Simple method to assess foam structure and stability using hydrophobin and BSA as model systems

The properties and arrangement of surface-active molecules at air-water interfaces influence foam stability and bubble shape. Such multiscale-relationships necessitate a well-conducted analysis of microscopic foam properties. We introduce a novel automated and precise method to characterize bubble growth, size distribution and shape based on image analysis and using the machine learning algorithm Cellpose. Studying the temporal evolution of bubble size and shape facilitates conclusions on foam stability. The addition of two sets of masks, for tiny bubbles and large bubbles, provides for a high precision of analysis. A python script for analysis of the evolution of bubble diameter, circularity and dispersity is provided in the supplementary information. Using foams stabilized by bovine serum albumin (BSA), hydrophobin (HP), and blends thereof, we show how this technique can be used to precisely characterize foam structures. Foams stabilized by HP show a significantly increased foam stability and rounder bubble shape than BSA-stabilized foams. These differences are induced by the different molecular structure of the two proteins. Our study shows that the proposed method provides an efficient way to analyse relevant foam properties in detail and at low cost, with higher precision than conventional methods of image analysis.

Measurement of Ice Nucleation Activity of Biological Samples

Experimentation with ice-nucleating biomolecules is needed to advance the fundamental understanding of biotic heterogeneous ice nucleation. Standard experimental procedures vary with sample type. Here we describe a generalized primary purification and analysis process to measure ice nucleation activity of biological samples using an advanced freezing droplet assay.

Functional aggregation of cell-free proteins enables fungal ice nucleation

Biological ice nucleation plays a key role in the survival of cold-adapted organisms. Several species of bacteria, fungi, and insects produce ice nucleators (INs) that enable ice formation at temperatures above -10 °C. Bacteria and fungi produce particularly potent INs that can promote water crystallization above -5 °C. Bacterial INs consist of extended protein units that aggregate to achieve superior functionality. Despite decades of research, the nature and identity of fungal INs remain elusive. Here, we combine ice nucleation measurements, physicochemical characterization, numerical modeling, and nucleation theory to shed light on the size and nature of the INs from the fungus Fusarium acuminatum. We find ice-binding and ice-shaping activity of Fusarium IN, suggesting a potential connection between ice growth promotion and inhibition. We demonstrate that fungal INs are composed of small 5.3 kDa protein subunits that assemble into ice-nucleating complexes that can contain more than 100 subunits. Fusarium INs retain high ice-nucleation activity even when only the ~12 kDa fraction of size-excluded proteins are initially present, suggesting robust pathways for their functional aggregation in cell-free aqueous environments. We conclude that the use of small proteins to build large assemblies is a common strategy among organisms to create potent biological INs.

True Origin of Amide I Shifts Observed in Protein Spectra Obtained with Sum Frequency Generation Spectroscopy

Accurate determination of protein structure at interfaces is critical for understanding protein interactions, which is directly relevant to a molecular-level understanding of interfacial proteins in biology and medicine. Vibrational sum frequency generation (VSFG) spectroscopy is often used for probing the protein amide I mode, which reports protein structures at interfaces. Observed peak shifts are attributed to conformational changes and often form the foundation of hypotheses explaining protein working mechanisms. Here, we investigate structurally diverse proteins using conventional and heterodyne-detected VSFG (HD-VSFG) spectroscopy as a function of solution pH. We reveal that blue-shifts of the amide I peak observed in conventional VSFG spectra upon lowering the pH are governed by the drastic change of the nonresonant contribution. Our results highlight that connecting changes in conventional VSFG spectra to conformational changes of interfacial proteins can be arbitrary, and that HD-VSFG measurements are required to draw unambiguous conclusions about structural changes in biomolecules.

AlphaFold2 models indicate that protein sequence determines both structure and dynamics

AlphaFold 2 (AF2) has placed Molecular Biology in a new era where we can visualize, analyze and interpret the structures and functions of all proteins solely from their primary sequences. We performed AF2 structure predictions for various protein systems, including globular proteins, a multi-domain protein, an intrinsically disordered protein (IDP), a randomized protein, two larger proteins (> 1000 AA), a heterodimer and a homodimer protein complex. Our results show that along with the three dimensional (3D) structures, AF2 also decodes protein sequences into residue flexibilities via both the predicted local distance difference test (pLDDT) scores of the models, and the predicted aligned error (PAE) maps. We show that PAE maps from AF2 are correlated with the distance variation (DV) matrices from molecular dynamics (MD) simulations, which reveals that the PAE maps can predict the dynamical nature of protein residues. Here, we introduce the AF2-scores, which are simply derived from pLDDT scores and are in the range of [0, 1]. We found that for most protein models, including large proteins and protein complexes, the AF2-scores are highly correlated with the root mean square fluctuations (RMSF) calculated from MD simulations. However, for an IDP and a randomized protein, the AF2-scores do not correlate with the RMSF from MD, especially for the IDP. Our results indicate that the protein structures predicted by AF2 also convey information of the residue flexibility, i.e., protein dynamics.

