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PubMed1990

Measurement of active-site homology between potato and rabbit muscle alpha-glucan phosphorylases through use of a linear free energy relationship.

The Michaelis-Menten parameters (Vmax and Km) for turnover of an extensive series of deoxy and deoxyfluoro derivatives of alpha-D-glucopyranosyl phosphate by the alpha-glucan phosphorylase from potato tuber have been determined. Very large rate reductions are observed as a consequence of each substitution, primarily due to losses in specific binding interactions, most likely hydrogen bonding, at the enzymic transition state. Comparison of the Vmax/Km values so determined with those measured for rabbit muscle alpha-glucan phosphorylase [Street et al. (1989) Biochemistry 28, 1581] reveals an astonishingly similar specificity, especially in light of the phylogenetic separation of their host organisms. This indicates that very similar hydrogen-bonding interactions between the enzyme and the substrate must be present at the transition states for the two enzymic reactions; therefore, they have very similar active sites. Quantitation of this similarity is achieved by plotting the logarithm of the Vmax/Km value for each substrate analogue with the potato enzyme against the same parameter for the muscle enzyme, yielding straight lines (p = 0.998 and 0.999) of slope 1.0 and 1.2 for the deoxy and deoxyfluoro substrates, respectively. Since the correlation coefficient of such plots is a direct measure of the similarity of the two transition-state complexes, thus of the enzyme active sites, it can be used as a measure of active-site homology between the two enzymes. The extremely high homology observed in this case is consistent with the observed sequence homology at the active site.

Animals↗
PubMed1994

Effect of phosphate activating group on oligonucleotide formation on montmorillonite: the regioselective formation of 3',5'-linked oligoadenylates.

The effects of amine structure on the montmorillonite-catalyzed oligomerization of the 5'-phosphoramidates of adenosine are investigated. 4-Aminopyridine derivatives yielded oligoadenylates as long as dodecamers with a regioselectivity for 3',5'-phosphodiester bond formation averaging 88%. Linear and cyclic oligomers are obtained and no A5'ppA-containing products are detected. Oligomers as long as the hexanucleotide are obtained using 2-aminobenzimidazole as the activating group. A predominance of pA2'pA is detected in the dimer fraction along with cyclic 3',5'-trimer; no A5'ppA-containing oligomers were detected. Little or no oligomer formation was observed when morpholine, piperidine, pyrazole, 1,2,4-triazole, and 2-pyridone are used as phosphate-activating groups. The effects of the structure of the phosphate activating group on the oligomer structure and chain lengths are discussed.

4-Aminopyridine↗
PubMed2003

Quantitative analysis and characterization of DNA immobilized on gold.

We describe the complementary use of X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FTIR) spectroscopy to quantitatively characterize the immobilization of thiolated (dT)(25) single-stranded DNA (ssDNA) on gold. When electron attenuation effects are accurately accounted for in the XPS analysis, the relative coverage values obtained by the two methods are in excellent agreement, and the absolute coverage can be calculated on the basis of the XPS data. The evolution of chemically specific spectral signatures during immobilization indicates that at lower coverages much of the DNA lies flat on the surface, with a substantial fraction of the thymine bases chemisorbed. At higher immobilization densities, the (dT)(25) film consists of randomly coiled ssDNA molecules each anchored via the thiol group and at possibly one or two other bases. We use two examples to demonstrate how the quantitative analysis can be applied to practical problems: the effects of different buffer salts on the immobilization efficiency; the immobilization kinetics. Buffers with divalent salts dramatically increase the efficiency of immobilization and result in very high surface densities (>5 x 10(13)/ cm(2)), densities that may only be possible if the divalent counterions induce strong attractive intermolecular interactions. In contrast with previous reports of alkanethiol adsorption kinetics on gold, ssDNA immobilization in 1 M phosphate buffer does not occur with Langmuir kinetics, a result attributable to rearrangement within the film that follows the initial adsorption.

