A molecular dynamics simulation of SNase and its hydration shell at high temperature and high pressure.
Temperature- and pressure-induced unfolding of staphylococcal nuclease (SNase) was studied by Royer, Winter et al. using a variety of experimental techniques (SAXS, FT-IR and fluorescence spectroscopy, DSC, PPC, densimetry). For a more detailed understanding of the underlying mechanistic processes of the different unfolding scenarios, we have carried out a series of molecular dynamics (MD) computer simulations on SNase. We investigated the initial changes of the structure of the protein upon application of pressure (up to 5 kbar) and discuss volumetric and structural differences between the native and pressure pre-denatured state. Additionally, we have obtained the compressibility of the protein and hydration water and compare these data with experimental results. As water plays a crucial role in determining the structure, dynamics and function of proteins, we undertook a detailed analysis of the structure of the interfacial water and the protein-solvent H-bond network as well. Moreover, we report here also MD results on the temperature-induced unfolding of SNase. The time evolution of the protein volume and solvent accessible surface area during thermal unfolding have been investigated, and we present a detailed discussion of the temperature-induced unfolding pathway of SNase in terms of secondary and tertiary structural changes.
Smolin
Nikolai
N
Physical Chemistry I-Biophysical Chemistry, Department of Chemistry, University of Dortmund, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany. nikolai.smolin @uni-dortmund.de
Winter
Roland
R
D003198:Computer Simulation; D006358:Hot Temperature; D008836:Micrococcal Nuclease / Q000737:chemistry*; D011312:Pressure; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013696:Temperature; D014867:Water / Q000737:chemistry
D014867:Water; D008836:Micrococcal Nuclease