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Ortega-Arzola E, Higgins PM, Cockell CS. The minimum energy required to build a cell. Sci Rep 2024; 14:5267. [PMID: 38438463 DOI: 10.1038/s41598-024-54303-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/11/2024] [Indexed: 03/06/2024] Open
Abstract
Understanding the energy requirements for cell synthesis accurately and comprehensively has been a longstanding challenge. We introduce a computational model that estimates the minimum energy necessary to build any cell from its constituent parts. This method combines omics and internal cell compositions from various sources to calculate the Gibbs Free Energy of biosynthesis independently of specific metabolic pathways. Our public tool, Synercell, can be used with other models for minumum species-specific energy estimations in any well-sequenced species. The energy for synthesising the genome, transcriptome, proteome, and lipid bilayer of four cell types: Escherichia coli, Saccharomyces cerevisiae, an average mammalian cell and JCVI-syn3A were estimated. Their modelled minimum synthesis energies at 298 K were 9.54 × 10 - 11 J/cell, 4.99 × 10 - 9 J/cell, 3.71 × 10 - 7 J/cell and 3.69 × 10 - 12 respectively. Gram-for-gram synthesis of lipid bilayers requires the most energy, followed by the proteome, genome, and transcriptome. The average per gram cost of biomass synthesis is in the 300s of J/g for all four cells. Implications for the generalisability of cell construction and applications to biogeosciences, cellular biology, biotechnology, and astrobiology are discussed.
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Affiliation(s)
- Edwin Ortega-Arzola
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK.
| | - Peter M Higgins
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
- Department of Earth Sciences, University of Toronto, Toronto, ON, Canada
| | - Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
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Sheehan JD, Abraham A, Savage PE. Reaction pathways and kinetics for tetra-alanine in hot, compressed liquid water. REACT CHEM ENG 2019. [DOI: 10.1039/c9re00023b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
pH alters the prevalence of the dissociation states of peptides, through acid–base equilibrium, and influences reaction selectivity under hydrothermal conditions.
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Affiliation(s)
- James D. Sheehan
- Department of Chemical Engineering
- Pennsylvania State University
- USA
| | - Ashwin Abraham
- Department of Chemical Engineering
- Pennsylvania State University
- USA
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Kitadai N. Predicting Thermodynamic Behaviors of Non-Protein Amino Acids as a Function of Temperature and pH. ORIGINS LIFE EVOL B 2016; 46:3-18. [PMID: 26286083 DOI: 10.1007/s11084-015-9457-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 07/27/2015] [Indexed: 10/23/2022]
Abstract
Why does life use α-amino acids exclusively as building blocks of proteins? To address that fundamental question from an energetic perspective, this study estimated the standard molal thermodynamic data for three non-α-amino acids (β-alanine, γ-aminobutyric acid, and ε-aminocaproic acid) and α-amino-n-butyric acid in their zwitterionic, negative, and positive ionization states based on the corresponding experimental measurements reported in the literature. Temperature dependences of their heat capacities were described based on the revised Helgeson-Kirkham-Flowers (HKF) equations of state. The obtained dataset was then used to calculate the standard molal Gibbs energies (∆G (o)) of the non-α-amino acids as a function of temperature and pH. Comparison of their ∆G (o) values with those of α-amino acids having the same molecular formula showed that the non-α-amino acids have similar ∆G (o) values to the corresponding α-amino acids in physiologically relevant conditions (neutral pH, <100 °C). In acidic and alkaline pH, the non-α-amino acids are thermodynamically more stable than the corresponding α-ones over a broad temperature range. These results suggest that the energetic cost of synthesis is not an important selection pressure to incorporate α-amino acids into biological systems.
