Water replacement hypothesis in atomic detail--factors determining the structure of dehydrated bilayer stacks

Extreme makeover: the incredible cell membrane adaptations of extremophiles to harsh environments

The existence of life beyond Earth has long captivated humanity, and the study of extremophiles-organisms surviving and thriving in extreme environments-provides crucial insights into this possibility. Extremophiles overcome severe challenges such as enzyme inactivity, protein denaturation, and damage of the cell membrane by adopting several strategies. This feature article focuses on the molecular strategies extremophiles use to maintain the cell membrane's structure and fluidity under external stress. Key strategies include homeoviscous adaptation (HVA), involving the regulation of lipid composition, and osmolyte-mediated adaptation (OMA), where small organic molecules protect the lipid membrane under stress. Proteins also have direct and indirect roles in protecting the lipid membrane. Examining the survival strategies of extremophiles provides scientists with crucial insights into how life can adapt and persist in harsh conditions, shedding light on the origins of life. This article examines HVA and OMA and their mechanisms in maintaining membrane stability, emphasizing our contributions to this field. It also provides a brief overview of the roles of proteins and concludes with recommendations for future research directions.

Molecular simulation on the interaction between trehalose and asymmetric lipid bilayer mimicking the membrane of human red blood cells

Trehalose is widely acknowledged for its ability to stabilize plasma membranes during dehydration. However, the exact mechanism by which trehalose interacts with lipid bilayers remains presently unclear. In this study, we conducted atomistic molecular dynamic simulations on asymmetric model bilayers that mimic the membrane of human red blood cells at various trehalose and water contents. We considered three different hydration levels mimicking the full hydration to desiccation scenarios. Results indicate that the asymmetric distribution of lipids did not significantly influence the computed structural characteristics at full and low hydration. At dehydration, however, the order parameter obtained from the symmetric bilayer is significantly higher compared to those obtained from asymmetric ones. Analysis of hydrogen bonds revealed that the protective ability of trehalose is well described by the water replacement hypothesis at full and low hydration, while at dehydration other interaction mechanisms associated with trehalose exclusion from the bilayer may involve. In addition, we found that trehalose exclusion is not attributed to sugar saturation but rather to the reduction in hydration levels. It can be concluded that the protective effect of trehalose is not only related to the hydration level of the bilayer, but also closely tied to the asymmetric distribution of lipids within each leaflet.

Lipid acyl chain protrusion induced by the influenza virus hemagglutinin fusion peptide detected by NMR paramagnetic relaxation enhancement

The glycoprotein spikes of membrane-enveloped viruses include a subunit that catalyzes fusion (joining) of the viral and target cell membranes. For influenza virus, this is subunit 2 of hemagglutinin which has a ∼ 20-residue N-terminal fusion peptide (Fp) region that binds target membrane. An outstanding question is whether there are associated membrane changes important for fusion. Several computational studies have found increased "protrusion" of lipid acyl chains near Fp, i.e. one or more chain carbons are closer to the aqueous region than the headgroup phosphorus. Protrusion may accelerate initial joining of outer leaflets of the two membranes into a stalk intermediate. In this study, higher protrusion probability in membrane with vs. without Fp is convincingly detected by larger Mn2+-associated increases in chain 13C NMR transverse relaxation rates (Γ2's). Data analysis provides a ratio Γ2,neighbor/Γ2,distant for lipids neighboring vs. more distant from the Fp. The calculated ratio depends on the number of Fp-neighboring lipids and the experimentally-derived range of 4 to 24 matches the range of increased protrusion probabilities from different simulations. For samples either with or without Fp, the Γ2 values are well-fitted by an exponential decay as the 13C site moves closer to the chain terminus. The decays correlate with free-energy of protrusion proportional to the number of protruded -CH2 groups, with free energy per -CH2 of ∼0.25 kBT. The NMR data support one major fusion role of the Fp to be much greater protrusion of lipid chains, with highest protrusion probability for chain regions closest to the headgroups.

