Peptides and the origin of life

Early assembly of cellular life

Popular hypotheses that attempt to explain the origin of prebiotic molecules and cellular life capable of growth and division are not always agreed upon. In this manuscript, information on early bacterial life on Earth is examined using information from several disciplines. For example, knowledge can be integrated from physics, thermodynamics, planetary sciences, geology, biogeochemistry, lipid chemistry, primordial cell structures, cell and molecular biology, microbiology, metabolism and genetics. The origin of life also required a combination of elements, compounds and environmental physical-chemical conditions that allowed cells to assemble in less than a billion years. This may have been widespread in the subsurface of the early Earth located at microscopic physical domains.

Magnesium chloride: an efficient 13C NMR relaxation agent for amino acids and some carboxylic acids

A series of amino acids and carboxylic acids were determined by 13C NMR spectroscopy. The results showed that addition of 3 M MgCl(2), led to shortening of relaxation time and 13C NMR integral area of samples was well proportional to the number of carbon atoms with reliability more than 95%. So MgCl(2) is proposed as an efficient relaxation agent for analysis of amino acids and some carboxylic acids.

Preferential amino acid sequences in alumina-catalyzed peptide bond formation

The catalytic effect of activated alumina on amino acid condensation was investigated. The readiness of amino acids to form peptide sequences was estimated on the basis of the yield of dipeptides and was found to decrease in the order glycine (Gly), alanine (Ala), leucine (Leu), valine (Val), proline (Pro). For example, approximately 15% Gly was converted to the dipeptide (Gly(2)), 5% to cyclic anhydride (cyc(Gly(2))) and small amounts of tri- (Gly(3)) and tetrapeptide (Gly(4)) were formed after 28 days. On the other hand, only trace amounts of Pro(2) were formed from proline under the same conditions. Preferential formation of certain sequences was observed in the mixed reaction systems containing two amino acids. For example, almost ten times more Gly-Val than Val-Gly was formed in the Gly+Val reaction system. The preferred sequences can be explained on the basis of an inductive effect that side groups have on the nucleophilicity and electrophilicity, respectively, of the amino and carboxyl groups. A comparison with published data of amino acid reactions in other reaction systems revealed that the main trends of preferential sequence formation were the same as those described for the salt-induced peptide formation (SIPF) reaction. The results of this work and other previously published papers show that alumina and related mineral surfaces might have played a crucial role in the prebiotic formation of the first peptides on the primitive earth.

Reaction behaviors of glycine under super- and subcritical water conditions

The influence of temperature and pressure on the dimerization and decomposition of glycine under simulated hydrothermal system conditions was studied by injecting a glycine solution into water in the sub- and supercritical state. The experiments at five different temperatures of supplied water--250, 300, 350, 374, and 400 degrees C--were performed at 22.2 and 40.0 MPa. At 350 degrees C, experiments under 15.0-40.0 MPa were conducted. Diglycine, triglycine (trace), diketopiperazine, and an unidentified product with a high molecular mass (433 Da) were the main products of oligomerization. The results show that temperature and pressure influence the extent of dimerization and decomposition of glycine. The maximum of dimers formation was observed at 350 and 375 degrees C at 22.2 and 40.0 MPa, respectively, and coincided with a high rate of glycine decomposition. Glycine, alanine, aspartic acid, as well as other amino acids, were obtained by injecting a mixture of formaldehyde and ammonia. The results support the oligomerization and synthesis of amino acids in a submarine hydrothermal system.

Primordial coding of amino acids by adsorbed purine bases

Scanning tunneling microscopy and chromatography experiments exploring the potential templating properties of nucleic acid bases adsorbed to the surface of crystalline graphite, revealed that the interactions of amino acids with the bare crystal surface are significantly modulated by the prior adsorption of adenine and hypoxanthine. These bases are the coding elements of a putative purine-only genetic alphabet and the observed effects are different for each of the bases. Such mapping between bases and amino acids provides a coding mechanism. These observations demonstrate that a simple pre-RNA amino acid discrimination mechanism could have existed on the prebiotic Earth providing critical functionality for the origin of life.

Life before RNA

The hypothesis that life originated and evolved from linear informational molecules capable of facilitating their own catalytic replication is deeply entrenched. However, widespread acceptance of this paradigm seems oblivious to a lack of direct experimental support. Here, we outline the fundamental objections to the de novo appearance of linear, self-replicating polymers and examine an alternative hypothesis of template-directed coding of peptide catalysts by adsorbed purine bases. The bases (which encode biological information in modern nucleic acids) spontaneously self-organize into two-dimensional molecular solids adsorbed to the uncharged surfaces of crystalline minerals; their molecular arrangement is specified by hydrogen bonding rules between adjacent molecules and can possess the aperiodic complexity to encode putative protobiological information. The persistence of such information through self-reproduction, together with the capacity of adsorbed bases to exhibit enantiomorphism and effect amino acid discrimination, would seem to provide the necessary machinery for a primitive genetic coding mechanism.

