Interfacial Glucose to Regulate Hydrated Lipid Bilayer Properties: Influence of Concentrations.

A series of atomistic molecular dynamics (MD) simulations were carried out with a hydrated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayer with the variation of glucose concentrations from 0 to 30 wt % in the presence of 0.3 M NaCl. The study suggested that although the thickness of the lipid bilayer dropped significantly with the increase in glucose concentration, it expanded laterally at high glucose levels due to the intercalation of glucose between the headgroups of adjacent lipids. We adopted the surface assessment via the grid evaluation method to compute the deviation of the bilayer's key structural features for the different amounts of glucose present. This suggested that the accumulation of glucose molecules near the headgroups influences the local lipid bilayer undulation and crimping of the lipid tails. We find that the area compressibility modulus increases with the glucose level, causing enhanced bilayer rigidity arising from the slow lateral diffusion of lipids. The restricted lipid motion at high glucose concentrations controls the sustainability of the curved bilayer surface. Calculations revealed that certain orientations of CO→ of interfacial glucose with the PN→ of lipid headgroups are preferred, which helps the glucose to form direct hydrogen bonds (HBs) with the lipid headgroups. Such lipid-glucose (LG) HBs relax slowly at low glucose concentrations and exhibit a higher lifetime, whereas fast structural relaxation of LG HBs with a shorter lifetime was noticed at a higher glucose level. In contrast, lipid-water (LW) HBs exhibited a higher lifetime at a higher glucose level, which gradually decreased with the glucose level lowering. The study interprets that the glucose concentration-driven LW and LG interactions are mutually inclusive. Our detailed analysis will exemplify small saccharide concentration-driven membrane stabilizing efficiency, which is, in general, helpful for drug delivery study.

Boron-containing fullerene-based salts with cyclic carbonate solvents as electrolytes for Li-ion batteries and beyond.

Replacement of carbon atoms by a heteroatom in fullerene is a promising route that enhances the electronic properties of fullerenes and results in hetero fullerene-based effective agents ensuring applications in vivid fields of the solar cell, cathode materials for batteries, etc. Towards the development of new electrolyte salts, attention has been paid to facilitating ion mobility in particular and moderate stability of the anions in addition. From the atomistic molecular dynamics simulation studies, for the first time, we uncover that the boron-containing hetero fullerene, C59B- anion-based LiC59B, and NaC59B salts in cyclic carbonate solvents can act as efficient electrolytes by improving the transport phenomenon of the metal ions in solution, importantly for Li+ and satisfactorily for Na+ as compared to their commonly used BF4- anion based salts. Additionally, our study revealed that apart from LiC59B, and NaC59B salts, C58B22- based MgC58B2 salt can facilitate the ionic conductivity of the electrolyte. The properties of the proposed electrolyte under an electric field and different temperatures were investigated. Some of the bulk properties of the used electrolytes to some extent were found to be improved in the presence of these salts. The first principle-based electrochemical calculations further justify the stability of the proposed anions. The initial investigation from the Reactive force-field (ReaxFF) based atomistic simulations study elucidates that LiC59B reduces the decomposition of the EC solvent compared to LiBF4 and facilitates solvent stability.

Sulfation Effects of Chondroitin Sulfate to Bind a Chemokine in Aqueous Medium: Conformational Heterogeneity and Dynamics from Molecular Simulation.