Yacon juice as culture and cryoprotectant medium for Latilactobacillus sakei and Staphylococcus vitulinus autochthonous strains

Abstract Yacon is mainly constituted of water and carbohydrates [single sugars and fructooligosaccharides (FOS)], thus being an excellent alternative for the growth and preservation of bacterial culture. Latilactobacillus sakei ACU-2 and Staphylococcus vitulinus ACU-10 comprised the autochthonous starter culture SAS-1 designed for the manufacture of dry sausages. This study evaluated the use of yacon juice as a potential growth medium and cryoprotectant for these bacteria. The growth medium was prepared with yacon juice supplemented with peptone and dipotassium phosphate. After growing, cells were resuspended in yacon juice (5, 10 and 25 mL/100 mL) and lyophilized. Viable cells were count before, immediately after lyophilization, and along 6 months of refrigerated storage. Both bacteria grew in every yacon concentration tested; however, juice concentration affected their growth. Latilactobacillus sakei grew at μ = 0.256 ± 0.01 giving the highest bacterial density at 10 mL/100 mL (Log DOmax 0.33 ± 0.01). While 5 mL/100 mL yacon juice provided the best conditions for S. vitulinus growth (μ = 0.215 ± 0.016; Log DOmax 0.32 ± 0.01). After lyophilization, the survival rate was 91.1% for L. sakei and 65.8% for S. vitulinus. Throughout storage, high cell counts suggested good stability of both bacteria. Results revealed that yacon juice comprises a nutritive substrate for the growth and cryopreservation of tested strains from the genus Latilactobacillus and Staphylococcus.

Effect of protective agents on the storage stability of freeze-dried Ligilactobacillus salivarius CECT5713

Ligilactobacillus salivarius is a lactic acid bacterium exhibiting several health benefits but remains commercially underexploited due to its inability to survive during long-term storage in the dried state. Our objective was to study the effect of various protective molecules (maltodextrin, trehalose, antioxidants, and fructooligosaccharides), being efficient on other bacteria, on the freeze-dried stability of L. salivarius CECT5713. The culturability was evaluated after freezing, freeze-drying, and subsequent storage at 37 °C, as well as the biochemical composition of cells in an aqueous environment using Fourier transform infrared (FTIR) micro-spectroscopy. The assignment of principal absorption bands to cellular components was performed using data from the literature on bacteria. The membrane fatty acid composition was determined after freeze-drying and storage. Glass transition temperature of the liquid and freeze-dried bacterial suspensions and water activity of the freeze-dried samples were measured. The best storage stability was observed for the formulations involving maltodextrin and antioxidants. The analysis of the FTIR spectra of freeze-thawed cells and rehydrated cells after freeze-drying and storage revealed that freeze-drying induced damage to proteins, peptidoglycans of the cell wall and nucleic acids. Storage stability appeared to be dependent on the ability of the protective molecules to limit damage during freeze-drying. The inactivation rates of bacteria during storage were analyzed as a function of the temperature difference between the product temperature during sublimation or during storage and the glass transition temperature, allowing a better insight into the stabilization mechanisms of freeze-dried bacteria. Maintaining during the process a product temperature well below the glass transition temperature, especially during storage, appeared essential for L. salivarius CECT5713 storage stability. KEY POINTS: • L. salivarius CECT5713 highly resisted freezing but was sensitive to freeze-drying and storage. • Freeze-drying and storage mainly altered cell proteins, peptidoglycans, and nucleic acids. • A glassy matrix containing maltodextrin and an antioxidant ensured the highest storage stability.

Ligilactobacillus salivarius functionalities, applications, and manufacturing challenges

Ligilactobacillus salivarius is a lactic acid bacteria that has been gaining attention as a promising probiotic. Numerous strains exhibit functional properties with health benefits such as antimicrobial activity, immunological effects, and the ability to modulate the intestinal microbiota. However, just a small number of them are manufactured at an industrial scale and included in commercial products. The under exploitation of L. salivarius strains that remain in the freezer of companies is due to their incapacity to overcome the environmental stresses induced by production and stabilization processes.The present study summarizes the functionalities and applications of L. salivarius reported to date. It aims also at providing a critical evaluation of the literature available on the manufacturing steps of L. salivarius concentrates, the bacterial quality after each step of the process, and the putative degradation and preservation mechanisms. Here, we highlight the principal issues and future research challenges for improving the production and long-term preservation at the industrial scale of this microorganism, and probably of other probiotics.Key points• L. salivarius beneficial properties and commercialized products.• Production conditions and viability of L. salivarius after stabilization processes.• Prospects for identifying preservation mechanisms to improve L. salivarius stability.

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.

