TY - JOUR AU - Bazaziyan, Behnaz AU - Bozorgmehr, Mohammad Reza AU - Momen-Heravi, Mohammad AU - Beyramabadi, S. Ali PY - 2020/08/21 Y2 - 2024/03/28 TI - Flavodoxin in a binary surfactant system consisting of the nonionic 1-decanoyl-rac-glycerol and the zwitterionic lauryldimethylamine-N-oxide: Molecular dynamics simulation approach JF - Papers in Physics JA - Pap. Phys. VL - 12 IS - SE - Traditional Review Articles DO - 10.4279/pip.120004 UR - https://www.papersinphysics.org/papersinphysics/article/view/531 SP - 120004 AB - <p>Due to the short time constant of the spin-spin relaxation process, there is a limitation in the preparation of NMR sample solution for large proteins. To overcome this problem, reverse micelle systems are used.&nbsp; Here, molecular dynamics simulation was used to study the structure of flavodoxin in a quaternary mixture of 1-decanoyl-rac-glycerol, lauryldimethylamine-N-oxide, pentane and hexanol.&nbsp; Hexanol was used as co-solvent. Simulations were performed at three different co-solvent concentrations.&nbsp; The proportion of components in the mixture was selected according to experimental conditions.&nbsp; For comparison, simulation of flavodoxin in water was also performed.&nbsp; The simulation results show that the C$\alpha$-RMSD for the protein in water is less than for the surfactant mixture.&nbsp; Also, the radius of gyration of flavodoxin increased in the presence of surfactants.&nbsp; The distance between the two residues trp-57 and phe-94, as a measure of protein activity, was obtained from the simulations.&nbsp; The results showed that in the surfactant mixtures this distance increases.&nbsp; Analysis of the secondary structure of the protein shows that the N-terminal part of the flavodoxin is more affected by surfactants.&nbsp; The flavodoxin diffusion coefficient in the surfactant mixture decreased in relation to its diffusion coefficient in water.</p> ER -