The sulfation patterns and degree of sulfation of chondroitin sulfate (CS), an important class of glycosaminoglycans (GAG), and their interactions with chemokines are accountable for various diseases. To realize the underlying mechanism of such complex biological phenomena at a molecular level and their application in rational drug design, a study on conformations and dynamics of CSs is necessary. To explore this, in this study, we performed a series of atomistic molecular dynamics (MD) simulations with different sulfated variants of octadecasaccharide CS, like CS-C, CS-E, and CS-T, in their free forms and when bound to the protein chemokine CXCL8 dimer in an aqueous medium. The calculated binding free energy of CSs with the CXCL8 dimer is favorable, and the degree of sulfation favors the complexation process further with prominent hydrophobic and hydrogen-bonded interactions. We find that the recognition is associated with the configurational entropy loss of the CS molecules as calculated from the Gaussian mixture approach, which supports that the degree of sulfation regulates the process. Cluster analysis through the k-means algorithm and end-to-end distance measurement revealed that although the free CS molecules adopted linear conformations, the nonlinear conformations during binding with protein were noted. Adaptation of nonlinear forms in the bound forms is noteworthy for the less-sulfated CS-C and CS-E. Apart from favorable 4C1 conformations, the occasional appearance of skew-boat forms from the free-energy map of ring pucker for the GlcUA unit was observed, which remains unaffected by the sulfation. We find that during recognition, the average relaxation time of intra-CS and inter-CS-CXCL8 hydrogen bonds (HBs) is about a magnitude lesser than that of CS-water HBs, most prominent on the involvement of higher sulfated CS-T analogues. The translational motion of surrounded water molecules in CSs exhibited sublinear diffusion, and the degree of sublinearity increases around the heavily sulfated molecules due to the hindrance created by them as well as the presence of the chemokine and exhibited markedly slow heterogeneous diffusion.

Selective Sensing of Epinephrine by Phenylboronic Acid Tethered Carbon Dot.

The present work depicts development of phenylboronic acid (PBA) derived and appended carbon dots (CD1-PBAs) to detect epinephrine with high sensitivity and selectivity against structurally analogous biomolecules like norepinephrine, L-Dopa and glucose. Carbon dots were synthesized by hydrothermal method. Microscopic and spectroscopic studies ensured the suitability of CD1-PBAs for diol sensing. Catecholic-OH groups of epinephrine primarily form covalent adduct with CD1-PBAs via boronate-diol linkage that caused change in absorption intensity of CD1-PBAs. The limit of detection (LOD) for epinephrine was found to be 2.0 nM. For other analogous biomolecules, formation of boronate-diol linkage might have got retarded by the dominant participation of secondary interactions like hydrogen bonding owing to the presence of varying functional moieties. Subsequently, responsiveness in the change in absorbance intensity of CD1-PBAs was weaker compared to that for epinephrine. Hence, a selective and efficient carbon dot (CD1-PBAs) based epinephrine sensor was developed simply by utilizing boronate-diol linkage.

Conformational Features and Hydration Dynamics of Proteins in Cosolvents: A Perspective from Computational Approaches.

The importance of solvent in stabilizing protein structures has long been recognized. Water is the common solvent for proteins, and hydration is elemental in governing protein stability, flexibility, and function through various interactions. The addition of small organic molecules known as cosolvents may deploy stabilization (folding) or destabilization (unfolding) effects on native protein conformations. Despite exhaustive literature, the molecular mechanism by which cosolvents regulate protein conformations and dynamics is controversial. Specifically, the cosolvent behavior has been unpredictable with the nature and concentrations that lead to protein stabilizing/destabilizing effects as it changes in water content near the vicinity of proteins. With the massive development of computational resources, advancement of computational methods, and the availability of numerous experimental techniques, various theoretical and computational studies of proteins in a mixture of solvents have been instigated. The growing interest in such studies has been to unravel the underlying mechanism of protein folding and cosolvent/solvent-protein interactions that have significant implications in biomedical and biotechnological applications. In this mini-review, apart from the brief overview of important theories and force-field model-based cosolvent effects on proteins, we present the current state of knowledge and recent advances in the field to describe cosolvent-guided conformational features of proteins and hydration dynamics from computational approaches. The mini-review further explains the mechanistic details of protein stability in various popularly used cosolvents, including limitations of present studies and future outlooks. The counteracting effects of cosolvent on the proteins in the mixture of stabilizing and destabilizing cosolvents are also presented and discussed.

Understanding Conformational Properties and Role of Hydrogen Bonds in Glycosaminoglycans-Interleukin8 Complexes in Aqueous Medium by Molecular Dynamics Simulation.

