Hydration dynamics of protein molecules in aqueous solution: Unity among diversity

Dielectric dispersion and NMRD experiments have revealed that a significant fraction of water molecules in the hydration shell of various proteins do not exhibit any slowing down of dynamics. This is usually attributed to the presence of the hydrophobic residues (HBR) on the surface, although HBRs alone cannot account for the large amplitude of the fast component. Solvation dynamics experiments and also computer simulation studies, on the other hand, repeatedly observed the presence of a non-negligible slow component. Here we show, by considering three well-known proteins (lysozyme, myoglobin and adelynate kinase), that the fast component arises partly from the response of those water molecules that are hydrogen bonded with the backbone oxygen (BBO) atoms. These are structurally and energetically less stable than those with the side chain oxygen (SCO) atoms. In addition, the electrostatic interaction energy distribution (EIED) of individual water molecules (hydrogen bonded to SCO) with side chain oxygen atoms shows a surprising two peak character with the lower energy peak almost coincident with the energy distribution of water hydrogen bonded to backbone oxygen atoms (BBO). This two peak contribution appears to be quite general as we find it for lysozyme, myoglobin and adenylate kinase (ADK). The sharp peak of EIED at small energy (at less than 2 k(B)T) for the BBO atoms, together with the first peak of EIED of SCO and the HBRs on the protein surface, explain why a large fraction (similar to 80%) of water in the protein hydration layer remains almost as mobile as bulk water Significant slowness arises only from the hydrogen bonds that populate the second peak of EIED at larger energy (at about 4 k(B)T). Thus, if we consider hydrogen bond interaction alone, only 15-20% of water molecules in the protein hydration layer can exhibit slow dynamics, resulting in an average relaxation time of about 5-10 ps. The latter estimate assumes a time constant of 20-100 ps for the slow component. Interestingly, relaxation of water molecules hydrogen bonded to back bone oxygen exhibit an initial component faster than the bulk, suggesting that hydrogen bonding of these water molecules remains frustrated. This explanation of the heterogeneous and non-exponential dynamics of water in the hydration layer is quantitatively consistent with all the available experimental results, and provides unification among diverse features.

Microbially induced separation of quartz from hematite using yeast cells and metabolites

The utility of yeast, Saccharomyces cerevisiae, in the separation of quartz from hematite is demonstrated. Yeast cells; as well as their metabolites, functioned as flotation collectors, depressants or flocculants and dispersants for hematite and quartz. Interaction between yeast and the above minerals resulted in significant surface chemical changes, rendering quartz surfaces hydrophobic and hematite hydrophilic. Mineral-specific extracellular proteins and exopolysaccharides were secreted by yeast cells when grown in the presence of quartz and hematite, respectively. Quartz could be efficiently separated from hematite through microbially induced flotation and selective flocculation.

Structural characterization of folded pentapeptides containing centrally positioned beta(R)Val, gamma(R)Val and gamma(S)Val residues

A cylindrical pore of similar to 7.5 angstrom diameter containing a one-dimensional water wire, within the confines of a hydrophobic channel lined with the valine side chain, has been observed in crystals of the peptide Boc-D-Pro-Aib-Val-Aib-Val-OMe (1) (Raghavender et al., 2009, 2010). The synthesis and structural characterization in crystals of three backbone homologated analogues Boc-D-Pro-Aib-beta(3)(R) Val-Aib-Val-OMe (2), Boc-D-Pro-Aib-gamma(4)(R)Val-Aib-Val-OMe (3), Boc-D-Pro-Aib-gamma(4)(S)Val-Aib-Val-OMe (4) are described. Crystal structures of peptides 2, 3 and 4 reveal close-packed arrangements in which no pore was formed. In peptides 2 and 3 the N-terminus D-Pro-Aib segment adopted conformations closely related to Type II' beta-turns, while residues 2-4 form one turn of an alpha beta right-handed C-11 helix in 2 and an alpha gamma C-12 helix in 3. In peptide 4, a continuous left-handed helical structure was observed with the D-Pro-Aib segment forming a Type III' beta-turn, followed by one turn of a left-handed alpha gamma C-12 helix. (C) 2012 Elsevier Ltd. All rights reserved.

Dilithium phthalocyanine as a catalyst for oxygen reduction in non-aqueous Li-O-2 cells

The electrochemical performance of Li-O-2 cells depends mainly on the kinetics of the cathode reaction, namely, oxygen reduction reaction in non-aqueous electrolytes. The catalyst plays an important role on the kinetics of the reaction. In the present work, dilithium phthalocyanine is used as the catalyst in the cathode of Li-O-2 cells. Dual-layer O-2 electrodes are fabricated employing a high surface area microporous carbon with Ni gauge current collector present between the two layers. Discharge capacity of Li-O-2 cell measured at 0.2 mA.cm(-2) is about 30 mAh.cm(-2). Phthalocyanine ring is considered to interact with O-2 producing Li2Pc+delta - O-2(-delta) as a reaction intermediate, which facilitates the electron-transfer reaction.

