LassoProt: server to analyze biopolymers with lassos

Abstract

The LassoProt server, http://lassoprot.cent.uw.edu.pl/, enables analysis of biopolymers with entangled configurations called lassos. The server offers various ways of visualizing lasso configurations, as well as their time trajectories, with all the results and plots downloadable. Broad spectrum of applications makes LassoProt a useful tool for biologists, biophysicists, chemists, polymer physicists and mathematicians. The server and our methods have been validated on the whole PDB, and the results constitute the database of proteins with complex lassos, supported with basic biological data. This database can serve as a source of information about protein geometry and entanglement-function correlations, as a reference set in protein modeling, and for many other purposes.

Figure 1.

The number of lasso structures deposited in the PDB over years. The first occurrence of a given lasso type is shown by an arrow. Note that the complexity of discovered structures grows with time. The schemes represent lasso types L₁, L₂, L₃, LS₂, LL and LS₃ (from left to right), which are characterized in the text.

Figure 2.

The main panel presenting detected lasso structures (supercoiling LS₂, two sided LL_{1, 1}) in protein with cysteine bridges.

Figure 3.

Comparison between (A) visualization of a smoothed protein and (B) visualization in VMD of the same protein.

Figure 4.

A sample trajectory output. The charts present L₀ → L_+2N → L_−1N → L₀ process shown schematically in the bottom. The top plot presents changes in lasso type. The bottom plot shows changes of crossing residue indices, with R_gyr dependence for comparison (orange plot). For each frame an additional information is displayed upon pointing the cursor in an appropriate position (small gray frames). Each frame can be analyzed in detail upon entering its number.