Atomistic molecular dynamics simulations were performed under ambient conditions to explore the conformational features and binding affinities of hexameric glycosaminoglycans (GAGs) with chemokine Interleukin8 (IL8) in an aqueous medium. We tried to understand the role of hydrogen bonds (HBs) involving conserved water in mediating the interactions. The Luzar-Chandler model was adopted to study the kinetics of HB breaking and formation concerning different water-mediated HBs. The conformational flexibilities of bound GAGs are due to the flexible glycosidic linkages than the occasional/rare ring pucker conformation. The free energy landscape constructed with ϕ, and ψ, depicted that different conformational minima associated with the glycosidic linkage flexibility of the GAGs in bound states are separated by energy barriers. The binding affinities of IL8 towards GAGs are favored through the electrostatic and non-polar solvation interactions. 4-different types of conserved water were explored in the solvent-mediated binding of GAGs with IL8. The average lifetime of the IL8-GAG direct HB pairs was ∼ten times less than the IL8-GAG-shared water HBs. This is due to the rapid establishment of HB breaking and reformation kinetics involving water of a shared layer. We find that despite the highly negatively charged surface of GAGs, the IL8 surface populated by non-cationic amino acids could serve as a promising binding site in addition to the cationic surface of the protein.

Influence of Aqueous Arginine Solution on Regulating Conformational Stability and Hydration Properties of the Secondary Structural Segments of a Protein at Elevated Temperatures: A Molecular Dynamics Study.

The effects of aqueous arginine solution on the conformational stability of the secondary structural segments of a globular protein, ubiquitin, and the structure and dynamics of the surrounding water and arginine were examined by performing atomistic molecular dynamics (MD) simulations. Attempts have been made to identify the osmolytic efficacy of arginine solution, and its influence in guiding the hydration properties of the protein at an elevated temperature of 450 K. The similar properties of the protein in pure water at elevated temperatures were computed and compared. Replica exchange MD simulation was performed to explore the arginine solution's sensitivity in stabilizing the protein conformations for a wide range of temperatures (300-450 K). It was observed that although all the helices and strands of the protein undergo unfolding at elevated temperature in pure water, they exhibited native-like conformational dynamics in the presence of arginine at both ambient and elevated temperatures. We find that the higher free energy barrier between the folded native and unfolded states of the protein primarily arises from the structural transformation of α-helix, relative to the strands. Our study revealed that the water structure around the secondary segments depends on the nature of amino acid compositions of the helices and strands. The reorientation of water dipoles around the helices and strands was found hindered due to the presence of arginine in the solution; such hindrance reduces the possibility of exchange of hydrogen bonds that formed between the secondary segments of protein and water (PW), and as a result, PW hydrogen bonds take longer time to relax than in pure water. On the other hand, the origin of slow relaxation of protein-arginine (PA) hydrogen bonds was identified to be due to the presence of different types of protein-bound arginine molecules, where arginine interacts with the secondary structural segments of the protein through multiple/bifurcated hydrogen bonds. These protein-bound arginine formed different kinds of bridged PA hydrogen bonds between amino acid residues of the same secondary segments or among multiple bonds and helped protein to conserve its native folded form firmly.

Predicting the evolution of number of native contacts of a small protein by using deep learning approach.

Native contacts (NCs) are one of the most vital parameters in order to define the resemblance of a protein conformation with its native state. Prediction of number of native contacts in a protein is useful in protein folding mechanism. In this work, we focused to predict the time series of the number of NCs of a small protein, insulin monomer by using three neural network based models, namely; Multi-Layer Perceptron (MLP), Long Short Term Memory (LSTM) and Gated Recurrent Unit (GRU). The input data used in the study was the time evolution of NC values of the folded and unfolded protein conformations computed from the equilibrated trajectories of atomistic molecular dynamics (MD) simulations performed with the aqueous solution of the protein at ambient as well as at an elevated temperature. The evolutionary prediction accuracy of the three models was tested by calculating two error parameters; Root Mean Square Error (RMSE) and Mean Absolute Error (MAE). Our study revealed that, although these three models are successful in forecasting the time evolutions of the NCs in terms of lower RMSE and MAE, the prediction through static memoryless artificial neural network, MLP was relatively less precise as compared to other two recurrent units, LSTM and GRU. The study infers that by using the available input data generated from the MD trajectories; these neural network based models could be used to predict the complex evolution pattern of distanced based structural parameters of a protein with a satisfactory level.

Molecular recognition of two bioactive coumarin derivatives 7-hydroxycoumarin and 4-methyl-7-hydroxycoumarin by hen egg white lysozyme: Exploring the binding mechanism, thermodynamic parameters and structural changes using multispectroscopic and computational approaches.

