Water Dynamics in Cytoplasm-Like Crowded Environment Correlates with the Conformational Transition of the Macromolecular Crowder

Origin of Strong Hydrogen Bonding and Preferred Orientation of Water at Uncharged Polyethylene Glycol Polymer/Water Interface

Polyethylene glycol (PEG), a water-soluble non-ionic polymer, finds diverse applications from Li-ion batteries to drug delivery. The effectiveness of PEG in these contexts hinges on water's behavior at PEG/water interfaces. Employing heterodyne-detected vibrational sum frequency generation and Raman spectroscopy along with a novel analytical approach, termed difference spectroscopy with simultaneous curve-fitting analysis, we observed that water exhibits both "hydrogen-up" and "hydrogen-down" orientations at PEG(≥400u)/water interfaces. As the molar mass of PEG increases, the contribution of the strongly hydrogen-bonded and H-up-oriented water rises. We propose that the PEG-affected interfacial water originates from the asymmetrical hydration of the surface-adsorbed PEG, as evidenced by the resemblance between the water spectra in the hydration shell of PEG and those at the PEG/water interface. These findings elucidate the molecular mechanism underlying PEG's catalytic role in water splitting at membrane interfaces.

The explicit role of interfacial hydration during polyethylene glycol induced lipid fusion: a THz spectroscopic investigation

While the phenomenon of excipient mediated membrane fusion has been studied widely, the inherent role of interfacial hydration involved in the process has mostly remained unaddressed. Here we report the experimental validation of the fact that PEG-induced membrane fusion is associated with the dehydration of the membrane(s). We explore the explicit hydration behavior at three different lipids (DOPC, POPC and DPPC) membranes with different aliphatic tails as they undergo fusogenic transition in the presence of PEG of average molecular weight of 4000 using THz-FTIR spectroscopy in the frequency window of 1.5-13.5 THz. Dynamic light scattering and electron microscopic measurements confirm the formation of different intermediate steps of the liposomes during the fusion process: bilayer aggregation, destabilization and finally lipid fusion. We observe that membrane hydration follows a systematic trend with the lipid specificity as the fusion process sets in.

PEG mediated destabilization of holo α-lactalbumin probed by in silico and in vitro studies: deviation from excluded volume effect

Crowded and confined macromolecular milieus surround proteins, and both are stabilizing if the nature of the interaction between crowder and proteins are considered hard-core repulsive interactions. However, non-specific chemical interactions between a protein and its surroundings also play a significant role and the sum effect of both hard-core repulsion and soft interaction balances the overall effect of crowding/confinement. Previous studies showing the effect of polyethylene glycol (PEG) on protein and nucleic acid may be interpreted as either primarily excluded volume effect or, in some cases, chemical effect by changing solvent properties. In case of destabilizing interactions, charge-charge and hydrophobic contact have to gain more attention. For instance, in vitro and in vivo studies using protein as crowding agent revealed the destabilization of proteins induced by charge-charge interactions. To investigate the effect of PEG 10 kDa on holo α-lactalbumin (holo α-LA), structure and thermal stability of the protein were measured at different pH values using several techniques. Structural characterization by Trp-fluorescence, near-UV CD and far-UV measurements at different pH values clearly shows perturbation of tertiary and secondary structure of holo α-LA by PEG 10 kDa. Furthermore, the dynamic light scattering measurement shows that the protein is homogeneous under all experimental conditions. Analysis of the heat-induced denaturation profile in the presence of the crowder shows destabilization of the protein in terms of T_m (midpoint of denaturation) and ΔG_D⁰ (Gibbs free energy change at 25 °C). To evaluate the interaction of PEG 10 kDa with holo α-LA and stability of PEG-α-LA complex, docking and molecular dynamic simulation were carried out for 100 ns.Communicated by Ramaswamy H. Sarma.

Effects of External Perturbations on Protein Systems: A Microscopic View

Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.

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.

Macromolecular Crowding Effect on the Structure, Function, Conformational Dynamics and Relative Domain Movement of a Multi-Domain Protein as a function of Crowder Shape and Interaction

The cellular environment is crowded by macromolecules of various sizes, shapes, and charges, which modulate protein structure, function and dynamics. Herein, we contemplated the effect of three different macromolecular crowders:...

