A distinct, high-affinity, alkaline phosphatase facilitates occupation of P-depleted environments by marine picocyanobacteria.

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus, the two most abundant phototrophs on Earth, thrive in oligotrophic oceanic regions. While it is well known that specific lineages are exquisitely adapted to prevailing in situ light and temperature regimes, much less is known of the molecular machinery required to facilitate occupancy of these low-nutrient environments. Here, we describe a hitherto unknown alkaline phosphatase, Psip1, that has a substantially higher affinity for phosphomonoesters than other well-known phosphatases like PhoA, PhoX, or PhoD and is restricted to clade III Synechococcus and a subset of high light I-adapted Prochlorococcus strains, suggesting niche specificity. We demonstrate that Psip1 has undergone convergent evolution with PhoX, requiring both iron and calcium for activity and likely possessing identical key residues around the active site, despite generally very low sequence homology. Interrogation of metagenomes and transcriptomes from TARA oceans and an Atlantic Meridional transect shows that psip1 is abundant and highly expressed in picocyanobacterial populations from the Mediterranean Sea and north Atlantic gyre, regions well recognized to be phosphorus (P)-deplete. Together, this identifies psip1 as an important oligotrophy-specific gene for P recycling in these organisms. Furthermore, psip1 is not restricted to picocyanobacteria and is abundant and highly transcribed in some α-proteobacteria and eukaryotic algae, suggesting that such a high-affinity phosphatase is important across the microbial taxonomic world to occupy low-P environments.

Quantum Dynamics of Oblique Vibrational States in the Hénon-Heiles System.

In this paper, we study the quantum time evolution of oblique nonstationary vibrational states in a Hénon-Heiles oscillator system with two dissociation channels, which models the stretching vibrational motions of triatomic molecules. The oblique nonstationary states we are interested in are the eigenfunctions of the anharmonic zero-order Hamiltonian operator resulting from the transformation to oblique coordinates, which are defined as those coming from nonorthogonal coordinate rotations that express the matrix representation of the second-order Hamiltonian in a block diagonal form characterized by the polyadic quantum number n = n1 + n2. The survival probabilities calculated show that the oblique nonstationary states evolve within their polyadic group with a high degree of coherence up to the dissociation limits on the short time scale. The degree of coherence is certainly much higher than that exhibited by the local nonstationary states extracted from the conventional orthogonal rotation of the original normal coordinates. We also show that energy exchange between the oblique vibrational modes occurs in a much more regular way than the exchange between the local modes.

Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates.

BACKGROUND: Cyanobacteria are the major prokaryotic primary producers occupying a range of aquatic habitats worldwide that differ in levels of salinity, making them a group of interest to study one of the major unresolved conundrums in aquatic microbiology which is what distinguishes a marine microbe from a freshwater one? We address this question using ecogenomics of a group of picocyanobacteria (cluster 5) that have recently evolved to inhabit geographically disparate salinity niches. Our analysis is made possible by the sequencing of 58 new genomes from freshwater representatives of this group that are presented here, representing a 6-fold increase in the available genomic data. RESULTS: Overall, freshwater strains had larger genomes (≈2.9 Mb) and %GC content (≈64%) compared to brackish (2.69 Mb and 64%) and marine (2.5 Mb and 58.5%) isolates. Genomic novelties/differences across the salinity divide highlighted acidic proteomes and specific salt adaptation pathways in marine isolates (e.g., osmolytes/compatible solutes - glycine betaine/ggp/gpg/gmg clusters and glycerolipids glpK/glpA), while freshwater strains possessed distinct ion/potassium channels, permeases (aquaporin Z), fatty acid desaturases, and more neutral/basic proteomes. Sulfur, nitrogen, phosphorus, carbon (photosynthesis), or stress tolerance metabolism while showing distinct genomic footprints between habitats, e.g., different types of transporters, did not obviously translate into major functionality differences between environments. Brackish microbes show a mixture of marine (salt adaptation pathways) and freshwater features, highlighting their transitional nature. CONCLUSIONS: The plethora of freshwater isolates provided here, in terms of trophic status preference and genetic diversity, exemplifies their ability to colonize ecologically diverse waters across the globe. Moreover, a trend towards larger and more flexible/adaptive genomes in freshwater picocyanobacteria may hint at a wider number of ecological niches in this environment compared to the relatively homogeneous marine system.

