Analysis of noninvasive macromolecular transport measurements in the lung

Several groups of investigators are measuring transcapillary protein flux in the lung using noninvasive methods. Results from these studies are reported using several different protein transport indexes, including pulmonary transvascular transfer coefficient, relative extravascular protein, pulmonary transcapillary escape rate, protein leak index, lung transferrin index, slope index, and lung-to-heart count ratios. The purpose of this study is to discover the relationships between these indexes by employing a two-compartment theory of protein transcapillary transport in the lung. We found that all the above indexes can be related to a single index, which we call the normalized slope index. This index is the time rate of change of radioactivity originating from protein in lung interstitium divided by radioactivity arising from protein in lung plasma, normalized by this ratio at time 0, and corrected for blood volume changes. In particular the normalized slope index is shown to be the same as pulmonary transcapillary escape rate under normal sampling conditions and is relatively unaffected by changes in interstitial volume. The response of the normalized slope index to changes in microvascular pressure and microvascular permeability is explored by applying a two-pore model of the microvascular barrier. Results indicate that the normalized slope index is relatively insensitive to changes in microvascular pressure but is greatly affected by changes in microvascular permeability (i.e., changes in large-pore size or number). Since all published leak indexes are related, we would encourage all investigators in the field to adopt a single leak index. We recommend that when a two-compartment model is applied to external detection data, the results be expressed as pulmonary transcapillary escape rate.(ABSTRACT TRUNCATED AT 250 WORDS)     

Evaluating pulmonary vascular permeability with radiolabeled proteins: an error analysis

Using techniques of mathematical simulation, we compared two methods of evaluating pulmonary vascular permeability, i.e., transvascular protein flux. Both methods calculate a transport rate constant [pulmonary transcapillary escape rate (PTCER)] after making external radiation detection measurements of an intravenously administered radiolabeled protein. With one method, lung tissue time-activity data are acquired by positron emission tomography (PET) and are interpreted with a two-compartment model. With the other method, the time-activity data are acquired with simple detector probes and are interpreted by linear regression after normalizing for various physical factors (slope-intercept or SI method). The results show that significant errors in calculating PTCER can result from using the SI method, because it ignores the effects of back-flux on the tissue time-activity measurements. Both methods produce errors if the data analysis includes activity from vascular volumes not involved in tracer exchange with the extravascular compartment. Significant errors can also occur with the PET method, particularly when permeability is nearly normal, if pulmonary vascular volume changes significantly during the period of data collection. On balance, the PET method appears to be the method of choice for accurately evaluating pulmonary vascular permeability by protein flux measurements, although both methods may be useful in clinical applications.     

Evaluating flux of labeled albumin into the pulmonary interstitium of sheep lungs.

A noninvasive method was used to measure the movement of 131I-labeled albumin across the pulmonary microvascular barrier of a blood-perfused in situ sheep lung lymph preparation. After injection of labeled albumin into the blood, external measurements of gamma activity were taken for 2 h. The interstitial concentrations were calculated by applying the external activities and sampled lung lymph concentrations to a mass transport model. For the external activities and lymph activities to yield the same quantitative results, two modifications were necessary. First, lymph concentrations were corrected for transport delay from the lymphatic system. Second, externally detected radioactivity had to be corrected for the contribution of unbound nuclide. Application of a mathematical model to the data indicated the extravascular distribution volume for albumin was 79% of the pulmonary blood volume, and the extravascular distribution volume for radiolabeled iodide was 4.42 times greater than the pulmonary blood volume. The permeability-surface area product for iodide in the lung was estimated to be 0.274 ml.min-1.g blood-free dry lung wt-1. The transport delay in the lymphatic system was approximately 30-45 min and represented a volume of 1.44-2.80 ml.     

