Role of Associated Water Dynamics on Protein Stability and Activity in Crowded Milieu

Macromolecular crowding bridges in vivo and in vitro studies by simulating cellular complexities such as high viscosity and limited space while maintaining the experimental feasibility. Over the last two decades, the impact of macromolecular crowding on protein stability and activity has been a significant topic of study and discussion, though still lacking a thorough mechanistic understanding. This article investigates the role of associated water dynamics on protein stability and activity within crowded environments, using bromelain and Ficoll-70 as the model systems. Traditional crowding theory primarily attributes protein stability to entropic effects (excluded volume) and enthalpic interactions. However, our recent findings suggest that water structure modulation plays a crucial role in a crowded environment. In this report, we strengthen the conclusion of our previous study, i.e., rigid-associated water stabilizes proteins via entropy and destabilizes them via enthalpy, while flexible water has the opposite effect. In the process, we addressed previous shortcomings with a systematic concentration-dependent study using a single-domain protein and component analysis of solvation dynamics. More importantly, we analyze bromelain's hydrolytic activity using the Michaelis-Menten model to understand kinetic parameters like maximum velocity (Vmax) achieved by the system and the Michaelis-Menten coefficient (KM). Results indicate that microviscosity (not the bulk viscosity) controls the enzyme-substrate (ES) complex formation, where an increase in the microviscosity makes the ES complex formation less favorable. On the other hand, flexible associated water dynamics were found to favor the rate of product formation significantly from the ES complex, while rigid associated water hinders it. This study improves our understanding of protein stability and activity in crowded environments, highlighting the critical role of associated water dynamics.

Aspartame and Its Microhydrated Aggregates Revealed by Laser Spectroscopy: Water-Sweetener Interactions in the Gas Phase

The popular sweetener, aspartame, is an agonist of the tongue's sweet taste receptor. How water molecules affect its conformation or which aspartame atoms are more prone to interact with solvent are helpful questions to understand its activity in different environments. Here, the combination of IR-UV spectroscopic techniques with computational simulations has been successfully applied to characterize aspartame·water0-2 clusters, showing that the addition of water molecules simplifies the conformational panorama of aspartame, favoring the formation of folded structures by interaction with the polar part of the molecule.

Do Ionic Liquids Exhibit the Required Characteristics to Dissolve, Extract, Stabilize, and Purify Proteins? Past-Present-Future Assessment

Proteins are highly labile molecules, thus requiring the presence of appropriate solvents and excipients in their liquid milieu to keep their stability and biological activity. In this field, ionic liquids (ILs) have gained momentum in the past years, with a relevant number of works reporting their successful use to dissolve, stabilize, extract, and purify proteins. Different approaches in protein-IL systems have been reported, namely, proteins dissolved in (i) neat ILs, (ii) ILs as co-solvents, (iii) ILs as adjuvants, (iv) ILs as surfactants, (v) ILs as phase-forming components of aqueous biphasic systems, and (vi) IL-polymer-protein/peptide conjugates. Herein, we critically analyze the works published to date and provide a comprehensive understanding of the IL-protein interactions affecting the stability, conformational alteration, unfolding, misfolding, and refolding of proteins while providing directions for future studies in view of imminent applications. Overall, it has been found that the stability or purification of proteins by ILs is bispecific and depends on the structure of both the IL and the protein. The most promising IL-protein systems are identified, which is valuable when foreseeing market applications of ILs, e.g., in "protein packaging" and "detergent applications". Future directions and other possibilities of IL-protein systems in light-harvesting and biotechnology/biomedical applications are discussed.

Understanding the intricacy of protein in hydrated deep eutectic solvent: Solvation dynamics, conformational fluctuation dynamics, and stability

Deep eutectic solvents (DESs) are potential biocatalytic media due to their easy preparation, fine-tuneability, biocompatibility, and most importantly, due to their ability to keep protein stable and active. However, there are many unanswered questions and gaps in our knowledge about how proteins behave in these alternate media. Herein, we investigated solvation dynamics, conformational fluctuation dynamics, and stability of human serum albumin (HSA) in 0.5 Acetamide/0.3 Urea/0.2 Sorbitol (0.5Ac/0.3Ur/0.2Sor) DES of varying concentrations to understand the intricacy of protein behaviour in DES. Our result revealed a gradual decrease in the side-chain flexibility and thermal stability of HSA beyond 30 % DES. On the other hand, the associated water dynamics around domain-I of HSA decelerate only marginally with increasing DES content, although viscosity rises considerably. We propose that even though macroscopic solvent properties are altered, a protein feels only an aqueous type of environment in the presence of DES. This is probably the first experimental study to delineate the role of the associated water structure of the enzyme for maintaining its stability inside DES. Although considerable effort is necessary to generalize such claims, it might serve as the basis for understanding why proteins remain stable and active in DES.

