Transport Dynamics of Water Molecules Confined between Lipid Membranes.

Water molecules confined between biological membranes exhibit a distinctive non-Gaussian displacement distribution, far different from that of bulk water. Here, we introduce a new transport equation for water molecules in the intermembrane space, quantitatively explaining molecular dynamics simulation results. We find that the unique transport dynamics of water molecules stems from the lateral diffusion coefficient fluctuation caused by their longitudinal motion in the direction perpendicular to the membranes. We also identify an interfacial region where water possesses distinct physical properties, which is unaffected by changes in the intermembrane separation.

How cryoprotectants work: hydrogen-bonding in low-temperature vitrified solutions.

Dimethyl sulfoxide (DMSO) increases cell and tissue viability at low temperatures and is commonly used as a cryoprotectant for cryogenic storage of biological materials. DMSO disorders the water hydrogen-bond networks and inhibits ice-crystal growth, though the specific DMSO interactions with water are difficult to characterize. In this study, we use a combination of Fourier Transform infrared spectroscopy (FTIR), molecular dynamics simulations, and vibrational frequency maps to characterize the temperature-dependent hydrogen bonding interactions of DMSO with water from 30 °C to -80 °C. Specifically, broad peaks in O-D stretch vibrational spectra of DMSO and deuterated water (HDO) cosolvent systems show that the hydrogen bond networks become increasingly disrupted compared to pure water. Simulations demonstrated that these disrupted hydrogen bond networks remain largely localized to the first hydration shell of DMSO, which explains the high DMSO concentrations needed to prevent ice crystal formation in cryopreservation applications.

Origin of thiocyanate spectral shifts in water and organic solvents.

Vibrational spectroscopy is a useful technique for probing chemical environments. The development of models that can reproduce the spectra of nitriles and azides is valuable because these probes are uniquely suited for investigating complex systems. Empirical vibrational spectroscopic maps are commonly employed to obtain the instantaneous vibrational frequencies during molecular dynamics simulations but often fail to adequately describe the behavior of these probes, especially in its transferability to a diverse range of environments. In this paper, we demonstrate several reasons for the difficulty in constructing a general-purpose vibrational map for methyl thiocyanate (MeSCN), a model for cyanylated biological probes. In particular, we found that electrostatics alone are not a sufficient metric to categorize the environments of different solvents, and the dominant features in intermolecular interactions in the energy landscape vary from solvent to solvent. Consequently, common vibrational mapping schemes do not cover all essential interaction terms adequately, especially in the treatment of van der Waals interactions. Quantum vibrational perturbation (QVP) theory, along with a combined quantum mechanical and molecular mechanical potential for solute-solvent interactions, is an alternative and efficient modeling technique, which is compared in this paper, to yield spectroscopic results in good agreement with experimental FTIR. QVP has been used to analyze the computational data, revealing the shortcomings of the vibrational maps for MeSCN in different solvents. The results indicate that insights from QVP analysis can be used to enhance the transferability of vibrational maps in future studies.

Interfacial dynamics in inverted-headgroup lipid membranes.

Inverted-headgroup (choline-phosphate) lipids are synthetic lipids that are not found in nature and are used as model systems to understand the role of headgroup dipole orientation. Recently, studies revealed that the net orientation of interfacial water strongly depends on the headgroup electrostatics, i.e., the charges and dipole generated by the phosphate and the choline groups. In order to characterize interfacial H-bond dynamics, we measured two-dimensional infrared spectra of the ester carbonyl band and performed molecular dynamics simulations in fully hydrated 1,2-dioleoyl-sn-glycero-3-phosphocholine and 2-((2,3-bis(oleoyloxy)propyl)-dimethyl-ammonio)ethyl ethyl phosphate (DOCPe) lipid bilayers. The experiments and simulations suggest that the reverse dipole generated by the inverted-headgroup in DOCPe does not affect the carbonyl H-bond populations or the interfacial water H-bond dynamics. However, while phosphate-associated waters in both lipids appear to show a similar H-bond structure, carbonyl-associated waters are characterized by a slightly disrupted H-bond structure in the DOCPe bilayer, especially within the second hydration shell. Our findings show that changes in net water orientation perturb the water H-bonds at the linker region between the headgroup and the lipid tail, although this perturbation is weak.

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

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

Water hydrogen-bonding structure and dynamics near lipid multibilayer surface: Molecular dynamics simulation study with direct experimental comparison.