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".

Polyglycerol for Half-Life Extension of Proteins-Alternative to PEGylation?

Since several decades, PEGylation is known to be the clinical standard to enhance pharmacokinetics of biotherapeutics. In this study, we introduce polyglycerol (PG) of different lengths and architectures (linear and hyperbranched) as an alternative polymer platform to poly(ethylene glycol) (PEG) for half-life extension (HLE). We designed site-selective N-terminally modified PG-protein conjugates of the therapeutic protein anakinra (IL-1ra, Kineret) and compared them systematically with PEG analogues of similar molecular weights. Linear PG and PEG conjugates showed comparable hydrodynamic sizes and retained their secondary structure, whereas binding affinity to IL-1 receptor 1 decreased with increasing polymer length, yet remained in the low nanomolar range for all conjugates. The terminal half-life of a 40 kDa linear PG-modified anakinra was extended 4-fold compared to the unmodified protein, close to its PEG analogue. Our results demonstrate similar performances of PEG- and PG-anakinra conjugates and therefore highlight the outstanding potential of polyglycerol as a PEG alternative for half-life extension of biotherapeutics.

Insights into the behavior of ethylene oxide-1,2-epoxybutane diblock copolymers in water as a function of temperature and the presence of colloidal silica

HYPOTHESIS

Nonionic surfactants have been widely used for many consumer products and industrial processes, and their applications often involve temperature-cycling across cloud point temperature (T_cloud). To explore the behavior of nonionic surfactants across T_cloud and when mixed with colloidal silica at a very dilute concentration around 0.1 wt%, a series of 1,2-epoxybutane-capped alcohol ethoxylates (BAEs) with various cloud points is used as a model system.

EXPERIMENTS

BAEs with cloud points from 15 to 64 °C were successfully prepared by varying the lengths of 1,2-epoxybutane (BO) and ethylene oxide (EO) blocks and their phase behavior across T_cloud was studied using nuclear magnetic resonance spectroscopy (NMR), dynamic light scattering (DLS) and differential scanning calorimetry (DSC).

FINDINGS

In the absence of silica, the NMR signals are not greatly affected by the cloud point transition, but both the water and surfactant exhibit a decrease in spin-spin relaxation time once the temperature reaches the T_cloud. In the presence of silica, the NMR spectra indicate significantly reduced mobility of the EO portion relative to the alkyl and BO segments. Furthermore, our results suggest that the BAE surfactants are not fractionally clouding out or precipitating with a portion of the compositional distribution during the cloud point transition.

Molecular crowding electrolytes for high-voltage aqueous batteries

Developing low-cost and eco-friendly aqueous electrolytes with a wide voltage window is critical to achieve safe, high-energy and sustainable Li-ion batteries. Emerging approaches using highly concentrated salts (21-55 m (mol kg^-1)) create artificial solid-electrode interfaces and improve water stability; however, these approaches raise concerns about cost and toxicity. Molecular crowding is a common phenomenon in living cells where water activity is substantially suppressed by molecular crowding agents through altering the hydrogen-bonding structure. Here we demonstrate a 'molecular crowding' electrolyte using the water-miscible polymer poly(ethylene glycol) as the crowding agent to decrease water activity, thereby achieving a wide electrolyte operation window (3.2 V) with low salt concentration (2 m). Aqueous Li₄Ti₅O₁₂/LiMn₂O₄ full cells with stable specific energies between 75 and 110 W h kg^-1 were demonstrated over 300 cycles. Online electrochemical mass spectroscopy revealed that common side reactions in aqueous Li-ion batteries (hydrogen/oxygen evolution reactions) are virtually eliminated. This work provides a path for designing high-voltage aqueous electrolytes for low-cost and sustainable energy storage.

