Macrodipoles. Unusual electric properties of biological macromolecules

Exaggerated trans-membrane charge of ammonium transporters in nutrient-poor marine environments

Transporter proteins are a vital interface between cells and their environment. In nutrient-limited environments, microbes with transporters that are effective at bringing substrates into their cells will gain a competitive advantage over variants with reduced transport function. Microbial ammonium transporters (Amt) bring ammonium into the cytoplasm from the surrounding periplasm space, but diagnosing Amt adaptations to low nutrient environments solely from sequence data has been elusive. Here, we report altered Amt sequence amino acid distribution from deep marine samples compared to variants sampled from shallow water in two important microbial lineages of the marine water column community-Marine Group I Archaea (Thermoproteota) and the uncultivated gammaproteobacterial lineage SAR86. This pattern indicates an evolutionary pressure towards an increasing dipole in Amt for these clades in deep ocean environments and is predicted to generate stronger electric fields facilitating ammonium acquisition. This pattern of increasing dipole charge with depth was not observed in lineages capable of accessing alternative nitrogen sources, including the abundant alphaproteobacterial clade SAR11. We speculate that competition for ammonium in the deep ocean drives transporter sequence evolution. The low concentration of ammonium in the deep ocean is therefore likely due to rapid uptake by Amts concurrent with decreasing nutrient flux.

Relevance of the protein macrodipole in the membrane-binding process. Interactions of fatty-acid binding proteins with cationic lipid membranes

The fatty acid-binding proteins L-BABP and Rep1-NCXSQ bind to anionic lipid membranes by electrostatic interactions. According to Molecular Dynamics (MD) simulations, the interaction of the protein macrodipole with the membrane electric field is a driving force for protein binding and orientation in the interface. To further explore this hypothesis, we studied the interactions of these proteins with cationic lipid membranes. As in the case of anionic lipid membranes, we found that both proteins, carrying a negative as well as a positive net charge, were bound to the positively charged membrane. Their major axis, those connecting the bottom of the β-barrel with the α-helix portal domain, were rotated about 180 degrees as compared with their orientations in the anionic lipid membranes. Fourier transform infrared (FTIR) spectroscopy of the proteins showed that the positively charged membranes were also able to induce conformational changes with a reduction of the β-strand proportion and an increase in α-helix secondary structure. Fatty acid-binding proteins (FABPs) are involved in several cell processes, such as maintaining lipid homeostasis in cells. They transport hydrophobic molecules in aqueous medium and deliver them into lipid membranes. Therefore, the interfacial orientation and conformation, both shown herein to be electrostatically determined, have a strong correlation with the specific mechanism by which each particular FABP exerts its biological function.

Free energy calculations and molecular properties of substrate translocation through OccAB porins

We investigated with molecular modeling the translocation of simple substrates through four similar specific bacterial porins from the Acinetobacter baumannii pathogen providing structure–function analysis at the molecular level.

Electric Destabilization of Supramolecular Lipid Vesicles Subjected to Fast Electric Pulses

Biological membranes are weakly permeable to hydrophilic molecules and ions and electric pulses can induce their transient permeabilization, but this process is not well characterized. We directly assay the electropermeabilization process, on the minimum model of lipid vesicles, by using a highly sensitive fluorescence method based on manganese ion transport. The approach gives access, at the single-lipid self-assembly level, to the transmembrane potential needed to detect divalent ion permeabilization on supramolecular giant unilamellar lipid vesicles. The critical values are strongly dependent on the lipid composition and are observed to vary from 10 to 150 mV. These values appear to be much lower than those previously reported in the literature for cells and vesicles. The detection method appears to be a decisive parameter as it is controlled by the transport of the reporter dye. We also provide evidence that the electropermeabilization process is a transient transition of the lipid self-organization due to the loss of assembly cohesion induced by bioelectrochemical perturbations of the zwitterionic interface with the solution.

