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Characterization of Lipid–Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

“…346 To quantify membrane deformation around LeuT, driven by the hydrophobic mismatch, the hybrid continuummolecular dynamics (CTMD) approach was applied to calculate the associated energy cost at the continuum level. 347 The study showed that the hydrophobic mismatch is different in distinct conformations (outward-open, occluded, inward-open) of LeuT, and that the differences are connected to the structural elements involved in the conformational transitions during the transport cycle. 347,348 Beyond hydrophobic-hydrophilic contacts between the membrane and the embedded protein, specific lipids can regulate the dynamics and conformational transitions of the LeuT-fold NSSs upon direct interactions.…”

“…347 The study showed that the hydrophobic mismatch is different in distinct conformations (outward-open, occluded, inward-open) of LeuT, and that the differences are connected to the structural elements involved in the conformational transitions during the transport cycle. 347,348 Beyond hydrophobic-hydrophilic contacts between the membrane and the embedded protein, specific lipids can regulate the dynamics and conformational transitions of the LeuT-fold NSSs upon direct interactions. Microsecond AA simulations of human dopamine transporter (hDAT) in a PIP 2 -enriched membrane revealed an inward opening of the transporter triggered by PIP 2 -mediated electrostatic association of specific structural motifs.…”

“…While many of the systems highlighted here are peripheral proteins, given the prevalence and involvement of anionic lipids in drawing peripheral proteins to the membrane, many simulations have also been performed with PG or PS in the membrane for channels 15,295,306,307,310,330,347,355,375,387,452,[791][792][793][794][795][796][797][798][799][800][801][802] and receptors. 387,437,803 Preference of proteins to bind anionic membranes has been frequently shown by demonstrating clustering of anionic lipids around a protein using both CG 483,496,676,804,805 and AA simulations.…”

Faculty Opinions recommendation of Ultrafast Dynamics of Water-Protein Coupled Motions around the Surface of Eye Crystallin.

“…[2][3][4][5][6] Over the past decades considerable strides have been made in understanding water-protein interactions in the socalled hydration layers composed of water near the protein surface and their effect on protein structure and function. 5,[7][8][9][10][11] Water in this region experiences slow, distinct dynamics compared to bulk water. 8 Many techniques, including NMR, 12,13 neutron scattering, 14,15 laser spectroscopies, 9,16 and molecular dynamics simulations (MD) 11,17,18 have studied the hydration layer water molecules at different time and length scales and have sought to clarify the essential nature of the hydration layers and their interactions with protein dynamics.…”

“…5,[7][8][9][10][11] Water in this region experiences slow, distinct dynamics compared to bulk water. 8 Many techniques, including NMR, 12,13 neutron scattering, 14,15 laser spectroscopies, 9,16 and molecular dynamics simulations (MD) 11,17,18 have studied the hydration layer water molecules at different time and length scales and have sought to clarify the essential nature of the hydration layers and their interactions with protein dynamics.…”