Ultrafast Hydration Dynamics in the Lipidic Cubic Phase: Discrete Water Structures in Nanochannels

Universality in the Structure and Dynamics of Water under Lipidic Mesophase Soft Nanoconfinement

Water under soft nanoconfinement features physical and chemical properties fundamentally different from bulk water; yet, the multitude and specificity of confining systems and geometries mask any of its potentially universal traits. Here, we advance in this quest by resorting to lipidic mesophases as an ideal nanoconfinement system, allowing inspecting the behavior of water under systematic changes in the topological and geometrical properties of the confining medium, without altering the chemical nature of the interfaces. By combining Terahertz absorption spectroscopy experiments and molecular dynamics simulations, we unveil the presence of universal laws governing the physics of nanoconfined water, recapitulating the data collected at varying levels of hydration and nanoconfinement topologies. This geometry-independent universality is evidenced by the existence of master curves characterizing both the structure and dynamics of simulated water as a function of the distance from the lipid-water interface. Based on our theoretical findings, we predict a parameter-free law describing the amount of interfacial water against the structural dimension of the system (i.e., the lattice parameter), which captures both the experimental and numerical results within the same curve, without any fitting. Our results offer insight into the fundamental physics of water under soft nanoconfinement and provide a practical tool for accurately estimating the amount of nonbulk water based on structural experimental data.

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.

Interplay of Hydropathy and Heterogeneous Diffusion in the Molecular Transport within Lamellar Lipid Mesophases

Lipid mesophases are being intensively studied as potential candidates for drug-delivery purposes. Extensive experimental characterization has unveiled a wide palette of release features depending on the nature of the host lipids and of the guest molecule, as well as on the environmental conditions. However, only a few simulation works have addressed the matter, which hampers a solid rationalization of the richness of outcomes observed in experiments. Particularly, to date, there are no theoretical works addressing the impact of hydropathy on the transport of a molecule within lipid mesophases, despite the significant fraction of hydrophobic molecules among currently-available drugs. Similarly, the high heterogeneity of water mobility in the nanoscopic channels within lipid mesophases has also been neglected. To fill this gap, we introduce here a minimal model to account for these features in a lamellar geometry, and systematically study the role played by hydropathy and water-mobility heterogeneity by Brownian-dynamics simulations. We unveil a fine interplay between the presence of free-energy barriers, the affinity of the drug for the lipids, and the reduced mobility of water in determining the net molecular transport. More in general, our work is an instance of how multiscale simulations can be fruitfully employed to assist experiments in release systems based on lipid mesophases.

Slowdown of Water Dynamics from the Top to the Bottom of the GroEL Cavity

The GroE molecular chaperone system is a critical protein machine that assists the folding of substrate proteins in its cavity. Water in the cavity is suspected to play a role in substrate protein folding, but the mechanism is currently unknown. Herein, we report measurements of water dynamics in the equatorial and apical domains of the GroEL cavity in the apo and football states, using site-specific tryptophanyl mutagenesis as an intrinsic optical probe with femtosecond resolution combined with molecular dynamics simulations. We observed clearly different water dynamics in the two domains with a slowdown of the cavity water from the apical to equatorial region in the football state. The results suggest that the GroEL cavity provides a unique water environment that may facilitate substrate protein folding.

Probing n-Octyl α-d-Glycosides Using Deuterated Water in the Lyotropic Phase by Deuterium NMR