Osmolyte induced protein stabilization: modulation of associated water dynamics might be a key factor

The mechanism of protein stabilization by osmolytes remains one of the most important and long-standing puzzles. The traditional explanation of osmolyte-induced stability through the preferential exclusion of osmolytes from the protein surface has been seriously challenged by the observations like the concentration-dependent reversal of osmolyte-induced stabilization/destabilization. The more modern explanation of protein stabilization/destabilization by osmolytes considers an indirect effect due to osmolyte-induced distortion of the water structure. It provides a general mechanism, but there are numerous examples of protein-specific effects, i.e., a particular osmolyte might stabilize one protein, but destabilize the other, that could not be rationalized through such an explanation. Herein, we hypothesized that osmolyte-induced modulation of associated water might be a critical factor in controlling protein stability in such a medium. Taking different osmolytes and papain as a protein, we proved that our proposal could explain protein stability in osmolyte media. Stabilizing osmolytes rigidify associated water structures around the protein, whereas destabilizing osmolytes make them flexible. The strong correlation between the stability and the associated water dynamics, and the fact that such dynamics are very much protein specific, established the importance of considering the modulation of associated water structures in explaining the osmolyte-induced stabilization/destabilization of proteins. More interestingly, we took another protein, bromelain, for which a traditionally stabilizing osmolyte, sucrose, acts as a stabilizer at higher concentrations but as a destabilizer at lower concentrations. Our proposal successfully explains such observations, which is probably impossible by any known mechanisms. We believe this report will trigger much research in this area.

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.

Number of Hydrogen Bonds per Unit Solvent Accessible Surface Area: A Descriptor of Functional States of Proteins

Proteins function close to native and near-native conformations. These states are evolutionarily selected to ensure the effect of mutations is minimized. The structural organization of a protein is hierarchical and modular, which reduces the dimensionality of the configurational space of the native states. Thus, finding appropriate descriptors that define the native state among all possible states of a protein is a problem of immense interest. The present study explores the correlation between solvent accessible surface areas (SASAs) and different intraprotein as well as protein-water hydrogen bonds of 55 single-chain globular proteins from four different structural classes (all α, all β, α+β, and α/β), 16 multichain proteins, and 4 macromolecular complexes. A systematic analysis of the solvent accessible surface area and intraprotein and protein-water hydrogen bonds suggests a linear relationship between SASAs and hydrogen bonds. The number of protein-water hydrogen bonds per unit SASA ranges from 3 to 4 for all the different structural protein classes. In contrast, the number of intramolecular hydrogen bonds per unit SASA, including the mainchain-mainchain, mainchain-sidechain, and sidechain-sidechain, varies between 0.75 to 2. The solvation free energy of a protein linearly decreases with SASA. Our study also shows that the solvation free energy/SASA varies from -75 to -105 kJ mol^-1 nm^-2 across all the native states studied here. The number conservancy of intraprotein hydrogen bonds per unit SASA possibly imparts structural stability to the native structure. On the other hand, 3-4 protein-water hydrogen bonds per unit SASA are possibly required to maintain a balance between the solubility and functionality of the native states. This study provides a basis for synthetic biologists to design new folds with improved functionality.

Ultraslow Biological Water-Like Dynamics in Waterless Liquid Protein

Fluorescence correlation spectroscopy and time-dependent fluorescence Stokes shift have been employed to elucidate dynamics in different time scales, ranging from picoseconds to nanoseconds, for human serum albumin, in its native and cationized forms as well as in the self-assembled complex of the cationized protein with the polymer surfactant (PS) glycolic acid ethoxylate lauryl ether. The effect of crowding in this complex, especially in the waterless condition, is of prime importance in this context. Excellent correlation of the dynamics with the structures, obtained by circular dichroism and Fourier transform infrared spectroscopy, has been observed. Slow solvation, associated classically with biological water, has been observed in these systems, even in the waterless condition. This apparently intriguing observation has been rationalized by the relaxation of segments of the protein and the PS in the microenvironment of the fluorescent probe.

Dynamic Heterogeneity at the Interface of an Intrinsically Disordered Peptide

It is believed that water around an intrinsically disordered protein or peptide (IDP) in an aqueous environment plays an important role in guiding its conformational properties and aggregation behavior. However, despite its importance, only a handful of studies exploring the correlation between the conformational motions of an IDP and the microscopic properties of water at its surface are reported. Attempts have been made in this work to study the dynamic properties of water present in the vicinity of α-synuclein, an IDP associated with Parkinson's disease (PD). Room temperature molecular dynamics (MD) simulations of eight α-synuclein_1-95 peptides with a wide range of initial conformations have been carried out in aqueous media. The calculations revealed that due to solid-like caging motions, the translational and rotational mobility of water molecules near the surfaces of the peptide repeat unit segments R1 to R7 are significantly restricted. A small degree of dynamic heterogeneity in the hydration environment around the repeat units has been observed with water near the hydrophobic R6 unit exhibiting relatively more restricted diffusivity. The time scales involving the overall structural relaxations of peptide-water and water-water hydrogen bonds near the peptide have been found to be correlated with the time scale of diffusion of the interfacial water molecules. We believe that the relatively more hindered dynamic environment near R6 can help create water-mediated contacts centered around R6 between peptide monomers at a higher concentration, thereby enhancing the early stages of peptide aggregation.

