Sugar-Driven Prebiotic Synthesis of Ammonia from Nitrite

Reaction of 3–5 carbon sugars, glycolaldehyde, and α-ketoaldehydes with nitrite under mild anaerobic aqueous conditions yielded ammonia, an essential substrate for the synthesis of nitrogen-containing molecules during abiogenesis. Under the same conditions, ammonia synthesis was not driven by formaldehyde, glyoxylate, 2-deoxyribose, and glucose, a result indicating that the reduction process requires an organic reductant containing either an accessible α-hydroxycarbonyl group or an α-dicarbonyl group. Small amounts of aqueous Fe⁺³ catalyzed the sugar-driven synthesis of ammonia. The glyceraldehyde concentration dependence of ammonia synthesis, and control studies of ammonia’s reaction with glyceraldehyde, indicated that ammonia formation is accompanied by incorporation of part of the synthesized ammonia into sugar-derived organic products. The ability of sugars to drive the synthesis of ammonia is considered important to abiogenesis because it provides a way to generate photochemically unstable ammonia at sites of sugar-based origin-of-life processes from nitrite, a plausible prebiotic nitrogen species.     

Homochirality in Life: Two Equal Runners,One Tripped

Strong arguments can be found in the literature addressed to the question of the origin of homochirality in life, supporting the hypothesis that primordial life could have evolved in both homochiral forms and that early on when life was still rarely found, random events led to the survival of only one of these living mirror images. This proposal is an alternative to the generally accepted view that small enantiomeric excesses of biologically important molecules were amplified to homochirality prior to life’s origin. Acceptance of the possibility of “two equal runners” leads to the importance of research investigations on routes to formation of ensembles of racemic mixtures of isotactic biologically interesting polymers, supramolecular entities and aggregates.     

Question 4: Basic Questions About the Origin of Life: On Chirobiogenesis

Some experimental aspects concerning either the enantio-enrichment of α-amino acids starting from non-racemic mixtures or the formation of homochiral oligopeptides and oligonucleotides starting from racemic precursors are described. In principle, it is possible that more than one of these processes had played a role in chirobiogenesis. Presented at the International School of Complexity – 4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.     

Chiral Amplification of Oligopeptides via Polymerization in Two-dimensional Crystallites on Water

A possible role that might have been played by ordered clusters at the air/water interface for the generation of homochiral oligopeptides under prebiotic conditions has been probed by a catalyzed polymerization of amphiphilic activated alpha-amino acids that assembled as two-dimensional (2-D) crystallites at this interface. Three type of processes are described: (i) polymerization of racemates of activated alpha-amino acids that undergo spontaneous resolution into enantiomorphous 2-D crystallites to yield racemic mixtures of oligopeptides enriched with the oligomers of homochiral sequence, (ii) enhanced formation of racemic mixtures of homochiral oligopeptides via lattice-controlled polymerization within 2-D racemic compounds and (iii) generation of homochiral oligopeptides of a single handedness from chiral non-racemic mixtures of monomers that self-assemble into two different phases, racemic crystallites composed from both enantiomers and enantiomorphous crystallites of the enantiomer in excess. The structures of the 2-D crystallites have been determined by grazing incidence X-ray diffraction and the diastereoisomeric composition of the oligopeptides by matrix-assisted laser-desorption time-of-flight mass spectrometry with enantio-labeling.     

