A stochastic model for the synthesis and degradation of natural organic matter part II: molecular property distributions

A stochastic biogeochemical model has been developed to simulate the transformation and degradation of natural organic matter (NOM) using an agent-based algorithm which treats each molecule as a separate and potentially unique entity. Molecules react when a pseudo-random number is lower than the calculated reaction probability in a given time step; repeated time steps simulate the transformation of precursor molecules into a complex NOM assemblage. The data for each molecule—elemental and functional group composition—can be used to calculate many properties directly and exactly for each molecule in the assemblage, e.g., molecular weight (MW), fraction of aromatic C (Ar), and charge at pH 7 (Z). Empirical quantitative structure activity relationships (QSARs) are developed which permit the estimation of thermodynamic quantities K _ow (the octanol–water partition coefficient) and pK _a (acidity) for each molecule. Root mean square errors for these QSARs are 0.39 log units for log K _ow and 0.45 log units for pK _a. Distributions of both exactly calculated (MW, Ar, Z) and estimated thermodynamic (K _ow, pK _a) properties are examined and compared with published experimental data. Molecular weight distributions from size exclusion HPLC experiments on aquatic NOM are quantitatively similar to simulation results. pH titrations and polarity distributions from reversed-phase HPLC are qualitatively similar to simulation results. This agreement suggests that the agent-based model can be used to explore hypotheses regarding both compositional and thermodynamic properties of NOM. Robert Wetzel—deceased.     

Oligonucleotide aptamers that recognize small molecules.

Nucleic acid receptors ('aptamers'), which recognize a large variety of organic molecules of low molecular weight, have been isolated from combinatorial nucleic acid libraries by in vitro selection methods. Structural studies of nucleic acid-small molecule complexes provide insight into both the principles of molecular recognition by this class of biopolymers and the architecture of tertiary motifs in nucleic acid folding. Aptamers that recognize small molecules are increasingly applied as tools in molecular biology, from the detection of oxidative damage in DNA to conditional gene expression and from their use as modules for the engineering of allosteric ribozymes to biosensors.     

Biochemical research on oogenesis. The storage particles of the teleost fish Tinca tinca

Oocytes ofTinca tinca and other Teleosts accumulate small and large molecules of RNA in noncoordinate fashion. Previtellogenic oocytes synthesize far less 28 S and 18 S RNA than tRNA and 5 S RNA, so that the latter molecules make up 50 to 90% of total RNA in these cells. As inXenopus laevis, tRNA and 5 S RNA made in excess by small oocytes ofT. tinca are stored in two kinds of nucleoprotein particles, sedimenting at 7 S and 42 S. In this paper we describe the biochemical and physical properties of the storage particles ofT. tinca. The 7 S particles are made up of one 5 S RNA and one 32,000 M_r protein (c). The molecular weight of this protein is lower by 8,000 than itsX. laevis counterpart. In contrast, the 42 S particles have the same size and composition inT. tinca andX. laevis. The 42 S particles of both species are made up of four subunits, each of which contains three molecules of tRNA, one molecule of 5 S RNA, two molecules of a 50,000-M_r protein (a), and one molecule of a 40,000-M_r protein (b). We present evidence showing that in the 42 S particles protein a is associated with tRNA, whereas protein b is associated with 5 S RNA, and suggesting that protein c is a cleavage product of protein b.     

Contribution to the reduction‐induced fluorescence enhancement of natural organic matter: Aromatic ketones outweigh quinones

This work involves the comparison of the fluorescence excitation ? emission matrices of different low‐molecular‐weight carbonyl compounds and natural organic matter (NOM). The aim is to determine if quinone or aromatic ketone groups are more responsible for the reduction‐induced fluorescence enhancement of NOM. After reduction, the aromatic ketones showed a significantly greater fluorescence change than the quinones, proving that the former play a more important role. Further analysis of the fluorescence of the NOM samples after re‐oxidization by oxygen with a Cu²⁺ catalyst, provided additional reliable evidence in support of the dominant role of aromatic ketones in the fluorescence change. This work demonstrates that aromatic ketone moieties should be given more attention when considering the physicochemical properties of NOM and related environmental processes.     

