Spectroscopic and Molecular Dynamics Simulation Study of Lysozyme in the Aqueous Mixture of Ethanol: Insights into the Nonmonotonic Change of the Structure of Lysozyme

Structural change of lysozyme in the aqueous mixture of ethanol (ETH) has been investigated using emission, circular dichroism spectroscopy, free-energy molecular dynamics (MD) simulation, and contact map analysis methods. The emission and circular dichroism data of protein depict the nonmonotonic change suggesting that the structure as well as local environment near the Trp of lysozyme modifies differently for different compositions of the ETH–water mixture. The free-energy MD simulation shows that the change in the average size of lysozyme in the aqueous mixture of ETH also shows a nonmonotonic nature. The free-energy profile of lysozyme in the low concentration of ETH suggests that the distance between helices increases (χ_ETH ≈ 0.07) first and decreases again (χ_ETH ≈ 0.2) becoming almost similar to the native structure. Around χ_ETH ≈ 0.5, the size of lysozyme increases significantly probably leading to the unfolding of the protein. With further increase of ETH (χ_ETH ≈ 0.7), size of lysozyme decreases suggesting the refolding of the protein. Contact map as well as solvent organization analysis depicts that ETH gets preferentially solvated by the hydrophobic core of lysozyme which weaken the hydrophobic interactions of protein, resulting in the increase in its size. The aggregation of ETH dominated at the higher concentration of ETH (χ_ETH ≈ 0.7); hence, the, weakening of hydrophobic core of protein by ETH is reduced, which probably lead to the refolding of lysozyme

Theoretical Study on the Microhydration of Atmospherically Important Carbonyl Sulfide in Its Neutral and Anionic Forms: Bridging the Gap between the Bulk and Finite Size Microhydrated Cluster

Carbonyl sulfide (OCS) is the most abundant and stable sulfur-containing triatomic gas present in the atmosphere that plays an important role in aerosol formation. Structure, energetics, and photoelectron spectral properties of the microhydrated OCS in its neutral and anionic forms have been studied by using the BP86, B3LYP, and MP2 methods. OCS is linear in the neutral state but bent in the anionic state. Water binds with the OCS through a single hydrogen bond (O–H···O) in the OCS-(H₂O)_<i>n</i> [<i>n</i> = 1–6], whereas binding of OCS^– with water takes place through single as well as double hydrogen bonds (O–H···S and O–H···O). Energy decomposition analysis shows that electrostatic and exchange energies are the main contributors to the stabilization energy of the microhydrated OCS and OCS^– clusters. Detachment as well as solvation energies are calculated with different levels of theory and compared with the existing experimental values. Finally, an analytical expression has been used to obtain the bulk value of the detachment and solvation energies from the existing information on the finite size clusters. The present study reveals that hydration increases the detachment energy of the OCS^– by 3.2 eV. In the absence of experimental bulk values of the detachment and solvation energies for this system, the values obtained by the solvent-number-dependent theoretical expression will definitely reduce this gap and may be used for the modeling of the OCS in the atmosphere

pH Regulates Ligand Binding to an Enzyme Active Site by Modulating Intermediate Populations

Understanding the mechanism of ligands binding to their protein targets and the influence of various factors governing the binding thermodynamics is essential for rational drug design. The solution pH is one of the critical factors that can influence ligand binding to a protein cavity, especially in enzymes whose function is sensitive to the pH. Using computer simulations, we studied the pH effect on the binding of a guanidinium ion (Gdm+) to the active site of hen egg-white lysozyme (HEWL). HEWL serves as a model system for enzymes with two acidic residues in the active site and ligands with Gdm+ moieties, which can bind to the active sites of such enzymes and are present in several approved drugs treating various disorders. The computed free energy surface (FES) shows that Gdm+ binds to the HEWL active site using two dominant binding pathways populating multiple intermediates. We show that the residues close to the active site that can anchor the ligand could play a critical role in ligand binding. Using a Markov state model, we quantified the lifetimes and kinetic pathways connecting the different states in the FES. The protonation and deprotonation of the acidic residues in the active site in response to the pH change strongly influence the Gdm+ binding. There is a sharp jump in the ligand-binding rate constant when the pH approaches the largest pKa of the acidic residue present in the active site. The simulations reveal that, at most, three Gdm+ can bind at the active site, with the Gdm+ bound in the cavity of the active site acting as a scaffold for the other two Gdm+ ions binding. These results can aid in providing greater insights into designing novel molecules containing Gdm+ moieties that can have high binding affinities to inhibit the function of enzymes with acidic residues in their active site

Understanding the Role of Hydrophobic Terminal in the Hydrogen Bond Network of the Aqueous Mixture of 2,2,2-Trifluoroethanol: IR, Molecular Dynamics, Quantum Chemical as Well as Atoms in Molecules Studies

The aqueous mixture of 2,2,2-trifluoroethanol (TFE) is one of the important alcoholic solvents which has been extensively used for understanding the stability of proteins as well as several chemical reactions. In this paper, the deconvolution of the IR lines in the OH-stretching region has been applied to understand the local structure of water–water, alcohol–water, and alcohol–alcohol interactions in the water mixture of TFE and ethanol (ETH). Further, molecular dynamics simulations, quantum chemical calculations, and atoms in molecules analysis have been performed to encode the local structure information obtained from the experimental data. Addition of a small amount of alcohol in a pure aqueous medium enhances the aggregation of water molecules for the case of ETH, whereas the hydrogen bond between TFE and water is the dominant contributor for TFE. The −CF₃ substitution changes the orientation and hydrogen-bonding site of water molecules from the hydrophilic OH terminal to the hydrophobic −CF₃ terminal of TFE, which decreases the clustering of water molecules as well as enhances the hydrogen bonding between TFE and water. In the TFE-rich region of the water mixture of TFE, the fluorine of the TFE molecules interacts with each other through a weak fluorous interaction which reduces the hydrogen bonding between the −CF₃ of TFE and water molecules. These findings about the hydrogen bond network of the water mixture of TFE induced by the hydrophobic −CF₃ group provide a stepwise explanation of the unique hydrophobic properties of the trifluoromethyl group containing pharmaceutical molecules

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. It has also been observed that the time scale of solvation dynamics of C6H in ETH and MFE is higher than that of C153 in the same solvents. MD simulation results show a qualitative agreement with the experimental data in terms of the time scale of the slow components of the solvation for all the systems. The experimental and simulation studies combined lead to the conclusion that the solvation dynamics of C6H in all solvents as well as C153 in ETH and MFE is mostly governed by the charge distribution of ester moieties (CO and O) of dye molecules whereas the solvation of C153 in TFE is predominantly due to the dispersive fluorous interaction (F···F) between the perfluoro groups of the C153 and solvent molecules