Dynamics of water in biological recognition

Elucidation of the Ultrafast Origin of Multiphasic Dynamics in a Far-Red-Sensing Cyanobacteriochrome

Cyanobacteriochromes are photoreceptors that constitute a significant subset of phycocyanobilin-bound proteins, yet the details of their excited-state photochemical and structural dynamics have not been fully elucidated. Here, we investigate the photoisomerization dynamics of a newly identified far-red/orange light-absorbing cyanobacteriochrome using femtosecond-resolved fluorescence and absorption methods. We observed active-site relaxations ranging from a few to hundreds of picoseconds for both far-red and orange-absorbing states. As such relaxations modulate the potential energy landscape of the chromophore, we also observed a unique dynamic spectral tuning in the far-red-absorbing state and an apparent dynamic Stokes shift in the orange-absorbing state in the femtosecond-resolved fluorescence spectra. We found that the isomerization reactions in both states occur within 320-400 ps. The observed correlation of the local relaxation and the phycocyanobilin twisting can be critical to the subsequent conformational changes after isomerization through the conical intersection to reach the final biological functions. Understanding of the time scales of the local relaxations and isomerization reactions is important to guide the design and engineering of phycocyanobilin-based light-sensitive systems of desired optical properties via synthetic biology.

Probing the Degree of Restriction in Solvent Dynamics at the Interface of a Protein-RNA Complex

Protein-RNA complexation is an important step for the regulation of numerous biological processes. Water present at the interface of a protein-RNA complex plays a critical role in guiding its structure, stability, and function. Therefore, studying the microscopic properties of interfacial water is essential to gain molecular insights into the formation of such complexes. In this study, we present results obtained from molecular dynamics (MD) simulations of poly(A)-binding protein (PABP) bound with poly(A) RNA, which is an essential regulatory step to control the deadenylation process, thereby stabilizing cellular mRNAs from degradation. Efforts have been made to explore how such complexation alters the regular dynamical and hydrogen bond properties of water present at the interface. The calculations revealed restricted water dynamics at the interface, characterized by heterogeneous time scales, with the extent of restriction being more pronounced for residues directly involved in protein-RNA binding. In particular, water molecules around the protein's linker, RRM2, and the RNA strand exhibit significantly more restricted motion compared to RRM1 upon complexation. Further, longer relaxation times of hydrogen bonds at the interface due to complex formation have been found to be correlated with increasingly restricted water motions. Notably, the kinetics of hydrogen bonds around the protein's linker, RRM2, and the RNA strand are more strongly influenced by complex formation, underscoring their critical role in mediating protein-RNA interactions.

Elucidating the microscopic properties of a β-barrel protein and the solvent confined in and around it

Intracellular lipid binding proteins (iLBPs) possess different characteristics, including a rigid protein structure consisting of a β-barrel, an α-helix cap, and a substantial internalized water cluster. Despite X-ray crystallographic research providing insights into the three-dimensional structures of iLBPs, the protein conformations, and the function of the internal water molecules inside the protein remain uncertain. In this study, we conducted molecular dynamics (MD) simulations on free (apo) and oleate-bound (holo) rat liver fatty acid binding proteins (rLFABPs), which are common intracellular lipid binding proteins (iLBPs) found in the liver of rats. Efforts have been made to obtain a comprehensive microscopic understanding of the conformational motions of different segments of the protein, namely, the β-strands, the helix-turn-helix (HTH) motif, and the loop regions, along with the impact of ligand binding on the microscopic structure and ordering of water molecules confined within the core and at the exterior surface of the protein. The calculations revealed fluctuating nature of the HTH region, characterized by the development and disruption of distinct secondary structural components. Furthermore, the coexistence of spatially heterogeneous ordered and disordered water molecules within the core regions of the apo and holo forms has been observed. A high degree of ordering of core water molecules has been attributed to those that are doubly coordinated. In contrast, the randomly oriented ones are found to be surrounded by three neighboring water molecules in their first coordination shells. Such non-uniform ordering of core water molecules suggests their important role in the ligand binding process for this class of proteins.

Hyperspectral Metachip-Based 3D Spatial Map for Cancer Cell Screening and Quantification

In this paper, compact terahertz (THz) metachips for hyperspectral screening and quantitative evaluation of human cancer cells is reported. This pixelated resonant metachips feature the resonance channel from 1 and 3 THz frequency with a record-high quality factor (up to 230). Through the interactions of various cancer cells of different concentrations, high-dimensional spectral signatures are obtained, which are further transformed into a spatial map for labelling and quantification purposes. The screening of up to 15 cancer cells is experimentally reported, with very high detecting accuracy of 93.33% and with attractive quantitative concentration sensitivity up to 1320 kHz cell mL-1. This hyperspectral metachips are low-cost, highly compact, and label-free for fast, high-throughput and high-sensitivity detections and evaluation of human cancer cells. This technology does not require clinical experience, representing an accessible technology for early diagnosis of cancer.

The role of water in mediating DNA structures with epigenetic modifications, higher-order conformations and drug-DNA interactions

Water is arguably one of the most important chemicals essential for the functioning of biological molecules. In the context of DNA, it plays a crucial role in stabilizing and modulating its structure and function. The discovery of water-bound motifs in crystal structures has greatly improved our understanding of the interactions between structured water molecules and DNA. In this manuscript, we review the role of water in mediating biologically relevant DNA structures, in particular those arising from epigenetic modifications and higher-order structures such as G-quadruplexes and i-motifs. We also examine water-mediated interactions between DNA and various small molecules, including groove binders and intercalators, and emphasize their importance for DNA function and therapeutic development. Finally, we discuss recent advances in tools and techniques for predicting water interactions in nucleic acid structures. By offering a fresh perspective on the role of water, this review underscores its importance as a molecular modulator of DNA structure and function.

Protein Crowding Effects on Hydration Water Dynamics

We propose a time-resolved optical Kerr effect study of the structural and vibrational dynamics of the hydration water surrounding the lysozyme on a very fast time scale. Measurements as a function of lysozyme concentration make it possible to distinguish the hydration water contribution from that of both the bulk water and the protein. Our results provide experimental evidence of the existence of two structural dynamics of hydration water, associated with a hydrogen bond exchange relaxation process and with the reorganization of water molecules induced by protein structural fluctuations. Likewise, we evaluated the vibrational dynamics of the water hydration layer at subpicosecond time scales. Our measurements of hydration water properties reveal the presence of a crossover point at a specific protein concentration. This crossover marks the transition between two clustering regimes with distinct hydration characteristics and establishes a possible threshold for protein crowding.