Electric field as a disaggregating agent for amyloid fibrils

Folding and aggregation lie on competing reaction pathways in proteins. Altering the occupancy of one pathway is automatically relayed to the other pathway, leading to a shift in the balance between the two processes. In particular, it is known that the stabilization of the native state through mutations or solvent alterations is able to halt aggregation. In this work, we explore the feasibility of using external electric field as an agent preventing aggregation through the promotion of folding. We use an atomically accurate protein model and computer simulations to investigate folding and aggregation of alanine polypeptides in electric field of varying strength. The studied peptides are mostly unstructured in the absence of the field but experience a transition into α-helical states when the field is applied. The transition is accompanied by the disassembly of preseeded stacked β-sheets, which are used as a model of amyloid fibrils, suggesting that electric field can be employed to control aggregation propensity of intrinsically disordered peptides. According to our calculations, the strength of the field required for the disaggregation could be suitable for both controlled in vitro experiments as well as for experiments on live cells. Additionally, our estimates suggest that endogenous electric fields may have a significant effect on in vivo amyloid formation.

Fabrication and characterization of a radiation sensor based on bacteriorhodopsin

Available techniques of X-ray detection have been under development due to specific shortcomings such as finite lifetime, low sensitivity, and post-processing requirements. Here we report on the fabrication of an X-ray sensor based on bacteriorhodopsin (BR) with a radius of r=3mm as the sensing area on a flexible substrate. The flexible X-ray detector can be placed on the targeted area for real-time monitoring of radiation dosage. We show that BR sensor is a potential candidate for such a powerful sensing device. For this purpose, we measure the electrical current generated by the BR sensor under different radiation dosages, energies and dose rates. This averaged current is in the range of nanoampere and is proportional to the dose rate of the received X-ray. The current also increases with the increase of radiation energy. BR radiation sensor can be readily miniaturized and is relatively easy to fabricate. The capability for real-time data collection and reusability are other advantages of this radiation sensor.

Field-induced alignment of flexible polyelectrolytes in solution

Molecular dynamics simulations are used to study dynamical coupling between conformational fluctuations of a highly charged flexible macromolecule and its surrounding ionic cloud. We find that the basic model of a polyelectrolyte as a chain of charged monomers captures the main experimental findings on the field-induced alignment of polyelectrolytes despite its simplicity. Contrary to current theories, the correlated local charge and field fluctuations in the vicinity of the macromolecule are found to dominate alignment along an external field. We suggest that short-lived monomer-counterion clustering can be probed by measuring the field-induced anisotropy of x-ray and neutron scattering from polymer solutions.

PHEMTO: protein pH-dependent electric moment tools

PHEMTO (protein pH-dependent electric moment tools) is released in response to the high demand in protein science community for evaluation of electrostatic characteristics in relations to molecular recognition. PHEMTO will serve protein scientists with new advanced features for analysis of protein molecular interactions: Electric/dipole moments, their pH-dependence and in silico charge mutagenesis effects on these properties as well as alternative algorithms for electric/dipole moment computation--Singular value decomposition of electrostatic potential (EP) to account for reaction field. The implementation is based on long-term experience--PHEI mean field electrostatics and PHEPS server for evaluation of global and local pH-dependent properties. However, PHEMTO is not just an update of our PHEPS server. Besides standard electrostatics, we offer new, advanced and useful features for analysis of protein molecular interactions. In addition our algorithms are very fast. Special emphasis is given to the interface--intuitive and user-friendly. The input is comprised of the atomic coordinate file in Protein Data Bank format. The advanced user is provided with a special input section for addition of non-polypeptide charges. The output covers actually full electrostatic characteristics but special emphasis is given to electric/dipole moments and their interactive visualization. PHEMTO server can be accessed at http://phemto.orgchm.bas.bg/.

