The Origin of Life: Revealing the Role of Mineral Surfaces in Prebiotic Synthesis

Overview

The origin of life through the transition from physics to organic geochemistry and then to biochemistry is one of the remaining fundamental questions in science (see Figure 1) [1]. Despite progress made in recent decades through the combined efforts of both experimental research and computational modelling, the solution to this enduring question remains elusive. It is clear that life on Earth is dependent on the transfer of information through polymeric systems, i.e., nucleic acids and peptides, interconverting structure into information, and information into structure [2]. A variety of pathways have been proposed for the origin of life through molecular evolution, where simple organic molecules, such as amino acids, carbohydrates or nucleosides, are initially formed from simple abiotic reactants. The synthesis of these simple starting components is followed by the subsequent polymerisation of organic monomers into biomolecules of increasing complexity and function [3]. However, this raises an important question, how do such molecules form in the absence of biological catalysts and enzymes?

One potential answer is that mineral surfaces can effectively replace these catalysts by offering sites where simple monomers can accumulate and begin to form more complex molecules. This is the central focus of this IAPETUS2 DTP studentship, which seeks to combine the strengths of computational and experimental geochemistry to provide new insights into the role of mineral-organic interactions in the origin of life. In particular, we will focus on the interaction of amino acids with mineral surfaces to elucidate the mechanisms for peptide bond formation, which is known to be kinetically and thermodynamically unfavourable in both the gas and liquid phases yet represents a critical step in the origin of life [4]. These findings will then be extended to consider the more complex secondary structures of proteins. The key objectives of this proposal are to identify the possible mechanisms through which amino acids absorb on mineral surfaces and then how these surfaces enable the formation of peptides and more complex biological structures.

Methodology

This multidisciplinary project includes both computational and experiment methods (the successful candidate will be thoroughly trained in both). Within the School of Natural and Environmental Sciences at Newcastle University, under the supervision of Dr. Dawson, the candidate will use both classical and quantum mechanical modelling methods, primarily molecular dynamics and density functional theory, to setup and analyse the absorption, polymerisation and formation of small organic molecules (primarily amino acids) on mineral surfaces (e.g., hydroxides, silicates, carbonates and borates), as exemplified in Figure 2. The student will have access to a variety of local and national high-performance computing facilities.

At the University of St. Andrews Isotope Geochemistry Laboratory, under the supervision of Dr. Stueeken, experiments will be conducted to assess how much total organic material adsorbs to mineral surfaces. A variety of mineral assemblages, organic monomers and fluid compositions will be explored, mimicking conditions found in natural environments on a prebiotic world. The student will utilise a wide range of experimental characterisation methods, including elemental analyser-isotopic ratio mass spectrometry, scanning electron microscopy, electron probe microanalysis and gas chromatography-mass spectrometry.

Through Dr. Dawson’s extensive international research network, there will opportunities for the successful candidate to undertake placements and visits at leading computational materials research groups in the US and Asia.

Project Timeline

Year 1

– Literature review and project proposal (mandatory requirement of Newcastle University) (3 months)
– In-depth training on density functional theory simulations and preliminary simulations (2 months)
– Preparation of optimised low-energy mineral surface models with DFT (3 months)
– DFT simulation of absorption and behaviour of amino acids on mineral surfaces (4 months)

Year 2

– DFT simulation of absorption and stability of amino acids on mineral surfaces (continued) (2 months)
– DFT simulations of peptide bond formation mechanisms between amino acids (4 months)
– Development of experimental setup at St. Andrews; experiments on organic partitioning between mineral types using elemental analyser-isotopic ratio mass spectrometry; detailed characterisation of mineral surfaces by scanning electron microscopy and electron probe microanalysis (6 months)

Year 3

– Completion of experimental work, exploring wider ranges of fluid and mineral compositions; scope for development of compound-specific analyses of organics by gas chromatography-mass spectrometry (5 months)
– In-depth training on classical molecular dynamics and preliminary simulations (2 months)
– Molecular dynamics simulations of the absorption and formation of secondary protein structures (5 months)

Year 3.5

– Completion of any final remaining simulations and experiments, thesis writing and preparation of manuscripts (a minimum of two first authored) (6 months)

Training
& Skills

By the end of the studentship, the candidate will have a large array of skills in computational materials modelling, geochemistry and the experimental characterisation of bulk minerals and their surfaces. Such a multidisciplinary background will place them in a strong position for both academic and industrial careers, not online in the remit of geochemistry and the natural environment but also in engineering and the physical sciences. This is further strengthened by the fact that the accurate simulation of material interfaces is widely regarded as a vital step towards the understanding and design of various natural phenomena and technologies, yet it is a skill that is lacking not only in the UK but indeed globally.

Over the course of the studentship, the candidate will have opportunities to attend in-person and online training and professional development courses organised by the Royal Society and the Royal Society of Chemistry (RSC) on leadership, management, mentorship, communication and media skills. These activities will be supplemented by numerous in-kind training events available at Newcastle University and the University of St Andrews, including the three-day residential ACTION for Impact course for developing personal and research impact and courses on scientific writing and public speaking.

References & further reading

[1] J.-M. Lehn, Angew. Chem. Int. Ed., 2013, 52, 2836–2850.[2] V. Erastova, M. T. Degiacomi, D. G. Fraser, H. C. Greenwell, Nat. Commun., 2017, 8, 2033.[3] J. F. Lambert, Orig. Life Evol. Biospheres, 2008, 38, 211–242.[4] B. Martinez-Bachs, A. Rimola, Life, 2019, 9, 75.

Further Information

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