A Rhodanine Derivative CCR-11 Inhibits Bacterial Proliferation by Inhibiting the Assembly and GTPase Activity of FtsZ

A perturbation of FtsZ assembly dynamics has been shown to inhibit bacterial cytokinesis. In this study, the antibacterial activity of 151 rhodanine compounds was assayed using Bacillus subtilis cells. Of 151 compounds, eight strongly inhibited bacterial proliferation at 2 mu M. Subsequently, we used the elongation of B. subtilis cells as a secondary screen to identify potential FtsZ-targeted antibacterial agents. We found that three compounds significantly increased bacterial cell length. One of the three compounds, namely, CCR-11 (E)-2-thioxo-5-({3-(trifluoromethyl)phenyl]furan-2-yl}methylene) thiazolidin-4-one], inhibited the assembly and GTPase activity of FtsZ in vitro. CCR-11 bound to FtsZ with a dissociation constant of 1.5 +/- 0.3 mu M. A docking analysis indicated that CCR-11 may bind to FtsZ in a cavity adjacent to the T7 loop and that short halogen oxygen, H-bonding, and hydrophobic interactions might be important for the binding of CCR-11 with FtsZ. CCR-11 inhibited the proliferation of B. subtilis cells with a half-maximal inhibitory concentration (IC50) of 1.2 +/- 0.2 mu M and a minimal inhibitory concentration of 3 mu M. It also potently inhibited proliferation of Mycobacterium smegmatis cells. Further, CCR-11 perturbed Z-ring formation in B. subtilis cells; however, it neither visibly affected nucleoid segregation nor altered the membrane integrity of the cells. CCR-11 inhibited HeLa cell proliferation with an IC50 value of 18.1 +/- 0.2,mu M (similar to 15 x IC50 of B. subtilis cell proliferation). The results suggested that CCR-11 inhibits bacterial cytokinesis by inhibiting FtsZ assembly, and it can be used as a lead molecule to develop FtsZ-targeted antibacterial agents.

Photocytotoxic Oxidovanadium(IV) Complexes of Polypyridyl Ligands Showing DNA-Cleavage Activity in Near-IR Light

Oxidovanadium(IV) complexes VO(pyphen)(L)]Cl2 (1, 2) and VO(pydppz)(L)]Cl2 (3, 4), where L is 1,10-phenanthroline (phen in 1 and 3) and dipyrido3,2-a:2',3'-c]phenazine (dppz in 2 and 4) are prepared and characterized. The crystal structure of VO(pyphen)(phen)](ClO4)2 (1a) shows a six-coordinate VN5O geometry with a VO2+ moiety in which the polypyridyl ligand binds in a meridional fashion and the phen ligand displays a chelating binding mode with an N-donor site trans to the oxidovanadyl group. The complexes show a dd band within 720-750 nm in DMF. The one-electron paramagnetic complexes are 1:2 electrolytes in DMF. The complexes exhibit an irreversible VIV/VIII redox response near -0.85 V vs. SCE in DMF/0.1 M TBAP. The complexes bind to calf thymus (ct) DNA giving Kb values within 7.5 x 104 to 1.1 x 106 M1. The complexes show poor chemical nuclease activity in the dark and exhibit significant DNA-photocleaving activity in near-IR light of 705 and 785 nm forming .OH radicals. Complexes 2-4 show remarkable photocytotoxicity in HeLa cancer cells. FACS analysis of the HeLa cells treated with complex 4 shows cell death as highlighted by the sub G1 peak. Propidium iodide staining data indicate apoptosis as the primary mode of cell death.

Self-Assembled Pd6 Open Cage with Triimidazole Walls and the Use of Its Confined Nanospace for Catalytic Knoevenagel- and Diels-Alder Reactions in Aqueous Medium

The two-component self-assembly of a 90 degrees PdII acceptor and a triimidazole donor led to the formation of a water-soluble semi-cylindrical cage with a hydrophobic cavity, which was separately crystallized with hydrophilic- and hydrophobic guests. The parent cage was found to catalyze the Knoevenagel condensation reaction of a series of aromatic mono-aldehydes with active methylene compounds, such as Meldrum's acid or 1,3-dimethylbarbituric acid. The confined hydrophobic nanospace within this cage was also used in the catalytic DielsAlder reactions of 9-hydroxymethylanthracene with N-phenylmaleimide or N-cyclohexylmaleimide.