Generalized stern models of the electric double layer considering the spatial variation of permittvity and finite size of ions in saturation regime

The interaction between a charged metal implant surface and a surrounding body fluid (electrolyte solution) leads to ion redistribution and thus to formation of an electrical double layer (EDL). The physical properties of the EDL contribute essentially to the formation of the complex implant-biosystem interface. Study of the EDL began in 1879 by Hermann von Helmholtz and still today remains a scientific challenge. The present mini review is focused on introducing the generalized Stern theory of an EDL, which takes into account the orientational ordering of water molecules. To ascertain the plausibility of the generalized Stern models described, we follow the classical model of Stern and introduce two Langevin models for spatial variation of the relative permittivity for point-like and finite sized ions. We attempt to uncover the subtle interplay between water ordering and finite sized ions and their impact on the electric potential near the charged implant surface. Two complementary effects appear to account for the spatial dependency of the relative permittivity near the charged implant surface — the dipole moment vectors of water molecules are predominantly oriented towards the surface and water molecules are depleted due to the accumulation of counterions. At the end the expressions for relative permittivity in both Langevin models were generalized by also taking into account the cavity and reaction field.     

Chiral Selection in Oligoadenylate Formation in the Presence of a Metal ion Catalyst or Poly(U) Template

The lead ion-catalyzed oligomerization of 5′-phosphorimidazolides of D-, L- or racemic DL-adenosine (D-ImpA, L-ImpA and DL-ImpA) gave oligoadenylates up to a pentamer. The oligomers resulting from racemic ImpA were comparable in yields and length to those from chiral D- or L-ImpA. A complex mixture of homochiral and heterochiral oligomers was formed in the reaction from racemic ImpA. Total dimer product from racemic ImpA by the lead ion catalyst showed homochiral selectivity. The reaction catalyzed by uranyl ion yielded oligoadenylates up to 15mer from chiral D- or L-ImpA in over 95% yield. A complex mixture of isomeric oligoadenylates was formed from racemic DL-ImpA in the presence of uranyl ion catalyst in comparable yields to those from D- or L-ImpA. The analysis of the dimer product from DL-ImpA showed that the homochiral 2′ –5′ linked dimer was selectively formed. D-ImpA polymerized effectively on a poly(U) template, which is exclusively composed of D-uridine, yielding oligoadenylates up to a pentamer. In contrast, L-ImpA or racemic DL-ImpA polymerized far less efficiently on the poly(U) template, demonstrating that chiral selection takes place in the poly(U) template-directed oligoadenylate formation.     

Progress in demonstrating total homochiral selection in montmorillonite-catalyzed RNA synthesis

The Na⁺-montmorillonite-catalyzed reactions of 5′-phosphorimidazolides of nucleosides generates RNA oligomers. The question arises as to how chiral selectivity was introduced into this biopolymer from a simple chemical system. We have demonstrated homochiral selection in quaternary reactions of a racemic mixture of d,l-ImpA and d,l-ImpU on Na⁺-montmorillonite. The dimer, trimer, tetramer and pentamer fractions were investigated for homochiral selection. The products were collected via ion exchange HPLC and their terminal 5′-phosphate was cleaved by alkaline phosphatase. These fractions were analyzed by reverse phase HPLC for the identification of homochiral and heterochiral isomers. Encouraged by favorable homochiral excesses of dimer (63.5 ± 0.8%) and trimer (74.3 ± 1.7%), the study was extended to the analysis of higher oligomers. The tetramer and pentamer of the quaternary reaction were separated into 26 and 22 isomers, respectively, on a reverse phase column. Their co-elution with those formed in the binary reactions of d-ImpA and d-ImpU on Na⁺-montmorillonite revealed 92.7 ± 2.0% and 97.2 ± 0.5% homochirality of the tetramer and pentamer, respectively. These results suggest that Na⁺-montmorillonite not only catalyzes the prebiotic synthesis of RNA but it also facilitates homochiral selection.     