Lipid multibilayers are excellent model systems for studying water structures and dynamics near biological membrane surfaces. In particular, the orientational distribution and rotational dynamics of water molecules near hydrophilic lipid groups are found to be sensitive to the chemical nature and charge distributions of the amphiphilic lipids. To elucidate how different parts of these lipids affect the water hydrogen-bonding structure and dynamics and to directly compare with recent experimental results, we carried out molecular dynamics (MD) simulations of lipid multibilayer systems. We found that the water molecules close to positively charged choline groups have a broad distribution of orientations due to the clathratelike shell formation around the choline groups but that those associated with phosphate groups, even in the second hydration shell, are orientationally restricted due to their strong hydrogen bonding with the phosphate group. These MD simulation results are in excellent agreement with our time-resolved infrared pump-probe anisotropy measurements, and we believe that they provide valuable insights into the role of water molecules in maintaining lipid bilayer integrity.

Fluorescence enhancement of a ligand-activated fluorescent protein induced by collective noncovalent interactions.

Fluorescent proteins contain an internal chromophore constituted of amino acids or an external chromophore covalently bonded to the protein. To increase their fluorescence intensities, many research groups have attempted to mutate amino acids within or near the chromophore. Recently, a new type of fluorescent protein, called UnaG, in which the ligand binds to the protein through many noncovalent interactions was discovered. Later, a series of mutants of the UnaG protein were introduced, which include eUnaG with valine 2 mutated to leucine emitting significantly stronger fluorescence than the wild type and V2T mutant, in which valine 2 is mutated to threonine, emitting weaker fluorescence than the wild type. Interestingly, the single mutation sites of both eUnaG and V2T mutants are distant from the fluorophore, bilirubin, which renders the mechanism of such fluorescence enhancement or reduction unclear. To elucidate the origin of fluorescence intensity changes induced by the single mutations, we carried out extensive analyses on MD simulations for the original UnaG, eUnaG and V2T, and found that the bilirubin ligand bound to eUnaG is conformationally more rigid than the wild-type, particularly in the skeletal dihedral angles, possibly resulting in the increase of quantum yield through a reduction of non-radiative decay. On the other hand, the bilirubin bound to the V2T appears to be flexible than that in the UnaG. Furthermore, examining the structural correlations between the ligand and proteins, we found evidence that the bilirubin ligand is encapsulated in different environments composed of protein residues and water molecules that increase or decrease the stability of the ligand. The changed protein stability affects the mobility and confinement of water molecules captured between bilirubin and the protein. Since the flexible ligand contains multiple hydrogen bond (H-bond) donors and acceptors, the H-bonding structure and dynamics of bound water molecules are highly correlated with the rigidity of the bound ligand. Our results suggest that, to understand the fluorescence properties of protein mutants, especially the ones with noncovalently bound fluorophores with internal rotations, the interaction network among protein residues, ligand, and water molecules within the binding cavity should be investigated rather than focusing on the local structure near the fluorescing moiety. Our in-depth simulation study may offer a foundation for the design principles for engineering this new class of fluorescent proteins.

The effect of Hofmeister anions on water structure at protein surfaces.

To understand the effects of specific ions on protein-water interactions and the thermodynamic stability of proteins in salt solutions, we use a molecular dynamics (MD) simulation to examine the water structure, orientational distribution, and dynamics near the surface of ubiquitin. In particular, we consider NaCl, NaBF4, NaSCN, and NaClO4 salt solutions containing ubiquitin, where the anions of the latter three salts are well-known chaotropic ions in the Hofmiester anion series. The number of hydrogen bonds (H-bonds) per water molecule is found to decrease significantly at the ubiquitin-water interface, indicating a significant disruption of the water H-bonding network. The distribution of the water H-bond numbers near the protein surface is modulated by dissolved ions, and the extent of the ion effect on the H-bonding network structure follows the order of the Hofmeister anion series, while there are no specific ion effects on water properties at distances larger than 5 Å from the protein surface. From detailed analyses of the surface area, volume, and root-mean-square deviation (RMSD) of ubiquitin, we show that changes in the properties of the protein could originate from the disruption of the water H-bond network induced by ions with a higher affinity for the protein surface instead of direct protein residue-ion interactions. An interesting observation made here is that the orientational distribution of water molecules at the protein-water interface is close to random, but there is a slight preference for interfacial water molecules with a straddle structure within 2.5 Å of the protein surface, where one of the two OH groups points away from the protein surface and the other points toward the surface. In addition, comparing the MD simulation results for ubiquitin solutions with dissolved NaSCN and KSCN, we show that Na+ affects the water H-bonding structure at the protein surface more than K+. It is clear that the H-bonding network structure of water more than one water layer away from the protein surface is not distinguishably different from that of neat water. We thus anticipate that the present work will provide insights into the scale of specific ion effects on the H-bonding structure and orientational distribution of water in the vicinity of protein surfaces in aqueous solutions.