Considerations for using fluorescence polarization in the screening of G protein-coupled receptors

Fluorescence polarization must be classified as a unique detection method relative to other intensity-based methods because both bound and unbound tracer is measured. Other fluorescence techniques require either physical removal of unbound tracer or a means for distinguishing only bound tracer. The presence of unbound tracer in the detection volume has profound consequences on how assay performance is gauged. The intent here is to provide tools for accurate assay performance assessment and to discuss some of the practical considerations necessary for understanding the advantages and limitations of the technology. An emphasis is placed on applications using G protein-coupled receptors.     

Modeling of palmitate transport in the heart

Summary Transport of palmitate from the albumin-palmitate complex in the plasma to inside mitochondria where it undergoes -oxidation is a multistep process. Albumin's large size prevents permeation via interendothelial clefts. Palmitate dissociation from albumin in solution is too slow to provide an adequate supply of the unbound palmitate. The discovery that the dissociation occurs upon albumin binding to an endothelial surface receptor resolves the conundrum. Palmitate transport across the luminal surface membrane may be either carrier-mediated or passive. Fatty-acid binding protein inside endothelial and cardiac muscle cells facilitates diffusion through cytosol while maintaining the unbound palmitate concentration at a very low level. Within the interstitium, albumin is again the palmitate carrier. Still controversial is whether or not there is a saturable sarcolemmal transporter or simply passive exchange. Inside the myocyte palmitate is again bound to the fatty acid binding protein which buffers the free palmitate concentration, facilitates diffusion, and may facilitate further intracellular reactions.     

An ultrastructural study of the blood/air barrier in the guinea-pig

Horseradish peroxidase (HRP) was intravenously injected into guinea-pigs to ultrastructurally examine the permeability of the blood/air barrier. Adults were given 300 mg/kg of the tracer in a small volume of saline, anesthetized and sacrificed at intervals by either intratracheal filling or right ventricular perfusion with 3% glutaraldehyde. The reaction product had passed through endothelial clefts and accumulated in the interstitium as early as 1.5 min after injection. This same degree of penetration occurred with either fixation method used. Tight junctions between pneumocytes prevented passage of the reaction product into alveoli. Pinocytotic vesicles were numerous in both endothelial and epithelial cells, but did not significantly contribute to tracer transport. Ten minutes post-injection was selected as optimal for this model since the highest concentration of tracer was found in the tissues at this time.     

Reassessing buried surface areas in protein–protein complexes

The buried surface area (BSA), which measures the size of the interface in a protein–protein complex may differ from the accessible surface area (ASA) lost upon association (which we call DSA), if conformation changes take place. To evaluate the DSA, we measure the ASA of the interface atoms in the bound and unbound states of the components of 144 protein–protein complexes taken from the Protein–Protein Interaction Affinity Database of Kastritis et al. (2011). We observe differences exceeding 20%, and a systematic bias in the distribution. On average, the ASA calculated in the bound state of the components is 3.3% greater than in their unbound state, and the BSA, 7% greater than the DSA. The bias is observed even in complexes where the conformation changes are small. An examination of the bound and unbound structures points to a possible origin: local movements optimize contacts with the other component at the cost of internal contacts, and presumably also the binding free energy.     

Carrier facilitated diffusion

The concept of a mobile carrier combining reversibly with a substrate is considered as a possible mechanism for facilitated transport across biological membranes. The mathematical model is a system of three reaction diffusion equations with certain boundary conditions. Two limiting cases are discussed in detail: The case of a "thin" membrane where the diffusion of bound and unbound carrier from one surface to the other may be simulated by a single jump. If the diffusion rate of the substance to be transported is small, then an approximate stationary solution is derived using singular perturbation theory. Finally, the results of numerical simulations are presented for a wide range of parameters.     