Multi-Site Red-Edge Excitation Shift Reveals the Residue-Specific Solvation Dynamics during the Native to Amyloid-like Transition of an Amyloidogenic Protein

Changes in water-protein interactions are crucial for proteins to achieve functional and nonfunctional conformations during structural transitions by modulating local stability. Amyloid-like protein aggregates in deteriorating neurons are hallmarks of neurodegenerative disorders. These aggregates form through significant structural changes, transitioning from functional native conformations to supramolecular cross-β-sheet structures via misfolded and oligomeric intermediates in a multistep process. However, the site-specific dynamics of water molecules from the native to misfolded conformations and further to oligomeric and compact amyloid structures remain poorly understood. In this study, we used the fluorescence method known as red-edge excitation shift (REES) to investigate the solvation dynamics at specific sites in various equilibrium conformations en route to the misfolding and aggregation of the functional domain of the TDP-43 protein (TDP-43tRRM). We generated three single tryptophan-single cysteine mutants of TDP-43tRRM, with the cysteines at different positions and tryptophan at a fixed position. Each sole cysteine was fluorescently labeled and used as a site-specific fluorophore along with the single tryptophan, creating four monitorable sites for REES studies. By investigating the site-specific extent of REES, we developed a residue-specific solvation dynamics map of TDP-43tRRM during its misfolding and aggregation. Our observations revealed that solvation dynamics progressively became more rigid and heterogeneous to varying extents at different sites during the transition from native to amyloid-like conformations.

Critical Role of Water beyond the Media to Maintain Protein Stability and Activity in Hydrated Deep Eutectic Solvent

Hydrated deep eutectic solvents (DESs) are recognized for their potential in biocatalysis due to their tunability, biocompatibility, greenness, and ability to keep protein stable and active. However, the mechanisms governing enzyme stability and activity in DES remain poorly understood. Herein, using bromelain as the model enzyme and acetamide (0.5)/urea(0.3)/sorbitol(0.2) as the model DES, we provide experimental evidence that modulation of associated water plays a key role in dictating protein stability and activity in hydrated DES. Specifically, rigid associated water at higher DES concentrations (beyond 40% v/v) stabilizes bromelain through entropy but destabilizes it through enthalpy. On the other hand, flexible associated water dynamics at lower DES concentrations result in an opposite thermodynamic outcome. Importantly, the bulk water dynamics cannot explain the stability trend, which emphasizes the critical role of water near the protein surface. Strikingly, associated water dynamics also correlates strongly with bromelain's proteolytic activity. An increasing flexibility of the associated water dynamics leads to the enhancement of the activity. This is the first study to experimentally link associated water dynamics to enzyme behavior in hydrated DES, offering insights that could guide future developments in solvent engineering for enzyme catalysis.

Unveiling the Effect of Myo-inositol on Primitive Cell Models Derived from Fatty Acid

Early forms of life on Earth were most likely not complex. Simple non-living molecules may have formed aggregates, orunderwent spontaneous complex organic reactions resulting in build-up of molecular complexity leading to origin of life. Protocell (hypothetical first live cell) models based on fatty acid self-assemblies have been used in many experiments. Sugars, amino acids and nucleic acids are the backbone of any living creature. Myo-inositol (InOH), is structurally similar to pyranose form of d-glucose. InOH not only has higher stability than simple sugars, but also not easily degraded under extreme conditions. Therefore, InOH would have persisted in the hostile environment of early Earth. Here, our objective is to study the effect of varying concentrations of InOH, a prebiotic sugar-like biomolecule, on the self-assemblies derived from oleic acid using solvation dynamics as a major experimental tool. We have demonstrated that InOH does indeed perturb the membrane of oleic acid/oleate vesicles, which is characterized by more negative zeta potential of vesicles, and faster solvation dynamics of the solvation probe C153. Overall, our results provide significant insight towards understanding the role of carbohydrate osmolytes in relation to protocell models.

Hidden water's influence on rhodopsin activation

Structural biology relies on several powerful techniques, but these tend to be limited in their ability to characterize protein fluctuations and mobility. Overreliance on structural approaches can lead to omission of critical information regarding biological function. Currently there is a need for complementary biophysical methods to visualize these mobile aspects of protein function. Here, we review hydrostatic and osmotic pressure-based techniques to address this shortcoming for the paradigm of rhodopsin. Hydrostatic and osmotic pressure data contribute important examples, which are interpreted in terms of an energy landscape for hydration-mediated protein dynamics. We find that perturbations of rhodopsin conformational equilibria by force-based methods are not unrelated phenomena; rather they probe various hydration states involving functional proton reactions. Hydrostatic pressure acts on small numbers of strongly interacting structural or solvent-shell water molecules with relatively high energies, while osmotic pressure acts on large numbers of weakly interacting bulk-like water molecules with low energies. Local solvent fluctuations due to the hydration shell and collective water interactions affect hydrogen-bonded networks and domain motions that are explained by a hierarchical energy landscape model for protein dynamics.

Progress of the Impact of Terahertz Radiation on Ion Channel Kinetics in Neuronal Cells

In neurons and myocytes, selective ion channels in the plasma membrane play a pivotal role in transducing chemical or sensory stimuli into electrical signals, underpinning neural and cardiac functionality. Recent advancements in biomedical research have increasingly spotlighted the interaction between ion channels and electromagnetic fields, especially terahertz (THz) radiation. This review synthesizes current findings on the impact of THz radiation, known for its deep penetration and non-ionizing properties, on ion channel kinetics and membrane fluid dynamics. It is organized into three parts: the biophysical effects of THz exposure on cells, the specific modulation of ion channels by THz radiation, and the potential pathophysiological consequences of THz exposure. Understanding the biophysical mechanisms underlying these effects could lead to new therapeutic strategies for diseases.

Macromolecular crowding effects on protein dynamics

Macromolecular crowding experiments bridge the gap between in-vivo and in-vitro studies by mimicking some of the cellular complexities like high viscosity and limited space, while still manageable for experiments and analysis. Macromolecular crowding impacts all biological processes and is a focus of contemporary research. Recent reviews have highlighted the effect of crowding on various protein properties. One of the essential characteristics of protein is its dynamic nature; however, how protein dynamics get modulated in the crowded milieu has been largely ignored. This article discusses how protein translational, rotational, conformational, and solvation dynamics change under crowded conditions, summarizing key observations in the literature. We emphasize our research on microsecond conformational and water dynamics in crowded milieus and their impact on enzymatic activity and stability. Lastly, we provided our outlook on how this field might move forward in the future.