Pharmacological Inhibition of Nicotinamide Phosphoribosyltransferase (NAMPT), an Enzyme Essential for NAD+ Biosynthesis,in Human Cancer Cells: METABOLIC BASIS AND POTENTIAL CLINICAL IMPLICATIONS*

Nicotinamide phosphoribosyltransferase (NAMPT) catalyzes the first rate-limiting step in converting nicotinamide to NAD⁺, essential for cellular metabolism, energy production, and DNA repair. NAMPT has been extensively studied because of its critical role in these cellular processes and the prospect of developing therapeutics against the target, yet how it regulates cellular metabolism is not fully understood. In this study we utilized liquid chromatography-mass spectrometry to examine the effects of FK866, a small molecule inhibitor of NAMPT currently in clinical trials, on glycolysis, the pentose phosphate pathway, the tricarboxylic acid (TCA) cycle, and serine biosynthesis in cancer cells and tumor xenografts. We show for the first time that NAMPT inhibition leads to the attenuation of glycolysis at the glyceraldehyde 3-phosphate dehydrogenase step due to the reduced availability of NAD⁺ for the enzyme. The attenuation of glycolysis results in the accumulation of glycolytic intermediates before and at the glyceraldehyde 3-phosphate dehydrogenase step, promoting carbon overflow into the pentose phosphate pathway as evidenced by the increased intermediate levels. The attenuation of glycolysis also causes decreased glycolytic intermediates after the glyceraldehyde 3-phosphate dehydrogenase step, thereby reducing carbon flow into serine biosynthesis and the TCA cycle. Labeling studies establish that the carbon overflow into the pentose phosphate pathway is mainly through its non-oxidative branch. Together, these studies establish the blockade of glycolysis at the glyceraldehyde 3-phosphate dehydrogenase step as the central metabolic basis of NAMPT inhibition responsible for ATP depletion, metabolic perturbation, and subsequent tumor growth inhibition. These studies also suggest that altered metabolite levels in tumors can be used as robust pharmacodynamic markers for evaluating NAMPT inhibitors in the clinic.     

Symmetry-breaking in Chiral Polymerisation

We propose a model for chiral polymerisation and investigate its symmetric and asymmetric solutions. The model has a source species which decays into left- and right-handed types of monomer, each of which can polymerise to form homochiral chains; these chains are susceptible to ‘poisoning’ by the opposite-handed monomer. Homochiral polymers are assumed to influence the proportion of each type of monomer formed from the precursor. We show that for certain parameter values a positive feedback mechanism makes the symmetric steady-state solution unstable. The kinetics of polymer formation are then analysed in the case where the system starts from zero concentrations of monomers and chains. We show that following a long induction time, extremely large concentrations of polymers are formed for a short time, during this time an asymmetry introduced into the system by a random external perturbation may be massively amplified. The system then approaches one of the steady-state solutions described above.     

New Pathway for Nonphosphorylated Degradation of Gluconate by Aspergillus niger

A new nonphosphorylative pathway for gluconate degradation was found in extracts of a strain of Aspergillus niger. The findings indicate that gluconate is dehydrated into 2-keto-3-deoxy-gluconate (KDG), which then is cleaved into glyceraldehyde and pyruvate. 6-Phosphogluconate was not degraded under the same conditions. In addition, KDG was formed from glyceraldehyde and pyruvate. Very weak activity was obtained when glyceraldehyde 3-phosphate replaced glyceraldehyde in this reaction.     

A tool for the prediction of structures of complex sugars

In two recent back to back articles(Xia et al., J Chem Theory Comput 3:1620–1628 and 1629–1643, 2007a, b) we have started to address the problem of complex oligosaccharide conformation and folding. The scheme previously presented was based on exhaustive searches in configuration space in conjunction with Nuclear Overhauser Effect (NOE) calculations and the use of a complex rotameric library that takes branching into account. NOEs are extremely useful for structural determination but only provide information about short range interactions and ordering. Instead, the measurement of residual dipolar couplings (RDC), yields information about molecular ordering or folding that is long range in nature. In this article we show the results obtained by incorporation RDC calculations into our prediction scheme. Using this new approach we are able to accurately predict the structure of six human milk sugars: LNF-1, LND-1, LNF-2, LNF-3, LNnT and LNT. Our exhaustive search in dihedral configuration space combined with RDC and NOE calculations allows for highly accurate structural predictions that, because of the non-ergodic nature of these molecules on a time scale compatible with molecular dynamics simulations, are extremely hard to obtain otherwise (Almond et al., Biochemistry 43:5853–5863, 2004). Molecular dynamics simulations in explicit solvent using as initial configurations the structures predicted by our algorithm show that the histo-blood group epitopes in these sugars are relatively rigid and that the whole family of oligosaccharides derives its conformational variability almost exclusively from their common linkage (β-d-GlcNAc-(1→3)-β-d-Gal) which can exist in two distinct conformational states. A population analysis based on the conformational variability of this flexible glycosidic link indicates that the relative population of the two distinct states varies for different human milk oligosaccharides. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Unifying and distinguishing diversity ordering methods for comparing communities

