ABSTRACT Molecular dynamics calculations demonstrated the conformational change in the prion protein due to Ala^sup 117^-->Val mutation, which is related to Gerstmann-Straussler-Sheinker disease, one of the familial prion diseases. Three kinds of model structures of human and mouse prion proteins were examined: (model 1) nuclear magnetic resonance structures of human prion protein HuPrP (125-228) and mouse prion protein MoPrP (124-224), each having a globular domain consisting of three a-helices and an antiparallel beta-sheet; (model 2) extra peptides including Ala^sup 117^ (109-124 in HuPrP and 109-123 in MoPrP) plus the nuclear magnetic resonance structures of model 1; and (model 3) extra peptides including Val"' 17 (109-124 in HuPrP and 109-123 in MoPrP) plus the nuclear magnetic resonance structures of model 1. The results of molecular dynamics calculations indicated that the globular domains of models 1 and 2 were stable and that the extra peptide in model 2 tended to form a new alpha-helix. On the other hand, the globular domain of model 3 was unstable, and the 1-sheet region increased especially in HuPrP.
Prion diseases are manifested as familial infections or sporadic diseases, and they cause neurodegenerative disorders such as kuru, Creutzfeldt-Jacob disease, Gerstmann-Straussler-Sheinker syndrome (GSS), and fatal familial insomnia in humans and scrapie and bovine spongiform encephalopathy (BSE) in animals (Prusiner and DeArmond, 1994). These disorders are thought to be caused by the transformation of a normal prion protein (PrP^sup C^) into an abnormal prion protein (PrP^sup C^), which accumulates in plaques in the brain (Borchelt et al., 1990). The replication of PrP^sup C^ is thought to occur through interaction between PrP^sup C^ and PrP^sup C^ with the assistance of a protein X acting as a chaperon (Telling et al., 1995). PrP^sup c^ has one disulfide bridge (Fig. 1) and is anchored to the cell membrane via a glycosyl phosphatidyl inositol anchor (Stahl et al., 1987, 1992). The important point is that no chemical difference between PrP^sup C^ and PrP^sup SC^ has been identified (Stahl et al., 1993). However, experiments using circulator dichroism and Fourier-transform infrared analyses have shown that PrPc has a low beta-sheet content (~3%) and is sensitive to proteases, whereas PrP^sup SC^ has a high beta-sheet content (~30%) and is protease-resistant (Pan et al., 1993; Safar et al., 1993). Recently, nuclear magnetic resonance (NMR) experiments have revealed the three-dimensional structures of mouse prion protein MoPrP (Riek et al., 1996, 1997, 1998), Syrian hamster prion protein ShPrP (Donne et al., 1997; Liu et al., 1999; James et al., 1997), bovine prion protein (Garcia et al., 2000), and human prion protein HuPrP (Zahn et al., 2000), all of which correspond to PrPc. These structural data have indicated that the N-terminal region (~125) is flexible and that the C-terminal region containing the globular domain (125-228) is rigid. The globular domain consists of three alpha-helices and a short antiparalell beta-sheet (Fig. 2).
Most cases of human prion diseases occur spontaneously by unknown causes. However, familial prion diseases such as GSS, fatal familial insomnia, and Creutzfeldt-Jacob disease are related to distinct point mutants within the human gene of PrPc (PRNP) (Hsiao et al., 1989; Kretzschmar 1993). Point mutations in the PRNP gene are seen in 102, 105, 117, 145, 198, and 217 in GSS and 178, 200, and 210 in most cases of Creutzfeldt-Jacob disease. Some mutations related to GSS occur only in a few families (Tateishi et al., 1990; Hsiao et al., 1991; Mastrianni et al., 1995), e.g., P102L mutation was detected in more than 30 families, whereas Ala^sup 117^-->Val mutation was detected in only three families (Trenchant et al., 1997). It is interesting that Ala^sup 117^-Val mutation requires two changes in the genetic code to generate an amino acid change. It is known that Ala^sup 117^--> Val mutation is coupled with Val , which is Met/Val heterozygous at codon 129 (Trenchant et al., 1997). Other experiments on peptides with Ala^sup 117^-->Val mutation have shown that the beta-sheet region tended to increase (Brown 2000). In the current work, focusing on the Ala^sup 117^-Val mutation, we tried to elucidate the correlation between Ala^sup 117^-->Val mutation and prion protein (PrP) structure using molecular dynamics (MD) and quantum chemical calculations. CONCLUSIONS
We provide the following conclusion from this study. Ala^sup 117^--> Val mutation deforms the structures of the globular domains on HuPrP and MoPrP. Especially in HuPrP containing Val 17, the extension of the P-sheet and the collapse of HI occur. PrPc containing Ala^sup 117^ tended to form a-helix in the extra peptide chain (109-124 in HuPrP and 109-123 in MoPrP). The extra peptide chain 119-122) containing Val^sup 117^ takes high electron distribution in some frontier molecular orbitals and had a high reactivity. These would be the driving force for the flexible motion of the N-terminal region of the mutant structure.
This work was supported by the super computer VPP700 in RIKEN. The computations were also carried out by the DRIA System at the Graduate School of Pharmaceutical Sciences, Chiba University.
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Noriaki Okimoto,* Kazunori Yamanaka,t Atsushi Suenaga,* Masayuki Hata,t and Tyuji Hoshinot
*Advanced Computing Center, Computational Science Division, Institute of Physical and Chemical Research (RIKEN), 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan; tGraduate School of Pharmaceutical Sciences, 1-33 Yayoi-cho, lnage-ku, Chiba University, Chiba 263-8522, Japan; and Computational Research Biology Center, 2-41-6 Ohme, Koutou-ku, Tokyo 135-0064, Japan
Address reprint requests to Noriaki Okimoto, Advanced Computing Center Computational Science Division, Institute of Physical and Chemical Research (RIKEN), 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan. Tel.: 81-48. 467-9417; Fax: 81-48-467-4078; E-mail: firstname.lastname@example.org.
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