Correlating the Local and Global Dynamics of an Enzyme in the Crowded Milieu

Enzymes are dynamic biological macromolecules, with their catalytic function(s) being largely influenced by the changes in local fluctuations of amino acid side chains as well as global structural modulations that the enzyme undergoes. Such local and global motions can be highly affected inside the crowded physiological interior of the cell. Here, we have addressed the role of dynamic structural flexibility in affecting the activation energy barrier of a flexible multidomain enzyme adenylate kinase (AK3L1, UniProtKB: Q9UIJ7). Activation energy profiles of both local (at three different sites along the polypeptide backbone) and global dynamics of the enzyme have been monitored using solvation studies on the subnanosecond time scale and tryptophan quenching studies over the temperature range of 278-323 K, respectively, under crowded conditions (Ficoll 70, Dextran 40, Dextran 70, and PEG 8). This study not only provides the site-specific mapping of dynamics but reveals that the activation energies associated with these local motions undergo a significant decrease in the presence of macromolecular crowders, providing new insights into how crowding affects internal protein dynamics. The crowded scenario also aids in enhancing the coupling between the local and global motions of the enzyme. Moreover, select portions/regions of the enzyme when taken together can well mirror the overall dynamics of the biomolecule, showing possible energy hotspots along the polypeptide backbone.

How Far Is "Bulk Water" from Interfaces? Depends on the Nature of the Surface and What We Measure

Using systematic molecular dynamics (MD) simulations, we revisit the question: At what distance from an interface do the properties of "bulk water" get recovered? We have considered three different kinds of interfaces: nonpolar (hydrophobic; isooctane-water interface), charged (negative; AOT bilayer), and polar (zwitterionic; POPC bilayer). In order to interrogate the extent of perturbation of the interfacial water molecules as a function of the distance from the interface, we utilize a diverse range of structural and dynamical parameters. To capture the structural perturbations, we look into local density (translational order), local tetrahedral order parameter, and dipolar orientation of the water molecules. We also explore the anisotropic diffusion of the water molecules in the direction perpendicular to the interface as well as the planar diffusion parallel to the interface in a distance dependent manner. In addition, the orientational time correlation functions have been computed to understand the extent of slowdown in the rotational dynamics. As expected, the electrostatic field emanating from the charged AOT interface seems to have the highest long-range effect on the orientational order and dynamics of the water molecules, whereas specific interactions like hydrogen bonding and electrostatic interaction lead to significant trapping and kinetic slowdown for both AOT and POPC (zwitterionic) very close to the interface. Our analysis highlights that not only the length-scale of perturbation depends on the nature of the interfaces and specific interactions but also the type of water property that we measure/calculate. Different water properties seem to have widely different length-scale of perturbation. Orientational order parameters seem to be perturbed to a much longer length-scale as compared to translational order parameters. The global orientational order of water can be perturbed even up to ∼4-5 nm near the negatively charged AOT surface in the absence of any extra electrolyte. This observation has significant implication toward the interpretation of experimental measurements as well since different spectroscopic techniques would probe different parameters or water properties with possible mutual disagreement and inconsistency between different types of measurements. Thus, our study provides a broader and unifying perspective toward the aspect of "context dependent" structural and dynamical perturbation of "interfacial water".

What Does Time-Dependent Fluorescence Shift (TDFS) in Biomembranes (and Proteins) Report on?

The organization of biomolecules and bioassemblies is highly governed by the nature and extent of their interactions with water. These interactions are of high intricacy and a broad range of methods based on various principles have been introduced to characterize them. As these methods view the hydration phenomena differently (e.g., in terms of time and length scales), a detailed insight in each particular technique is to promote the overall understanding of the stunning “hydration world.” In this prospective mini-review we therefore critically examine time-dependent fluorescence shift (TDFS)—an experimental method with a high potential for studying the hydration in the biological systems. We demonstrate that TDFS is very useful especially for phospholipid bilayers for mapping the interfacial region formed by the hydrated lipid headgroups. TDFS, when properly applied, reports on the degree of hydration and mobility of the hydrated phospholipid segments in the close vicinity of the fluorophore embedded in the bilayer. Here, the interpretation of the recorded TDFS parameters are thoroughly discussed, also in the context of the findings obtained by other experimental techniques addressing the hydration phenomena (e.g., molecular dynamics simulations, NMR spectroscopy, scattering techniques, etc.). The differences in the interpretations of TDFS outputs between phospholipid biomembranes and proteins are also addressed. Additionally, prerequisites for the successful TDFS application are presented (i.e., the proper choice of fluorescence dye for TDFS studies, and TDFS instrumentation). Finally, the effects of ions and oxidized phospholipids on the bilayer organization and headgroup packing viewed from TDFS perspective are presented as application examples.

