Molecular dipole effects on tuning electron transfer in a porphine–quinone complex: a DFT and TDDFT study

The effect of a strong electric field generated by molecular dipoles on the ground state electronic structure and the Q and B states as well as the lowest charge transfer (CT) excited state of porphine–2,5-dimethyl-1,4-benzoquinone (PQ) complex has been investigated theoretically. Density functional theory DFT and time-dependent DFT (TDDFT) with the BH&HLYP hybrid functional have been applied in these calculations. The molecular dipole effect was generated by imposing one or two helical homopeptides consisting of eight α-aminoisobutyric acid residues (Aib₈) close to the PQ complex. The molecular dipoles in a close proximity to the PQ complex expose it to an electric field of the order of magnitude of 10⁹ V/m. The presence of the ambient molecular dipoles affects mainly the energy of the lowest CT state and barely the energies of the Q and B states. The molecular dipoles affect the energies of the excited states in a similar way as an external electrostatic field. Hence, the electric field induced by the molecular dipoles of the helical peptides could be used analogously to the external electrostatic field to control electron transfer (ET) in the PQ complex.     

Effects of ELF Inductively Coupled Weak Magnetic Fields on Proliferation of 6B1 Cells

To determine the effects of extremely low-frequency (ELF) inductively coupled weak magnetic fields on the proliferation of 6B 1 hybridoma cells, we adopted 3–[4,5–dimethylthiazolyl]-2,5–diphenyl tetrazolium bromide (MTIJ colorimetry for determination of dehydrogenase production. The result shows that 0.8 mT, 30 Hz (Helmholtz coils) significantly inhibits proliferation on the order of -40%. At lower and higher frequencies, this restriction decreases to zero, or even changes to positive values. This outcome is rather rare for proliferation responses and is discussed with other “electromagentic field windows.”     

Analysis of an electrostatic mechanism for ΔpH dependent gating of the voltage-gated proton channel,HV1, supports a contribution of protons to gating charge

Voltage-gated proton channels (H_V1) resemble the voltage-sensing domain of other voltage-gated ion channels, but differ in containing the conduction pathway. Essential to the functions of H_V1 channels in many cells and species is a unique feature called ΔpH dependent gating. The pH on both sides of the membrane strictly regulates the voltage range of channel opening, generally resulting in exclusively outward proton current. Two types of mechanisms could produce ΔpH dependent gating. The “countercharge” mechanism proposes that protons destabilize salt bridges between amino acids in the protein that stabilize specific gating configurations (closed or open). An “electrostatic” mechanism proposes that protons bound to the channel alter the electrical field sensed by the protein. Obligatory proton binding within the membrane electrical field would contribute to measured gating charge. Estimations on the basis of the electrostatic model explain ΔpH dependent gating, but quantitative modeling requires calculations of the electric field inside the protein which, in turn, requires knowledge of its structure. We conclude that both mechanisms operate and contribute to ΔpH dependent gating of H_V1.     

The role of electrostatics in TrxR electron transfer mechanism: A computational approach

Thioredoxin reductase (TrxR) is an important enzyme in the control of the intracellular reduced redox environment. It transfers electrons from NADPH to several molecules, including its natural partner, thioredoxin. Although there is a generally accepted model describing how the electrons are transferred along TrxR, which involves a flexible arm working as a “shuttle,” the molecular details of such mechanism are not completely understood. In this work, we use molecular dynamics simulations with Poisson–Boltzmann/Monte Carlo pKa calculations to investigate the role of electrostatics in the electron transfer mechanism. We observed that the combination of redox/protonation states of the N‐terminal (FAD and Cys59/64) and C‐terminal (Cys497/Selenocysteine498) redox centers defines the preferred relative positions and allows for the flexible arm to work as the desired “shuttle.” Changing the redox/ionization states of those key players, leads to electrostatic triggers pushing the arm into the pocket when oxidized, and pulling it out, once it has been reduced. The calculated pKa values for Cys497 and Selenocysteine498 are 9.7 and 5.8, respectively, confirming that the selenocysteine is indeed deprotonated at physiological pH. This can be an important advantage in terms of reactivity (thiolate/selenolate are more nucleophilic than thiol/selenol) and ability to work as an electrostatic trigger (the “shuttle” mechanism) and may be the reason why TrxR uses selenium instead of sulfur. Proteins 2016; 84:1836–1843. © 2016 Wiley Periodicals, Inc.     