Multispectroscopic and computational methods of exploring the interaction between a carrier protein and therapeutic compounds provide a preliminary investigation into establishing the efficacy of such compounds. Here, two coumarin derivatives, 7-hydroxycoumarin (7-HC) and 4-methyl-7-hydroxycoumarin (4-Me-7-HC), were selected to carry out numerous biophysical interaction studies with a model carrier protein, hen egg white lysozyme (HEWL). Fluorescence spectroscopy studies conducted between HEWL and 7-HC/4-Me-7-HC revealed the binding constants (Kb) were in the range of 104 M-1, indicating a moderate nature of binding. The quenching mechanism observed during complexation process was an unusual static quenching due to the effect of temperature on the rate constant. Thermodynamic parameters revealed a positive ΔH and ΔS for HEWL-7-HC/4-Me-7-HC, indicating hydrophobic forces played a dominant role in the interaction process. FRET studies suggested a possible non-radiative energy transfer from the donor (HEWL) to the acceptor (coumarins). Molecular docking studies revealed the interaction of 7-HC/4-Me-7-HC with intrinsic fluorophores, Trp63 and Trp108, Trp108 being an essential residue for binding as proven by molecular dynamic (MD) simulation. MD simulation studies also indicated conformational stability gained by HEWL upon interaction with 7-HC and 4-Me-7-HC. The microenvironment surrounding the Trp residues showed a significant Stoke's shift on carrying out 3-D fluorescence. CD studies revealed a decrease in the alpha helical content of HEWL upon interacting with the ligands. Enzymatic assay conducted for HEWL in the presence of 7-HC/4-Me-7-HC saw an increase in the activity of HEWL, suggesting a change in structural conformation and stability of the protein, altering its activity.Communicated by Ramaswamy H. Sarma.

Conformational changes of GDNF-derived peptide induced by heparin, heparan sulfate, and sulfated hyaluronic acid - Analysis by circular dichroism spectroscopy and molecular dynamics simulation.

Glial-cell-line-derived neurotrophic factor (GDNF) is a protein that has therapeutic potential in the treatment of Parkinson's disease and other neurodegenerative diseases. The activity of GDNF is highly dependent on the interaction with sulfated glycans which bind at the N-terminus consisting of 19 residues. Herein, we studied the influence of different glycosaminoglycan (i.e., glycan; GAG) molecules on the conformation of a GDNF-derived peptide (GAG binding motif, sixteen amino acid residues at the N-terminus) using both experimental and theoretical studies. The GAG molecules employed in this study are heparin, heparan sulfate, hyaluronic acid, and sulfated hyaluronic acid. Circular dichroism spectroscopy was employed to detect conformational changes induced by the GAG molecules; molecular dynamics simulation studies were performed to support the experimental results. Our results revealed that the sulfated GAG molecules bind strongly with GDNF peptide and induce alpha-helical structure in the peptide to some extent.

Analyzing the driving forces of insulin stability in the basic amino acid solutions: A perspective from hydration dynamics.

Amino acids having basic side chains, as additives, are known to increase the stability of native-folded state of proteins, but their relative efficiency and the molecular mechanism are still controversial and obscure as well. In the present work, extensive atomistic molecular dynamics simulations were performed to investigate the hydration properties of aqueous solutions of concentrated arginine, histidine, and lysine and their comparative efficiency on regulating the conformational stability of the insulin monomer. We identified that in the aqueous solutions of the free amino acids, the nonuniform relaxation of amino acid-water hydrogen bonds was due to the entrapment of water molecules within the amino acid clusters formed in solutions. Insulin, when tested with these solutions, was found to show rigid conformations, relative to that in pure water. We observed that while the salt bridges formed by the lysine as an additive contributed more toward the direct interactions with insulin, the cation-π was more prominent for the insulin-arginine interactions. Importantly, it was observed that the preferentially more excluded arginine, compared to histidine and lysine from the insulin surface, enriches the hydration layer of the protein. Our study reveals that the loss of configurational entropy of insulin in arginine solution, as compared to that in pure water, is more as compared to the entropy loss in the other two amino acid solutions, which, moreover, was found to be due to the presence of motionally bound less entropic hydration water of insulin in arginine solution than in histidine or lysine solution.