Altered relaxation dynamics of excited state reactions by confinement in reverse micelles probed by ultrafast fluorescence up-conversion

Chemical reactions in confined environments are important in areas as diverse as heterogenous catalysis, environmental chemistry and biochemistry, yet they are much less well understood than the equivalent reactions in either the gas phase or in free solution. The understanding of chemical reactions in solution was greatly enhanced by real time studies of model reactions, through ultrafast spectroscopy (especially when supported by molecular dynamics simulation). Here we review some of the efforts that have been made to adapt this approach to the investigation of reactions in confined media. Specifically, we review the application of ultrafast fluorescence spectroscopy to measure reaction dynamics in the nanoconfined water phase of reverse micelles, as a function of the droplet radius and the charge on the interface. Methods of measurement and modelling of the reactions are outlined. In all of the cases studied (which are focused on ultrafast intramolecular reactions) the effect of confinement was to suppress the reaction. Even in the largest micelles the result in the bulk aqueous phase was not usually recovered, suggesting an important role for specific interactions between reactant and environment, for example at the interface. There was no simple one-to-one correspondence with direct measures of the dynamics of the confined phase. Thus, understanding the effect of confinement on reaction rate appears to require not only knowledge of the dynamics of the reaction in solutions and the effect of confinement on the medium, but also of the interaction between reactant and confining medium.

Molecular Mechanism of Cell Membrane Protection by Sugars: A Study of Interfacial H-Bond Networks

Sugars function as bioprotectants by stabilizing biomolecules during dehydration, thermal stress, and freeze-thaw cycles. A buildup of sugars occurs in many organisms upon their exposure to extreme conditions. Understanding sugar's bioprotective effects on membranes is achieved by characterizing the H-bond networks at the lipid-water interface. Here, we report the headgroup H-bond populations, structures, and dynamics of 1,2-dimyristoyl-sn-glycero-3-phosphocholine vesicles in concentrated glucose solutions using ultrafast two-dimensional infrared spectroscopy in conjunction with molecular dynamics simulations. H-Bond populations and dynamics at the ester carbonyl positions are largely unaffected even at very high, 600 mg/mL, sugar concentrations. In addition, dynamics exhibit a slight nonmonotonic dependence on sugar concentration. Simulations, which are in near-quantitative agreement with measured dynamics, show that the H-bond structure remains largely intact by the existence of sugar. This study shows that the bioprotection of sugar is realized through stable lipid-saccharide-water H-bond networks at the membrane interface that mimic the H-bond networks in pure water.

Understanding enzyme behavior in a crowded scenario through modulation in activity, conformation and dynamics

Macromolecular crowding, inside the physiological interior, modulates the energy landscape of biological macromolecules in multiple ways. Amongst these, enzymes occupy a special place and hence understanding the function of the same in the crowded interior is of utmost importance. In this study, we have investigated the manner in which the multidomain enzyme, AK3L1 (PDB ID: 1ZD8), an isoform of adenylate kinase, has its features affected in presence of commonly used crowders (PEG 8, Dextran 40, Dextran 70, and Ficoll 70). Michaelis Menten plots reveal that the crowders in general enhance the activity of the enzyme, with the K_m and V_max values showing significant variations. Ficoll 70, induced the maximum activity for AK3L1 at 100 g/L, beyond which the activity reduced. Ensemble FRET studies were performed to provide insights into the relative domain (LID and CORE) displacements in presence of the crowders. Solvation studies reveal that the protein matrix surrounding the probe CPM (7-diethylamino-3-(4-maleimido-phenyl)-4-methylcoumarin) gets restricted in presence of the crowders, with Ficoll 70 providing the maximum rigidity, the same being linked to the decrease in the activity of the enzyme. Through our multipronged approach, we have observed a distinct correlation between domain displacement, enzyme activity and associated dynamics. Thus, keeping in mind the complex nature of enzyme activity and the surrounding bath of dense soup that the biological entity remains immersed in, indeed more such approaches need to be undertaken to have a better grasp of the "enzymes in the crowd".