On the longitudinal distribution of electric field in the acceleration zones of plasma accelerators and thrusters with closed electron drift

The long-term experience in controlling the electric field distribution in the discharge gaps of plasma accelerators and thrusters with closed electron drift and the key ideas determining the concepts of these devices and tendencies of their development are analyzed. It is shown that an electrostatic mechanism of ion acceleration in plasma by an uncompensated space charge of the cloud of magnetized electrons “kept” to the magnetic field takes place in the acceleration zones and that the electric field distribution can be controlled by varying the magnetic field in the discharge gap. The role played by the space charge makes the mechanism of ion acceleration in this type of thrusters is fundamentally different from the acceleration mechanism operating in purely electrostatic thrusters.     

Direct Evidence for a Similar Molecular Mechanism Underlying Shaker Kv Channel Fast Inactivation and Clustering

The fast inactivation and clustering functions of voltage-dependent potassium channels play fundamental roles in electrical signaling. Recent evidence suggests that both these distinct channel functions rely on intrinsically disordered N- and C-terminal cytoplasmic segments that function as entropic clocks to time channel inactivation or scaffold protein-mediated clustering, both relying on what can be described as a “ball and chain” binding mechanism. Although the mechanisms employed in each case are seemingly analogous, both were put forward based on bulky chain deletions and further exhibit differences in reaction order. These considerations raised the question of whether the molecular mechanisms underlying Kv channel fast inactivation and clustering are indeed analogous. By taking a “chain”-level chimeric channel approach involving long and short spliced inactivation or clustering “chain” variants of the Shaker Kv channel, we demonstrate the ability of native inactivation and clustering “chains” to substitute for each other in a length-dependent manner, as predicted by the “ball and chain” mechanism. Our results thus provide direct evidence arguing that the two completely unrelated Shaker Kv channel processes of fast inactivation and clustering indeed occur according to a similar molecular mechanism.     

Zebrafish “personality” influences sensitivity to magnetic fields

How animals integrate different sensory information for orientation is a complex process involving interactions between a variety of internal and external factors. Due to this complexity, each component of a suite of factors is typically studied in isolation. Here, we examine how an internal factor (personality of fish) influences the response of zebrafish (Danio rerio) to the magnetic field, while swimming in a flow chamber. Our previous work demonstrated that the orientation to the water current (rheotaxis) of zebrafish individuals is influenced by variations of the magnetic field only when fish are part of a shoal. In this study, we evaluated the rheotactic behavior of 20 fish, grouped in shoals of “proactive” or “reactive” individuals, under magnetic fields of different directions. We found that the magnetic field influenced at which water speed rheotaxis was elicited in zebrafish with “reactive” personality, but not in those with “proactive” personality. These results suggest that fish personality influences response to or weighing of sensory inputs and provides some insight on the variation in behavioral responses to environmental stimuli in both laboratory and natural settings.     

Electrodissociation of clathrate-like structures

In the present work, we develop molecular dynamics (MD) simulations in the NPT (isobaric–isothermic) ensemble to analyse the effect of an external electrostatic field over a cubic methane hydrate crystallite. The amplitude of the field is in the range 0.5–3.0 V/nm. For the simulations, we used the SPC/E rigid water model and a single-site model for methane at a temperature of 248 K and a pressure of 20 bar. When the external electrostatic field is applied, the water dipoles are oriented in such a way that the methane molecules can diffuse far away from the water cages, hence the clathrate dissociation takes place. This last phenomenon was observed for intensities above 1.5 V/nm. Taking the final configuration of each run as input, we develop a new set of MD simulations, and we observe that the stable clathrate is not recovered immediately when the external electrostatic field is turned off due to limitations in the simulation time.     

