Dataset Information

The missing link between thermodynamics and structure in F1-ATPase.

ABSTRACT: F(1)F(o)-ATP synthase is the enzyme responsible for most of the ATP synthesis in living systems. The catalytic domain F(1) of the F(1)F(o) complex, F(1)-ATPase, has the ability to hydrolyze ATP. A fundamental problem in the development of a detailed mechanism for this enzyme is that it has not been possible to determine experimentally the relation between the ligand binding affinities measured in solution and the different conformations of the catalytic beta subunits (beta(TP), beta(DP), beta(E)) observed in the crystal structures of the mitochondrial enzyme, MF(1). Using free energy difference simulations for the hydrolysis reaction ATP+H(2)O --> ADP+P(i) in the beta(TP) and beta(DP) sites and unisite hydrolysis data, we are able to identify beta(TP) as the "tight" (K(D) = 10(-12) M, MF(1)) binding site for ATP and beta(DP) as the "loose" site. An energy decomposition analysis demonstrates how certain residues, some of which have been shown to be important in catalysis, modulate the free energy of the hydrolysis reaction in the beta(TP) and beta(DP) sites, even though their structures are very similar. Combined with the recently published simulations of the rotation cycle of F(1)-ATPase, the present results make possible a consistent description of the binding change mechanism of F(1)-ATPase at an atomic level of detail.

SUBMITTER: Yang W

PROVIDER: S-EPMC298694 | biostudies-literature | 2003 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

The missing link between thermodynamics and structure in F1-ATPase.

Yang W W Gao Y Q YQ Cui Q Q Ma J J Karplus M M

Proceedings of the National Academy of Sciences of the United States of America 20030127 3

F(1)F(o)-ATP synthase is the enzyme responsible for most of the ATP synthesis in living systems. The catalytic domain F(1) of the F(1)F(o) complex, F(1)-ATPase, has the ability to hydrolyze ATP. A fundamental problem in the development of a detailed mechanism for this enzyme is that it has not been possible to determine experimentally the relation between the ligand binding affinities measured in solution and the different conformations of the catalytic beta subunits (beta(TP), beta(DP), beta(E) ...[more]

PMID: 12552084

Similar Datasets

Project description:BackgroundFunctional traits are the primary biotic component driving organism influence on ecosystem functions; in consequence, traits are widely used in ecological research. However, most animal trait-based studies use easy-to-measure characteristics of species that are at best only weakly associated with functions. Animal-mediated pollination is a key ecosystem function and is likely to be influenced by pollinator traits, but to date no one has identified functional traits that are simple to measure and have good predictive power.MethodsHere, we show that a simple, easy to measure trait (hairiness) can predict pollinator effectiveness with high accuracy. We used a novel image analysis method to calculate entropy values for insect body surfaces as a measure of hairiness. We evaluated the power of our method for predicting pollinator effectiveness by regressing pollinator hairiness (entropy) against single visit pollen deposition (SVD) and pollen loads on insects. We used linear models and AICC model selection to determine which body regions were the best predictors of SVD and pollen load.ResultsWe found that hairiness can be used as a robust proxy of SVD. The best models for predicting SVD for the flower species Brassica rapa and Actinidia deliciosa were hairiness on the face and thorax as predictors (R2 = 0.98 and 0.91 respectively). The best model for predicting pollen load for B. rapa was hairiness on the face (R2 = 0.81).DiscussionWe suggest that the match between pollinator body region hairiness and plant reproductive structure morphology is a powerful predictor of pollinator effectiveness. We show that pollinator hairiness is strongly linked to pollination-an important ecosystem function, and provide a rigorous and time-efficient method for measuring hairiness. Identifying and accurately measuring key traits that drive ecosystem processes is critical as global change increasingly alters ecological communities, and subsequently, ecosystem functions worldwide.

Dataset Information

The missing link between thermodynamics and structure in F1-ATPase.

Publications

The missing link between thermodynamics and structure in F1-ATPase.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure