On the direction of the diffusional electric field in a mucous layer

A simple model of the mucous layer is used to illustrate the complex relationship of the diffusional electric field direction in the layer and parameters of the latter. It is shown that the field direction may depend not only on the ratios of mobile microion diffusivities but also on the characteristics of the layer (carboxylic group concentration and dissociation constant). The electric field direction is also shown to vary across the layer under appropriate conditions. The results are used to interpret the electrophoretic mechanism of the transport of macromolecules across the mucous layer on the surface of the digestive tract wall.     

Free solution mobility of oligomeric DNA

The free solution electrophoretic mobility of a charged oligomer in an ionic solvent that approximately takes into account relaxation field effects, screening of the velocity field, and the hydrodynamic interactions resulting from motions of the charges due to an electric field is described. For double‐stranded DNA, the free solution electrophoretic mobility under ionic strengths determined by the buffer and pH conditions relevant to capillary electrophoresis increases with increasing molecular weight up to few hundred base pairs. © 1999 John Wiley & Sons, Inc. Biopoly 49: 209–214, 1999     

Nucleocytoplasmic transport: cargo trafficking across the border

Transport of macromolecules between the cytoplasm and the nucleus is mediated by at least three different classes of soluble transport receptors, members of the importin-beta protein family, the Mex67/Tap family and the small nuclear transport factor 2 (NFT2). All nuclear transport factors can bidirectionally traverse the nuclear pore complex through specific interactions with phenylalanine/glycine-rich nuclear pore complex components. Recent kinetic and structural analyses revealed novel insight into the details of these interactions. In addition, new biochemical and genetic studies have dramatically improved our understanding of ribosomal and messenger RNA export, unveiling a tight coupling between RNA processing and transport.     

Solubilization of Minerals by Bacteria: Electrophoretic Mobility of Thiobacillus ferrooxidans in the Presence of Iron, Pyrite, and Sulfur

Thiobacillus ferroxidans is an obligate acidophile that respires aerobically on pyrite, elemental sulfur, or soluble ferrous ions. The electrophoretic mobility of the bacterium was determined by laser Doppler velocimetry under physiological conditions. When grown on pyrite or ferrous ions, washed cells were negatively charged at pH 2.0. The density of the negative charge depended on whether the conjugate base was sulfate, perchlorate, chloride, or nitrate. The addition of ferric ions shifted the net charge on the surface asymptotically to a positive value. When grown on elemental sulfur, washed cells were close to their isoelectric point at pH 2.0. Both pyrite and colloidal sulfur were negatively charged under the same conditions. The electrical double layer around the bacterial cells under physiological conditions exerted minimal electrostatic repulsion in possible interactions between the cell and either of its charged insoluble substrates. When Thiobacillus ferrooxidans was mixed with either pyrite or colloidal sulfur at pH 2.0, the mobility spectra of the free components disappeared with time to be replaced with a new colloidal particle whose electrophoretic properties were intermediate between those of the starting components. This new particle had the charge and size properties anticipated for a complex between the bacterium and its insoluble substrates. The utility of such measurements for the study of the interactions of chemolithotrophic bacteria with their insoluble substrates is discussed.     

A contribution to the theory of biological staining based on the principles for structural organization of biological macromolecules

Biological staining is to a large degree explainable based on the principles governing folding and aggregation of macromolecules in aqueous solution. Most macromolecules are polyions, which, except for heteropolysaccharides, have a large proportion of nonpolar or only slightly polar residues. Because they are amphiphilic, they react in water by a complex set of hydrophobic interactions involving charged residues, nonpolar residues and water molecules. The hydrophobic interactions lead to complex folding systems or micelle-like structures. Dyes are amphiphilic molecules with a tendency to form micelles, but with limitations due to geometric constraints and charge repulsion. Macromolecules and dyes react with each other in aqueous solution following the same principles as for the structural organization of macromolecules, as in protein folding for example. Dye binding requires near contact between nonpolar groups in both the dye and macromolecule, and this is accomplished by choosing a pH at which the dye and macromolecule have opposite net charges. Charge attraction is insufficient for binding in most cases, but it is directive because it determines which macromolecules a given dye ion is able to contact. These considerations apply to the staining of globular (cytoplasmic) proteins and to nucleic acid staining. The staining mechanism is by hydrophobic interactions. Above approximately pH 3.5, DNA may also bind dyes by hydrophobic intercalation between the bases of the double helix; at lower pH the double helix opens and dye binding is as for RNA and globular proteins. Heteroglycans (mucins) have virtually no nonpolar groups, so nonpolar interactions are restricted to the dye molecules. Metachromatic staining of heteroglycans is due to hydrophobic bonding or micelle formation between the monovalent planar dye molecules aided by charge neutralization by the negatively charged heteroglycans. Alternatively, as the charge attraction increases with the number of closely placed charges, acidic heteroglycans may be stained by a polycation such as alcian blue or colloidal iron. For elastic fiber and collagen staining, actual hydrophobic interactions are less important and hydrogen bonding and simple nonpolar interactions play a major role. These macromolecules may therefore be stained using a nonaqueous alcoholic solution.     