Influence of Substrate Hydrophilicity on Structural Properties of Supported Lipid Systems on Graphene, Graphene Oxides, and Silica

Pristine graphene, a range of graphene oxides, and silica substrates were used to investigate the effect of surface hydrophilicity on supported lipid bilayers by means of all-atom molecular dynamics simulations. Supported 1,2-dioleoyl-sn-glycero-3-phosphocholine lipid bilayers were found in close-contact conformations with hydrophilic substrates with as low as 5% oxidation level, while self-assembled monolayers occur on pure hydrophobic graphene only. Lipids and water at the surface undergo large redistribution to maintain the stability of the supported bilayers. Deposition of bicelles on increasingly hydrophilic substrates shows the continuous process of reshaping of the supported system and makes intermediate stages between self-assembled monolayers and supported bilayers. The bilayer thickness changes with hydrophilicity in a complex manner, while the number of water molecules per lipid in the hydration layer increases together with hydrophilicity.

Probiotic nasal spray development by spray drying

The upper respiratory tract (URT) is the main entrance point for many viral and bacterial pathogens, and URT infections are among the most common infections in the world. Recent evidences by our own group and others imply the importance of lactobacilli as gatekeepers of a healthy URT. However, the benefits of putting health-promoting microbes or potential probiotics, such as these URT lactobacilli, in function of URT disease control and prevention is underestimated, among others because of the absence of adequate formulation modalities. Therefore, this study entails important aspects in probiotic nasal spray development with a novel URT-derived probiotic strain by spray drying. We report quantitative and qualitative analysis of several spray-dried formulations, i.e. powders for reconstitution, based on disaccharide or sugar alcohol combinations with a polymer, including their long-term stability. Four formulations with the highest survival of >10⁹ (Colony Forming Units) CFU/g after 28 weeks were further examined upon reconstitution which confirmed sufficiency of one bottle/dosage form during 7 days and rheological properties of shear-thinning. Tests also demonstrated maintained viability and cell morphology overall upon spraying through a nasal spray bottle in all 4 formulations. Lastly, application suitability in terms of high adherence to Calu-3 cells and antimicrobial activity against common URT pathogens was demonstrated and was not impacted neither by powder production process nor by spraying of reconstituted powder through a nasal spray device.

BioSentinel: Long-Term Saccharomyces cerevisiae Preservation for a Deep Space Biosensor Mission

The biological risks of the deep space environment must be elucidated to enable a new era of human exploration and scientific discovery beyond low earth orbit (LEO). There is a paucity of deep space biological missions that will inform us of the deleterious biological effects of prolonged exposure to the deep space environment. To safely undertake long-term missions to Mars and space habitation beyond LEO, we must first prove and optimize autonomous biosensors to query the deep space radiation environment. Such biosensors must contain organisms that can survive for extended periods with minimal life support technology and must function reliably with intermittent communication with Earth. NASA's BioSentinel mission, a nanosatellite containing the budding yeast Saccharomyces cerevisiae, is such a biosensor and one of the first biological missions beyond LEO in nearly half a century. It will help fill critical gaps in knowledge about the effects of uniquely composed, chronic, low-flux deep space radiation on biological systems and in particular will provide valuable insight into the DNA damage response to highly ionizing particles. Due to yeast's robustness and desiccation tolerance, it can survive for periods analogous to that of a human Mars mission. In this study, we discuss our optimization of conditions for long-term reagent storage and yeast survival under desiccation in preparation for the BioSentinel mission. We show that long-term yeast cell viability is maximized when cells are air-dried in trehalose solution and stored in a low-relative humidity and low-temperature environment and that dried yeast is sensitive to low doses of deep space-relevant ionizing radiation under these conditions. Our findings will inform the design and development of improved future long-term biological missions into deep space.

Do Osmolytes Impact the Structure and Dynamics of Myoglobin?

Osmolytes are small organic compounds that can affect the stability of proteins in living cells. The mechanism of osmolytes' protective effects on protein structure and dynamics has not been fully explained, but in general, two possibilities have been suggested and examined: a direct interaction of osmolytes with proteins (water replacement hypothesis), and an indirect interaction (vitrification hypothesis). Here, to investigate these two possible mechanisms, we studied myoglobin-osmolyte systems using FTIR, UV-vis, CD, and femtosecond IR pump-probe spectroscopy. Interestingly, noticeable changes are observed in both the lifetime of the CO stretch of CO-bound myoglobin and the spectra of UV-vis, CD, and FTIR upon addition of the osmolytes. In addition, the temperature-dependent CD studies reveal that the protein's thermal stability depends on molecular structure, hydrogen-bonding ability, and size of osmolytes. We anticipate that the present experimental results provide important clues about the complicated and intricate mechanism of osmolyte effects on protein structure and dynamics in a crowded cellular environment.