Tutorial Review on the Set-Up and Running of Quantum Mechanical Cluster Models for Enzymatic Reaction Mechanisms

Enzymes turnover substrates into products with amazing efficiency and selectivity and as such have great potential for use in biotechnology and pharmaceutical applications. However, details of their catalytic cycles and the origins surrounding the regio- and chemoselectivity of enzymatic reaction processes remain unknown, which makes the engineering of enzymes and their use in biotechnology challenging. Computational modelling can assist experimental work in the field and establish the factors that influence the reaction rates and the product distributions. A popular approach in modelling is the use of quantum mechanical cluster models of enzymes that take the first- and second coordination sphere of the enzyme active site into consideration. These QM cluster models are widely applied but often the results obtained are dependent on model choice and model selection. Herein, we show that QM cluster models can give highly accurate results that reproduce experimental product distributions and free energies of activation within several kcal mol-1, regarded that large cluster models with >300 atoms are used that include key hydrogen bonding interactions and charged residues. In this tutorial review, we give general guidelines on the set-up and applications of the QM cluster method and discuss its accuracy and reproducibility. Finally, several representative QM cluster model examples on metal-containing enzymes are presented, which highlight the strength of the approach.

Comparative Bindings of Glycosaminoglycans with CXCL8 Monomer and Dimer: Insights from Conformational Dynamics and Kinetics of Hydrogen Bonds

GAGs bind to both the monomeric and dimeric forms of CXCL8, helping to form a concentration gradient of the chemokine that facilitates the recruitment of neutrophils to an injury site and supports other biological functions. In this study, atomistic molecular dynamics simulations were conducted to investigate the binding behavior of two hexameric GAGs sulfated at two different positions, chondroitin sulfate (CS) and heparan sulfate (HS), with the monomer (SIL8) and dimer (DIL8) forms of the CXCL8 protein. The results support that the conformational diversity of CS and HS appeared to be more when binding with monomer SIL8 than dimer DIL8. CS gained more configurational entropy from glycosidic linkage flexibility when bound to SIL8 than DIL8, with a higher energy barrier, whereas HS exhibited a lower energy barrier for configurational entropy when bound to SIL8 and DIL8. The monomer SIL8 exhibited more favorable and preferential binding with GAGs compared to DIL8. Formation of hydrogen bonds with the basic amino acids of SIL8 and GAG was more rigid and required higher activation energy to break than the other identified hydrogen bondings. Water molecules involved in hydrogen bonding with GAGs, excluding those with basic amino acids of DIL8, showed longer lifetimes and slower relaxation compared to SIL8. This suggests that water-mediated interactions also favor binding of DIL8 with GAGs. Despite having more basic amino acids, DIL8 did not display stronger binding than SIL8, indicating the significant role of basic residues in stabilizing the GAG-protein interactions in the monomers. The reason could be that the greater number of nonbasic amino acids in dimeric CXCL8 stabilizes the complex by forming water-mediated hydrogen bonds, reducing the conformational preferences for binding with GAGs. In contrast, the monomeric form of CXCL8 exhibits a higher conformational preference for protein-GAG interactions.

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.

Insights into dynamic properties of water in lipidic cubic phases by 2D nuclear Overhauser effect (NOE) NMR spectroscopy

Two-dimensional NOE (nuclear Overhauser effect) NMR spectroscopy was employed to investigate the dynamic properties of water within lyotropic bicontinuous lipidic cubic phases (LCPs) formed by monoolein (MO). Experiments observed categorically different effective residence times of water molecules: (i) in proximity to the glycerol moiety of MO, and (ii) adjacent to the hydrophobic chain towards the hydrocarbon tail of MO, as evidenced by the opposite signs of intermolecular NOE cross peaks between protons of water and those of MO in 2D 1H-1H NOESY spectra. Spectroscopic data delineating the different effective residence times of water molecules within both the gyroid (QIIG) and diamond (QIID) phase groups corresponding to hydration levels of 35 and 40 wt%, respectively, are presented. Additionally, an increase in effective residence time of water molecules in proximity to the glycerol moiety of MO in LCPs was observed upon storage at ambient temperature and in the presence of an additive lipid, cholesterol. Atom-specific NOE build-up curves for protons of water and those of MO are also given. The results presented herein provide new insight into the physicochemical properties and behaviour of water in LCPs, and demonstrate an additional avenue for experimental study of water-lipid interactions and hydration dynamics in model membranes and nanomaterials using 2D NOE NMR spectroscopy.

Insight from Boric Acid into Bioskeleton Formation: Inscribed Circle Effect on the Edge-Base Plate Growth

Complex morphologies in nature often arise from the assembly of elemental building blocks, leading to diverse and intricate structures. Understanding the mechanisms that govern the formation of these complex morphologies remains a significant challenge. In particular, the edge-base plate growth of biogenic crystals plays a crucial role in directing the development of intricate bioskeleton morphologies. However, the factors and regulatory processes that govern edge-base plate growth remain insufficiently understood. Inspired by biological skeletons and based on the soluble property of boric acid (BA) in both water and alcohols, we obtained a series of novel BA morphologies, including coccolith, and anemone biological skeletons. Here, we unveil the "inscribed circle effect", a concise mathematical model that reveals the underlying causative factors and regulatory mechanisms driving edge-base plate growth. Our findings illuminate how variations in solvent environments can exert control over the edge-base plate growth pathways, thereby resulting in the formation of diverse and complex morphologies. This understanding holds significant potential for guiding the chemical synthesis of bioskeleton materials.

Modeling of the Hydrogen Bond-Induced Frequency Shifts of the HOH and HOD Bending Modes of Water

The intramolecular bending mode of water is a possible useful probe of the hydrogen-bond situations in aqueous systems, but the behavior of its frequency and intensity should be further elucidated for better understanding on its nature and, hence, for its better utilization as a probe. Here, an analysis toward this goal is conducted by doing theoretical calculations on molecular clusters of normal isotopic and deuterated species of water and examining the correlations among the vibrational, structural, and electrostatic properties. It is shown that electrostatic interactions, particularly both of the in-plane components of the electric field along the OH bond and perpendicular to it, play a major role in controlling the hydrogen bond-induced shifts of the force constant, but additional factors, including the intermolecular structural and/or charge-transfer properties, are also important. Models of the hydrogen bond-induced shifts of the force constant are presented in a form that may be combined with classical molecular dynamics. With regard to the infrared intensity changes, it is shown on the basis of the electron density analysis that the intermolecular charge flux and polarization effect play an important role, depending on the angular characteristics of the hydrogen bond.