High affinity central benzodiazepine receptor ligands. Part 2: quantitative structure-activity relationships and comparative molecular field analysis of pyrazolo[4,3-c]quinolin-3-ones

A large series of 2-aryl(heteroaryl)-2,5-dihydropyrazolo[4,3-c]quinolin-3(3H)-ones (PQ, 106 compounds), carrying appropriate substituents at the quinoline and N2-phenyl rings, were designed, prepared and tested as central benzodiazepine receptor ligands. Compounds with an affinity significantly higher than the parent compound CGS-8216 were obtained, the most active ligand showing a pIC50 = 10.35. Hansch and comparative molecular field analyses gave coherent results suggesting the main structural requirements of high receptor binding affinity. The possible formation of a three-centred hydrogen bond (HB) at the HB donor site H2, as a key interaction for high receptor binding affinity, was assessed by the calculation and comparison of the molecular electrostatic potentials of a series of selected ligands.     

Reductive activation in periplasmic nitrate reductase involves chemical modifications of the Mo-cofactor beyond the first coordination sphere of the metal ion

In Rhodobacter sphaeroides periplasmic nitrate reductase NapAB, the major Mo(V) form (the “high g” species) in air-purified samples is inactive and requires reduction to irreversibly convert into a catalytically competent form (Fourmond et al., J. Phys. Chem., 2008). In the present work, we study the kinetics of the activation process by combining EPR spectroscopy and direct electrochemistry. Upon reduction, the Mo (V) “high g” resting EPR signal slowly decays while the other redox centers of the protein are rapidly reduced, which we interpret as a slow and gated (or coupled) intramolecular electron transfer between the [4Fe–4S] center and the Mo cofactor in the inactive enzyme. Besides, we detect spin–spin interactions between the Mo(V) ion and the [4Fe–4S]^1 + cluster which are modified upon activation of the enzyme, while the EPR signatures associated to the Mo cofactor remain almost unchanged. This shows that the activation process, which modifies the exchange coupling pathway between the Mo and the [4Fe–4S]^1 + centers, occurs further away than in the first coordination sphere of the Mo ion. Relying on structural data and studies on Mo-pyranopterin and models, we propose a molecular mechanism of activation which involves the pyranopterin moiety of the molybdenum cofactor that is proximal to the [4Fe–4S] cluster. The mechanism implies both the cyclization of the pyran ring and the reduction of the oxidized pterin to give the competent tricyclic tetrahydropyranopterin form.     

Consequences of one-electron oxidation and one-electron reduction for 4-aminopyrimidine—DFT studies

The consequences of one-electron oxidation and one-electron reduction were studied for 4-aminopyrimidine (4APM), which displays prototropic tautomerism. Since experimental techniques are incapable of detecting less than 0.1% of minor tautomers, quantum-chemical calculations [DFT(B3LYP)/6-311+G(d,p)] were carried out for all possible tautomers of neutral 4AMP and its redox forms, 4APM (+ ?) and 4APM (- ?). Four tautomers were considered: one amine and three imine tautomers (two NH and one CH form). Geometric isomerism of the exo?=?NH group was also taken into account. One-electron oxidation (4APM - e → 4APM (+??)) has no significant effect on the tautomeric preferences; it influences solely the composition of the tautomeric mixture. The amine tautomer is favored for both 4APM (+??) and 4APM. An interesting change in the tautomeric preference occurs for 4APM (- ?). One-electron reduction (4APM?+?e → 4APM (- ?)) favors the C5 atom for the labile proton. The preference of the imine CH tautomer in the tautomeric mixture of 4APM (- ?) may partially explain the origin of CH tautomers in nucleobases.     

The role of the environment around the catalytic triad in β-trypsin: A molecular orbital study

In the enzymatic reaction of β-trypsin the role of environment around the catalytic triad is studied by means of ab initio molecular orbital calculations. The triple ion form of the catalytic triad (Asp 102(?)-His 57(+)-Ser 195(?)) is considerably more stable than the double proton-transferred form (Asp 102(neutral)-His 57(neutral)-Ser 195(?)), due to the environment around it, rather than its nature. The “electrostatic mechanism” is more favorable than the “charge relay mechanism” owing to the nature of the enzyme as a biopolymer.     

