Standard thermodynamic formation properties for the adenosine 5'-triphosphate series

Alberty, Robert A.; Goldberg, Robert N.

doi:10.1021/bi00158a025

Cited by 185 publications

(189 citation statements)

References 12 publications

Supporting

Mentioning

184

Contrasting

Unclassified

Order By: Relevance

“…The reduction in electron density between the migrating P G and O 3B in the TS model in the mutant complex relative to WT (Figure 4) indicates that the loss of the H‐bond from Arg85′‐N η to O 3B in the Arg85′Ala complex (Figure 1) is of secondary importance. O 3B of GDP (p K a3 is ≈7.2)11 is still fully competent to act as a leaving group for nucleophilic attack on P G in the absence of a H‐bond from Arg85′. Moreover, replacing three H‐bonds from Arg85′ by one involving Tyr34 maintains the H‐bond network identified in our earlier study of the WT complex 1h.…”

mentioning

confidence: 73%

Assessing the Influence of Mutation on GTPase Transition States by Using X‐ray Crystallography, ¹⁹F NMR, and DFT Approaches

et al. 2017

View full text Add to dashboard Cite

We report X‐ray crystallographic and 19F NMR studies of the G‐protein RhoA complexed with MgF3 −, GDP, and RhoGAP, which has the mutation Arg85′Ala. When combined with DFT calculations, these data permit the identification of changes in transition state (TS) properties. The X‐ray data show how Tyr34 maintains solvent exclusion and the core H‐bond network in the active site by relocating to replace the missing Arg85′ sidechain. The 19F NMR data show deshielding effects that indicate the main function of Arg85′ is electronic polarization of the transferring phosphoryl group, primarily mediated by H‐bonding to O3G and thence to PG. DFT calculations identify electron‐density redistribution and pinpoint why the TS for guanosine 5′‐triphosphate (GTP) hydrolysis is higher in energy when RhoA is complexed with RhoGAPArg85′Ala relative to wild‐type (WT) RhoGAP. This study demonstrates that 19F NMR measurements, in combination with X‐ray crystallography and DFT calculations, can reliably dissect the response of small GTPases to site‐specific modifications.

show abstract

mentioning

confidence: 73%

Assessing the Influence of Mutation on GTPase Transition States by Using X‐ray Crystallography, ¹⁹F NMR, and DFT Approaches

et al. 2017

View full text Add to dashboard Cite

show abstract

“…The authors in [4,[41][42][43] proposed modifications of the reference that account for the effects of reactant and product concentrations, acid and base dissociation, free magnesium ion interaction, ionic interactions, effects of electrical potential, and so on. Based on these authors' results, the actual free energy change of ATP hydrolysis (∆g ATP ) in the reverse Equation (19) is −56 kJ/mol.…”

Section: Thermodynamic Modelmentioning

confidence: 99%

Exergy Analysis of the Musculoskeletal System Efficiency during Aerobic and Anaerobic Activities

Spanghero

Neto

Fernandes

et al. 2018

Entropy

View full text Add to dashboard Cite

Abstract:The first and second laws of thermodynamics were applied to the human body in order to evaluate the quality of the energy conversion during muscle activity. Such an implementation represents an important issue in the exergy analysis of the body, because there is a difficulty in the literature in evaluating the performed power in some activities. Hence, to have the performed work as an input in the exergy model, two types of exercises were evaluated: weight lifting and aerobic exercise on a stationary bicycle. To this aim, we performed a study of the aerobic and anaerobic reactions in the muscle cells, aiming at predicting the metabolic efficiency and muscle efficiency during exercises. Physiological data such as oxygen consumption, carbon dioxide production, skin and internal temperatures and performed power were measured. Results indicated that the exergy efficiency was around 4% in the weight lifting, whereas it could reach values as high as 30% for aerobic exercises. It has been shown that the stationary bicycle is a more adequate test for first correlations between exergy and performance indices.

show abstract

“…Data for organophosphates are from Alberty (40)(41)(42). We evaluate the direction of reactions using both equilibrium and nonequilibrium chemistry coupled to the law of mass balance.…”

Section: Methodsmentioning

confidence: 99%

Redox chemistry in the phosphorus biogeochemical cycle

Pasek

Sampson

Atlas

2014

Proc. Natl. Acad. Sci. U.S.A.

