Coupling between Catalytic Loop Motions and Enzyme Global Dynamics

Abstract

Catalytic loop motions facilitate substrate recognition and binding in many enzymes. While these motions appear to be highly flexible, their functional significance suggests that structure-encoded preferences may play a role in selecting particular mechanisms of motions. We performed an extensive study on a set of enzymes to assess whether the collective/global dynamics, as predicted by elastic network models (ENMs), facilitates or even defines the local motions undergone by functional loops. Our dataset includes a total of 117 crystal structures for ten enzymes of different sizes and oligomerization states. Each enzyme contains a specific functional/catalytic loop (10–21 residues long) that closes over the active site during catalysis. Principal component analysis (PCA) of the available crystal structures (including apo and ligand-bound forms) for each enzyme revealed the dominant conformational changes taking place in these loops upon substrate binding. These experimentally observed loop reconfigurations are shown to be predominantly driven by energetically favored modes of motion intrinsically accessible to the enzyme in the absence of its substrate. The analysis suggests that robust global modes cooperatively defined by the overall enzyme architecture also entail local components that assist in suitable opening/closure of the catalytic loop over the active site.

Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase

“…Only three residues located on the catalytic loop (P166 at the N-terminus, T175 and A176 at the C-terminus) show higher mobility in the complex. PCA reveals that in apo enzyme, counter-clockwise rotation -the dominant mode-drives the opening/closure of the catalytic loop, in conformity with our previous findings [8][9][10]. In contrast, this mode is suppressed in the complex and the bending of the subunits appears in the dominant PCs coupled to loop opening/closure.…”

“…Solid (lower) and dashed (upper) horizontal lines in Figure 2 refer to the I170-Y208 distances in the ligand-bound/closed (1TPH, smallest distance among the two chains) and apo/open (8TIM, largest distance) X-ray structures, respectively. In previous MD studies on apo TIM from chicken [7,9] and Trypanosoma cruzi [10], multiple opening/closure events of loop 6 have been observed during independent 60-100 ns runs. It is known that for effective catalysis this loop should stay closed so that the active site is shielded from solvent [1,2].…”

“…More recently, several studies have appeared that emphasize such coupling between energetically-favored global modes of motion and functional loop dynamics [10][11][12] for a larger set of proteins. Specifically, for a set of 10 enzymes with different sizes and oligomerization states, it has been shown through ENM that the experimentally determined catalytic loop (10-20 residue-long) reconfigurations are driven, at least to a certain extent, by collective modes of the intact enzyme in the apo state [10].…”

“…Specifically, for a set of 10 enzymes with different sizes and oligomerization states, it has been shown through ENM that the experimentally determined catalytic loop (10-20 residue-long) reconfigurations are driven, at least to a certain extent, by collective modes of the intact enzyme in the apo state [10]. It must be noted that ENM is a purely entropic model based on non-specific harmonic interactions between closely spaced residue pairs in the protein.…”

How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics

“…Previous computational studies, including both coarse-grained elastic network modeling (ENM) and classical MD simulations (9,10,(14)(15)(16)(17), have indicated that the loop dynamics are coupled with the global modes of TIM, which can be identified as counterrotation and bending of subunits. Similar coupling has been observed in other enzymes with functional loops (17), suggesting that the global modes of such enzymes enable or facilitate the functional loop motions.…”