Dynamics and Local Ordering of Spin-Labeled Prion Protein: An ESR Simulation Study of a Highly PH-Sensitive Site

• Published in: Journal of biomolecular structure & dynamics 2008-12, Vol.26 (3), p.355-365
• Main Authors: Chiang, Yun-Wei, Otoshima, Yuki, Watanabe, Yasuko, Inanami, Osamu, Shimoyama, Yuhei
• Format: Article
• Language: English
• Subjects: Animals; Computer Simulation; Electron spin resonance; Electron Spin Resonance Spectroscopy; Hydrogen-Ion Concentration; Mice; Models, Molecular; Prion protein; Protein Conformation; Protein dynamics; PrPC Proteins - chemistry; Site-directed spin labeling; Slow motional regime; Spin Labels; Stochastic Liouville equation
• ISSN: 0739-1102; 1538-0254
• DOI: 10.1080/07391102.2008.10507250

Valine 160 on β-sheet-2 (S2) of mouse prion (moPrP C ) has been previously identified as the most highly pH-sensitive site on moPrP C by ESR spectroscopy using site-directed spin labeling (SDSL) technique. However, no further theoretical analysis to reveal the molecular dynamics reported on the experimental ESR spectra is available. The X-band ESR spectra of R1 nitroxide spin label at V160 and four other sites are carefully analyzed over large pH and temperature ranges using a spectral simulation method based upon stochastic Liouville equation (SLE). The results clearly reveal the dynamics and ordering of the local environment of V160R1 showing that (i) molecular mobility of V160R1 on S2 gradually increases with a decrease of pH from 7.5 to 4.5; (ii) two distinctly different spectral components are simultaneously present in all spectra of V160R1 studied. The spectral components are, respectively, denoted as immobile (Im), characterized by lower molecular mobility and higher ordering, and mobile (Mb) component of high mobility and low ordering. The population ratio (Im/Mb) increases with increasing pH, while Im remains dominant in all V160R1 spectra. It suggests a more mobile and disordered dynamic molecular structure for mouse PrP C , which is very likely correlated with increased β-sheet content at low pH, as the environment changes from neutral to acidic pH. Together with the results of the SLE-based analyses on the spectra of other sites that appear pH-insensitive, we suggest that the simultaneous presence of the spectral components for V160R1 is strongly correlated with the coexistence of multiple protein conformations in local structure of PrP C over the varied pH range. It demonstrates that the combined approach of the SDSL technique and the SLE-based analysis leads to a powerful method for unraveling the complexity of protein dynamics.