Bulk-like and Interfacial Water Dynamics in Nafion Fuel Cell Membranes Investigated with Ultrafast Nonlinear IR Spectroscopy

The water confined in the hydrophilic domains of Nafion fuel cell membranes is central to its primary function of ion transport. Water dynamics are intimately linked to proton transfer and are sensitive to the structural features and length scales of confinement. Here, ultrafast polarization-selective pump-probe and two-dimensional infrared vibrational echo (2D IR) experiments were performed on fully hydrated Nafion membranes with sodium counterions to explicate the water dynamics. Like aerosol-OT reverse micelles (AOT RMs), the water dynamics in Nafion are attributed to bulk-like core water in the central region of the hydrophilic domains and much slower interfacial water. Population and orientational dynamics of water in Nafion are slowed by polymer confinement. Comparison of the observed dynamics to those of AOT RMs helps identify local interactions between water and sulfonate anions at the interface and among water molecules in the core. This comparison also demonstrates that the well-known spherical cluster morphology of Nafion is not appropriate. Spectral diffusion of the interfacial water, which arises from structural dynamics, was obtained from the 2D IR experiments taking the core water to have dynamics similar to bulk water. Like the orientational dynamics, spectral diffusion was found to be much slower at the interface compared to bulk water. Together, the dynamics indicate slow reorganization of weakly hydrogen-bonded water molecules at the interface of Nafion. These results provide insights into proton transport mechanisms in fuel cell membranes, and more generally, water dynamics near the interface of confining systems.

On the origin of the extremely different solubilities of polyethers in water

The solubilities of polyethers are surprisingly counter-intuitive. The best-known example is the difference between polyethylene glycol ([-CH₂-CH₂-O-]_n) which is infinitely soluble, and polyoxymethylene ([-CH₂-O-]_n) which is completely insoluble in water, exactly the opposite of what one expects from the C/O ratios of these molecules. Similar anomalies exist for oligomeric and cyclic polyethers. To solve this apparent mystery, we use femtosecond vibrational and GHz dielectric spectroscopy with complementary ab initio calculations and molecular dynamics simulations. We find that the dynamics of water molecules solvating polyethers is fundamentally different depending on their C/O composition. The ab initio calculations and simulations show that this is not because of steric effects (as is commonly believed), but because the partial charge on the O atoms depends on the number of C atoms by which they are separated. Our results thus show that inductive effects can have a major impact on aqueous solubilities.

Water Structure and Dynamics in the Stern Layer of Micelles: Femtosecond Mid-Infrared Pump-Probe Spectroscopy Study

Molecular-level understanding of the water structure and dynamics in the Stern layer of micelles is important to elucidate the active role of water in biological processes on membrane surfaces. Micelles and reverse micelles are considered to be excellent membrane model systems. Here, to address the question of whether or not the spatial confinement effect on water in reverse micelles and nanometric water pool systems plays a role in modulating water dynamics, we consider four different aqueous micelle solutions and study the water dynamics in the Stern layer of micelles using a femtosecond mid-infrared pump-probe spectroscopy technique. Vibrational energy relaxation and rotational dynamics of the O?D stretch mode of HDO and the azido stretch mode of hydrazoic acid are critically dependent on the charge, polarity, and chemical structure of the surfactant head group. In particular, water molecules in the Stern layer of micelles, which are not in spatially confined environments, are notably different from those in bulk water. This finding clearly indicates that changes in the vibrational and rotational dynamics of water molecules, even in spatially confined systems, are mainly induced by surface effects instead of spatial confinement effects. We believe that the present experimental results are of importance for understanding water-involved biochemical processes on biological membranes.

Programming in situ accelerated DNA walkers in diffusion-limited microenvironments

Macromolecule diffusion in cellular microenvironments dictates the kinetics of biochemical processes, yet inevitably limiting the assembly and operation of biomimetic motors. Herein we program in situ accelerated DNA walkers in diffusion-limited microenvironments such as molecularly crowded solutions and cytoplasm. All DNA components, including single-foot walkers, chemically damaged tracks and calibration elements, are anchored on individual gold nanoparticles. Two endogenous enzymes participating in base repair pathways are used to actuate on-particle walking via a base excision/hydrolyzation coupled reaction. The walkers are in situ driven without requiring external drivers and accelerated several times. They also avoid low-efficiency diffusion/assembly procedures and respond to heterogeneous cellular milieus with calibration function. We further regulated the walking kinetics via DNA densities and sets of enzymes, and demonstrated cytoplasmic behaviors of three kinds of walkers. They were utilized to profile DNA repair pathways and monitor enzyme catalysis in living cells.

