Aqueous hydration of nucleic acid constituents: Monte Carlo computer simulation studies

Monte Carlo computer simulations were performed on dilute aqueous solutions of thymine, cytosine, uracil, adenine, guanine, the dimethyl phosphate anion in the gauche-gauche conformation and a ribose and deoxyribose derivative. The aqueous hydration of each molecule was analysed in terms of quasi-component distribution functions based on the Proximity Criterion, and partitioned into hydrophobic, hydrophilic and ionic contributions. Color stereo views of selected hydration complexes are also presented. A preliminary discussion of the transferability of functional group coordination numbers is given. The results enable to comment on two current problems related to the hydration of nucleic acids: a) the theory of Dickerson and coworkers on the role of water in the relative stability of the A and B form of DNA and b) the idea of water bridges and filaments emerging from the computer simulation results on the hydration of DNA fragments by Clementi.     

Aqueous Hydration of Nucleic Acid Constituents: Monte Carlo Computer Simulation Studies

Abstract

Monte Carlo computer simulations were performed on dilute aqueous solutions of thymine, cytosine, uracil, adenine, guanine, the dimethyl phosphate anion in the gauche-gauche conformation and a ribose and deoxyribose derivative. The aqueous hydration of each molecule was analysed in terms of quasi-component distribution functions based on the Proximity Criterion, and partitioned into hydrophobic, hydrophilic and ionic contributions. Color stereo views of selected hydration complexes are also presented. A preliminary discussion of the transferability of functional group coordination numbers is given. The results enable to comment on two current problems related to the hydration of nucleic acids: a) the theory of Dickerson and coworkers on the role of water in the relative stability of the A and B forms of DNA and b) the idea of water bridges and filaments emerging from the computer simulation results on the hydration of DNA fragments by Clementi.     

Diketopiperazine-mediated peptide formation in aqueous solution

Though diketopiperazines (DKP) are formed in most experiments concerning the prebiotic peptide formation, the molecules have not been paid attention in the studies of chemical evolution. We have found that triglycine, tetraglycine or pentaglycine are formed in aqueous solution of glycine anhydride (DKP) and glycine, diglycine or triglycine, respectively. A reaction of alanine with DKP resulted in the formation of glycylglycylalanine under the same conditions. These results indicate that the formation of the peptide bonds proceeds through the nucleophilic attack of an amino group of the amino acids or the oligoglycines on the DKP accompanied by the ring-opening.The formation of glycine anhydride, di-, tri- and tetraglycine was also observed in a mixed aqueous solution of urea and glycine in an open system to allow the evaporation of ammonia. A probable pathway is proposed for prebiotic peptide formation through diketopiperazine on the primitive Earth.     

Effect of alcohol on the solubility of amino acid in water

In a previous work, the parameters of the statistical associating fluid theory (SAFT) equation of state for amino acids were determined by using the method developed. The solubility of amino acids in water was modeled. In this work, the SAFT equation of state has been applied to describe the solubility of amino acids in aqueous alcohol solutions. The systems include dl-alanine/ethanol/water, glycine/ethanol/water, dl-valine/ethanol/water, dl-serine/ethanol/water, glycine/1-propanol/water, glycine/2-propanol/water, l-alanine/2-propanol/water, l-leucine/ethanol/water. Binary interaction parameters between amino acid and alcohol are needed by the SAFT model to get good modeling results.     

Computer simulation studies of the fully solvated wild-type and mutated GnRH in extended and beta-turn conformations

The conformational preference of the gonadotropin-releasing hormone (GnRH) and its Lys-8 mutant, studied earlier with a continuum model, was revisited using an explicit solvent model and thermodynamic integration to calculate the solvents contribution to the conformation-dependence of its free energy. In addition, the Proximity Criterion was used to further analyze the effects of conformational changes.     