Size-dependent trajectories of DNA macromolecules due to insulative dielectrophoresis in submicrometer-deep fluidic channels

In this paper, we demonstrate for the first time that insulative dielectrophoresis can induce size-dependent trajectories of DNA macromolecules. We experimentally use lambda (48.5 kbp) and T4GT7 (165.6 kbp) DNA molecules flowing continuously around a sharp corner inside fluidic channels with a depth of 0.4 mum. Numerical simulation of the electrokinetic force distribution inside the channels is in qualitative agreement with our experimentally observed trajectories. We discuss a possible physical mechanism for the DNA polarization and dielectrophoresis inside confining channels, based on the observed dielectrophoresis responses due to different DNA sizes and various electric fields applied between the inlet and the outlet. The proposed physical mechanism indicates that further extensive investigations, both theoretically and experimentally, would be very useful to better elucidate the forces involved at DNA dielectrophoresis. When applied for size-based sorting of DNA molecules, our sorting method offers two major advantages compared to earlier attempts with insulative dielectrophoresis: Its continuous operation allows for high-throughput analysis, and it only requires electric field strengths as low as approximately 10 Vcm.

Dielectrophoretic Manipulation of DNA: Separation and Polarizability

Although separation of polymers based on the combination of dielectrophoretic trapping and electrophoretic forces was proposed 15 years ago, experimental proof has not yet been reported. Here, we address this problem for long DNA fragments in a simple and easy-to-fabricate microfluidic device, in which the DNA is manipulated by electrophoresis and by electrodeless dielectrophoresis. By slowly increasing the strength of the dielectrophoretic traps in the course of the separation experiments, we are able to perform efficient and fast DNA separation according to length for two different DNA conformations: linear DNA (lambda (48.5-kbp) and T2 (164-kbp) DNA) and supercoiled covalently closed circular plasmid DNA (7 and 14 kbp). The underlying migration mechanism-thermally induced escape processes out of the dielectrophoretic traps in the direction of the electrophoretic force-is sensitive to different DNA fragments because of length-dependent DNA polarizabilities. This is analyzed in a second series of experiments, where the migration mechanism is exploited for the quantitative measurement of the DNA polarizabilities. This new and simple technique allows for the systematic characterization of the polarizability not only for DNA but also for other biomolecules like proteins. Furthermore, our results have direct implications to future biotechnological applications such as gene therapy and DNA vaccination.

Dielectric properties of Bauhinia monandra and concanavalin A lectin monolayers, part I

The dielectric properties of the galactose-binding lectins Bauhinia monandra (BmoLL) and Concanavalin A (Con A) were assessed by surface potential measurements of their spread monolayers on an aqueous subphase containing a monovalent electrolyte. For both lectins the curves of surface potential versus mean molecular area (DeltaV-A) and the independently recorded isotherms of surface pressure versus mean molecular area (Pi-A) were shown to be pH-dependent. As the subphase pH changed from 2 to 9, a noticeable trend to higher surface pressures accompanied the compression of the monolayers. Conversely, the surface potentials values of both monolayers decreased with increasing pH. For Con A, with the single exception of the pH 9 case, lowering the pH yielded DeltaV values higher than those for BmoLL. The contribution of the electric double layer (Psi0) to the overall DeltaV values at a given Pi (15 mN/m) was calculated using a modified Davies equation and assuming that at this surface pressure the monolayers of both studied lectins were stable. While at all studied pHs the Psi0 values for Con A exceeded those calculated for BmoLL, for both lectins they were insensitive to pH changes. This provided evidence that the reorientation of lectin molecules, during compression predominantly contributed to the alteration of the overall DeltaV values. The calculated Psi0 values made possible the evaluation of the dipole moments for BmoLL and Con A, and it has been estimated that the decrease in the pH of the subphase from 9 to 2 produced a 1.6-fold (twofold) increase in the value of for BmoLL (Con A). The differences in dielectric properties between the two film-forming lectins have been attributed to the differences in their structures. Indeed, the circular dichroism (CD) spectrum of Con A showed the predominance of beta-plated sheet structures while that of BmoLL was typically rich in alpha-helix structures.