The lyotropic phase behavior of four common and easily accessible glycosides, n-octyl α-d-glycosides, namely, α-Glc-OC₈, α-Man-OC₈, α-Gal-OC₈, and α-Xyl-OC₈, was investigated. The presence of normal hexagonal (H_I), bicontinuous cubic (V_I), and lamellar (L_α) phases in α-Glc-OC₈ and α-Man-OC₈ including their phase diagrams in water reported previously was verified by deuterium nuclear magnetic resonance (²H NMR), via monitoring the D₂O spectra. Additionally, the partial binary phase diagrams and the liquid crystal structures formed by α-Gal-OC₈ and α-Xyl-OC₈ in D₂O were constructed and confirmed using small- and wide-angle X-ray scattering and ²H NMR. The average number of bound water molecules (n_b) per headgroup in the L_α phase was determined by the systematic measurement of the quadrupolar splitting of D₂O over a wide range of molar ratio values (glycoside/D₂O), especially at high glucoside composition. The number of bound water molecules bound to the headgroup was found to be around 1.5-2.0 for glucoside, mannoside, and galactoside, all of which possesses four OH groups. In the case of xyloside, which has only three OH groups, the bound water content is ∼2.0. Our findings confirmed that the bound water content of all n-octyl α-d-glycosides studied is lower compared to the number of possible hydrogen bonding sites possibly due to the fact that most of the OH groups are involved in intralayer interaction that holds the lipid assembly together.

Proton-Coupled Electron Transfer in the Aqueous Nanochannels of Lyotropic Liquid Crystals: Interplay of H-Bonding and Polarity Effects

A molecular-level description of the aqueous nanochannels in lyotropic liquid crystals (LLCs) is crucial for their widespread utilization in diverse fields. Herein, the polarity and hydrogen bonding effects of LLC water molecules have been simultaneously explored using a single probe, 4'-N,N-dimethylamino-3-hydroxyflavone (DMA3HF), by the unique multiparametric sensitivity of the excited state proton-coupled electron transfer (PCET) phenomenon. The decreased ESIPT efficiency and the significantly retarded ESIPT dynamics (>20 times) of DMA3HF in the LLC phases suggests the dominant influence of strong hydrogen-bonded solute-solvent complexes that leads to a high activation barrier for ESIPT in the mesophases. The effects of hydrogen bonding on ESIPT have been elucidated by enhanced sampling techniques based on classical MD simulations of DMA3HF in explicit water. ESIPT via an extended hydrogen-bonded water wire is associated with a significantly high ESIPT activation barrier, substantiating the experimentally observed slow ESIPT dynamics inside the LLCs.

Ultrafast Dynamics of Water-Protein Coupled Motions around the Surface of Eye Crystallin

Water dynamics on the protein surface mediate both protein structure and function. However, many questions remain about the role of the protein hydration layers in protein fluctuations and how the dynamics of these layers relate to specific protein properties. The fish eye lens protein γM7-crystallin (γM7) is found in vivo at extremely high concentrations nearing the packing limit, corresponding to only a few water layers between adjacent proteins. In this study, we conducted a site-specific probing of hydration water motions and side-chain dynamics at nine selected sites around the surface of γM7 using a tryptophan scan with femtosecond spectroscopy and NMR nuclear spin relaxation (NSR). We observed correlated fluctuations between hydration water and protein side chains on the time scales of a few picoseconds and hundreds of picoseconds, corresponding to local reorientations and network restructuring, respectively. These motions are heterogeneous over the protein surface and relate to the various steric and chemical properties of the local protein environment. Overall, we found that γM7 has relatively slower water dynamics within the hydration shell than a similar β-sheet protein, which may contribute to the high packing limit of this unique protein.

Peculiar hydrogen bonding behaviour of water molecules inside the aqueous nanochannels of lyotropic liquid crystals

The hydrogen bonding abilities of the LLC water molecules and their effects on intramolecular hydrogen bonds of the target probe molecules.

Soft biomimetic nanoconfinement promotes amorphous water over ice

Water is a ubiquitous liquid with unique physicochemical properties, whose nature has shaped our planet and life as we know it. Water in restricted geometries has different properties than in bulk. Confinement can prevent low-temperature crystallization of the molecules into a hexagonal structure and thus create a state of amorphous water. To understand the survival of life at subzero temperatures, it is essential to elucidate this behaviour in the presence of nanoconfining lipidic membranes. Here we introduce a family of synthetic lipids with designed cyclopropyl modifications in the hydrophobic chains that exhibit unique liquid-crystalline behaviour at low temperature, which enables the maintenance of amorphous water down to ~10 K due to nanoconfinement. The combination of experiments and molecular dynamics simulations unveils a complex lipid-water phase diagram in which bicontinuous cubic and lamellar liquid crystalline phases that contain subzero liquid, glassy or ice water emerge as a competition between the two components, each pushing towards its thermodynamically favoured state.