Toward Understanding Bacterial Ice Nucleation

Bacterial ice nucleators (INs) are among the most effective ice nucleators known and are relevant for freezing processes in agriculture, the atmosphere, and the biosphere. Their ability to facilitate ice formation is due to specialized ice-nucleating proteins (INPs) anchored to the outer bacterial cell membrane, enabling the crystallization of water at temperatures up to −2 °C. In this Perspective, we highlight the importance of functional aggregation of INPs for the exceptionally high ice nucleation activity of bacterial ice nucleators. We emphasize that the bacterial cell membrane, as well as environmental conditions, is crucial for a precise functional INP aggregation. Interdisciplinary approaches combining high-throughput droplet freezing assays with advanced physicochemical tools and protein biochemistry are needed to link changes in protein structure or protein–water interactions with changes on the functional level.

Ice Recrystallization Inhibition Is Insufficient to Explain Cryopreservation Abilities of Antifreeze Proteins

Antifreeze proteins (AFPs) and glycoproteins (AFGPs) are exemplary at modifying ice crystal growth and at inhibiting ice recrystallization (IRI) in frozen solutions. These properties make them highly attractive for cold storage and cryopreservation applications of biological tissue, food, and other water-based materials. The specific requirements for optimal cryostorage remain unknown, but high IRI activity has been proposed to be crucial. Here, we show that high IRI activity alone is insufficient to explain the beneficial effects of AF(G)Ps on human red blood cell (hRBC) survival. We show that AF(G)Ps with different IRI activities cause similar cell recoveries of hRBCs and that a modified AFGP variant with decreased IRI activity shows increased cell recovery. The AFGP variant was found to have enhanced interactions with a hRBC model membrane, indicating that the capability to stabilize cell membranes is another important factor for increasing the survival of cells after cryostorage. This information should be considered when designing novel synthetic cryoprotectants.

Cryofouling avoidance in the Antarctic scallop Adamussium colbecki

The presence of supercooled water in polar regions causes anchor ice to grow on submerged objects, generating costly problems for engineered materials and life-endangering risks for benthic communities. The factors driving underwater ice accretion are poorly understood, and passive prevention mechanisms remain unknown. Here we report that the Antarctic scallop Adamussium colbecki appears to remain ice-free in shallow Antarctic marine environments where underwater ice growth is prevalent. In contrast, scallops colonized by bush sponges in the same microhabitat grow ice and are removed from the population. Characterization of the Antarctic scallop shells revealed a hierarchical micro-ridge structure with sub-micron nano-ridges which promotes directed icing. This concentrates the formation of ice on the growth rings while leaving the regions in between free of ice, and appears to reduce ice-to-shell adhesion when compared to temperate species that do not possess highly ordered surface structures. The ability to control the formation of ice may enable passive underwater anti-icing protection, with the removal of ice possibly facilitated by ocean currents or scallop movements. We term this behavior cryofouling avoidance. We posit that the evolution of natural anti-icing structures is a key trait for the survival of Antarctic scallops in anchor ice zones.

Membranes Are Decisive for Maximum Freezing Efficiency of Bacterial Ice Nucleators

Ice-nucleating proteins (INPs) from Pseudomonas syringae are among the most active ice nucleators known, enabling ice formation at temperatures close to the melting point of water. The working mechanisms of INPs remain elusive, but their ice nucleation activity has been proposed to depend on the ability to form large INP aggregates. Here, we provide experimental evidence that INPs alone are not sufficient to achieve maximum freezing efficiency and that intact membranes are critical. Ice nucleation measurements of phospholipids and lipopolysaccharides show that these membrane components are not part of the active nucleation site but rather enable INP assembly. Substantially improved ice nucleation by INP assemblies is observed for deuterated water, indicating stabilization of assemblies by the stronger hydrogen bonds of D₂O. Together, these results show that the degree of order/disorder and the assembly size are critically important in determining the extent to which bacterial INPs can facilitate ice nucleation.