Analysis of the decarboxylation step in mammalian histidine decarboxylase. A computational study

We report a hybrid quantum mechanics/molecular mechanics theoretical study on the reaction mechanism of mammalian histidine decarboxylase that allows us to obtain valuable insights on the structure of the cofactor-substrate adduct (external aldimine) in the active site of rat histidine decarboxylase. By means of molecular dynamics simulations, we traced the potential of mean force corresponding to the decarboxylation reaction of the adduct both in the active site of the enzyme and in aqueous solution. By comparing this process in both media, we have identified the key electrostatic interactions that explain the lowering of the free energy barrier in the enzyme. Our analysis also offers a validation of Dunathan's hypothesis (Dunathan, H. (1966) Proc. Natl. Acad. Sci. U. S. A. 55, 712-716) regarding the role of stereoelectronic effects in the enzymatic decarboxylation process.     

Molecular dynamics simulation,binding free energy calculation and unbinding pathway analysis on selectivity difference between FKBP51 and FKBP52: Insight into the molecular mechanism of isoform selectivity

As co‐chaperones of the 90‐kDa heat shock protein(HSP90), FK506 binding protein 51 (FKBP51) and FK506 binding protein 52 (FKBP52) modulate the maturation of steroid hormone receptor through their specific FK1 domains (FKBP12‐like domain 1). The inhibitors targeting FK1 domains are potential therapies for endocrine‐related physiological disorders. However, the structural conservation of the FK1 domains between FKBP51 and FKBP52 make it difficult to obtain satisfactory selectivity in FK506‐based drug design. Fortunately, a series of iFit ligands synthesized by Hausch et al exhibited excellent selectivity for FKBP51, providing new opportunity for design selective inhibitors. We performed molecular dynamics simulation, binding free energy calculation and unbinding pathway analysis to reveal selective mechanism for the inhibitor iFit4 binding with FKBP51 and FKBP52. The conformational stability evaluation of the “Phe67‐in” and “Phe67‐out” states implies that FKBP51 and FKBP52 have different preferences for “Phe67‐in” and “Phe67‐out” states, which we suggest as the determinant factor for the selectivity for FKBP51. The binding free energy calculations demonstrate that nonpolar interaction is favorable for the inhibitors binding, while the polar interaction and entropy contribution are adverse for the inhibitors binding. According to the results from binding free energy decomposition, the electrostatic difference of residue 85 causes the most significant thermodynamics effects on the binding of iFit4 to FKBP51 and FKBP52. Furthermore, the importance of substructure units on iFit4 were further evaluated by unbinding pathway analysis and residue‐residue contact analysis between iFit4 and the proteins. The results will provide new clues for the design of selective inhibitors for FKBP51.     

1,6-Diamino-2,5-anhydro-1,6-dideoxy-dl-glucitol and some derivatives thereof

1,6-Diamino-2,5-anhydro-1,6-dideoxy-dl-glucitol dihydrochloride and some derivatives were synthesized from 3,5-di-O-acetyl-1,6-dibromo-1,6-dideoxy-d-mannitol. Introduction of the 2,5-anhydro ring and subsequent replacement of the terminal bromine atoms by azide gave low yields of the diazide; therefore, a reverse reaction-sequence was applied. The azido groups were reduced with hydrogen sulfide-pyridine, and the amino groups formed were methylated by using formaldehyde-formic acid and subsequently treating with borohydride. According to ¹³C-n.m.r. investigations, the symmetrically substituted, 2,5-anhydroglucitol derivatives are present mainly in the ⁴T₃ [“north” (N) type of twist] conformation, whereas the analogous l-iditol derivatives mainly adopt the ³T₄ [“south” (S)] type. The different quaternary salts obtained on methylation of the corresponding 1,6-bis(dimethylamino)derivatives with methyl iodide (aiming at the structure of epi-muscarine) showed no muscarine-like, biological activity.     