Diversity indices have been widely used in ecological research, but they remain problematic in that different indices may rank communities inconsistently. This problem can be solved by using diversity ordering methods, the output of which is a diversity profile in graphical form for each community being compared. In this paper, we demonstrate that existing diversity ordering methods can be classified into four groups and that within-group methods are essentially equivalent, while among-group methods are not. We find that the intrinsic diversity-related methods—i.e., the group containing the right tail-sum method, the logarithmic dominance plot, the majorization method, and the k-dominance plot—provide the most stringent test of diversity ordering, and we recommend the right tail-sum method as the method of preference for practical purposes.     

Sugar-Driven Prebiotic Synthesis of 3,5(6)-Dimethylpyrazin-2-one: A Possible Nucleobase of a Primitive Replication Process

Reaction of glyceraldehyde with alanine amide (or ammonia) under anaerobic aqueous conditions yielded 3,5(6)-dimethylpyrazin-2-one that is considered a possible complementary residue of a primitive replicating molecule that preceded RNA. Synthesis of the dimethylpyrazin-2-one isomers under mild aqueous conditions (65 degrees C, pH 5.5) from 100 mM glyceraldehyde and alanine amide (or ammonia) was complete in about 5 days. This synthesis using 25 mM glyceraldehyde and alanine amide gave a total pyrazinone yield of 9.3% consisting of 42% of the 3,5-dimethylprazin-2-one isomer and 58% of the 3,6-dimethylpyrazin-2-one isomer. The related synthesis of the dimethylpyrazin-2-one isomers from glyceraldehyde and ammonia was about 200-fold less efficient than the alanine amide reaction. This synthetic process is considered a reasonable model of origin-of-life chemistry because it uses plausible prebiotic substrates, and resembles modern biosynthesis by employing the energized carbon groups of sugars to drive the synthesis of small organic molecules. Possible sugar-driven pathways for the prebiotic synthesis of polymerizable 2-pyrazinone monomers are discussed.     

Amplification of Chirality at Solid Surfaces

Symmetry-breaking phenomena in two-dimensional crystallization at surfaces are reviewed and the potential impact to chiral amplification in three-dimensional systems in connection with the origin of homochirality in the biomolecular world is discussed. Adsorption of prochiral molecules leads to two-dimensional conglomerates, i.e., on a local scale spontaneously to homochiral crystal structures. Small enantiomeric excess or chiral impurities in this environment install homochirality on a global scale, that is, on the entire surface.     

The structural analysis of three‐dimensional fibrous collagen hydrogels by raman microspectroscopy