pH effects on the molecular structure and charging state of β-Escin biosurfactants at the air-water interface

Saponins like β-escin exhibit an unusually high surface activity paired with a remarkable surface rheology which makes them as biosurfactants highly interesting for applications in soft matter colloids and at interfaces. We have applied vibrational sum-frequency generation (SFG) to study β-escin adsorption layers at the air-water interface as a function of electrolyte pH and compare the results from SFG spectroscopy to complementary experiments that have addressed the surface tension and the surface dilational rheology. SFG spectra of β-escin modified air-water interfaces demonstrate that the SFG intensity of OH stretching vibrations from interfacial water molecules is a function of pH and dramatically increases when the pH is increased from acidic to basic conditions and reaches a plateau at a solution pH of > 6. These changes are attributable to the interfacial charging state and to the deprotonation of the carboxylic acid group of β-escin. Thus, the change in OH intensity provides qualitative information on the degree of protonation of this group at the air-water interface. At pH < 4 the air-water interface is dominated by the charge neutral form of β-escin, while at pH > 6 its carboxylic acid group is fully deprotonated and, consequently, the interface is highly charged. These observations are corroborated by the change in equilibrium surface tension which is qualitatively similar to the change in OH intensity as seen in the SFG spectra. Further, once the surface layer is charge neutral, the surface elasticity drastically increases. This can be attributed to a change in prevailing intermolecular interactions that change from dominating repulsive electrostatic interactions at high pH, to dominating attractive interactions, such as hydrophobic and dispersive interactions, as well as, hydrogen bonding at low pH values. In addition to the clear changes in OH intensity from interfacial H₂O, the SFG spectra exhibit drastic changes in the CH bands from interfacial β-escin which we relate to differences in the net molecular orientation. This orientation change is driven by tighter packing of β-escin adsorption layers when the β-escin moiety is in its charge neutral form (pH < 4).

Disaccharide Residues are Required for Native Antifreeze Glycoprotein Activity

Antifreeze glycoproteins (AFGPs) are able to bind to ice, halt its growth, and are the most potent inhibitors of ice recrystallization known. The structural basis for AFGP’s unique properties remains largely elusive. Here we determined the antifreeze activities of AFGP variants that we constructed by chemically modifying the hydroxyl groups of the disaccharide of natural AFGPs. Using nuclear magnetic resonance, two-dimensional infrared spectroscopy, and circular dichroism, the expected modifications were confirmed as well as their effect on AFGPs solution structure. We find that the presence of all the hydroxyls on the disaccharides is a requirement for the native AFGP hysteresis as well as the maximal inhibition of ice recrystallization. The saccharide hydroxyls are apparently as important as the acetyl group on the galactosamine, the α-linkage between the disaccharide and threonine, and the methyl groups on the threonine and alanine. We conclude that the use of hydrogen-bonding through the hydroxyl groups of the disaccharide and hydrophobic interactions through the polypeptide backbone are equally important in promoting the antifreeze activities observed in the native AFGPs. These important criteria should be considered when designing synthetic mimics.

Specific Ion-Protein Interactions Influence Bacterial Ice Nucleation

Ice nucleation‐active bacteria are the most efficient ice nucleators known, enabling the crystallization of water at temperatures close to 0 °C, thereby overcoming the kinetically hindered phase transition process at these conditions. Using highly specialized ice‐nucleating proteins (INPs), they can cause frost damage to plants and influence the formation of clouds and precipitation in the atmosphere. In nature, the bacteria are usually found in aqueous environments containing ions. The impact of ions on bacterial ice nucleation efficiency, however, has remained elusive. Here, we demonstrate that ions can profoundly influence the efficiency of bacterial ice nucleators in a manner that follows the Hofmeister series. Weakly hydrated ions inhibit bacterial ice nucleation whereas strongly hydrated ions apparently facilitate ice nucleation. Surface‐specific sum‐frequency generation spectroscopy and molecular dynamics simulations reveal that the different effects are due to specific interactions of the ions with the INPs on the surface of the bacteria. Our results demonstrate that heterogeneous ice nucleation facilitated by bacteria strongly depends upon the nature of the ions, and specific ion–protein interactions are essential for the complete description of heterogeneous ice nucleation by bacteria.