Human root dentin microhardness and degradation by triple antibiotic paste and calcium hydroxide.

PURPOSE: To investigate and compare the effects of the two widely used regenerative endodontics medicaments: Triple antibiotic paste (ciprofloxacine-metronidazole-clindamycin) and calcium hydroxide on the microhardness and degradation of human root dentin. METHODS: Following ethical approval and subject consent to use teeth in this research study, 60 singled-rooted permanent human teeth were randomly divided into six groups:(1) Tri-antibiotic paste with distilled water, or with (2) propylene glycol, (3) calcium hydroxide with distilled water, (4) calcium hydroxide propylene glycol, (5) untreated extracted teeth as negative controls, or (6) teeth instrumented and filled with calcium hydroxide or tri-antibiotic paste as positive controls. The microhardness tests were conducted after 1 and 2 months of exposure to the medicaments using a Vickers microhardness tester. Raman spectroscopy and energy dispersive x-ray spectroscopy were used to evaluate the chemistry and structure of the root dentin. RESULTS: There were differences in the dentin microhardness following treatment with the medicaments or controls (P< 0.05). The time of root dentin exposure to the medicaments was similar (P> 0.05). The root dentin microhardness was lower in the teeth treated with the triple antibiotic paste or calcium hydroxide when combined with propylene glycol. The root dentin collagen in these treated teeth were also significantly degraded when viewed with Raman spectroscopy and energy dispersive x-ray spectroscopy, whereas the inorganic phase (dentin) remained unaltered. Samples exposed to the antimicrobial agents with water as a vehicle exhibited stronger microhardness and less degradation. CLINICAL SIGNIFICANCE: These ex vivo results suggest that the triple antibiotic paste and calcium hydroxide should be used with propylene glycol if a fast diffusion is desired or with water to avoid degrading the collagen and weakening the microhardness of the teeth. Clinical trials are needed of new formulations of medicaments with propylene glycol to disinfect teeth for regenerative endodontic procedures, to help strengthen the teeth to prevent the loss of children's permanent immature teeth by fracture following caries or trauma.

Ab Initio Partition Functions and Thermodynamic Quantities for the Molecular Hydrogen Isotopologues.

In this work, we calculate the partition functions and thermodynamic quantities of molecular hydrogen isotopologues using the rovibrational energy levels provided by the highly accurate ab initio adiabatic potential energy functions recently determined by Pachucki and Komasa (Pachucki, K.; Komasa, J. J. Chem. Phys. 2014, 141, 224103). The partition functions are calculated by including all bound energy levels of the isotopologues, up to their dissociation limits, plus the quasi-bound levels lying below the centrifugal potential barriers. For the homonuclear isotopologues, H2, D2, and T2, we also determine the partition functions and thermodynamic quantities of the normal mixtures using the statistical treatment recently proposed by Colonna et al. (Colonna, G.; D'Angola, A.; Capitelli, M. Int. J. Hydrogen Energy 2012, 37, 9656) based on the definition of the partition function of the mixture, which avoids inconsistencies in the values of the thermodynamic quantities depending directly on the internal partition function, in the high-temperature limit.

On the Role of Entropy in the Stabilization of α-Helices.

Protein folding evolves by exploring the conformational space with a subtle balance between enthalpy and entropy changes which eventually leads to a decrease of free energy upon reaching the folded structure. A complete understanding of this process requires, therefore, a deep insight into both contributions to free energy. In this work, we clarify the role of entropy in favoring the stabilization of folded structures in polyalanine peptides with up to 12 residues. We use a novel method referred to as K2V that allows us to obtain the potential-energy landscapes in terms of residue conformations extracted from molecular dynamics simulations at conformational equilibrium and yields folding thermodynamic magnitudes, which are in agreement with the experimental data available. Our results demonstrate that the folded structures of the larger polyalanine chains are stabilized with respect to the folded structures of the shorter chains by both an energetic contribution coming from the formation of the intramolecular hydrogen bonds and an entropic contribution coming from an increase of the entropy of the solvent with approximate weights of 60 and 40%, respectively, thus unveiling a key piece in the puzzle of protein folding. In addition, the ability of the K2V method to provide the enthalpic and entropic contributions for individual residues along the peptide chain makes it clear that the energetic and entropic stabilizations are basically governed by the nearest neighbor residue conformations, with the folding propensity being rationalized in terms of triads of residues.

