Channel structures in synthetic polypeptides with alternating configurations. Conformational analysis of poly(DL-proline)

Theoretical conformational analysis of L,D alternating sequences of poly alpha-amino acids is reported in connection with the ability of naturally occurring peptide and depsipeptide having alternating configurations to increase selectively the ion permeability across membranes. The most stable structures of poly(DL-proline), of which the conformational variability is practically limited to the choice between cis and trans conformations of the peptide bonds, were characterized. The all-trans conformation results in a flat helical structure possessing the main features for acting as an ion channel across membranes as actually found experimentally. Random cis-trans conformational sequences provide an alternative mechanism of ion transport intermediate between the ion channel and the ion carrier.     

Electrochemical study of ion channel behavior in incorporated poly L-glutamate bilayer lipid membranes

The lipid layer membranes were fabricated on the glassy carbon electrode (GC) and demonstrated to be bilayer lipid membranes by impedance spectroscopy. The formation of incorporated poly L-glutamate bilayer lipid membrane was achieved. The ion channel behavior of the incorporated poly L-glutamate membrane was determined. When the stimulus calcium cations were added into the electrolyte, the ion channel was opened immediately and exhibited distinct channel current. Otherwise, the ion channel was closed. The cyclic voltammogram at the GC electrode coated with incorporated poly L-glutamate DMPC film response to calcium ion is very fast compared with that at the GC electrode coated only with DMPC film. Ion channel current is not dependent on the time but on the concentration of calcium. The mechanism of the ion channel formation was investigated.     

Plant prolyl hydroxylase recognizes poly(L-proline) II helix

Substrate specificity of a prolyl hydroxylase from Vinca rosea suspension-cultured cells was studied using synthetic oligo(L-proline)s and their t-butyloxycarbonyl derivatives (Pron and Boc-Pron; n = 2-8) as peptidyl substrates. All peptides with a residual number of 5 or greater served as substrates in the enzyme reaction at 30 degrees C, after the preincubation of the enzyme and peptides at 0 degrees C prior to addition of cofactors and cosubstrate. Under the same conditions, the hydroxylation of Pro5 reached a plateau within 10 min, but that of Boc-Pro8 and poly(L-proline) increased linearly up to 40 min. If the preincubation temperature was raised to 30 degrees C, only Pro5 among the peptides was unable to serve as a substrate. The optimum temperature of the enzyme was 30 degrees C toward Boc-Pro8 and poly(L-proline) but it decreased to 15 degrees C using Pro5. These data suggest that the enzyme can bind Pro5 only at low temperature. Poly(L-proline) and Boc-Pron (n greater than or equal to 5) in aqueous solution are known to have a left-handed helical structure (poly(L-proline) II helix). Moreover, Pro5 was indicated as forming this helix below 10 degrees C. Accordingly, the enzyme recognizes the poly(L-proline) II helix, that is, the secondary structure of a substrate rather than the primary structure.     

Poly(L-proline)-binding proteins from chick embryos are a profilin and a profilactin

Two poly(L-proline)-binding proteins (PBP-1 and PBP-2) were purified from chick embryos by using a poly(L-proline)-agarose column. PBP-1 was composed of two different polypeptides (molecular masses of 42 kDa and 15 kDa). The molar ratio of the two proteins in the complex was 1:1. The other poly(L-proline)-binding protein, PBP-2, was the 15-kDa protein itself. The 42-kDa protein was confirmed to be an actin from the amino acid composition, by immunochemical evidence and by its ability to self-polymerize. In addition, the 42 + 15-kDa protein complex (PBP-1) inhibited DNase I, just as a monomeric actin did. The amino acid composition of the 15-kDa protein was similar to that of mammalian profilin and it inhibited the salt-induced polymerization of rabbit skeletal muscle actin. Therefore, we conclude that the two poly(L-proline)-binding proteins from the chick embryo are a profilactin and a profilin in chick embryo. The ability of profilactin to bind poly(L-proline) must be due to profilin itself, because the profilin has a greater affinity for poly(L-proline) than does profilactin. Additionally, both the monomeric and filamentous actin from rabbit skeletal muscle have no affinity for poly(L-proline).     

