title: Microscopic hydration properties of the aβ1-42 Peptide monomer and the globular protein ubiquitin: a comparative molecular dynamics study.
abstract: Atomistic molecular dynamics simulations of eight selected conformations of a disordered protein, amyloid beta (1-42) (Aβ), and a globular protein, ubiquitin (UBQ), have been carried out in aqueous media at 310 K. Detailed analyses were carried out to compare the microscopic properties of water molecules present in the hydration layers of these systems. It is noticed that irrespective of the conformational heterogeneity among the Aβ monomers, water molecules hydrating their surfaces exhibit relatively faster dynamics as compared to water molecules hydrating UBQ. Importantly, the conformational heterogeneity of the Aβ monomers has been found to affect the translational and rotational motions of hydration water molecules in a nonuniform manner. Detailed investigation of the timescale of hydrogen bond relaxations at the surface and their energetics revealed the possibility of heterogeneous confinement around different Aβ conformations. The distribution of water density fluctuation around Aβ conformations are broader compared to UBQ because of its predominant hydrophobic nature. Significant heterogeneity in the density fluctuation among the Aβ monomers suggests that the structural propensities could affect the peptide's effective surface hydrophobicity.
authors.affiliation: Physical Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhaba Road, Pune 411008, India.
authors.forename: Jaya C
authors.initials: JC
authors.lastname: Jose
authors.forename: Prabir
authors.initials: P
authors.lastname: Khatua
authors.forename: Nupur
authors.initials: N
authors.lastname: Bansal
authors.forename: Neelanjana
authors.initials: N
authors.lastname: Sengupta
authors.forename: Sanjoy
authors.initials: S
authors.lastname: Bandyopadhyay
mesh_terms: D016229:Amyloid beta-Peptides / Q000737:chemistry*; D006801:Humans; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D025801:Ubiquitin / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
chemical_list: D016229:Amyloid beta-Peptides; D010446:Peptide Fragments; D025801:Ubiquitin; C075222:amyloid beta-protein (1-42); D014867:Water