Exploration of the secondary structure specific differential solvation dynamics between the native and molten globule states of the protein HP-36

Recent experiments have shown that the time dependence of fluorescence Stokes shift of a chromophore is substantially different when the chromophore is located in a molten globule (MG) state and in the native state of the same protein. To understand the origin of this difference, particularly the role of water in the differential solvation of the protein in the native and the MG states, we have carried out fully atomistic molecular dynamics simulations with explicit water of a partially unfolded MG state of the protein HP-36 and compared the results with the solvation dynamics of the protein in the folded native state. It is observed that the polar solvation dynamics of the three helical segments of the protein is influenced in a nonuniform heterogeneous manner in the MG state. While the equilibrium solvation time correlation function for helix-3 has been found to relax faster in the MG state as compared to that in the native state, the decay of the corresponding function for the other two helices slows down in the MG state. A careful analysis shows that the origin of such heterogeneous relative solvation behavior lies in the differential location of the polar probe residues and their exposure to bulk solvent. We find a significant negative cross-correlation between the contribution (to the solvation energy of a tagged amino acid residue) of water and the other groups of the protein, indicating a competing role in solvation. The sensitivity of solvation dynamics to the secondary structure and the immediate environment can be used to discriminate the partially unfolded and folded states. These results therefore should be useful in explaining recent solvation dynamics experiments on native and MG states of proteins.     

Photoinduced intramolecular charge transfer reaction in (E)-3-(4-Methylamino-phenyl)-acrylic acid methyl ester: A fluorescence study in combination with TDDFT calculation

A donor-acceptor substituted aromatic system (E)-3-(4-Methylamino-phenyl)-acrylic acid methyl ester (MAPAME) has been synthesized, and its photophysical behavior obtained spectroscopically has been compared with the theoretical results. The observed dual fluorescence from MAPAME has been assigned to emission from locally excited and twisted intramolecular charge transfer states. The donor and acceptor angular dependency on the ground and excited states potential energy surfaces have been calculated both in vacuo and in acetonitrile solvent using time dependent density functional theory (TDDFT) and TDDFT polarized continuum model (TDDFT-PCM), respectively. Calculation predicts that a stabilized twisted excited state is responsible for red shifted charge transfer emission.     

Thermodynamics of Black Holes in Einstein-Maxwell-Gauss-Bonnet Theory

We study the black hole solution in Einstein-Maxwell-Gauss-Bonnet (EMGB) gravity theory with a cosmological constant in five dimension. It is a generalization of the Reissner-Nordström-de Sitter (RNdS) or RNAdS (Reissner-Nordström-Anti-de Sitter) black hole solutions (according as the cosmological constant is positive or negative) in the Einstein-Gauss-Bonnet (EGB) theory. We analyze the thermodynamic quantities of EMGB black hole and find a restriction involving the charge and the cosmological constant for the existence of an extremal black hole. Finally, Hawking-Page phase transition has been discussed for the present black hole.     

Emergent Universe in Einstein-Gauss-Bonnet Theory

In this work, Emergent Universe scenario has been developed in Einstein-Gauss-Bonnet (EGB) theory. The universe is chosen as homogeneous and isotropic FRW model and the matter in the universe has two components—the first one is a perfect fluid with barotropic equation of state p=ω ρ (ω, a constant) and the other component is a real or phantom (or tachyonic) scalar field. Various possibilities for the existence of emergent scenario has been discussed and the results are compared with those in Einstein gravity.     

DsbA is a redox-switchable mechanical chaperone

DsbA is a ubiquitous bacterial oxidoreductase that associates with substrates during and after translocation, yet its involvement in protein folding and translocation remains an open question. Here we demonstrate a redox-controlled chaperone activity of DsbA, on both cysteine-containing and cysteine-free substrates, using magnetic tweezers-based single molecule force spectroscopy that enables independent measurements of oxidoreductase activity and chaperone behavior. Interestingly we found that this chaperone activity is tuned by the oxidation state of DsbA; oxidized DsbA is a strong promoter of folding, but the effect is weakened by the reduction of the catalytic CXXC motif. We further localize the chaperone binding site of DsbA using a seven-residue peptide which effectively blocks the chaperone activity. We found that the DsbA assisted folding of proteins in the periplasm generates enough mechanical work to decrease the ATP consumption needed for periplasmic translocation by up to 33%.

Protein translocation is facilitated by DsbA chaperone in a redox-dependent manner.     

Charge transfer via a two-strand superexchange bridge in DNA

Charge transfer in a DNA duplex chain is studied by constructing a system with virtual electrodes connected at the ends of each DNA strand. The system is described by the tight-binding model and its transport is analyzed by the transfer matrix method. The very weak distance dependence in a long (G:C)(T:A)M(G:C)3 DNA chain observed in experiment [B. Giese, Nature (London) 412, 318 (2001)] is explained by a unistep two-strand superexchange bridge without the need for the multistep thermally induced hopping mechanism or the dephasing effect. The crossover number Mc of the (T:A) base pairs, where crossover between the strong and weak distance dependence occurs, reflects the ratio of intra- and interstrand neighboring base-base couplings.     

Variable Modified Chaplygin Gas in Anisotropic Universe with Kaluza-Klein Metric

In this work, we have considered Kaluza-Klein Cosmology for anisotropic universe where the universe is filled with Variable Modified Chaplygin Gas (VMCG). Here we find normal scalar field ? and the self interacting potential V(?) to describe the VMCG Cosmology. We have also graphically analyzed the geometrical parameters named Statefinder Parameters in anisotropic Kaluza-Klein model. Next, we have considered a Kaluza-Klein model of interacting VMCG with dark matter in the Einstein gravity framework. Here we construct the three dimensional autonomous dynamical system of equations for this interacting model with the assumption that the dark energy and the dark matter interacts between themselves and for that we also choose the interaction term. We convert that interaction term to its dimensionless form and perform stability analysis and solve them numerically. We obtain a stable scaling solution of the equations in Kaluza-Klein model and graphically represent solutions.