Ice Nucleation Activity of Perfluorinated Organic Acids

Perfluorinated acids (PFAs) are widely used synthetic chemical compounds, highly resistant to environmental degradation. The widespread PFA contamination in remote regions such as the High Arctic implies currently not understood long-range atmospheric transport pathways. Here, we report that perfluorooctanoic acid (PFOA) initiates heterogeneous ice nucleation at temperatures as high as -16 °C. In contrast, the eight-carbon octanoic acid, perfluorooctanesulfonic acid, and deprotonated PFOA showed poor ice nucleating capabilities. The ice nucleation ability of PFOA correlates with the formation of a PFOA monolayer at the air-water interface, suggesting a mechanism in which the aligned hydroxyl groups of the carboxylic acid moieties provide a lattice matching to ice. The ice nucleation capabilities of fluorinated compounds like PFOA might be relevant for cloud glaciation in the atmosphere and the removal of these persistent pollutants by wet deposition.

Interfacial Water Ordering Is Insufficient to Explain Ice-Nucleating Protein Activity

Ice-nucleating proteins (INPs) found in bacteria are the most effective ice nucleators known, enabling the crystallization of water at temperatures close to 0 °C. Although their function has been known for decades, the underlying mechanism is still under debate. Here, we show that INPs from Pseudomonas syringae in aqueous solution exhibit a defined solution structure and show no significant conformational changes upon cooling. In contrast, irreversible structural changes are observed upon heating to temperatures exceeding ∼55 °C, leading to a loss of the ice-nucleation activity. Sum-frequency generation (SFG) spectroscopy reveals that active and heat-inactivated INPs impose similar structural ordering of interfacial water molecules upon cooling. Our results demonstrate that increased water ordering is not sufficient to explain INPs' high ice-nucleation activity and confirm that intact three-dimensional protein structures are critical for bacterial ice nucleation, supporting a mechanism that depends on the INPs' supramolecular interactions.

Freezing of Aqueous Carboxylic Acid Solutions on Ice

We study the properties of acetic acid and propionic acid solutions at the surface of monocrystalline ice with surface-specific vibrational sum-frequency generation (VSFG) and heterodyne-detected vibrational sum-frequency generation spectroscopy (HD-VSFG). When we decrease the temperature toward the eutectic point of the acid solutions, we observe the formation of a freeze concentrated solution (FCS) of the carboxylic acids that is brought about by a freeze-induced phase separation (FIPS). The freeze concentrated solution freezes on top of the ice surface as we cool the system below the eutectic point. We find that for freeze concentrated acetic acid solutions the freezing causes a strong decrease of the VSFG signal, while for propionic acid an increase and a blue-shift are observed. This different behavior points at a distinct difference in molecular-scale behavior when cooling below the eutectic point. We find that cooling of the propionic acid solution below the eutectic point leads to the formation of hydrogen-bonded dimers with an opposite alignment of the carboxylic acid O–H groups.

Inhibition of Bacterial Ice Nucleators Is Not an Intrinsic Property of Antifreeze Proteins

Cold-adapted organisms use antifreeze proteins (AFPs) or ice-nucleating proteins (INPs) for the survival in freezing habitats. AFPs have been reported to be able to inhibit the activity of INPs, a property that would be of great physiological relevance. The generality of this effect is not understood, and for the few known examples of INP inhibition by AFPs, the molecular mechanisms remain unclear. Here, we report a comprehensive evaluation of the effects of five different AFPs on the activity of bacterial ice nucleators using a high-throughput ice nucleation assay. We find that bacterial INPs are inhibited by certain AFPs, while others show no effect. Thus, the ability to inhibit the activity of INPs is not an intrinsic property of AFPs, and the interactions of INPs and different AFPs proceed through protein-specific rather than universal molecular mechanisms.

Decoding the molecular water structure at complex interfaces through surface-specific spectroscopy of the water bending mode

The structure of interfacial water determines atmospheric chemistry, wetting properties of materials, and protein folding. The challenge of investigating the properties of specific interfacial water molecules has frequently been confronted using surface-specific sum-frequency generation (SFG) vibrational spectroscopy using the O-H stretch mode. While perfectly suited for the water-air interface, for complex interfaces, a potential complication arises from the contribution of hydroxyl or amine groups of non-water species present at the surface, such as surface hydroxyls on minerals, or O-H and N-H groups contained in proteins. Here, we present a protocol to extract the hydrogen bond strength selectively of interfacial water, through the water bending mode. The bending mode vibrational frequency distribution provides a new avenue for unveiling the hydrogen bonding structure of interfacial water at complex aqueous interfaces. We demonstrate this method for the water-CaF₂ and water-protein interfaces. For the former, we show that this method can indeed single out water O-H groups from surface hydroxyls, and that with increasing pH, the hydrogen-bonded network of interfacial water strengthens. Furthermore, we unveil enhanced hydrogen bonding of water, compared to bulk water, at the interface with human serum albumin proteins, a prototypical bio-interface.

