Structural parsimony in endonuclease active sites: should the number of homing endonuclease families be redefined?

Homing endonucleases are classified into four families based on active site sequence motifs. Through structural comparisons we have found structural similarities between the endonuclease domain of colicin E9, an H-N-H motif-containing enzyme, and both the non-specific nuclease from Serratia and I-PpoI, a His-Cys box-containing homing endonuclease. Our comparison identifies conservation at the heart of all three enzyme active sites and so argues for a re-classification of H-N-H and His-Cys box homing endonucleases as a single family. We suggest the 'betabetaalpha-Me family' of homing enzymes to reflect the three elements of secondary structure and the metal ion that define the motif.     

Transformation of the θ-phase in Mg-Li-Al alloys: a density functional theory study

In Mg-Li-Al alloys, θ-phase MgAlLi₂ is a strengthening and metastable phase which is liable to be transformed to the equilibrium phase AlLi on overaging. While the structural details of the θ-phase MgAlLi₂ and the microscopic transformation are still unknown. In this paper, the structure of MgAlLi₂ unit cell was determined through X-ray powder diffraction simulation. Microscopic transformation process of θ-phase MgAlLi₂ was discussed in detail using first principles method.     

The effects of tautomerization and protonation on the adenine–cytosine mismatches: a density functional theory study

In the present work, we demonstrate the results of a theoretical study concerned with the question how tautomerization and protonation of adenine affect the various properties of adenine–cytosine mismatches. The calculations, in gas phase and in water, are performed at B3LYP/6-311++G(d,p) level. In gas phase, it is observed that any tautomeric form of investigated mismatches is more stabilized when adenine is protonated. As for the neutral mismatches, the mismatches containing amino form of cytosine and imino form of protonated adenine are more stable. The role of aromaticity on the stability of tautomeric forms of mismatches is investigated by NICS(1)_ZZ index. The stability of mispairs decreases by going from gas phase to water. It can be explained using dipole moment parameter. The influence of hydrogen bonds on the stability of mismatches is examined by atoms in molecules and natural bond orbital analyses. In addition to geometrical parameters and binding energies, the study of the topological properties of electron charge density aids in better understanding of these mispairs.     

Coarse-grained modeling study of nonpeptide RGD ligand density and PEG molecular weight on the conformation of poly(γ-glutamyl-glutamate) paclitaxel conjugates

Molecular shape, flexibility, and surface hydrophilicity are thought to influence the ability of nanoparticles to cross biological barriers during drug delivery. In this study, coarse-grained (CG) molecular dynamics (MD) simulations were used to study these properties of a polymer-drug construct in potential clinical development: poly(γ-glutamyl-glutamate)-paclitaxel-poly(ethylene glycol) nonpeptide RGD (PGG-PTX-PEG-npRGD), a linear glutamyl-glutamate polymer with paclitaxel and poly(ethylene glycol)-nonpeptide RGD side groups. It was hypothesized that the PEG molecular weight (MW) (500 Da; 1,000 Da; and 2,000 Da) and nonpeptide RGD ligand density (4, 8, 12, and 16 per molecule), respectively, may have advantageous effects on the shape, flexibility, and surface hydrophilicity of PGG-PTX-PEG-npRGD. Circular dichroism spectroscopy was used to suggest initial structures for the all-atom (AA) models of PGG-PTX-PEG-npRGD, which were further converted to CG models using a commercially available mapping algorithm. Due to its semi-flexibility, PGG-PTX-PEG-npRGD is not limited to one specific conformation. Thus, CG MD simulations were run until statistical equilibrium, at which PGG-PTX-PEG-npRGD is represented as an ensemble of statistically similar conformations. The size of a PGG-PTX-PEG-npRGD molecule is not affected by the PEG MW or the nonpeptide RGD density, but higher PEG MW results in increased surface density of a PGG-PTX-PEG-npRGD molecule. Most PGG-PTX-PEG-npRGD shapes are globular, although filamentous shapes were also observed in the PEG500 and PEG1000 molecules. PEG500 and PEG1000 molecules are more flexible than PEG2000 systems. A higher presence of npRGD ligands results in decrease surface hydrophilicity of PGG-PTX-PEG-npRGD. These results indicate that the PGG-PTX-PEG1000-npRGD₄ and PGG-PTX-PEG1000-npRGD₈ molecules are the most efficacious candidates and are further recommended for experimental preclinical studies.     

