* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Klauda-NCTU-Oct31
Bimolecular fluorescence complementation wikipedia , lookup
Protein design wikipedia , lookup
Structural alignment wikipedia , lookup
Protein folding wikipedia , lookup
Protein domain wikipedia , lookup
Circular dichroism wikipedia , lookup
Implicit solvation wikipedia , lookup
Trimeric autotransporter adhesin wikipedia , lookup
Protein purification wikipedia , lookup
Homology modeling wikipedia , lookup
Cooperative binding wikipedia , lookup
ATP-binding cassette transporter wikipedia , lookup
Protein structure prediction wikipedia , lookup
Protein mass spectrometry wikipedia , lookup
List of types of proteins wikipedia , lookup
Protein–protein interaction wikipedia , lookup
Intrinsically disordered proteins wikipedia , lookup
Nuclear magnetic resonance spectroscopy of proteins wikipedia , lookup
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.