Structural dynamics

AID/APOBECs and many other DNA/RNA-editing enzymes are challenging to obtain as a pure, crystalized or soluble compound, making 3D structure resolution using crystallography and NMR analyses challenging. We have been tackling the problem of these enzymes’ structures using a novel “computational-biochemical-evolutionary” research pipeline which complements the standard methods of structure elucidation. This method combines computational mod eling with rigorous testing of model predictions by generating and assaying a library of hundreds of variants (mutants, orthologs and chimeras). Using this method, we provided the first insights into the native/functional/dynamic structure of AID in 2015. We discovered that AID’s catalytic pocket shifts between open and closed conformations and ~70% of the conformations exhibit a closed pocket that is unable to mutate. The discovery that the pocket can open and close itself is a novel concept in DNA/RNA -modifying enzymes-. We called this novel dynamic state the “Schrodinger’s CATalytic pocket” as homage to the pioneering quantum physics concept of dual states. This discovery was the first demonstration that a tremendous level of regulation is built into movem ent of the monomeric AID/APOBECs structure. More recent crystallographic and NMR structural analysis by multiple groups have confirmed the structure and the pocket duality. The combined computational-biochemical-evolutionary methodology integrates pocket dynamics, functional information and “3D” results to provide insight into the relative time the enzyme spends in many possible active or inactive conformations and the relevance of this mobility to function, as well as its development in the evolutionary context. Having demonstrated the utility of this approach to AID’s structure, we apply the same method to other DNA/RNA-editing enzymes to map out their dynamic/functional structure.

Representative publications in this area:

  1. King JJ, Larijani M. Structural plasticity of substrate selection by activation-induced cytidine deaminase as a regulator of its genome-wide mutagenic activity. FEBS Letters. 2020. 2020 Oct 21. doi: 10.1002/1873-3468.13962
  2. King JJ, Larijani M. A novel regulator of AID/APOBECs: Schrödinger's CATalytic pocket, Frontiers Imm. 2017, Apr 6;8:351
  3. King JJ, Manuel CA, Barrett CV, Raber S, Lucas HM, Sutter P, Larijani M. Catalytic pocket inaccessibility of activation induced cytidine deaminases a safeguard against excessive mutagenic activity, Structure. 2015. Apr 7; 23(4):615-27
  4. Abdouni H, King J, Suliman Mw, Quinlan M, Fifield H, Larijani M. Zebrafish AID is capable of deaminating methylated deoxycytidines. Nucleic Acids Research. 2013.1; 41(10):5457-68