Composition dependent multiple structural transformations of myoglobin in aqueous ethanol solution: a combined experimental and theoretical study.

Experimental studies (circular dichroism and ultra-violet (UV) absorption spectra) and large scale atomistic molecular dynamics simulations (accompanied by order parameter analyses) are combined to establish a number of remarkable (and unforeseen) structural transformations of protein myoglobin in aqueous ethanol mixture at various ethanol concentrations. The following results are particularly striking. (1) Two well-defined structural regimes, one at xEtOH ∼ 0.05 and the other at xEtOH ∼ 0.25, characterized by formation of distinct partially folded conformations and separated by a unique partially unfolded intermediate state at xEtOH ∼ 0.15, are identified. (2) Existence of non-monotonic composition dependence of (i) radius of gyration, (ii) long range contact order, (iii) residue specific solvent accessible surface area of tryptophan, and (iv) circular dichroism spectra and UV-absorption peaks are observed. Interestingly at xEtOH ∼ 0.15, time averaged value of the contact order parameter of the protein reaches a minimum, implying that this conformational state can be identified as a molten globule state. Multiple structural transformations well known in water-ethanol binary mixture appear to have considerably stronger effects on conformation and dynamics of the protein. We compare the present results with studies in water-dimethyl sulfoxide mixture where also distinct structural transformations are observed along with variation of co-solvent composition.

Synthesis and characterization of Cu/Ag nanoparticle loaded mullite nanocomposite system: A potential candidate for antimicrobial and therapeutic applications.

BACKGROUND: Microbial resistance to antibiotics has triggered the development of nanoscale materials as an alternative strategy. To stabilize these particles an inert support is needed. METHOD: Porous nanomullite developed by sol-gel route is loaded with copper and silver nanoparticle by simple adsorption method. These nanocomposites are characterized using XRD, FTIR, TEM, SEM, EDAX and UV-visible spectrophotometer. Antibacterial activity of these nanocomposites against Gram positive and Gram negative bacteria are performed by bactericidal kinetics, flow cytometry and MTT assay. The underlying mechanisms behind the antimicrobial property and cell death are also investigated by EPR spectroscopy, intracellular ROS measurement and ß-galactosidase assay. The cytocompatibility of the nanocomposites is investigated by cell viability (MTT), proliferation (Alamar blue) and wound healing assay of mammalian fibroblast cell line. RESULTS: Nanocomposites show a fairly uniform distribution of metal nanoparticle within mullite matrix. They show excellent antibacterial activity. Metal ions/nanoparticle is found to be released from the materials (CM and SM). Treated cells manifested high intracellular oxidative stress and ß-galactosidase activity in the growth medium. The effect of nanocomposites on mammalian cell line depends on exposure time and concentration. The scratch assay shows normal cell migration with respect to control. CONCLUSION: The fabricated nanoparticles possess diverse antimicrobial mechanism and exhibit good cytocompatibility along with wound healing characteristics in mouse fibroblast cell line (L929). GENERAL SIGNIFICANCE: The newly synthesized materials are promising candidates for the development of antimicrobial ceramic coatings for biomedical devices and therapeutic applications.

2D QSAR Studies of Several Potent Aminopyridine, Anilinopyrimidine and Pyridine Carboxamide-based JNK Inhibitors.

The c-Jan N-terminal kinases are members of the mitogen activated protein kinase family of signaling proteins. Amino pyridine based compounds, 4-anilino pyrimidine derivatives, and 2-pyridine carboxamide derivatives have been identified as potent JNK inhibitors with good cellular activity. In this study we calculated molecular topological and quantum chemical descriptors of 15 training compounds and three quantitative structure activity relationships models have been constructed. The significance of three models is judged on the basis of correlation, Fischer F test and quality factor (Q). This study is helpful for screening potent inhibitors of protein kinases.

Electrostatic relaxation and hydrodynamic interactions for self-diffusion of ions in electrolyte solutions.

The concentration dependence of self-diffusion of ions in solutions at large concentrations has remained an interesting yet unsolved problem. Here we develop a self-consistent microscopic approach based on the ideas of mode-coupling theory. It allows us to calculate both contributions which influence the friction of a moving ion: the ion atmosphere relaxation and hydrodynamic interactions. The resulting theory provides an excellent agreement with known experimental results over a wide concentration range. Interestingly, the mode-coupling self-consistent calculation of friction reveal a nonlinear coupling between the hydrodynamic interactions and the ion atmosphere relaxation which enhances ion diffusion by reducing friction, particularly at intermediate ion concentrations. This rather striking result has its origin in the similar time scales of the relaxation of the ion atmosphere relaxation and the hydrodynamic term, which are essentially given by the Debye relaxation time. The results are also in agreement with computer simulations, with and without hydrodynamic interactions.

