Pairwise Hydrophobicity at Low Temperature: Appearance of a Stable Second Solvent-Separated Minimum with Possible Implication in Cold Denaturation

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

5-(tert-Butyl)-2-hydroxy-1,3-isophthalaldehyde (5-tBHI) 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. It has been found that 5-tBHI forms mixed aggregates of different orders, owing to the presence of both enolic and tautomeric forms, to yield tunable emission, although the emission intensity is quenched. These findings suggest that the intramolecular hydrogen bonding of 5-tBHI not only limits intermolecular interactions but also promotes nonradiative deactivation pathways. Hence, designing and structural engineering, with a focus to suppressing intramolecular hydrogen bonding as well as increasing through space conjugation by replacing the aldehydic moieties with bulky aliphatic or aromatic ketonic groups, can be a plausible approach to yielding improved probes with tunable emission and higher fluorescence quantum yields.

Correlation between protein conformations and water structure and thermodynamics at high pressure: A molecular dynamics study of the Bovine Pancreatic Trypsin Inhibitor (BPTI) protein

Pressure-induced perturbation of a protein structure leading to its folding-unfolding mechanism is an important yet not fully understood phenomenon. The key point here is the role of water and its coupling with protein conformations as a function of pressure. In the current work, using extensive molecular dynamics simulation at 298 K, we systematically examine the coupling between protein conformations and water structures of pressures of 0.001, 5, 10, 15, 20 kbar, starting from (partially) unfolded structures of the protein Bovine Pancreatic Trypsin Inhibitor (BPTI). We also calculate localized thermodynamics at those pressures as a function of protein-water distance. Our findings show that both protein-specific and generic effects of pressure are operating. In particular, we found that (1) the amount of increase in water density near the protein depends on the protein structural heterogeneity; (2) the intra-protein hydrogen bond decreases with pressure, while the water-water hydrogen bond per water in the first solvation shell (FSS) increases; protein-water hydrogen bonds also found to increase with pressure, (3) with pressure hydrogen bonds of waters in the FSS getting twisted; and (4) water's tetrahedrality in the FSS decreases with pressure, but it is dependent on the local environment. Thermodynamically, at higher pressure, the structural perturbation of BPTI is due to the pressure-volume work, while the entropy decreases with the increase of pressure due to the higher translational and rotational rigidity of waters in the FSS. The local and subtle effects of pressure, found in this work, are likely to be typical of pressure-induced protein structure perturbation.

Absorption of Volatile Organic Compounds Toluene and Acetaldehyde in Choline Chloride-Based Deep Eutectic Solvents

Unrestricted emission of volatile organic compounds (VOCs)─a threat to human health and the environment─can be controlled to a large extent by the capturing mechanism. Few recent experimental studies explored the efficacy of the deep eutectic solvent (DES), a designer solvent with some fascinating properties, as a VOC-capturing medium. Through the partition coefficient measurement, it was found that the choline chloride-based DESs exhibit excellent VOC-capturing potencies. However, a molecular picture of the above absorption process is still lacking. Here, we study the molecular mechanism of the absorption of two commonly occurring VOCs, toluene and acetaldehyde, in two different choline chloride-based DESs with varying donor molecules, urea, and levulinic acid via the molecular dynamics simulation technique. Strong absorption of the VOCs is observed in both the DESs. The free energy profile for the absorption process has been explored using the umbrella sampling method. The VOCs are preferentially solvated near the liquid/vapor interface. The simulated partition coefficients for the VOCs from the vapor to the liquid phase show good agreement with the experimental results. Detailed analyses of the spatial and orientational structure of the VOCs and different components of DESs are performed to elucidate the interaction among them. The above analyses have indicated that DES is a better VOC-capturing medium compared to a room-temperature ionic liquid, which is more extensively studied in the literature.

Structural characteristics of low-density environments in liquid water

The existence of two structural forms in liquid water has been a point of discussion for a long time. A phase transition between these two forms of liquid water has been proposed based on evidence from molecular simulations, and experiments have also been very recently able to track the proposed transition of the low-density liquid form to the high-density liquid form. We propose to use the average angle an oxygen atom makes with its neighbors to describe the structural environment of a water molecule. The distribution of this order parameter is observed to have two peaks with one peak at ∼109.5^{∘}, corresponding to the internal angle of a regular tetrahedron, indicating tetrahedral arrangement. The other peak corresponds to an environment with a tighter arrangement of neighboring molecules. The distribution of O-O-O angles is decomposed into two skewed distributions to estimate the fractions of the two liquid forms in water. A good similarity is observed between the temperature and pressure trends of fractions of locally favored tetrahedral structure (LFTS) form estimated using the new order parameter and the reports in the literature, over a range of temperatures and pressures. We also compare the structural environments indicated by different order parameters and find that the order parameter proposed in this paper captures the structure of first solvation shell of the LFTS accurately.

