Abstract
Site-directed spin labeling (SDSL) combined with continuous-wave electron paramagnetic resonance (CW-EPR) spectroscopy has become a useful approach to investigate the structural and dynamical properties of biomolecules, especially membrane protein. In this method, spin label side chains due to their motion highly depending on the local environment were employed as external molecules to probe the structure and dynamics of the membrane protein. The close relationships between the dynamics of the spin label side chain and protein structure have been studied for T4 lysozyme. Besides, molecular dynamics (MD) simulations were widely applied as a powerful tool to study the microscopic behavior of the proteins, completing experimental approaches. Here, we presented an all-atom MD simulation study of the nitroxide spin label (MTSSL) in the X-ray structure of a potassium channel voltage-sensor domain (VSD) from Aeropyrum Pernix (KvAP).
Highlights
We aim to model structures of cysteine-mutated membrane protein with nitroxide spin label attaching at various positions and investigate typical structural and dynamical features of spin label in membrane protein
A spin label was covalently attaching to one amino acid of the X-ray structure of KvAP-voltage-sensing domain (VSD) (5) by site-directed mutagenesis
It was found that the dynamics from Root-Mean-Square Fluctuation (RMSF) calculations and mobilities data from EPR (6) had similar patterns as shown in graphical abstract
Summary
We aim to model structures of cysteine-mutated membrane protein with nitroxide spin label attaching at various positions and investigate typical structural and dynamical features of spin label in membrane protein. Research Highlights This work is one of the pioneer computational investigations applying SDSL for all residues in a membrane protein and performing MD simulations. ̈ The dynamics of spin label side chains were well consistent with the experimental EPR data. ̈ Spin label side chain can reflect the conformational changes and flexibilities of membrane protein.
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