Structure of the ATP synthase catalytic complex (F(1)) from Escherichia coli in an autoinhibited conformation.

ATP synthase is a membrane-bound rotary motor enzyme that is critical for cellular energy metabolism in all kingdoms of life. Despite conservation of its basic structure and function, autoinhibition by one of its rotary stalk subunits occurs in bacteria and chloroplasts but not in mitochondria. The crystal structure of the ATP synthase catalytic complex (F(1)) from Escherichia coli described here reveals the structural basis for this inhibition. The C-terminal domain of subunit ɛ adopts a heretofore unknown, highly extended conformation that inserts deeply into the central cavity of the enzyme and engages both rotor and stator subunits in extensive contacts that are incompatible with functional rotation. As a result, the three catalytic subunits are stabilized in a set of conformations and rotational positions distinct from previous F(1) structures

Continuous representations of proteins: construction of coordinate models from curvature profiles.

A representation of proteins based on the geometry of space curves is described. This representation enables the application of continuum methods to the analysis of macromolecular structure and form that cannot be applied to the more familiar discrete atomic coordinate models. It is shown that the continuous modeling method defines the geometry of the protein fold very efficiently. An analytical solution for curve construction is employed from which both continuous and coordinate models can be obtained. The method is applied to five representative test proteins which are used to assess the accuracy and efficiency of the modeling procedure

The Fourier transforms of curves and filaments and their application to low-resolution protein crystallography

A numerical method for computing the Fourier transform of an arbitrary space curve is described. The method is applicable to all sufficiently smooth curves and relies on the local geometric parameters describing a curve. The numerical results for a helical curve are compared with the exact analytical theory for the transform of a helix. It is shown that the transform of a filamentary density distribution radially symmetric around a curve is equivalent to the transform of that curve scaled by an appropriately defined weight function. These filamentary density distributions in conjunction with the numerical transform evaluation method can be used for simulating low-resolution diffraction data for protein crystals. Crystallographic structure factors obtained from a filament model representing a simple three-helix-bundle protein are compared with those calculated from conventional coordinate models. At low resolution, the filamentary representation provides an excellent approximation of the structure factors obtained from the standard coordinate model, but requires far fewer independent parameters. © International Union of Crystallography 2009

Chirality of coiled coils: elasticity matters.

Coiled coils are important protein-protein interaction motifs with high specificity that are used to assemble macromolecular complexes. Their simple geometric organization, consisting of alpha helices wrapped around each other, confers remarkable mechanical properties. A geometrical and mechanical continuous model taking into account sequence effects and based on the superhelical winding of the constituent helices is introduced, and a continuous family of solutions in which the oligomerization interactions are satisfied is derived. From these solutions, geometric and structural properties, such as the chirality and pitch of the coiled coil and the location of residues, are obtained. The theoretical predictions are compared to x-ray data from the leucine zipper motif

Elastic coiled-coils act as energy buffers in the ATP synthase

In the ATP synthase, transmission of energy from the membrane-embedded F0 sector to the catalytic F1 sector is accomplished by two stalks composed of coiled-coils. The great efficiency of the enzyme, despite the presence of a symmetry mismatch between the F1 and F0 sectors, suggests the involvement of elastic elements that store energy during the catalytic cycle. Here, the stalk subunits γ and b are investigated as the source of this elastic compliance using a continuum mechanical model of coiled-coils and energy arguments. The analysis shows that the compliance of both subunits is required for efficient energy transmission between F0 and F1. In addition, the predicted mechanical properties of coiled-coils in the ATP synthase suggest mechanisms whereby regulatory subunits influence the enzyme activity. © 2008 Elsevier Ltd. All rights reserved

The effect of NBD-Cl in nucleotide-binding of the major subunit alpha and B of the motor proteins F1FO ATP synthase and A(1)A(O) ATP synthase.

Subunit alpha of the Escherichia coli F(1)F(O) ATP synthase has been produced, and its low-resolution structure has been determined. The monodispersity of alpha allowed the studies of nucleotide-binding and inhibitory effect of 4-Chloro-7-nitrobenzofurazan (NBD-Cl) to ATP/ADP-binding. Binding constants (K ( d )) of 1.6 microM of bound MgATP-ATTO-647N and 2.9 microM of MgADP-ATTO-647N have been determined from fluorescence correlation spectroscopy data. A concentration of 51 microM and 55 microM of NBD-Cl dropped the MgATP-ATTO-647N and MgADP-ATTO-647N binding capacity to 50% (IC(50)), respectively. In contrast, no effect was observed in the presence of N,N'-dicyclohexylcarbodiimide. As subunit alpha is the homologue of subunit B of the A(1)A(O) ATP synthase, the interaction of NBD-Cl with B of the A-ATP synthase from Methanosarcina mazei Gö1 has also been shown. The data reveal a reduction of nucleotide-binding of B due to NBD-Cl, resulting in IC(50) values of 41 microM and 42 microM for MgATP-ATTO-647N and MgADP-ATTO-647N, respectively