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.

Disruption of myelin leads to ectopic expression of K(V)1.1 channels with abnormal conductivity of optic nerve axons in a cuprizone-induced model of demyelination

The molecular determinants of abnormal propagation of action potentials along axons and ectopic conductance in demyelinating diseases of the central nervous system, like multiple sclerosis (MS), are poorly defined. Widespread interruption of myelin occurs in several mouse models of demyelination, rendering them useful for research. Herein, considerable myelin loss is shown in the optic nerves of cuprizone-treated demyelinating mice. Immuno-fluorescence confocal analysis of the expression and distribution of voltage-activated K⁺ channels (K(V)1.1 and 1.2 α subunits) revealed their spread from typical juxta-paranodal (JXP) sites to nodes in demyelinated axons, albeit with a disproportionate increase in the level of K(V)1.1 subunit. Functionally, in contrast to monophasic compound action potentials (CAPs) recorded in controls, responses derived from optic nerves of cuprizone-treated mice displayed initial synchronous waveform followed by a dispersed component. Partial restoration of CAPs by broad spectrum (4-aminopyridine) or K(V)1.1-subunit selective (dendrotoxin K) blockers of K⁺ currents suggest enhanced K(V)1.1-mediated conductance in the demyelinated optic nerve. Biophysical profiling of K⁺ currents mediated by recombinant channels comprised of different K(V)1.1 and 1.2 stoichiometries revealed that the enrichment of K(V)1 channels K(V)1.1 subunit endows a decrease in the voltage threshold and accelerates the activation kinetics. Together with the morphometric data, these findings provide important clues to a molecular basis for temporal dispersion of CAPs and reduced excitability of demyelinated optic nerves, which could be of potential relevance to the patho-physiology of MS and related disorders.

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.

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.

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.

Neurospheres derived from human embryoid bodies treated with retinoic Acid show an increase in nestin and ngn2 expression that correlates with the proportion of tyrosine hydroxylase-positive cells

In the central nervous system (CNS), generation of phenotypic diversity within the neuronal lineage is precisely regulated in a spatial and temporal fashion. Neural basic helix-loop-helix (bHLH) transcription factors are cell intrinsic factors that control commitment to neuronal lineage and play an important role in neuronal cell type specification. The ability to differentiate human embryonic stem (hES) cells into neurons provides a good model system to address human neuronal specification. Previous studies have shown neurogenin-2 (Ngn2) to be involved in the development of mesencephalic dopaminergic neurons. Toward the goal of correlating neuronal phenotype with early gene expression pattern, we have characterized the expression of Ngn2 during hES cell differentiation. Our results show that treatment of embryoid bodies (EBs) with retinoic acid (RA) leads to the greatest proportion of tyrosine hydroxylase (TH)-positive cells followed by vasoactive intestinal peptide (VIP)-treated EBs as compared to untreated EBs. This increase in the proportion of TH-positive neurons was correlated with the unique morphology of RA-treated aggregates and the spatial delocalization of the expression of Ngn2 within the EB. Neurospheres derived from RA-treated EBs contained many nestin-positive cells within regions that expressed Ngn2. We show that the extent of nestin-positive cells that arise from the region of Ngn2 expression is correlated with the appearance of TH-positive neurons. Our results show for the first time the expression of Ngn2 during the differentiation of hES cells.

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.

CMV promotor activity during ES cell differentiation: potential insight into embryonic stem cell differentiation

The activity of the P(CMV IE) promoter was studied during the differentiation of ES cells into neurons. In order to do this, stable embryonic stem (ES) cell lines that express enhanced green fluorescent protein (EGFP) under the control of P(CMV IE) were created and these ES cells were differentiated by aggregation of cells in the presence of retinoic acid (RA). Based on our observations that the activity of P(CMV IE) was highest in undifferentiated cells, and that cell-cell interaction and addition of RA that lead to enhanced cell proliferation also increased expression from P(CMV IE), we hypothesized that the activity of P(CMV IE) was positively regulated in cycling cells. However, when analysis was done at the single cell level it was found that BrdU label and EGFP expression were not correlated. EGFP expression was found to be down-regulated in many cells that were BrdU positive and conversely there were significant numbers of BrdU negative cells that were EGFP positive. Further, P(CMV IE) activity was not observed in cells that were nestin positive or in differentiated neurons, but P(CMV IE) was active in cells with a fibroblast-like morphology. Finally, several proteins present in undifferentiated ES cells were found to bind to regulatory regions of P(CMV IE). These were absent when cells were aggregated in the presence of RA. The above results have implications for expression of transgenes in ES cells as well as providing new insight into the mechanism of lineage restriction.

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.

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.