A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks

The study of protein binding mechanisms is a major topic of research in structural biology. Here, we implement a combination of metrics to systematically assess the cost of backbone conformational changes that protein domains undergo upon association. Through the analyses of 2090 unique unbound → bound transitions, from over 12,000 structures, we show that two-thirds of these proteins do not suffer significant structural changes upon binding, and could thus fit the lock-and-key model well. Among the remaining proteins, one-third explores the bound conformation in the unbound state (conformational selection model) and, while most transitions are possible from an energetic perspective, a few do require external help to break the thermodynamic barrier (induced fit model). We also analyze the relationship between conformational transitions and protein connectivity, finding that, in general, domains interacting with many partners undergo smaller changes upon association, and are less likely to freely explore larger conformational changes.     

Transient transcapillary exchange of water driven by osmotic forces in the heart

Osmotic transient responses in organ weight after changes in perfusate osmolarity have implied steric hindrance to small-molecule transcapillary exchange, but tracer methods do not. We obtained osmotic weight transient data in isolated, Ringer-perfused rabbit hearts with NaCl, urea, glucose, sucrose, raffinose, inulin, and albumin and analyzed the data with a new anatomically and physicochemically based model accounting for 1) transendothelial water flux, 2) two sizes of porous passages across the capillary wall, 3) axial intracapillary concentration gradients, and 4) water fluxes between myocytes and interstitium. During steady-state conditions approximately 28% of the transcapillary water flux going to form lymph was through the endothelial cell membranes [capillary hydraulic conductivity (Lp) = 1.8 +/- 0.6 x 10-8 cm. s-1. mmHg-1], presumably mainly through aquaporin channels. The interendothelial clefts (with Lp = 4.4 +/- 1.3 x 10-8 cm. s-1. mmHg-1) account for 67% of the water flux; clefts are so wide (equivalent pore radius was 7 +/- 0.2 nm, covering approximately 0.02% of the capillary surface area) that there is no apparent hindrance for molecules as large as raffinose. Infrequent large pores account for the remaining 5% of the flux. During osmotic transients due to 30 mM increases in concentrations of small solutes, the transendothelial water flux was in the opposite direction and almost 800 times as large and was entirely transendothelial because no solute gradient forms across the pores. During albumin transients, gradients persisted for long times because albumin does not permeate small pores; the water fluxes per milliosmolar osmolarity change were 200 times larger than steady-state water flux. The analysis completely reconciles data from osmotic transient, tracer dilution, and lymph sampling techniques.     

Monte Carlo simulation of simultaneous gas flow and diffusion in an asymmetric distal pulmonary airway model

In order to evaluate the effect of anatomic asymmetries on the gas concentration distribution in the pulmonary airways, a Monte Carlo simulation of combined bulk flow and molecular diffusion was carried out in a realistic distal airway model (Parkeret al., 1971). This airway model, composed of branches distal to the 0.5-ram diameter airways, contained an upper symmetric segment consisting of four generations of conducting airways and a lower asymmetric segment of alveolar ducts and sacs arranged in five transport paths of varying lengths. In accounting for the volume increases of these ducts and sacs occurring during normal respiration, uniform alveolar filling rates and a fixed length-to-diameter ratio of all airways were assumed. For a pulse injection of inert tracer gas, the simulation was employed to determine the longitudinal concentration profiles in the conducting airways. In the alveolated airways, not only were the longitudinal profiles determined along each path, but radial transport from the core to the periphery of the airways was considered. The results of the simulations indicate that geometric asymmetries alone contribute substantially to regional concentration variations in the distal airways. For example, when a gas bolus is injected at mid*inspiration, there are concentration differences as great as 40% between two points along different transport paths located equi-distant from the proximal end of the model. As viewed from the terminal end of the model (acinus), average concentration differences as large as 6-to-1 exist between the longest and shortest transport paths respectively for gas boli introduced near the end of inspiration. The results further indicate because of large radial diffusion rates, no significant concentration differences exist between the periphery a-ld the central core of alveolated airways. Simulation of the expired concentration profiles indicate that boll injected very late during inspiration exhibit a sloping tail, unlike the earlier injected boll whose tails are virtually horizontal. Through the use of superposition teehniqnes, it was found that these sloping tails correspond to an alveolar slope of 1.5 vol% between 750 and 1250 ml expired for a continuous washing of tracer. This result is in disagreement with other transport analyses which did not directly account for the effect of geometric asymmetries.     

