Our Research
Structural Biology and Molecular Biophysics:Experimental Projects
• Structural topology and functional dynamics of bio-medically essential membrane proteins (KCNE3, KCNE1, KCNQ1) in different membrane environments, including lipid bilayer vesicles and lipoids nanoparticles/styrene maleic acid-lipid particles (SMALPs).
• Innovative structure biology techniques are used to determine the three-dimensional structure of membrane protein in a membrane environment using DEER distance restraints and simulated annealing molecular dynamics simulation.
• Effect of disease-causing mutations on structural dynamics of KCNE3 in different environments.
• Advanced Magnetic Resonance techniques: CW-EPR power saturation, Double electron-electron resonance (DEER), Electron spin echo envelope modulation (ESEEM), CW-dipolar broadening EPR, SS-NMR for the study of biological systems.
• Molecular Biology techniques for membrane protein sample preparation: Plasmid preparation, Gene cloning, Site-directed mutagenesis, Polymerase chain reaction (PCR), SDS-PAGE, Protein synthesis and purification (FPLC (fast protein liquid chromatography), HPLC (high-performance liquid chromatography)), Deuterium Isotopic labeling, Spin labeling (mono-functional spin labeling, bi-functional spin labeling), Protein reconstitutions in bilayered lipid vesicles, bicelles, lipodisq nanoparticles.
Figure: (A) Chemical structure of the MTSL spin label probe, (B) a predicted topology of KCNE3 in lipid bilayers based on previous solution NMR studies(3, 20), (C) CW-EPR spectra on KCNE3 mutants in 0.5% DPC micelles (left panel) and POPC/POPG bilayered vesicles (right panel). Spectra were normalized to the highest intensity of the spectrum. (Campbell et al. BBA-Biomembrane, 2024, 1864, 183974)
Computational Modeling of Membrane Proteins:
• Computational methods are used for molecular modeling for the structure and dynamics of biochemical and biomedical systems (KCNE3 and KCNE3/KCNQ1) in various membrane environments.
• Effect of Cholesterol on Structural Dynamics of KCNE3 and KCNE3/KCNQ1 in lipid bilayer membrane.
Principal Component Analysis of WT-KCNE3. Dynamic cross-correlation matrix (DCCM) is computed from PCA analysis for the first (PC1) and second (PC2) principal components (left panel). The blue color represents a positive correlation, and the red color represents a negative correlation on the vertical color bar (left panel). Vector arrows depicting the motion are mapped onto the protein structure, and the corresponding percentage contribution of the first and second principal components are indicated (middle panel). The green arrows represent the direction of the movement of the amino acid residue, and the length represents the relative magnitude of the movement for each residue (middle panel). Individual residue fluctuations (b-factors) are shown for each principal component.
E3 simulations