Experimental data and modelling of apparent molar volumes, isentropic compressibilities and refractive indices in aqueous solutions of glycine + NaCl

Experiments have been performed at 298.15 K to measure the density, sound velocity and refractive index of glycine in aqueous solutions of NaCl over a wide range of both glycine and NaCl concentrations. The values of apparent molar volume and isentropic compressibility of glycine were calculated from the measured data. The results show a positive transfer volume of glycine from an NaCl solution to a more concentrated NaCl solution. This indicates that the size of a glycine molecule is larger in a solution with higher NaCl concentration. The negative values of apparent isentropic compressibility imply that the water molecules around the glycine molecules are less compressible than the water molecules in the bulk solution. These effects are attributed to the doubly charged behaviour of glycine and to the formation of physically bonded ion-pairs between the charged groups of glycine and sodium and chloride ions. The formation of ion-pairs, whose extents of binding reactions depend on the concentrations of both NaCl and glycine, alter the hydration number of glycine. This also explains the reason for the increase in the size of glycine with an increase in the NaCl concentration. A model based on the Pitzer formalism has been developed to correlate the activity coefficient, apparent molar volume and isentropic compressibility of glycine in aqueous solutions of NaCl. The results show that the model can accurately correlate the interactions in aqueous solutions of glycine and NaCl.     

Stoichiometry of sodium- and chloride-coupled glycine transport in synaptic plasma membrane vesicles derived from rat brain

The stoichiometric properties of the glycine transporter were studied in synaptic plasma membrane vesicles from rat brain. The present results, together with previous data from our laboratory, allow us to suggest a stoichiometry of 2 Na+ and 1 Cl- per glycine zwitterion for the translocation cycle catalyzed by the glycine carrier. We propose a kinetic model with an ordered mechanism for the binding/debinding of solutes.     

Synthesis and photochemistry of photolabile N-glycine derivatives and effects of one on the glycine receptor.

Three photolabile precursors of glycine containing a photosensitive 2-nitrobenzyl moiety attached to the amino group have been synthesized. When exposed to ultraviolet radiation between 308 and 350 nm, the compounds photolyze to release glycine, an important inhibitory neurotransmitter in the central nervous system. The identification of glycine as a photolysis product was determined by two different methods: separation of the photolyzed sample by thin-layer chromatography followed by a reaction with ninhydrin, and recognition of derivatized glycine using the Waters pico-tag method in conjunction with high-performance liquid chromatography. The photolysis of these compounds at 22 degrees C has been investigated, and the rate of decay of a transient intermediate in the reaction, which is assumed to reflect product release, has been measured. For N-(alpha-carboxy-2-nitrobenzyl)glycine this decay rate was found to be 940 s-1 at pH 6.8 and 600 s-1 at pH 7.5. Additionally, this compound was found to exhibit biological activity upon photolysis; cultured mouse spinal cord cells containing neuronal glycine receptors were used to detect the glycine liberation. The approach adopted here is useful in demonstrating the utility of photolabile precursors of neurotransmitters that have the protecting group linked to the neurotransmitter through the amino group. The rapid photolysis of such compounds to release free neurotransmitter is valuable in gaining access to chemical kinetic studies of neurotransmitter receptors. Previously, such studies have been limited because the available methods for neurotransmitter delivery did not give a sufficiently high time resolution.     

Conformations of the glycine dipeptide

Integral equation theory is applied to the determination of the intramolecular potential of mean force for the glycine dipeptide, N-acetyl glycyl-N-methylamide, in aqueous solution. The solvated free energy for the dipeptide as a function of the dihedral angles ? and ψ (Ramachandran plot) is determined and compared with the vacuum surface. Conformations forbidden in vacuum are found to be populated in aqueous solution. The results of the glycine dipeptide are compared to a parallel study on the alanine dipeptide. Solvent effects are found to be responsible for the extent of many of glycines properties related to flexibility.     

