Plasticization of protein dynamics by water, a molecular dynamics study

Abstract

Previous research has suggested that protein dynamics is ‘slaved’ to the dynamics of the solvent. However, the extent of this modulation of the protein dynamics by water is not currently known. In this work, we have modeled three representative proteins having rather different sizes and shapes (ubiquitin (4XOF), lysozyme (5LSH), and serum albumin (6M4R)) in TIP4P water to gain insight into the interfacial water of the protein in comparison to bulk water. For all three systems, we compared trends in the average local protein density to the average mean square atomic displacement on a ps timescale <u2>, the Debye-Waller parameter.