A contribution to the theory of biological staining based on the principles for structural organization of biological macromolecules

Biological staining is to a large degree explainable based on the principles governing folding and aggregation of macromolecules in aqueous solution. Most macromolecules are polyions, which, except for heteropolysaccharides, have a large proportion of nonpolar or only slightly polar residues. Because they are amphiphilic, they react in water by a complex set of hydrophobic interactions involving charged residues, nonpolar residues and water molecules. The hydrophobic interactions lead to complex folding systems or micelle-like structures. Dyes are amphiphilic molecules with a tendency to form micelles, but with limitations due to geometric constraints and charge repulsion. Macromolecules and dyes react with each other in aqueous solution following the same principles as for the structural organization of macromolecules, as in protein folding for example. Dye binding requires near contact between nonpolar groups in both the dye and macromolecule, and this is accomplished by choosing a pH at which the dye and macromolecule have opposite net charges. Charge attraction is insufficient for binding in most cases, but it is directive because it determines which macromolecules a given dye ion is able to contact. These considerations apply to the staining of globular (cytoplasmic) proteins and to nucleic acid staining. The staining mechanism is by hydrophobic interactions. Above approximately pH 3.5, DNA may also bind dyes by hydrophobic intercalation between the bases of the double helix; at lower pH the double helix opens and dye binding is as for RNA and globular proteins. Heteroglycans (mucins) have virtually no nonpolar groups, so nonpolar interactions are restricted to the dye molecules. Metachromatic staining of heteroglycans is due to hydrophobic bonding or micelle formation between the monovalent planar dye molecules aided by charge neutralization by the negatively charged heteroglycans. Alternatively, as the charge attraction increases with the number of closely placed charges, acidic heteroglycans may be stained by a polycation such as alcian blue or colloidal iron. For elastic fiber and collagen staining, actual hydrophobic interactions are less important and hydrogen bonding and simple nonpolar interactions play a major role. These macromolecules may therefore be stained using a nonaqueous alcoholic solution.     

Macromolecular crowding in biological systems: hydrodynamics and NMR methods

Most biologically relevant environments involve highly concentrated macromolecular solutions and most biological processes involve macromolecules that diffuse and interact with other macromolecules. Macromolecular crowding is a general phenomenon that strongly affects the transport properties of macromolecules (rotational and translational diffusion) as well as the position of their equilibria. NMR methods can provide information on molecular interactions, as well as on translational and rotational diffusion. In fact, rotational diffusion, through its determinant role in NMR relaxation, places a practical limit on the systems that can be studied by NMR. While in dilute solutions of non-aggregating macromolecules this limit is set by macromolecular size, in crowded solutions excluded volume effects can have a strong effect on the observed diffusion rates. Hydrodynamic theory offers some insight into the magnitude of crowding effects on NMR observable parameters.     

Electroosmosis Dominates Electrophoresis of Antibiotic Transport Across the Outer Membrane Porin F

We report that the dynamics of antibiotic capture and transport across a voltage-biased OmpF nanopore is dominated by the electroosmotic flow rather than the electrophoretic force. By reconstituting an OmpF porin in an artificial lipid bilayer and applying an electric field across it, we are able to elucidate the permeation of molecules and their mechanism of transport. This field gives rise to an electrophoretic force acting directly on a charged substrate but also indirectly via coupling to all other mobile ions, causing an electroosmotic flow. The directionality and magnitude of this flow depends on the selectivity of the channel. Modifying the charge state of three different substrates (norfloxacin, ciprofloxacin, and enoxacin) by varying the pH between 6 and 9 while the charge and selectivity of OmpF is conserved allows us to work under conditions in which electroosmotic flow and electrophoretic forces add or oppose. This configuration allows us to identify and distinguish the contributions of the electroosmotic flow and the electrophoretic force on translocation. Statistical analysis of the resolvable dwell times reveals rich kinetic details regarding the direction and the stochastic movement of antibiotics inside the nanopore. We quantitatively describe the electroosmotic velocity component experienced by the substrates and their diffusion coefficients inside the porin with an estimate of the energy barrier experienced by the molecules caused by the interaction with the channel wall, which slows down the permeation by several orders of magnitude.     

Fractionation of macromolecules in an alternating transverse electric field: simulation of the method

An electric field of alternating polarity applied in a direction transverse to the direction of solute transport is used as the basis of a method for the separation of biological macromolecules. The method derives directly from the ability of an electric field to induce movement of a charged macromolecule and from the physics of laminar fluid flow; no adsorptive immobile phase component is involved.