Partitioning of Differently Sized Poly(ethylene glycol)s into OmpF Porin

To understand the physics of polymer equilibrium and dynamics in the confines of ion channel pores, we study partitioning of poly(ethylene glycol)s (PEGs) of different molecular weights into the bacterial porin, OmpF. Thermodynamic and kinetic parameters of partitioning are deduced from the effects of polymer addition on ion currents through single OmpF channels reconstituted into planar lipid bilayer membranes. The equilibrium partition coefficient is inferred from the average reduction of channel conductance in the presence of PEG; rates of polymer exchange between the pore and the bulk are estimated from PEG-induced conductance noise. Partition coefficient as a function of polymer weight is best fitted by a “compressed exponential” with the compression factor of 1.65. This finding demonstrates that PEG partitioning into the OmpF channel pore has sharper dependence on polymer molecular weight than predictions of hard-sphere, random-flight, or scaling models. A 1360-Da polymer separates regimes of partitioning and exclusion. Comparison of its characteristic size with the size of a 2200-Da polymer previously found to separate these regimes for the α-toxin shows good agreement with the x-ray structural data for these channels. The PEG-induced conductance noise is compatible with the polymer mobility reduced inside the OmpF pore by an order of magnitude relatively to its value in bulk solution.     

Reassessment of the random coil conformation: vibrational CD study of proline oligopeptides and related polypeptides.

The "random coil" conformational problem is examined by comparison of vibrational CD (VCD) spectra of various polypeptide model systems with that of proline oligomers [(Pro)n] and poly(L-proline). VCD, ir and uv CD spectra of blocked L-proline oligopeptides [(Pro)n, n = 2-12] in different solvents are reported and compared to the spectra of poly(L-proline) II, poly(L-glutamic acid), and unblocked proline oligomers. Based on the chain-length dependence of the VCD and electronic CD (ECD) spectra of proline oligomers, it is established that VCD spectra are dominated by short-range interactions. The VCD of random coil model polypeptides is shown to be identical in shape but smaller in magnitude than poly(L-proline) II and of similar magnitude to that of (Pro)n (n = 3, 4). Based on the spectral evidence, it is concluded that the "random coil" conformation has a large fraction of helical regions, conformationally similar to the left-handed, 3(1) polyproline II helix, as was previously suggested by Krimm and co-workers. This conclusion is further supported by studies of effects of salt (CaCl2, LiBr, LiClO4), temperature (5-75 degrees C), and pH on the VCD spectra of L-proline oligomers, poly(L-proline) II, and poly(L-glutamic acid). These show that, after each of these perturbations, a significant local ordering remains in the oligomers and polymers studied, and that charged polypeptides such as poly(L-glutamic acid) are more flexible than are polyproline or even L-proline oligomers.     

Poly(DL-proline), a synthetic polypeptide behaving as an ion channel across bilayer membranes

The synthesis and characterization of poly(DL-proline) are reported in relation with its predicted property of forming ion channels across membranes. The analysis of the conductance induced in synthetic bilayer membranes doped with poly(DL-proline) shows ionic permeoselectivity and the characteristic time course of fluctuations of ion channels, according to the similarity with the active structure of gramicidin A in membranes during the ion passage. An alternative mechanism of ion transport across bilayer membranes is also advanced.     

Thermocontrol of solute permeation across polymer membrane composed of poly(N,N-dimethylaminoethyl methacrylate) and its copolymers

Polymer membranes composed ofN,N-dimethylaminoethyl methacrylate (DMAEMA) and acrylamide (AAm) (or ethyl acrylamide (EAAm)) were prepared to demonstrate the thermocontrol of solute permeation. Poly DMEMA has a lower critical solution temperature (LCST) at around 50°C in water. With the copolymerization of DMAEMA with AAm (or EAAm), a shift in the LCST to a lower temperature was observed, probably due to the formation of hydrogen bonds between the amide andN,N-dimethylamino groups. However, the temperature-induced phase transition of poly (DMAEMA-co-EAAm) did not show a similar trend to that of poly (DMAEMA-co-AAm) in the gel state. The hydrogen bonds in poly (DMAEMA-co-EAAm) were significantly disrupted with the formation of a gel network, which led to a difference in the swelling behavior of polymer gels in response to temperature. To apply these polymers to temperature-sensitive solute permeation, polymer membranes were prepared. The permeation pattern of hydrocortisone, used as the model solute, was explained based on the temperature-sensitive swelling behavior of the polymer membranes.     