DNA, Single-Stranded↗
PubMed1990

Photochemical cycloaddition reactions of cyanoacetylene and dicyanoacetylene.

Photolysis of cyanoacetylene with 185- or 206-nm light yields 1,3,5-tricyanobenzene while 254-nm radiation yields a mixture of tetracyanocyclooctatetraenes, 1,2,4- and 1,3,5-tricyanobenzene. A polymer of cyanoacetylene is the major photoproduct. 1,3,5-Tricarbomethoxybenzene was the only photoproduct identified from the irradiation of methyl propiolate at 254 nm. Mono-, di-, and tricyanobenzenes are formed by irradiation of mixtures of acetylene and cyanoacetylene at 185, 206, and 254 nm along with trace amounts of cyclooctatetraenes. No photoadducts were detected on photolysis of mixtures of cyanoacetylene and CO or HCN. The tetracyanocyclooctatetraene structures were established by UV, MS, and NMR analyses. The 1H NMR of the product mixture exhibited a singlet at delta 7.028 consistent with either 1 or 2 and two singlets at delta 6.85 and 6.91 assigned to 3. Photolysis of mixtures of dicyanoacetylene and acetylene with either 185- or 206-nm light yielded 1,2-dicyanobenzene and (E,Z)-1-buten-3-yne-1,4-dicarbonitrile. These products were also obtained using 254-nm light along with a mixture of tetracyanocyclooctatetraenes. The same three singlets were observed in this product mixture as were observed in the tetracyanocyclooctatetraenes obtained from cyanoacetylene. From this observation it was concluded that the delta 7.02 signal is due to 2 and not 1. The photolysis of cyanoacetylene and dicyanoacetylene in the presence of ethylene with 185-nm light yields 1-cyanocylobutene and 1,2-dicyanocyclobutene, respectively. 2-Cyanobutadiene and 2,3-dicyanobutadiene are the photoproducts with 254-nm light. Reaction pathways are proposed to explain these findings.

Acetonitriles↗
PubMed1997

Glycolonitrile oligomerization: structure of isolated oxazolines, potential heterocycles on the early earth.

A study of glycolonitrile polymerization has led to the isolation and characterization of two 2,5-dihydro-4-aminooxazoles, 4 and 5. Previous reports have misassigned these structures as s-triazines or pyrimidines. X-ray diffraction analysis of crystals of 4 and an acetylated oxazole derivative of 5 (6) confirm the proposed structures. Ab initio computations are used to assess the relative thermodynamic stability of three trimer isomers (an s-triazine, an aminohydroxypyrimidine, and an aminooxazoline), and the results indicate that 4 is a novel kinetic product. Mechanistic considerations rationalize kinetic oxazole formation over the more customary triazine or pyrimidine trimers.

Acetonitriles↗
PubMed2007

Cytochrome c(2) Exit Strategy: Dissociation Studies and Evolutionary Implications.

Small, water-soluble, type c cytochromes form a transient network connecting major bioenergetic membrane protein complexes in both photosynthesis and respiration. In the photosynthesis cycle of Rhodobacter sphaeroides, cytochrome c2 (cyt c2) docks to the reaction center (RC), undergoes electron transfer, and exits for the cytochrome bc1 complex. Translations of cyt c2 about the RC-cyt c2 docking interface and surrounding membrane reveal possible exit pathways. A pathway at a minimal elevation allowed by the architecture of the RC is analyzed using both an all-atom steered molecular dynamics simulation of the RC-cyt c2 complex and a bioinformatic analysis of the structures and sequences of cyt c. The structure-based phylogenetic analysis allows for the identification of structural elements that have evolved to satisfy the requirements of having multiple functional partners. The patterns of evolutionary variation obtained from the phylogenetic analysis of both docking partners of cyt c2 reveal conservation of key residues involved in the interaction interfaces that would be candidates for further experimental studies. Additionally, using the molecular mechanics Poisson-Boltzmann surface area method we calculate that the binding free energy of reduced cyt c2 to the RC is nearly 6 kcal/mol more favorable than with oxidized cyt c2. The redox-dependent variations lead to changes in structural flexibility, behavior of the interfacial water molecules, and eventually changes in the binding free energy of the complex.