The method is simulated by computer for the case of solute molecules in a solvent flowing through a narrow chamber of recta generates an electric field orthogonal to the direction of solvent flow. Solute molecules repetitively traverse the solvent channel at rates determined by their electrophoretic mobility. During the transit across the channel, solute molecules are transported in the direction of solvent flow; at the channel wall, solvent velocity is negligible and solute transport is limited to that provided by transient diffusion into a mobile solvent zone. Molecules of different intrinsic electrophoretic mobility are separated.

The computer model was used to illustrate the process and to demonstrate the ‘tunability’ of the method as a function of the oscillation frequency and voltage wave form. Because of this tunability, a single instrument can function as the equivalent of several different chromatographic systems. Because fractionation is effected by direct physicochemical phenomena rather than via interaction with chromatographic sites, variations in fractionation results arising from formation of polymers for gel electrophoresis, packing of chromatography columns, or deterioration of columns with use are avoided. This method may be of particular use for the purification of nucleic acid fragments and for the analysis of protei: nucleic acid interactions.     

A pathway separate from the central channel through the nuclear pore complex for inorganic ions and small macromolecules

Nuclear pore complexes (NPCs) are supramolecular nanomachines that mediate the exchange of macromolecules and inorganic ions between the nucleus and the cytosol. Although there is no doubt that large cargo is transported through the centrally located channel, the route of ions and small molecules remains debatable. We thus tested the hypothesis that there are two separate pathways by imaging NPCs using atomic force microscopy, NPC electrical conductivity measurements, and macromolecule permeability assays. Our data indicate a spatial separation between the active transport of macromolecules through the central channel and the passive transport of ions and small macromolecules through the pore periphery.     

Nucleocytoplasmic transport of proteins

In eukaryotic cells, the movement of macromolecules between the nucleus and cytoplasm occurs through the nuclear pore complex (NPC)--a large protein complex spanning the nuclear envelope. The nuclear transport of proteins is usually mediated by a family of transport receptors known as karyopherins. Karyopherins bind to their cargoes via recognition of nuclear localization signal (NLS) for nuclear import or nuclear export signal (NES) for export to form a transport complex. Its transport through NPC is facilitated by transient interactions between the karyopherins and NPC components. The interactions of karyopherins with their cargoes are regulated by GTPase Ran. In the current review, we describe the NPC structure, NLS, and NES, as well as the model of classic Ran-dependent transport, with special emphasis on existing alternative mechanisms; we also propose a classification of the basic mechanisms of protein transport regulation.     

Passive and facilitated transport in nuclear pore complexes is largely uncoupled

Nuclear pore complexes provide the sole gateway for the exchange of material between nucleus and cytoplasm of interphase eukaryotic cells. They support two modes of transport: passive diffusion of ions, metabolites, and intermediate-sized macromolecules and facilitated, receptor-mediated translocation of proteins, RNA, and ribonucleoprotein complexes. It is generally assumed that both modes of transport occur through a single diffusion channel located within the central pore of the nuclear pore complex. To test this hypothesis, we studied the mutual effects between transporting molecules utilizing either the same or different modes of translocation. We find that the two modes of transport do not interfere with each other, but molecules utilizing a particular mode of transport do hinder motion of others utilizing the same pathway. We therefore conclude that the two modes of transport are largely segregated.     

Isotope effects on electron tunneling reactions in biological systems conformational mobility of proteins

Effects of D2O substitution on electron transport reactions in proteins were analysed on the basis of generally adopted ideas of electronic vibration interactions and conformational mobility of macromolecules. At the molecular level, a mechanism for cytochrome c oxidation was established. On the basis of general viscosity and elasticity properties of proteins, the effects of temperature and chemical composition of the medium on conformational relaxation were analysed. For chromatophores of photosynthetising bacteria, a mechanism is discussed by which abnormal effects of temperature and abnormal isotope effects may be exercised on charge recombination.     

Nuclear-pore-complex dynamics and transport in higher eukaryotes

Summary The nuclear-pore complex controls the passage of macromolecules to and from the nucleus. It is a complex structure spanning the double-membrane nuclear envelope, consisting of many proteins and structural components. Structurally it consists of a series of stacked rings and associated filaments and a central cylinder which appears to contain the transport channel. Much of the pore complex appears to be dynamic, altering conformationally during transport. We review what is known about pore complex structure and dynamics and attempt to relate this to recent new information on transport pathways and the interactions of transport factors with each other and with components of the nuclear-pore complex.     