Combined effects of osmotic and hydrostatic pressure on multilamellar lipid membranes in the presence of PEG and trehalose

We studied the interaction of lipid membranes with the disaccharide trehalose (TRH), which is known to stabilize biomembranes against various environmental stress factors. Generally, stress factors include low/high temperature, shear, osmotic and hydrostatic pressure. Small-angle X-ray-scattering was applied in combination with fluorescence spectroscopy and calorimetric measurements to get insights into the influence of trehalose on the supramolecular structure, hydration level, and elastic and thermodynamic properties as well as phase behavior of the model biomembrane DMPC, covering a large region of the temperature, osmotic and hydrostatic pressure phase space. We observed distinct effects of trehalose on the topology of the lipid's supramolecular structure. Trehalose, unlike osmotic pressure induced by polyethylene glycol, leads to a decrease of lamellar order and a swelling of multilamellar vesicles, which is attributable to direct interactions between the membrane and trehalose. Our results revealed a distinct biphasic concentration dependence of the observed effects of trehalose. While trehalose intercalates between the polar head groups at low concentrations, the effects after saturation are dominated by the exclusion of trehalose from the membrane surface.

Activity of the α-glucoside transporter Agt1 in Saccharomyces cerevisiae cells during dehydration-rehydration events

Microbial cells can enter a state of anhydrobiosis under desiccating conditions. One of the main determinants of viability during dehydration-rehydration cycles is structural integrity of the plasma membrane. Whereas much is known about phase transitions of the lipid bilayer, there is a paucity of information on changes in activity of plasma membrane proteins during dehydration-rehydration events. We selected the α-glucoside transporter Agt1 to gain insights into stress mechanisms/responses and ecophysiology during anhydrobiosis. As intracellular water content of S. cerevisiae strain 14 (a strain with moderate tolerance to dehydration-rehydration) was reduced to 1.5 g water/g dry weight, the activity of the Agt1 transporter decreased by 10-15 %. This indicates that functionality of this trans-membrane and relatively hydrophobic protein depends on water. Notably, however, levels of cell viability were retained. Prior incubation in the stress protectant xylitol increased stability of the plasma membrane but not Agt1. Studies were carried out using a comparator yeast which was highly resistant to dehydration-rehydration (S. cerevisiae strain 77). By contrast to S. cerevisiae strain 14, there was no significant reduction of Agt1 activity in S. cerevisiae strain 77 cells. These findings have implications for the ecophysiology of S. cerevisiae strains in natural and industrial systems.

Towards water-free biobanks: long-term dry-preservation at room temperature of desiccation-sensitive enzyme luciferase in air-dried insect cells

Desiccation-tolerant cultured cells Pv11 derived from the anhydrobiotic midge embryo endure complete desiccation in an ametabolic state and resume their metabolism after rehydration. These features led us to develop a novel dry preservation technology for enzymes as it was still unclear whether Pv11 cells could preserve an exogenous enzyme in the dry state. This study shows that Pv11 cells protect an exogenous desiccation-sensitive enzyme, luciferase (Luc), preserving the enzymatic activity even after dry storage for 372 days at room temperature. A process including preincubation with trehalose, dehydration, storage, and rehydration allowed Pv11 (Pv11-Luc) cells stably expressing luciferase to survive desiccation and still emit luminescence caused by luciferase after rehydration. Luminescence produced by luciferase in Pv11-Luc cells after rehydration did not significantly decrease in presence of a translation inhibitor, showing that the activity did not derive from de novo enzyme synthesis following the resumption of cell metabolism. These findings indicate that the surviving Pv11 cells almost completely protect luciferase during desiccation. Lacking of the preincubation step resulted in the loss of luciferase activity after rehydration. We showed that preincubation with trehalose associated to induction of desiccation tolerance-related genes in Pv11 cells allowed effective in vivo preservation of enzymes in the dry state.