Origins of life: a route to nanotechnology

The origins of life and nanotechnology are two seemingly disparate areas of scientific investigation. However, the fundamental questions of life's beginnings and the applied construction of a Drexlerian nanotechnology both share a similar problem; how did and how can self-reproducing molecular machines originate? Here we draw attention to the coincidence between nanotechnology and origins research with particular attention paid to the spontaneous adsorption and scanning tunneling microscopy investigation of purine and pyrimidine bases self-organized into monolayers, adsorbed to the surfaces of crystalline solids. These molecules which encode biological information in nucleic acids, can form supramolecular architectures exhibiting enantiomorphism with the complexity to store and encode putative protobiological information. We conclude that the application of nanotechnology to the investigation of life's origins, and vice versa, could provide a viable route to an evolution-driven synthetic life.

Syntheses and properties of zinc and calcium complexes of valinate and isovalinate: metal alpha-amino acidates as possible constituents of the early Earth's chemical inventory

We have studied the ligand behavior of racemic isovalinate (iva) and valinate (val) towards zinc(II) and calcium(II). The following solid metal amino acidates were obtained from aqueous solutions: Zn3Cl2(iva)4 (1), Zn3Cl2(val)4 (2). Zn(val)2 (3), Zn(iva)2 x 2H2O (4), Zn(iva)2 x 3.25H2O (5), Zn(iva)2 (6), Ca(iva)2x xH2O (7), and Ca(val)2 x H2O (8). Except for complex 3, these were hitherto unknown compounds. The conditions under which they formed, together with current ideas of the conditions on early Earth, support the assumption that alpha-amino acidate complexes of zinc and calcium might have belonged to early Earth's prebiotic chemical inventory. The zinc isovalinates 1, 4, and 5 were characterized by X-ray crystal structure analyses. Complex 1 forms a layer structure containing four- and five-coordinate metal atoms, whereas the zinc atoms in 4 and 5 are five-coordinate. Compound 5 possesses an unprecedented nonpolymeric structure built from cyclic [Zn6(iva)12] complexes, which are separated by water molecules. The thermolyses of solids 1. 3, and 8 at 320 degrees C in an N2 atmosphere yielded numerous organic products, including the cyclic dipeptide of valine from 3 and 8. Condensation, C-C bond breaking and bond formation, aromatization, decarboxylation, and deamination reactions occurred during the thermolyses. Such reactions of metal-bound a-amino acidates that are abiotically formed could already have contributed to an organic-geochemical diversity before life appeared on Earth.

Structure of cationized glycine, gly.m (m = be, mg, ca, sr, ba), in the gas phase: intrinsic effect of cation size on zwitterion stability

Interactions between divalent metal ions and biomolecules are common both in solution and in the gas phase. Here, the intrinsic effect of divalent alkaline earth metal ions (Be, Mg, Ca, Sr, Ba) on the structure of glycine in the absence of solvent is examined. Results from both density functional and Moller-Plesset theories indicate that for all metal ions except beryllium, the salt-bridge form of the ion, in which glycine is a zwitterion, is between 5 and 12 kcal/mol more stable than the charge-solvated structure in which glycine is in its neutral form. For beryllium, the charge-solvated structure is 5-8 kcal/mol more stable than the salt-bridge structure. Thus, there is a dramatic change in the structure of glycine with increased metal cation size. Using a Hartree-Fock-based partitioning method, the interaction between the metal ion and glycine is separated into electrostatic, charge transfer and deformation components. The charge transfer interactions are more important for stabilizing the charge-solvated structure of glycine with beryllium relative to magnesium. In contrast, the difference in stability between the charge-solvated and salt-bridge structure for magnesium is mostly due to electrostatic interactions that favor formation of the salt-bridge structure. These results indicate that divalent metal ions dramatically influence the structure of this simplest amino acid in the gas phase.

Are prions a relic of an early stage of peptide evolution?

The rather unique properties of prions and their presence in very different kinds of living species suggest that this type of molecule was created at a very early stage of evolution and may even represent a relic from a time where peptide evolution was ongoing and RNA/DNA did not yet exist. A comparison of the most frequently occurring amino acid sequences in known prions with the sequences preferentially formed in the salt-induced peptide formation reaction, the most simple mechanism enabling the formation of peptides under primitive earth conditions, shows a remarkable coincidence that strongly supports this hypothesis.