Statistical analysis of a small set of time-ordered gene expression data using linear splines

MOTIVATION: Recently, the temporal response of genes to changes in their environment has been investigated using cDNA microarray technology by measuring the gene expression levels at a small number of time points. Conventional techniques for time series analysis are not suitable for such a short series of time-ordered data. The analysis of gene expression data has therefore usually been limited to a fold-change analysis, instead of a systematic statistical approach. METHODS: We use the maximum likelihood method together with Akaike's Information Criterion to fit linear splines to a small set of time-ordered gene expression data in order to infer statistically meaningful information from the measurements. The significance of measured gene expression data is assessed using Student's t-test. RESULTS: Previous gene expression measurements of the cyanobacterium Synechocystis sp. PCC6803 were reanalyzed using linear splines. The temporal response was identified of many genes that had been missed by a fold-change analysis. Based on our statistical analysis, we found that about four gene expression measurements or more are needed at each time point.     

Assessment of sustainable forest management criteria using indicators of the international programme ICP forests

This article gives an assessment of the international criteria for the sustainable management of forests on the basis of indicators according to the International Cooperative Programme on Assessment and Monitoring of Air Pollution Effects on Forests (ICP Forests). The given program allows us to assess Criterion 2: Maintenance of Forest Health and Vitality and Criterion 4: Conservation and Improvement of the Biological Diversity of the Forest Ecosystem. The informative indicators of Criterion 2 are the degrees of the tree crown defoliation and the composition parameters of atmospheric deposition, soils, and dominant tree plant photosynthetic organs. The assessment of Criterion 4 is carried out on the basis of biodiversity items, including forest distribution by age and species composition, sets of forest community major groups (groups of forest types) and their quantitative representation in the area, number of tree and shrub species found in the forests, and species richness and species saturation. An attempt has been made to show whether the network of the permanent observation posts reflects in full measure the forest typological and age structure in Karelia and Karelian Isthmus.     

Thermodynamics of vanadyl(IV)—carboxylate complex formation in aqueous solution

The stability constants and the heats of formation of vanadyl(IV)—acetate, —glycolate, and —glycine complexes have been determined in aqueous solution by means of potentiometric and calorimetric measurements. In the pH range where the protolitic equilibria of VO²⁺ is certainly negligible the acetate forms two mononuclear complexes, the glycolate three whereas the glycine reacts in its zwitterionic form. The stabilities of the glycolate complexes are considerably higher than the acetate ones, in spite of its lower basicity, indicating that the complex formation involves the coordination of the hydroxyl group to the metal ion. The enthalpy changes are positive except for the glycolate where a small negative value is found. For all systems the entropy changes are positive and therefore favourable to the complex formation.     

Condensation of oligoglycines with trimeta- and tetrametaphosphate in aqueous solutions

The dehydration condensation of glycine with trimetaphosphate in aqueous solution has been reinvestigated. Although it has been reported that the condensation of glycine under the alkaline conditions was brought about through the formation of cyclic acylphosphoramidate and hence the condensation of polyglycines could not occur, we found that the condensation of oligoglycines with trimeta- and tetrametaphosphate in aqueous solution are possible through the formation of their acylphosphates under the neutral or weak acidic conditions.Aqueous solutions of 1.0 M glycylglycine and 1.0 M trimetaphosphate in the various pH from 4.0 to 9.0 were incubated at 38 °C. The solutions were analyzed by HPLC with ninhydrin reaction system. Tetraglycine and hexaglycine were detected and their maximum yields were given in the reaction carried out around pH 7. They are approximately 15% and 4% after 30 days, respectively. Analogous experiments were performed with tetrametaphosphate. The results showed a similar pH dependence for the condensation, but the yields were about one-tenth of those of corresponding experiments with trimetaphosphate.Relative rates of dimerization of glycine, diglycine and triglycine in the equimolar concentration were also investigated at pH 6.0 at 38 °C. The rates for digylcine and triglycine were approximately twice and four times as large as that for glycine.Relevance of the experiments to chemical evolution is discussed.     