Electrostatic Interactions Control the Functionality of Bacterial Ice Nucleators

Bacterial ice-nucleating proteins (INPs) promote heterogeneous ice nucleation more efficiently than any other material. The details of their working mechanism remain elusive, but their high activity has been shown to involve the formation of functional INP aggregates. Here we reveal the importance of electrostatic interactions for the activity of INPs from the bacterium Pseudomonas syringae by combining a high-throughput ice nucleation assay with surface-specific sum-frequency generation spectroscopy. We determined the charge state of nonviable P. syringae as a function of pH by monitoring the degree of alignment of the interfacial water molecules and the corresponding ice nucleation activity. The net charge correlates with the ice nucleation activity of the INP aggregates, which is minimal at the isoelectric point. In contrast, the activity of INP monomers is less affected by pH changes. We conclude that electrostatic interactions play an essential role in the formation of the highly efficient functionally aligned INP aggregates, providing a mechanism for promoting aggregation under conditions of stress that prompt the bacteria to nucleate ice.

Determination of the Solution Structure of Antifreeze Glycoproteins Using Two-Dimensional Infrared Spectroscopy

We study the solution structure of antifreeze glycoproteins (AFGPs) with linear and two-dimensional infrared spectroscopy (2D-IR). With 2D-IR, we study the coupling between the amide I and amide II vibrations of AFGPs. The measured nonlinear spectral response constitutes a much more clearly resolved amide I spectrum than the linear absorption spectrum of the amide I vibrations and allows us to identify the different structural elements of AFGPs in solution. We find clear evidence for the presence of polyproline II (PPII) helical structures already at room temperature, and we find that the fraction of PPII structures increases when the temperature is decreased to the biological working temperature of AFGP. We observe that inhibition of the antifreeze activity of AFGP using borate buffer or enhancing the antifreeze activity using sulfate buffer does not lead to significant changes in the protein conformation. This finding indicates that AFGPs bind to ice with their sugar side chains.

Surface Structure of Solutions of Poly(vinyl alcohol) in Water

We use surface-specific heterodyne-detected vibrational sum-frequency generation spectroscopy (HD-VSFG) and surface tension measurements to investigate the molecular structure of the surface of aqueous solutions of poly(vinyl alcohol) (PVA) polymers with average molecular weights of 10000 and 125000 g/mol. We find that the interfacial water molecules have a preferred orientation with their hydrogen-bonded O-H groups pointing away from the bulk, for both PVA₁₀₀₀₀ and PVA₁₂₅₀₀₀. This observation is explained from the ongoing hydrolysis of the acetyl impurities on the PVA polymer chains. This hydrolysis yields negatively charged acetate ions that have a relatively high surface propensity. For both PVA₁₀₀₀₀ and PVA₁₂₅₀₀₀ the strong positive signal vanishes when the pH is decreased, due to the neutralization of the acetate ions. For solutions with a high concentration of PVA₁₀₀₀₀ the interfacial water signal becomes very small, indicating that the surface gets completely covered with a disordered PVA polymer film. In contrast, for high concentrations of PVA₁₂₅₀₀₀, the strong positive water signal persists at high pH, which shows that the water surface does not get completely covered. The HD-VSFG data combined with surface tension data indicate that concentrated PVA₁₂₅₀₀₀ solutions form a structured surface layer with pores containing a high density of interfacial water.

Antifreeze Glycoproteins Bind Irreversibly to Ice

Antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs) inhibit ice growth via an adsorption-inhibition mechanism that assumes irreversible binding of AF(G)Ps to embryonic ice crystals and the inhibition of further growth. The irreversible binding of antifreeze glycoproteins (AFGPs) to ice has been questioned and remains poorly understood. Here, we used microfluidics and fluorescence microscopy to investigate the nature of the binding of small and large AFGP isoforms. We found that both AFGP isoforms bind irreversibly to ice, as evidenced by microfluidic solution exchange experiments. We measured the adsorption rate of the large AFGP isoform and found it to be 50% faster than that of AFP type III. We also found that the AFGP adsorption rate decreased by 65% in the presence of borate, a well-known inhibitor of AFGP activity. Our results demonstrate that the adsorption rate of AFGPs to ice is crucial for their ice growth inhibition capability.