Influence of Temperature and Salt Concentration on the Hydrophobic Interactions of Adamantane and Hexane

One of the definitions of hydrophobic interactions is the aggregation of nonpolar particles in a polar solvent, such as water. While this phenomenon appears to be very simple, it is crucial for many complex processes, such as protein folding, to take place. In this work, the hydrophobic association of adamantane and hexane at various temperatures and ionic strengths was studied using molecular dynamics simulations with the AMBER 16.0 program and the GAFF force field. The potentials of mean force of hydrophobic dimer formation, as well as the excess free energy, excess energy, excess entropy, and excess heat capacity corresponding to the formation of the contact minimum, were determined and analyzed. For both systems, the depth of the contact minimum in the potential of mean force was found to increase with both temperature and ionic strength. The excess heat capacity of the association at the contact minimum and T = 298 K was found to be negative and to decrease, while the excess entropy and energy were found to be positive and to increase for both systems, the changes being more pronounced for the hexane dimer. The excess heat capacity is also greater in absolute value for the hexane dimer.

Deciphering the Role of the Non-ice-binding Surface in the Antifreeze Activity of Hyperactive Antifreeze Proteins

Antifreeze proteins (AFPs) show thermal hysteresis through specific interaction with the ice crystal. Hyperactive AFPs interact with the ice surface through a threonine-rich motif present at their ice-binding surface (IBS). Ordering of water around the IBS was extensively investigated. However, the role of non-IBS in ice growth inhibition is yet to be understood completely. The present study explores the nature of hydration and its length-scale evaluation around the non-IBS for hyperactive AFPs. We observed that the hydration layer of non-IBS is liquid-like, even in highly supercooled conditions, and the nature of hydration is drastically different from the hydration pattern of non-AFP surfaces. In similar conditions, the hydration layer around the IBS is ice-like ordered. Non-IBS of the hyperactive AFP exposes toward the bulk and is able to maintain the liquid-like character of its hydration water up to 15 Å. We also find that the amino acid compositions and their spatial distribution on the non-IBS are markedly different from those of the IBS and non-AFP surfaces. These results elucidate the combined role of IBS and non-IBS in ice-growth inhibition. While IBS is required to adsorb on ice efficiently, the exposed non-IBS may prevent ice nucleation/growth on top of the bound AFPs.

Translocation of a hydroxyl functionalized carbon dot across a lipid bilayer: an all-atom molecular dynamics simulation study

Passive permeation of CD across lipid bilayer is almost impossible. Forced permeation results membrane rupture.

Factors Promoting the Formation of Clathrate-Like Ordering of Water in Biomolecular Structure at Ambient Temperature and Pressure

Clathrate hydrate forms when a hydrophobic molecule is entrapped inside a water cage or cavity. Although biomolecular structures also have hydrophobic patches, clathrate-like water is found in only a limited number of biomolecules. Also, while clathrate hydrates form at low temperature and moderately higher pressure, clathrate-like water is observed in biomolecular structure at ambient temperature and pressure. These indicate presence of other factors along with hydrophobic environment behind the formation of clathrate-like water in biomolecules. In the current study, we presented a systematic approach to explore the factors behind the formation of clathrate-like water in biomolecules by means of molecular dynamics simulation of a model protein, maxi, which is a naturally occurring nanopore and has clathrate-like water inside the pore. Removal of either confinement or hydrophobic environment results in the disappearance of clathrate-like water ordering, indicating a coupled role of these two factors. Apart from these two factors, clathrate-like water ordering also requires anchoring groups that can stabilize the clathrate-like water through hydrogen bonding. Our results uncover crucial factors for the stabilization of clathrate-like ordering in biomolecular structure which can be used for the development of new biomolecular structure promoting clathrate formation.

Ordered hydration layer mediated ice adsorption of a globular antifreeze protein: mechanistic insight

The ice binding surface of a type III AFP induces water ordering at lower temperature, which mediates its adsorption on the ice surface.

Influence of glycerol on the cooling effect of pair hydrophobicity in water: relevance to proteins’ stabilization at low temperature

Glycerol reduces the cooling effect of pair hydrophobicity (reduction of hydrophobicity with decreasing temperature) in water.