Solvent-exposed lipid tail protrusions depend on lipid membrane composition and curvature

The stochastic protrusion of hydrophobic lipid tails into solution, a subclass of hydrophobic membrane defects, has recently been shown to be a critical step in a number of biological processes like membrane fusion. Understanding the factors that govern the appearance of lipid tail protrusions is critical for identifying membrane features that affect the rate of fusion or other processes that depend on contact with solvent-exposed lipid tails. In this work, we utilize atomistic molecular dynamics simulations to characterize the likelihood of tail protrusions in phosphotidylcholine lipid bilayers of varying composition, curvature, and hydration. We distinguish two protrusion modes corresponding to atoms near the end of the lipid tail or near the glycerol group. Through potential of mean force calculations, we demonstrate that the thermodynamic cost for inducing a protrusion depends on tail saturation but is insensitive to other bilayer structural properties or hydration above a threshold value. Similarly, highly curved vesicles or micelles increase both the overall frequency of lipid tail protrusions as well as the preference for splay protrusions, both of which play an important role in driving membrane fusion. In multi-component bilayers, however, the incidence of protrusion events does not clearly depend on the mismatch between tail length or tail saturation of the constituent lipids. Together, these results provide significant physical insight into how system components might affect the appearance of protrusions in biological membranes, and help explain the roles of composition or curvature-modifying proteins in membrane fusion.

A combination of hydroxypropyl cellulose and trehalose as supplementation for vitrification of human oocytes: a retrospective cohort study

PURPOSE

This study aimed to determine whether the new formulation of vitrification solutions containing a combination of hydroxypropyl cellulose (HPC) and trehalose does not affect outcomes in comparison with using conventional solutions made of serum substitute supplement (SSS) and sucrose.

METHODS

Ovum donation cycles were retrospectively compared regarding the solution used for vitrification and warming of human oocytes. The analysis included 218 cycles (N = 2532 oocytes) in the study group (HPC + trehalose) and 214 cycles (N = 2353 oocytes) in the control group (SSS + sucrose).

RESULTS

No statistical differences were found in ovarian stimulation parameters and baseline characteristics of donors and recipients. The survival rate was 91.3% (95% confidence interval (CI) = 89.8-92.9) in the HPC + trehalose group vs. 92.1% (95% CI = 90.4-93.7) in the SSS + sucrose group (NS). The implantation rate (42.8%, 95% CI = 37.7-47.9 vs. 41.2%, 95% CI = 36.0-46.4), clinical pregnancy rate (CPR) per transfer (60.7%, 95% CI = 53.9-67.5 vs. 56.4%, 95% CI = 49.3-63.5), and ongoing pregnancy rate (OPR) per transfer (48.5%, 95% CI = 41.5-55.5 vs. 46.3%, 95% CI = 39.2-53.4) were similar for patients who received either HPC + trehalose-vitrified oocytes or SSS + sucrose-vitrified oocytes. Statistical differences were found when analyzing blastocyst rate both per injected oocyte (30.2%, 95% CI = 28.3-32.1 vs. 24.1%, 95% CI = 22.3-25.9) and per fertilized oocyte (40.8%, 95%CI = 38.5-43.1 vs. 33.2%, 95% CI = 30.8-35.5) (P < 0.0001). Delivery rate was comparable between groups (37.2%, 95% CI = 30.8-46.6 vs. 36.9%, 95% CI = 30.4-43.4; NS).

CONCLUSIONS

Our data demonstrate that HPC and trehalose are suitable and safe substitutes for serum and sucrose. Therefore, the new commercial media can be used efficiently in the vitrification of human oocytes avoiding viral and endotoxin contamination risk.

Force Field Development for Lipid Membrane Simulations

With the rapid development of computer power and wide availability of modelling software computer simulations of realistic models of lipid membranes, including their interactions with various molecular species, polypeptides and membrane proteins have become feasible for many research groups. The crucial issue of the reliability of such simulations is the quality of the force field, and many efforts, especially in the latest several years, have been devoted to parametrization and optimization of the force fields for biomembrane modelling. In this review, we give account of the recent development in this area, covering different classes of force fields, principles of the force field parametrization, comparison of the force fields, and their experimental validation. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Structural and functional stabilization of protein entities: state-of-the-art

Within the context of biomedicine and pharmaceutical sciences, the issue of (therapeutic) protein stabilization assumes particular relevance. Stabilization of protein and protein-like molecules translates into preservation of both structure and functionality during storage and/or targeting, and such stabilization is mostly attained through establishment of a thermodynamic equilibrium with the (micro)environment. The basic thermodynamic principles that govern protein structural transitions and the interactions of the protein molecule with its (micro)environment are, therefore, tackled in a systematic fashion. Highlights are given to the major classes of (bio)therapeutic molecules, viz. enzymes, recombinant proteins, (macro)peptides, (monoclonal) antibodies and bacteriophages. Modification of the microenvironment of the biomolecule via multipoint covalent attachment onto a solid surface followed by hydrophilic polymer co-immobilization, or physical containment within nanocarriers, are some of the (latest) strategies discussed aiming at full structural and functional stabilization of said biomolecules.

