments. Sodium alginate powder was also treated by both gamma-irradiation and ethylene oxide sterilization. The effects of these treatments on the viscosities of sodium alginate solutions and both the diameter and strength of the beads formed in 0.1 M CaCl2 solutions were determined quantitatively. The viscosity of sodium alginate solutions and the gel strength of the calcium alginate beads decreased with increasing sterilization temperature while the bead diameters were found to increase. All these effects can be attributable to a reduction in the degree of polymerization of the alginate molecules as a result of the heat treatments. Ethylene oxide and gamma-irradiation treatments caused similar effects. Standard conditions for sterilization are necessary for comparative studies with alginate beads.     

Exclusion in hyaluronate gels.

Osmotic pressures of solutions of hyaluronate (HA) (mol wt 117,000) and mixtures of HA and bovine serum albumin (BSA) in phosphate-buffered saline, pH 7.2 were measured with a membrane osmometer. The data were fit with a virial expansion in integral powers of total nondiffusible solute concentration. Values of number average molecular weight were calculated for HA and the mixtures from the first virial coefficients. The excluded volume of HA in the single nondiffusible solute solution was calculated from the second virial coefficient extracted from the data on the HA solution. The excluded volume of HA with respect to BSA was estimated from the "osmotic parameters" of HA and BSA by an approach developed in 1976 by Shaw. The resulting excluded volume of HA with respect to BSA was compared with those obtained from a lightly cross-linked HA gel and from solutions of HA (mol wt 1.5 x 10(6)) studied in 1964 by Laurent. The development of this cross-linked HA gel and its subsequent calibration are described.