Spontaneous Curvature Induction in an Artificial Bilayer Membrane

Maintaining lipid asymmetry across membrane leaflets is critical for functions like vesicular traffic and organelle homeostasis. However, a lack of molecular-level understanding of the mechanisms underlying membrane fission and fusion processes in synthetic systems precludes their development as artificial analogs. Here, we report asymmetry induction of a bilayer membrane formed by an extended π-conjugated molecule with oxyalkylene side chains bearing terminal tertiary amine moieties (BA1) in water. Autogenous protonation of the tertiary amines in the periphery of the bilayer by water induces anisotropic curvature, resulting in membrane fission to form vesicles and can be monitored using time-dependent spectroscopy and microscopy. Interestingly, upon loss of the induced asymmetry by extensive protonation using an organic acid restored bilayer membrane. The mechanism leading to the compositional asymmetry in the leaflet and curvature induction in the membrane is validated by density functional theory (DFT) calculations. Studies extended to control molecules having changes in hydrophilic (BA2) and hydrophobic (BA3) segments provide insight into the delicate nature of molecular scale interactions in the dynamic transformation of supramolecular structures. The synergic effect of hydrophobic interaction and the hydrated state of BA1 aggregates provide dynamicity and unusual stability. Our study unveils mechanistic insight into the dynamic transformation of bilayer membranes into vesicles.

Molecular Origin of Distinct Hydration Dynamics in Double Helical DNA and RNA Sequences

Water molecules are essential to determine the structure of nucleic acids and mediate their interactions with other biomolecules. Here, we characterize the hydration dynamics of analogous DNA and RNA double helices with unprecedented resolution and elucidate the molecular origin of their differences: first, the localization of the slowest hydration water molecules─in the minor groove in DNA, next to phosphates in RNA─and second, the markedly distinct hydration dynamics of the two phosphate oxygen atoms OR and OS in RNA. Using our Extended Jump Model for water reorientation, we assess the relative importance of previously proposed factors, including the local topography, water bridges, and the presence of ions. We show that the slow hydration dynamics at RNA OR sites is not due to bridging water molecules but is caused by both the larger excluded volume and the stronger initial H-bond next to OR, due to the different phosphate orientations in A-form double helical RNA.

Formation of H-bonding networks in the solid state structure of a trinuclear cobalt(iii/ii/iii) complex with N2O2 donor Schiff base ligand and glutaric acid as bridging co-ligand: synthesis, structure and DFT study

A trinuclear linear mixed-valence centrosymmetric cobalt(iii)-cobalt(ii)-cobalt(iii) complex, [CoII{(μ-L)(μ-Hglu)CoIII(OH2)}2](ClO4)2·6H2O has been synthesized during tetradentate N2O2 donor 'Schiff base' ligand, H2L {N,N'-bis(salicylidene)-1,3-diaminopropane} and glutaric acid (H2glu) as anionic co-ligand. The complex has been characterized by spectroscopic measurements and its solid state structure has been determined by single crystal X-ray diffraction analysis. The supra-molecular assembly formed by the hydrogen bonding interactions in the solid state of the complex has been analysed using DFT calculations.

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.

The elementary reactions for incorporation into crystals

The growth rates of crystals are largely dictated by the chemical reaction between solute and kinks, in which a solute molecule severs its bonds with the solvent and establishes new bonds with the kink. Details on this sequence of bond breaking and rebuilding remain poorly understood. To elucidate the reaction at the kinks we employ four solvents with distinct functionalities as reporters on the microscopic structures and their dynamics along the pathway into a kink. We combine time-resolved in situ atomic force microscopy and x-ray and optical methods with molecular dynamics simulations. We demonstrate that in all four solvents the solute, etioporphyrin I, molecules reach the steps directly from the solution; this finding identifies the measured rate constant for step growth as the rate constant of the reaction between a solute molecule and a kink. We show that the binding of a solute molecule to a kink divides into two elementary reactions. First, the incoming solute molecule sheds a fraction of its solvent shell and attaches to molecules from the kink by bonds distinct from those in its fully incorporated state. In the second step, the solute breaks these initial bonds and relocates to the kink. The strength of the preliminary bonds with the kink determines the free energy barrier for incorporation into a kink. The presence of an intermediate state, whose stability is controlled by solvents and additives, may illuminate how minor solution components guide the construction of elaborate crystal architectures in nature and the search for solution compositions that suppress undesirable or accelerate favored crystallization in industry.

Bridging Soft Interaction and Excluded Volume in Crowded Milieu through Subtle Protein Dynamics

The impact of macromolecular crowding on biological macromolecules has been elucidated through the excluded volume phenomenon and soft interactions. However, it has often been difficult to provide a clear demarcation between the two regions. Here, using temperature-dependent dynamics (local and global) of the multidomain protein human serum albumin (HSA) in the presence of commonly used synthetic crowders (Dextran 40, PEG 8, Ficoll 70, and Dextran 70), we have shown the presence of a transition that serves as a bridge between the soft and hard regimes. The bridging region is independent of the crowder identity and displays no apparent correlation with the critical overlap concentration of the polymeric crowding agents. Moreover, the dynamics of domains I and II and the protein gating motion respond differently, thereby bringing to the fore the asymmetry underlying the crowder influence on HSA. In addition, solvent-coupled and decoupled protein motions indicate the heterogeneity of the dynamic landscape in the crowded milieu. We also propose an intriguing correlation between protein stability and dynamics, with increased global stability being accompanied by eased local domain motion.

Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data

Biological macromolecules in solution are surrounded by a hydration shell, whose structure differs from the structure of bulk solvent. While the importance of the hydration shell for numerous biological functions is widely acknowledged, it remains unknown how the hydration shell is regulated by macromolecular shape and surface composition, mainly because a quantitative probe of the hydration shell structure has been missing. We show that small-angle scattering in solution using X-rays (SAXS) or neutrons (SANS) provide a protein-specific probe of the protein hydration shell that enables quantitative comparison with molecular simulations. Using explicit-solvent SAXS/SANS predictions, we derived the effect of the hydration shell on the radii of gyration Rg of five proteins using 18 combinations of protein force field and water model. By comparing computed Rg values from SAXS relative to SANS in D2O with consensus SAXS/SANS data from a recent worldwide community effort, we found that several but not all force fields yield a hydration shell contrast in remarkable agreement with experiments. The hydration shell contrast captured by Rg values depends strongly on protein charge and geometric shape, thus providing a protein-specific footprint of protein-water interactions and a novel observable for scrutinizing atomistic hydration shell models against experimental data.