Specificity in the genetic code. The role of nucleotide base-amino acid interaction

The mechanism of the unique and specific association of a given amino acid to its t-RNA is investigated by theoretical methods. Several possible schemes are proposed to explain specificity. The physical forces which act within these mechanisms are illustrated by the computer simulation of probable interactions between glycine and nucleotide bases and base pairs. It is demonstrated that glycine has direct and selective affinities for the nucleotide bases and that these interactions are principally determined by the polar groups. Energies have been calculated for the interaction of glycine with several base pairs. From these, the possibility that specificity arises through direct complexing of an amino acid with its anticodon is evaluated.     

A new photolabile precursor of glycine with improved properties: A tool for chemical kinetic investigations of the glycine receptor

The synthesis and characterization of a new photolabile precursor of glycine (caged glycine) is described. The alpha-carboxyl group of glycine is covalently coupled to the alpha-carboxy-2-nitrobenzyl (alphaCNB) protecting group. Photolysis of the caged glycine with UV light produces free glycine. At 308 nm, the compound photolyzes with a quantum yield of 0.38. The absorption spectrum and the pH dependence of a transient absorption produced after laser-flash illumination are typical for aci-nitro intermediates of alphaCNB-protected compounds. The time constant for the major component of the aci-nitro intermediate decay ( approximately 84% of the total aci-nitro absorbance) was determined to be 7 micros at physiological pH. A minor component ( approximately 16%) decays with a rate constant of 170 micros. The compound does not activate or inhibit the alpha(1)-homomeric glycine receptor transiently expressed in HEK293 cells. After photolysis with a 10 ns pulse of 325 nm laser light, the glycine released from the caged compound activates glycine-mediated whole-cell currents in the same cells. The rise of these currents can be measured in a time-resolved fashion and occurs on a millisecond to sub-millisecond time scale. It can be described with a single-exponential function over >85% of the total current. The rate constant of the current rise is about 2 orders of magnitude slower than the rate constant of caged glycine photolysis. Thermal hydrolysis of the alphaCNB-caged glycine takes place with a half-life of 15.6 h at physiological pH. The new caged glycine is the first in a series of photoprotected glycine derivatives that has the required properties for use with chemical kinetic methods for investigation of glycine-activated cell surface receptors. Photolysis is rapid and efficient with respect to the receptor reactions to be studied; hydrolysis in aqueous solution is sufficiently slow, and the compound is biologically inert. It will, therefore, be a useful tool for investigation of the processes leading to channel opening of glycine receptor channels and the effects of mutations of the glycine receptor and of inhibitors on these processes.     

Extending the modified bayesian information criterion (mBIC) to dense markers and multiple interval mapping

SUMMARY: The modified version of Bayesian Information Criterion (mBIC) is a relatively simple model selection procedure that can be used when locating multiple interacting quantitative trait loci (QTL). Our earlier work demonstrated the statistical properties of mBIC for situations where the average genetic map interval is at least 5 cM. In this work mBIC is adapted to genome searches based on a dense map and, more importantly, to the situation where consecutive QTL and interactions are located by multiple interval mapping. Easy to use formulas for the extended mBIC are given. A simulation study, as well as the analysis of real data, confirm the good properties of the extended mBIC.     

Cloning and mapping of platypus SOX2 and SOX14: insights into SOX group B evolution

Group B SOX genes, the closest relatives to the sex-determining gene SRY, are thought to have evolved from a single ancestral SOX B by a series of duplications and translocations. The two SOX B genes SOX2 and SOX14 co-localize to chromosome 3q in humans. SOX2 and SOX14 homologues were cloned and characterized in the platypus, a monotreme mammal distantly related to man. The two genes were found to co-localize to chromosome 1q in this species. Proximity of the two related genes has therefore been conserved for 170 Myr, since humans and platypus diverged. The sequence similarity and conserved synteny of these group B genes provide clues to their origin. A simple model of SOX group B gene evolution is proposed.     

