[PyMOL] Morphing NMR structures

Solution NMR determines protein structures showing both static and dynamic features. The secondary structural elements and tertiary structure of protein are commonly stable though the loop and termini are often dynamic. Therefore, NMR spectroscopists determine protein structure, collect 10-20 lowest energy profiled coordinates/structures and put them together as one ensemble.

However, in the downloaded PDB coordinate file, the NMR structure ensemble is not shown as multiple conformers by default. In PDB, the NMR ensemble is presented as “states” and PyMOL automatically opens and displays the first state.

To view all states in one time, one should click "A (action)" --> "states" --> "all states". Please see example figure below.

Alternatively, type "set all_states, on" in the command panel to turn on the display function.

The image above is an example that I display protein GB1 (PDB ID: 1GB1). The protein is colored in “rainbow” gradient with cartoon (as a tube) mode. The sidechains are shown in sticks to present the inconsistent sidechain rotamers, especially some long sidechains such as Ile, Leu, Lys and Arg.

It is not easy to sense the conformational dynamics for a new comer and PyMOL’s morphing plugin provides an excellent solution to present how protein moves in solution. To make a morphing movie objecy, go to PyMOL toolbar, click “Plugin”, then “Morphing”.

At here, I turned off the “all states”, by switching back to “freeze”. Then use “morphing” window to show the protein dynamics of GB1 in cartoon mode. The overall shape and size of GB1 are unchanged. The helix and strands of GB1 are stable but not constantly located at same spacial position all through the 60 conformers. The slightly changes of helix and strands present how a protein behaves in solution
–> it moves around all the time.

On the other hand, I change the cartoon mode from “automatic” to “tube” by typing “cartoon tube”. Then display sticks and sphere of sidechains. Rescale the sphere from 1.0 to 0.3 (set sphere_scale, 0.3). Generate the second morphing movie of protein GB1. Several long sidechains of GB1 residues are changing through the 60 conformers. This is an easy way to present concept of protein dynamics for students in my lectures.

A more complicated case is a 82-kDa protein named malate synthase G. This protein has been studied using NMR spectroscopy and its solution structures have been determined by NMR or combined method. I used MSG NMR structure PDB ID 1Y8B (10 conformers in the ensemble) to generate a morphing movie from the first to the last (10th) structure in 1Y8B. MSG is shown in cartoon mode. In this movie, parts of MSG moves round randomly and frequently, in particular several loops displace dramatically. The overall shape doesn’t change vividly. The same morphing movie can be done for conformational change upon binding.