Time-Temperature Scaling of Conductivity Spectra of Organic Plastic Crystalline Conductors

Organic plastic crystalline soft matter ion conductors are interesting alternatives to liquid electrolytes in electrochemical storage devices such as Lithium-ion batteries. The solvent dynamics plays a major role in determining the ion transport in plastic crystalline ion conductors. We present here an analysis of the frequency-dependent ionic conductivity of succinonitrile-based plastic crystalline ion conductors at varying salt composition (0.005 to 1 M) and temperature (-20 to 60 degrees C) using time-temperature superposition principle (TTSP). The main motivation of the work has been to establish comprehensive insight into the ion transport mechanism from a single method viz, impedance spectroscopy rather than employing cluster of different characterization methods probing various length and time scales. The TTSP remarkably aids in explicit identification of the extent of the roles of solvent dynamics and ion-ion interactions on the effective conductivity of the orientationally disordered plastic crystalline ion conductors.

PEO|Sncl(2)|PANI composites: as an electrolyte in solid-state battery

Solid-state polymer electrolytes possess high conductivity and have advantages compared with their liquid counterparts. The polyethylene oxide (PEO)-based polymer is a good candidate for this purpose. The PEO/SnCl2/polyaniline composite (PSP composites) at different weight percentages were prepared in anhydrous acetonitrile media. Structural studies were carried out of the prepared composites by X-ray diffraction, Fourier transmission infrared spectroscopy, and surface morphology by scanning electron microscopy. The sigma (dc) was carried out by a two-probe method, and it is found that the conductivity increases with an increase in temperature. The temperature-dependent conductivity of the composites exhibits a typical semi-conducting behavior and hence can be explained by the 1D variable range hopping model proposed by Mott. The electrochemical cell parameters for battery applications at room temperature have also been determined. The samples are fabricated for battery application in the configuration of Na: (PSP): (I-2 + C + sample), and their experimental data are measured using Wagner's polarization technique. The cell parameters result in an open-circuit voltage of 0.83 V and a short-circuit current of 912 mu A for PSP (70:30:10) composite. Hence, these composites can be used in polymer electrolyte studies.

Reactivities of Modified and Unmodified Exfoliated Graphite Electrodes in Selected Redox Systems

The electrochemical profiles of exfoliated graphite electrodes (EG) and glassy carbon electrodes (GCE) were recorded using cyclic voltammetry and square wave voltammetry in the presence of various supporting electrolytes and Fe(CN)(6)](3-/4-), Ru(NH3)(6)](2+/3+), ferrocene redox probes. In the supporting electrolytes (KCl, H2SO4, NaOH, tetrabutylammoniumtetraflouroborate, phosphate buffers), the potential windows of EG were found in some cases to be about 200 mV larger than that of GCE. The electroactive surface area of EG was estimated to be 19.5 % larger than the GCE which resulted in higher peak currents on the EG electrode. Furthermore, EG was modified with various nanomaterials such as poly (propylene imine) dendrimer, gold nanoparticles, and dendrimer-gold nanoparticles composite. The morphologies of the modified electrodes were studied using scanning electron microscopy and their electrochemical reactivities in the three redox probes were investigated. The current and the reversibility of redox probes were enhanced with the presence of modifiers in different degrees with dendrimer and gold nanoparticles having a favorable edge.

A 12 V Substrate-Integrated PbO2-Activated Carbon Asymmetric Hybrid Ultracapacitor with Silica-Gel-Based Inorganic-Polymer Electrolyte

A 12 V Substrate-Integrated PbO2-Activated Carbon hybrid ultracapacitor (SI-PbO2-AC HUCs) with silica-gel sulfuric acid electrolyte is developed and performance tested. The performance of the silica-gel based hybrid ultracapacitor is compared with flooded and AGM-based HUCs. These HUCs comprise substrate-integrated PbO2 (SI-PbO2) as positive electrodes and high surface-area activated carbon with dense graphite-sheet substrate as negative electrodes. 12 V SI-PbO2-AC HUCs with flooded, AGM and gel electrolytes are found to have capacitance values of 308 F, 184 F, and 269 F at C-rate and can be pulse charged and discharged for 100,000 cycles with only a nominal decrease in their capacitance values. The best performance is exhibited by gel-electrolyte HUCs.