Intraresidual Correlated Motions in Peptide Chains.

We investigate the interresidual and intraresidual correlations between dihedral displacements of adjacent residues within model polyalanine peptides by analyzing extensive molecular dynamics trajectories. Correlations are evaluated individually at different residue conformations covering the whole (ϕi,ψi)-space. From these, we draw maps that unveil an unprecedented strong intramolecular correlation displaying opposite (correlated/anticorrelated) behaviors at different conformations. Both interresidual and intraresidual correlations arise from the propensity of the peptide to minimize the overall atomic displacements.

Tuning the Optical Properties of Novel Antitumoral Drugs Based on Cyclometalated Iridium(III) Complexes.

Most of the current efforts in drug discovery are devoted to the design of molecules able to mitigate side effects by concentrating the biological action in the targeted tissue. One promising strategy is photodynamic therapy, which is based on the in situ generation of reactive singlet oxygen upon radiation exposure. However, such an approach requires the use of an efficient photosensitizer. This contribution deals with the optical properties of an Ir(III) complex, [Ir(pbz)2(N^N)] (pbz = 2-phenylbenzimidazole; N^N = methyl 1-butyl-2-pyridyl-benzimidazole-5-carboxylate), which has recently been shown to exhort a strong photoactivity, but still needs further improvements to reach clinical applications. We performed density functional theory calculations at the M06, PBE0, ωB97xD, and CAM-B3LYP levels to predict the impact of introducing electron donor-acceptor groups into the nature of the lowest excited states. The simulations performed demonstrate that the presence of a NH2 at the pbz ligand and a NO2 group at the N^N ligand yield a bathochromic shift of absorption spectrum. We report the most sensitive positions to tune the optical signatures of this family of complexes.

Structure, Spectra, and DFT Simulation of Nickel Benzazolate Complexes with Tris(2-aminoethyl)amine Ligand.

Benzazolate complexes of Ni(II), [Ni(pbz)(tren)]ClO4 (pbz = 2-(2'-hydroxyphenyl)-benzimidazole (pbm), 1, 2-(2'-hydroxyphenyl)-benzoxazole (pbx), 2, 2-(2'-hydroxyphenyl)-benzothiazole (pbt), 3; tren = tris(2-aminoethyl)amine), are prepared by self-assembly reaction and structurally characterized. Theoretical DFT simulations are carried out to reproduce the features of their crystal structures and their spectroscopic and photophysic properties. The three complexes are moderately luminescent at room temperature both in acetonitrile solution and in the solid state. The simulations indicate that the absorption spectrum is dominated by two well-defined transitions, and the electronic density concentrates in three MOs around the benzazole ligands. The Stokes shifts of the emission spectra of complexes 1-3 are determined by optimizing the electronic excited state.

Understanding the connection between conformational changes of peptides and equilibrium thermal fluctuations.

Despite the increasing evidence that conformational transitions in peptides and proteins are driven by specific vibrational energy pathways along the molecule, the current experimental techniques of analysis do as yet not allow to study these biophysical processes in terms of anisotropic energy flows. Computational methods offer a complementary approach to obtain a more detailed understanding of the vibrational and conformational dynamics of these systems. Accordingly, in this work we investigate jointly the vibrational energy distribution and the conformational dynamics of trialanine peptide in water solution at room temperature by applying the Instantaneous Normal Mode analysis to the results derived from equilibrium molecular dynamics simulations. It is shown that conformational changes in trialanine are triggered by the vibrational energy accumulated in the low-frequency modes of the molecule, and that excitation is caused exclusively by thermal fluctuations of the solute-solvent system, thus excluding the possibility of an intramolecular vibrational energy redistribution process.

Relaxation pathways of the OD stretch fundamental of HOD in liquid H2O.