The 4,5-double bond of ceramide regulates its dipole potential, elastic properties, and packing behavior

The biological activities of ceramides show a large variation with small changes in molecular structure. To help understand how the structure regulates the activity of this important lipid second messenger, we investigated the interfacial features of a series of synthetic ceramide analogs in monomolecular films at the argon-buffer interface. To minimize differences arising from the N-acyl moiety, each analog had either a N-hexadecanoyl or a N-cis-4-hexadecenoyl moiety amide linked to the nitrogen of the sphingosine backbone. We found that the trans 4,5-unsaturation in the sphingosine backbone promoted closer packing and lower compressibilities of ceramide analogs in interfaces relative to comparable saturated species. Moreover, structures with this feature exhibited dipole potentials as much as 150-250 mV higher than comparable compounds lacking 4,5-unsaturation. The results support the hypothesis by M.C. Yappert and co-workers that trans unsaturation in the vicinity of C4 of the sphingoid backbone augments intramolecular hydration/hydrogen bonding in the polar region. This intramolecular hydration may allow the close packing of the ceramide molecules and engender their high dipole potentials. These properties of ceramides and their analogs may be important determinants of biological function.

DNA deposition on carbon electrodes under controlled dc potentials

The native calf-thymus DNA molecule fully dispersed in solution was deposited onto highly oriented pyrolytic graphite, carbon fiber column and disk electrodes under controlled dc potentials. X-ray photoelectron spectroscopy, atomic force microscopy and electrochemical investigations indicated that network structures of DNA could be formed on various carbon electrode surfaces resulting in significant surface enlargement. The conformation, conductivity and stability of the deposited DNA layer largely depended on the concentration of the DNA deposition solution, the applied dc potential and the mode of electric field. The optimal condition for deposition of the DNA on carbon fiber disk electrode was determined as a deposition potential of 1.8 +/- 0.3 V versus 50 mM NaCl-Ag/AgCl and a deposition DNA solution of 0.1 mg ml(-1). Under this condition, the DNA was covalently bonded on the electrode surface forming a three-dimensional modified layer, generating a 500-fold enlarged effective electrode surface area and similarly enlarged current sensitivity for redox species, such as Co(phen)3(3+). A possible mechanism for the formation of DNA networks is proposed.

Adsorption of alpha-chymotrypsin onto mica in laminar flow conditions. Adsorption kinetic constant as a function of tris buffer concentration at pH 8.6

We examined the adsorption kinetics of alpha-chymotrypsin (pH 8.6, 10(-2) to 0.5 M Tris buffer) on muscovite mica in conditions of laminar flow through a slit. The range of buffer concentrations is between two limits: (i) no adsorption in 1 M Tris and (ii) no desorption in 10(-3) M Tris. Studying the dependence of adsorption kinetics on the wall shear rate leads to the determination of the interfacial adsorption kinetic constant ka and the diffusion coefficient. The obtained value for the diffusion coefficient is close to the one expected from the molecular size of alpha-chymotrypsin. The interfacial adsorption kinetic constant of alpha-chymotrypsin decreases when ionic strength increases, while the initial desorption constant (over a part of all the adsorbed population) shows the contrary. Although alpha-chymotrypsin is almost at its isoelectric point, the effect of ionic strength on the adsorption kinetics suggests the importance of electrostatic interactions between the protein and mica. We observed an increase in the adsorption rate, at a surface coverage near 0.14 microg cm(-2), for adsorption in 10(-2) M Tris and the low wall shear rates (<300 s(-1)). This change in the adsorption rate suggests a structural transition, that we assume again to be due to electrostatic interactions, but between proteins. The large dipole moment of the protein may induce this transition, illustrated here by the ferroelectric/antiferroelectric pattern. The variation of the zeta potential with interfacial concentration seems to be in agreement with such a model.

DNA heterogeneity and phosphorylation unveiled by single-molecule electrophoresis

Broad-spectrum analysis of DNA and RNA samples is of increasing importance in the growing field of biotechnology. We show that nanopore measurements may be used to assess the purity, phosphorylation state, and chemical integrity of nucleic acid preparations. In contrast with gel electrophoresis and mass spectrometry, an unprecedented dynamic range of DNA sizes and concentrations can be evaluated in a single data acquisition process that spans minutes. Because the molecule information is quantized and digitally recorded with single-molecule resolution, the sensitivity of the system can be adjusted in real time to detect trace amounts of a particular DNA species.