Self-Adapting Peripherally Heterofunctionalized Hyperbranched Polymers: Formation of Janus and Tripodal Structures

A peripherally clickable hyperbranched polyester carrying numerous propargyl terminal groups was prepared by a simple melt transesterification polycondensation of a suitably designed AB(2) monomer; this clickable hyperscaffold was then transformed into a variety of different derivatives by using the Cu-catalyzed azide-yne click reaction. Functionalization of the periphery with equimolar quantities of mutually immiscible segments, such as hydrocarbon, fluorocarbon, and PEG, yielded frustrated molecular systems that readapt and form structures wherein the immiscible segments appear to self-segregate to generate either Janus structures (when two immiscible segments are present) or tripodal structures (when three immiscible segments are present). Evidence for such self-segregation was obtained from a variety of studies, such as differential scanning calorimetry, Langmuir isotherms, AFM imaging, and small-angle X-ray scattering measurements. Crystallization of one or more of the peripheral segments reinforced this self-segregation; the weight-fraction-normalized enthalpies of melting associated with the different domains revealed a competition between the segments to optimize their crystalline organization. When one or more of the segments are amorphous, the remaining segments crystallize more effectively and consequently exhibit a higher melting enthalpy. AFM images of monolayers, transferred from the Langmuir trough, revealed that the thickness matches the expected values; furthermore, contact angle measurements clearly demonstrated that the monolayer films are fairly hydrophobic, and in the case of the tripodal hybramers, the presence of domains of hydrocarbon and fluorocarbon appears to impart nanoscale chemical heterogeneity that is reflected in the strong hysteresis in the advancing and receding contact angles.

Sustainability of apparent slip in micro-channel flows

In the present work, we experimentally study the flow of water over textured hydrophobic surfaces in a micro-channel. Shear stress measurements are done along with direct visualization of trapped air pockets on the hydrophobic surface. The trapped air pockets on such surfaces are known to be responsible for apparent slip at these surfaces and hence in significant drag reduction. In typical circumstances, the apparent slip reduces over time as seen, for example, from our shear stress measurements. This implies that the drag reduction will not be sustained. We have performed extensive visualizations of the trapped air pockets while varying flow parameters like the flow rate and the pressure. We present here direct visualizations that show that under some conditions, the air pockets can grow with time. The variation of the air pocket size with time is found to change qualitatively and quantitatively as the flow rate is varied. These measured changes in the air pocket size with time have a direct bearing on the sustainability of apparent slip in micro-channel flows.

Time dependent superhydrophobicity of drag reducing surfaces

Air can be trapped on the crevices of specially textured hydrophobic surfaces immersed in water. This heterogenous state of wetting in which the water is in contact with both the solid surface and the entrapped air is not stable. Diffusion of air into the surrounding water leads to gradual reduction in the size and numbers of the air bubbles. The sustainability of the entrapped air on such surfaces is important for many underwater applications in which the surfaces have to remain submersed for longer time periods. In this paper we explore the suitability of different classes of surface textures towards the drag reduction application by evaluating the time required for the disappearance of the air bubbles under hydrostatic conditions. Different repetitive textures consisting of holes, pillars and ridges of different sizes have been generated in silicon, aluminium and brass by isotropic etching, wire EDM and chemical etching respectively. These surfaces were rendered hydrophobic with self-assembled layer of fluorooctyl trichlorosilane for silicon and aluminium surfaces and 1-dodecanethiol for brass surfaces. Using total internal reflection the air bubbles are visualized with the help of a microscope and time lapse photography. Irrespective of the texture, both the size and the number of air pockets were found to decrease with time gradually and eventually disappear. In an attempt to reverse the diffusion we explore the possibility of using electrolysis to generate gases at the textured surfaces. The gas bubbles are nucleated everywhere on the surface and as they grow they coalesce with each other and get pinned at the texture edges.

Packing in molten globules and native states

Close packing of hydrophobic residues in the protein interior is an important determinant of protein stability. Cavities introduced by large to small substitutions are known to destabilize proteins. Conversely, native states of proteins and protein fragments can be stabilized by filling in existing cavities. Molten globules (MGs) were initially used to describe a state of protein which has well-defined secondary structure but little or no tertiary packing. Subsequent studies have shown that MGs do have some degree of native-like topology and specific packing. Wet molten globules (WMGs) with hydrated cores and considerably decreased packing relative to the native state have been studied extensively. Recently there has been renewed interest in identification and characterization of dry molten globules (DMGs). These are slightly expanded forms of the native state which show increased conformational flexibility, native-like main-chain hydrogen bonding and dry interiors. The generality of occurrence of DMGs during protein unfolding and the extent and nature of packing in DMGs remain to be elucidated. Packing interactions in native proteins and MGs can be probed through mutations. Next generation sequencing technologies make it possible to determine relative populations of mutants in a large pool. When this is coupled to phenotypic screens or cell-surface display, it becomes possible to rapidly examine large panels of single-site or multi-site mutants. From such studies, residue specific contributions to protein stability and function can be estimated in a highly parallelized fashion. This complements conventional biophysical methods for characterization of packing in native states and molten globules.