The molecular dynamics with quantum transitions method is used to study the vibrational relaxation of the OD stretching mode of HOD dissolved in liquid H2O water at 303 K. All the vibrational modes of the solute and solvent molecules that participate in the relaxation process are described by quantum mechanics, while the rotational and translational degrees of freedom are treated classically. A modification of the water intramolecular SPC/E (Simple Point Charge/Extended) force field providing vibrational frequencies in solution closer to the experimental values is proposed to analyze the influence of the vibrational energy gaps on the relaxation channels. The relaxation times obtained are in satisfactory agreement with experimental values. The energy transfer during the relaxation process alters significantly the H-bond network around the HOD molecule. The analysis of the vibrational transitions during the relaxation process reveals a complex mechanism which involves the participation of both intra- and intermolecular channels and provides a compromise for the different interpretations of the experimental data reported for this system in recent years.

Assessing the importance of proton transfer reactions in DNA.

Although engineered by millions of years of evolution, the cellular machinery is not flawless, and errors regularly appear during DNA replication. The subsequent alteration of the stored genetic message results in a mutation and might be the starting point of important health disorders. The question therefore is what causes DNA mutations? All living organisms are constantly exposed to a number of external agents such as free radicals and to radiation, which may lead to induced mutations. There are also mutations happening without invoking the action of any exogenous element, the so-called spontaneous mutations. The former can be partially controlled by avoiding exposure to high-risk environments, while the latter are more intriguing because their origin is unclear and difficult to determine. As noted by Watson and Crick when they first discovered the DNA structure, the correct replication of DNA rests on the assumption that the base pairs remain in their most stable, canonical form. However, protons along the interbase hydrogen-bond network are not static entities. They can in fact interchange their positions in DNA bases through proton transfer (PT) reactions before strands unwind, giving rise to noncanonical structures defined as rare tautomers. The importance of these rare tautomers was also cleverly anticipated by Watson and Crick and some years later claimed by Löwdin to be a source of spontaneous mutations. In Watson and Crick's words: "It would be of interest to know the precise difference in free energy between the various tautomeric forms under physiological conditions." Unfortunately, rare tautomeric forms are very difficult to detect, so no direct and accurate free energy measure has been discerned. In contrast, theoretical chemistry is making good progress toward the quantification of PT reactions in DNA and their biological consequences. This Account touches upon the theoretical studies devoted to appraising the importance of rare tautomers as promoters of spontaneous mutations. We focus in particular on the crucial role played by the biological environment on DNA stability. It has now been demonstrated that valuable macroscopic predictions require not only highly accurate theories but also refined chemical models. Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations performed on short but complete DNA sequence fragments emerge in this context as the most adequate tools. In addition, these methods can be used to quantify the effect of different external agents on the PT tautomeric equilibria and, eventually, to conveniently handle them. This is the case for the possible alteration of the naturally observed mutation rate by exposure to intense electric fields. Theoretical predictions envision in this respect promising applications of ultrashort electric pulses in medicine to selectively modify the mutated/canonical ratio in DNA.

Structure and spectroscopic properties of nickel benzazolate complexes with hydrotris(pyrazolyl)borate ligand.

The reaction of benzazole ligands 2-(2'-hydroxylphenyl)benzimidazole (Hpbm), 2-(2'-hydroxylphenyl)benzoxazole (Hpbx), and 2-(2'-hydroxylphenyl)benzothiazole (Hpbt), with [Ni(Tp*)(µ-OH)]2 (Tp* = hydrotris(3,5-dimethylpyrazolyl)borate), leads to pentacoordinate nickel complexes [Ni(Tp*)(pbz)] (pbz = pbm (1), pbx (2), pbt (3)). The structures of 1, 2, and 3 were determined by X-ray crystallography. The pentacoordinate nickel complexes have distorted trigonal bipyramidal geometries with Addison's τ parameter values of 0.63, 0.73, and 0.61 for 1, 2 and 3, respectively. The benzazolates are bonded in an η(2)(N,O) fashion to the nickel atoms. DFT calculations are carried out to optimize the structures of the three complexes giving a good agreement with the X-ray structures. The (1)H NMR spectra of complexes 1-3 exhibit sharp isotropically shifted signals. The complete assignment of these signals required an application of two-dimensional {(1)H-(1)H}-COSY techniques. The experimental absorption spectra of the three complexes in chloroform solution each show an intense absorption band in the ultraviolet region ca. 240 nm, followed by three less intense bands, the first two at ∼295 and ∼340 nm, and the last more disperse one, at wavelengths between 360 and 410 nm. The absorption spectra are simulated by TD-DFT and reproduce the main features of the experimental spectra well. The analysis of the electronic transitions by inspection of the frontier molecular orbitals and also the natural transition orbitals allowed us to characterize and assign the observed bands properly. The three complexes are moderately blue luminescent at room temperature, both in the solid state and in solution. Emission spectra at room temperature display broad structureless bands in chloroform solution at 460, 482, and 512 nm for complexes 1, 2 and 3, respectively, and structured emission in solid state with λmax values of 473, 486, and 516 nm. Complexes containing different donor atoms in the benzazole ligand are furthermore observed to give different luminescence responses in the presence of Zn(II), Cd(II), Hg(II), and Cu(II).