Antioxidant activity of phenolic and related compounds: a density functional theory study on the O–H bond dissociation enthalpy

Abstract

We report here on calculations at the hybrid DFT/HF (B3-LYP/6-31G(d, p)) level of the O–H bond dissociation enthalpy (O–H BDE) of phenylpropenoic acids (caffeic, ferulic, p-coumaric and cinnamic) and phenolic acids and related compounds (gallic, methylgallate, vanillic and gentisic) in order to gain insight into the understanding of structure–antioxidant activity relationships. The results were correlated and discussed mainly on the basis of experimental data in a companion work (Galato D, Giacomelli C, Ckless K, Susin MF, Vale RMR, Spinelli A. Antioxidant capacity of phenolic and related compounds: correlation among electrochemical, visible spectroscopy methods and structure-antioxidant activity. Redox Report 2001; 6: 243–250). The O–H BDE values showed remarkable dependence on the hydroxyl position in the benzene ring and the existence of additional interaction due to hydrogen bonding. For parent molecules, the experimental antioxidant activity (AA) order was properly obeyed only when intramolecular hydrogen bonding was present in the radicalized structures of o-dihydroxyl moieties. In structurally related compounds, excellent correlation with experimental data was in general observed (0.64 < ρ < 0.99). However, it is shown that excellent correlation can also be obtained for this series of compounds considering p-radicalized structures which were not stabilized by intramolecular hydrogen bonding, but this had no physical meaning. These findings suggested that the antioxidant activity evaluation of phenolic and related compounds must take into consideration the characteristics of each particular compound.     

Structural analysis and the effect of cyclo(His–Pro) dipeptide on neurotoxins—a dynamics and density functional theory study

The switching propensity and maximum probability of occurrence of the side chain imidazole group in the dipeptide cyclo(His–Pro) (CHP) were studied by applying molecular dynamics simulations and density functional theory. The atomistic behaviour of CHP with the neurotoxins glutamate (E) and paraquat (Pq) were also explored; E and Pq engage in hydrogen bond formation with the diketopiperazine (DKP) ring of the dipeptide, with which E shows a profound interaction, as confirmed further by NH and CO stretching vibrational frequencies. The effect of CHP was found to be greater on E than on Pq neurotoxin. A ring puckering study indicated a twist boat conformation for the six-membered DKP ring. Molecular electrostatic potential (MESP) mapping was also used to explore the hydrogen bond interactions prevailing between the neurotoxins and the DKP ring. The results of this study reveal that the DKP ring of the dipeptide CHP can be expected to play a significant role in reducing effects such as oxidative stress and cell death caused by neurotoxins.     

Should "handled" prey be considered? Some consequences for functional response, predator-prey dynamics and optimal foraging theory

Predator-prey models consider those prey that are free. They assume that once a prey is captured by a predator it leaves the system. A question arises whether in predator-prey population models the variable describing prey population shall consider only those prey which are free, or both free and handled prey together. In the latter case prey leave the system after they have been handled. The classical Holling type II functional response was derived with respect to free prey. In this article we derive a functional response with respect to prey density which considers also handled prey. This functional response depends on predator density, i.e., it accounts naturally for interference. We study consequences of this functional response for stability of a simple predator-prey model and for optimal foraging theory. We show that, qualitatively, the population dynamics are similar regardless of whether we consider only free or free and handled prey. However, the latter case may change predictions in some other cases. We document this for optimal foraging theory where the functional response which considers both free and handled prey leads to partial preferences which are not observed when only free prey are considered.     

