jp4026706_si_002.zip (5.32 MB)
Molecular Dynamics Simulations of Depth Distribution of Spin-Labeled Phospholipids within Lipid Bilayer
dataset
posted on 2013-05-16, 00:00 authored by Alexander Kyrychenko, Alexey S. LadokhinSpin-labeled
lipids are commonly used as fluorescence quenchers
in studies of membrane penetration of dye-labeled proteins and peptides
using depth-dependent quenching. Accurate calculations of depth of
the fluorophore rely on the use of several spin labels placed in the
membrane at various positions. The depth of the quenchers (spin probes)
has to be determined independently; however, experimental determination
of transverse distributions of spin probe depths is difficult. In
this Article, we use molecular dynamics (MD) simulations to study
the membrane behavior and depth distributions of spin-labeled phospholipids
in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
(POPC) bilayer. To probe different depths within the bilayer, a series
containing five Doxyl-labeled lipids (n-Doxyl PC)
has been studied, in which a spin moiety was covalently attached to nth carbon atoms (where n = 5, 7, 10, 12,
and 14) of the sn-2 stearoyl chain of the host phospholipid.
Our results demonstrate that the chain-attached spin labels are broadly
distributed across the model membrane and their environment is characterized
by a high degree of mobility and structural heterogeneity. Despite
the high thermal disorder, the depth distributions of the Doxyl labels
were found to correlate well with their attachment positions, indicating
that the distribution of the spin label within the model membrane
is dictated by the depth of the nth lipid carbon
atom and not by intrinsic properties of the label. In contrast, a
much broader and heterogeneous distribution was observed for a headgroup-attached
Tempo spin label of Tempo-PC lipids. MD simulations reveal that, due
to the hydrophobic nature, a Tempo moiety favors partitioning from
the headgroup region deeper into the membrane. Depending on the concentration
of Tempo-PC lipids, the probable depth of the Tempo moiety could span
a range from 14.4 to 18.2 Å from the membrane center. Comparison
of the MD-estimated immersion depths of Tempo and n-Doxyl labels with their suggested experimental depth positions allows
us to review critically the possible sources of error in depth-dependent
fluorescence quenching studies.