Cellular dynamics as a marker of normal-to-cancer transition in human cells

Normal-to-cancer (NTC) transition is known to be closely associated to cell´s biomechanical properties which are dependent on the dynamics of the intracellular medium. This study probes different human cancer cells (breast, prostate and lung), concomitantly to their healthy counterparts, aiming at characterising the dynamical profile of water in distinct cellular locations, for each type of cell, and how it changes between normal and cancer states. An increased plasticity of the cytomatrix is observed upon normal-to-malignant transformation, the lung carcinoma cells displaying the highest flexibility followed by prostate and breast cancers. Also, lung cells show a distinct behaviour relative to breast and prostate, with a higher influence from hydration water motions and localised fast rotations upon NTC transformation. Quasielastic neutron scattering techniques allowed to accurately distinguish the different dynamical processes taking place within these highly heterogeneous cellular systems. The results thus obtained suggest that intracellular water dynamics may be regarded as a specific reporter of the cellular conditions-either healthy or malignant.

Water molecule ordering on the surface of an intrinsically disordered protein

The dynamics and local structure of the hydration water on surfaces of folded proteins have been extensively investigated. However, our knowledge of the hydration of intrinsically disordered proteins (IDPs) is more limited. Here, we compare the local structure of water molecules hydrating a globular protein, lysozyme, and the intrinsically disordered N-terminal of c-Src kinase (SH4UD) using molecular dynamics simulation. The radial distributions from the protein surface of the first and the second hydration shells are similar for the folded protein and the IDP. However, water molecules in the first hydration shell of both the folded protein and the IDP are perturbed from the bulk. This perturbation involves a loss of tetrahedrality, which is, however, significantly more marked for the folded protein than the IDP. This difference arises from an increase in the first hydration shell of the IDP of the fraction of hydration water molecules interacting with oxygen. The water ordering is independent of the compactness of the IDP. In contrast, the lifetimes of water molecules in the first hydration shell increase with IDP compactness, indicating a significant impact of IDP configuration on water surface pocket kinetics, which here is linked to differential pocket volumes and polarities.

Terahertz Spectroscopy of Aqueous Solutions of Sodium Halides (NaX): Self- and Cross-Correlation Contributions of Ions and Hydration Shell Water for X- = F-, Cl-, Br-, and I. J Phys Chem B 2023;127:9323-9335. [PMID: 37871257 DOI: 10.1021/acs.jpcb.3c05228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

We investigated the terahertz (THz) absorption spectra of aqueous sodium halide solutions through molecular dynamics simulations using polarizable models of both water and ions. Specifically, we have considered aqueous solutions (∼1 M) of NaF, NaCl, NaBr, and NaI and calculated the difference THz spectrum of these solutions by subtracting the corresponding pure water contribution from the total THz spectrum of an ionic solution. The difference absorption spectrum of a given solution is then dissected into contributions from ion and ion-water correlations and also modifications of water-water correlations in the presence of the ions. The different components are further decomposed into induced dipole and permanent charge/dipole components and also into self- and cross-correlation components. The ion-water cross-correlation components are subsequently decomposed into contributions coming from different solvation shells through radially resolved calculations of such ion-water cross-correlations. Through all of these dissections, we could investigate the origin of different parts of the difference THz spectra of the sodium halide solutions studied here. It is found that while features below or around 100 cm-1 and also around 200 cm-1 arise mainly from ion and ion-water motion, that at the librational region above 600 cm-1 primarily originates from changes in water librational motion influenced by the ions. The variations of intensities of different components are also linked to the size and charge density of the anions in the solutions.

Contrasting Changes in Strongly and Weakly Bound Hydration Water of a Protein upon Denaturation

Water is considered integral for the stabilization and function of proteins, which has recently attracted significant attention. However, the microscopic aspects of water ranging up to the second hydration shell, including strongly and weakly bound water at the sub-nanometer scale, are not yet well understood. Here, we combined terahertz spectroscopy, thermal measurements, and infrared spectroscopy to clarify how the strongly and weakly bound hydration water changes upon protein denaturation. With denaturation, that is, the exposure of hydrophobic groups in water and entanglement of hydrophilic groups, the number of strongly bound hydration water decreased, while the number of weakly bound hydration water increased. Even though the constraint of water due to hydrophobic hydration is weak, it extends to the second hydration shell as it is caused by the strengthening of hydrogen bonds between water molecules, which is likely the key microscopic mechanism for the destabilization of the native state due to hydration.

Ultrafast Förster resonance energy transfer from tyrosine to tryptophan in monellin: potential intrinsic spectroscopic ruler

Ultrafast Förster Resonance Energy Transfer (FRET) between tyrosine (Tyr) and tryptophan (Trp) residues in the protein monellin has been investigated using picosecond and femtosecond time-resolved fluorescence spectroscopy. Decay associated spectra (DAS) and time-resolved emission spectra (TRES) taken with the different excitation wavelengths of 275, 290 and 295 nm were constructed via global analysis. At two of those three excitation loci (275 and 290 nm), earmarks of energy transfer from Tyr to Trp in monellin are seen, and particularly when the excitation is 275 nm, the energy transfer between Tyr and Trp clearly changes the signature emission DAS shape to that indicating excited state reaction (especially on the red side of fluorescence emission, near 380 nm). Those FRET signatures may overlap with the conventional signatory DAS in heterogeneous systems. When overlap and addition occur between FRET type DAS and "full positive" QSSQ (quasi-static self-quenching), mixed DAS shapes will emerge that still show "positive blue side and negative red sides", just with zero crossing shifted. In addition, excitation decay associated spectra (EDAS) taken with the different emission wavelengths of 330, 350 and 370 nm were constructed. In the study of protein dynamics, ultrafast FRET between Tyr and Trp could provide a basis for an intrinsic (non-perturbing) "spectroscopic ruler", potentially a powerful tool to detect even slight changes in protein structures.