Correspondence between Spectral-Derived and Viscosity-Derived Local Composition in Binary Liquid Mixtures Having Specific Interactions with Preferential Solvation Theory

Local interactions between unlike molecules (1-2) in solution are commonly measured with spectroscopy and used to estimate local composition. Herein, a viscosity model based on preferential solvation (PS) theory is developed for aqueous and nonaqueous binary liquid mixtures containing a dipolar aprotic solvent that provides local composition considering the hydration or solvation shell around complex (1-2) molecules. Spectral-derived and viscosity-derived local composition distributions showed similar trends with bulk composition, and their correspondence is attributed to characteristics of the hydration or solvation shell. Viscosity-derived local compositions were consistent with literature molecular simulations, whereas spectral-derived local composition distributions contained artifacts. The PS viscosity model is also applicable to nonpolar-polar mixtures for which self-association occurs, and it can be used to estimate solvent mixture dipolarity/polarizability. Since the PS viscosity model only requires bulk viscosity, it may provide a means to estimate microviscosity or the solvent environment around biomolecules.

How Molecular Crowding Differs from Macromolecular Crowding: A Femtosecond Mid-Infrared Pump-Probe Study

Crowding is an inherent property of living systems in which biochemical processes occur in highly concentrated solutions of various finite-sized species of both low (molecular crowding) and high (macromolecular crowding) molecular weights. Is molecular crowding fundamentally different from macromolecular crowding? To answer this question, we use a femtosecond mid-infrared pump-probe technique with three vibrational probes in molecular (diethylene glycol) and macromolecular (polyethylene glycol) solutions. In less crowded media, both molecular and macromolecular crowders fail to affect the dynamics of interstitial bulk-like water molecules and those at the crowder/water interface. In highly crowded media, interstitial water dynamics strongly depends on molecular crowding, but macromolecular crowding does not alter the bulk-like hydration dynamics and has a modest crowding effect on water at the crowder/water interface. The results of this study provide a molecular level understanding of the structural and dynamic changes to water and the water-mediated cross-linking of crowders.

Soft interaction and excluded volume effect compete as polyethylene glycols modulate enzyme activity

Polyethylene glycols (PEGs) can either preferentially bind to biomolecules or exert excluded volume effect depending upon their chain length and concentration. We have studied the effect of ethylene glycol (EG) and PEGs of different chain lengths (M_n 400 and 4000) on the enzyme efficiency of hen-egg-white lysozyme (HEWL) on Micrococcus lysodeikticus (M. Lys.) cell. The activity shows a bell-like profile as the turnover number increases from ~1.3 × 10⁵ s^-1 M^-1 in water to ~1.7 × 10⁵ s^-1 M^-1 in presence of 2% PEG-400 beyond which it decreases to ~0.7 × 10⁵ s^-1 M^-1 at 20% PEG-400. Solvent polarity, excluded volume effect, soft nonspecific interactions and structural flexibility are found to be the competing factors which govern the overall enzyme activity as evidenced from circular dichroism (CD) and fluorescence measurements. Thermal unfolding temperature (T_m) of HEWL also shows a bell-shaped profile with PEG concentration which establishes possible correlation with its activity. We also observe a minimum in the activation energy barrier for the catalysis at low osmolyte concentrations. The maximum in the enzyme efficiency has been explained on the basis of an optimization between excluded volume effect and soft interaction among the protein and the cosolutes.

