Domain Motion of Individual F₁-ATPase β-Subunits during Unbiased Molecular Dynamics Simulations

Abstract

F1-ATPase is the catalytic domain of F1Fo-ATP synthase and consists of an hexameric arrangement of three non-catalytic α and three catalytic β subunits. We have used unbiased molecular dynamics simulations with a total simulation time of 900 ns to investigate the dynamic relaxation properties of isolated β-subunits as a step toward explaining the function of the integral F1 unit. To this end, we simulated the open (βE) and the closed (βTP) conformations under unbiased conditions for up to 120 ns each using several samples. The simulations confirm that nucleotide-free βE retains its open configuration over the course of the simulations. The same is true when the neighbouring α subunits are included. The nucleotide-depleted as well as the nucleotide-bound isolated βTP subunits show a significant trend toward the open conformation during our simulations, with one trajectory per case opening completely. Hence, our simulations suggest that the equilibrium conformation of a nucleotide-free β-subunit is the open conformation and that the transition from the closed to the open conformation can occur on a timescale of a few tens of nanoseconds.

pH‐dependent molecular dynamics of vesicular stomatitis virus glycoprotein G

“…With these fixed reference points, the fourth residue tyrosine 73, located at the tip of the longer Domain IV β‐strand, serves to monitor the Domain IV motions with respect to the protein core (Domains I–III). Similar geometric criteria have been already used in previous investigations to study domain–hinge motions 42, 43…”

Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing

“…The soluble charge carrier cytochrome c 2 returns electrons back from the bc 1 -complex to the RC, thereby completing a circuit. The proton gradient drives ATP synthesis at the ATP synthase [11]. (See Fig.…”

Metal Fluorides: Tools for Structural and Computational Analysis of Phosphoryl Transfer Enzymes

“…There are three prime MF x complexes for the a 3 b 3 assembly at resolutions from C2.0 Å (PDB: 1w0j, 1h8e, and 1e1r). These have been starting points for multiple computational studies, of which the majority are concerned with energetics of the chemical step, coupling between the subunits and the rotor, and rotational behavior of the synthetic complex [102,[105][106][107]. More recent studies involve the juxtaposition of several structures from the PDB.…”