Structural and Vibrational Properties of Trehalose: A Density Functional Study

Laser Techniques on Acoustically Levitated Droplets

This work reports the results of an experimental study where laser techniques are applied to acoustically levitated droplets of trehalose aqueous solutions in order to perform spectroscopic analyses as a function of concentration and to test the theoretical diameter law. The study of such systems is important in order to better understand the behaviour of trehalose-synthesizing extremophiles that live in extreme environments. In particular, it will be shown how acoustic levitation, combined with optical spectroscopic instruments allows to explore a wide concentration range and to test the validity of the diameter law as a function of levitation lag time, i.e. the D2 vs t law. On this purpose a direct diameter monitoring by a video camera and a laser pointer was first performed; then the diameter was also evaluated by an indirect measure through an OH/CH band area ratio analysis of collected Raman and Infrared spectra. It clearly emerges that D2 vs t follows a linear trend for about 20 minutes, reaching then a plateau at longer time. This result shows how trehalose is able to avoid total water evaporation, this property being essential for the surviving of organisms under extreme environmental conditions.

Density functional study of adenine tetrads with N6-H6...N3 hydrogen bonds

The structure and energy of A-tetrads with N6-H6...N3 H-bonds was studied using B3LYP and BH&H density functional theory. The planar A-tetrad with C(4h) symmetry is more stable than the nonplanar structures at C4 and S4 symmetry. This structure corresponds to a local energy minimum. The energies of the structures with N6-H6...N1 and N6-H6...N7 H-bonds studied previously are of similar magnitude. Structures of A-tetrad complexes with sodium and potassium were most stable at S4 symmetry, and similarly, sandwich complexes consisting of two tetrads and a single cation were most stable at S8 symmetry. Relative energies of sandwich complexes with different symmetries obtained with the B3LYP and BH&H methods were quite different. BH&H overestimates the interaction energies between hydrogen-bonded neighbor bases relative to B3LYP.

Concentration dependence of vibrational properties of bioprotectant/water mixtures by inelastic neutron scattering

Neutron scattering has been demonstrated to be a powerful tool for characterizing the structure and dynamics of biological molecules and for investigating the physical and chemical mechanisms of biophysical processes. The aim of the present work is to investigate by inelastic neutron scattering (INS) the vibrational behaviour of a class of bioprotectant systems, such as homologous disaccharides, trehalose, maltose and sucrose, in water mixtures. INS measurements have been performed on trehalose/H2O, maltose/H2O and sucrose/H2O mixtures at very low temperature as a function of concentration by using the thermal original spectrometer with cylindrical analyzers (TOSCA) spectrometer at the ISIS Facility (DRAL, UK). The findings allow the analyses of the vibrational features of the INS spectra in order to study the effect of disaccharides on the H2O hydrogen-bonded tetrahedral network. The obtained neutron scattering findings point out that disaccharides, and in particular trehalose, have a destructuring effect on the water tetrahedral network, as emphasized by the analysis of the librational modes region from 50 to 130 meV energy transfer. On the other hand, the analysis of the bending modes region (130-225 meV) shows a locally ordered structure in the disaccharide/H2O mixtures.Finally, the observed experimental evidences are linked to the different bioprotective effectiveness of disaccharides as a function of concentration.

Changes in vibrational modes of water and bioprotectants in solution

Inelastic neutron scattering (INS) measurements have been performed on trehalose and sucrose/H(2)O mixtures at very low temperature as a function of concentration by using the TOSCA spectrometer at the ISIS Facility (DRAL, UK). The aim of this work is to investigate by INS the vibrational behaviour of water in presence of trehalose and sucrose in order to characterize the changes induced by these disaccharides on the H(2)O hydrogen-bonded network. In particular, we obtained information about the effects of the two disaccharides in the translational, librational and bending spectral regions of ice. The disaccharide bioprotective effectiveness can be linked by the high destructuring effect emphasised by the analysis of the librational modes region. On the other hand, the analysis of the vibrational region corresponding to the ice bending modes show a high "crystallinity" degree which can justify the cryptobiotic action of disaccharides.