Crowding Stabilizes DMSO-Water Hydrogen-Bonding Interactions

Up to 40% of intracellular water is confined due to the dense packing of macromolecules, ions, and osmolytes. Despite the large body of work concerning the effect of additives on the biomolecular structure and stability, the role of crowding and heterogeneity in these interactions is not well understood. Here, infrared spectroscopy and molecular dynamics simulations are used to describe the mechanisms by which crowding modulates hydrogen bonding interactions between water and dimethyl sulfoxide (DMSO). Specifically, we use formamide and dimethylformamide (DMF) as molecular crowders and show that the S═O hydrogen bond populations in aqueous mixtures are increased by both amides. These additives increase the amount of water within the DMSO first solvation shell through two mechanisms: (a) directly stabilizing water-DMSO hydrogen bonds; (b) increasing water exposure by destabilizing DMSO-DMSO self-interactions. Further, we quantified the hydrogen bond enthalpies between the different components: DMSO-water (61 kJ/mol) > DMSO-formamide (32 kJ/mol) > water-water (23 kJ/mol) ≫ formamide-water (4.7 kJ/mol). Spectra of carbonyl stretching vibrations show that DMSO induces the dehydration of amides as a result of strong DMSO-water interactions, which has been suggested as the main mechanism of protein destabilization.

Effect of Osmolytes on the Conformational Behavior of a Macromolecule in a Cytoplasm-like Crowded Environment: A Femtosecond Mid-IR Pump-Probe Spectroscopy Study

Osmolytes found endogenously in almost all living beings play an important role in regulating cell volume under harsh environment. Here, to address the longstanding questions about the underlying mechanism of osmolyte effects, we use femtosecond mid-IR pump-probe spectroscopy with two different IR probes that are the OD stretching mode of HDO and the azido stretching mode of azido-derivatized poly(ethylene glycol) dimethyl ether (PEGDME). Our experimental results show that protecting osmolytes bind strongly with water molecules and dehydrate polymer surface, which results in promoting intramolecular interactions of the polymer. By contrast, urea behaves like water molecules without significantly disrupting water H-bonding network and favors extended and random-coil segments of the polymer chain by directly participating in solvation of the polymer. Our findings highlight the importance of direct interaction between urea and macromolecule, while protecting osmolytes indirectly affect the macromolecule through enhancing the water-osmolyte interaction in a crowded environment, which is the case that is often encountered in real biological systems.

Origin of the blueshift of water molecules at interfaces of hydrophilic cyclic compounds

Water molecules at interfaces of materials exhibit enigmatic properties. A variety of spectroscopic studies have observed a high-frequency motion in these water molecules, represented by a blueshift, at both hydrophobic and hydrophilic interfaces. However, the molecular mechanism behind this blueshift has remained unclear. Using Raman spectroscopy and ab initio molecular dynamics simulations, we reveal the molecular mechanism of the blueshift of water molecules around six monosaccharide isomers. In the first hydration shell, we found weak hydrogen-bonded water molecules that cannot have a stable tetrahedral water network. In the water molecules, the vibrational state of the OH bond oriented toward the bulk solvent strongly contributes to the observed blueshift. Our work suggests that the blueshift in various solutions originates from the vibrational motions of these observed water molecules.

Role of Solvent Water in the Temperature-Induced Self-Assembly of a Triblock Copolymer

Water-soluble triblock copolymers have received much attention in industrial applications and scientific fields. We here show that femtosecond mid-IR pump-probe spectroscopy is useful to study the role of water in the temperature-induced self-assembly of triblock copolymers. Our experimental results suggest two distinct subpopulations of water molecules: those that interact with other water molecules and those involved in the hydration of a triblock copolymer surface. We find that the vibrational dynamics of bulk-like water is not affected by either micellation or gelation of triblock copolymers. The increased population of water interacting with ether oxygen atoms of the copolymer during the unimer to micelle phase transition is important evidence for the entropic role of water in temperature-induced micelle formation at a low copolymer concentration. In contrast, at the critical gelation temperature and beyond, the population of surface-associated water molecules interacting with ether oxygen atoms decreases, which indicates important enthalpic control by water. The present study on the roles of water in the two different phase transitions of triblock copolymers sheds new light on the underlying mechanisms of temperature-induced self-aggregation behaviors of amphiphiles that are ubiquitous in nature.

Role of solvent properties of water in crowding effects induced by macromolecular agents and osmolytes

Dipolarity/polarizability of water in polymer mixtures may be additive, reduced or enhanced depending on the composition of the mixture.