Molecular Structure of Hydrophobins Studied with Site-Directed Mutagenesis and Vibrational Sum-Frequency Generation Spectroscopy

Hydrophobins are surface-active fungal proteins that adsorb to the water-air interface and self-assemble into amphiphilic, water-repelling films that have a surface elasticity that is an order of magnitude higher than other molecular films. Here we use surface-specific sum-frequency generation spectroscopy (VSFG) and site-directed mutagenesis to study the properties of class I hydrophobin (HFBI) films from Trichoderma reesei at the molecular level. We identify protein specific HFBI signals in the frequency region 1200-1700 cm-1 that have not been observed in previous VSFG studies on proteins. We find evidence that the aspartic acid residue (D30) next to the hydrophobic patch is involved in lateral intermolecular protein interactions, while the two aspartic acid residues (D40, D43) opposite to the hydrophobic patch are primarily interacting with the water solvent.

Observation of pH-Induced Protein Reorientation at the Water Surface

Hydrophobins are surface-active proteins that form a hydrophobic, water-repelling film around aerial fungal structures. They have a compact, particle-like structure, in which hydrophilic and hydrophobic regions are spatially separated. This surface property renders them amphiphilic and is reminiscent of synthetic Janus particles. Here we report surface-specific chiral and nonchiral vibrational sum-frequency generation spectroscopy (VSFG) measurements of hydrophobins adsorbed to their natural place of action, the air-water interface. We observe that hydrophobin molecules undergo a reversible change in orientation (tilt) at the interface when the pH is varied. We explain this local orientation toggle from the modification of the interprotein interactions and the interaction of hydrophobin with the water solvent, following the pH-induced change of the charge state of particular amino acids.

Reduced Acid Dissociation of Amino-Acids at the Surface of Water

We use surface-specific intensity vibrational sum-frequency generation and attenuated total reflection spectroscopy to probe the ionization state of the amino-acids l-alanine and l-proline at the air/water surface and in the bulk. The ionization state is determined by probing the vibrational signatures of the carboxylic acid group, representing the nondissociated acid form, and the carboxylate anion group, representing the dissociated form, over a wide range of pH values. We find that the carboxylic acid group deprotonates at a significantly higher pH at the surface than in the bulk.

Identification of the response of protein N–H vibrations in vibrational sum-frequency generation spectroscopy of aqueous protein films

We study the response of protein N–H vibrations in aqueous hydrophobin films using vibrational sum- frequency generation spectroscopy.

Dynamics of the Hydration Water of Antifreeze Glycoproteins

Antifreeze glycoproteins (AFGPs) are unique proteins that inhibit the growth of ice by a mechanism that is still unclear. We study the dynamics of water in aqueous solutions of small and large isoforms of AFGPs using polarization-resolved femtosecond infrared spectroscopy. We find that a fraction of the water molecules is strongly slowed down by the interaction with the antifreeze glycoprotein surface. The fraction of slow water molecules scales with the size and concentration of AFGP, and is similar to the fraction of slow water observed for nonantifreeze proteins, both at room temperature and close to biologically relevant working temperatures. We observe that inhibiting AFGP antifreeze activity using borate buffer induces no changes in the dynamics of water hydrating the AFGP. Our findings support a mechanism in which the sugar unit of AFGP forms the active ice-binding site.

Self-Assembly and Conformational Changes of Hydrophobin Classes at the Air-Water Interface

We use surface-specific vibrational sum-frequency generation spectroscopy (VSFG) to study the structure and self-assembling mechanism of the class I hydrophobin SC3 from Schizophyllum commune and the class II hydrophobin HFBI from Trichoderma reesei. We find that both hydrophobins readily accumulate at the water-air interface and form rigid, highly ordered protein films that give rise to prominent VSFG signals. We identify several resonances that are associated with β-sheet structures and assign them to the central β-barrel core present in both proteins. Differences between the hydrophobin classes are observed in their interfacial self-assembly. For HFBI, we observe no changes in conformation upon adsorption to the water surface. For SC3, we observe an increase in β-sheet-specific signals that supports a surface-driven self-assembly mechanism in which the central β-barrel remains intact and stacks into a larger-scale architecture, amyloid-like rodlets.

Heterodyne-detected sum frequency generation spectroscopy of polyacrylic acid at the air/water-interface

A complete picture of the surface affinity and structure of polyacrylic acid at the air–water interface was determined.

Orientation of polar molecules near charged protein interfaces

We study the orientation of water and urea molecules and protein amide vibrations at aqueous α-lactalbumin and α-lactalbumin/urea interfaces using heterodyne-detected vibrational sum frequency generation.