136

105

View full text Add to dashboard Cite

The element phosphorus (P) controls growth in many ecosystems as the limiting nutrient, where it is broadly considered to reside as pentavalent P in phosphate minerals and organic esters. Exceptions to pentavalent P include phosphine-PH 3 -a trace atmospheric gas, and phosphite and hypophosphite, P anions that have been detected recently in lightning strikes, eutrophic lakes, geothermal springs, and termite hindguts. Reduced oxidation state P compounds include the phosphonates, characterized by C−P bonds, which bear up to 25% of total organic dissolved phosphorus. Reduced P compounds have been considered to be rare; however, the microbial ability to use reduced P compounds as sole P sources is ubiquitous. Here we show that between 10% and 20% of dissolved P bears a redox state of less than +5 in water samples from central Florida, on average, with some samples bearing almost as much reduced P as phosphate. If the quantity of reduced P observed in the water samples from Florida studied here is broadly characteristic of similar environments on the global scale, it accounts well for the concentration of atmospheric phosphine and provides a rationale for the ubiquity of phosphite utilization genes in nature. Phosphine is generated at a quantity consistent with thermodynamic equilibrium established by the disproportionation reaction of reduced P species. Comprising 10-20% of the total dissolved P inventory in Florida environments, reduced P compounds could hence be a critical part of the phosphorus biogeochemical cycle, and in turn may impact global carbon cycling and methanogenesis.phosphorus | redox chemistry | phosphonates | element cycling | biogeochemistry L ife as we know it is dependent on phosphate esters, which act in metabolism as energy-storing polyphosphates and cofactors, in replication and transcription as the backbone of RNA and DNA, and in cell structure as phospholipids. Phosphate minerals are the ultimate source of phosphate in the biosphere. However, most phosphate minerals are poorly soluble and slow to dissolve at neutral pH and at room temperature; hence phosphorus (P) is the limiting nutrient in many ecosystems. Phosphorus cycling is especially slow compared with carbon and nitrogen cycling (1).Although inorganic phosphate and phosphate esters (P 5+ ) are viewed as the prevalent compounds in nature, phosphonates, with C−P bonds, are ubiquitous, comprising up to 25% of the dissolved organic P in some natural samples (2). The P in phosphonates has a stronger potential for electron sharing than the P in phosphates, based on the electronegativity difference between C and P (2.5-2.2) compared with O (3.5) and P in phosphates. With a greater potential for electron sharing, the formal oxidation state of P in phosphonates is thus less than +5; hence phosphonates represent a reduced oxidation state P (hereafter, reduced P) speciation in the environment. Phosphonates appear to be critical to some biogeochemical pathways, including a role for methylphosphonate in aerobic methanogenesis in marine environme...

show abstract

Standard thermodynamic formation properties for the adenosine 5'-triphosphate series

Cited by 185 publications

References 12 publications

Assessing the Influence of Mutation on GTPase Transition States by Using X‐ray Crystallography, ¹⁹F NMR, and DFT Approaches

Assessing the Influence of Mutation on GTPase Transition States by Using X‐ray Crystallography, ¹⁹F NMR, and DFT Approaches

Exergy Analysis of the Musculoskeletal System Efficiency during Aerobic and Anaerobic Activities

Redox chemistry in the phosphorus biogeochemical cycle

Contact Info

Product

Resources

About

Standard thermodynamic formation properties for the adenosine 5'-triphosphate series

Cited by 185 publications

References 12 publications

Assessing the Influence of Mutation on GTPase Transition States by Using X‐ray Crystallography, 19F NMR, and DFT Approaches

Assessing the Influence of Mutation on GTPase Transition States by Using X‐ray Crystallography, 19F NMR, and DFT Approaches

Exergy Analysis of the Musculoskeletal System Efficiency during Aerobic and Anaerobic Activities

Redox chemistry in the phosphorus biogeochemical cycle

Contact Info

Product

Resources

About

Assessing the Influence of Mutation on GTPase Transition States by Using X‐ray Crystallography, ¹⁹F NMR, and DFT Approaches

Assessing the Influence of Mutation on GTPase Transition States by Using X‐ray Crystallography, ¹⁹F NMR, and DFT Approaches