Infrared absorption study of the heme pocket dynamics of carbonmonoxyheme proteins

The temperature dependencies of the infrared absorption CO bands of carboxy complexes of horseradish peroxidase (HRP(CO)) in glycerol/water mixture at pH 6.0 and 9.3 are interpreted using the theory of optical absorption bandshape. The bands' anharmonic behavior is explained assuming that there is a higher-energy set of conformational substates (CSS(h)), which are populated upon heating and correspond to the protein substates with disordered water molecules in the heme pocket. Analysis of the second moments of the CO bands of the carboxy complexes of myoglobin (Mb(CO)) and hemoglobin (Hb(CO)), and of HRP(CO) with benzohydroxamic acid (HRP(CO)+BHA), shows that the low energy CSS(h) exists also in the open conformation of Mb(CO), where the heme pocket is spacious enough to accommodate a water molecule. In the HRP(CO)+BHA and closed conformations of Mb(CO) and Hb(CO), the heme pocket is packed with BHA and different amino acids, the CSS(h) has much higher energy and is hardly populated even at the highest temperatures. Therefore only motions of these amino acids contribute to the band broadening. These motions are linked to the protein surface and frozen in the glassy matrix, whereas in the liquid solvent they are harmonic. Thus the second moment of the CO band is temperature-independent in glass and is proportional to the temperature in liquid. The temperature dependence of the second moment of the CO peak of HRP(CO) in the trehalose glass exhibits linear coupling to an oscillator. This oscillator can be a moving water molecule locked in the heme pocket in the whole interval of temperatures or a trehalose molecule located in the heme pocket.

Inelastic neutron scattering study on bioprotectant systems

We collected inelastic neutron scattering (INS) spectra of homologous disaccharide (C12H22O11)/H2O mixtures at a very low temperature by using indirect geometry time-of-flight spectrometer TOSCA at the ISIS pulse neutron facility (DRAL, UK). The aim of this work is to investigate the vibrational behaviour of trehalose, maltose and sucrose/H2O mixtures with INS in order to characterize the structural changes induced by these disaccharides on the H2O hydrogen-bonded network. A higher degree of 'crystallinity' for the trehalose/H2O system is observed in the vibrational region corresponding to the ice bending modes. This feature could justify the better cryptobiotic action of trehalose compared with maltose and sucrose. On the other hand, the better bioprotective effectiveness could be explained by the higher destructuring effect of trehalose, emphasized by the analysis of the librational modes region.

Substrate Distortion in the Michaelis Complex of Bacillus 1,3–1,4-β-Glucanase

The structure and dynamics of the enzyme-substrate complex of Bacillus 1,3-1,4-beta-glucanase, one of the most active glycoside hydrolases, is investigated by means of Car-Parrinello molecular dynamics simulations (CPMD) combined with force field molecular dynamics (QM/MM CPMD). It is found that the substrate sugar ring located at the -1 subsite adopts a distorted 1S3 skew-boat conformation upon binding to the enzyme. With respect to the undistorted 4C1 chair conformation, the 1S3 skew-boat conformation is characterized by: (a) an increase of charge at the anomeric carbon (C1), (b) an increase of the distance between C1 and the leaving group, and (c) a decrease of the intraring O5-C1 distance. Therefore, our results clearly show that the distorted conformation resembles both structurally and electronically the transition state of the reaction in which the substrate acquires oxocarbenium ion character, and the glycosidic bond is partially broken. Together with analysis of the substrate conformational dynamics, it is concluded that the main determinants of substrate distortion have a structural origin. To fit into the binding pocket, it is necessary that the aglycon leaving group is oriented toward the beta region, and the skew-boat conformation naturally fulfills this premise. Only when the aglycon is removed from the calculation the substrate recovers the all-chair conformation, in agreement with the recent determination of the enzyme product structure. The QM/MM protocol developed here is able to predict the conformational distortion of substrate binding in glycoside hydrolases because it accounts for polarization and charge reorganization at the -1 sugar ring. It thus provides a powerful tool to model E.S complexes for which experimental information is not yet available.