Amino Acid Sequence↗
PubMed2006

Stochastic analysis of the parity-violating energy differences between enantiomers and its implications for the origin of biological chirality.

A stochastic description of a racemic mixture is developed taking into account the slight energy difference between enantiomers originating from parity violation (DeltaE(PV) approximately equal to 10(-13) Jmol(-1)). The system can be described by an asymmetric binomial distribution. A method is developed to calculate the probability of forming the more-stable isomer in excess, which is not significantly larger than 50% under normal conditions. It is concluded that the parity-violating energy difference between enantiomers is very unlikely to be relevant in considerations about the origin of biological chirality.

Algorithms↗
PubMed1998

Biomarkers as tracers for life on early earth and Mars.

Biomarkers in geological samples are products derived from biochemical (natural product) precursors by reductive and oxidative processes (e.g., cholestanes from cholesterol). Generally, lipids, pigments and biomembranes are preserved best over longer geological times and labile compounds such as amino acids, sugars, etc. are useful biomarkers for recent times. Thus, the detailed characterization of biomarker compositions permits the assessment of the major contributing species of extinct and/or extant life. In the case of the early Earth, work has progressed to elucidate molecular structure and carbon isotropic signals preserved in ancient sedimentary rocks. In addition, the combination of bacterial biochemistry with the organic geochemistry of contemporary and ancient hydrothermal ecosystems permits the modeling of the nature, behavior and preservation potential of primitive microbial communities. This approach uses combined molecular and isotopic analyses to characterize lipids produced by cultured bacteria (representative of ancient strains) and to test a variety of culture conditions which affect their biosynthesis. On considering Mars, the biomarkers from lipids and biopolymers would be expected to be preserved best if life flourished there during its early history (3.5-4 x 10(9) yr ago). Both oxidized and reduced products would be expected. This is based on the inferred occurrence of hydrothermal activity during that time with the concomitant preservation of biochemically-derived organic matter. Both known biomarkers (i.e., as elucidated for early terrestrial samples and for primitive terrestrial microbiota) and novel, potentially unknown compounds should be characterized.

Bacteria↗
PubMed1998

Formation of RNA oligomers on montmorillonite: site of catalysis.

Certain montmorillonites catalyze the self condensation of the 5'-phosphorimidazolide of nucleosides in pH 8 aqueous electrolyte solutions at ambient temperatures leading to formation of RNA oligomers. In order to establish the nature of the sites on montmorillonite responsible for this catalytic activity, oligomerization reactions were run with montmorillonites which had been selectively modified (I) at the edges by (a) fluoride treatment, (b) silylation, (c) metaphosphate treatment of the anion exchange sites (II) in the interlayer by (a) saturation with quaternary alkylammonium ions of increasing size, (b) aluminum polyoxo cations. High pressure liquid chromatography, HPLC, analysis of condensation products for their chain lengths and yields indicated that modification at the edges did not affect the catalytic activity to a significant extent, while blocking the interlayer strongly inhibited product formation.

Bentonite↗
PubMed1998

Review and latest results of laboratory investigations of Titan's aerosols.

Titan, the largest satellite of Saturn, has an atmosphere chiefly made up of N2 and CH4, and including many organics. This atmosphere also partly consists of hazes and aerosol particles which shroud the surface of this satellite, giving it a reddish appearance. The aerosols observed in Titan's atmosphere are thought to be synthesized at high altitudes (>300 km) and fall to the surface. Varying with temperature profiles, condensation phenomena take place in the lower atmosphere, about 100 km below. These solid particles, often called 'tholins', have been currently investigated for many years by laboratory scientists and physics modellers. This paper assesses past research and results in different fields (elemental composition, optical constants, pyrolysis, particle size), hightlighting interests and questions aroused by these studies. It also presents the latest results and advances, and concludes with existing problems and future pathways.