Solid support membranes for ion channel arrays and sensors: application to rapid screening of pharmacological compounds

The use of solid supported membranes (SSM) was investigated for reconstitution of ion channels and for potential application to screen pharmacological reagents affecting ion channel function. The voltage-gated Kv1.5 K+ channel was reconstituted on an SSM and a current was measured. This current was dependent on the presence of K+, but not Na+, indicating that the Kv1.5 K+ channel maintained cation specificity when reconstituted on SSM. Two pharmacological reagents applied to Kv1.5 K+ channels reconstituted on SSM had similar inhibitory effects as those measured using Kv1.5 in biological membranes. SSM-mounted ion channels were stable enough to be washed with buffer solution and reused many times, allowing solution exchange essential for pharmacological drug screening.     

Conformations of oligoprolines with different configurational sequences and their association complexes with alkali and alkali-earth ions

To clarify the possible molecular mechanism of cation unit conductance of poly(D ,L -proline) across lipidic membranes, the structure and conformation of tetraproline derivatives with different configurational sequences in solid state, as well as in solution and in the presence of alkali and alkali-earth ions, were investigated using x-ray analysis, CD, and nmr spectroscopy. The tetraproline derivatives Boc(D -Pro-L -Pro-L -Pro-D -Pro)OBg and Boc(L -Pro)₄OBg show very different conformational versatilities in solutions as well as different propensities to form complexes with Ca²⁺ ion. This is interpreted, based on previous evidence, as due to different abilities to form ion complexing cavities. © 1998 John Wiley & Sons, Inc. Biopoly 45: 257–267, 1998     

Identification of a novel proline-rich peptide-binding domain in prolyl 4-hydroxylase.

Prolyl 4-hydroxylase (EC 1.14.11.2) catalyzes the hydroxylation of -X-Pro-Gly- sequences and plays a central role in the synthesis of all collagens. The [alpha(I)]2beta2 type I enzyme is effectively inhibited by poly(L-proline), whereas the [alpha(II)]2beta2 type II enzyme is not. We report here that the poly(L-proline) and (Pro-Pro-Gly)10 peptide substrate-binding domain of prolyl 4-hydroxylase is distinct from the catalytic domain and consists of approximately 100 amino acids. Peptides of 10-19 kDa beginning around residue 140 in the 517 residue alpha(I) subunit remained bound to poly(L-proline) agarose after limited proteolysis of the human type I enzyme tetramer. A recombinant polypeptide corresponding to the alpha(I) subunit residues 138-244 and expressed in Escherichia coli was soluble, became effectively bound to poly(L-proline) agarose and could be eluted with (Pro-Pro-Gly)10. This polypeptide is distinct from the SH3 and WW domains, and from profilin, and thus represents a new type of proline-rich peptide-binding module. Studies with enzyme tetramers containing mutated alpha subunits demonstrated that the presence of a glutamate and a glutamine in the alpha(II) subunit in the positions corresponding to Ile182 and Tyr233 in the alpha(I) subunit explains most of the lack of poly(L-proline) binding of the type II prolyl 4-hydroxylase. Keywords: collagen/dioxygenases/peptide-binding domain/ proline-rich/prolyl hydroxylase     

Phosphorylation of profilin regulates its interaction with actin and poly (L-proline)

Activation of bovine platelets with thrombin and phorbol 12,13-dibutyrate (PDBu) resulted in phosphorylation of profilin on serine. The phosphorylation was inhibited when platelets were pretreated with the PI 3-kinase inhibitor, LY294002, indicating that profilin phosphorylation is a downstream event with respect to PI 3-kinase activation. Phosphorylation of profilin resulted in significant decrease in actin polymerization (16.5%), indicating an increased affinity of phosphoprofilin towards actin. The critical actin monomer concentration (Cc) increased to 260 nM in the presence of phosphoprofilin in comparison with 200 nM in the presence of profilin. The interaction of phosphoprofilin with phosphatidylinositol 4,5-bisphosphate [PI (4,5)-P2] and poly (L-proline) (PLP) was examined by monitoring the quenching of tryptophan fluorescence. Scatchard plot and binding isotherm data obtained revealed no difference in PI (4,5)-P2 binding between profilin and phosphoprofilin (Kd=20.4 microM), while poly (L-proline)-binding studies indicated a sixfold decrease (27.34 microM for profilin and 4.73 microM for phosphoprofilin) in Kd with phosphoprofilin. In vivo studies with platelets indicated an increased association of p85alpha, the regulatory subunit of PI 3-kinase with phosphoprofilin over profilin. Overall, the data presented conclude that profilin phosphorylated under in vivo conditions and phosphorylation depends upon activation of PI 3-kinase. Phosphoprofilin exhibited increased affinity to poly (L-proline) sequences both in vitro and in vivo.     

