journal menu
![[Figure 2]](qr5005fig2mag.jpg)
|
|
Figure 2
Protein dynamics for (a) a Keap1 Kelch domain–peptide complex (left panel; PDB entry 2flu) and (b) a Keap1–small-molecule complex (left panel; PDB entry 4iqk); ligand dynamics for the systems are shown in the right panels and a movie of the Keap1–small-molecule complex is provided as supporting information. (c) The SARS-CoV-2 nsp13 helicase protein modelled from the SARS-CoV-1 structure (PDB entry 4jyt) is shown in the left (top view) and right (side view) panels. Each of the images shows dynamics sampled every 10 ns from 1 µs trajectories. Protein structures are shown in a cartoon representation, coloured by secondary structure, and the ligands (left and centre) are shown in liquorice representation, coloured by atom name, and indicated with arrows. Images were created using VMD. Over femtosecond to picosecond timescales, the main motion is atomic bond vibrations and local side-chain rearrangements. Over longer (nanosecond to microsecond) timescales, the protein and ligand undergo large-scale, overdamped, global motions around a free-energy minimum. Proteins have complex free-energy landscapes containing multiple minima, which give rise to different conformational states which may be functionally relevant. Over extended (microsecond to millisecond) timescales, the protein will diffuse between these conformations. Over even longer timescales, the ligand will repeatedly bind and unbind from the pocket. |
![[Figure 2]](qr5005fig2.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
Open 
access
access