Aerosols↗
PubMed1997

Condensation of glycylglycine to oligoglycines with trimetaphosphate in aqueous solution. II: catalytic effect of magnesium ion.

The previously reported condensation reaction of glycylglycine with trimetaphosphate (Yamanaka et al., 1988) was reinvestigated and shown to be catalyzed by magnesium ion. Aqueous solutions containing glycylglycine (0.5 M), trimetaphosphate (0.5 M) and magnesium chloride (0.5 M) were incubated at 38 degrees C at pH 4, 5, 6, 7 and 8. After incubation for ten days at pH 5, the maximum yields of tetraglycine and hexaglycine as condensation products were found to be about 12 and 1.4%, respectively. This result indicated the presence of a considerable catalytic effect of magnesium ion compared with the maximum yield of about 2% for tetraglycine and approximately 0% for hexaglycine in the absence of magnesium ion.

Evolution, Chemical↗
PubMed1997

Prebiotic transamination.

Biological amino acids and alpha keto acids directly condense with decarboxylation and transamination to yield product amino acids. This process is closely related to unusual amino acid decarboxylase enzymes in certain microorganisms and may represent a primordial mode of amino acid metabolism.

Alanine↗
PubMed1998

A fission-fusion origin for life.

To develop a comprehensive 'cells-first' approach to the origin of life, we propose that protocells form spontaneously and that the fission and fusion of these protocells drives the dynamics of their evolution. The fitness criterion for this evolution is taken to be the the stability (conservation) of domains in the protocellular membrane as determined by non-covalent molecular associations between the amphiphiles of the membrane and a subset of the macromolecules in the protocell. In the presence of a source of free energy the macromolecular content of the protocell (co-)evolves as the result of (domain-dependent) membrane-catalysed polymerisation of the prebiotic constituents delivered to the protocell by fusion. The metabolism of the cell therefore (co-)evolves on a rugged fitness landscape. We indicate how domain evolution with the same fitness criterion can potentially give rise to coding. Membrane domains may therefore provide the link between protocells and the RNA/DNA-world.

Amino Acids↗
PubMed1997

Attempted prebiotic synthesis of pseudouridine.

Pseudouridine is a modified base found in all tRNA and rRNA. Hence, it is reasonable to think that pseudouridine was important in the early evolution, if not the origin, of life. Since uracil reacts rapidly with formaldehyde and other aldehydes at the C-5 position, it is plausible that pseudouridine could be synthesized in a similar way by the reaction of the C-5 of uracil with the C-1 of ribose. The determining factor is whether the ribose could react with the uracil faster than ribose decomposes. However, both rates are determined by the amount of free aldehyde in the ribose. Various plausible prebiotic reactions were investigated and none showed pseudouridine above the detection limit (<0.01%). Only unreacted uracil and ribose decomposition products could be observed. Thus the rate of addition of ribose to uracil is much slower than the decomposition of ribose under any reasonable prebiotic conditions. Unless efficient non-biological catalysts for any of these reactions exist, pseudouridine would not have been synthesized to any significant extent without the use of biologically produced enzymes.

Deoxyribose↗
PubMed1999

Martian stable isotopes: volatile evolution, climate change and exobiological implications.

Measurements of the ratios of stable isotopes in the martian atmosphere and crust provide fundamental information about the evolution of the martian volatile and climate system. Current best estimates of the isotope ratios indicate that there has been substantial loss of gases to space and exchange of gases between the atmosphere and the crust throughout geologic time; exchange may have occurred through circulation of water in hydrothermal systems. Processes of volatile evolution and exchange will fractionate the isotopes in a manner that complicates the possible interpretation of isotopic data in terms of any fractionation that may have been caused by martian biota, and must be understood first. Key measurements are suggested that will enhance our understanding of the non-biological fractionation of the isotopes and of the evolution of the martian volatile system.

Climate↗