Formation versus hydrolysis of the peptide bond from a quantum-mechanical viewpoint: The role of mineral surfaces and implications for the origin of life (original) (raw)
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Catalytic peptide hydrolysis by mineral surface: Implications for prebiotic chemistry
Geochimica et Cosmochimica Acta, 2010
The abiotic polymerization of amino acids may have been important for the origin of life, as peptides may have been components of the first self-replicating systems. Though amino acid concentrations in the primitive oceans may have been too dilute for significant oligomerization to occur, mineral surface adsorption may have provided a concentration mechanism. As unactivated amino acid polymerization is thermodynamically unfavorable and kinetically slow in aqueous solution, we studied mainly the reverse reaction of polymer degradation to measure the impact of mineral surface catalysis on peptide bonds. Aqueous glycine (G), diglycine (GG), diketopiperazine (DKP), and triglycine (GGG) were reacted with minerals (calcite, hematite, montmorillonite, pyrite, rutile, or amorphous silica) in the presence of 0.05 M, pH 8.1, KHCO 3 buffer and 0.1 M NaCl as background electrolyte in a thermostatted oven at 25, 50 or 70°C. Below 70°C, reaction kinetics were too sluggish to detect catalytic activity over amenable laboratory timescales. Minerals were not found to have measurable effects on the degradation or elongation of G, GG or DKP at 70°C in solution. At 70°C pyrite was the most catalytic mineral with detectible effects on the degradation of GGG, although several others also displayed catalytic behavior. GGG degraded $1.5-4 times faster in the presence of pyrite than in control reactions, depending on the ratio of solution concentration to mineral surface area. The rate of pyrite catalysis of GGG hydrolysis was found to be saturable, suggesting the presence of discrete catalytic sites on the mineral surface. The mineral-catalyzed degradation of GGG appears to occur via a GGG ? DKP + G mechanism, rather than via GGG ? GG + G, as in solution-phase reactions. These results are compatible with many previous findings and suggest that minerals may have assisted in peptide synthesis in certain geological settings, specifically by speeding the approach to equilibrium in environments where amino acids were already highly concentrated, but that minerals may not significantly alter the expected solution-phase equilibria. Thus the abiotic synthesis of long peptides may have required activating agents, dry heating at higher temperatures, or some form of phase separation.
Role of Mineral Surfaces in Prebiotic Chemical Evolution. In Silico Quantum Mechanical Studies
Life, 2019
There is a consensus that the interaction of organic molecules with the surfaces of naturally-occurring minerals might have played a crucial role in chemical evolution and complexification in a prebiotic era. The hurdle of an overly diluted primordial soup occurring in the free ocean may have been overcome by the adsorption and concentration of relevant molecules on the surface of abundant minerals at the sea shore. Specific organic–mineral interactions could, at the same time, organize adsorbed molecules in well-defined orientations and activate them toward chemical reactions, bringing to an increase in chemical complexity. As experimental approaches cannot easily provide details at atomic resolution, the role of in silico computer simulations may fill that gap by providing structures and reactive energy profiles at the organic–mineral interface regions. Accordingly, numerous computational studies devoted to prebiotic chemical evolution induced by organic–mineral interactions have ...
International journal of molecular sciences, 2018
The interaction strength of progressively longer oligomers of glycine, (Gly), di-Gly, tri-Gly, and penta-Gly, with a natural pyrite surface was directly measured using the force mode of an atomic force microscope (AFM). In recent years, selective activation of abiotically formed amino acids on mineral surfaces, especially that of pyrite, has been proposed as an important step in many origins of life scenarios. To investigate such notions, we used AFM-based force measurements to probe possible non-covalent interactions between pyrite and amino acids, starting from the simplest amino acid, Gly. Although Gly itself interacted with the pyrite surface only weakly, progressively larger unbinding forces and binding frequencies were obtained using oligomers from di-Gly to penta-Gly. In addition to an expected increase of the configurational entropy and size-dependent van der Waals force, the increasing number of polar peptide bonds, among others, may be responsible for this observation. The...
2020
The chemical origins of life on Earth and perhaps elsewhere in the universe is not utterly unknowable, though the subject is incredibly complex. To endeavor to understand what events brought about life on early-Earth nearly 4 billion years ago, life itself must be broken down into its major processes, which themselves are constructed from increasingly simple and ordinary sub-units, and eventually, examined to describe the building blocks of life and how they might assemble. The presence of amino acids on extra-terrestrial bodies and in prebiotic simulation experiments suggests the plausibility of their existence on early Earth. In contrast to extant biological protein production, abiotic polypeptide formation presents several challenges, such as the thermodynamically disfavored condensation of non-activated amino acids in aqueous solution. Recent work has introduced α-hydroxy acids, a class of molecules found alongside amino acids in prebiotic contexts, into peptide forming systems....