Hydrogen-Bond Dynamics and Energetics of Biological Water

Water molecules in the immediate vicinity of biomacromolecules and biomimetic organized assemblies often exhibit a markedly distinct behavior from that of their bulk counterparts. The overall sluggish behavior of biological water substantially affects the stability and integrity of biomolecules, as well as the successful execution of various crucial water-mediated biochemical phenomena. In this Minireview, insights are provided into the features of truncated hydrogen-bond networks that grant biological water its unique characteristics. In particular, experimental results and theoretical investigations, based on chemical kinetics, are presented that have shed light on the dynamics and energetics governing such characteristics. It is emphasized how such details help us to understand the energetics of biological water, an aspect relatively less explored than its dynamics. For instance, when biological water at hydrophilic or charged protein surfaces was explored, the free energy of H-bond breakage was found to be of the order of 0.4 kcal mol^-1 higher than that of bulk water.

Hydrogen-Bond Free Energy of Local Biological Water

Here, we propose an experimental methodology based on femtosecond-resolved fluorescence spectroscopy to measure the hydrogen (H)-bond free energy of water at protein surfaces under isothermal conditions. A demonstration was conducted by installing a non-canonical isostere of tryptophan (7-azatryptophan) at the surface of a coiled-coil protein to exploit the photoinduced proton transfer of its chromophoric moiety, 7-azaindole. The H-bond free energy of this biological water was evaluated by comparing the rates of proton transfer, sensitive to the hydration environment, at the protein surface and in bulk water, and it was found to be higher than that of bulk water by 0.4 kcal mol^-1 . The free-energy difference is dominated by the entropic cost in the H-bond network among water molecules at the hydrophilic and charged protein surface. Our study opens a door to accessing the energetics and dynamics of local biological water to give insight into its roles in protein structure and function.

Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi

Our group has implemented a smooth Gaussian-based dielectric function in DelPhi (J. Chem. Theory Comput. 2013, 9 (4), 2126-2136) which models the solute as an object with inhomogeneous dielectric permittivity and provides a smooth transition of dielectric permittivity from surface-bound water to bulk solvent. Although it is well-understood that the protein hydrophobic core is less polarizable than the hydrophilic protein surface, less attention is paid to the polarizability of water molecules inside the solute and on its surface. Here, we apply explicit water simulations to study the behavior of water molecules buried inside a protein and on the surface of that protein and contrast it with the behavior of the bulk water. We selected a protein that is experimentally shown to have five cavities, most of which are occupied by water molecules. We demonstrate through molecular dynamics (MD) simulations that the behavior of water in the cavity is drastically different from that in the bulk. These observations were made by comparing the mean residence times, dipole orientation relaxation times, and average dipole moment fluctuations. We also show that the bulk region has a nonuniform distribution of these tempo-spatial properties. From the perspective of continuum electrostatics, we argue that the dielectric "constant" in water-filled cavities of proteins and the space close to the molecular surface should differ from that assigned to the bulk water. This provides support for the Gaussian-based smooth dielectric model for solving electrostatics in the Poisson-Boltzmann equation framework. Furthermore, we demonstrate that using a well-parametrized Gaussian-based model with a single energy-minimized configuration of a protein can also reproduce its ensemble-averaged polar solvation energy. Thus, we argue that the Gaussian-based smooth dielectric model not only captures accurate physics but also provides an efficient way of computing ensemble-averaged quantities.

Role of Different States of Solubilized Water on Solvation Dynamics and Rotational Relaxation of Coumarin 490 in Reverse Micelles of Gemini Surfactants, Water/12-s-12.2Br- (s = 5, 6, 8)/n-Propanol/Cyclohexane

The present study demonstrates how the different states of solubilized water viz. quaternary ammonium headgroup-bound, bulklike, counterion-bound, and free water in reverse micelles of a series of cationic gemini surfactants, water/12-s-12 (s = 5, 6, 8).2Br^-/n-propanol/cyclohexane, control the solvation dynamics and rotational relaxation of Coumarin 490 (C-490) and microenvironment of the reverse micelles. The relative number of solubilized water molecules of a given state per surfactant molecule decides major and minor components. A rapid increase in the number of bulklike water molecules per surfactant molecule as compared to the slow increase in the number of each of headgroup- and counterion-bound water molecules per surfactant molecule with increasing water content (W _o) in a given reverse micellar system is responsible for the increase in the rate of solvation and rotational relaxation of C-490. The increase in the number of counterion-bound water molecules per surfactant molecule and the concomitant decrease in the number of bulklike water molecules per surfactant molecule with increasing spacer chain length of gemini surfactants at a given W _o are ascribed to the slower rates of both solvation and rotational relaxation. Relative abundances of different states of water have a role on the microenvironment of the reverse micelles as well. Thus, a comprehensive effect of different states of water on dynamics in complex biomimicking systems has been presented here.