The Influence of Aqueous versus Glassy Solvents on Protein Dynamics: Vibrational Echo Experiments and Molecular Dynamics Simulations

Spectrally resolved infrared stimulated vibrational echo measurements are used to measure the vibrational dephasing of the CO stretching mode of carbonmonoxy-hemoglobin (HbCO), a myoglobin mutant (H64V), and a bacterial cytochrome c(552) mutant (Ht-M61A) in aqueous solution and trehalose glasses. The vibrational dephasing of the heme-bound CO is significantly slower for all three proteins embedded in trehalose glasses compared to that of aqueous protein solutions. All three proteins exhibit persistent but notably slower spectral diffusion when the protein surface is fixed by the glassy solvent. Frequency-frequency correlation functions (FFCFs) of the CO are extracted from the vibrational echo data to reveal that the structural dynamics, as sensed by the CO, of the three proteins in trehalose and aqueous solution are dominated by fast (tens of femtoseconds), motionally narrowed fluctuations. MD simulations of H64V in dynamic and "static" water are presented as models of the aqueous and glassy environments. FFCFs are calculated from the H64V simulations and qualitatively reproduce the important features of the experimentally extracted FFCFs. The suppression of long time scale (picoseconds to tens of picoseconds) frequency fluctuations (spectral diffusion) in the glassy solvent is the result of a damping of atomic displacements throughout the protein structure and is not limited to structural dynamics that occur only at the protein surface. The analysis provides evidence that some dynamics are coupled to the hydration shell of water, supporting the idea that the bioprotection offered by trehalose is due to its ability to immobilize the protein surface through a thin, constrained layer of water.

Mean-square displacement relationship in bioprotectant systems by elastic neutron scattering

Neutron intensity elastic scans on trehalose, maltose, and sucrose/H(2)O mixtures as a function of concentration, temperature, and exchanged wave vector are presented. The experimental findings show a crossover in molecular fluctuations between harmonic and anharmonic dynamical regimes. A new operative definition for the degree of fragility of glass-forming systems is furnished by using explicitly the connection between viscosity and mean-square displacement. The procedure is tested for the investigated mixtures and for a set of glass-forming systems. In this frame, the stronger character of trehalose/H(2)O mixture indicates a better attitude in respect to maltose and sucrose/H(2)O mixtures to encapsulate biostructures in a more rigid matrix.

Interaction of the disaccharide trehalose with a phospholipid bilayer: a molecular dynamics study

The disaccharide trehalose is well known for its bioprotective properties. Produced in large amounts during stress periods in the life of organisms able to survive potentially damaging conditions, trehalose plays its protective role by stabilizing biostructures such as proteins and lipid membranes. In this study, molecular dynamics simulations are used to investigate the interaction of trehalose with a phospholipid bilayer at atomistic resolution. Simulations of the bilayer in the absence and in the presence of trehalose at two different concentrations (1 or 2 molal) are carried out at 325 K and 475 K. The results show that trehalose is able to minimize the disruptive effect of the elevated temperature and stabilize the bilayer structure. At both temperature, trehalose is found to interact directly with the bilayer through hydrogen bonds. However, the water molecules at the bilayer surface are not completely replaced. At high temperature, the protective effect of trehalose is correlated with a significant increase in the number of trehalose-bilayer hydrogen bonds, predominantly through an increase in the number of trehalose molecules bridging three or more lipid molecules.

Selective binding of monovalent cations to the stacking G-quartet structure formed by guanosine 5'-monophosphate: a solid-state NMR study

We report a solid-state multinuclear ((23)Na, (15)N, (13)C, and (31)P) NMR study on the relative affinity of monovalent cations for a stacking G-quartet structure formed by guanosine 5'-monophosphate (5'-GMP) self-association at pH 8. Two major types of cations are bound to the 5'-GMP structure: one at the surface and the other within the channel cavity between two G-quartets. The channel cation is coordinated to eight carbonyl oxygen atoms from the guanine bases, whereas the surface cation is close to the phosphate group and likely to be only partially hydrated. On the basis of solid-state (23)Na NMR results from a series of ion titration experiments, we have obtained quantitative thermodynamic parameters concerning the relative cation binding affinity for each of the two major binding sites. For the channel cavity site, the values of the free energy difference (Delta G degrees at 25 degrees C) for ion competition between M(+) and Na(+) ions are K(+) (-1.9 kcal mol(-1)), NH(4)(+) (-1.8 kcal mol(-1)), Rb(+) (-0.3 kcal mol(-1)), and Cs(+) (1.8 kcal mol(-1)). For the surface site, the values Delta G degrees are K(+) (2.5 kcal mol(-1)), NH(4)(+) (-1.3 kcal mol(-1)), Rb(+) (1.1 kcal mol(-1)), and Cs(+) (0.9 kcal mol(-1)). Solid-state NMR data suggest that the affinity of monovalent cations for the 5'-GMP structure follows the order NH(4)(+) > Na(+) > Cs(+) > Rb(+) > K(+) at the surface site and K(+) > NH(4)(+) > Rb(+) > Na(+) > Cs(+) > Li(+) at the channel cavity site. We have found that the cation-induced stability of a 5'-GMP structure is determined only by the affinity of monovalent cations for the channel site and that the binding of monovalent cations to phosphate groups plays no role in 5'-GMP self-ordered structure. We have demonstrated that solid-state (23)Na and (15)N NMR can be used simultaneously to provide mutually complementary information about competitive binding between Na(+) and NH(4)(+) ions.