Coordinated transcriptional response to environmental stress by a Synechococcus virus.

Viruses are a major control on populations of microbes. Often, their virulence is examined in controlled laboratory conditions. Yet, in nature, environmental conditions lead to changes in host physiology and fitness that may impart both costs and benefits on viral success. Phosphorus (P) is a major abiotic control on the marine cyanobacterium Synechococcus. Some viruses infecting Synechococcus have acquired, from their host, a gene encoding a P substrate binding protein (PstS), thought to improve virus replication under phosphate starvation. Yet, pstS is uncommon among cyanobacterial viruses. Thus, we asked how infections with viruses lacking PstS are affected by P scarcity. We show that the production of infectious virus particles of such viruses is reduced in low P conditions. However, this reduction in progeny is not caused by impaired phage genome replication, thought to be a major sink for cellular phosphate. Instead, transcriptomic analysis showed that under low P conditions, a PstS-lacking cyanophage increased the expression of a specific gene set that included mazG, hli2, and gp43 encoding a pyrophosphatase, a high-light inducible protein and DNA polymerase, respectively. Moreover, several of the upregulated genes were controlled by the host's phoBR two-component system. We hypothesize that recycling and polymerization of nucleotides liberates free phosphate and thus allows viral morphogenesis, albeit at lower rates than when phosphate is replete or when phages encode pstS. Altogether, our data show how phage genomes, lacking obvious P-stress-related genes, have evolved to exploit their host's environmental sensing mechanisms to coordinate their own gene expression in response to resource limitation.

Conformational changes of ß-carotene and zeaxanthin immersed in a model membrane through atomistic molecular dynamics simulations.

In this work, we investigate systems formed by ß-carotene and zeaxanthin embedded separately in a model lipid bilayer of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) through molecular dynamics (MD) simulations. The study is conducted using an all-atoms model and by analyzing the structural changes that occur at both the carotenoid molecule and the membrane during the simulations. We concentrate specifically on the conformation of the conjugated chain, given the relevance that this feature has in modulating the spectroscopic and antioxidant properties of the carotenoids. The force fields of the carotenoids are parametrized accordingly in order to reproduce the rotation potentials of the conjugated chains calculated using quantum DFT methods. A model to quantify the effective conjugated chain length is presented. The MD simulations are carried out using the parameters adjusted for the carotenoids along with those provided by the CHARMM36 force field for the lipids of the membrane. A differentiating dynamic behavior of ß-carotene and zeaxanthin within the bilayer is observed in the simulations, which is analyzed in detail through umbrella sampling techniques. This behavior is driven basically by the interactions of the lipid polar heads with the hydroxyl groups of zeaxanthin, which are absent in ß-carotene. These interactions influence the carotenoid orientation, modify the conformational distribution of the dihedral angles of the conjugated chain significantly, and specifically distort the membrane structure.

Instantaneous normal mode analysis of the vibrational relaxation of the amide I mode of alanine dipeptide in water.