Molecular Insights into the Unusual Structure of an Antifreeze Protein with a Hydrated Core

The primary driving force for protein folding is the formation of a well-packed, anhydrous core. However, recently, the crystal structure of an antifreeze protein, maxi, has been resolved where the core of the protein is filled with water, which apparently contradicts the existing notion of protein folding. Here, we have performed standard molecular dynamics (MD) simulation, replica exchange MD (REMD) simulation, and umbrella sampling using TIP4P water at various temperatures (300, 260, and 240 K) to explore the origin of this unusual structural feature. It is evident from standard MD and REMD simulations that the protein is found to be stable at 240 K in its unusual state. The core of protein has two layers of semi-clathrate water separating the methyl groups of alanine residues from different helical strands. However, with increasing temperature (260 and 300 K), the stability decreases as the core becomes dehydrated, and methyl groups of alanine are tightly packed driven by hydrophobic interactions. Calculation of the potential of mean force by an umbrella sampling technique between a pair of model hydrophobes resembling maxi protein at 240 K shows the stabilization of second solvent-separated minima (SSM), which provides a thermodynamic rationale of the unusual structural feature in terms of weakening of the hydrophobic interaction. Because the stabilization of SSMs is implicated for cold denaturation, it suggests that the maxi protein is so designed by nature where the cold denatured-like state becomes the biologically active form as it works near or below the freezing point of water.

How do glycerol and dimethyl sulphoxide affect local tetrahedral structure of water around a nonpolar solute at low temperature? Importance of preferential interaction

Glycerol and dimethyl sulphoxide (DMSO) have vital roles in cryoprotection of living cells, tissues, etc. The above action has been directly linked with disruption of hydrogen (H-) bond structure and dynamics of water by these cosolvents at bulk region and around various complex units, such as peptide, amino acid, protein, and lipid membrane. However, the disruption of the local structure of the water solvent around a purely hydrophobic solute is still not studied extensively. The latter is also important in the context of stabilization of protein from cold denaturation. Through all-atom molecular dynamics simulation, we have investigated the comparative effect of glycerol and DMSO on the orientational order of water around a nonpolar solute at -5 °C. A steady reduction of the tetrahedral order of water is observed at bulk (>10 Å distance from the solute) and solute interface (<5.5 Å distance from the solute) with increasing the cosolvent concentration. Contrasting roles of glycerol and DMSO have been evidenced. While DMSO affects the H-bond structure of the interfacial water more than that of the bulk water, glycerol affects the water structure almost uniformly at all regions around the solute. Furthermore, while glycerol helps to retain water molecules at the interface, DMSO significantly reduces the water content in that region. We have put forward a plausible mechanism for these contrasting roles of these cosolvents. The solute-cosolvent hydrophobic-interaction-induced orientational alignment of an interfacial cosolvent molecule determines whether the involvement of the cosolvent molecules in H-bonding with solvent water in the interface is akin to the bulk region or not.

Optimum Number of Anchored Clathrate Water and Its Instantaneous Fluctuations Dictate Ice Plane Recognition Specificities of Insect Antifreeze Protein

Ice recognition by antifreeze proteins (AFPs) is a subject of topical interest. Among several classes of AFPs, insect AFPs are hyperactive presumably due to their ability to adsorb on basal plane. However, the origin of the basal plane binding specificity is not clearly known. Present work aims to provide atomistic insight into the origin of basal plane recognition by an insect antifreeze protein. Free energy calculations reveal that the order of binding affinity of the AFP toward different ice planes is basal plane > prism plane > pyramidal plane. Critical insight reveals that the observed plane specificity is strongly correlated with the number and their instantaneous fluctuations of clathrate water forming hydrogen bonds with both ice binding surface (IBS) of AFP and ice surface, thus anchoring AFP to the ice surface. On basal plane, anchored clathrate water array is highly stable due to exact match in the periodicity of oxygen atom repeat distances of the ice surface and the threonine repeat distances at the IBS. The stability of anchored clathrate water array progressively decreases upon prism and pyramidal plane adsorption due to mismatch between the threonine ladder and oxygen atom repeat distance. Further analysis reveals that hydration around the methyl side-chains of threonine residues becomes highly significant at low temperature which stabilizes the anchored clathrate water array and dual hydrogen-bonding is a consequence of this stability. Structural insight gained from this study paves the way for rational designing of highly potent antifreeze-mimetic with potential industrial applications.