Energetics of storage and diffusion of water and Cyclo-Octasulfur for a nonpolar cavity of RHCC Tetrabrachion by molecular dynamics simulations

Publication date: Available online 23 May 2019Source: Computational and Structural Biotechnology JournalAuthor(s): C. Harder-Viddal, M. McDougall, R.M. Roshko, J. StetefeldAbstractTetrabrachion forms the key component of the S-layer of Staphylothermus marinus. Molecular dynamics simulations have been used to study the energetics of occupancy of cavity 3 of the right-handed coiled-coil stalk of tetrabrachion by both water molecules and cyclooctasulfur S8 crowns, as well as to determine possible pathways and free energy barriers for the diffusion of both water and cyclooctasulfur through the peptide walls of RHCC tetrabrachion between cavity 3 and bulk solvent. Calculations of the transfer free energy from solvent to cavity show that clusters of six, seven and eight water molecules are marginally stable in cavity 3, but that occupancy of the cavity by a cyclooctasulfur ring is favoured significantly over water clusters of all sizes. Thermal activation simulations at T = 400K revealed that water molecules diffusing through the wall pass through a sequence of metastable configurations where they are temporarily immobilized by forming networks of hydrogen bonds with specific wall residues. Calculations of the free energy of these metastable configurations using multi-configurational thermodynamic integration yielded a free energy profile with a principal free energy maximum ∆G~50 kJ/mol and a slight activation asymmetry in favour of the direction from cavity to solvent. Pote...

Source: Computational and Structural Biotechnology Journal - May 24, 2019 Category: Biotechnology Source Type: research