Ubiquitin Dynamics in Complexes Reveal Molecular Recognition Mechanisms Beyond Induced Fit and Conformational Selection

Protein-protein interactions play an important role in all biological processes. However, the principles underlying these interactions are only beginning to be understood. Ubiquitin is a small signalling protein that is covalently attached to different proteins to mark them for degradation, regulate transport and other functions. As such, it interacts with and is recognised by a multitude of other proteins. We have conducted molecular dynamics simulations of ubiquitin in complex with 11 different binding partners on a microsecond timescale and compared them with ensembles of unbound ubiquitin to investigate the principles of their interaction and determine the influence of complex formation on the dynamic properties of this protein. Along the main mode of fluctuation of ubiquitin, binding in most cases reduces the conformational space available to ubiquitin to a subspace of that covered by unbound ubiquitin. This behaviour can be well explained using the model of conformational selection. For lower amplitude collective modes, a spectrum of zero to almost complete coverage of bound by unbound ensembles was observed. The significant differences between bound and unbound structures are exclusively situated at the binding interface. Overall, the findings correspond neither to a complete conformational selection nor induced fit scenario. Instead, we introduce a model of conformational restriction, extension and shift, which describes the full range of observed effects.     

Epithelial and endothelial flux after bypass in dogs: effect of positive end-expiratory pressure

Cardiopulmonary bypass (CPB) causes lung injury that occasionally progresses to the adult respiratory distress syndrome (ARDS). We measured the effect of 10 cmH2O of positive end-expiratory pressure (PEEP) on small solute and protein flux in dogs 1 wk before and 2 h after the completion of CPB. As an index of alveolar epithelial permeability, the clearance from lung to blood of inhaled technetium-99m-labeled diethylenetriaminepentaacetic acid (99mTc-DTPA) was measured. To assess microvascular endothelial integrity, the rate of accumulation in the lung interstitium of intravascular 113mIn-transferrin was measured. The clearance half time (t 1/2) for 99mTc-DTPA in the study dogs declined from 18.8 +/- 1.9 min (mean +/- SE) at base line to 9.4 +/- 2.0 min during PEEP (P less than 0.05). Two hours after CPB, the t 1/2 was 8.1 +/- 1.6 min at base line and unchanged during PEEP. The 113mIn-transferrin rate of accumulation was unchanged by PEEP before CPB. After CPB, the index was 3.25 +/- 0.95 slope/min X 10(-3) (P less than 0.05). Of the five dogs with a significant slope, four showed a decrease in microvascular flux during PEEP, although for the group the mean change in slope was not significant (P = 0.10). We conclude that the application of PEEP does not increase 99mTc-DTPA clearance in lungs already injured by CPB, and may actually decrease the apparent microvascular protein flux in some cases.     

Minimal ensembles of side chain conformers for modeling protein–protein interactions

The goal of this article is to reduce the complexity of the side chain search within docking problems. We apply six methods of generating side chain conformers to unbound protein structures and determine their ability of obtaining the bound conformation in small ensembles of conformers. Methods are evaluated in terms of the positions of side chain end groups. Results for 68 protein complexes yield two important observations. First, the end‐group positions change less than 1 Å on association for over 60% of interface side chains. Thus, the unbound protein structure carries substantial information about the side chains in the bound state, and the inclusion of the unbound conformation into the ensemble of conformers is very beneficial. Second, considering each surface side chain separately in its protein environment, small ensembles of low‐energy states include the bound conformation for a large fraction of side chains. In particular, the ensemble consisting of the unbound conformation and the two highest probability predicted conformers includes the bound conformer with an accuracy of 1 Å for 78% of interface side chains. As more than 60% of the interface side chains have only one conformer and many others only a few, these ensembles of low‐energy states substantially reduce the complexity of side chain search in docking problems. This approach was already used for finding pockets in protein–protein interfaces that can bind small molecules to potentially disrupt protein–protein interactions. Side‐chain search with the reduced search space will also be incorporated into protein docking algorithms. Proteins 2012. © 2011 Wiley Periodicals, Inc.     