The synthesis of amino acids and sugars on an inorganic template from constituents of the prebiotic atmosphere

Inelastic Electron Tunnelling Spectroscopy (IETS) has been used to identify the reaction products present on an alumina surface when it is exposed to likely components of the earth's prebiotic atmosphere. The alumina barrier of Al-AlO _x -Pb tunnelling junctions have been exposed to water; aqueous ammonia; wet carbon monoxide gas and to aqueous formaldehyde vapour under normal atmospheric conditions at room temperature. The water spectrum shows strong coincidence with that of a genuine sample of formic acid. It is proposed that atmospheric CO₂ is involved in this surface catalyzed reaction. The aqueous ammonia spectrum is assigned as an amino acid species produced from ammonia, water and atmospheric carbon dioxide. This spectrum compares very closely with the tunnelling spectrum of a genuine sample of glycine. The wet carbon monoxide spectrum and the aqueous formaldehyde spectrum have been produced by an infusion doping process. These spectra of CO and aqueous formaldehyde are assigned as a sugar like polymer or a sugar formed on the alumina surface. A tunnelling spectrum of D(–) fructose has been produced to aid this assignment. The role of an inorganic template such as alumina in the original prebiotic synthesis of amino acids and sugars is considered.     

Refined models for computer simulation of protein folding. Applications to the study of conserved secondary structure and flexible hinge points during the folding of pancreatic trypsin inhibitor

A new model and parameters are proposed for the computer simulation of protein folding, which satisfy requirements for a fully automatic simulation as discussed in recent critical reviews.The parameters were obtained, refined or checked by empirical observations on proteins of known sequence and conformation, in order to avoid as much as possible theoretical deductions about the nature of the interactions between groups in proteins, which may not be justified by the current status of the art.The major improvement over previous methods is to retain a more realistic and complete representation of the protein backbone, and to alternatively reduce the number of variables by coupling their behaviour. As an example, the method is applied to simulate the folding of pancreatic trypsin inhibitor, and leads to a root-mean-square fit of 6·0 Å with good secondary structure.This also allows a more detailed examination of secondary structure transitions during protein folding than has been possible hitherto. Although, in the simulation discussed most extensively, the advantage of initial statistical predictions is demonstrated, the secondary structure was free to change in the simulation. A simulation from an extended chain is also described, and refinements tested.By observing changes in secondary structure during the simulated folding, it is shown that α-helices and extended chain regions predicted at the outset, or formed early in the simulation, are conserved, and that certain residues are crucial as flexible hinge-points to bring the secondary structure together in order to achieve tertiary packing.In view of recent debate about the importance of glycyl residues as hinge-points, and the danger of imparting glycyl-like backbone behaviour to non-glycyl residues suspected to be hinge-points, it is of considerable interest that the hinge-point residues identified by us are not, in general, glycyl residues. This makes an important distinction between a “reverse turn region”, for which glycine is statistically a strong candidate, and a hinge-point in the protein backbone. It is discussed that reverse turns are locally determined and likely to be fairly stable during the folding process, while hinge-points are determined by tertiary interactions. This distinction, implicit in most papers concerned with statistical methods of secondary structure prediction, has not been made clearly in recent reports of folding simulations.     

N-Glycyl-glucosamine: A novel constituent in the cell wall of Halococcus morrhuae

The dinitrophenyl-derivative of N-glycylglucosamine was isolated from partially hydrolyzed dinitrophenylated cell walls of Halococcus morrhuae CCM 859. To increase the yield of amino-terminal glycine residues, halococcal cell walls were treated with alkali or acid prior to dinitrophenylation. Authentic N-glycyl-glucosamine was used as a reference substance. A substitution of the amino group of glucosamine by an amino acid has so far not been found in any other wall of a pro- or eucaryotic cell. Since only 5% of the glycine residues reveal an unsubstituted carboxyl group within intact cell walls, glycine may play a role in connecting glycan strands through peptidic linkages between the amino group of glucosamine and the carboxyl group of an uronic acid or gulosaminuronic acid.Abbreviations DNP dinitrophenyl