Bluelight-induced,flavin-mediated transport of redox equivalents across artificial bilayer membranes

Summary This paper continues our studies of physico-chemical properties of vesicle-bound flavins. Based on previous results, an advanced model system was designed in order to study the mechanisms underlying bluelight-induced redox transport across artificial membranes. The lumen of single-shelled vesicles was charged with cytochromec, and amphiphilic flavin (AF1 3, AF1 10) was bound to the membrane. Upon bluelight irradiation redox equivalents are translocated from exogeneous 1e ^–(EDTA)-and 2e ^–(BH₃CN^–) donors across the membrane finally reducing the trapped cytochromec both under aerobic and anaerobic conditions. The mechanisms involved are explored and evidence for the involvement of various redox states of oxygen, dihydroflavin and flavosemiquinone is presented.     

Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database

The study of mechanistically diverse enzyme superfamilies-collections of enzymes that perform different overall reactions but share both a common fold and a distinct mechanistic step performed by key conserved residues-helps elucidate the structure-function relationships of enzymes. We have developed a resource, the structure-function linkage database (SFLD), to analyze these structure-function relationships. Unique to the SFLD is its hierarchical classification scheme based on linking the specific partial reactions (or other chemical capabilities) that are conserved at the superfamily, subgroup, and family levels with the conserved structural elements that mediate them. We present the results of analyses using the SFLD in correcting misannotations, guiding protein engineering experiments, and elucidating the function of recently solved enzyme structures from the structural genomics initiative. The SFLD is freely accessible at http://sfld.rbvi.ucsf.edu.     

Apidaecin-type peptides: biodiversity, structure-function relationships and mode of action

Apidaecins (apidaecin-type peptides) refer to a series of small, proline-rich (Pro-rich), 18- to 20-residue peptides produced by insects. They are the largest group of Pro-rich antimicrobial peptides (AMPs) known to date. Structurally, apidaecins consist of two regions, the conserved (constant) region, responsible for the general antibacterial capacity, and the variable region, responsible for the antibacterial spectrum. The small, gene-encoded and unmodified apidaecins are predominantly active against many gram-negative bacteria by special antibacterial mechanisms. The mechanism of action by which apidaecins kill bacteria involves an initial non-specific binding of the peptides to an outer membrane (OM) component. This binding is followed by invasion of the periplasmic space, and by a specific and essentially irreversible combination with a receptor/docking molecule that may be a component of a permease-type transporter system on inner membrane (IM). In the final step, the peptide is translocated into the interior of the cell where it meets its ultimate target. Evidence that apidaecins are non-toxic for human and animal cells is a prerequisite for using them as novel antibiotic drugs. This review presents the biodiversity, structure-function relationships, and mechanism of action of apidaecins.     

Expression of band 3 anion exchanger induces chloride current and taurine transport: structure-function analysis.

Most, but not all, cell types release intracellular organic solutes (e.g. taurine) in response to cell swelling to achieve cell volume regulation. Although this efflux is blocked by classical inhibitors of the electroneutral anion exchanger band 3 (AE1), it is thought to involve an anion channel. The role of band 3 in volume-dependent taurine transport was determined by expressing, in Xenopus oocytes, band 3 from erythrocytes which do (trout) or do not (mouse) release taurine when swollen. AE1 of both species elicited anion exchange activity, but only trout band 3 showed chloride channel activity and taurine transport. Chimeras constructed from trout and mouse band 3 allowed the identification of some protein domains critically associated with channel activity and taurine transport. The data provide evidence that swelling-induced taurine movements occur via an anion channel which is dependent on, or controlled by, band 3. They suggest the involvement of proteins of the band 3 (AE) family in cell volume regulation.     