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Affiliation(s)
- Norio Kitadai
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
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Kitadai N. Energetics of Amino Acid Synthesis in Alkaline Hydrothermal Environments. ORIGINS LIFE EVOL B 2015; 45:377-409. [PMID: 25796392 DOI: 10.1007/s11084-015-9428-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 01/27/2015] [Indexed: 01/01/2023]
Abstract
Alkaline hydrothermal systems have received considerable attention as candidates for the origin and evolution of life on the primitive Earth. Nevertheless, sufficient information has not yet been obtained for the thermodynamic properties of amino acids, which are necessary components for life, at high temperatures and alkaline pH. These properties were estimated using experimental high-temperature volume and heat capacity data reported in the literature for several amino acids, together with correlation algorithms and the revised Helgeson-Kirkham-Flowers (HKF) equations of state. This approach enabled determination of a complete set of the standard molal thermodynamic data and the revised HKF parameters for the 20 protein amino acids in their zwitterionic and ionization states. The obtained dataset was then used to evaluate the energetics of amino acid syntheses from simple inorganic precursors (CO2, H2, NH3 and H2S) in a simulated alkaline hydrothermal system on the Hadean Earth. Results show that mixing between CO2-rich seawater and the H2-rich hydrothermal fluid can produce energetically favorable conditions for amino acid syntheses, particularly in the lower-temperature region of such systems. Together with data related to the pH and temperature dependences of the energetics of amino acid polymerizations presented in earlier reports, these results suggest the following. Hadean alkaline hydrothermal settings, where steep pH and temperature gradients may have existed between cool, slightly acidic Hadean ocean water and hot, alkaline hydrothermal fluids at the vent-ocean interface, may be energetically the most suitable environment for the synthesis and polymerization of amino acids.
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Affiliation(s)
- Norio Kitadai
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan,
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Kitadai N. Thermodynamic prediction of glycine polymerization as a function of temperature and pH consistent with experimentally obtained results. J Mol Evol 2014; 78:171-87. [PMID: 24652580 DOI: 10.1007/s00239-014-9616-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/08/2014] [Indexed: 11/26/2022]
Abstract
Prediction of the thermodynamic behaviors of biomolecules at high temperature and pressure is fundamental to understanding the role of hydrothermal systems in the origin and evolution of life on the primitive Earth. However, available thermodynamic dataset for amino acids, essential components for life, cannot represent experimentally observed polymerization behaviors of amino acids accurately under hydrothermal conditions. This report presents the thermodynamic data and the revised HKF parameters for the simplest amino acid "Gly" and its polymers (GlyGly, GlyGlyGly and DKP) based on experimental thermodynamic data from the literature. Values for the ionization states of Gly (Gly(+) and Gly(-)) and Gly peptides (GlyGly(+), GlyGly(-), GlyGlyGly(+), and GlyGlyGly(-)) were also retrieved from reported experimental data by combining group additivity algorithms. The obtained dataset enables prediction of the polymerization behavior of Gly as a function of temperature and pH, consistent with experimentally obtained results in the literature. The revised thermodynamic data for zwitterionic Gly, GlyGly, and DKP were also used to estimate the energetics of amino acid polymerization into proteins. Results show that the Gibbs energy necessary to synthesize a mole of peptide bond is more than 10 kJ mol(-1) less than previously estimated over widely various temperatures (e.g., 28.3 kJ mol(-1) → 17.1 kJ mol(-1) at 25 °C and 1 bar). Protein synthesis under abiotic conditions might therefore be more feasible than earlier studies have shown.
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Affiliation(s)
- Norio Kitadai
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan,
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Amend JP, LaRowe DE, McCollom TM, Shock EL. The energetics of organic synthesis inside and outside the cell. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120255. [PMID: 23754809 PMCID: PMC3685458 DOI: 10.1098/rstb.2012.0255] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Thermodynamic modelling of organic synthesis has largely been focused on deep-sea hydrothermal systems. When seawater mixes with hydrothermal fluids, redox gradients are established that serve as potential energy sources for the formation of organic compounds and biomolecules from inorganic starting materials. This energetic drive, which varies substantially depending on the type of host rock, is present and available both for abiotic (outside the cell) and biotic (inside the cell) processes. Here, we review and interpret a library of theoretical studies that target organic synthesis energetics. The biogeochemical scenarios evaluated include those in present-day hydrothermal systems and in putative early Earth environments. It is consistently and repeatedly shown in these studies that the formation of relatively simple organic compounds and biomolecules can be energy-yielding (exergonic) at conditions that occur in hydrothermal systems. Expanding on our ability to calculate biomass synthesis energetics, we also present here a new approach for estimating the energetics of polymerization reactions, specifically those associated with polypeptide formation from the requisite amino acids.
