Data from: The intrinsically disordered N-terminus of the voltage-dependent anion channel

The voltage-dependent anion channel (VDAC) is a beta-barrel membrane
protein of the mitochondrial outer membrane (MOM), which controls the
transport of ions and ATP between mitochondria and the
cytoplasm. The present dataset includes all data and
scripts generated in the study "The
intrinsically-disordered N-terminus of the voltage-dependent anion
channel" by J. Preto and I. Krimm, where we performed
all-atom simulations to investigate the disordered properties of VDAC’s
N-terminus (i) as a free peptide in solution (ii) as part of the channel
(mVDAC1-WT) or (iii) as part of a mVDAC1 mutant (mVDAC1-Cys) characterized
by a disulfide bond affixing the N-terminus against the beta-barrel wall.
The last two studies involve the channel embedded in a DOPC/DOPE lipid
bilayer representing the MOM. Our data comprise molecular dynamics (MD)
and accelerated MD (aMD) trajectories of the three systems performed for
exploratory purposes. In the case of mVDAC1-Cys, MD/aMD simulations were
performed upon different transmembrane (TM) potential values (0mV, +40mV
and -40mV). At all voltages, GCMC/BD calculations were run to probe for
possible low-conducting conformers of the channel. At +40mV, our aMD
trajectory shows detachment of the N-terminus from the
beta-barrel and the emergence of long-lived
subconducting conformations. The stability of these conformations is
further confirmed from standard MD simulations at +40mV, starting from
each of the subconducting conformers identified in GCMC/BD. For each
trajectory, the numbers of cations and anions crossing the channel were
recorded to keep track of the intensity and of the conductance of each
state.