Pulsatile flow and oxygen transport past cylindrical fiber arrays for an artificial lung: computational and experimental studies

The influence of time-dependent flows on oxygen transport from hollow fibers was computationally and experimentally investigated. The fluid average pressure drop, a measure of resistance, and the work required by the heart to drive fluid past the hollow fibers were also computationally explored. This study has particular relevance to the development of an artificial lung, which is perfused by blood leaving the right ventricle and in some cases passing through a compliance chamber before entering the device. Computational studies modeled the fiber bundle using cylindrical fiber arrays arranged in in-line and staggered rectangular configurations. The flow leaving the compliance chamber was modeled as dampened pulsatile and consisted of a sinusoidal perturbation superimposed on a steady flow. The right ventricular flow was modeled to depict the period of rapid flow acceleration and then deceleration during systole followed by zero flow during diastole. Experimental studies examined oxygen transfer across a fiber bundle with either steady, dampened pulsatile, or right ventricular flow. It was observed that the dampened pulsatile flow yielded similar oxygen transport efficiency to the steady flow, while the right ventricular flow resulted in smaller oxygen transport efficiency, with the decrease increasing with Re. Both computations and experiments yielded qualitatively similar results. In the computational modeling, the average pressure drop was similar for steady and dampened pulsatile flows and larger for right ventricular flow while the pump work required of the heart was greatest for right ventricular flow followed by dampened pulsatile flow and then steady flow. In conclusion, dampening the artificial lung inlet flow would be expected to maximize oxygen transport, minimize work, and thus improve performance.     

Lipids, curvature stress, and the action of lipid prodrugs: free fatty acids and lysolipid enhancement of drug transport across liposomal membranes

Molecular shape and its impact on bilayer curvature stress are powerful concepts for describing the effects of lipids and fatty acids on fundamental membrane properties, such as passive permeability and derived properties like drug transport across liposomal membranes. We illustrate these relationships by studying the effects of fatty acids and lysolipids on the permeation of a potent anti-cancer drug, doxorubicin, across the bilayer of a liposome in which the drug is encapsulated. Using a simple fluorescence assay, we have systematically studied the passive permeation of doxorubicin across liposomal membranes in different lipid phases: the solid-ordered phase (DPPC bilayers), the liquid-disordered phase (POPC lipid bilayers), and the liquid-ordered phase induced by high levels of cholesterol (DOPC + cholesterol lipid bilayers). The effect of different free fatty acids (FA) and lysolipids (LL), separately and in combination, on permeability was assessed to elucidate the possible mechanism of phospholipase A₂-triggered release in cancer tissue of liposomal doxorubicin formulations. In all cases, FAs applied separately lead to significant enhancement of permeability, most pronounced in liquid-disordered bilayers and less pronounced in solid and solid-ordered bilayers. LLs applied separately had only a marginal effect on permeability. FA and LL applied in combination lead to a synergistic enhancement of permeability in solid bilayers, whereas in liquid-disordered bilayers, the combined effect suppressed the otherwise strong permeability enhancement due to the FAs.     

Structural and functional relationships of natural and artificial dimeric bovine ribonucleases: New scaffolds for potential antitumor drugs

Protein aggregation via 3D domain swapping is a complex mechanism which can lead to the acquisition of new biological, benign or also malignant functions, such as amyloid deposits. In this context, RNase A represents a fascinating model system, since by dislocating different polypeptide chain regions, it forms many diverse oligomers. No other protein displays such a large number of different quaternary structures. Here we report a comparative structural analysis between natural and artificial RNase A dimers and bovine seminal ribonuclease, a natively dimeric RNase with antitumor activity, with the aim to design RNase A derivatives with improved pharmacological potential.     

The nucleobase-ascorbate transporter (NAT) family: genomics, evolution, structure-function relationships and physiological role

This review summarizes knowledge concerning a ubiquitous plasma transmembrane protein family that mediates nucleobase or ascorbate secondary active transport (NAT). We show that prototype bacterial and mostly fungal members have become unique model systems to unravel structure-function relationships and regulation of expression, using classical and reverse genetics, as well as biochemical approaches. We discuss the importance of NAT-mediated ascorbate transport in mammals and how changes in substrate specificity, from different nucleobases to ascorbate, might have evolved at the molecular level. Finally, we also discuss how modelling NAT-purine interactions might constitute a step towards the use of NAT proteins as specific gateways for targeting pathogenic microbes.     