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

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

Controlling Water Delivery to an Electrochemical Interface with Surfactants

Most electrochemical reactions require delivery of protons, often from water, to surface-adsorbed species. However, water also acts as a competitor to many such processes by directly reacting with the electrode, which necessitates using water in small amounts. Controlling the water content and structure near the surface is an important frontier in directing the reactivity and selectivity of electrochemical reactions. Surfactants accumulate near surfaces, and therefore, they can be used as agents to control interfacial water. Using mid-IR spectro-electrochemistry, we show that a modest concentration (1 mM) of the cationic surfactant CTAB in mixtures of 10 M water in an organic solvent (dDMSO) has a large effect on the interfacial water concentration, changing it by up to ∼35% in the presence of an applied potential. The major cause of water content change is displacement due to the accumulation or depletion of surfactants driven by potential. Two forces drive the surfactants to the electrode: the applied potential and the hydrophobic interactions with the water in the bulk. We have quantified their competition by varying the water content in the bulk. To our knowledge, for the first time, we have identified the electrochemical equivalent of the hydrophobic drive. For our system, a change in applied potential of 1 V has the same effect as adding a 0.55 mole fraction of water to the bulk. This work illustrates the significance of surfactants in the partitioning of water between the bulk and the surface and paves the way toward engineering interfacial water structures for controlling electrochemical reactions.

Theory of Protein Charge Transfer: Electron Transfer between Tryptophan Residue and Active Site of Azurin

One reaction step in the conductivity relay of azurin, electron transfer between the Cu-based active site and the tryptophan residue, is studied theoretically and by classical molecular dynamics simulations. Oxidation of tryptophan results in electrowetting of this residue. This structural change makes the free energy surfaces of electron transfer nonparabolic as described by the Q-model of electron transfer. We analyze the medium dynamical effect on protein electron transfer produced by coupled Stokes-shift dynamics and the dynamics of the donor-acceptor distance modulating electron tunneling. The equilibrium donor-acceptor distance falls in the plateau region of the rate constant, where it is determined by the protein-water dynamics, and the probability of electron tunneling does not affect the rate. The crossover distance found here puts most intraprotein electron-transfer reactions under the umbrella of dynamical control. The crossover between the medium-controlled and tunneling-controlled kinetics is combined with the effect of the protein-water medium on the activation barrier to formulate principles of tunability of protein-based charge-transfer chains. The main principle in optimizing the activation barrier is the departure from the Gaussian-Gibbsian statistics of fluctuations promoting activated transitions. This is achieved either by incomplete (nonergodic) sampling, breaking the link between the Stokes-shift and variance reorganization energies, or through wetting-induced structural changes of the enzyme's active site.

Hydrophobicity of arginine leads to reentrant liquid-liquid phase separation behaviors of arginine-rich proteins

Intrinsically disordered proteins rich in cationic amino acid groups can undergo Liquid-Liquid Phase Separation (LLPS) in the presence of charge-balancing anionic counterparts. Arginine and Lysine are the two most prevalent cationic amino acids in proteins that undergo LLPS, with arginine-rich proteins observed to undergo LLPS more readily than lysine-rich proteins, a feature commonly attributed to arginine's ability to form stronger cation-π interactions with aromatic groups. Here, we show that arginine's ability to promote LLPS is independent of the presence of aromatic partners, and that arginine-rich peptides, but not lysine-rich peptides, display re-entrant phase behavior at high salt concentrations. We further demonstrate that the hydrophobicity of arginine is the determining factor giving rise to the reentrant phase behavior and tunable viscoelastic properties of the dense LLPS phase. Controlling arginine-induced reentrant LLPS behavior using temperature and salt concentration opens avenues for the bioengineering of stress-triggered biological phenomena and drug delivery systems.

A Mechanoelastic Glimpse on Hyaluronan-Coated Extracellular Vesicles

Cancer cells secrete extracellular vesicles (EVs) covered with a carbohydrate polymer, hyaluronan (HA), linked to tumor malignancy. Herein, we have unravelled the contour lengths of HA on a single cancer cell-derived EV surface using single-molecule force spectroscopy (SMFS), which divulges the presence of low molecular weight HA (LMW-HA < 200 kDa). We also discovered that these LMW-HA-EVs are significantly more elastic than the normal cell-derived EVs. This intrinsic elasticity of cancer EVs could be directly allied to the LMW-HA abundance and associated labile water network on EV surface as revealed by correlative SMFS, hydration dynamics with fluorescence spectroscopy, and molecular dynamics simulations. This method emerges as a molecular biosensor of the cancer microenvironment.

Importance of Hydrogen Bonding in Crowded Environments: A Physical Chemistry Perspective

Cells are heterogeneous on every length and time scale; cytosol contains thousands of proteins, lipids, nucleic acids, and small molecules, and molecular interactions within this crowded environment determine the structure, dynamics, and stability of biomolecules. For decades, the effects of crowding at the atomistic scale have been overlooked in favor of more tractable models largely based on thermodynamics. Crowding can affect the conformations and stability of biomolecules by modulating water structure and dynamics within the cell, and these effects are nonlocal and environment dependent. Thus, characterizing water's hydrogen-bond (H-bond) networks is a critical step toward a complete microscopic crowding model. This perspective provides an overview of molecular crowding and describes recent time-resolved spectroscopy approaches investigating H-bond networks and dynamics in crowded or otherwise complex aqueous environments. Ultrafast spectroscopy combined with atomistic simulations has emerged as a powerful combination for studying H-bond structure and dynamics in heterogeneous multicomponent systems. We discuss the ongoing challenges toward developing a complete atomistic description of macromolecular crowding from an experimental as well as a theoretical perspective.

Solvent effects on the NMR shieldings of stacked DNA base pairs

Stacking effects are among the most important effects in DNA. We have recently studied their influence in fragments of DNA through the analysis of NMR magnetic shieldings, firstly in vacuo. As a continuation of this line of research we show here the influence of solvent effects on the shieldings through the application of both explicit and implicit models. We found that the explicit solvent model is more appropriate for consideration due to the results matching better in general with experiments, as well as providing clear knowledge of the electronic origin of the value of the shieldings. Our study is grounded on a recently developed theoretical model of our own, by which we are able to learn about the magnetic effects of given fragments of DNA molecules on selected base pairs. We use the shieldings of the atoms of a central base pair (guanine-cytosine) of a selected fragment of DNA molecules as descriptors of physical effects, like π-stacking and solvent effects. They can be taken separately and altogether. The effect of π-stacking is introduced through the addition of some pairs above and below of the central base pair, and now, the solvent effect is considered including a network of water molecules that consist of two solvation layers, which were fixed in the calculations performed in all fragments. We show that the solvent effects enhance the stacking effects on the magnetic shieldings of atoms that belong to the external N-H bonds. The net effect is of deshielding on both atoms. There is also a deshielding effect on the carbon atoms that belong to CO bonds, for which the oxygen atom has an explicit hydrogen bond (HB) with a solvent water molecule. Solvent effects are found to be no higher than a few percent of the total value of the shieldings (between 1% and 5%) for most atoms, although there are few for which such an effect can be higher. There is one nitrogen atom, the acceptor of the HB between guanine and cytosine, that is more highly shielded (around 15 ppm or 10%) when the explicit solvent is considered. In a similar manner, the most external nitrogen atom of cytosine and the hydrogen atom that is bonded to it are highly deshielded (around 10 ppm for nitrogen and around 3 ppm for hydrogen).