Packing and electrostatic behavior of sn-2-docosahexaenoyl and -arachidonoyl phosphoglycerides

Mammalian synaptic membranes appear to contain high proportions of specific, sn-1-stearoyl-2-docosahexaenoyl- and sn-1-stearoyl-2-arachidonoyl phosphoglycerides, but the structural significance of this is unclear. Here we used a standardized approach to compare the properties of homogeneous monolayers of the corresponding phosphatidylcholines, phosphatidylethanolamines, phosphatidylserines, and phosphatidic acids with those of control monolayers of sn-1-stearoyl-2-oleoyl- and sn-1-palmitoyl-2-oleoyl phosphoglycerides. Major findings were: 1), that the presence of an sn-2-docosahexaenoyl group or an sn-2-arachidonoyl group increases the molecular areas of phosphoglycerides by 3.8 A(2) (7%) relative to the presence of an sn-2-oleoyl group; 2), that the phosphorylcholine headgroup independently increases molecular areas by a larger amount, 7.1 A(2) (13%); and 3), that the dipole moments of species having an arachidonoyl moiety or an oleoyl moiety are 83 mD (19%) higher than those of comparable docosahexaenoic acid-containing phosphoglycerides. These and other results provide new information about the molecular packing properties of polyenoic phosphoglycerides and raise important questions about the role of these phosphoglycerides in synapses.

Effect of protonation of the N-acetyl neuraminic acid residue of sialyl Lewis(X): a molecular orbital study with insights into its binding properties toward the carbohydrate recognition domain of E-selectin

Semiempirical molecular orbital (MO) calculations with an implicit treatment of the water environment were employed in order to assess whether the sialyl Lewis(X) (sLe(X)) tetrasaccharide binds to E-selectin in the anionic or neutral (i.e., protonated) state. The analysis of the frontier molecular orbitals, electrostatic potential surfaces, and conformational behavior of the sugar indicates that its neutral form possesses the necessary characteristics for binding. In particular, the LUMO level of the neutral sLe(X) molecule is localized both on the carboxylic group of the N-acetyl neuraminic acid (NeuNAc) residue and on the nearby glycosidic linkage. These two moieties interact with the Arg97 residue of E-selectin, as revealed by a recent crystal structure analysis of the E-selectin/sLe(X) complex. The energetics of this specific interaction was investigated with the aid of ab initio Hartree-Fock MO calculations, which resulted in a BSSE-corrected binding energy of 16.63 kcal/mol. Our observations could open up new perspectives in the design of sLe(X) mimics.

Dual effect of high electric field in capillary electrophoresis study of the conformational stability of Bungarus fasciatus acetylcholinesterase

The effect of high electric field in capillary zone electrophoresis (CZE) was evaluated for the study of the thermally induced unfolding of Bungarus fasciatus acetylcholinesterase. This monomer enzyme is characterised by two interdependent uncommon structural features, the asymmetrical distribution of charged residues and a relatively low thermal denaturation temperature. Both traits were presumed to interfere in the thermal unfolding of this enzyme as investigated by CZE. This paper analyses the effect of high electric field on the behaviour of the enzyme native state. It is shown that increasing the applied field causes denaturation-like transition of the enzyme at a current power which does not induce excessive Joule heating in the capillary. The susceptibility to electric field of proteins like cholinesterases, with charge distribution anisotropy, large permanent dipole moment and notable molecular flexibility associated with moderate thermal stability, was subsequently discussed.