Orientational relaxation in a dispersive dynamic medium: generalization of the Kubo-Ivanov-Anderson jump-diffusion model to include fractional environmental dynamics.

The Ivanov-Anderson model (and an earlier treatment by Kubo) envisages a decay of the orientational correlation by random but large amplitude molecular jumps, as opposed to infinitesimal small jumps assumed in Brownian diffusion. Recent computer simulation studies on water and viscous liquids have shown that large amplitude motions may indeed be more of a rule than exception. Existing theoretical studies on jump diffusion mostly assume an exponential (Poissonian) waiting time distribution for jumps, thereby again leading to an exponential decay. Here we extend the existing formalism of Ivanov and Anderson to include an algebraic waiting time distribution between two jumps. As a result, the first (l=1) and second (l=2) rank orientational time correlation functions show the same long time power law, but their short time decay behavior is quite different. The predicted Cole-Cole plot of dielectric relaxation reproduces various features of non-Debye behavior observed experimentally. We also developed a theory where both unrestricted small jumps and large angular jumps coexist simultaneously. The small jumps are shown to have a large effect on the long time decay, particularly in mitigating the effects of algebraic waiting time distribution, and in giving rise to an exponential-like decay, with a time constant, surprisingly, less than the time constant that arises from small amplitude decay alone.

Water inertial reorientation: hydrogen bond strength and the angular potential.

The short-time orientational relaxation of water is studied by ultrafast infrared pump-probe spectroscopy of the hydroxyl stretching mode (OD of dilute HOD in H(2)O). The anisotropy decay displays a sharp drop at very short times caused by inertial orientational motion, followed by a much slower decay that fully randomizes the orientation. Investigation of temperatures from 1 degrees C to 65 degrees C shows that the amplitude of the inertial component (extent of inertial angular displacement) depends strongly on the stretching frequency of the OD oscillator at higher temperatures, although the slow component is frequency-independent. The inertial component becomes frequency-independent at low temperatures. At high temperatures there is a correlation between the amplitude of the inertial decay and the strength of the O-D O hydrogen bond, but at low temperatures the correlation disappears, showing that a single hydrogen bond (OD O) is no longer a significant determinant of the inertial angular motion. It is suggested that the loss of correlation at lower temperatures is caused by the increased importance of collective effects of the extended hydrogen bonding network. By using a new harmonic cone model, the experimentally measured amplitudes of the inertial decays yield estimates of the characteristic frequencies of the intermolecular angular potential for various strengths of hydrogen bonds. The frequencies are in the range of approximately 400 cm(-1). A comparison with recent molecular dynamics simulations employing the simple point charge-extended water model at room temperature shows that the simulations qualitatively reflect the correlation between the inertial decay and the OD stretching frequency.

Dynamics of barrierless and activated chemical reactions in a dispersive medium within the fractional diffusion equation approach.

Barrierless chemical reactions have often been modeled as a Brownian motion on a one-dimensional harmonic potential energy surface with a position-dependent reaction sink or window located near the minimum of the surface. This simple (but highly successful) description leads to a nonexponential survival probability only at small to intermediate times but exponential decay in the long-time limit. However, in several reactive events involving proteins and glasses, the reactions are found to exhibit a strongly nonexponential (power law) decay kinetics even in the long time. In order to address such reactions, here, we introduce a model of barrierless chemical reaction where the motion along the reaction coordinate sustains dispersive diffusion. A complete analytical solution of the model can be obtained only in the frequency domain, but an asymptotic solution is obtained in the limit of long time. In this case, the asymptotic long-time decay of the survival probability is a power law of the Mittag-Leffler functional form. When the barrier height is increased, the decay of the survival probability still remains nonexponential, in contrast to the ordinary Brownian motion case where the rate is given by the Smoluchowski limit of the well-known Kramers' expression. Interestingly, the reaction under dispersive diffusion is shown to exhibit strong dependence on the initial state of the system, thus predicting a strong dependence on the excitation wavelength for photoisomerization reactions in a dispersive medium. The theory also predicts a fractional viscosity dependence of the rate, which is often observed in the reactions occurring in complex environments.

Ion dynamics in compacted clays: derivation of a two-state diffusion-reaction scheme from the lattice Fokker-Planck equation.

We show how a two-state diffusion-reaction description of the mobility of ions confined within compacted clays can be constructed from the microscopic dynamics of ions in an external field. The diffusion-reaction picture provides the usual interpretation of the reduced ionic mobility in clays, but the required partitioning coefficient K(d) between trapped and mobile ions is generally an empirical parameter. We demonstrate that it is possible to obtain K(d) from the microscopic dynamics of ions interacting with the clay surfaces by evaluating the ionic mobility using a novel lattice implementation of the Fokker-Planck equation. The resulting K(d) allows a clear-cut characterization of the trapping sites on the clay surfaces and determines the adsorption/desorption rates. The results highlight the limitations of standard approximation schemes and pinpoint the crossover from jump to Brownian diffusion regimes.