Investigation of the Ice-Binding Site of an Insect Antifreeze Protein Using Sum-Frequency Generation Spectroscopy

We study the ice-binding site (IBS) of a hyperactive antifreeze protein from the beetle Dendroides canadensis (DAFP-1) using vibrational sum-frequency generation spectroscopy. We find that DAFP-1 accumulates at the air-water interface due to the hydrophobic character of its threonine-rich IBS while retaining its highly regular β-helical fold. We observe a narrow band at 3485 cm(-1) that we assign to the O-H stretch vibration of threonine hydroxyl groups of the IBS. The narrow character of the 3485 cm(-1) band suggests that the hydrogen bonds between the threonine residues at the IBS and adjacent water molecules are quite similar in strength, indicating that the IBS of DAFP-1 is extremely well-ordered, with the threonine side chains showing identical rotameric confirmations. The hydrogen-bonded water molecules do not form an ordered ice-like layer, as was recently observed for the moderate antifreeze protein type III. It thus appears that the antifreeze action of DAFP-1 does not require the presence of ordered water but likely results from the direct binding of its highly ordered array of threonine residues to the ice surface.

Non-invasive chemical assessment of living human spermatozoa

Confocal Raman microspectroscopy was used to chemically image single and living human spermatozoa under near-physiological conditions.

Assessing the public health impacts of urban air pollution in 25 European cities: results of the Aphekom project

INTRODUCTION

The Aphekom project aimed to provide new, clear, and meaningful information on the health effects of air pollution in Europe. Among others, it assessed the health and monetary benefits of reducing short and long-term exposure to particulate matter (PM) and ozone in 25 European cities.

METHOD

Health impact assessments were performed using routine health and air quality data, and a common methodology. Two scenarios were considered: a decrease of the air pollutant levels by a fixed amount and a decrease to the World Health Organization (WHO) air quality guidelines. Results were economically valued by using a willingness to pay approach for mortality and a cost of illness approach for morbidity.

RESULTS

In the 25 cities, the largest health burden was attributable to the impacts of chronic exposure to PM2.5. Complying with the WHO guideline of 10 μg/m(3) in annual mean would add up to 22 months of life expectancy at age 30, depending on the city, corresponding to a total of 19,000 deaths delayed. The associated monetary gain would total some €31 billion annually, including savings on health expenditures, absenteeism and intangible costs such as well-being, life expectancy and quality of life.

CONCLUSION

European citizens are still exposed to concentrations exceeding the WHO recommendations. Aphekom provided robust estimates confirming that reducing urban air pollution would result in significant health and monetary gains in Europe. This work is particularly relevant now when the current EU legislation is being revised for an update in 2013.

Long-range protein-water dynamics in hyperactive insect antifreeze proteins

Antifreeze proteins (AFPs) are specific proteins that are able to lower the freezing point of aqueous solutions relative to the melting point. Hyperactive AFPs, identified in insects, have an especially high ability to depress the freezing point by far exceeding the abilities of other AFPs. In previous studies, we postulated that the activity of AFPs can be attributed to two distinct molecular mechanisms: (i) short-range direct interaction of the protein surface with the growing ice face and (ii) long-range interaction by protein-induced water dynamics extending up to 20 Å from the protein surface. In the present paper, we combine terahertz spectroscopy and molecular simulations to prove that long-range protein-water interactions make essential contributions to the high antifreeze activity of insect AFPs from the beetle Dendroides canadensis. We also support our hypothesis by studying the effect of the addition of the osmolyte sodium citrate.

Functional importance of short-range binding and long-range solvent interactions in helical antifreeze peptides

Short-range ice binding and long-range solvent perturbation both have been implicated in the activity of antifreeze proteins and antifreeze glycoproteins. We study these two mechanisms for activity of winter flounder antifreeze peptide. Four mutants are characterized by freezing point hysteresis (activity), circular dichroism (secondary structure), Förster resonance energy transfer (end-to-end rigidity), molecular dynamics simulation (structure), and terahertz spectroscopy (long-range solvent perturbation). Our results show that the short-range model is sufficient to explain the activity of our mutants, but the long-range model provides a necessary condition for activity: the most active peptides in our data set all have an extended dynamical hydration shell. It appears that antifreeze proteins and antifreeze glycoproteins have reached different evolutionary solutions to the antifreeze problem, utilizing either a few precisely positioned OH groups or a large quantity of OH groups for ice binding, assisted by long-range solvent perturbation.