Do the phenology and functional stem attributes of woody species allow for the identification of functional groups in the semiarid region of Brazil?

The phenology of tree species in environments that are subject to strong climatic seasonality is mainly determined by water availability, which may vary as a function of wood density. The relationship among phenology, water potential, wood density and the capacity of water storage in the stem were determined for woody species of caatinga vegetation (dry forest) in the semiarid region of NE Brazil. Leaf flush and fall, flowering and fruiting events were recorded over a 31-month period, and the water potential was measured over a two-year period. These data were related to precipitation, water availability in the soil and photoperiod. Seven deciduous species exhibited low wood density (DLWD,?<0.5?g?cm^?3), high capacity of water storage in the stem (until 250?% of the dry weight) and high water potential during the year, as opposed to 15 deciduous species that showed high wood density (DHWD,?≥0.5?g?cm^?3). Leaf flush, flowering and the fruiting of DHWD species were related to precipitation, whereas these phenological events occurred at the end of the dry season and/or the beginning of the rainy season for DLWD species and were related to the photoperiod. The two evergreen species showed variations of water potential that were intermediate between those of DHWD and DLWD deciduous species, leaf flush during the dry season and flowering at the end of dry season. These results suggest the existence of three functional groups: evergreen species, DHWD deciduous species and DLWD deciduous species.     

Bryophytes and their microhabitats in coniferous forest pastures: should they be considered in the pasture management?

Forest pastures, like many other semi-natural (traditional) rural biotopes, have undergone a drastic decline both in area and quality during the last century in many areas. We explored the bryophyte flora of Finnish coniferous forest pastures on acidic soil and aimed to recognize the most important microsites (rocks, coarse woody debris, tree bases, mineral soil patches and closed vegetation) for bryophyte diversity. The effects of microhabitat heterogeneity (microsite entropy) on bryophytes was also examined. We found altogether 83 bryophyte species. The only red-listed species, Tayloria tenuis, was frequently found on dung patches and a few rare ruderal species grew exclusively on bare mineral soil. Rocks comprised the most species rich microsite and many common forest floor species showed preference for this microsite. Microhabitat heterogeneity explained bryophyte species richness on both alpha (plot average) and gamma (pasture total) scales. The results suggest that certain individual bryophyte species and their microsites should be taken into account in the management of this biotope, rather than guiding the management solely on the basis of the overall bryophyte diversity.     

Cyano or o-nitrophenyl? Which is the optimal electron-withdrawing group for the acrylic acid acceptor of D-π-A sensitizers in DSSCs? A density functional evaluation

We report a DFT, TDDFT and DFTB investigation of the performance of two donor-π-acceptor (D-π-A)-type organic dyes bearing different electron-withdrawing groups (EWG) for dye-sensitized solar cells (DSSCs) to evaluate which EWG is better for an acrylic acid acceptor, i.e., Cyano (–CN) or o-nitrophenyl (o-NO₂–Ph). A series of theoretical criteria applied successfully in our previous work to explain the different performance of organic dyes related to open-circuit photovoltage (V _oc) and short-circuit current density (J _sc) were used to evaluate the performance of the dyes with just different EWG. Our calculated results reveal that dye 2 with o-NO₂–Ph has a larger vertical dipole moment, more electrons transferred from the dye to the semiconductor and a lower degree of charge recombination, which could lead to larger V _oc; while the larger driving force and comparable light harvesting efficiency could lead to higher J _sc , highlighting the potential of o-NO₂–Ph as an EWG in an acrylic acid acceptor.

Are density functional theory predictions of the Raman spectra accurate enough to distinguish conformational transitions during amyloid formation?

We report density functional theory (DFT) calculations of the Raman spectra for hexapepetides of glutamic acid and lysine in three different conformations (α, β and PPII). The wave numbers of amide I, amide II and amide III bands of all three conformations predicted at B3LYP/6-31G and B3LYP/6-31G* are in good agreement with previously reported experimental values of polyglutamic acid and polylysine. Agreement with experiment improves when polarization functions are included in the basis set. Explicit water molecules, H-bonded to the backbone amide groups were found to be absolutely necessary to obtain this agreement. Our results indicate that DFT is a promising tool for assignment of the spectral data on kinetics of conformational changes for peptides during amyloid formation.     