Natural organic matter (NOM) has the potential to modify the multixenobiotic resistance (MXR) activity in freshwater amphipods Eulimnogammarus cyaneus and E. verrucosus

Based on the chemical features of natural organic matter (NOM) with its variety of functional groups, we hypothesized that NOM will modify the multixenobiotic-resistance (MXR) of an organism as xenobiotic chemicals do. The MXR system is a general first rather non-specific line of defense against environmental contaminants. The aim of this study was to compare the impacts on MXR activity in amphipod species (Eulimnogammarus cyaneus and E. verrucosus, from Lake Baikal) stressed by cadmium chloride or dissolved NOM for 24 h. NOM exposure concentrations were environmentally realistic. MXR activity was assessed based on rhodamine B efflux; its specificity was proven by a verapamil inhibition assay. It was shown that both NOM and CdCl₂ lead to substantial reduction of the rhodamine B efflux. This suggests that NOM may be regarded as a chemosensor which is able to reduce the efficiency of the MXR system. Possible mechanisms of direct NOM impact on MXR processes are discussed, such as peroxidation of the membranes (including P-glycoproteins) or internal blockage of the MXR pump by bioconcentrated NOM. In general, our results show that well-developed depuration pathways of freshwater organisms in contaminated environments may be impaired by strong chemical stressors and, more important, by natural biogeochemical matrices such as humic substances — humic substances are present in all freshwater systems.     

Resolution of Two Sub-Populations of Conformers and Their Individual Dynamics by Time Resolved Ensemble Level FRET Measurements

Most active biopolymers are dynamic structures; thus, ensembles of such molecules should be characterized by distributions of intra- or intermolecular distances and their fast fluctuations. A method of choice to determine intramolecular distances is based on Förster resonance energy transfer (FRET) measurements. Major advances in such measurements were achieved by single molecule FRET measurements. Here, we show that by global analysis of the decay of the emission of both the donor and the acceptor it is also possible to resolve two sub-populations in a mixture of two ensembles of biopolymers by time resolved FRET (trFRET) measurements at the ensemble level. We show that two individual intramolecular distance distributions can be determined and characterized in terms of their individual means, full width at half maximum (FWHM), and two corresponding diffusion coefficients which reflect the rates of fast ns fluctuations within each sub-population. An important advantage of the ensemble level trFRET measurements is the ability to use low molecular weight small-sized probes and to determine nanosecond fluctuations of the distance between the probes. The limits of the possible resolution were first tested by simulation and then by preparation of mixtures of two model peptides. The first labeled polypeptide was a relatively rigid Pro₇ and the second polypeptide was a flexible molecule consisting of (Gly-Ser)₇ repeats. The end to end distance distributions and the diffusion coefficients of each peptide were determined. Global analysis of trFRET measurements of a series of mixtures of polypeptides recovered two end-to-end distance distributions and associated intramolecular diffusion coefficients, which were very close to those determined from each of the pure samples. This study is a proof of concept study demonstrating the power of ensemble level trFRET based methods in resolution of subpopulations in ensembles of flexible macromolecules.     

Determination of the elastic properties of short ssDNA molecules by mechanically folding and unfolding DNA hairpins

The characterization of elastic properties of biopolymers is crucial to understand many molecular reactions determined by conformational bending fluctuations of the polymer. Direct measurement of such elastic properties using single‐molecule methods is usually hindered by the intrinsic tendency of such biopolymers to form high‐order molecular structures. For example, single‐stranded deoxyribonucleic acids (ssDNA) tend to form secondary structures such as local double helices that prevent the direct measurement of the ideal elastic response of the ssDNA. In this work, we show how to extract the ideal elastic response in the entropic regime of short ssDNA molecules by mechanically pulling two‐state DNA hairpins of different contour lengths. This is achieved by measuring the force dependence of the molecular extension and stiffness on mechanically folding and unfolding the DNA hairpin. Both quantities are fit to the worm‐like chain elastic model giving values for the persistence length and the interphosphate distance. This method can be used to unravel the elastic properties of short ssDNA and RNA sequences and, more generally, any biopolymer that can exhibit a cooperative two‐state transition between mechanically folded and unfolded states (such as proteins). © 2014 Wiley Periodicals, Inc. Biopolymers 101: 1193–1199, 2014.     

Comparative investigations of biopolymer hydration by physicochemical and modeling techniques.

The comparative investigation of biopolymer hydration by physicochemical techniques, particularly by small-angle X-ray scattering, has shown that the values obtained differ over a wide range, depending on the nature of the polymer and the environmental conditions. In the case of simple proteins, a large number of available data allow the derivation of a realistic average value for the hydration (0.35 g of water per gram of protein). As long as the average properties of proteins are considered, the use of such a default value is sufficient. Modeling approaches may be used advantageously, in order to differentiate between different assumptions and hydration contributions, and to correctly predict hydrodynamic properties of biopolymers on the basis of their three-dimensional structure. Problems of major concern are the positioning and the properties of the water molecules on the biopolymer surface. In this context, different approaches for calculating the molecular volume and surface of biopolymers have been applied, in addition to the development of appropriate hydration algorithms.     