Antifreeze glycoprotein activity correlates with long-range protein-water dynamics

Antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs) enable the survival of organisms living in subfreezing habitats and serve as preservatives. Although their function is known, the underlying molecular mechanism was not understood. Mutagenesis experiments questioned the previous assumption of hydrogen bonding as the dominant mechanism. We use terahertz spectroscopy to show that antifreeze activity is directly correlated with long-range collective hydration dynamics. Our results provide evidence for a new model of how AFGPs prevent water from freezing. We suggest that antifreeze activity may be induced because the AFGP perturbs the aqueous solvent over long distances. Retarded water dynamics in the large hydration shell does not favor freezing. The complexation of the carbohydrate cis-hydroxyl groups by borate suppresses the long-range hydration shell detected by terahertz absorption. The hydration dynamics shift toward bulk water behavior strongly reduces the AFGP antifreeze activity, further supporting our model.

Confocal Raman microspectroscopy as an analytical tool to assess the mitochondrial status in human spermatozoa

Confocal Raman microspectroscopy was used to investigate human sperm cells. Raman mapping with a 532 nm excitation laser allowed to unambiguously characterize the nucleus, the neck, and, in particular, the mitochondria-rich middle piece of a human sperm cell. The effect of ultraviolet radiation on different organelles of the sperm was quantified by localized spectral Raman signatures obtained within milliseconds. Chemical changes within the sub-cellular structure of the sperm cells were recorded as a function of ultraviolet light exposure time, showing the proof-of-principle that Raman microspectroscopy can be a fast diagnostic method for detecting the mitochondrial and motility status of human spermatozoa.

[Dual diagnosis psychosis and substance use disorders in adolescents--part 1]

Epidemiological studies suggest that 20 % to 50 % of patients with schizophrenia have a lifetime comorbid substance use disorder (SUD). In first-episode psychosis this prevalence is even higher and varies between 20 % and 75 % with cannabis being the most widely used illicit drug. These difficult to treat patients usually have a worse prognosis as compared with non-substance abusing schizophrenic patients. Despite multiple theories proposed such as the self medication hypothesis, common or bidirectional factor models or genetic vulnerability, there is no consensus on the aetiology of increased rates of substance use in people with psychosis which is important to treat these patients. The dually diagnosed population is a heterogeneous group and it is likely that different models may explain comorbidity in different subgroups. The present review part one gives an overview on prevalence and explanation models for dual diagnosis psychosis and substance use with focus in adolescent and young adult populations, the second part reviews the clinical course for both disorders and current psychosocial treatment options.

Fast folding of an RNA tetraloop on a rugged energy landscape detected by a stacking-sensitive probe

We investigate the microsecond-timescale kinetics of the RNA hairpin ga*cUUCGguc. The fluorescent nucleotide 2-aminopurine (a*) reports mainly on base stacking. Ten kinetic traces and the temperature denaturation curve are globally fitted to four-state models of the free-energy surface. In the best-fitting sequential model, the hairpin unfolds over successively larger barriers in at least three stages: stem fraying and increased base-stacking fluctuations; concerted loss of hydrogen bonding and partial unstacking; and additional unstacking of single strands at the highest temperatures. Parallel and trap models also provide adequate fits: such pathways probably also play a role in the complete free-energy surface of the hairpin. To interpret the model states structurally, 200 ns of molecular dynamics, including six temperature-jump simulations, were run. Although the sampling is by no means comprehensive, five different states were identified using hydrogen bonding and base stacking as reaction coordinates. The four to five states required to explain the experiments or simulations set a lower limit on the complexity of this small RNA hairpin's energy landscape.

MATSim-T

Micro-simulations for transport planning are becoming increasingly important in traffic simulation, traffic analysis, and traffic forecasting. In the last decades the shift from using typically aggregated data to more detailed, individual based, complex data (e.g. GPS tracking) andthe continuously growing computer performance on fixed price level leads to the possibility of using microscopic models for large scale planning regions. This chapter presents such a micro-simulation. The work is part of the research project MATSim (Multi Agent Transport Simulation, http://matsim.org). In the chapter here the focus lies on design and implementation issues as well as on computational performance of different parts of the system. Based on a study of Swiss daily traffic – ca. 2.3 million individuals using motorized individual transport producing about 7.1 million trips, assigned to a Swiss network model with about 60,000 links, simulated and optimized completely time-dynamic for a complete workday – it is shown that the system is able to generate those traffic patterns in about 36 hours computation time.