Antagonist Effects of l-Phenylalanine and the Enantiomeric Mixture Containing d-Phenylalanine on Phospholipid Vesicle Membrane

One of the congenital flaws of metabolism, phenylketonuria (PKU), is known to be related to the self-assembly of toxic fibrillar aggregates of phenylalanine (Phe) in blood at elevated concentrations. Our experimental findings using l-phenylalanine (l-Phe) at millimolar concentration suggest the formation of fibrillar morphologies in the dry phase, which in the solution phase interact strongly with the model membrane composed of 1,2-diacyl-sn-glycero-phosphocholine (LAPC) lipid, thereby decreasing the rigidity (or increasing the fluidity) of the membrane. The hydrophobic interaction, in addition to the electrostatic attraction of Phe with the model membrane, is found to be responsible for such phenomena. On the contrary, various microscopic observations reveal that such fibrillar morphologies of l-Phe are severely ruptured in the presence of its enantiomer d-phenylalanine (d-Phe), thereby converting the fibrillar morphologies into crushed flakes. Various biophysical studies, including the solvation dynamics experiment, suggest that this l-Phe in the presence of d-Phe, when interacting with the same model membrane, now reverts the rigidity of the membrane, i.e., increases the rigidity of the membrane, which was lost due to interaction with l-Phe exclusively. Fluorescence anisotropy measurements also support this reverse rigid character of the membrane in the presence of an enantiomeric mixture of amino acids. A comprehensive understanding of the interaction of Phe with the model membrane is further pursued at the single-molecular fluorescence detection level using fluorescence correlation spectroscopy (FCS) experiments. Therefore, our experimental conclusion interprets a linear correlation between increased permeability and enhanced fluidity of the membrane in the presence of l-Phe and certifies d-Phe as a therapeutic modulator of l-Phe fibrillar morphologies. Further, the study proposes that the rigidity of the membrane lost due to interaction with l-Phe was reinstated-in fact, increased-in the presence of the enantiomeric mixture containing both d- and l-Phe.

Expulsion of a potent cancer-cell photosensitizer from its micelle-bound state using β-cyclodextrin: A tenable model for efficient drug release

The present study delves into the interaction of a potent cancer-cell photosensitizer Norharmane (NHM) with non-ionic triblock copolymer P123, followed by the assessment of the stability of the formed complex in the presence of β-cyclodextrin (β-CD). Spectroscopic results unveil the modulation of the prototropic equilibrium of NHM within the constrained microheterogeneous medium of the copolymer micelle to be favoured towards the neutral species of NHM over the cationic counterpart; which has been aptly rationalized invoking the key role of hydrophobic interaction in the association process and is further reinforced from steady-state and time-resolved spectroscopic measurements. The micropolarity of the probe-binding site has been evaluated by the archetypal E_T(30) analysis revealing that the cationic probe remains in the corona region of the micelle instead of penetrating deeper into the micellar core. Moreover, the effect of β-CD on the stability of the NHM-bound P123 aggregates has also been investigated, revealing that β-CD can be used as a potential host for the release of the micelle-encapsulated drug through an inclusion complex formation with the P123 monomers. The result is expected to be of potential interest from medical perspective owing to the context of efficient drug release at their potential sites.

Origin of Slow Solvation Dynamics in DNA: DAPI in Minor Groove of Dickerson-Drew DNA

The measurement and understanding of collective solvation dynamics in DNA have vital biological implications, as protein and ligand binding to DNA can be directly controlled by complex electrostatic interactions of anionic DNA and surrounding dipolar water, and ions. Time-resolved fluorescence Stokes shift (TRFSS) experiments revealed anomalously slow solvation dynamics in DNA much beyond 100 ps that follow either power-law or slow multiexponential decay over several nanoseconds. The origin of such dispersed dynamics remains difficult to understand. Here we compare results of TRFSS experiments to molecular dynamics (MD) simulations of well-known 4',6-diamidino-2-phenylindole (DAPI)/Dickerson-Drew DNA complex over five decades of time from 100 fs to 10 ns to understand the origin of such dispersed dynamics. We show that the solvation time-correlation function (TCF) calculated from 200 ns simulation trajectory (total 800 ns) captures most features of slow dynamics as measured in TRFSS experiments. Decomposition of TCF into individual components unravels that slow dynamics originating from dynamically coupled DNA-water motion, although contribution from coupled water-Na⁺ motion is non-negligible. The analysis of residence time of water molecules around the probe (DAPI) reveals broad distribution from ∼6 ps to ∼3.5 ns: Several (49 nos.) water molecules show residences time greater than 500 ps, of which at least 14 water molecules show residence times of more than 1 ns in the first solvation shell of DAPI. Most of these slow water molecules are found to occupy two hydration sites in the minor groove near DAPI binding site. The residence time of Na⁺, however, is found to vary within ∼17-120 ps. Remarkably, we find that freezing the DNA fluctuations in simulation eliminates slower dynamics beyond ∼100 ps, where water and Na⁺ dynamics become faster, although strong anticorrelation exists between them. These results indicate that primary origin of slow dynamics lies within the slow fluctuations of DNA parts that couple with nearby slow water and ions to control the dispersed collective solvation dynamics in DNA minor groove.