The human skin as a sub-THz receiver - Does 5G pose a danger to it or not?

In the interaction of microwave radiation and human beings, the skin is traditionally considered as just an absorbing sponge stratum filled with water. In previous works, we showed that this view is flawed when we demonstrated that the coiled portion of the sweat duct in upper skin layer is regarded as a helical antenna in the sub-THz band. Experimentally we showed that the reflectance of the human skin in the sub-THz region depends on the intensity of perspiration, i.e. sweat duct's conductivity, and correlates with levels of human stress (physical, mental and emotional). Later on, we detected circular dichroism in the reflectance from the skin, a signature of the axial mode of a helical antenna. The full ramifications of what these findings represent in the human condition are still unclear. We also revealed correlation of electrocardiography (ECG) parameters to the sub-THz reflection coefficient of human skin. In a recent work, we developed a unique simulation tool of human skin, taking into account the skin multi-layer structure together with the helical segment of the sweat duct embedded in it. The presence of the sweat duct led to a high specific absorption rate (SAR) of the skin in extremely high frequency band. In this paper, we summarize the physical evidence for this phenomenon and consider its implication for the future exploitation of the electromagnetic spectrum by wireless communication. Starting from July 2016 the US Federal Communications Commission (FCC) has adopted new rules for wireless broadband operations above 24 GHz (5 G). This trend of exploitation is predicted to expand to higher frequencies in the sub-THz region. One must consider the implications of human immersion in the electromagnetic noise, caused by devices working at the very same frequencies as those, to which the sweat duct (as a helical antenna) is most attuned. We are raising a warning flag against the unrestricted use of sub-THz technologies for communication, before the possible consequences for public health are explored.

Dynamics of different steps of the photopyrolytic cycle of an eminent anticancer drug topotecan inside biocompatible lyotropic liquid crystalline systems

Dynamics of different steps of photopyrolytic processes of an eminent anticancer drug topotecan have been investigated inside different lyotropic liquid crystalline systems.

Probe-location dependent resonance energy transfer at lipid/water interfaces: comparison between the gel- and fluid-phase of lipid bilayer

Effect of dielectric environment and lipid fluidity/rigidity in multi-chromophoric FRET from a series of donors to acceptors at lipid/water interfaces are monitored by tailored donor–acceptor pairs.

Comparative study of the inverse versus normal bicontinuous cubic phases of the β-d-glucopyranoside water-driven self-assemblies using fluorescent probes

This work investigates the head group region of the inverse and normal bicontinuous cubic phases (Ia3d space group) of the glucopyranoside/water system using 2-(2′-hydroxyphenyl)benzoxazole and its derivatives as fluorescent probes.

New insight into probe-location dependent polarity and hydration at lipid/water interfaces: comparison between gel- and fluid-phases of lipid bilayers

Location dependent polarity and hydration probed by a new series of 4-aminophthalimide-based fluorescent molecules (4AP-Cn;n= 2–10, 12) show different behaviour at gel- and fluid-phase lipid/water interfaces.

Detecting local heterogeneity and ionization ability in the head group region of different lipidic phases using modified fluorescent probes

Local heterogeneity in lipid self-assembly is important for executing the cellular membrane functions. In this work, we chemically modified 2-(2'-hydroxyphenyl)benzoxazole (HBO) and attached a C8 alkyl chain in two different locations to probe the microscopic environment of four lipidic phases of dodecyl β-maltoside. The fluorescence change in HBO and the new probes (HBO-1 and HBO-2) shows that in all phases (micellar, hexagonal, cubic and lamellar) three HBO tautomeric species (solvated syn-enol, anionic, and closed syn-keto) are stable. The formation of multi tautomers reflects the heterogeneity of the lipidic phases. The results indicate that HBO and HBO-1 reside in a similar location within the head group region, whereas HBO-2 is slightly pushed away from the sugar-dominated area. The stability of the solvated syn-enol tautomer is due to the formation of a hydrogen bond between the OH group of the HBO moiety and an adjacent oxygen atom of a sugar unit. The detected HBO anions was proposed to be a consequence of this solvation effect where a hydrogen ion abstraction by the sugar units is enhanced. Our results point to a degree of local heterogeneity and ionization ability in the head group region as a consequence of the sugar amphoterism.