Insights from modeling three-dimensional structures of the human potassium and sodium channels

Ion channels allow the movement of ions across cell membranes. Nearly all cells have membranes spanned by ion channels, without which human nerves simply would not work. Ion channels are formed by the aggregation of subunits into a cylindrical configuration that allows a pore, thus forming a kind of tube for ion trafficking. In the present study, the subunits of the human potassium channel are formed by four identical protein chains, whereas for the case of the human sodium channel, the corresponding subunits are actually four hetero-domains formed by the folding of a very large but single protein chain. Since both of the two ion channels are important targets for drug discovery, the 3D (dimensional) structures of their pore regions were developed. On the basis of the 3D models, some important molecular biological mechanisms were discussed that may stimulate novel strategies for therapeutic treatment of the diseases related to ion channel disorders, such as long QT syndrome and chronic pain.     

Ion channels in human macrophages compared with the U-937 cell line

Summary The human cell line U-937 has been used extensively to model many macrophage functions. We have examined the cell membranes of human monocyte-derived macrophages (HMDM) and U-937 cells to compare membrane properties as expressed by single ion channel currents. The patch-clamp technique was applied to isolated, nonactivated, inside-out patches of cell membranes obtained from HMDM and from the U-937 cell line. Voltage-gated potassium channels of similar conductance but different kinetics are present in both types of cells, and a calcium-activated potassium channel is present only in the HMDM. These differences in ion channel properties suggest fundamentally different behavior between these two cell types at the level of the cell membrane.     

Helix-coil stability constants for the naturally occurring amino acids in water. XXIII. Proline parameters from random poly (hydroxybutylglutamine-co-L-proline)

Water-soluble random copolymers containing L-proline and N5-(4-hydroxybutyl)-L-glutamine were synthesized by copolymerization of the tripeptides H-L-Glu(OBzl)-L-Glu(OBzl)-L-Glu(OBzl)-OH and H-L-Glu(OBzl)-L-Pro-L-Glu(OBzl)-OH, using benzotriazolyl-N-oxy-tris(dimethylamino)-phosphonium hexafluorophosphate as condensing reagent, and subsequent aminolysis of the Bzl ester groups with 4-amino-1-butanol. These copolymers were found to contain significant amounts of N5-(4-hydroxybutyl)-D-glutamine, thus requiring the synthesis of a binary copolymer containing only D- and L-N5-(4-hydroxybutyl)glutamine residues in order to evaluate the possible effects of the D-residues on the conformational properties of poly(hydroxybutylglutamine-co-L-proline). The different copolymers were fractionated, and their thermally induced helix-coil transition curves were obtained in water at neutral pH. When proper corrections were applied for the helix-destabilizing properties of N5-(4-hydroxybutyl)-D-glutamine, the Zimm-Bragg parameters sigma and s for L-proline could be deduced from the melting curves of poly(hydroxybutylglutamine-co-L-proline). The results indicate that L-proline acts as a very strong helix breaker over the entire temperature range from 0 to 60 degrees C.     

Evaluation of surface tension and ion occupancy effects on gramicidin A channel lifetime.

The surface tension of glycerylmonooleate-hexadecane lipid bilayer membranes and the lifetime of gramicidin A channels were measured at various concentrations of the surrounding solutions. For HCl the surface tension is essentially constant at approximately 5 mN/m up to approximately 1 M, whereas the average lifetime increases approximately 40-fold. At higher concentrations the surface tension decreases markedly. For CsCl the surface tension is constant up to about 1 M then increases with salt level. The average lifetime in this case increases about sixfold. In both cases the lifetime levels off and even decreases at higher salt levels. The increase in lifetime observed with ion activity is therefore qualitatively different from, and not explained by, the established dependence of lifetime on membrane properties (Elliot, J.R., D. Needham, J.P. Dilger, and D.A. Haydon. 1983. Biochim. Biophys. Acta. 735:95-103). We have previously proposed that ion occupancy is a determinant of channel stability, and to test this hypothesis the voltage dependence of channel lifetime was measured in asymmetrical solutions. For the case of a potassium chloride solution on one side of the membrane and a hydrogen chloride solution, on the other, the voltage dependence of the lifetime is asymmetrical. The asymmetry is such that when the electrical field is applied in the direction of the chemical gradient for each of the ions, the channel lifetime approaches, at increasing field strengths, that of a symmetrical solution of the respective ion. The voltage dependence of the surface tension, on the other hand, is negligible for the range of voltages used.(ABSTRACT TRUNCATED AT 250 WORDS)     