3D-QSAR analysis of antimalarial farnesyltransferase inhibitors based on a 2,5-diaminobenzophenone scaffold

With annual death tolls in the millions and emerging resistance to existing drugs, novel therapies are needed against malaria. Wiesner et al. recently developed a novel class of antimalarials derived from farnesyltransferase inhibitors based on a 2,5-diaminobenzophenone scaffold. The compounds displayed a wide range of activity, including submicromolar, against the multi-drug resistant Plasmodium falciparum strain Dd2. In order to investigate quantitatively the local physicochemical properties involved in the interaction between drug and biotarget, we used the 3D-QSAR methods CoMFA and CoMSIA to study some of the series, including the screened lead compound 2,5-bis-acylaminobenzophenone, 28 cinnamic acid derivatives, 29 N-(3-benzoyl-4-tolylacetylaminophenyl)-3-(5-aryl-2-furyl)acrylic acid amides, and 34 N-(4-substituted-amino-3-benzoylphenyl)-[5-(4-nitrophenyl)-2-furyl]acrylic acid amides. We found that steric, electrostatic, and hydrophobic properties of substituent groups play key roles in the bioactivity of the series of compounds, while hydrogen bonding interactions show no obvious impact. We built several highly predictive 3D-QSAR models, including a CoMSIA one composed of steric, electrostatic, and hydrophobic fields, with r(2)=0.94, q(2)=0.63, and r(pred)(2)=0.63. The results provide insight for optimization of this class of antimalarials for better activity and may prove helpful for further lead optimization.     

Protein-protein complexation in bioluminescence

In this review we summarize the progress made towards understanding the role of protein-protein interactions in the function of various bioluminescence systems of marine organisms, including bacteria, jellyfish and soft corals, with particular focus on methodology used to detect and characterize these interactions. In some bioluminescence systems, protein-protein interactions involve an “accessory protein” whereby a stored substrate is efficiently delivered to the bioluminescent enzyme luciferase. Other types of complexation mediate energy transfer to an “antenna protein” altering the color and quantum yield of a bioluminescence reaction. Spatial structures of the complexes reveal an important role of electrostatic forces in governing the corresponding weak interactions and define the nature of the interaction surfaces. The most reliable structural model is available for the protein-protein complex of the Ca²⁺-regulated photoprotein clytin and green-fluorescent protein (GFP) from the jellyfish Clytia gregaria, solved by means of X-ray crystallography, NMR mapping and molecular docking. This provides an example of the potential strategies in studying the transient complexes involved in bioluminescence. It is emphasized that structural studies such as these can provide valuable insight into the detailed mechanism of bioluminescence.     

Site of bicarbonate effect in Hill reaction. Evidence from the use of artificial electron acceptors and donors

Using artificial electron donors and acceptors, it is shown here that the major HCO₃^? effect in the Hill reaction is after the “primary” electron acceptor (Q) of Photosystem II and before the site of action of 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (at the plastoquinone pool). Chloroplasts in the presence of both 3-(3′,4′-dichlorophenyl)-1,1-dimethylurea, which blocks electron flow from the reduced primary acceptor Q^? to the plastoquinone pool, and silicomolybdate, which accepts electrons from Q^?, show no significant bicarbonate stimulation of electron flow. However, a 6–7-fold stimulation is clearly observed when oxidized diaminodurene, as an electron acceptor, and dibromothymoquinone, as an inhibitor of electron flow beyond the plastoquinone pool, are used. In the same chloroplast preparation no measurable effect of bicarbonate is observed in a Photosystem I reaction as monitored by electron flow from reduced diaminodurene to methyl viologen in the presence of 3-(3′,4′-dichlorophenyl)-1,1-dimethylurea. The insensitivity of the bicarbonate effect to uncouplers of photophosphorylation and the dependence of this effect on the presence of a weak acid anion and on external pH are also reported.     

Follow the money: international donors,external homelands and their effect on Romani media and advocacy

ABSTRACT

While Roma are both Europe’s largest minority, there is no “homeland” state that claims to guard their interest. The lack of “an external national homeland” [Brubaker, R. 1996. Nationalism Reframed: Nationhood and the National Question in the New Europe. Cambridge: Cambridge University Press] to watchdog and safeguard their rights has a particular effect on how Roma engage as political actors and subjects. International donors/foundations have assumed the role of “external homeland”. This article explores the effect that donors’ funding priorities have on Romani advocacy – specifically Romani journalism. Drawing upon multi-sited fieldwork in five countries, extensive document analysis, and interviews, Idemonstrate that the change in Romani media content over the past two decades reflects the shift in funders’ priorities, particularly in relation to the European project. “The Roma” become a tool for donors and European institutions to build a “European” identity while Romani-led advocacy becomes increasingly marganilized.