An ab initio force field for the cofactors of bacterial photosynthesis

This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, namely quinones and bacteriochlorophylls. The parameters has been designed to be suitable for molecular dynamics simulations of photosynthetic proteins by being compatible with the AMBER force field. To our knowledge, this is the first force field for photosynthetic cofactors based on a reliable set of ab initio density functional reference data for methyl bacteriochlorophyll a, methyl bacteriopheophytin a, and of a derivative of ubiquinone. Indeed, the new molecular mechanics force field is able to reproduce very well not only the experimental and ab initio structural properties and the vibrational spectra of the molecules, but also the eigenvectors of the molecular normal modes. For this reason it might also be helpful to understand vibrational spectroscopy results obtained on reaction center proteins.

The trehalose myth revisited: introduction to a symposium on stabilization of cells in the dry state

This essay is an introduction to a series of papers arising from a symposium on stabilization of cells in the dry state. Nearly all of these investigations have utilized the sugar trehalose as a stabilizing molecule. Over the past two decades a myth has grown up about special properties of trehalose for stabilization of biomaterials. We review many of such uses here and show that under ideal conditions for drying and storage trehalose has few, if any, special properties. However, under suboptimal conditions trehalose has some distinct advantages and thus may remain the preferred excipient. We review the available mechanisms for introducing trehalose into the cytoplasm of living cells as an introduction to the papers that follow.

Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations

Large-scale molecular dynamics (MD) simulations have been utilized to study G-DNA quadruplex molecules containing mixed GCGC and all-guanine GGGG quartet layers. Incorporation of mixed GCGC quartets into G-DNA stems substantially enhances their sequence variability. The mixed quadruplexes form rigid assemblies that require integral monovalent cations for their stabilization. The interaction of cations with the all-guanine quartets is the leading contribution for the stability of the four-stranded assemblies, while the mixed quartets are rather tolerated within the structure. The simulations predict that two cations are preferred to stabilize a four-layer quadruplex stem composed of two GCGC and two all-guanine quartets. The distribution of cations in the structure is influenced by the position of the GCGC quartets within the quadruplex, the presence and arrangement of thymidine loops connecting the guanine/cytosine stretches forming the stems, and the cation type present (Na(+) or K(+)). The simulations identify multiple nanosecond-scale stable arrangements of the thymidine loops present in the molecules investigated. In these thymidine loops, several structured pockets are identified capable of temporarily coordinating cations. However, no stable association of cations to a loop has been observed. The simulations reveal several paths through the thymidine loop regions that can be followed by the cations when exchanging between the central ion channel in the quadruplex stem and the surrounding solvent. We have carried out 20 independent simulations while the length of simulations reaches a total of 90 ns, rendering this study one of the most extensive MD investigations carried out on nucleic acids so far. The trajectories provide a largely converged characterization of the structural dynamics of these four-stranded G-DNA molecules.

A lead-filled G-quadruplex: insight into the G-Quartet's selectivity for Pb(2+) over K(+)

The lipophilic nucleoside, G 1, extracts Pb(2+) picrate from water into organic solvents to give structures based on the hydrogen-bonded G-quartet. Crystal structures indicate important differences between (G 1)(8)-Pb(2+) and (G 1)(8)-K(+). The divalent Pb(2+) templates a smaller G(8) cage than does K(+), as judged by the M-O6 bond length, O6-O6 diagonal distance, and inter-tetramer separation. The more compact Pb(2+) octamer correlates with NMR data indicating that N2-N7 hydrogen bonds in (G 1)(8)-Pb(2+) are kinetically more stable than in (G 1)(8)-K(+).