Wu YiBing, Migliorini Molly, Walsh Joseph, Yu Ping, Strickland Dudley K, Wang Yun-Xing
Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702, USA.
J Biomol NMR. 2004 Jul;29(3):271-9. doi: 10.1023/B:JNMR.0000032507.96325.6d.
The 39 kDa receptor-associated protein (RAP) is an endoplasmic reticulum resident protein that binds tightly to the low-density lipoprotein receptor-related protein (LRP) as well as to other members of the low-density lipoprotein receptor superfamily. The association of RAP with LRP prevents this receptor from interacting with ligands. RAP is a three-domain protein that contains two independent LRP binding sites; one located within domains 1 and 2, and one located within domain 3. As the first step toward defining the structure of the full-length protein and understanding the interaction between RAP and this family of receptors, we have determined the 3D structure of domain 1 using constraints derived from heteronuclear multi-dimensional NMR spectra, including NOEs, dihedral angles, J-couplings and chemical shifts, as well as two sets of non-correlated residual dipolar couplings measured from the protein solutions in anisotropic media of Pf1 and 6% polyacrylamide gel. The backbone C(alpha) rmsd between the current structure and a homo-nuclear NOE-based structure is about 2 A. The large rmsd mainly reflects the significant differences in helical orientation and in the structural details of the long helix (helix 2) between the two structures.
39 kDa受体相关蛋白（RAP）是一种内质网驻留蛋白，它与低密度脂蛋白受体相关蛋白（LRP）以及低密度脂蛋白受体超家族的其他成员紧密结合。RAP与LRP的结合会阻止该受体与配体相互作用。RAP是一种三结构域蛋白，包含两个独立的LRP结合位点；一个位于结构域1和2内，另一个位于结构域3内。作为确定全长蛋白结构以及理解RAP与该受体家族之间相互作用的第一步，我们利用从异核多维核磁共振谱推导的约束条件，包括核Overhauser效应（NOE）、二面角、J耦合和化学位移，以及从Pf1和6%聚丙烯酰胺凝胶的各向异性介质中的蛋白质溶液测量的两组不相关的残余偶极耦合，确定了结构域1的三维结构。当前结构与基于同核NOE的结构之间的主链Cα均方根偏差约为2 Å。较大的均方根偏差主要反映了两种结构之间螺旋取向以及长螺旋（螺旋2）结构细节上的显著差异。
