Thermodynamics,the structure of integral membrane proteins,and transport

Membranes are structures whose lipid and protein components are at, or close to, equilibrium in the plane of the membrane, but are not at equilibrium across the membrane. The thermodynamic tendency of ionic and highly polar molecules to be in contact with water rather than with nonpolar media (hydrophilic interactions) is important in determining these equilibrium and nonequilibrium states. In this paper, we speculate about the structures and orientations of integral proteins in a membrane, and about how the equilibrium and nonequilibrium features of such structures and orientations might be influenced by the special mechanisms of biosynthesis, processing, and membrane insertion of these proteins. The relevance of these speculations to the mechanisms of the translocation event in membrane transport is discussed, and specific protein models of transport that have been proposed are analyzed.     

Fluorescence microscopy applied to intracellular transport by microtubule motors

Long-distance transport of many organelles inside eukaryotic cells is driven by the dynein and kinesin motors on microtubule filaments. More than 30 years since the discovery of these motors, unanswered questions include motor–organelle selectivity, structural determinants of processivity, collective behaviour of motors and track selection within the complex cytoskeletal architecture, to name a few. Fluorescence microscopy has been invaluable in addressing some of these questions. Here we present a review of some efforts to understand these sub-microscopic machines using fluorescence.     

Thermodynamics of competitive molecular channel transport: application to artificial nuclear pores

In an analytical model channel transport is analyzed as a function of key parameters, determining efficiency and selectivity of particle transport in a competitive molecular environment. These key parameters are the concentration of particles, solvent-channel exchange dynamics, as well as particle-in-channel- and interparticle interaction. These parameters are explicitly related to translocation dynamics and channel occupation probability. Slowing down the exchange dynamics at the channel ends, or elevating the particle concentration reduces the in-channel binding strength necessary to maintain maximum transport. Optimized in-channel interaction may even shift from binding to repulsion. A simple equation gives the interrelation of access dynamics and concentration at this transition point. The model is readily transferred to competitive transport of different species, each of them having their individual in-channel affinity. Combinations of channel affinities are determined which differentially favor selectivity of certain species on the cost of others. Selectivity for a species increases if its in-channel binding enhances the species' translocation probability when compared to that of the other species. Selectivity increases particularly for a wide binding site, long channels, and fast access dynamics. Recent experiments on competitive transport of in-channel binding and inert molecules through artificial nuclear pores serve as a paradigm for our model. It explains qualitatively and quantitatively how binding molecules are favored for transport at the cost of the transport of inert molecules.     

Non‐homogeneous biofilm modeling applied to bioleaching processes

A two‐dimensional non‐homogeneous biofilm model is proposed for the first time to study chemical and biochemical reactions at the microorganism scale applied to biological metal leaching from mineral ores. The spatial and temporal relation between these reactions, microorganism growth and the morphological changes of the biofilm caused by solid inorganic precipitate formation were studied using this model. The model considers diffusion limitations due to accumulation of inorganic particles over the mineral substratum, and allows the study of the effect of discrete phases on chemical and microbiological mineral solubilization. The particle‐based modeling strategy allowed representation of contact reactions between the microorganisms and the insoluble precipitates, such as those required for sulfur attack and solubilization. Time‐dependent simulations of chemical chalcopyrite leaching showed that chalcopyrite passivation occurs only when an impervious solid layer is formed on the mineral surface. This mineral layer hinders the diffusion of one kinetically determinant mineral‐attacking chemical species through a nearly irreversible chemical mechanism. Simulations with iron and sulfur oxidizing microorganisms revealed that chemolithoautotrophic biofilms are able to delay passivation onset by formation of corrosion pits and increase of the solid layer porosity through sulfur dissolution. The model results also show that the observed flat morphology of bioleaching biofilms is favored preferentially at low iron concentrations due to preferential growth at the biofilm edge on the surface of sulfur‐forming minerals. Flat biofilms can also be advantageous for chalcopyrite bioleaching because they tend to favor sulfur dissolution over iron oxidation. The adopted modeling strategy is of great interest for the numerical representation of heterogeneous biofilm systems including abiotic solid particles. Biotechnol. Bioeng. 2010;106: 660–676. © 2010 Wiley Periodicals, Inc.     

