Solvent interactions and protein dynamics in spin-labeled T4 lysozyme.
Aspects of T4 lysozyme dynamics and solvent interaction are investigated using atomically detailed Molecular Dynamics (MD) simulations. Two spin-labeled mutants of T4 lysozyme are analyzed (T4L-N40C and T4L-K48C), which have been found from electronic paramagnetic resonance (EPR) experiments to exhibit different mobilities at the site of spin probe attachment (N- and C-terminus of helix B, respectively). Similarities and differences in solvent distribution and diffusion around the spin label, as well as around exposed and buried residues within the protein, are discussed. The purpose is to capture possible strong interactions between the spin label (ring) and solvent molecules, which may affect EPR lineshapes. The effect of backbone motions on the water density profiles is also investigated. The focus is on the domain closure associated with the T4 lysozyme hinge-bending motion, which is analyzed by Essential Dynamics (ED). The N-terminus of helix B is found to be a "hinge" residue, which explains the high degree of flexibility and motional freedom at this site.
Stoica
I
I
University of Ottawa, Ottawa, Ontario, Canada. istoica@physics.cornell.edu
D017122:Bacteriophage T4 / Q000737:chemistry*; D004578:Electron Spin Resonance Spectroscopy; D008433:Mathematics; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry*; D013113:Spin Labels; D014867:Water / Q000737:chemistry
D010446:Peptide Fragments; D012997:Solvents; D013113:Spin Labels; D014867:Water; D009113:Muramidase