Long-Range Lipid-Water Interaction as Observed by ATR-FTIR Spectroscopy

It is commonly assumed that the structure of water at a lipid-water interface is influenced mostly in the first hydration layer. However, recent results from different experimental methods show that perturbation extends through several hydration layers. Due to its low light penetration depth, attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy is specifically suited to study interlamellar water structure in multibilayers. Results obtained by this technique confirm the long-range water structure disturbance. Consequently, in confined membrane environments nearly all water molecules can be perturbed. It is important to note that the behavior of confined water molecules differs significantly in samples prepared in excess water and in partially hydrated samples. We show in what manner the interlamellar water perturbation is influenced by the hydration level and how it is sequentially modified with a step-by-step dehydration of samples either by water evaporation or by osmotic pressure. Our results also indicate that besides different levels of hydration the lipid-water interaction is modulated by different lipid headgroups and different lipid phases as well. Therefore, modification of interlamellar water properties may clarify the role of water-mediated effects in biological processes.

Photodynamics of a Proton-Transfer Dye in Solutions and Confined Within NaX and NaY Zeolites

We report on steady-state, picosecond and femtosecond time-resolved emission studies of 2-(2'-hydroxyphenyl)benzoxazole (HBO) in solutions and interacting with NaX and NaY zeolites. In solutions, an ultrafast (less than 150 fs) excited-state intramolecular proton-transfer (ESIPT) reaction takes place in syn-enol form, and leads to keto-type tautomer. We also observed a torsional motion in the keto form (~20 ps in dichloromethane, DCM). For NaX and NaY DCM suspensions, anionic forms interacting with the zeolites at S0 and S1 states are generated. They show two fluorescence lifetimes in both zeolites (720 ps and 2.4 ns for NaY and 960 ps and 2.7 ns for NaX), while those of the enol bonded to the zeolite framework and of the free keto forms are ~100 and 250 ps, respectively. The ultrafast dynamics of the anion in alkaline solutions reveals two deactivation pathways: an intramolecular charge transfer (ICT, 1.2 ps) and a twisting motion, affected by the viscosity of the solvent (12 and 20 ps for MeOH and ethylene glycol). When HBO is interacting with NaX and NaY the twisting motion is cancelled, while the ICT becomes slower as a result of a combination of several environment effects. HBO anions within the faujasite framework show also a ~ 30 ps decay associated to a non-fluorescent (n, π*) state. Our results demonstrate how intermolecular H-bonds, the confinement and the electrostatic interactions of HBO with the used materials, affect its ground as well as its excited state properties. Our findings add new knowledge on the interactions of silica-based nanomaterials containing the H-bonding guests.

Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of myoglobin

Over the past few years, time-dependent ultrafast fluorescence spectroscopy method has been applied to the study of protein dynamics. However, observations from these experiments are in a controversy with other experimental studies. Participating of theoretical methods in this debate has not reconciled the contradiction, because the predicted initial relaxation from computer simulations is one-order faster than the ultrafast fluorescence spectroscopy experiment. In those simulations, pairwise force fields are employed, which have been shown to underestimate the roughness of the free energy landscape. Therefore, the relaxation rate of protein and water molecules under pairwise force fields is falsely exaggerated. In this work, we compared the relaxations of tryptophan/environment interaction under linear response approximation employing pairwise, polarized, and polarizable force fields. Results show that although the relaxation can be slowed down to a certain extent, the large gap between experiment and theory still cannot be filled.