Elastin-like polypeptides as a promising family of genetically-engineered protein based polymers

Elastin-like polypeptides (ELP) are artificial, genetically encodable biopolymers, belonging to elastomeric proteins, which are widespread in a wide range of living organisms. They are composed of a repeating pentapeptide sequence Val–Pro–Gly–Xaa–Gly, where the guest residue (Xaa) can be any naturally occurring amino acid except proline. These polymers undergo reversible phase transition that can be triggered by various environmental stimuli, such as temperature, pH or ionic strength. This behavior depends greatly on the molecular weight, concentration of ELP in the solution and composition of the amino acids constituting ELPs. At a temperature below the inverse transition temperature (T_t), ELPs are soluble, but insoluble when the temperature exceeds T_t. Furthermore, this feature is retained even when ELP is fused to the protein of interest. These unique properties make ELP very useful for a wide variety of biomedical applications (e.g. protein purification, drug delivery etc.) and it can be expected that smart biopolymers will play a significant role in the development of most new materials and technologies. Here we present the structure and properties of thermally responsive elastin-like polypeptides with a particular emphasis on biomedical and biotechnological application.     

A singular state of membrane lipids at cell growth temperatures.

Cells adjust their membrane lipid composition when they adapt to grow at different temperatures. The consequences of this adjustment for membrane properties and functions are not well understood. Our report shows that the temperature dependence of the diffusion of a probe molecule in multilayers formed from total lipid extracts of E. coli has an anomalous maximum at a temperature corresponding to the growth temperature of each bacterial preparation (25, 29, and 32 degrees C). This increase in the lateral diffusion coefficient, D, is characteristic of membrane lipids in a critical state, for which large fluctuations of molecular area in the plane of the bilayer are expected. Therefore, changes in lipid composition may be due to a requirement that cells maintain their membranes in a state where molecular interactions and reaction rates are readily modulated by small, local perturbations of membrane organization.     

Influence of Cooperativity on Hydrogen Bond Networks

Abstract

Cooperative effects are known to strongly affect the geometrical, energetic and vibrational properties of hydrogen bonded systems. In particular, such effects strongly favor molecular arrangements where each molecule is simultaneously a donor and an acceptor of hydrogen bonds (HBs), regardless of the chemical nature of the monomer subunits. In the particular case of water systems, it has been shown that the more a molecule is a proton donor in HBs, the more the HBs where it is a proton acceptor are reinforced. Such a property could be at the origin of the equilibrium between the two species of hydrogen bonded water molecules in liquid water (one with a strong hydrogen bonding character, and one with a weaker one), as experimentally evidenced and as a molecular dynamic study of the small (H₂O)₂₄ cluster clearly suggests.     

The structure of form I crystals of D-ribulose-1,5-diphosphate carboxylase.

Single crystals of d-ribulose-1,5-diphosphate carboxylase from tobacco leaves, Nicotiana tabacum (variety Turkish Samsun), have been examined by X-ray diffraction, electron microscopy, and optical diffraction. Twelve molecules are loosely packed into a body-centered cubic unit cell, space group I4¹32 with cell dimension $\text{a = 383}\text{A}\text{̊}$. The asymmetric unit is one quarter of a molecule, and the minimum molecular symmetry is 222. This symmetry when combined with estimates of the two subunit masses and stoichiometry is compatible with a molecular structure of the composition L₈S₈ (L is large subunit, S is small). If all bonds between large and small subunits are equivalent, the true molecular symmetry is 422; this symmetry is consistent with molecular images in micrographs.     

Parametrization scheme with accuracy and transferability for tight-binding electronic structure calculations with extended Hückel approximation and molecular dynamics simulations

A transferable tight-binding parametrization procedure for extended Hückel approximation is proposed, with the charge self-consistent scheme, that could be applied to the quantum molecular dynamics (MD) simulation for long-time dynamics of large-scale systems. In this procedure, either a target molecule is divided into small molecules or another realistic set of small molecules characterizing chemical bonds in the complicated target molecule is adopted. Then, the parameters for these small molecules are adjusted and compared with reference results of energy levels and wave functions by, for example, density functional theory. Upon application to the large target molecule, these parameters are then readjusted directly in the target molecule. An example is demonstrated with MD simulation applied to the ionic liquid molecule N-methyl-N-propylpiperidinium bis trifluoromethanesulfonyl imide (PP13-TFSI). The origin and stability of HOMO–LUMO gap are discussed.     

