Energy Transfer from Adenosine Triphosphate: Quantitative Analysis and Mechanistic Insights

Abstract

The ATP-ADP thermodynamic cycle is the fundamental mode of energy exchange in oxidative phosphorylation, photophosphorylation, muscle contraction, and intracellular transport by various molecular motors and is therefore of vital importance in biological energy transduction and storage. Following a recent suggestion in the pages of this journal (Ross, J. J. Phys. Chem. B 2006, 110, 6987-6990), we have carried out a simple quantitative analysis of a direct molecular mechanism of energy transfer from adenosine triphosphate (ATP). The simulation provides new insights into the mechanistic events following terminal phosphorus-oxygen bond cleavage during ATP hydrolysis. This approach also allows for the division of the energy-transfer process into elementary steps and for the prediction of the distribution of the standard-state Gibbs free energy of the overall ATP hydrolysis process among the various steps of substrate binding, bond cleavage, and product release in the enzymatic cycle, which had proved very difficult to specify previously. These predictions are consistent with available experimental data on ATP hydrolysis by protein biomolecular machines. The fundamental biological implications arising from our results are also discussed in detail. The aspects considered in this work enable us to look at the entire process of ATP synthesis/hydrolysis and energy transduction and storage in various biological molecular machines in a logically consistent and unified way.

The probability distribution function of the Lyman transmitted flux from a sample of Sloan Digital Sky Survey quasars

“…At the present epoch, this fraction might be as large as 40 per cent (e.g. Cen & Ostriker 1999; Davé et al 2001; see also Nath & Silk 2001). At redshift z ∼ 3, however, these simulations indicate that this fraction falls below 10 per cent, and that most of the WHIM baryons reside in overdensities δ b ≳ 10 (Davé et al 2001).…”

The advantage of channeling nucleotides for very processive functions

“…The three main kinds of biological work are: mechanical work (such as the beating of cilia, muscle contraction, and movement of chromosomes during cell division), transport work (such as pumping substances across membranes against the direction of spontaneous movement), and chemical work that drives thermodynamically unfavourable reactions (such as the synthesis of polypeptides and nucleic acids). In most cases, the source of chemical energy that powers biological work is ATP, the predominant form of chemical energy in all living cells 12 . ATP is composed of the nitrogenous base, adenine, the five-carbon sugar ribose, and a chain of three phosphate groups.…”

“…The hydrolysis of ATP to ADP (adenosine diphosphate) and P i (inorganic phosphate) is a strongly exergonic reaction, i.e. it releases a large amount of energy (called Gibbs free energy, ΔG), which is used to perform much of the biological work described above 12– 14 . The other nucleoside triphosphate (NTP)s have similar chemical properties as ATP, but they are used for different tasks in the cell: GTP, which has a guanine base in the place of the adenine in ATP, is important in protein synthesis as well as in signal transduction through G proteins and in tubulin polymerisation 15 , whereas UTP (uridine 5’-triphosphate) and CTP (cytidine 5’-triphosphate) are used in polysaccharide and phospholipid synthesis, respectively.…”

A non‐enzymatic model based on an acyl transfer reaction for the formation of energy‐rich acetyl phosphate in organic solvents and in a biphasic system

“…Living beings need energy in order to perform a series of biochemical events, and some energy‐rich phosphate compounds, such as adenosine triphosphate (ATP) and acetyl phosphate (AcP), play a very important role in these processes 1–7. While mechanistic aspects of the hydrolysis of these phosphate compounds have been extensively studied,8–20 the literature registers relatively few enzymatic models responsible for the synthesis of energy‐rich phosphate compounds. A classical example was shown by Lehn and co‐workers who utilized a macrocyclic polyamine as an artificial enzyme able not only to hydrolyze of ATP,21–23 but also to mediate, using AcP and via a phosphoramidate intermediate, the formation of ATP from ADP and inorganic phosphate 24–27…”