New Concept on the Phase Space of the Protein : Experiments and Theory

我们使用高压NMR方法发现并结构表征了仓鼠朊病毒蛋白的折叠中间体（K.Kuwata，Biochemistry，2002），并将其命名为PrP^*。我们发现，在PrP^* 中，B-和C-螺旋优先无序，而A-螺旋保持完整。特别是位于与β折叠（S2）的界面处的残基是极其不稳定的。PrP^C到PrP^C的结构转换反应很可能是部分未折叠的PrP^* 参与<Sc>的。我们还利用电子显微镜、圆二色性、NMR和分子动力学模拟（KKuwata Proc.Natl.Acad.Sci，2003）阐明了PrP 106 -126（一种对应于朊病毒蛋白疏水簇的肽）的寡聚簇的三维结构。在仓鼠朊病毒中，使用CPMG弛豫分散法在微米至毫秒的时间尺度上交换的残基，一些对应于在高压NMR方法中表现出低稳定性的那些（Kuwata等人，Biochemistry，2004）。此外，这些不稳定残基的分布与致病突变相关。因此，这些残基可能是导致PrPC构象转变为PrP^的主要原因<Sc>。

We found and structurally characterized the folding intermediate of hamster prion protein using high-pressure NMR method (K.Kuwata, Biochemistry, 2002) and designated it as PrP^*. We found that in PrP^*, B-and C-helices are preferentially disordered, while A-helix remains intact. Especially residues locate at the interface with the beta sheet (S2) are extremely unstable. It is highly possible that partially unfolded PrP^* is involved in the structural conversion reaction from PrP^C to PrP^<Sc>.We also clarified the three dimensional structure of oligomeric duster of PrP106-126, a peptide corresponding to the hydrophobic cluster of prion protein, using electron microscopy, circular dichroism, NMR and molecular dynamics simulation (K Kuwata Proc.Natl.Acad.Sci, 2003). The oligomeric conformation of PrP106-126 dusterwas stabilized by the hydrophobic interaction between methyl moieties.In hamster prion, residues exchanging on a time scale of micro-to milliseconds using CPMG relaxation dispersion method some what correspond to those exhibit low stability in high-pressure NMR method (Kuwata et al., Biochemistry, 2004). Moreover the distribution of those unstable residues is correlated with those involved in the causative mutation. Thus these residues may be responsible for the conformational conversion from PrPC to PrP^<Sc>.Furthermore we formulated a novel mathematical representation of the protein dynamics using the number theoretical description.