Molecular dynamics simulations and NMR spectroscopy studies of trehalose-lipid bilayer systems

The disaccharide trehalose (TRH) strongly affects the physical properties of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH using NMR spectroscopy and molecular dynamics (MD) computer simulations. We compare dipolar couplings derived from DMPC/TRH trajectories with those determined (i) experimentally in TRH using conventional high-resolution NMR in a weakly ordered solvent (bicelles), and (ii) by solid-state NMR in multilamellar vesicles (MLV) formed by DMPC. Analysis of the experimental and MD-derived couplings in DMPC indicated that the force field used in the simulations reasonably well describes the experimental results with the exception for the glycerol fragment that exhibits significant deviations. The signs of dipolar couplings, not available from the experiments on highly ordered systems, were determined from the trajectory analysis. The crucial step in the analysis of residual dipolar couplings (RDCs) in TRH determined in a bicelle-environment was access to the conformational distributions derived from the MD trajectory. Furthermore, the conformational behavior of TRH, investigated by J-couplings, in the ordered and isotropic phases is essentially identical, indicating that the general assumptions in the analyses of RDCs are well founded.

Anhydrobiosis in yeast: FT-IR spectroscopic studies of yeast grown under conditions of severe oxygen limitation

Anhydrobiosis is a unique state of living organisms when metabolism is temporarily and reversibly delayed in response to the extreme desiccation of cells. The production of dry active preparations of yeast grown under anaerobic conditions is not currently possible because preparations are extremely sensitive to the dehydration procedure, though they could be very helpful in different biotechnological processes, including bioethanol production. To characterize mechanisms responsible for such sensitivity to the dehydration procedure, Fourier transform infrared spectroscopy was used to study the composition of aerobically grown yeast Saccharomyces cerevisiae resistant to dehydration and grown under conditions of severe oxygen limitation and sensitive to dehydration. Results indicated that significantly lower amounts of lipids in cells, grown under conditions of severe oxygen limitation, may be related to the mechanisms of sensitivity. Dehydration of both resistant and sensitive S. cerevisiae cells was accompanied by similar changes in main cellular compounds. Amounts of nucleic acids and proteins decreased slightly, whereas that of lipids and carbohydrates increased. Artificially reduced sensitivity to dehydration in S. cerevisiae cells, grown under conditions of severe oxygen limitation, led to the increase in the lipid concentration. The chemical composition of S. cerevisiae membranes is proposed to dictate the resistance to dehydration in resistant and sensitive cells.

Anhydrobiosis in yeast: is it possible to reach anhydrobiosis for yeast grown in conditions with severe oxygen limitation?

The yeast Saccharomyces cerevisiae was shown to be extremely sensitive to dehydration-rehydration treatments when stationary phase cells were subjected to conditions of severe oxygen limitation, unlike the same cells grown in aerobic conditions. The viability of dehydrated anaerobically grown yeast cells never exceeded 2 %. It was not possible to increase this viability using gradual rehydration of dry cells in water vapour, which usually strongly reduces damage to intracellular membranes. Specific pre-dehydration treatments significantly increased the resistance of anaerobic yeast to drying. Thus, incubation of cells with trehalose (100 mM), increased the viability of dehydrated cells after slow rehydration in water vapour to 30 %. Similarly, pre-incubation of cells in 1 M xylitol or glycerol enabled up to 50-60 % of cells to successfully enter a viable state of anhydrobiosis after subsequent rehydration. We presume that trehalose and sugar alcohols function mainly according to a water replacement hypothesis, as well as initiating various protective intracellular reactions.

Interspecies interaction extends bacterial survival at solid-air interfaces

Despite the ubiquity of biofilms in natural and man-made environments, research on surface-associated cells has focused primarily on solid-liquid interfaces. This study evaluated the extent to which bacterial cells persist on inanimate solid-air interfaces. The desiccation tolerance of bacterial strains isolated from indoor air, as well as of a test strain (Pseudomonas aeruginosa), was determined at different levels of relative humidity (RH) using the large droplet inoculation method in an aerosol chamber. The cells survived longer at lower (25 and 42%) than at high RH (95%). Four of the seven indoor strains selected for further study showed extended period of survival following deposition as 0.05-0.1 ml of washed culture followed by desiccation, each with different effects on the survival of the test strain, P. aeruginosa. A strain closely related to Arthrobacter species afforded the highest level of protection to the test strain. Even though the desiccation-tolerant strains survived when they were deposited as bioaerosols, the protective role towards the test strain was not observed when the latter was deposited as a bioaerosol. These, which are often-unculturable, bacteria may go undetected during routine monitoring of biofouling, thereby allowing them to act as reservoirs and extending the habitat range of undesired microorganisms.