Orig. Life Evol. Biosphere, 2013
Many studies have reported condensation reactions of prebiotic molecules, such as the formation of peptide bonds between amino acids, to occur to some degree on mineral surfaces.We have studied several such reactions on the same divided silica. When drying steps are applied, the equilibria of peptide formation from glycine, and polyphosphate formation from monophosphate, are displaced to the right because these reactions are dehydrating condensations, accompanied by the emission of water. In contrast, the equilibrium of AMP dismutation is not significantly favored by drying. The silica surface plays little role (if any) in the thermochemistry of the condensation reactions, but is does play a significant kinetic role by acting as a catalyst, lowering the condensation temperatures with respect to bulk solids. Of course, the surface also catalyzes the inverse hydrolysis reactions
Tracing the Primordial Chemical Life of Glycine: A Review from Quantum Chemical Simulations
International Journal of Molecular Sciences
Glycine (Gly), NH2CH2COOH, is the simplest amino acid. Although it has not been directly detected in the interstellar gas-phase medium, it has been identified in comets and meteorites, and its synthesis in these environments has been simulated in terrestrial laboratory experiments. Likewise, condensation of Gly to form peptides in scenarios resembling those present in a primordial Earth has been demonstrated experimentally. Thus, Gly is a paradigmatic system for biomolecular building blocks to investigate how they can be synthesized in astrophysical environments, transported and delivered by fragments of asteroids (meteorites, once they land on Earth) and comets (interplanetary dust particles that land on Earth) to the primitive Earth, and there react to form biopolymers as a step towards the emergence of life. Quantum chemical investigations addressing these Gly-related events have been performed, providing fundamental atomic-scale information and quantitative energetic data. Howev...
Surface charges and interfaces: implications for mineral roles in prebiotic chemistry
Anais da Academia Brasileira de Ciências, 2000
There exists an extensive literature on the possible roles of minerals in the prebiotic stages of the chemical evolution of life , see Lahav (1994 for a review). Among the original proposals, minerals have been considered in: (a) processes that would discriminate molecular chirality; (b) condensation reactions of biomolecular precursors; (c) prebiotic catalysis; (d) biochemical templates; and (e) autocatalytic metabolism. In this communication it is emphazised the complex properties of both surface reactions and interfaces between minerals and aqueous solutions simulating Archean scenarios. The properties of pyrite surface net charge and of its interface with a solution simulating primitive seawater are discussed and their implications to the autocatalytic model are presented in order to demonstrate their relevance. The proposed roles of iron-sulfide minerals (mainly pyrite) as physical support for primitive bidimensional metabolism and chiral discriminator are revised. It is shown that: (a) the net surface charge can be modulated by the pyrite-aqueous solution interface; (b) mononucleotides attachment to pyrite require a cationic bridge; and (c) direct absorption of acetate -a molecule proposed as carbon source in primitive aqueous environments -also modulates the interface properties and would have masked pyrite's bulk structure. These results indicate that physicochemical changes of mineral surfaces -caused by environments simulating Archean aqueous scenarios -should be taken into account in the proposals of mineral prebiotic roles.
Origins of Life and Evolution of Biospheres, 1999
Two reactions with suggested prebiotic relevance for peptide evolution, the saltinduced peptide formation reaction and the peptide chain elongation/stabilization on clay minerals have been combined in experimental series starting from dipeptides and dipeptide/amino acid mixtures. The results show that both reactions can take place simultaneously in the same reaction environment and that the presence of mineral catalysts favours the formation of higher oligopeptides. These findings lend further support to the relevance of these reactions for peptide evolution on the primitive earth. The detailed effects of the specific clay mineral depend both on the nature of the mineral and the reactants in solution.
ACS Earth and Space Chemistry, 2020
In current living matter, biopolymers follow specific sequences that give them special properties, such as the sequence of amino acids in proteins and peptides. A major challenge for the elucidation of the origins of life lies in understanding how e.g. non-random polypeptides have been selected among all the possible ones. While many investigations established plausible prebiotic polymerization pathways, surprisingly, only a few attempted to study the selectivity of these processes. We studied a mineral surface polymerization scenario based on moderate thermal activation of leucine + glutamic acid mixtures on silica. Oligopeptides up to octamers were quantitatively formed in a "clean" prebiotic reaction and analyzed by high-resolution mass spectrometry, using FT-ICR spectrometry for unambiguous molecular assignments. Nontrivial oligomerization selectivities are evidenced in both stoichiometric compositions and AA sequence, while comparable selectivities are not observed in other polymerization scenarios. They must therefore be due to specific catalytic reaction pathways occurring on the SiO2 surface. A statistical measure of information contained in oligopeptide distributions is proposed. It could be used to follow the evolution of potentially meaningful complexity in biopolymers from the mineral to the biochemical world.
Physical Chemistry Chemical Physics, 2011
It has always been a question of considerable scientific interest why amino acids (and other biomolecule building blocks) formed and accumulated in the prebiotic ocean. In this study, we suggest an answer to this question for the simplest amino acid, glycine. We have shown for the first time that classical equilibrium thermodynamics can explain the most likely selection of glycine (and the derivative of its dipeptide) in aqueous media, although glycine is not the lowest free energy structure among all (404) possible constitutional isomers. Species preceding glycine in the free energy order are either supramolecular complexes of small molecules or such molecules likely to dissociate and thus get back to the gas phase. Then, 2-hydroxyacetamide condensates yielding a thermodynamically favored derivative of glycine dipeptide providing an alternative way for peptide formation. It is remarkable that a simple equilibrium thermodynamic model can explain the accumulation of glycine and provide a reason for the importance of water in the formation process.