A density functional theory study of phenyl formation initiated by ethynyl radical (C2H•) and ethyne (C2H2)

An ab initio computational density functional theory (DFT) was used to study the formation of the first cyclic molecule (phenyl) initiated by the ethynyl radical (C₂H•). The study covers a competition reaction between the addition reactions of C₂H• with ethyne (C₂H₂) and some molecular re-arrangement schemes. The minimum energy paths of the preferred cyclic formation route were characterized. A thorough thermochemical analysis was performed by evaluating the differences in the energy of activation (ΔE), enthalpy (ΔH), and Gibb's free energy (ΔG) of the optimized stable and transition state (TS) molecules. The reaction temperatures were set to normal (T = 298 K) and combustion (T = 1,200 K) conditions.

The evolution of parental and alloparental effort in cooperatively breeding groups: when should helpers pay to stay?

We used a reproductive skew framework to consider the evolutionof parental and alloparental effort in cooperatively breedinggroups. The model provides the first theoretical treatmentof rent payment (the "pay-to-stay" hypothesis) for the evolutionof helping behavior of subordinates. According to this hypothesis,not all helping behavior is kin selected, but group membershelp in order to be allowed to stay in the group and potentiallygain breeding positions later in life. We show that reproductiveconcessions may be replaced by complete skew and voluntary,costly alloparental effort by subordinates once future prospectsare included in fitness calculations. This suggests that incompleteskew observed in long-lived species is not due to dominantcontrol over reproduction. Rent payment is predicted to occurwhen relatedness between subordinate and dominant is low, survivalis high, ecological constraints are at least moderately tight,and retaining nonhelping subordinates harms the dominant'sfitness. Rent may also be required from related subordinatesif helping is very costly (leading to low voluntary helpingeffort) and ecological constraints are moderately tight. However, related subordinates do not need to have a positive net effecton the dominant's direct fitness to be accepted as group members.We also consider compensatory responses of dominant group membersas a potential threat to the stability of renting behavior.If dominants trade off parental effort against their own survival,they may selfishly reduce their own parental effort as a responseto increased help. As this improves their own survival, theprospects of territorial inheritance diminish for the subordinate,and subordinates should hence be less willing to accept therent agreement. However, we show that compensatory responsesby "lazy" parents prevent group formation only in borderlinecases.     

Structural relationship between the active sites of β-lactam-recognizing and amidase signature enzymes: convergent evolution?

The β-lactam-recognizing enzymes (BLRE) make up a superfamily of largely bacterial proteins that include, principally, the dd-peptidases and β-lactamases. The former enzymes catalyze the final step in bacterial cell wall biosynthesis and are inhibited by β-lactam antibiotics, while the latter enzymes catalyze the hydrolytic destruction of β-lactams and represent a major source of bacterial resistance to these antibiotics. The active site of this superfamily of enzymes includes a Ser1/Ser2(Tyr)/Lys1(His)/Lys2 tetrad in which Ser1 is a nucleophilic catalyst that becomes acylated in the formation of an acyl-enzyme intermediate. An oxyanion hole is also present. The amidase signature (AS) enzymes represent another serine amidohydrolase superfamily with no overall structural resemblance to the BLRE. The active site is characterized by a Ser1/Ser2/Lys1/NH tetrad and an oxyanion hole. We point out that there is a close spatial overlap between the two tetrads and speculate that this has arisen from a process of convergent evolution driven by a mechanistic imperative. Conversion of the backbone NH group of the AS tetrad into Lys2 of the BLRE is rationalized and leads to another mechanistic possibility that may dominate BLRE catalysis. The active site triads of other serine amidohydrolases are also briefly and comparatively discussed.