Aggregation-Induced Modulation of Ground and Excited State Photophysics of 5-(-Butyl)-2-Hydroxy-1,3-Isophthalaldehyde (5-BHI).

5-(-Butyl)-2-hydroxy-1,3-isophthalaldehyde (5-BHI) is a photochromic material susceptible to either excited state proton transfer or excited state intramolecular proton transfer, depending upon the solvent. However, it has also been found to aggregate in the presence of sodium dodecyl sulfate. In this current study, based on the steady-state and time-resolved spectroscopy, supported by crystallography, quantum chemical density functional theory calculation, and molecular dynamics (MD) simulation, we report on the aggregation of this potential single benzene-based emitter (SBBE) in neat solvents as well as solid phase to modulate its photophysics.

Energetic and structural insights behind calcium induced conformational transition in calmodulin.

Calmodulin (CaM) is a key signaling protein that triggers several cellular and physiological processes inside the cell. Upon binding with calcium ion, CaM undergoes large scale conformational transition from a closed state to an open state that facilitates its interaction with various target protein and regulates their activity. This work explores the origin of the energetic and structural variation of the wild type and mutated CaM and explores the molecular origin for the structural differences between them.

How soluble misfolded proteins bypass chaperones at the molecular level.

Subpopulations of soluble, misfolded proteins can bypass chaperones within cells. The extent of this phenomenon and how it happens at the molecular level are unknown. Through a meta-analysis of the experimental literature we find that in all quantitative protein refolding studies there is always a subpopulation of soluble but misfolded protein that does not fold in the presence of one or more chaperones, and can take days or longer to do so.

Exploring the role of hydrophilic amino acids in unfolding of protein in aqueous ethanol solution.

Hydrophobic association is the key contributor behind the formation of well packed core of a protein which is often believed to be an important step for folding from an unfolded chain to its compact functional form. While most of the protein folding/unfolding studies have evaluated the changes in the hydrophobic interactions during chemical denaturation, the role of hydrophilic amino acids in such processes are not discussed in detail. Here we report the role of the hydrophilic amino acids behind ethanol induced unfolding of protein.

On the Correlation between Pair Hydrophobicity and Mixing Enthalpies in Water-Alcohol Binary Mixtures.

In this article, we have explored the extent of pair hydrophobicity in water-alcohol binary mixtures upon varying the chain length of the alcohol at several compositions. We have measured the pair hydrophobicity in water-methanol, water-propanol, and water-butanol mixtures. The pair hydrophobicity is measured by the depth of the first minimum (contact minimum) in the potential of mean force profile between a pair of neopentanes.

Exploring and Engineering the Conformational Landscape of Calmodulin through Specific Interactions.

Conformational fluctuations often play paramount role in the function and activity of proteins. Calmodulin (CaM) is a calcium sensing protein that shows significant conformational flexibility on going from a ligand-free open state to a ligand-bound closed state. By employing large-scale equilibrium molecular dynamics simulations and free energy calculations, we have shown that apo CaM frequently visits a state that is neither fully open nor fully closed and referred to as half-open half-closed (HOHC) state.

Unravelling the Composition-Dependent Anomalies of Pair Hydrophobicity in Water-Ethanol Binary Mixtures.

Aqueous binary mixtures have received immense attention in recent years because of their extensive application in several biological and industrial processes. The water-ethanol binary mixture serves as a unique system because it exhibits composition-dependent alteration of dynamic and thermodynamic properties. Our present work demonstrates how different compositions of water-ethanol binary mixtures affect the pair hydrophobicity of different hydrophobes.

Interaction of proteins with ionic liquid, alcohol and DMSO and in situ generation of gold nano-clusters in a cell.

In this review, we give a brief overview on how the interaction of proteins with ionic liquids, alcohols and dimethyl sulfoxide (DMSO) influences the stability, conformational dynamics and function of proteins/enzymes. We present experimental results obtained from fluorescence correlation spectroscopy on the effect of ionic liquid or alcohol or DMSO on the size (more precisely, the diffusion constant) and conformational dynamics of lysozyme, cytochrome c and human serum albumin in aqueous solution. The interaction of ionic liquid with biomolecules (e.

Role of Dispersive Fluorous Interaction in the Solvation Dynamics of the Perfluoro Group Containing Molecules.

Perfluoro group containing molecules possess an important self-aggregation property through the fluorous (F···F) interaction which makes them useful for diverse applications such as medicinal chemistry, separation techniques, polymer technology, and biology. In this article, we have investigated the solvation dynamics of coumarin-153 (C153) and coumarin-6H (C6H) in ethanol (ETH), 2-fluoroethanol (MFE), and 2,2,2-trifluoroethanol (TFE) using the femtosecond upconversion technique and molecular dynamics (MD) simulation to understand the role of fluorous interaction between the solute and solvent molecules in the solvation dynamics of perfluoro group containing molecules. The femtosecond upconversion data show that the time scales of solvation dynamics of C6H in ETH, MFE, and TFE are approximately the same whereas the solvation dynamics of C153 in TFE is slow as compared to that of ETH and MFE.

Modulation of the Conformational Dynamics of Apo-Adenylate Kinase through a π-Cation Interaction.

Large-scale conformational transition from open to closed state of adenylate kinase (ADK) is essential for its catalytic cycle. Apo-ADK undergoes conformational transition in a way that closely resembles an open-to-closed conformational transition. Here, equilibrium simulations, free-energy simulations, and quantum mechanics/molecular mechanics (QM/MM) calculations in combination with several bioinformatics approaches have been used to explore the molecular origin of this conformational transition in apo-ADK.

Effect of alcohol on the structure of cytochrome C: FCS and molecular dynamics simulations.

Effect of ethanol on the size and structure of a protein cytochrome C (Cyt C) is investigated using fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulations. For FCS studies, Cyt C is covalently labeled with a fluorescent probe, alexa 488. FCS studies indicate that on addition of ethanol, the size of the protein varies non-monotonically.

Solvent organization around the perfluoro group of coumarin 153 governs its photophysical properties: An experimental and simulation study of coumarin dyes in ethanol as well as fluorinated ethanol solvents.

The self-aggregation property of the perfluoro group containing molecules makes it important in the research fields of biology and polymer and organic synthesis. In the quest of understanding the role of the perfluoro group on the photophysical properties of perfluoro-containing molecules in biologically important fluoroethanol solvents, we have applied photophysical as well as molecular dynamics simulation techniques to explore the properties of perfluoro groups containing molecule coumarin-153 (C153) in ethanol (ETH), monofluoroethanol (MFE), difluoroethanol (DFE), and trifluoroethanol (TFE) and compared them with the molecules without perfluoro moiety, namely coumarin-6H (C6H) and coumarin-480 (C480). In contrast to C6H and C480, the excited state lifetime of C153 in fluorinated ETHs is not monotonic.

Structural relaxation of acridine orange dimer in bulk water and inside a single live lung cell.

Structural relaxation of the acridine orange (AO) dimer in bulk water and inside a single live lung cell is studied using time resolved confocal microscopy and molecular dynamics (MD) simulations. The emission maxima (λem (max)∼ 630 nm) of AO in a lung cancer cell (A549) and a non-cancer lung fibroblast cell (WI38) suggest that AO exists as a dimer inside the cell. Time-dependent red shift in emission maximum indicates dynamic relaxation of the AO dimer (in the excited state) with a time constant of 500-600 ps, both in bulk water and inside the cell.