Synthesis and structure-function study of artificial nucleases on the basis of hemin conjugates with peptide fragments of cell differentiation factor HLDF

A series of octa-hexapeptide fragments of HLDF and their conjugates with hemin were obtained by solid phase peptide synthesis. A relationship between the structure and the nuclease activity of the compounds was established. The effect of various factors (medium pH, the presence of metal ions, complexons, reducers, and buffer composition) on DNA destruction with hemin peptides was studied. Preliminary information confirming an oxidative mechanism of this process was obtained. The cleavage of plasmid DNA under the action of hemin peptides was studied by the methods of electron microscopy, gel electrophoresis, and atomic force microscopy.     

Synthesis and structure-function study of artificial nucleases on the basis of hemin conjugates with peptide fragments of cell differentiation factor HLDF

A series of octa-hexapeptide fragments of HLDF and their conjugates with hemin were obtained by solid phase peptide synthesis. A relationship between the structure and the nuclease activity of the compounds was established. The effect of various factors (medium pH, the presence of metal ions, complexons, reducers, and buffer composition) on the DNA destruction with hemin peptides was studied. Preliminary information confirming an oxidative mechanism of this process was obtained. The cleavage of plasmid DNA under the action of hemin peptides was studied by the methods of electron microscopy, gel electrophoresis, and atomic force microscopy.     

Superoxide organic chemistry within the liposomal bilayer, part II: a correlation between location and chemistry

Coumarin ester derivatives 1, substituted at C-4 and/or C-12 with alkyl chains, were synthesized and intercalated within DMPC liposomal bilayers. By correlating the 13C chemical shift with medium polarity [E(T)(30)], the relative location of these substrates within the liposomal bilayer was determined. The length of the alkyl chain substituents clearly influences the lipophilicity of the substrates and their location and orientation within the liposome: Superoxide readily saponifies the C-12 esteric linkage of 1, when this reaction site lies in a polar region of the liposome (E(T)(30) > 45 kcal/mol), to give the corresponding 7-hydroxy coumarin derivatives 2. However, when C-12 lies deeper and is hence less available to O(2)(*-), the lactonic carbon C-2, which lies in a shallower region (E(T)(30) = 43-49), is the preferred site for superoxide-mediated cleavage. When coumarin 1 is disubstituted with long chains at both C-12 and C-4, these derivatives lie deep within the bilayer and react only slowly with O(2)(*-). These results indicate there is indeed a correlation between location within the bilayer and substrate reactivity. Contrary to the suggestion of Dix and Aikens (Chem. Res. Toxicol.6:2-18; 1993) superoxide can penetrate deep within the liposomal bilayer. Nevertheless, its concentration drops precipitously (to approximately 16% of what it is near the interface) below E(T) values of 38, thereby precluding substantial reaction with many highly lipophilic substrates. This work also confirms the findings of others that reactions of small oxy-radicals occur within cellular membranes and appear to be of significant biological importance.     

Active oxygen chemistry within the liposomal bilayer. Part III: Locating Vitamin E, ubiquinol and ubiquinone and their derivatives in the lipid bilayer

We have previously shown that the location and orientation of compounds intercalated within the lipid bilayer can be qualitatively determined using an NMR chemical shift-polarity correlation. We describe herein the results of our application of this method to analogs of Vitamin E, ubiquinol and ubiquinone. The results indicate that tocopherol--and presumably the corresponding tocopheroxyl radical--reside adjacent to the interface, and can, therefore, abstract a hydrogen atom from ascorbic acid. On the other hand, the decaprenyl substituted ubiquinol and ubiquinone lie substantially deeper within the lipid membrane. Yet, contrary to the prevailing literature, their location is far from being the same. Ubiquinone-10 is situated above the long-chain fatty acid "slab". Ubiquinol-10 dwells well within the lipid slab, presumably out of "striking range" of Vitamin C. Nevertheless, ubiquinol can act as an antioxidant by reducing C- or O-centered lipid radicals or by recycling the lipid-resident tocopheroxyl radical.     