Effects of diffusion on the electrophoretic behavior of associating systems: the Gilbert-Jenkins theory revisited

The Gilbert-Jenkins theory predicts the asymptotic shape of moving-boundary sedimentation and electrophoretic patterns and broad zone molecular sieve chromatographic elution profiles for the class of interacting systems, A + B in equilibrium C, in which two dissimilar macromolecules react reversibly to form a complex. A particularly provocative case is the one in which the complex has a greater migration velocity than that of either reactant, each of which has a different velocity. Depending upon conditions, this case predicts, for example, that in the asymptotic limit an ascending electrophoretic pattern or a frontal gel chromatographic elution profile can show two hypersharp reaction boundaries separated by a plateau. This prediction is now confirmed by numerical solution of transport equations which retain the second-order diffusional term and extrapolation of the computed patterns to zero diffusion coefficient. For finite diffusion coefficient, however, the two hypersharp reaction boundaries are separated by a weak negative gradient. These calculations are extended to an examination of the transitions between the three types of patterns admitted by the case under consideration in order to gain physical understanding and to define criteria for recognizing the transitions. Studies of this kind not only establish confidence in the Gilbert-Jenkins theory, but, in addition, they provide new insights which make for more effective application of the theory to real systems.     

In vivo mimicking model for solid tumor towards hydromechanics of tissue deformation and creation of necrosis

The present work addresses transvascular and interstitial fluid transport inside a solid tumor surrounded by normal tissue (close to an in vivo mimicking setup). In general, biological tissues behave like a soft porous material and show mechanical behavior towards the fluid motion through the interstitial space. In general, forces like viscous drag that are associated with the fluid flow may compress the tissue material. On the macroscopic level, we try to model the motion of fluids and macromolecules through the interstitial space of solid tumor and the normal tissue layer. The transvascular fluid transport is assumed to be governed by modified Starling’s law. The poroelastohydrodynamics (interstitial hydrodynamics and the deformation of tissue material) inside the tumor and normal tissue regions is modeled using linearized biphasic mixture theory. Correspondingly, the velocity distribution of fluid is coupled to the displacement field of the solid phase (mainly cellular phase and extracellular matrix) in both the normal and tumor tissue regions. The corresponding velocity field is used within the transport reaction equation for fluids and macromolecules through interstitial space to get the overall solute (e.g., nutrients, drug, and other macromolecules) distribution. This study justifies that the presence of the normal tissue layer plays a significant role in delaying/assisting necrosis inside the tumor tissue. It is observed that the exchange process of fluids and macromolecules across the interface of the tumor and normal tissue affects the effectiveness factor corresponding to the tumor tissue.     

Transport properties and hydrodynamic centers of rigid macromolecules with arbitrary shapes

A general formalism, which includes translation–rotation coupling, is proposed for calculating translational and rotational transport properties, as well as intrinsic viscosities, of rigid macromolecules with an arbitrary shape. This formalism is based on Brenner's theory of translational–rotational dynamics and on methods for the calculation of hydrodynamic properties that have been already presented, and can be regarded as a generalization of the one proposed by Nakajima and Wada. The calculated transport properties depend on the origin as predicted by Brenner's theory, but in a disagreement with him, the center of resistance and the center of diffusion do not coincide. As one can define several hydrodynamic centers, which in practice turn out to be located at different points, the influence of the choice of the center on the calculated transport properties is discussed. An analysis of the translation–rotation coupling effects in translational diffusion reveals that they arise exclusively from hydrodynamic interactions and are rather small in some cases of interest. Finally, we present a study of the rotational diffusion of rigid bent rods with a fixed length-to-diameter ratio. The diffusion coefficients obtained can be useful to estimate changes with respect to a straight rod.     

Effects of diffusion on the electrophoretic behavior of associating systems: The Gilbert-Jenkins theory revisited

The Gilbert-Jenkins theory predicts the asymptotic shape of moving-boundary sedimentation and electrophoretic patterns and broad zone molecular sieve chromatographic elution profiles for the class of interacting systems, A + B ⇄ C, in which two dissimilar macromolecules react reversibly to form a complex. A particularly provocative case is the one in which the complex has a greater migration velocity than that of either reactant, each of which has a different velocity. Depending upon conditions, this case predicts, for example, that in the asymptotic limit an ascending electrophoretic pattern or a frontal gel chromatographic elution profile can show two hypersharp reaction boundaries separated by a plateau. This prediction is now confirmed by numerical solution of transport equations which retain the second-order diffusional term and extrapolation of the computed patterns to zero diffusion coefficient. For finite diffusion coefficient, however, the two hypersharp reaction boundaries are separated by a weak negative gradient. These calculations are extended to an examination of the transitions between the three types of patterns admitted by the case under consideration in order to gain physical understanding and to define criteria for recognizing the transitions. Studies of this kind not only establish confidence in the Gilbert-Jenkins theory, but, in addition, they provide new insights which make for more effective application of the theory to real systems.