Mechanism of Solvent Control of Protein Dynamics

We find that the coupled interactions between protein and water polarization fluctuations play a dominant role in driving the configuration space random walk of solvated proteins. We perform atomistic molecular dynamics simulations on five proteins. Owing to a very low dielectric constant of protein, its dipolar groups experience forces from water along with local forces due to protein atoms. Energy fluctuations reveal a pronounced anticorrelation between protein and water contributions. The protein energy spectrum shows bimodal 1/f noise, which can be attributed to the influence of water on the dynamics of protein.

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.

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.

Modulation of probe-genomic DNA interaction within the confined interior of a reverse micelle: Is the bulk-like properties of water truly achieved in large reverse micelles?

The prime motivation of the present study is to explore the effect of reverse micellar confinement on the binding interaction of an anthracene-based probe 9-methyl anthroate with herring-sperm DNA. The structural modification of the genomic DNA from its native B-form to the non-native C-form and subsequently to the condensed Ψ-form as a function of the level of hydration (W₀, defined as [water] / [surfactant]) of the reverse micellar core is found to reveal a remarkable regulatory role on the stability of the stacking interaction (intercalation) of the probe within the DNA helix; the interaction being progressively stabilized at higher W₀. Particularly, a close perusal of the dynamical aspects of the interaction is found to be counter-intuitive to the popular notion of the properties of the confined water within the reverse micelles typically approaching bulk-like properties at sufficiently high hydration levels (W₀ > 10).

Distinguishing dynamical features of water inside protein hydration layer: Distribution reveals what is hidden behind the average

Since the pioneering works of Pethig, Grant, and Wüthrich on a protein hydration layer, many studies have been devoted to find out if there are any "general and universal" characteristic features that can distinguish water molecules inside the protein hydration layer from bulk. Given that the surface itself varies from protein to protein, and that each surface facing the water is heterogeneous, search for universal features has been elusive. Here, we perform an atomistic molecular dynamics simulation in order to propose and demonstrate that such defining characteristics can emerge if we look not at average properties but the distribution of relaxation times. We present results of calculations of distributions of residence times and rotational relaxation times for four different protein-water systems and compare them with the same quantities in the bulk. The distributions in the hydration layer are unusually broad and log-normal in nature due to the simultaneous presence of peptide backbones that form weak hydrogen bonds, hydrophobic amino acid side chains that form no hydrogen bond, and charged polar groups that form a strong hydrogen bond with the surrounding water molecules. The broad distribution is responsible for the non-exponential dielectric response and also agrees with large specific heat of the hydration water. Our calculations reveal that while the average time constant is just about 2-3 times larger than that of bulk water, it provides a poor representation of the real behaviour. In particular, the average leads to the erroneous conclusion that water in the hydration layer is bulk-like. However, the observed and calculated lower value of static dielectric constant of hydration layer remained difficult to reconcile with the broad distribution observed in dynamical properties. We offer a plausible explanation of these unique properties.

Origin of diverse time scales in the protein hydration layer solvation dynamics: A simulation study

In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics, we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems, namely, lysozyme, myoglobin, and sweet protein monellin. In these experiments, we mutate the charges of the neighbouring amino acid side chains of certain natural probes (tryptophan) and also freeze the side chain motions. In order to distinguish between different contributions, we decompose the total solvation energy response in terms of various components present in the system. This allows us to capture the interplay among different self- and cross-energy correlation terms. Freezing the protein motions removes the slowest component that results from side chain fluctuations, but a part of slowness remains. This leads to the conclusion that the slow component approximately in the 20-80 ps range arises from slow water molecules present in the hydration layer. While the more than 100 ps component has multiple origins, namely, adjacent charges in amino acid side chains, hydrogen bonded water molecules and a dynamically coupled motion between side chain and water. In addition, the charges enforce a structural ordering of nearby water molecules and helps to form a local long-lived hydrogen bonded network. Further separation of the spatial and temporal responses in solvation dynamics reveals different roles of hydration and bulk water. We find that the hydration layer water molecules are largely responsible for the slow component, whereas the initial ultrafast decay arises predominantly (approximately 80%) due to the bulk. This agrees with earlier theoretical observations. We also attempt to rationalise our results with the help of a molecular hydrodynamic theory that was developed using classical time dependent density functional theory in a semi-quantitative manner.

