Determining and visualizing flexibility in protein structures

作者：Scott Walter R P; Straus Suzana K^*

来源：Proteins: Structure, Function, and Genetics , 2015, 83(5): 820-826.

DOI：10.1002/prot.24776

• protein structure
• protein dynamics
• protein mobility
• protein structure comparison
• geometric algebra

How to compare the structures of an ensemble of protein conformations is a fundamental problem in structural biology. As has been previously observed, the widely used RMSD measure due to Kabsch, in which a rigid-body superposition minimizing the least-squares positional deviations is performed, has its drawbacks when comparing and visualizing a set of flexible protein structures. Here, we develop a method, fleximatch, of protein structure comparison that takes flexibility into account. Based on a distance matrix measure of flexibility, a weighted superposition of distance matrices rather than of atomic coordinates is performed. Subsequently, this allows a consistent determination of (a) a superposition of structures for visualization, (b) a partitioning of the protein structure into rigid molecular components (core atoms), and (c) an atomic mobility measure. The method is suitable for highlighting both particularly flexible and rigid parts of a protein from structures derived from NMR, X-ray diffraction or molecular simulation. Proteins 2015; 83:820-826.

• 出版日期2015-5