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Preventing Misfolding of the Prion Protein by Trimethylamine N-Oxide^†

Brian J. Bennion,^‡^§ Mari L. DeMarco,^‡ and Valerie Daggett*^‡

Department of Medicinal Chemistry and Biomolecular Structure and Design Program, University of Washington, Seattle, Washington 98195-7610

Biochemistry, 2004, 43 (41), pp 12955–12963

DOI: 10.1021/bi0486379

Publication Date (Web): September 25, 2004

†

We gratefully acknowledge support from the National Institutes of Health (Grant RO1 GM-50789 to V.D.) and a National Institute of General Medical Sciences National Research Service Award (Grant GM-07750 to B.J.B. and M.L.D.).

‡

Department of Medicinal Chemistry.

Current address: Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA 94551.

Biomolecular Structure and Design Program.

To whom correspondence should be addressed: Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195-7610. E-mail: daggett@u.washington.edu. Fax: (206) 685-3252.

Abstract

Transmissible spongiform encephalopathies are a class of fatal neurodegenerative diseases linked to the prion protein. The prion protein normally exists in a soluble, globular state (PrP^C) that appears to participate in copper metabolism in the central nervous system and/or signal transduction. Infection or disease occurs when an alternatively folded form of the prion protein (PrP^Sc) converts soluble and predominantly α-helical PrP^C into aggregates rich in β-structure. The structurally disordered N-terminus adopts β-structure upon conversion to PrP^Sc at low pH. Chemical chaperones, such as trimethylamine N-oxide (TMAO), can prevent formation of PrP^Sc in scrapie-infected mouse neuroblastoma cells [Tatzelt, J., et al. (1996) EMBO J. 15, 6363−6373]. To explore the mechanism of TMAO protection of PrP^C at the atomic level, molecular dynamics simulations were performed under conditions normally leading to conversion (low pH) with and without 1 M TMAO. In PrP^C simulations at low pH, the helix content drops and the N-terminus is brought into the small native β-sheet, yielding a PrP^Sc-like state. Addition of 1 M TMAO leads to a decreased radius of gyration, a greater number of protein−protein hydrogen bonds, and a greater number of tertiary contacts due to the N-terminus forming an Ω-loop and packing against the structured core of the protein, not due to an increase in the level of extended structure as with the PrP^C to PrP^Sc simulation. In simulations beginning with the “PrP^Sc-like” structure (derived from PrP^C simulated at low pH in pure water) in 1 M TMAO, similar structural reorganization at the N-terminus occurred, disrupting the extended sheet. The mechanism of protection by TMAO appears to be exclusionary in nature, consistent with previous theoretical and experimental studies. The TMAO-induced N-terminal conformational change prevents residues that are important in the conversion of PrP^C to PrP^Sc from assuming extended sheet structure at low pH.