Download Klauda-NCTU-Oct31

Molecular Modeling of a Curvature-Sensing Peptide and Structural Changes in a Secondary Active
Transporter
Molecular simulations at the atomistic level have been able to probe biologically relevant behaviors of
lipids and proteins. However, there still is a need to further enhance conformational sampling in simulation
for timescales that are not reachable with traditional computational approaches. One aspect of our research
is understanding the mechanism of lipid exchange between cell organelles. This involves proteins that aid
in lipid transport by forming membrane contact sites. One example is the oxysterol binding protein
homologues (Osh) with Osh4 known to exchange phosphatidylinositol 4-phosphate (PI4P) lipids regulated
by ergosterol. This protein contains a lipid packing sensing peptide classified as an amphipathic lipid
packing sensor (ALPS) like motif that is believe to sense membrane curvature. To probe peptide sampling
at the membrane surface, the Anton1 computational resource was used to obtain microsecond simulations
using molecular dynamics (MD). We have found dual motifs of binding at the hydrophobic/hydrophilic
interface (vertical and horizontal orientations). For some simulations when a hydrophobic residue
approaches a bilayer packing defect in the correct orientation, it embeds itself even into a small defect by
expanding it upon binding. Since Anton1 is limited in use by the field, we also tested the Highly Mobile
Membrane-Mimetic Model (BJ, 102: p2130) to enhance peptide binding. Almost all systems showed stable
binding conformations before 100ns. These binding events were an order of magnitude faster than with the
all-atom membrane and agree with its bound structure demonstrating the accuracy of this enhanced
approach.
Lactose permease (LacY) of E. coli has been a historical model transmembrane protein for secondary
active transporters, but its crystal structure is only know in the inward facing and occluded state. We have
used an enhanced sampling technique to predict the outward-facing state of this protein. Our results agree
well with various biophysical and biochemical experimental results. However, there appeared to be some
discrepancies with recent Double Electron-Electron Resonance (DEER) experiments that measure the
distance between two nitroxide spin labels. Our molecular simulation results show that the orientation and
movement of the spin labels significantly affect the residue pair distance. Therefore, careful interpretation
of DEER experimental results is needed and molecular modeling is likely required to fully understand
distance measurements from DEER on proteins.