Taste of sugar at the membrane: thermodynamics and kinetics of the interaction of a disaccharide with lipid bilayers

Sugar recognition at the membrane is critical in various physiological processes. Many aspects of sugar-membrane interaction are still unknown. We take an integrated approach by combining conventional molecular-dynamics simulations with enhanced sampling methods and analytical models to understand the thermodynamics and kinetics of a di-mannose molecule in a phospholipid bilayer system. We observe that di-mannose has a slight preference to localize at the water-phospholipid interface. Using umbrella sampling, we show the free energy bias for this preferred location to be just -0.42 kcal/mol, which explains the coexistence of attraction and exclusion mechanisms of sugar-membrane interaction. Accurate estimation of absolute entropy change of water molecules with a two-phase model indicates that the small energy bias is the result of a favorable entropy change of water molecules. Then, we incorporate results from molecular-dynamics simulation in two different ways to an analytical diffusion-reaction model to obtain association and dissociation constants for di-mannose interaction with membrane. Finally, we verify our approach by predicting concentration dependence of di-mannose recognition at the membrane that is consistent with experiment. In conclusion, we provide a combined approach for the thermodynamics and kinetics of a weak ligand-binding system, which has broad implications across many different fields.

Effect of carrageenans of different chemical structures in biointerfaces: a Langmuir film study

Carrageenans have unique properties in the pharmaceutical and food industries that involve interactions with lipid interfaces, which may be accessed if surface chemistry techniques are employed. The interaction between three different types of carrageenans with dipalmitoylphosphatidylcholine (DPPC) was investigated using Langmuir monolayers as biointerface models. With a combination of data on Surface Pressure-Area Isotherms and Polarization Modulation Infrared Reflection-Absorption Spectroscopy (PM-IRRAS), the effect of different fractions on DPPC monolayers was compared by considering the chemical and structural differences as well as the anticoagulant activity of each fraction. Thus, a model is proposed in which carrageenans can encompass interactions that are maximized due to geometrical adaptations on behalf of the interactions between polysaccharide sulfate groups and lipid polar heads.

Xeroprotectants for the stabilization of biomaterials

With the advancement of science and technology, it is crucial to have effective preservation methods for the stable long-term storage of biological material (biomaterials). As an alternative to cryopreservation, various techniques have been developed, which are based on the survival mechanism of anhydrobiotic organisms. In this sense, it has been found that the synthesis of xeroprotectants can effectively stabilize biomaterials in a dry state. The most widely studied xeroprotectant is trehalose, which has excellent properties for the stabilization of certain proteins, bacteria, and biological membranes. There have also been attempts to apply trehalose to the stabilization of eukaryotic cells but without conclusive results. Consequently, a xeroprotectant or method that is useful for the stable drying of a particular biomaterial might not necessarily be suitable for another one. This article provides an overview of recent advances in the use of new techniques to stabilize biomaterials and compare xeroprotectants with other more standard methods.

Carbohydrate force fields

Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion.

An NMR database for simulations of membrane dynamics

Computational methods are powerful in capturing the results of experimental studies in terms of force fields that both explain and predict biological structures. Validation of molecular simulations requires comparison with experimental data to test and confirm computational predictions. Here we report a comprehensive database of NMR results for membrane phospholipids with interpretations intended to be accessible by non-NMR specialists. Experimental ¹³C-¹H and ²H NMR segmental order parameters (S(CH) or S(CD)) and spin-lattice (Zeeman) relaxation times (T(1Z)) are summarized in convenient tabular form for various saturated, unsaturated, and biological membrane phospholipids. Segmental order parameters give direct information about bilayer structural properties, including the area per lipid and volumetric hydrocarbon thickness. In addition, relaxation rates provide complementary information about molecular dynamics. Particular attention is paid to the magnetic field dependence (frequency dispersion) of the NMR relaxation rates in terms of various simplified power laws. Model-free reduction of the T(1Z) studies in terms of a power-law formalism shows that the relaxation rates for saturated phosphatidylcholines follow a single frequency-dispersive trend within the MHz regime. We show how analytical models can guide the continued development of atomistic and coarse-grained force fields. Our interpretation suggests that lipid diffusion and collective order fluctuations are implicitly governed by the viscoelastic nature of the liquid-crystalline ensemble. Collective bilayer excitations are emergent over mesoscopic length scales that fall between the molecular and bilayer dimensions, and are important for lipid organization and lipid-protein interactions. Future conceptual advances and theoretical reductions will foster understanding of biomembrane structural dynamics through a synergy of NMR measurements and molecular simulations.