Unraveling the origin of interactions of hydroxychloroquine with the receptor-binding domain of SARS-CoV-2 in aqueous medium.

Interactions of hydroxychloroquin (HCQ) with the receptor binding domain (RBD) of SARS-CoV-2 were studied from atomistic simulation and ONIOM techniques. The key-residues of RBD responsible for the human transmission are recognized to be blocked in a heterogeneous manner with the favorable formation of key-residue:HCQ (1:1) complex. Such heterogeneity in binding was identified to be governed by the differential life-time of the hydrogen bonded water network anchoring HCQ and the key-residues. The intermolecular proton transfer facilitates the most favorable Lys417:HCQ complexation. The study demonstrates that off-target bindings of HCQ need to be minimized to efficiently prevent the transmission of SARS-CoV-2.

Non-enzymatic glycation of human serum albumin modulates its binding efficacy towards bioactive flavonoid chrysin: A detailed study using multi-spectroscopic and computational methods.

The non-enzymatic glycation of plasma proteins by reducing sugars have important consequences on the conformational and functional properties of protein. The formation of advanced glycation end products (AGEs) is responsible for cell death and other pathological conditions. We have synthesized the glycated human serum albumin (gHSA) and characterized the same by using differential spectroscopic measurements. The aim of the present study is to determine the effect of glycation on the binding of human serum albumin (HSA) with bioactive flavonoid chrysin, which possesses anti-cancer, anti-inflammatory and anti-oxidant activities. The interaction of chrysin with HSA and gHSA was studied using multi-spectroscopic, molecular docking and molecular dynamics (MD) simulation techniques. Chrysin quenched the intrinsic fluorescence of both HSA and gHSA by static quenching mechanism. The value of the binding constant (Kb) for the interaction of HSA-chrysin complex (4.779 ± 0.623 × 105 M-1 at 300 K) was found to be higher than that of gHSA-chrysin complex (2.206 ± 0.234 × 105 M-1 at 300 K). Hence, non-enzymatic glycation of HSA significantly reduced its binding affinity towards chrysin. The % α-helicity of HSA was found to get enhanced upon binding with chrysin, and minimal changes were observed for the gHSA-chrysin complex. Site marker probe studies indicated that chrysin binds to subdomain IIA and IIIA of both HSA and gHSA. The results from molecular docking and MD simulation studies correlated well with the experimental findings. Electrostatic interactions followed by hydrogen bonding and hydrophobic interactions played major roles in the binding process. These observations may have some useful insights into the field of pharmaceutics.

Insights into the Sensitivity of Arginine Concentration to Preserve the Folded Form of Insulin Monomer under Thermal Stress.

Arginine, although popularly known as aggregation suppressor additive, has been found to quench proteins' structure and function by destabilizing their conformations. Driven by such controversial evidence, in this work we performed a series of atomistic molecular dynamics simulations of insulin monomer, a biologically active hormone protein, in arginine solution of varying concentrations (0.5, 1, and 2 M) at ambient and elevated temperature (400 K) to explore the arginine concentration driven structure-based stability of the protein. Our study reveals that the flexibility of the protein's structure is dependent on the arginine concentration, and among all the used solutions, 2 M arginine, a "neutral crowder" that mimics the cellular environment, can preserve the native folded form of the protein at ambient temperature in an excellent manner. Further, while the protein unfolds at 400 K in pure water, this solution worked satisfactorily to preserve the protein's folded conformation more firmly than the other solutions. The replica-exchange MD of insulin in 2 M arginine solution further supports the fact. In this aspect an important issue in molecular pharmacology is to identify and recognize the physical origin of the stability of a protein, i.e, in this case, how arginine directs the conformational flexibility of the protein and preserves its native folded form. We identified that the exclusion of arginine from the protein surface increases the local structuration of water around the protein, thereby preserving its "biological water" layer, and makes the protein more hydrated at 2 M concentration as compared to the other arginine solutions. Additionally, our microscopic investigation on the interactions of the protein-solvation layer revealed that the structural heterogeneity of the protein surface, arising from the differential physicochemical nature of the amino acid residues, controls the favorable formation of sluggish water-arginine mixed solvation layer at higher arginine concentration that helps the protein to maintain its structural rigidity. Importantly, apart from the protein-solvent hydrogen-bonding interactions, the anion-pi interactions, established between the carboxyl group of arginine and the aromatic amino acid residues of insulin, were recognized to facilitate the protein to maintain its native folded form at the experimental temperatures.