Contributions of secondary active transport processes to membrane potentials

Summary Equations are developed to examine the effects of secondary active transport processes on the steady-state membrane potential of symmetrical cells. It is shown that, with suitable modifications, equations of the type developed by Goldman, Hodgkin and Katz may be derived to accommodate the contributions to the membrane potential of both electroneutral and electrogenic transporters. Where the membrane potential is function of the dominant medium ions (Na, K, and Cl), other contributions can come only from an electrogenic Na pump and from neutral co- and counter-transporters if, and only if, these involve the dominant ions. Experimental approaches to measure the parameters necessary to solve the equations developed here are discussed.     

Thermodynamics of electron transfer and its coupling to vectorial processes in biological membranes.

A method is developed to express the flux of an electron transfer reaction as a function of the conjugate force, the redox potential difference, throughout the nonlinear region. The flux can be expressed by a product of the hyperbolic sine of the force, a factor ("redox-poising parameter") determined by the redox potentials of subsystem (in certain cases by local pH's and pK's of subsystems), and some constants. This is analogous to the expression of the flux of a diffusion process by the product of its force and the concentration of the diffusing species. The redox-poising parameter corresponds to the concentration term. The expression is applied to redox chains in which electron transfers are coupled to vectorial processes such as proton translocation or electric current.     

Efficiency of electron transport processes

Efficiency of electron transport along the linear chain of molecules was investigated from a dynamic viewpoint. It was proposed that two kinds of efficiency are important for electron transport; one is energy efficiency, the other quantum efficiency. In this paper, these two efficiencies are defined for a linear chain system and the correlation between these quantities and the arrangement of various electron transfers is investigated. The optimization of energy and quantum efficiency is found to set different conditions on the arrangement of the rate constants of electron transfer, and there is strong correlation between neighboring electron transfers. In order to maximize both efficiencies, the rate constants of forward and backward transfers of electrons should be bounded by one another in a limited range. In particular, when there are some bypass reactions on the linear chain, as is the case for photosynthesis and respiration, the rate of the backward transfer should be the same order of magnitude as that of the next forward transfer. The present results are applied to some biological processes. In the early stage of photosynthetic electron transfer it seems that quantum efficiency is more important than energy efficiency. The quantum efficiency is close to unity, whereas a considerable part of the free energy is wasted as heat during the primary electron transfers. On the other hand, in the slower electron transfer processes in photosynthesis and respiration, which take place mostly near equilibrium, the energy efficiency seems to be more important than the quantum efficiency. The relation of these properties to biological function is discussed.     

Model of two noise source dependent Ornstein-Uhlenbeck processes applied to postural sway

In this study the postural control system is modeled in terms of two counteracting bio-subsystems. Their activities are described by two Ornstein-Uhlenbeck processes with different-in-magnitude noise sources. The model is constructed as a sum of these processes, where in each of them the same noise source with opposite sign of the noise coefficients was introduced. Since the friction coefficients are also different for these processes, the delay of a crossover from ballistic to diffusive motion for one of the subsystems is greater than for its counterpart. It turns out that for smaller time intervals a superdiffusive behavior is observed, whereas, counteraction of subsystems is called into play for a larger time intervals, what for investigated range of data, is exhibited as a slow, subdiffusive behavior.     