Ca(2+) bridging of apposed phospholipid bilayers

In an effort to provide insight into the mechanism of Ca(2+)-induced fusion of lipid vesicles, molecular dynamics simulations in the isobaric-isothermal ensemble are used to investigate interactions of Ca(2+) with apposed lipid bilayers in close proximity. Simulations reveal the formation of a Ca(2+)-phospholipid "anhydrous complex" between apposed bilayers, whereas similar calculations performed with Na(+) display only complexation between neighboring lipids within the same bilayer. The binding of Ca(2+) to apposed phospholipids brings large regions of the bilayers into close contact (<4 Å), displacing water from phospholipid head groups in the process and creating regions of local dehydration. Dehydration of the apposed bilayers leads to ordering of the phospholipid tails, which is partially disrupted by the presence of Ca(2+)-phospholipid bridges.

Lipid-protein correlations in nanoscale phospholipid bilayers determined by solid-state nuclear magnetic resonance

Nanodiscs are examples of discoidal nanoscale lipid-protein particles that have been extremely useful for the biochemical and biophysical characterization of membrane proteins. They are discoidal lipid bilayer fragments encircled and stabilized by two amphipathic helical proteins named membrane scaffolding protein (MSP), ~10 nm in size. Nanodiscs are homogeneous, easily prepared with reproducible success, amenable to preparations with a variety of lipids, and stable over a range of temperatures. Here we present solid-state nuclear magnetic resonance (SSNMR) studies on lyophilized, rehydrated POPC Nanodiscs prepared with uniformly (13)C-, (15)N-labeled MSP1D1 (Δ1-11 truncated MSP). Under these conditions, by SSNMR we directly determine the gel-to-liquid crystal lipid phase transition to be at 3 ± 2 °C. Above this phase transition, the lipid (1)H signals have slow transverse relaxation, enabling filtering experiments as previously demonstrated for lipid vesicles. We incorporate this approach into two- and three-dimensional heteronuclear SSNMR experiments to examine the MSP1D1 residues interfacing with the lipid bilayer. These (1)H-(13)C and (1)H-(13)C-(13)C correlation spectra are used to identify and quantify the number of lipid-correlated and solvent-exposed residues by amino acid type, which furthermore is compared with molecular dynamics studies of MSP1D1 in Nanodiscs. This study demonstrates the utility of SSNMR experiments with Nanodiscs for examining lipid-protein interfaces and has important applications for future structural studies of membrane proteins in physiologically relevant formulations.

Water replacement hypothesis in atomic details: effect of trehalose on the structure of single dehydrated POPC bilayers

We present molecular dynamics (MD) simulations to study the plausibility of the water replacement hypothesis (WRH) from the viewpoint of structural chemistry. A total of 256 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC) lipids were modeled for 400 ns at 11.7 or 5.4 waters/lipid. To obtain a single dehydrated bilayer relevant to the WRH, simulations were performed in the NP(xy)h(z)T ensemble with h(z) > 8 nm, allowing interactions between lipids in the membrane plane and preventing interactions between neighboring membranes via periodic boundary conditions. This setup resulted in a stable single bilayer in (or near) the gel state. Trehalose caused a concentration-dependent increase of the area per lipid (APL) accompanied by fluidizing the bilayer core. This mechanism has been suggested by the WRH. However, dehydrated bilayers in the presence of trehalose were not structurally identical to fully hydrated bilayers. The headgroup vector was in a more parallel orientation in dehydrated bilayers with respect to the bilayer plane and maintained this orientation in the presence of trehalose in spite of APL increase. The total dipole potential changed sign in dehydrated bilayers and remained slightly positive in the presence of trehalose. The model of a dehydrated bilayer presented here allows the study of the mechanisms of membrane protection against desiccation by different compounds.