Ionic liquid mediated micelle to vesicle transition of a cationic gemini surfactant: a spectroscopic investigation

In this contribution, we have examined a composition dependent self aggregated structural modification of a catanionic mixture of the surface active ionic liquid (IL) 1-butyl-3-methylimidazolium octyl sulphate and a cationic gemini surfactant (14-5-14) in aqueous medium. We have observed that the hydrodynamic diameter of the aggregates increases with increasing IL concentration and microscopic evidence (HRTEM, FESEM, and LCSM) shows the formation of vesicle like aggregates (Dh ≈ 200 nm) at XIL = 0.5. The steady state fluorescence anisotropy of the membrane binding probe DPH shows a micelle to vesicle transition at this composition. The viscosity of the solution shows a peak at XIL = 0.3, indicating the formation of a worm like micelle as an intermediate of the micelle to vesicle transition. The rotational dynamics shows a stiffer surfactant packing in the vesicles compared to the micelles, whereas, the solvation dynamics measurements indicate a higher abundance of bound type water in the vascular medium compared to that for the micelle. The formed vesicles also show stability towards temperature and biomolecules, which can be used for respective applications.

Live Cell Microscopy: A Physical Chemistry Approach

Probing dynamics of intracellular components using physical chemistry techniques is a remarkable bottom-up approach for understanding the structures and functions of a biological cell. In this "Feature Article", we give an overview on local polarity, solvation, viscosity, acid-base property, red-ox processes (thiol-disulfide exchange), and gene silencing at selected intracellular components inside a live cell. Significant differences have been observed between cancer cells and their noncancer counterparts. We demonstrate that thiol-disulfide exchange, calcium oscillation, and gene silencing are manifested in time dependence of fluorescence intensity. We show that fluorescent gold nanoclusters may be used in drug delivery (e.g., doxorubicin) and selective killing of cancer cells. Further, we discuss dynamics and structural changes of DNA quadruplexes and i-motifs, induced by different external conditions (e.g., pH) and additives (e.g., K⁺ and other target specific small molecules). We demonstrate that peptidomimetic analogues have high specificity over double-stranded DNA for binding with i-motifs and G-quadruplexes. These results may have significant biological implications.

Arm-First Approach toward Cross-Linked Polymers with Hydrophobic Domains via Hypervalent Iodine-Mediated Click Chemistry

In this work, synthesis of two cross-linked polymeric systems through isoxazoline ring formation using nitrile oxide-acrylate click chemistry has been described. In the first system, styrenic block copolymer with oxime-functionalized middle block was synthesized using S,S'-bis(α,α'-dimethyl-α″-acetic acid)trithiocarbonate as chain-transfer agent using reversible addition fragmentation chain-transfer technique. This block copolymer was further utilized to prepare core cross-linked star polymers by reacting with a four-arm acrylic cross-linker by employing environment-friendly, nontoxic PhI(OAc)2-mediated "click reaction" via the formation of isoxazoline ring. In the second system, two linear styrenic block copolymers, one containing oxime and another containing acrylate group, were reacted to form a cross-linked (CS) polymeric system. Formation of cross-linked polymers and isoxazoline ring was confirmed by Fourier transform infrared spectroscopy, gel permeation chromatography, NMR spectroscopy, and dynamic light scattering studies. Later, we also demonstrated that in aqueous medium these CS polymers produced polymeric nanoparticles (NPs), which can be used as potential carriers of hydrophobic drug molecules. The loading capacity of the hydrophobic domains has been investigated using coumarin dyes with varying hydrophobicity through steady-state and time-resolved spectroscopy studies. The polymeric NPs were also shown to successfully encapsulate a hydrophobic drug doxorubicin.

Hydration water dynamics around a protein surface: a first passage time approach

A stochastic noise-driven dynamic model is proposed to study the diffusion of water molecules around a protein surface, under the effect of thermal fluctuations that arise due to the collision of water molecules with the surrounding environment. The underlying dynamics of such a system may be described in the framework of the generalized Langevin equation, where the thermal fluctuations are assumed to be algebraically correlated in time, which governs the non-Markovian behavior of the system. Results of the calculations of mean-square displacement and the velocity autocorrelation function reveal that the hydration water around the protein surface follows subdiffusive dynamics at long times. Analytical expressions for the first passage time distribution, survival probability, mean residence time and mean first passage time of water molecules are derived for different boundary conditions, to analyze hydration water dynamics under the effect of thermally correlated noise. The results depict a unimodal distribution of the first passage time unlike Brownian motion. The survival probability of hydration water follows a stretched exponential decay for both boundary conditions. The mean residence time of the hydration water molecule for different initial positions increases with increase in the complexity/heterogeneity of the surrounding environment for both boundary conditions. The mean first passage time of the water molecule to reach the absorbing/reflecting boundary follows an asymptotic power law with respect to the thickness of the hydration layer, and increases with increase in the complexity/heterogeneity of the environment.