To investigate molecular effects of 1‐Ethyl‐3‐(3‐dimethylaminopropyl) carbodiimide (EDC), EDC/N‐hydroxysuccinimide (NHS), glyceraldehyde cross‐linking as well as polymerization temperature and concentration on the three‐dimensional (3D) collagen hydrogels, we analyzed the structures in situ by Raman microspectroscopy. The increased intensity of the 814 and 936 cm^?1 Raman bands corresponding to the C—C stretch of a protein backbone and a shift in the amide III bands from 1241 cm^?1/1268 cm^?1 in controls to 1247 cm^?1/1283 cm^?1 in glyceraldehyde‐treated gels indicated changes to the alignment of the collagen molecules, fibrils/fibers and/or changes to the secondary structure on glyceraldehyde treatment. The increased intensity of 1450 cm^?1 band and the appearance of a strong peak at 1468 cm^?1 reflected a change in the motion of lysine/arginine CH₂ groups. For the EDC‐treated collagen hydrogels, the increased intensity of 823 cm^?1 peak corresponding to the C—C stretch of the protein backbone indicated that EDC also changed the packing of collagen molecules. The 23% decrease in the ratio of 1238 cm^?1 to 1271 cm^?1 amide III band intensities in the EDC‐modified samples compared with the controls indicated changes to the alignment of the collagen molecules/fibrils and/or the secondary structure. A change in the motion of lysine/arginine CH₂ groups was detected as well. The addition of NHS did not induce additional Raman shifts compared to the effect of EDC alone with the exception of a 1416 cm^?1 band corresponding to a COO^? stretch. Overall, the Raman spectra suggest that glyceraldehyde affects the collagen states within 3D hydrogels to a greater extent compared to EDC and the effects of temperature and concentration are minimal and/or not detectable. © 2012 Wiley Periodicals, Inc. Biopolymers 99: 349–356, 2013.     

Cholesterol Induces Specific Spatial and Orientational Order in Cholesterol/Phospholipid Membranes

Background

In lipid bilayers, cholesterol facilitates the formation of the liquid-ordered phase and enables the formation of laterally ordered structures such as lipid rafts. While these domains have an important role in a variety of cellular processes, the precise atomic-level mechanisms responsible for cholesterol''s specific ordering and packing capability have remained unresolved.

Methodology/Principal Findings

Our atomic-scale molecular dynamics simulations reveal that this ordering and the associated packing effects in membranes largely result from cholesterol''s molecular structure, which differentiates cholesterol from other sterols. We find that cholesterol molecules prefer to be located in the second coordination shell, avoiding direct cholesterol-cholesterol contacts, and form a three-fold symmetric arrangement with proximal cholesterol molecules. At larger distances, the lateral three-fold organization is broken by thermal fluctuations. For other sterols having less structural asymmetry, the three-fold arrangement is considerably lost.

Conclusions/Significance

We conclude that cholesterol molecules act collectively in lipid membranes. This is the main reason why the liquid-ordered phase only emerges for Chol concentrations well above 10 mol% where the collective self-organization of Chol molecules emerges spontaneously. The collective ordering process requires specific molecular-scale features that explain why different sterols have very different membrane ordering properties: the three-fold symmetry in the Chol-Chol organization arises from the cholesterol off-plane methyl groups allowing the identification of raft-promoting sterols from those that do not promote rafts.     

Does glyceraldehyde enter pancreatic islet metabolism via both the triokinase and the glyceraldehyde phosphate dehydrogenase reactions? A study of these enzymes in islets