Computer simulation of small molecule permeation across a lipid bilayer: dependence on bilayer properties and solute volume, size, and cross-sectional area

Cell membrane permeation is required for most drugs to reach their biological target, and understanding this process is therefore crucial for rational drug design. Recent molecular dynamics simulations have studied the permeation of eight small molecules through a phospholipid bilayer. Unlike experiments, atomistic simulations allow the direct calculation of diffusion and partition coefficients of solutes at different depths inside a lipid membrane. Further analyses of the simulations suggest that solute diffusion is less size-dependent and solute partitioning more size-dependent than was commonly thought.     

A computational study of odorant transport and deposition in the canine nasal cavity: implications for olfaction

Olfaction begins when an animal draws odorant-laden air into its nasal cavity by sniffing, thus transporting odorant molecules from the external environment to olfactory receptor neurons (ORNs) in the sensory region of the nose. In the dog and other macrosmatic mammals, ORNs are relegated to a recess in the rear of the nasal cavity that is comprised of a labyrinth of scroll-like airways. Evidence from recent studies suggests that nasal airflow patterns enhance olfactory sensitivity by efficiently delivering odorant molecules to the olfactory recess. Here, we simulate odorant transport and deposition during steady inspiration in an anatomically correct reconstructed model of the canine nasal cavity. Our simulations show that highly soluble odorants are deposited in the front of the olfactory recess along the dorsal meatus and nasal septum, whereas moderately soluble and insoluble odorants are more uniformly deposited throughout the entire olfactory recess. These results demonstrate that odorant deposition patterns correspond with the anatomical organization of ORNs in the olfactory recess. Specifically, ORNs that are sensitive to a particular class of odorants are located in regions where that class of odorants is deposited. The correlation of odorant deposition patterns with the anatomical organization of ORNs may partially explain macrosmia in the dog and other keen-scented species.     

Potassium transport in the rabbit renal proximal tubule: Effects of barium,ouabain, valinomycin,and other ionophores

Summary Potassium fluxes in a suspension of rabbit proximal tubules were monitored using a potassium-sensitive extracellular electrode. Ouabain (10^–4 m) and barium (5mm) were used to selectively quantitate the potassium efflux pathway (105±5 nmol K⁺·mg protein^–1·min^–1) and the sodium pump-related potassium influx (108±7), respectively. These equal and opposite fluxes suggest that potassium accumulation in the cell occurs mainly through the sodium pump and that potassium efflux occurs mainly through barium-sensitive potassium channels. Thus the activity of the sodium pump (Na, K-ATPase) in the basolateral membrane of the proximal tubule is balanced by the efflux of potassium, presumably across the basolateral membrane, which has a high potassium permeability. In addition, the effect of valinomycin and other ionophores was examined on potassium fluxes and several metabolic parameters [oxygen consumption (QO₂), ATP content]. The addition of valinomycin to the tubules produced a net efflux of potassium which was quantitatively equivalent to the efflux produced by the addition of ouabain. The valinomycin-induced efflux was mainly due to the activity of valinomycin as a mitochondrial uncoupler, which indirectly inhibited the sodium pump by allowing a rapid reduction of the intracellular ATP. Amphotericin, nystatin, and monensin all produced large net releases of intracellular potassium. The action of the ionophores could be localized to the plasma or mitochondrial membrane and classified into three groups, as follows: (a) those which demonstrated full mitochondrial uncoupler activity (FCCP, valinomycin), (b) those which had no uncoupler activity (amphotericin B, nystatin); and (c) those which displayed partial uncoupler activity (monensin, nigericin).     