Theoretical investigation of auxiliary electronic acceptors in modifying D-D-π-A sensitizers for dye-sensitized solar cells

In light of the performance of the SD2 pigments in DSSC, in order to expand the absorption spectral scope, decrease the energy difference between the highest occupied and the lowest unoccupied molecular orbitals, with SD2 dye molecular electron donor and electron acceptor as the fundamental framework, the indole fragment and thiophene derivative in the prototype dye molecule were replaced by the two π-bridges (labeled PA, PB, respectively) and the four auxiliary electron acceptors (labeled A1, A2, A3, A4, respectively). For the sake of characterizing dye molecules as thoroughly as possible in DSSC, the frontier orbital energy levels, ultraviolet absorption spectra, natural bond orbital analysis, intramolecular charge transfer, charge and hole reorganization energies, parameters influencing the short-circuit current density and the open-circuit photovoltage for these eight individual dye molecules are carried out to try to fully characterize the properties of these dye molecules. According to these computational results of physical quantities and based on the performance of these dye molecules in the above aspects, in this paper, six free molecular models were picked out to combine with titanium dioxide cluster to calculate their geometrical structures, frontier orbital distributions, electron excitation energies, ultraviolet absorption spectra and the composition of the electronic transitions in chloroform solvent with polarizable continuum model. The results of these calculations show that the PA-A2 and PB-A4 dye molecule has better properties in electron transfer and spectral absorption range before and after the adsorption on the titanium dioxide.     

NMR evidence for an acetylcholine ATP complex.

The interaction of acetylcholine with ATP was studied using proton NMR. T₁ measurements indicate the formation of a complex with a probable composition of four (4) acetylcholine molecules for each ATP molecule.     

Designing polymers that mimic biomolecules.

A new field is emerging. Chemists are beginning to synthesize polymers with properties that are similar to those of proteins and RNA. Recent studies have identified oligomer backbones that form stable secondary structures. It is now possible to assemble specific sequences of diverse monomer sets into chain lengths that are nearly sufficient for tertiary structure formation. Such molecules will teach us how natural biopolymers fold; they will also enable us to design synthetic heteropolymers with novel structures and desirable functions.     

Computer modeling and analysis of heterogeneous structures of microporous carbonaceous materials

The aim of this work was to study the problems connected with computer modeling and analysis of heterogeneous structures of microporous carbonaceous materials. The research was focused on the numerical properties of original mathematical models for heterogeneous multilayer adsorption on microporous carbonaceous materials presented in our earlier papers and their applicability to examination of real microporous materials. These models are aimed at drawing information on pore structure and capacity on the basis of adsorption isotherms of small molecule adsorbates. They easily fit typical adsorption data in wide relative pressure ranges. In the theory presented, adsorption of small nearly spherical molecules in irregular pores of molecular size has been considered and side adsorbate–adsorbate interactions are neglected. The molecules mentioned are located in pores by forming aggregates, the size of which is limited by the geometry of the pores. The set of adsorbate molecules, which were adsorbed mainly due to adhesive interactions with the adsorbent matter, is treated as the first layer adsorption. Joining further molecules is viewed as the second, third,... layer adsorption. The main idea of the approach to modeling microporous structure presented, consists of introducing of realistic relationships between geometrical properties of pores and adsorption energy. Special attention was focused on the analysis of the influence of the number of model parameters on identification reliability and evaluation errors of porous structure parameters. This paper gives more information on properties of the identification technique presented in our earlier papers. The five-parameter and six-parameter identification reliability is analyzed in more detail, for different values of the system parameters. In this context, the efficiency of simultaneous examination of two isotherms is also studied.     

Relationship between the lifetime of an enzyme-substrate complex and the properties of the molecular environment.

A theoretical discussion of the decomposition rate constants of enzyme substrate complexes is presented, based upon an enzyme model published earlier (Damjanovich &; Somogyi,1973). These rate constants are expressed by the aid of molecular parameters characteristic for the enzyme-substrate complexes and the molecules in the surrounding liquid phase.Both the exponential and pre-exponential factors of the expressions describing the composition rate constants contain parameters depending on the mass distribution of the reaction mixture in a specific way which is characteristic for the enzyme-substrate complex. The findings suggest a new kind of the enzyme regulation generated by the surrounding medium.