Lysozyme-luteolin binding: molecular insights into the complexation process and the inhibitory effects of luteolin towards protein modification.

In the proposed work, the complexation of bioactive flavonoid luteolin with hen egg white lysozyme (HEWL) along with its inhibitory influence on HEWL modification has been explored with the help of multi-spectroscopic and computational methods. The binding affinity has been observed to be moderate in nature (in the order of 104 M-1) and the static quenching mechanism was found to be involved in the fluorescence quenching process. The binding constant (Kb) shows a progressive increase with the increase in temperature from (4.075 ± 0.046 × 104 M-1) at 293 K to (6.962 ± 0.024 × 104 M-1) at 313 K under experimental conditions. Spectroscopic measurements along with molecular docking calculations suggest that Trp62 is involved in the binding site of luteolin within the geometry of HEWL. The positive changes in enthalpy (ΔH = +19.99 ± 0.65 kJ mol-1) as well as entropy (ΔS = +156.28 ± 2.00 J K-1 mol-1) are indicative of the presence of hydrophobic forces that stabilize the HEWL-luteolin complex. The micro-environment around the Trp residues showed an increase in hydrophobicity as indicated by synchronous fluorescence (SFS), three dimensional fluorescence (3D) and red edge excitation (REES) studies. The % α-helix of HEWL showed a marked reduction upon binding with luteolin as indicated by circular dichroism (CD) and Fourier-transform infrared spectroscopy (FTIR) studies. Moreover, luteolin is situated at a distance of 4.275 ± 0.004 nm from the binding site as indicated by FRET theory, and the rate of energy transfer kET (0.063 ± 0.004 ns-1) has been observed to be faster than the donor decay rate (1/τD = 0.606 ns-1), which is indicative of the non-radiative energy transfer during complexation. Leaving aside the binding study, luteolin showed promising inhibitory effects towards the d-ribose mediated glycation of HEWL as well as towards HEWL fibrillation as studied by fluorescence emission and imaging studies. Excellent correlation with the experimental observations as well as precise location and dynamics of luteolin within the binding site has been obtained from molecular docking and molecular dynamics simulation studies.

Superhalogens as Building Blocks of Super Lewis Acids.

Lewis acids play an important role in synthetic chemistry. Using first-principle calculations on some newly designed molecules containing boron and organic heterocyclic superhalogen ligands, we show that the acid strength depends on the charge of the central atom as well as on the ligands attached to it. In particular, the strength of the Lewis acid increases with increasing electron withdrawing power of the ligand. With this insight, we highlight the importance of superhalogen-based ligands in the design of strong Lewis acids. Calculated fluoride ion affinity (FIA) values of B[C2 BNO(CN)3 ]3 and B[C2 BNS(CN)3 ]3 show that these are super Lewis acids.

A New Class of Superhalogen Based Anion Receptor in Li-Ion Battery Electrolytes.

In the search for new additives (anion receptors) in Li-ion battery electrolytes especially for LiPF6 and LiClO4, we have theoretically designed boron-based complexes by coupling with different heterocyclic ligands. The validation of the formation of modeled compounds involves reproduction of available experimentally reported absolute magnetic shielding and chemical shift values for different boron complexes. As compared to the commonly used tris(pentafluorophenyl) borane, our designed compounds suggest that the complexes like B[C2HBNO(CN)2]3, B[C2HBNS(CN)2]3, and B[C4H3BN(CN)2]3 are promising additives.

An insight into the binding of 6-hydroxyflavone with hen egg white lysozyme: a combined approach of multi-spectroscopic and computational studies.