ESR study of interfacial hydration layers of polypeptides in water-filled nanochannels and in vitrified bulk solvents

There is considerable evidence for the essential role of surface water in protein function and structure. However, it is unclear to what extent the hydration water and protein are coupled and interact with each other. Here, we show by ESR experiments (cw, DEER, ESEEM, and ESE techniques) with spin-labeling and nanoconfinement techniques that the vitrified hydration layers can be evidently recognized in the ESR spectra, providing nanoscale understanding for the biological interfacial water. Two peptides of different secondary structures and lengths are studied in vitrified bulk solvents and in water-filled nanochannels of different pore diameter (6.1∼7.6 nm). The existence of surface hydration and bulk shells are demonstrated. Water in the immediate vicinity of the nitroxide label (within the van der Waals contacts, ∼0.35 nm) at the water-peptide interface is verified to be non-crystalline at 50 K, and the water accessibility changes little with the nanochannel dimension. Nevertheless, this water accessibility for the nanochannel cases is only half the value for the bulk solvent, even though the peptide structures remain largely the same as those immersed in the bulk solvents. On the other hand, the hydration density in the range of ∼2 nm from the nitroxide spin increases substantially with decreasing pore size, as the density for the largest pore size (7.6 nm) is comparable to that for the bulk solvent. The results demonstrate that while the peptides are confined but structurally unaltered in the nanochannels, their surrounding water exhibits density heterogeneity along the peptide surface normal. The causes and implications, especially those involving the interactions between the first hydration water and peptides, of these observations are discussed. Spin-label ESR techniques are proven useful for studying the structure and influences of interfacial hydration.

Solvation dynamics of biological water in a single live cell under a confocal microscope

Time-resolved confocal microscopy has been applied to study the cytoplasm and nucleus region of a single live Chinese hamster ovary (CHO) cell. To select the cytoplasm and the nucleus region, two different fluorescent probes are used. A hydrophobic fluorescent dye, DCM, localizes preferentially in the cytoplasm region of a CHO cell. A DNA binding dye, DAPI, is found to be inside the nucleus of the cell. The locations of the probes are clearly seen in the image. Emission maxima of the dyes (DCM in cytoplasm and DAPI in the nucleus) are compared to those of the same dyes in different solvents. From this, it is concluded that the polarity (dielectric constant, ε) of the microenvironment of DCM in the cytoplasm is ~15. The nucleus is found to be much more polar with ε ≈ 60 (as reported by DAPI). The diffusion coefficient (and hence viscosity) in the cytoplasm and the nucleus was determined using fluorescence correlation spectroscopy (FCS). The diffusion coefficient (D(t)) of the dye (DCM) in the cytoplasm is 2 μm(2) s(-1) and is ~150 times slower than that in bulk water (buffer). D(t) of DAPI in the nucleus (15 μm(2) s(-1)) is 30 times slower than that in bulk water (buffer). The extremely slow diffusion inside the cell has been ascribed to higher viscosity and also to the binding of the probes (DCM and DAPI) to large biological macromolecules. The solvation dynamics of water in the cytoplasm (monitored by DCM) exhibits an average relaxation time [τ(sol)] of 1250 ± 50 ps, which is about 1000 times slower than in bulk water (1 ps). The solvation dynamics inside the nucleus (studied using DAPI) is about 2-fold faster, [τ(sol)] ≈ 775 ps. The higher polarity, faster diffusion, and faster solvation dynamics in the nucleus indicates that it is less crowded and less restricted than the cytoplasm.

Validation of response function construction and probing heterogeneous protein hydration by intrinsic tryptophan

Protein solvation dynamics usually occur on multiple time scales with site specificity, and the characterization of such heterogeneous dynamics requires a convenient optical probe. We proposed a tryptophan methodology, and with site-directed mutagenesis we can use a tryptophan scan to probe any desirable position around protein surfaces. Here, we report our extended solvation model for construction of response functions for probes such as tryptophan with multiple emission peaks and lifetimes. We show our systematic construction procedure and careful analyses of the possible missing percentage of an initial ultrafast component with the established zero-time emission spectrum and limited temporal resolution through two methods of the direct mapping of femtosecond-resolved fluorescence spectra (3D FRES) and the constructed FRES (2D) from the fluorescence transients. We unambiguously validate our extended model with reexamination of solvation dynamics (methanol, water, and proteins) using conventional dye coumarin, intrinsic tryptophan, and cofactor flavin. Using mutant proteins of GB1, we show again the generality of the powerful probe tryptophan for protein hydration (solvation) and the slowdown of the hydration layer dynamics especially at the water-protein interface. These results justify the necessity of our extended solvation model, clarify the confusion of protein hydration in the recent literature, and establish the universal optical probe of tryptophan for heterogeneous protein dynamics.