Global structure and flexibility of hairpin ribozymes with extended terminal helices

Global structure and flexibility of three different hairpin ribozyme constructs have been analyzed by measuring their electric dichroism decay in various buffers at temperatures between 2 and 30 degrees C. The hairpin ribozyme is characterized by two independently folding domains A and B that are connected through a hinge and have to interact to enable catalysis. The analyzed constructs feature extended terminal helices 1 and 4 with 27 and 25 bp, respectively, to increase the sensitivity of the molecular rotational diffusion time constants with respect to the interdomain bending angle. Constructs HP1 and HP2 cannot cleave because of a G+1A change at the 3'-side of the cleavage site; in HP1 the helices 2 and 3 that flank the hinge form a continuous double helical segment; in HP2 and HP3, a six nucleotide bulge confers flexibility to the expected bending site; HP3 is a cleavable form of HP2 with a G+1-base. For comparison, a standard RNA double helix with 72 bp was included in our analysis. The dichroism decay curves of the hairpin constructs after pulses of low electric field strengths can be fitted to single exponentials taus, whereas the curves after pulses of high field strengths require two exponentials. In all cases, time constants increase with RNA concentration, indicating intermolecular interactions. Extrapolation of the tausvalues measured in standard buffer (50 mM Tris (pH 7.5) and 12 mM MgCl2) to zero RNA concentration provide values of 112, 93, and 73 ns for HP1, HP2 and HP3, respectively, at 30 degrees C, indicating increasingly compact structures. The 72 bp RNA reference under corresponding conditions did not show a dependence of its decay time constant on the RNA concentration nor on the field strength; its time constant is 175 ns (standard buffer, 30 degrees C). The observation of two relaxation processes for the hairpin constructs at high field strengths indicates stretching to a more elongated state; the fast process with a time constant of the order of 50 ns is assigned to reversion of stretching, the slow process to overall rotation. The overall rotational time of the stretched state at 20 degrees C is close to that for a completely stretched rigid state; at 30 degrees C the experimental values are around 70 % of that expected for a completely stretched rigid state, indicating flexibility and/or residual bending. Bead models were constructed to simulate dichroism decay curves. The time constants observed for the 72 bp RNA are as expected for a rigid rod with a rise of 2.8 A per base-pair. Based on this rise per base-pair for models of a V and a Y-shape, we estimate average bending angles of 80(+/-20) degrees and 105 (+/-25) degrees, respectively, for the catalytically active hairpin ribozyme HP3. The energy required for stretching is of the order of the thermal energy.

The apparently symmetrical hexagonal bilayer hemoglobin from Lumbricus terrestris has a large dipole moment

The giant approximately 3.6 MDa hexagonal bilayer hemoglobin (HBL Hb) from Lumbricus terrestris consists of 12 213-kDa dodecamers of four globin chains ([b + a + c]3[d]3) tethered to a central scaffold of approximately 36 non-globin, linker subunits L1-L4 (24-32 kDa). Three-dimensional reconstructions obtained by electron cryomicroscopy showed it to have a D6 point-group symmetry, with the two layers rotated approximately 16 degrees relative to each other. Measurement of the dielectric constants of the Hb and the dodecamer over the frequency range 5-100 kHz indicated relaxation frequencies occurring at 20-40 and 300 kHz, respectively, substantially lower than the 700-800 kHz in HbA. The dipole moments calculated using Oncley's equation were 17,300 +/- 2300 D and 1400 D for the Hb and dodecamer, respectively. The approximately threefold higher dipole moment of the dodecamer relative to HbA is consistent with an asymmetric shape in solution suggested by small-angle X-ray scattering. Although a two-term Debye equation and a prolate ellipsoid of revolution model provided a good fit to the experimental dielectric dispersion of the dodecamer, a three-term Debye equation based on an oblate ellipsoid of revolution model was required to fit the asymmetric dielectric dispersion curve of the Hb: the required additional term may represent either an induced dipole moment or a substructure which rotates independently of the main permanent dipole component of the Hb. The D6 point-group symmetry implies that the dipole moments of the dodecamers cancel out. Thus, in addition to a possible contribution from fluctuations of the proton distribution, the large dipole moment of the Hb may be due to an asymmetric distribution of the heterogeneous linker subunits.