Potluri Shobha, Yan Anthony K, Chou James J, Donald Bruce R, Bailey-Kellogg Chris
Department of Computer Science, Dartmouth College, Hanover, New Hampshire 03755, USA.
Proteins. 2006 Oct 1;65(1):203-19. doi: 10.1002/prot.21091.
Structural studies of symmetric homo-oligomers provide mechanistic insights into their roles in essential biological processes, including cell signaling and cellular regulation. This paper presents a novel algorithm for homo-oligomeric structure determination, given the subunit structure, that is both complete, in that it evaluates all possible conformations, and data-driven, in that it evaluates conformations separately for consistency with experimental data and for quality of packing. Completeness ensures that the algorithm does not miss the native conformation, and being data-driven enables it to assess the structural precision possible from data alone. Our algorithm performs a branch-and-bound search in the symmetry configuration space, the space of symmetry axis parameters (positions and orientations) defining all possible C(n) homo-oligomeric complexes for a given subunit structure. It eliminates those symmetry axes inconsistent with intersubunit nuclear Overhauser effect (NOE) distance restraints and then identifies conformations representing any consistent, well-packed structure to within a user-defined similarity level. For the human phospholamban pentamer in dodecylphosphocholine micelles, using the structure of one subunit determined from a subset of the experimental NMR data, our algorithm identifies a diverse set of complex structures consistent with the nine intersubunit NOE restraints. The distribution of determined structures provides an objective characterization of structural uncertainty: backbone RMSD to the previously determined structure ranges from 1.07 to 8.85 A, and variance in backbone atomic coordinates is an average of 12.32 A(2). Incorporating vdW packing reduces structural diversity to a maximum backbone RMSD of 6.24 A and an average backbone variance of 6.80 A(2). By comparing data consistency and packing quality under different assumptions of oligomeric number, our algorithm identifies the pentamer as the most likely oligomeric state of phospholamban, demonstrating that it is possible to determine the oligomeric number directly from NMR data. Additional tests on a number of homo-oligomers, from dimer to heptamer, similarly demonstrate the power of our method to provide unbiased determination and evaluation of homo-oligomeric complex structures.
对称同型寡聚体的结构研究为其在细胞信号传导和细胞调控等基本生物学过程中的作用提供了机制性见解。本文提出了一种给定亚基结构来确定同型寡聚体结构的新算法，该算法既完整，因为它评估所有可能的构象，又由数据驱动，因为它分别评估构象以与实验数据保持一致并考虑堆积质量。完整性确保算法不会错过天然构象，而由数据驱动则使其能够仅根据数据评估可能的结构精度。我们的算法在对称配置空间中进行分支定界搜索，对称配置空间是定义给定亚基结构所有可能的C(n)同型寡聚体复合物的对称轴参数（位置和方向）空间。它消除那些与亚基间核Overhauser效应（NOE）距离限制不一致的对称轴，然后识别出在用户定义的相似性水平内代表任何一致且堆积良好结构的构象。对于十二烷基磷酸胆碱胶束中的人磷酸受磷蛋白五聚体，使用从实验NMR数据子集中确定的一个亚基的结构，我们的算法识别出一组与九个亚基间NOE限制一致的不同复杂结构。所确定结构的分布提供了结构不确定性的客观表征：相对于先前确定结构的主链RMSD范围为1.07至8.85 Å，主链原子坐标的方差平均为12.32 Ų。纳入范德华堆积将结构多样性降低到最大主链RMSD为6.24 Å，平均主链方差为6.80 Ų。通过在不同寡聚体数量假设下比较数据一致性和堆积质量，我们的算法将五聚体识别为磷酸受磷蛋白最可能的寡聚状态，表明可以直接从NMR数据确定寡聚体数量。对从二聚体到七聚体的多种同型寡聚体的额外测试同样证明了我们的方法在无偏确定和评估同型寡聚体复合物结构方面的能力。