Amyloids Formed by Nonaromatic Amino Acid Methionine and Its Cross with Phenylalanine Significantly Affects Phospholipid Vesicle Membrane: An Insight into Hypermethioninemia Disorder

The incorrect metabolic breakdown of the nonaromatic amino acid methionine (Met) leads to the disorder called hypermethioninemia via an unknown mechanism. To understand the molecular level pathogenesis of this disorder, we prepared a DMPC lipid membrane, the mimicking setup of the cell membrane, and explored the effect of the millimolar level of Met on it. We found that Met forms toxic fibrillar aggregates that disrupt the rigidity of the membrane bilayer, and increases the dynamic response of water molecules surrounding the membrane as well as the heterogeneity of the membrane. Such aggregates strongly deform red blood cells. This opens the requirement to consider therapeutic antagonists either to resist or to inhibit the toxic amyloid aggregates against hypermethioninemia. Moreover, such disrupting effect on membrane bilayer and cytotoxicity along with deformation effect on RBC by the cross amyloids of Met and Phenylalanine (Phe) was found to be most virulent. This exclusive observation of the enhanced virulent effect of the cross amyloids is expected to be an informative asset to explain the coexistence of two amyloid disorders.

Multidimensional insights into the repeated electromagnetic field stimulation and biosystems interaction in aging and age-related diseases

We provide a multidimensional sequence of events that describe the electromagnetic field (EMF) stimulation and biological system interaction. We describe this process from the quantum to the molecular, cellular, and organismal levels. We hypothesized that the sequence of events of these interactions starts with the oscillatory effect of the repeated electromagnetic stimulation (REMFS). These oscillations affect the interfacial water of an RNA causing changes at the quantum and molecular levels that release protons by quantum tunneling. Then protonation of RNA produces conformational changes that allow it to bind and activate Heat Shock Transcription Factor 1 (HSF1). Activated HSF1 binds to the DNA expressing chaperones that help regulate autophagy and degradation of abnormal proteins. This action helps to prevent and treat diseases such as Alzheimer's and Parkinson's disease (PD) by increasing clearance of pathologic proteins. This framework is based on multiple mathematical models, computer simulations, biophysical experiments, and cellular and animal studies. Results of the literature review and our research point towards the capacity of REMFS to manipulate various networks altered in aging (Reale et al. PloS one 9, e104973, 2014), including delay of cellular senescence (Perez et al. 2008, Exp Gerontol 43, 307-316) and reduction in levels of amyloid-β peptides (Aβ) (Perez et al. 2021, Sci Rep 11, 621). Results of these experiments using REMFS at low frequencies can be applied to the treatment of patients with age-related diseases. The use of EMF as a non-invasive therapeutic modality for Alzheimer's disease, specifically, holds promise. It is also necessary to consider the complicated and interconnected genetic and epigenetic effects of the REMFS-biological system's interaction while avoiding any possible adverse effects.

Comparative analysis of hydration layer reorientation dynamics of antifreeze protein and protein cytochrome P450

Antifreeze proteins (AFPs) inhibit ice re-crystallization by a mechanism remaining largely elusive. Dynamics of AFPs’ hydration water and its involvement in the antifreeze activity have not been identified conclusively. We herein, by simulation and theory, examined the water reorientation dynamics in the first hydration layer of an AFP from the spruce budworm, Choristoneura fumiferana, compared with a protein cytochrome P450 (CYP). The increase of potential acceptor water molecules around donor water molecules leads to the acceleration of hydrogen bond exchange between water molecules. Therefore, the jump reorientation of water molecules around the AFP active region is accelerated. Due to the mutual coupling and excitation of hydrogen bond exchange, with the acceleration of hydrogen bond exchange, the rearrangement of the hydrogen bond network and the frame reorientation of water are accelerated. Therefore, the water reorientation dynamics of AFP is faster than that of CYP. The results of this study provide a new physical image of antifreeze protein and a new understanding of the antifreeze mechanism of antifreeze proteins.

Spatiotemporal control of l-phenyl-alanine crystallization in microemulsion: the role of water in mediating molecular self-assembly

Water confined or constrained in a cellular environment can exhibit a diverse structural and dynamical role and hence will affect the self-assembly behavior of biomolecules. Herein, the role of water in the formation of l-phenyl-alanine crystals and amyloid fibrils was investigated. A microemulsion biomimetic system with controllable water pool size was employed to provide a microenvironment with different types of water, which was characterized by small-angle X-ray scattering, attenuated total reflectance-Fourier transform infrared spectroscopy and differential scanning calorimetry. In a bound water environment, only plate-like l-phenyl-alanine crystals and their aggregates were formed, all of which are anhydrous crystal form I. However, when free water dominated, amyloid fibrils were observed. Free water not only stabilizes new oligomers in the initial nucleation stage but also forms bridged hydrogen bonds to induce vertical stacking to form a fibrous structure. The conformational changes of l-phenyl-alanine in different environments were detected by NMR. Different types of water trigger different nucleation and growth pathways, providing a new perspective for understanding molecular self-assembly in nanoconfinement.

Hydration Dynamics of Model Peptides with Different Hydrophobic Character

The multi-scale dynamics of aqueous solutions of the hydrophilic peptide N-acetyl-glycine-methylamide (NAGMA) have been investigated through extended frequency-range depolarized light scattering (EDLS), which enables the broad-band detection of collective polarizability anisotropy fluctuations. The results have been compared to those obtained for N-acetyl-leucinemethylamide (NALMA), an amphiphilic peptide which shares with NAGMA the same polar backbone, but also contains an apolar group. Our study indicates that the two model peptides induce similar effects on the fast translational dynamics of surrounding water. Both systems slow down the mobility of solvating water molecules by a factor 6–8, with respect to the bulk. Moreover, the two peptides cause a comparable far-reaching spatial perturbation extending to more than two hydration layers in diluted conditions. The observed concentration dependence of the hydration number is explained considering the random superposition of different hydration shells, while no indication of solute aggregation phenomena has been found. The results indicate that the effect on the dynamics of water solvating the amphiphilic peptide is dominated by the hydrophilic backbone. The minor impact of the hydrophobic moiety on hydration features is consistent with structural findings derived by Fourier transform infrared (FTIR) measurements, performed in attenuated total reflectance (ATR) configuration. Additionally, we give evidence that, for both systems, the relaxation mode in the GHz frequency range probed by EDLS is related to solute rotational dynamics. The rotation of NALMA occurs at higher timescales, with respect to the rotation of NAGMA; both processes are significantly slower than the structural dynamics of hydration water, suggesting that solute and solvent motions are uncoupled. Finally, our results do not indicate the presence of super-slow water (relaxation times in the order of tens of picoseconds) around the peptides investigated.