Feasible and optimal retrofitting of batch-soluble to continuous-immobilized enzyme processes applied to adsorbed enzymes

The advantages of retrofitting an in situ soluble enzyme batch process to an immobilized enzyme continuous process are contrasted against the disadvantages by means of a dimensionless feasibility/optimization analysis. The general analysis is applied to the case of an adsorbed enzyme system where a maximum in activity occurs with respect to loading. For this case, a minimum in the ratio of enzyme-carrier complex working lifetime to in situ batch process time and a maximum in the cost difference between the in situ and retrofit processes occurs with respect to loading and retrofit process conversion. For the maximization of cost difference, the analysis also suggests a criterion that can be used to determine whether the values for optimal loading and retrofit conversion will result in the retrofit being economically feasible. When infeasibility occurs, qualitative sensitivity analysis for a variety of situations points out whether a catalyst or process modification will improve feasibility the most. Apart from forming the basis for an iterative retrofit process design algorithm, the modeling approach's ability to specify optimal values of catalyst properties such as loading lends itself to defining process-specific, catalyst design "targets" would be useful for those developing immobilized enzyme preparation methodology and those investigating enzyme-carrier interactions.     

Phosphate transport processes in eukaryotic cells

Conclusion Much more work has been done on P_i transport processes, even in the last five years, than we have been able to mention in the space available. We have restricted our discussion to studies on mechanisms of transport or transport regulation, identification of transport proteins and their essential amino acids, and isolation, purification, and reconstitution of P_i transport systems. Many valuable studies on the physiology of P_i transport and its regulation and P_i transport in nonepithelial cells have also been conducted. Transport of P_i into and out of organelles other than the mitochondrion is gaining well-deserved attention, as are transport processes in fungi and plants. It is hoped that in another five years many P_i transport processes will be understood in true molecular terms and that this will increase our knowledge of cellular bioenergetics and metabolism.     

Nitrate transport processes in Fagus- Laccaria-Mycorrhizae

The contribution of influx and efflux of NO₃ ^- on NO₃ ^- net uptake has been studied in excised mycorrhizae of 18–20 week old beech (Fagus sylvatica L.) trees. Net uptake rates of NO₃ ^- followed uniphasic Michaelis-Menten kinetics in the concentration range between 10 μM and 1.0 mM external NO₃ ^-, with an apparent K_m of 88±7 μM, and a V_max of 110±7 nmol g^-1 root f.wt. h^-1. The relative xylem loading of N, i.e. the portion of NO₃ ^- taken up that was loaded into the xylem vessels as NO₃ ^- plus reduced N, was constant over the concentration range tested (4.6–7.7%). NO₃ ^- influx proceeded linearly with increasing external NO₃ ^- supply. When the assumed regulators of net NO₃ ^- uptake, i.e. NH₄ ⁺ or L-glutamate, were applied together with NO₃ ^-, net uptake rates of NO₃ ^- decreased. This inhibitory effect was caused by a reduction of NO₃ ^- influx rather than an enhanced efflux. The comparison of the present data with a recent study with non-mycorrhizal beech roots (Kreuzwieser et al., 1997; J. Exp. Bot. 48, 1431–1438) revealed that mycorrhization leads to reduced rates of NO₃ ^- net uptake. This effect is caused by reduced influx plus enhanced efflux of NO₃ ^- as compared with non-mycorrhizal beech roots. This revised version was published online in June 2006 with corrections to the Cover Date.     

Energetics of active transport processes.

Active sodium transport across epithelial membranes has been analyzed by means of linear nonequilibirium thermodynamics. In this formulation the rates of active sodium transport JNa and the associated metabolic reaction Jr are postulated to be linear functions of both the electrochemical potential difference of sodium--XNa and the affinity A (negative free energy) of the metabolic reaction of driving transport. Experimental studies in various epithelia demonstrate that both JNa and Jr (oxygen consumption) are indeed linear functions of XNa. Theoretical considerations and experimental studies in other systems suggest that likelihood of linearity in A as well. If so, A may be evaluated. Several observations indicate that the quantity A evaluated from the thermodynamic formalism does in fact reflect the substrate-product ratio of the metabolic reaction which supports transport. This is in contrast to measurements of mean cellular concentrations, which may not reflect conditions at the site of transport. Associated studies of isotope kinetics permit the distinction between effects on the permeability of the active and passive transport pathways. With these combined approaches, it may prove possible to characterize both the energetic and permeability factors which regulate transport. The formulation has been applied to an analysis of the mechanism of action of the hormone aldosterone.