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Affiliation(s)
- Jan P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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Hutt M, Kulschewski T, Pleiss J. Molecular modelling of the mass density of single proteins. J Biomol Struct Dyn 2012; 30:318-27. [DOI: 10.1080/07391102.2012.680031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Dick JM, Shock EL. Calculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring. PLoS One 2011; 6:e22782. [PMID: 21853048 PMCID: PMC3154912 DOI: 10.1371/journal.pone.0022782] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 06/29/2011] [Indexed: 11/23/2022] Open
Abstract
Uncovering the chemical and physical links between natural environments and microbial communities is becoming increasingly amenable owing to geochemical observations and metagenomic sequencing. At the hot spring known as Bison Pool in Yellowstone National Park, the cooling of the water in the outflow channel is associated with an increase in oxidation potential estimated from multiple field-based measurements. Representative groups of proteins whose sequences were derived from metagenomic data also exhibit an increase in average oxidation state of carbon in the protein molecules with distance from the hot-spring source. The energetic requirements of reactions to form selected proteins used in the model were computed using amino-acid group additivity for the standard molal thermodynamic properties of the proteins, and the relative chemical stabilities of the proteins were investigated by varying temperature, pH and oxidation state, expressed as activity of dissolved hydrogen. The relative stabilities of the proteins were found to track the locations of the sampling sites when the calculations included a function for hydrogen activity that increases with temperature and is higher, or more reducing, than values consistent with measurements of dissolved oxygen, sulfide and oxidation-reduction potential in the field. These findings imply that spatial patterns in the amino acid compositions of proteins can be linked, through energetics of overall chemical reactions representing the formation of the proteins, to the environmental conditions at this hot spring, even if microbial cells maintain considerably different internal conditions. Further applications of the thermodynamic calculations are possible for other natural microbial ecosystems.
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Affiliation(s)
- Jeffrey M Dick
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, United States of America.
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Sirimulla S, Lerma M, Herndon WC. Prediction of Partial Molar Volumes of Amino Acids and Small Peptides: Counting Atoms versus Topological Indices. J Chem Inf Model 2010; 50:194-204. [PMID: 20058884 DOI: 10.1021/ci900318c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Suman Sirimulla
- Department of Chemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968
| | - Maricarmen Lerma
- Department of Chemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968
| | - William C. Herndon
- Department of Chemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968
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Lemke KH, Rosenbauer RJ, Bird DK. Peptide synthesis in early Earth hydrothermal systems. ASTROBIOLOGY 2009; 9:141-146. [PMID: 19371157 DOI: 10.1089/ast.2008.0166] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report here results from experiments and thermodynamic calculations that demonstrate a rapid, temperature-enhanced synthesis of oligopeptides from the condensation of aqueous glycine. Experiments were conducted in custom-made hydrothermal reactors, and organic compounds were characterized with ultraviolet-visible procedures. A comparison of peptide yields at 260 degrees C with those obtained at more moderate temperatures (160 degrees C) gives evidence of a significant (13 kJ . mol(-1)) exergonic shift. In contrast to previous hydrothermal studies, we demonstrate that peptide synthesis is favored in hydrothermal fluids and that rates of peptide hydrolysis are controlled by the stability of the parent amino acid, with a critical dependence on reactor surface composition. From our study, we predict that rapid recycling of product peptides from cool into near-supercritical fluids in mid-ocean ridge hydrothermal systems will enhance peptide chain elongation. It is anticipated that the abundant hydrothermal systems on early Earth could have provided a substantial source of biomolecules required for the origin of life.