Conformational and Solvation Dynamics of an Amyloidogenic Intrinsically Disordered Domain of a Melanosomal Protein

The conformational plasticity of intrinsically disordered proteins (IDPs) allows them to adopt a range of conformational states that can be important for their biological functions. The driving force for the conformational preference of an IDP emanates from an intricate interplay between chain-chain and chain-solvent interactions. Using ultrafast femtosecond and picosecond time-resolved fluorescence measurements, we characterized the conformational and solvation dynamics around the N- and C-terminal segments of a disordered repeat domain of a melanosomal protein Pmel17 that forms functional amyloid responsible for melanin biosynthesis. Our time-resolved fluorescence anisotropy results revealed slight compaction and slower rotational dynamics around the amyloidogenic C-terminal segment when compared to the proline-rich N-terminal segment of the repeat domain. The compaction of the C-terminal region was also associated with the restrained mobility of hydration water as indicated by our solvation dynamics measurements. Our findings indicate that sequence-dependent chain-solvent interactions govern both the conformational and solvation dynamics that are crucial in directing the conversion of a highly dynamic IDP into an ordered amyloid assembly. Such an interplay of amino acid composition-dependent conformational and solvation dynamics might have important physicochemical consequences in specific water-protein, ion-protein, and protein-protein interactions involved in amyloid formation and phase transitions.

Solvent-Dependent Excited-State Evolution of Prodan Dyes

Excited-state character and dynamics of two 6-(dimethylamino)-2-acylnaphthalene dyes (Prodan and Badan-SCH₂CH₂OH) were studied by picosecond time-resolved IR spectroscopy (TRIR) in solvents of different polarity and relaxation times: hexane, CD₃OD, and glycerol-d₈. In all these solvents, near-UV excitation initially produced the same S₁(ππ*) excited state characterized by a broad TRIR signal. A very fast decay (3, ∼100 ps) followed in hexane, whereas conversion to a distinct IR spectrum with a ν(C═O) band downshifted by 76 cm^-1 occurred in polar/H-bonding solvents, slowing down on going from CD₃OD (1, 23 ps) to glycerol-d₈ (5.5, 51, 330 ps). The final relaxed excited state was assigned as planar Me₂N → C═O intramolecular charge transfer S₁(ICT) by comparing experimental and TDDFT-calculated spectra. TRIR conversion kinetics are comparable to those of early stages of multiexponential fluorescence decay and dynamic fluorescence red-shift. This work presents a strong evidence that Prodan-type dyes undergo solvation-driven charge separation in their S₁ state, which is responsible for the dynamic fluorescence Stokes shift observed in polar/H-bonding solvents. The time evolution of the optically prepared S₁(ππ*) state to the S₁(ICT) final state reflects environment relaxation and solvation dynamics. This finding rationalizes the widespread use of Prodan-type dyes as probes of environment dynamics and polarity.

The Dietary Nutrient Trimethylamine N-Oxide Affects the Phospholipid Vesicle Membrane: Probable Route to Adverse Intake

Trimethylamine N-oxide (TMAO), a choline-containing dietary supplement obtained from red meat, egg, and other animal resources, on excess accumulation is known to cause cardiovascular diseases (CVDs) like atherosclerosis. To understand the molecular mechanism of the pathogenesis of TMAO-induced CVDs, we have set up 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) membrane in water that mimicked the endothelial cell membrane-blood interface of the artery wall and investigated the effect of an elevated concentration of TMAO on the membrane. We found that TMAO exerts an "action at a distance" mechanism through electrostatic force of attraction that significantly alters various properties of the membrane, like hydrophobicity, lateral organization, and interfacial water dynamics, which elevates the rigidity of the membrane. Such an effect was found to be further amplified in the presence of known causes of CVDs, i.e., high content of cholesterol (Chol). Therefore, TMAO-induced membrane rigidity may restrict the intrinsic elasticity of an artery membrane, expected to be introducing "hardening of the arteries", which makes the membrane atherosclerotic.

The mutual interactions of RNA, counterions and water - quantifying the electrostatics at the phosphate-water interface

The structure and dynamics of polyanionic biomolecules, like RNA, are decisively determined by their electric interactions with the water molecules and the counterions in the environment. The solvation dynamics of the biomolecules involves a subtle balance of non-covalent and many-body interactions with structural fluctuations due to thermal motion occurring in a femto- to subnanosecond time range. This complex fluctuating many particle scenario is crucial in defining the properties of biological interfaces with far reaching significance for the folding of RNA structures and for facilitating RNA-protein interactions. Given the inherent complexity, suited model systems, carefully calibrated and benchmarked by experiments, are required to quantify the relevant interactions of RNA with the aqueous environment. In this feature article we summarize our recent progress in the understanding of the electrostatics at the biological interface of double stranded RNA (dsRNA) and transfer RNA (tRNA). Dimethyl phosphate (DMP) is introduced as a viable and rigorously accessible model system allowing the interaction strength with water molecules and counterions, their relevant fluctuation timescales and the spatial reach of interactions to be established. We find strong (up to ≈90 MV cm-1) interfacial electric fields with fluctuations extending up to ≈20 THz and demonstrate how the asymmetric stretching vibration νAS(PO2)- of the polarizable phosphate group can serve as the most sensitive probe for interfacial interactions, establishing a rigorous link between simulations and experiment. The approach allows for the direct interfacial observation of interactions of biologically relevant Mg2+ counterions with phosphate groups in contact pair geometries via the rise of a new absorption band imposed by exchange repulsion interactions at short interatomic distances. The systematic extension to RNA provides microscopic insights into the changes of the hydration structure that accompany the temperature induced melting of the dsRNA double helix and quantify the ionic interactions in the folded tRNA. The results show that pairs of negatively charged phosphate groups and Mg2+ ions represent a key structural feature of RNA embedded in water. They highlight the importance of binding motifs made of contact pairs in the electrostatic stabilization of RNA structures that have a strong impact on the surface potential and enable the fine tuning of the local electrostatic properties which are expected to be relevant for mediating the interactions between biomolecules.