The interaction of 6-hydroxyflavone (6HF) with hen egg white lysozyme (HEWL) has been executed using multi-spectroscopic and computational methods. Steady state fluorescence studies indicated that static quenching mechanism is involved in the binding of 6HF with HEWL, which was further supported by excited state lifetime and UV-vis absorption studies. The binding constant (Kb) of the HEWL-6HF complex was observed to be 6.44 ± 0.09 × 104 M-1 at 293 K, which decreases with the increase in temperature. The calculation of the thermodynamic quantities showed that the binding is exothermic in nature with a negative enthalpy change (ΔH = -11.91 ± 1.02 kJ mol-1) along with a positive entropy change (ΔS = +51.36 ± 2.43 J K-1 mol-1), and the major forces responsible for the binding are hydrogen bonding and hydrophobic interactions. The possibility of energy transfer from tryptophan (Trp) residue to the 6HF ligand was observed from Fo¨rster's theory. The inclusion of 6HF within the binding site of HEWL induces some micro-environmental changes around the Trp residues as indicated by synchronous and three-dimensional (3D) fluorescence studies. The changes in secondary structural components of HEWL are observed on binding with 6HF along with a reduction in % α-helical content. Computational studies correlate well with the experimental finding, and the ligand 6HF is found to bind near to Trp 62 and Trp 63 residues of HEWL. Altogether, the present study provides an insight into the interaction dynamics and energetics of the binding of 6HF to HEWL. Communicated by Ramaswamy H. Sarma.

Can 2,2,2-trifluoroethanol be an efficient protein denaturant than methanol and ethanol under thermal stress?

Monohydric alcohols, such as methanol (MEH), ethanol (ETH) and 2,2,2-trifluoroethanol (TFE), have significant effects on biological processes including the protein folding-unfolding phenomenon. Among the several monohydric alcohols, TFE, a fluorine-substituted alcohol, is known to induce a helical structure in proteins. In this work, we report the heterogeneous unfolding phenomenon of a small protein Chymotrypsin Inhibitor 2 in various concentrations of methanol, ethanol and TFE solutions by performing atomistic molecular dynamics simulation studies. Our study reveals that the unfolding phenomenon of CI2 under thermal stress majorly depends on the concentration and the nature of the alcohol. The presence of alcohols in general has been noted to accelerate the unfolding process compared to pure water and TFE, among them all, has been found to speed up the unfolding time scale at low concentrations. The molecular contact frequency between protein and alcohol follows the trend, MEH < ETH < TFE at low concentrations, whereas the trend becomes MEH ∼ ETH > TFE at more concentrated solutions. The differential water-mediated and self-clustering phenomena of alcohols, diverse protein-alcohol hydrogen bond strengths and the concentration dependent restricted inhomogeneous protein-water as well as protein-alcohol hydrogen bond dynamics suggest that TFE, a well known α-helix stabilizer, could be a good competitor among its class of denaturants.

Picosecond Solvation Dynamics in Nanoconfinement: Role of Water and Host-Guest Complexation.

The dynamics of solvation of an excited chromophore, 5-(4″-dimethylaminophenyl)-2-(4'-sulfophenyl)oxazole, sodium salt (DMO), has been explored in confined nanoscopic environments of ß-cyclodextrin (ßCD) and heptakis(2,6-di- O-methyl)-ß-cyclodextrin (DIMEB). Solvation occurs on a distinctly slower time scale (τS3 ∼ 47 ps, τS4 ∼ 517 ps) in the host cavity of DIMEB than in that of ßCD (τS3 ∼ 20 ps, τS4 ∼ 174 ps). The calculated equilibrium solvation response of DMO was characterized by four relaxation components (τS1 ∼ 0.46-0.48 ps, τS2 ∼ 3.2-3.4 ps, τS3 ∼ 32.3-37.7 ps, and τS4 ∼ 232-485 ps), of which the longer ones (τS3, τS4) are well-consistent with experiments, whereas the ultrafast components (τS1, τS2) are unresolved. The observed time constant (τS3) within the ∼20-47 ps range arises from slow water molecules in the primary hydration layers of the host CDs and is slower for DIMEB than for ßCD presumably due to longer-lived and stronger hydrogen bonds that water forms with the former host relative to the latter. Decomposition of the calculated solvation response of DMO has revealed that conformational fluctuations of the macrocyclic hosts give rise to the observed long-time relaxation component (τS4), which is much slower for the inclusion complexes with DIMEB than for those with ßCD because of slower conformational dynamics of the former host than that of the latter.