Femtosecond conical intersection dynamics of tryptophan in proteins and validation of slowdown of hydration layer dynamics

Water motion probed by intrinsic tryptophan shows the significant slowdown around protein surfaces, but it is unknown how the ultrafast internal conversion of two nearly degenerate states of Trp ((1)L(a) and (1)L(b)) affects the initial hydration in proteins. Here, we used a mini-protein with 10 different tryptophan locations one at a time through site-directed mutagenesis and extensively characterized the conversion dynamics of the two states. We observed all the conversion time scales in 40-80 fs by measurement of their anisotropy dynamics. This result is significant and shows no noticeable effect on the initial observed hydration dynamics and unambiguously validates the slowdown of hydration layer dynamics as shown here again in two mutant proteins.

Membrane protein structure determination using crystallography and lipidic mesophases: recent advances and successes

The crystal structure of the β(2)-adrenergic receptor in complex with an agonist and its cognate G protein has just recently been determined. It is now possible to explore in molecular detail the means by which this paradigmatic transmembrane receptor binds agonist, communicates the impulse or signaling event across the membrane, and sets in motion a series of G protein-directed intracellular responses. The structure was determined using crystals of the ternary complex grown in a rationally designed lipidic mesophase by the so-called in meso method. The method is proving to be particularly useful in the G protein-coupled receptor field where the structures of 13 distinct receptor types have been determined in the past 5 years. In addition to receptors, the method has proven to be useful with a wide variety of integral membrane protein classes that include bacterial and eukaryotic rhodopsins, light-harvesting complex II (LHII), photosynthetic reaction centers, cytochrome oxidases, β-barrels, an exchanger, and an integral membrane peptide. This attests to the versatility and range of the method and supports the view that the in meso method should be included in the arsenal of the serious membrane structural biologist. For this to happen, however, the reluctance to adopt it attributable, in part, to the anticipated difficulties associated with handling the sticky, viscous cubic mesophase in which crystals grow must be overcome. Harvesting and collecting diffraction data with the mesophase-grown crystals are also viewed with some trepidation. It is acknowledged that there are challenges associated with the method. Over the years, we have endeavored to establish how the method works at a molecular level and to make it user-friendly. To these ends, tools for handling the mesophase in the pico- to nanoliter volume range have been developed for highly efficient crystallization screening in manual and robotic modes. Methods have been implemented for evaluating the functional activity of membrane proteins reconstituted into the bilayer of the cubic phase as a prelude to crystallogenesis. Glass crystallization plates that provide unparalleled optical quality and sensitivity to nascent crystals have been built. Lipid and precipitant screens have been designed for a more rational approach to crystallogenesis such that the method can now be applied to an even wider variety of membrane protein types. In this work, these assorted advances are outlined along with a summary of the membrane proteins that have yielded to the method. The prospects for and the challenges that must be overcome to further develop the method are described.

Fluorescence probing of the temperature-induced phase transition in a glycolipid self-assembly: hexagonal ↔ micellar and cubic ↔ lamellar