Structure and morphology changes during in vitro degradation of electrospun poly(glycolide-co-lactide) nanofiber membrane

Electrospun poly(glycolide-co-lactide) (PLA10GA90, LA/GA ratio 10/90) biodegradable nanofiber membranes possessed very high surface area to volume ratios and were completely noncrystalline with a relatively lowered glass transition temperature. These characteristics led to very different structure, morphology, and property changes during in vitro degradation, which were examined systematically. A shrinkage study showed that the electrospun crystallizable but amorphous PLA10GA90 membranes exhibited a very small shrinkage percentage when compared with the electrospun membranes of noncrystallizable poly(lactide-co-glycolide) (PLA75GA25, LA/GA 75/25) and poly(d,l-lactide). Although the weight loss of electrospun PLA10GA90 membranes exhibited a similar degradation behavior as cast thin films, detailed studies showed that the structure and morphology changes in electrospun membranes followed different pathways during the hydrolytic degradation. After 1 day of degradation in buffer solution at 37 degrees C, electrospun PLA10GA90 membranes exhibited a sudden increase in crystallinity and glass transition temperature, due to the fast thermally induced crystallization process. The continuous increase in crystallinity and apparent crystal size, as well as the decrease in long period and lamellae thickness, indicated that the thermally induced crystallization was followed by a chain cleavage induced crystallization process. The mass loss rate was accelerated after 6 days of degradation. The increase in glass transition temperature during this period further confirmed that the degradation of PLA10GA90 nanofibers was initiated from the amorphous region within the lamellar superstructures. A mechanism of structure and morphology changes during in vitro degradation of electrospun PLA10GA90 nanofibers is proposed.     

ATP transport through a single mitochondrial channel, VDAC, studied by current fluctuation analysis.

The "molecular Coulter counter" concept has been used to study transport of ATP molecules through the nanometer-scale aqueous pore of the voltage-dependent mitochondrial ion channel, VDAC. We examine the ATP-induced current fluctuations and the change in average current through a single fully open channel reconstituted into a planar lipid bilayer. At high salt concentration (1 M NaCl), the addition of ATP reduces both solution conductivity and channel conductance, but the effect on the channel is several times stronger and shows saturation behavior even at 50 mM ATP concentration. These results and simple steric considerations indicate pronounced attraction of ATP molecules to VDAC's aqueous pore and permit us to evaluate the effect of a single ATP molecule on channel conductance. ATP addition also generates an excess noise in the ionic current through the channel. Analysis of this excess noise shows that its spectrum is flat in the accessible frequency interval up to several kilohertz. ATP exchange between the pore and the bulk is fast enough not to display any dispersion at these frequencies. By relating the low-frequency spectral density of the noise to the equilibrium diffusion of ATP molecules in the aqueous pore, we calculate a diffusion coefficient D = (1.6-3.3)10(-11) m2/s. This is one order of magnitude smaller than the ATP diffusion coefficient in the bulk, but it agrees with recent results on ATP flux measurements in multichannel membranes using the luciferin/luciferase method.     

The influence of a membrane environment on the structure and stability of a prokaryotic potassium channel, KcsA

The lack of a membrane environment in membrane protein crystals is considered one of the major limiting factors to fully imply X-ray structural data to explain functional properties of ion channels [Gulbis, J.M. and Doyle, D. (2004) Curr. Opin. Struct. Biol. 14, 440-446]. Here, we provide infrared spectroscopic evidence that the structure and stability of the potassium channel KcsA and its chymotryptic derivative 1-125 KcsA reconstituted into native-like membranes differ from those exhibited by these proteins in detergent solution, the latter taken as an approximation of the mixed detergent-protein crystal conditions.