Synthesis and structure-activity relationships of the halovirs, antiviral natural products from a marine-derived fungus

The halovirs are linear, lipophilic peptides produced by a marine-derived fungus of the genus Scytalidium. We recently reported that these molecules possess potent in vitro activity against the herpes simplex viruses 1 and 2. Here we present structure-activity relationships defining key structural elements for optimal viral inhibition. Results demonstrate that an N(alpha)-acyl chain of at least 14 carbons and an Aib-Pro dipeptide are critical for maintaining the antiviral activity.     

Electron paramagnetic resonance probing of macromolecules: a comparison of structure-function relationships in chymotrypsinogen, -chymotrypsin and anhydrochymotrypsin

Chymotrypsinogen, chymotrypsin and anhydrochymotrypsin have been covalently spin-labeled by an analog of bromoacetamide, and the latter two proteins have been labeled by an analog of 1-chloro-3-tosylamido-4-phenyl butanone. The electron paramagnetic resonance spectra of the labeled proteins indicate protein conformational changes accompanying (1) activation of the zymogen and (2) the binding of protons and substrates by the native and anhydro enzymes, and tertiary structural differences between these protein forms which are at once informative and predictable. A spin-label linked to the thioether side-chain of methionine 192 in Chymotrypsinogen may be in contact with a hydrophobic surface. This interaction is lost upon zymogen activation with little change in the isotropic rotational freedom of the nitroxide group. The rotational freedom of the group increases sigmoidally with pH; a spectral dependence upon an ionizing group (pK_a = 8.9) is demonstrated. The binding of indole to the labeled enzyme raises the pK_a of the ionizing group to 10.2. A spin-label linked to histidine 57 in chymotrypsin senses both indole binding and pH changes directly; the same label in anhydrochymotrypsin responds directly only to changes in pH. Neither histidine-labeled derivative exhibits enzymic activity. The electron paramagnetic resonance spectra of these two labeled proteins at high pH indicate a decrease in the motional freedom of the spin label. The spectral data show that the conformational state of the labeled zymogen is not similar to the high-pH conformational state of the labeled enzyme. Furthermore, the pH-dependent conformational transition of labeled chymotrypsin requires neither the serine 195 hydroxyl nor the histidine 57 imidazole, since the transition occurs normally in derivatized and chemically modified protein forms. The chemical reactivity of histidine 57 in anhydrochymotrypsin is evaluated and the catalytic activities of two histidine alkylated enzymes are compared.     

Isomeric iodinated analogs of nimesulide: Synthesis,physicochemical characterization,cyclooxygenase-2 inhibitory activity,and transport across Caco-2 cells

Isomeric iodinated derivatives of nimesulide, with an iodine substituent on the phenoxy ring, were prepared with the aim of identifying potential candidate compounds for the development of imaging agents targeting cyclooxygenase-2 (COX-2) in the brain. Both the experimental log P_7.4 and pK_a values for these iodinated analogs were in the acceptable range for passive brain penetration. The para-iodo-substituted analog was a more potent and selective COX-2 inhibitor than nimesulide, with a potency that was comparable to the reference drug, celecoxib. Iodination at the ortho- or meta-position of the phenoxy ring was associated with a substantial loss of COX-2 inhibitory activity. Transport studies across Caco-2 cell monolayers in the presence and absence of a P-glycoprotein (P-gp) inhibitor, verapamil, indicated that the para-iodo-substituted analog was not a P-gp transport substrate; this feature is a prerequisite for potential in vivo brain imaging compounds. The para-iodo-substituted analog of nimesulide appears to be an attractive candidate for the development of radioiodine-labeled tracers for in vivo brain imaging of COX-2 levels.