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Affiliation(s)
- Kono H Lemke
- Department of Geological and Environmental Sciences, Stanford University, Stanford, California, USA.
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Dick JM. Calculation of the relative metastabilities of proteins using the CHNOSZ software package. GEOCHEMICAL TRANSACTIONS 2008; 9:10. [PMID: 18834534 PMCID: PMC2654789 DOI: 10.1186/1467-4866-9-10] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2008] [Accepted: 10/03/2008] [Indexed: 05/09/2023]
Abstract
BACKGROUND Proteins of various compositions are required by organisms inhabiting different environments. The energetic demands for protein formation are a function of the compositions of proteins as well as geochemical variables including temperature, pressure, oxygen fugacity and pH. The purpose of this study was to explore the dependence of metastable equilibrium states of protein systems on changes in the geochemical variables. RESULTS A software package called CHNOSZ implementing the revised Helgeson-Kirkham-Flowers (HKF) equations of state and group additivity for ionized unfolded aqueous proteins was developed. The program can be used to calculate standard molal Gibbs energies and other thermodynamic properties of reactions and to make chemical speciation and predominance diagrams that represent the metastable equilibrium distributions of proteins. The approach takes account of the chemical affinities of reactions in open systems characterized by the chemical potentials of basis species. The thermodynamic database included with the package permits application of the software to mineral and other inorganic systems as well as systems of proteins or other biomolecules. CONCLUSION Metastable equilibrium activity diagrams were generated for model cell-surface proteins from archaea and bacteria adapted to growth in environments that differ in temperature and chemical conditions. The predicted metastable equilibrium distributions of the proteins can be compared with the optimal growth temperatures of the organisms and with geochemical variables. The results suggest that a thermodynamic assessment of protein metastability may be useful for integrating bio- and geochemical observations.
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Affiliation(s)
- Jeffrey M Dick
- Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA.
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Hedwig GR, Hinz HJ. Group additivity schemes for the calculation of the partial molar heat capacities and volumes of unfolded proteins in aqueous solution. Biophys Chem 2003; 100:239-60. [PMID: 12646369 DOI: 10.1016/s0301-4622(02)00284-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A critical review is given of the present state of group additivity schemes for the calculation of partial molar volumes and heat capacities of unfolded proteins. The comparison between the experimental values and the predictions based on the different models shows clearly that only the peptide-based additivity scheme represents properly both the absolute values and the temperature dependence of these thermodynamic quantities.
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Affiliation(s)
- Gavin R Hedwig
- Institute of Fundamental Sciences-Chemistry, Massey University, Private Bag 11222, Palmerston North, New Zealand.
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Hakin AW, Hedwig GR. Group additivity calculations of the thermodynamic properties of unfolded proteins in aqueous solution: a critical comparison of peptide-based and HKF models. Biophys Chem 2001; 89:253-64. [PMID: 11254218 DOI: 10.1016/s0301-4622(00)00229-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A recent paper in this journal [Amend and Helgeson, Biophys. Chem. 84 (2000) 105] presented a new group additivity model to calculate various thermodynamic properties of unfolded proteins in aqueous solution. The parameters given for the revised Helgeson-Kirkham-Flowers (HKF) equations of state for all the constituent groups of unfolded proteins can be used, in principle, to calculate the partial molar heat capacity, C(o)p.2, and volume, V2(0), at infinite dilution of any polypeptide. Calculations of the values of C(o)p.2 and V2(0) for several polypeptides have been carried out to test the predictive utility of the HKF group additivity model. The results obtained are in very poor agreement with experimental data, and also with results calculated using a peptide-based group additivity model. A critical assessment of these two additivity models is presented.
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Affiliation(s)
- A W Hakin
- Department of Chemistry and Biochemistry, University of Lethbridge, Alberta, Canada.
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