Ionic self-diffusion in concentrated aqueous electrolyte solutions.

A self-consistent microscopic theory is developed to understand the anomalously weak concentration dependence of ionic self-diffusion coefficient D(ion) in electrolyte solutions. The self-consistent equations are solved by using the mean spherical approximation expressions of the static pair correlation functions for unequal sizes. The results are in excellent agreement both with the known experimental results for many binary electrolytes and also with the new Brownian dynamics simulation results. The calculated velocity time correlation functions also show quantitative agreement with simulations. The theory also explains the reason for observing different D(ion) in recent NMR and neutron scattering experiments.

Reentrant behavior of relaxation time with viscosity at varying composition in binary mixtures.

In order to understand the long known anomalies in the composition dependence of diffusion and viscosity of binary mixtures, we introduce here two new models and carry out extensive molecular dynamics simulations. In these models, the two molecular species (A and B) have the same diameter and mass. In model I the interspecies interaction is more attractive than that between the pure components, while the reverse is true for model II. Simulations and mode coupling theory calculations reveal that the models can capture a wide variety of behavior observed in experiments, including the reentrant viscosity dependence of relaxation time.

Power law mass dependence of diffusion: A mode coupling theory analysis

The self-diffusion coefficient of a tagged molecule is known to exhibit a weak mass dependence, especially for solutes with size comparable to or larger than the size of the solvent molecules. Sometimes this mass dependence can be fitted to a power law, with a small exponent, less than 0.1. This weak mass dependence has often been considered as supportive of the hydrodynamic picture (that is, the Stokes-Einstein relation) of diffusion rather than the kinetic theory approach, which predicts a stronger mass dependence, for example, via the Enskog theory. Neither can explain the weak power-law mass dependence. In order to understand this, we have carried out a mode coupling theory (MCT) analysis of diffusion. It is found that a straightforward application of the existing mode coupling theory expressions lead to an inaccurate mass dependence-it predicts an increase of diffusion coefficient with an increase of the mass. We find that this is because of the inadequate description of the initial decay of the collective contributions to the friction. We have proposed a new prescription to accurately describe the short time dynamics of the density and the current term. In addition, we have modified the existing MCT by imposing the full self-consistency between the frequency-dependent friction and the mean square displacement over the whole time and frequency plane. Previously the self-consistency was performed only at the zero frequency level between the zero frequency friction and the diffusion coefficient. With these two generalizations, the mode coupling theory is found to provide a fairly accurate description of the mass dependence. In particular, the theory can correctly reproduce the power-law dependence of solvent-solute diffusion ratio on solute-solvent mass ratio, observed in computer simulations of Bearman and Jolly [Mol. Phys. 44, 665 (1981)]. Another important result is that the current mode is found to play no significant role in determining the diffusion. Thus the hydrodynamic argument of weak mass dependence has little validity for same size solute-solvent systems.

Collapse of stiff conjugated polymers with chemical defects into ordered, cylindrical conformations

The optical, electronic and mechanical properties of synthetic and biological materials consisting of polymer chains depend sensitively on the conformation adopted by these chains. The range of conformations available to such systems has accordingly been of intense fundamental as well as practical interest, and distinct conformational classes have been predicted, depending on the stiffness of the polymer chains and the strength of attractive interactions between segments within a chain. For example, flexible polymers should adopt highly disordered conformations resembling either a random coil or, in the presence of strong intrachain attractions, a so-called 'molten globule'. Stiff polymers with strong intrachain interactions, in contrast, are expected to collapse into conformations with long-range order, in the shape of toroids or rod-like structures. Here we use computer simulations to show that the anisotropy distribution obtained from polarization spectroscopy measurements on individual poly[2-methoxy-5-(2'-ethylhexyl)oxy-1,4-phenylenevinylene] polymer molecules is consistent with this prototypical stiff conjugated polymer adopting a highly ordered, collapsed conformation that cannot be correlated with ideal toroid or rod structures. We find that the presence of so-called 'tetrahedral chemical defects', where conjugated carbon-carbon links are replaced by tetrahedral links, divides the polymer chain into structurally identifiable quasi-straight segments that allow the molecule to adopt cylindrical conformations. Indeed, highly ordered, cylindrical conformations may be a critical factor in dictating the extraordinary photophysical properties of conjugated polymers, including highly efficient intramolecular energy transfer and significant local optical anisotropy in thin films.

Levinthal's paradox.

Levinthal's paradox is that finding the native folded state of a protein by a random search among all possible configurations can take an enormously long time. Yet proteins can fold in seconds or less. Mathematical analysis of a simple model shows that a small and physically reasonable energy bias against locally unfavorable configurations, of the order of a few kT, can reduce Levinthal's time to a biologically significant size.