title: Model Dependency of TMAO's Counteracting Effect Against Action of Urea: Kast Model versus Osmotic Model of TMAO.
abstract: Classical molecular dynamics simulation of GB1 peptide (a 16-residue β-hairpin) in different osmotic environments is studied. Urea is used for denaturation of the peptide, and trimethylamine-N-oxide (TMAO) is used to offset the effect of urea. Protein-urea electrostatic interactions are found to play a major role in protein-denaturation. To emphasize on protein protecting action of TMAO against urea, two different models of TMAO are used, viz., the Kast model and the Osmotic model. We observe that the Osmotic model of TMAO gives the best protection to counteract urea's action when used in ratio 1:2 of urea:TMAO (i.e., reverse ratio). This is because the presence of TMAO makes urea-protein electrostatic interactions more unfavorable. Preferential solvation of TMAO molecules by urea (and water) molecules is also observed, which causes depletion in the number of urea molecules in the vicinity of the protein. The calculations of intraprotein hydrogen bonds between different residues of protein further reveal the breaking of backbone hydrogen bonds of residues 2 and 15 in the presence of urea, and the same is preserved in the presence of TMAO. Free energy landscapes show that the narrowest distribution is obtained for the osmotic TMAO model when used in reverse ratio.
authors.affiliation: Department of Chemistry, Indian Institute of Technology , Guwahati 781039, India.
authors.forename: Gargi
authors.initials: G
authors.lastname: Borgohain
authors.affiliation: Department of Chemistry, Indian Institute of Technology , Guwahati 781039, India.
authors.forename: Sandip
authors.initials: S
authors.lastname: Paul
mesh_terms: D006860:Hydrogen Bonding; D008744:Methylamines / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009995:Osmosis; D055672:Static Electricity; D014508:Urea / Q000737:chemistry*
chemical_list: D008744:Methylamines; D014508:Urea; C005855:trimethyloxamine