Water-driven self-assembly of lipids displays a variety of liquid crystalline phases that are crucial for membrane functions. Herein, we characterize the temperature-induced phase transitions in two compositions of an aqueous self-assembly system of the octyl β-D-glucoside (βGlcOC(8)) system, using steady-state and time-resolved fluorescence measurements. The phase transitions hexagonal ↔ micellar and cubic ↔ lamellar were investigated using tryptophan (Trp) and two of its ester derivatives (Trp-C(4) and Trp-C(8)) to probe the polar headgroup region and pyrene to probe the hydrophobic tail region. The polarity of the headgroup region was estimated to be close to that of simple alcohols (methanol and ethanol) for all phases. The pyrene fluorescence indicates that the pyrene molecules are dispersed among the tails of the hydrophobic region, yet remain in close proximity to the polar head groups. Comparing the present results with our previously reported one for βMaltoOC(12), increasing the tail length of the hexagonal phase from C(8) to C(12) leads to less interaction with pyrene, which is attributed to the more random and wobbling motion of the longer alkyl tail. We measured a reduction (more hydrophobic) in the ratio of the vibronic peak intensities of pyrene (I(1)/I(3)) for the lamellar phase compared to that of the cubic phase. The higher polarity in the cubic phase can be correlated to the nature of its interface, which curves toward the bulk water. This geometry also explains the slight reduction in polarity of the headgroup region compared to the other phases. Upon the addition of Trp-C(8), the fluorescence lifetime of pyrene is reduced by 28% in the lamellar and cubic phases, whereas the I(1)/I(3) value is only slightly reduced. The results reflect the dominant role of dynamic interaction mechanism between the C(8) chain of Trp-C(8) and pyrene. This mechanism may be important for these two phases since they participate in the process of membrane fusion. Both lipid compositions show completely reversible temperature-induced phase transitions, reflecting the thermodynamic equilibrium structures of their mesophases. Probing both regions of the different lipid phases reveals a large degree of heterogeneity and flexibility of the lipid self-assembly. These properties are crucial for carrying out different biological functions such as the ability to accommodate various molecular sizes.

Nucleotide recognition and phosphate linkage hydrolysis at a lipid cubic interface

Mononucleotides, when entrapped within a mono-olein-based cubic Ia3d liquid crystalline phase, have been found to undergo hydrolysis at the sugar-phosphate ester bond in spite of their natural inertness toward hydrolysis. Here, kinetics of the hydrolysis reaction and interactions between the lipid matrix and the mononucleotide adenosine 5'-monophosphate disodium salt (AMP) and its 2'-deoxy derivative (dAMP) are thoroughly investigated in order to shed some light on the mechanism of the nucleotide recognition and phosphate ester hydrolysis. Experiments evidenced that molecular recognition occurs essentially through the sn-2 and the sn-3 alcoholic OH groups of mono-olein. As deduced from the apparent activation energies, the mechanism underlying the hydrolysis reaction is the same for AMP and dAMP. Nevertheless, the reaction proceeds slower for the latter, highlighting a substantial difference in the chemical behavior of the two nucleotides. A model that explains the hydrolysis reaction is presented. Remarkably, the hydrolysis mechanism appears to be highly specific for the Ia3d phase.

Water on graphene surfaces

In this paper, we summarize the main results obtained in our group about the behavior of water confined inside or close to different graphene surfaces by means of molecular dynamics simulations. These include the inside and outside of carbon nanotubes, and the confinement inside a slit pore or a single graphene sheet. We paid special attention to some thermodynamical (binding energies), structural (hydrogen-bond distributions) and dynamic (infrared spectra) properties, and their comparison to their bulk counterparts.

Protein hydration dynamics and molecular mechanism of coupled water-protein fluctuations

Protein surface hydration is fundamental to its structural stability and flexibility, and water-protein fluctuations are essential to biological function. Here, we report a systematic global mapping of water motions in the hydration layer around a model protein of apomyoglobin in both native and molten globule states. With site-directed mutagenesis, we use intrinsic tryptophan as a local optical probe to scan the protein surface one at a time with single-site specificity. With femtosecond resolution, we examined 16 mutants in two states and observed two types of water-network relaxation with distinct energy and time distributions. The first water motion results from the local collective hydrogen-bond network relaxation and occurs in a few picoseconds. The initial hindered motions, observed in bulk water in femtoseconds, are highly suppressed and drastically slow down due to structured water-network collectivity in the layer. The second water-network relaxation unambiguously results from the lateral cooperative rearrangements in the inner hydration shell and occurs in tens to hundreds of picoseconds. Significantly, this longtime dynamics is the coupled interfacial water-protein motions and is the direct measurement of such cooperative fluctuations. These local protein motions, although highly constrained, are necessary to assist the longtime water-network relaxation. A series of correlations of hydrating water dynamics and coupled fluctuations with local protein's chemical and structural properties were observed. These results are significant and reveal various water behaviors in the hydration layer with wide heterogeneity. We defined a solvation speed and an angular speed to quantify the water-network rigidity and local protein flexibility, respectively. We also observed that the dynamic hydration layer extends to more than 10 A. Finally, from native to molten globule states, the hydration water networks loosen up, and the protein locally becomes more flexible with larger global plasticity and partial unfolding.