STUDIES ON THE PERMEABILITY OF LYMPHATIC CAPILLARIES

The passageway for interstitial fluids and large molecules across the connective tissue lymph interface has been investigated in dermal lymphatic capillaries in the ears of guinea pigs. Numerous endothelial cells overlap extensively at their margins and lack adhesion devices at many points. The observations suggest that these sites are free to move as a result of slight pressure changes. Immediately following interstitial injections of tracer particles (ferritin, thorium, carbon, and latex spheres), many of the overlapped endothelial cells are separated and thus passageways are provided between the interstitium and lymphatic lumen. Tracer particles also occur in plasmalemmal invaginations along both connective tissue and luminal fronts. All of the tracer particles accumulate within large autophagic-like vacuoles. Very few particles of ferritin are observed in the endothelium after 24 hr; however, the vesicles containing the nonprotein tracer particles (carbon, thorium, and latex) increase in size and content and remain within the lymphatic endothelial cells up to 6 months. The role of vesicles in the transport of large molecules and particles is discussed in relation to the accretion of tracer particles within large vesicles and autophagic-like vacuoles in the endothelial cytoplasm.     

Cardiac adenosine 3':5'-monophosphate. Free and bound forms in the isolated rat atrium.

Adenosine 3':5'-monophosphate (cyclic AMP), a mediator of hormone action in a variety of tissues, has been measured in its free and bound forms in intact cardiac tissue. We have used a rapid high dilution technique which involves tissue homogenization, subcellular fractionation, and separation of bound from free cyclic AMP by Millopore filtration. The precision of this method is dependent upon minimization of binding and dissociation of cyclic AMP that occur during the preparation and handling of tissue homogenates. In each experiment, a tracer of cyclic [3H]AMP prebound to isolated cardiac binding protein was freed of unbound cyclic [3H]AMP by Sephadex gel filtration and added to the tissue just prior to homogenization in cold EDTA buffer. This tracer was therefore treated identically to the sample through all subsequent dilution, fractionation, and filtration procedures, and provided an acurate internal monitor for total cyclic AMP dissociation during the course of the free-bound determination. Each tissue sample was then individually corrected for dissociation. Rapid dilution to produce a 1:1000 homogenate was found to lower endogenous cyclic AMP levels sufficiently to make binding (or rebinding) during the procedure negligible (less than 5%). Spontaneously beating rat right atria (controls) contained 5.96 +/- 0.28 pmol of cyclic AMP/mg of protein (n = 19) of which 41 and 14% were bound to soluble and particulate proteins, respectively. The remaining cyclic AMP was free. Pretreatment of the tissue with 1 muM isoproterenol (30 s at 30 degrees) increased both the bound and free forms of cyclic AMP (n = 8). While free cyclic AMP increased 420% with the catecholamine, the bound forms increased 240% (soluble) and 60% (particulate). Similar results were obtained when atria (n = 6) were treated with the phosphodiesterase inhibitor, methylisobutylxanthine (0.5 mM, 10 min at 30 degrees). When both agents were used together, cyclic AMP bound to soluble proteins was elevated 4-fold over control while free cyclic AMP increased 27-fold (n = 7), indicating saturation of the soluble sites. It could be calculated that less than one-third of these sites are occupied in the unstimulated cell. These sites may represent the R subunit of cyclic AMP-dependent protein kinase. The data suggest that half-maximal binding in vivo occurs at an intracellular free cyclic AMP concentration of about 1 muM.     

