Department of Biomathematical Sciences, Mount Sinai School of Medicine, Box 1023, One Gustave L. Levy Place, New York, NY 10029, USA
1 To whom correspondence should be addressed at: Department of Molecular Biosciences, 2034 Haworth Hall, 1200 Sunnyside Avenue, The University of Kansas, Lawrence, KS 66045, USA. e-mail: igor{at}ku.edu
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Abstract |
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Keywords: alignment/conformational transition/Doppel/sequence profile
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Introduction |
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The cellular form of the prion protein is a GPI-anchored outer-membrane glycoprotein that undergoes rapid endocytosis (Lehmann et al., 1999). A number of NMR and X-ray studies aimed to detect the structure of PrPC have revealed that the C-terminal domain of the protein is structured, whereas the N-terminal domain, which contains Gly- and Pro-rich octarepeats, is highly flexible and cannot be assigned a particular conformation (Riek et al., 1998
). Recently, a paralog of the prion protein, PrP-Doppel, was identified (Mo et al., 2001
). This protein and the C-terminal domain of PrP share
25% sequence identity and have very similar structures which consist of three
-helices (A, B and C) and a short ß-sheet. However, despite its structural similarity to PrP, Doppel does not undergo a structural transition into a ß-sheet-rich conformation (Nicholson et al., 2002
).
Little is known about the pathogenic conformation of the prion protein, PrPSc, except for its approximate secondary structure content, protease resistance and the insolubility of some forms (Prusiner et al., 1998). Owing to the insolubility of PrPSc, characterization of its structure by NMR or X-ray crystallography has been problematic. A number of attempts to model the structure of PrPSc using spectroscopic and electron crystallography data have been undertaken (Huang et al., 1995
; Wille et al., 2003
). Improvement of the quality of such knowledge-based models, and progress in determining the structure of PrPSc, can be achieved by using information derived from proteins that share a weak but significant sequence similarity with PrP. The structural properties of such proteins, especially if they adopt a mainly-ß fold, may be used to gain insight into the conformation of PrPSc. Sequence profiles obtained from a multiple sequence alignment of related proteins represent one of the most sensitive methods used to detect structural similarity between proteins with a low degree of sequence identity (Gribskov and Veretnik, 1996
). Our aim here is to use sequence profiles to identify proteins that share a significant sequence similarity with the structured C-terminal domain of the prion protein.
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Methods and results |
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The random scores were fitted to the extreme value distribution using the STATISTICA software package (Statistica version 6.0; StatSoft, Inc., 2300 East 14 St., Tulsa, OK 74104, USA), giving a = 20.5557 and b = 2.971 (Equation 1). The profile alignment score for UL9 is 53.17, and the probability of observing a score of this magnitude or larger in the sequences with the same amino acid composition and length as those of UL9 obtained using Equation 1 is very low, P(S 53.17) = 1.7x105. Therefore, we conclude that the observed sequence similarity between UL9 and prion protein is highly significant. The local alignment between UL9 and the prion protein profile comprises residues 67172 of UL9 and is shown in Figure 1A. Pairwise local alignment of chicken PrP and UL9 shows that the best alignment comprises residues 80130 of UL9, and helices A and B of PrP (Figure 1B). It should be noted that the loop connecting helices A and B is thought to participate in binding the hypothetical PrP ligand, protein X, which may be involved in conformational transition (Kaneko et al., 1997
).
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We used the mGenThreader fold recognition server (McGuffin and Jones, 2003), which has been shown to have the lowest rate of false positive predictions among all automated fold recognition servers (Bujnicki et al., 2001
), to make predictions for UL9 protein. It should be noted that all highest scoring templates (E-value from 0.03 to 0.06) belong to mainly-ß proteins involved in substrate binding: immunoglobulin antigen-binding domains (PDB i.d. 8fab, 12e8, 1a3l, 32c2, 1igt) and T-cell receptors (PDB i.d. 1tcr, 1hxm, 1bec). A different fold recognition method, SAM_T02 (Karplus et al., 2001
), also assigns highest scoring hits for UL9 to immunoglobulin antigen-binding domains and T-cell receptors. The same two methods do not find any significant matches for the C-terminal domain of the prion protein, except for the match between PrP and Doppel. The evidence of a putative mainly-ß fold of the UL9 protein and its sequence similarity with the prion protein, which undergoes a conformational transition into mainly-ß conformation, identify UL9 as a potential target for experimental structure determination aimed at obtaining a template for modeling the structure of PrPSc. Further progress in structural and functional annotation of UL9 may help understand the function of PrP and what type of substrate it binds.
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Acknowledgements |
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References |
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Received September 2, 2003; accepted September 12, 2003