Glyceraldehyde has been known to be an insulin secretagogue for more than 15 years. It has been (reasonably) assumed that glyceraldehyde enters the glycolytic pathway via its phosphorylation by ATP to form glyceraldehyde phosphate, a reaction catalyzed by the enzyme triokinase, and that subsequent metabolism is identical to that of glucose. glucose. However, up to now there have been no studies verifying the presence of triokinase in the pancreatic beta cell. We report here that (1) the activity of triokinase in pancreatic islets is very low, indicating that the activity is intrinsically low and/or the enzyme was rapidly inactivated during the preparation of tissue for assay; (2) the activity is much lower than glucose phosphorylating activity (hexokinase plus glucokinase) in islets, even though glyceraldehyde is a more efficient insulin secretagogue than glucose; (3) glyceraldehyde phosphate dehydrogenase from pancreatic islets can use glyceraldehyde as a substrate in place of glyceraldehyde phosphate (the Vmax of glyceraldehyde phosphate dehydrogenase from islets when glyceraldehyde is the substrate is 20-fold that of triokinase when glyceraldehyde is the substrate); and (4) the Km of glyceraldehyde phosphate dehydrogenase with respect to glyceraldehyde (4.8 mM) is similar to the concentration of glyceraldehyde that gives one-half maximal rates of insulin release from pancreatic islets, whereas the Km of triokinase with respect to glyceraldehyde is much lower (less than 50 microM). These data suggest that besides stimulating insulin release in islets via its entering metabolism by phosphorylation to glyceraldehyde phosphate in the triokinase reaction, glyceraldehyde could be phosphorylated by Pi in the glyceraldehyde phosphate dehydrogenase reaction to form glycerate 1-phosphate which is probably unmetabolizable in islets. The second reaction could drastically increase the NADH/NAD ratio in islets without providing substrates for hydrogen shuttles that reoxidize cytosolic NADH. Since an increased NAD(P)H/NAD(P) ratio is believed to be a key part of the signal for insulin release, such a mechanism would explain the potent insulinotropism of glyceraldehyde in short-term experiments. In addition, the formation of unmetabolizable acids may explain the toxic effects of long-term exposure of islets to glyceraldehyde and why glyceraldehyde causes the beta cell to become acidic, whereas glucose does not.     

Effects of aluminum on membrane fluidity of the mycorrhizal fungus Amanita muscaria

The effect of aluminum on the ordering and dynamics of lipid molecules in plasmalemma was studied by electron paramagnetic resonance via the membrane-inserted reporter spin label molecules (methyl ester of 5-doxyl-hexadecanoic acid) in situ in mycelia of the ectomycorrhizal fungus Amanita muscaria . It was found, first, that the plasmalemma is structured into coexistent regions of lipids with different ordering and dynamics, and second, that aluminum stress is accompanied by the corresponding relative decrease of the proportion of the less ordered membrane domains. This effect is opposite to that found previously for Lactarius piperatus , where the membrane responded by an increase of the portion of the less ordered membrane domains. Such qualitatively diverse effects of aluminum at the membrane level is of interest as it coincides with the opposite effect on growth, i. e. inhibition of Amanita muscaria and stimulation of Lactarius piperatus .     

Microtubules bind glyceraldehyde 3-phosphate dehydrogenase and modulate its enzyme activity and quaternary structure

Glyceraldehyde 3-phosphate dehydrogenase, a tetramer of 140,000 Da, interacts with in vitro reconstituted microtubules. It results in a partial inhibition of the activity of the microtubule-bound enzyme. After cold depolymerization of the microtubule-glyceraldehyde 3-phosphate dehydrogenase complexes, a fraction of the enzyme is recovered in an active form in the disassembly supernatant; the other fraction devoid of activity, identified by polyacrylamide gel electrophoresis, remains associated with the undepolymerizable microtubule protein pellet. The inactivation of the microtubule-bound enzyme is related to the concentration of microtubule protein. Higher the concentration of microtubule protein, lower the fraction of inactivated enzyme; consequently, glyceraldehyde 3-phosphate dehydrogenase is able to copolymerize quantitatively with microtubule protein through one assembly-disassembly cycle, provided that the concentration of microtubule protein is high. Monomeric glyceraldehyde 3-phosphate dehydrogenase (molecular weight: 35,000) devoid of enzyme activity, prepared by reversible dissociation of the tetrameric enzyme, also binds to microtubules and is quantitatively recovered in the undepolymerizable microtubule protein fraction after cold treatment. These results indicate that interacting with microtubules, glyceraldehyde 3-phosphate dehydrogenase partly dissociates into inactive monomers, this process is regulated by the concentration of assembled microtubule protein, and active and inactive glyceraldehyde 3-phosphate dehydrogenase bound to microtubules have different fate at the step of microtubule disassembly. These data suggest that an association of glyceraldehyde 3-phosphate dehydrogenase to microtubules could play a role in modulating the activity of the glycolytic enzyme in intact cells.