Quasi-static self-quenching of Trp-X and X-Trp dipeptides in water: ultrafast fluorescence decay

Time-resolved fluorescence decay profiles of N-acetyl-l-tryptophanamide (NATA) and tryptophan (Trp) dipeptides of the form Trp-X and X-Trp, where X is another aminoacyl residue, have been investigated using an ultraviolet upconversion spectrophoto fluorometer with time resolution better than 350 fs, together with a time-correlated single photon counting apparatus on the 100 ps to 20 ns time scale. We analyzed the set of fluorescence decay profiles at multiple wavelengths using the global analysis technique. Nanosecond fluorescence transients for Trp dipeptides all show multiexponential decay, while NATA exhibits a monoexponential decay near 3 ns independent of pH. In the first 100 ps, a time constant for the water "bulk relaxation" around Trp, NATA and Trp dipeptides are seen near 1-2 ps, with an associated preexponential amplitude that is positive or negative, depending on emission wavelength, as expected for a population conserving spectral shift. The initial brightness (sub-picosecond) we measure for all these dipeptides is less than that of NATA, implying even faster (<200 fs) intramolecular (quasi-) static quenching occurs within them. A new, third, ultrafast decay, bearing an exponential time constant of 20-30 ps with positive amplitude, has been found in many of these dipeptides. We believe it verifies our previous predictions of dipeptide QSSQ ("quasi-static self-quenching")-the loss of quantum yield to sub-100-ps decay process (Chen, R. F.; et al. Biochemistry 1991, 30, 5184). Most important, this term is found in proteins as well (Xu, J.; et al. J. Am. Chem. Soc. 2006, 128, 1214; Biophys. J. 2008, 94, 546; 2009, 96, 46a), suggesting an ultrafast quenching mechanism must be common to both.

Hydration structure on crystalline silica substrates

The structure of interfacial water at the silica solid surfaces was investigated using molecular dynamics simulations. Different degrees of surface hydroxylation were employed to assess the effect of the surface chemistry on the structure of interfacial water. Density profiles, in-plane radial distribution functions, in-plane density distribution, and hydrogen-bond profiles were calculated. Our results show that the surface hydroxylation affects the structure, orientation, and hydrogen-bond network of interfacial water molecules. Data analysis suggests that the degree of hydroxylation controls the amount of water molecules in the first interfacial layer as well as the distance between the first adsorbed layer and the substrate. Well-organized and uniform structures of interfacial water appear on the homogeneously hydroxylated surface, while a heterogeneous interfacial structure, characterized by extensive water-water hydrogen bonds, forms on the partially hydroxylated surface. We demonstrate that both the local surface chemistry and water-water hydrogen bonds are the dominant factors that determine the structural properties of interfacial water.

Crystallizing membrane proteins for structure determination: use of lipidic mesophases

The principal route to determine the structure and the function and interactions of membrane proteins is via macromolecular crystallography. For macromolecular crystallography to be successful, structure-quality crystals of the target protein must be forthcoming, and crystallogenesis represents a major challenge. Several techniques are employed to crystallize membrane proteins, and the bulk of these techniques make direct use of solubilized protein-surfactant complexes by the more traditional, so-called in surfo methods. An alternative in meso approach, which employs a bicontinuous lipidic mesophase, has emerged as a method with considerable promise in part because it involves reconstitution of the solubilized protein back into a stabilizing and organizing lipid bilayer reservoir as a prelude to crystallogenesis. A hypothesis for how the method works at the molecular level and experimental evidence in support of the proposal are reviewed here. The latest advances, successes, and challenges associated with the method are described.