Nonequilibrium Molecular Dynamics (MD) simulations coupled to instantaneous normal modes (INMs) analysis are used to study the vibrational relaxation of the acetyl and amino-end amide I modes of the alanine dipeptide (AlaD) molecule dissolved in water (D2O). The INMs are assigned in terms of the equilibrium normal modes using the Effective Atomic Min-Cost algorithm as adapted to make use of the outputs of standard MD packages, a method which is well suited for the description of flexible molecules. The relaxation energy curves of both amide I modes show multiexponential decays, in good agreement with the experimental findings. It is found that ~85%-90% of the energy relaxes through intramolecular vibrational redistribution. The main relaxation pathways are also identified. The rate at which energy is transferred into the solvent is similar for the acetyl-end and amino-end amide I modes. The conformational changes occurring during relaxation are investigated, showing that the populations of the alpha and beta region conformers are altered by energy transfer in such a way that it takes 15 ps for the equilibrium conformational populations to be recovered after the initial excitation of the AlaD molecule.

Bacterial catabolism of membrane phospholipids links marine biogeochemical cycles.

In marine systems, the availability of inorganic phosphate can limit primary production leading to bacterial and phytoplankton utilization of the plethora of organic forms available. Among these are phospholipids that form the lipid bilayer of all cells as well as released extracellular vesicles. However, information on phospholipid degradation is almost nonexistent despite their relevance for biogeochemical cycling. Here, we identify complete catabolic pathways for the degradation of the common phospholipid headgroups phosphocholine (PC) and phosphorylethanolamine (PE) in marine bacteria. Using Phaeobacter sp. MED193 as a model, we provide genetic and biochemical evidence that extracellular hydrolysis of phospholipids liberates the nitrogen-containing substrates ethanolamine and choline. Transporters for ethanolamine (EtoX) and choline (BetT) are ubiquitous and highly expressed in the global ocean throughout the water column, highlighting the importance of phospholipid and especially PE catabolism in situ. Thus, catabolic activation of the ethanolamine and choline degradation pathways, subsequent to phospholipid metabolism, specifically links, and hence unites, the phosphorus, nitrogen, and carbon cycles.

Antioxidant properties of ß-carotene isomers and their role in photosystems: insights from Ab initio simulations.

In this work we investigate the effect of cis isomerizations and conformational changes on the antioxidant activity of ß-carotene, one of the most important pigments in nature. The electrodonating (ω(-)) and electroaccepting (ω(+)) powers of the most relevant isomers of ß-carotene are first evaluated in polar and nonpolar solvents using density functional theory (DFT), and these quantities are then used to establish an antioxidant scale of the isomers. The electrodonating power, which is directly related to the antioxidant activity, is shown to provide a very good correlation with the experimental data. Next, we compute the intermediate twisted structures of the ß-carotene isomers generated by partial rotation of every single bond in the polyenic chain. The electrodonating and electroaccepting powers are evaluated for each of these intermediate structures along with their maximum absorption wavelengths, which are computed using time-dependent DFT (TD-DFT). The trends observed for both the electrodonating power and the maximum absorption wavelength can be rationalized in terms of the effective conjugated chain length of the structure resulting from single bond rotations. The results obtained are used to analyze the conformational distribution of ß-carotene in the well-resolved photosystem I (PS-I) of purple cyanobacteria. It is then shown that the isomers present in this photosystem are those having the lowest calculated relative energies and that those with enhanced antioxidant activity are preferentially located in the inner core of the protein complex.

Molecular dynamics with quantum transitions study of the vibrational relaxation of the HOD bend fundamental in liquid D2O.

The molecular dynamics with quantum transitions method is used to study the vibrational relaxation of the HOD bend fundamental in liquid D(2)O. All of the vibrational bending degrees of freedom of the HOD and D(2)O molecules are described by quantum mechanics, while the remaining translational and rotational degrees of freedom are described classically. The effect of the coupling between the rotational and vibrational degrees of freedom of the deuterated water molecules is analyzed. A kinetic mechanism based on three steps is proposed in order to interpret the dynamics of the system. It is shown that intermolecular vibrational energy transfer plays an important role in the relaxation process and also that the transfer of energy into the rotational degrees of freedom is favored over the transfer of energy into the translational motions. The thermalization of the system after the relaxation is reached in a shorter time scale than that of the recovery of the hydrogen bond network. The relaxation and equilibration times obtained compare well with experimental and previous theoretical results.