The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts

Abstract

Protein motions play important roles in numerous biological processes such as enzyme catalysis, muscle contractions, antigen-antibody interactions, gene regulation and virus assembly. Knowledge of protein flexibility is also important in rational drug design, protein docking and protein engineering. However, the experimental measurement of protein motions is often difficult, requiring sophisticated experiments, complex data analysis and detailed information about the protein's tertiary structure. As a result, there is a considerable interest in developing simpler, more effective ways of quantifying protein flexibility. Recently, we described a method, called the random coil index (RCI), which is able to quantitatively estimate backbone root mean square fluctuations (RMSFs) of structural ensembles and order parameters using only chemical shifts. The RCI method is very fast (<5 s) and exceedingly robust. It also offers an excellent alternative to traditional methods of measuring protein flexibility. We have recently extended the RCI concept and implemented it as a web server. This server allows facile, accurate and fully automated predictions of MD RMSF values, NMR RMSF values and model-free order parameters (S2) directly from chemical shift assignments. It also performs automatic chemical shift re-referencing to ensure consistency and reproducibility. On average, the correlation between RCI predictions and experimentally obtained motional amplitudes is within the range from 0.77 to 0.82. The server is available at http://wishart.biology.ualberta.ca/rci.

Figure 1.

Sample screenshots of the RCI web server's input and output pages.

Figure 2.

A flow chart describing the RCI protocol.