An electrochemical model of the transport of charged molecules through the capillary glycocalyx

An electrochemical theory of the glycocalyx surface layer on capillary endothelial cells is developed as a model to study the electrochemical dynamics of anionic molecular transport within capillaries. Combining a constitutive relationship for electrochemical transport, derived from Fick's and Ohm's laws, with the conservation of mass and Gauss's law from electrostatics, a system of three nonlinear, coupled, second-order, partial, integro-differential equations is obtained for the concentrations of the diffusing anionic molecules and the cations and anions in the blood. With the exception of small departures from electroneutrality that arise locally near the apical region of the glycocalyx, the model assumes that cations in the blood counterbalance the fixed negative charges bound to the macromolecular matrix of the glycocalyx in equilibrium. In the presence of anionic molecular tracers injected into the capillary lumen, the model predicts the size- and charge-dependent electrophoretic mobility of ions and tracers within the layer. In particular, the model predicts that anionic molecules are excluded from the glycocalyx at equilibrium and that the extent of this exclusion, which increases with increasing tracer and/or glycocalyx electronegativity, is a fundamental determinant of anionic molecular transport through the layer. The model equations were integrated numerically using a Crank-Nicolson finite-difference scheme and Newton-Raphson iteration. When the concentration of the anionic molecular tracer is small compared with the concentration of ions in the blood, a linearized version of the model can be obtained and solved as an eigenvalue problem. The results of the linear and nonlinear models were found to be in good agreement for this physiologically important case. Furthermore, if the fixed-charge density of the glycocalyx is of the order of the concentration of ions in the blood, or larger, or if the magnitude of the anionic molecular valence is large, a closed-form asymptotic solution for the diffusion time can be obtained from the eigenvalue problem that compares favorably with the numerical solution. In either case, if leakage of anionic molecules out of the capillary occurs, diffusion time is seen to vary exponentially with anionic valence and in inverse proportion to the steady-state anionic tracer concentration in the layer relative to the lumen. These findings suggest several methods for obtaining an estimate of the glycocalyx fixed-charge density in vivo.     

Estimation of the binding affinities of FKBP12 inhibitors using a linear response method.

A series of non-immunosuppressive inhibitors of FK506 binding protein (FKBP12) are investigated using Monte Carlo statistical mechanics simulations. These small molecules may serve as scaffolds for chemical inducers of protein dimerization, and have recently been found to have FKBP12-dependent neurotrophic activity. A linear response model was developed for estimation of absolute binding free energies based on changes in electrostatic and van der Waals energies and solvent-accessible surface areas, which are accumulated during simulations of bound and unbound ligands. With average errors of 0.5 kcal/mol, this method provides a relatively rapid way to screen the binding of ligands while retaining the structural information content of more rigorous free energy calculations.     

A flow immunoassay for studies of human exposure and toxicity in biological samples

This paper describes a heterogeneous competitive flow immunoassay with a high sample throughput which can be used for the screening of smaller analytes in various samples. The method is based on off-line incubation of the analyte (Ag), a fluorescent labelled tracer (Ag*) and the corresponding antibody (Ab). The separation of bound (Ab-Ag*) and free tracer (Ag*) is based on a size exclusion and reversed phase mechanism utilizing a restricted access (RA) column. The column traps the free unbound tracer (Ag*) in its hydrophobic (C18) inner cavity but excludes the large Ab-Ag* complex, which is passed on and measured by the fluorescence detector. The flow immunoassay was developed using the triazine herbicide atrazine as a model compound owing to its human toxicity and widespread use. A sample throughput of 80 samples per hour and a detection limit of 300 pg ml-1 in water were obtained. Urine samples were successfully applied for direct injections into the flow system, while for human plasma samples an additional clean-up step using solid phase extraction was efficiently included where pure extract is obtained with the highly stable and biocompatible extracting column material. The resulting detection limits for atrazine in plasma and water samples using this clean-up and trace enrichment procedure were found to be 2 ng ml-1 and 20 pg ml-1 respectively.