Calculation of the standard molal thermodynamic properties of crystalline peptides

LaRowe, Douglas E.; Dick, Jeffrey M.

doi:10.1016/j.gca.2011.11.041

Cited by 33 publications

(35 citation statements)

References 96 publications

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“…Values of DG 0 r are calculated as a function of temperature and pressure using the revised-HKF equations of state (Helgeson et al, 1981;Tanger and Helgeson, 1988;Shock et al, 1992), the SUPCRT92 software package and thermodynamic data taken from Shock and Helgeson (1988); Shock et al (1989); Shock and Helgeson (1990);Shock (1995); Sverjensky et al (1997); Amend and Helgeson (1997a, b); Amend and Plyasunov (2001); Schulte et al (2001); Dick et al (2006); LaRowe and Helgeson (2006) and LaRowe and Dick (2012). Values of Q r are calculated using…”

Section: Computational Techniquesmentioning

confidence: 99%

The energetics of anabolism in natural settings

LaRowe

Amend

2016

The ISME Journal

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The environmental conditions that describe an ecosystem define the amount of energy available to the resident organisms and the amount of energy required to build biomass. Here, we quantify the amount of energy required to make biomass as a function of temperature, pressure, redox state, the sources of C, N and S, cell mass and the time that an organism requires to double or replace its biomass. Specifically, these energetics are calculated from 0 to 125°C, 0.1 to 500 MPa and − 0.38 to +0.86 V using CO 2 , acetate or CH 4 for C, NO 3 À or NH 4 þ for N and SO 4 2À or HS − for S. The amounts of energy associated with synthesizing the biomolecules that make up a cell, which varies over 39 kJ (g cell), are then used to compute energy-based yield coefficients for a vast range of environmental conditions. Taken together, environmental variables and the range of cell sizes leads to a~4 orders of magnitude difference between the number of microbial cells that can be made from a Joule of Gibbs energy under the most (5.06 × 10 11 cells J − 1) and least (5.21 × 10 7 cells J − 1 ) ideal conditions. When doubling/replacement time is taken into account, the range of anabolism energies can expand even further.

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Section: Computational Techniquesmentioning

confidence: 99%

The energetics of anabolism in natural settings

LaRowe

Amend

2016

The ISME Journal

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“…for crystalline compounds (Helgeson et al, 1998;LaRowe and Helgeson, 2006;LaRowe and Dick, 2012). In Eqs.…”

Section: Thermodynamic Calculations Of Reactions Of Amino Acids and Nmentioning

confidence: 99%

“…6, V o is the standard molal volume at the temperature and pressure of interest, and a, b, and c are temperature-independent coefficients. In this study, values of V o are equal to those of the standard molal volumes at the reference temperature and pressure of 298.15 K and 0.1 MPa, V o P r , T r , for all crystalline compounds (LaRowe and LaRowe and Dick, 2012). The data and parameters required to calculate the DG o as a function of temperature and pressure are presented in Tables 1 and 2 for aqueous species and crystalline compounds, respectively.…”

Section: Thermodynamic Calculations Of Reactions Of Amino Acids and Nmentioning

confidence: 99%

Polymerization of Building Blocks of Life on Europa and Other Icy Moons

Kimura

Kitadai

2015

Astrobiology

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The outer Solar System may provide a potential habitat for extraterrestrial life. Remote sensing data from the Galileo spacecraft suggest that the jovian icy moons-Europa, Ganymede, and possibly Callisto-may harbor liquid water oceans underneath their icy crusts. Although compositional information required for the discussion of habitability is limited because of significantly restricted observation data, organic molecules are ubiquitous in the Universe. Recently, in situ spacecraft measurements and experiments suggest that amino acids can be formed abiotically on interstellar ices and comets. These amino acids could be continuously delivered by meteorite or comet impacts to icy moons. Here, we show that polymerization of organic monomers, in particular amino acids and nucleotides, could proceed spontaneously in the cold environment of icy moons, in particular the jovian icy moon Europa as a typical example, based on thermodynamic calculations, though kinetics of formation are not addressed. Observed surface temperature on Europa is 120 and 80 K in the equatorial region and polar region, respectively. At such low temperatures, Gibbs energies of polymerization become negative, and the estimated thermal structure of the icy crust should contain a shallow region (i.e., at a depth of only a few kilometers) favorable for polymerization. Investigation of the possibility of organic monomer polymerization on icy moons could provide good constraints on the origin and early evolution of extraterrestrial life.

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“…At nearly the same time, progress was made in extending group contribution estimation procedures to biomolecules, including a new take on amino acids, polypeptides and unfolded proteins [74], nucleic-acid bases, nucleotides and nucleosides [75], and magnesium complexes of adenosine nucleotides, as well as oxidized and reduced nicotinamide adenosine dinucleotides (NAD) and NAD-phosphates [76]. Internally consistent data and group contribution estimation methods for crystalline forms of many of the same compounds can be found in the latter publications, and internally consistent thermodynamic data for crystalline peptides were also contributed recently [77].…”

Section: Sources Of Thermodynamic Data For Organic Compoundsmentioning

confidence: 90%

“…The group contribution algorithm used to calculate values of DG AABB refer to standard state Gibbs energies of formation of the protein backbone and amino acid backbone groups, respectively, which have been determined in the aqueous [61,74] and crystalline states [77]. Values of DG 0 1 are shown in figure 4 from 08C to 1508C at 500 bar (50 MPa) and at pressures corresponding to the liquidvapour saturation pressure for water, P SAT .…”

Section: Organic Synthesis Inside the Cellmentioning

confidence: 99%

The energetics of organic synthesis inside and outside the cell

Amend

LaRowe

McCollom

et al. 2013

Phil. Trans. R. Soc. B

Self Cite

108

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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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Calculation of the standard molal thermodynamic properties of crystalline peptides

Cited by 33 publications

References 96 publications

The energetics of anabolism in natural settings

The energetics of anabolism in natural settings

Polymerization of Building Blocks of Life on Europa and Other Icy Moons

The energetics of organic synthesis inside and outside the cell

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