Conformational Transitions in Protein-Protein Association: Binding of Fasciculin-2 to Acetylcholinesterase

Abstract

The neurotoxin fasciculin-2 (FAS2) is a picomolar inhibitor of synaptic acetylcholinesterase (AChE). The dynamics of binding between FAS2 and AChE is influenced by conformational fluctuations both before and after protein encounter. Submicrosecond molecular dynamics trajectories of apo forms of fasciculin, corresponding to different conformational substates, are reported here with reference to the conformational changes of loop I of this three-fingered toxin. This highly flexible loop exhibits an ensemble of conformations within each substate corresponding to its functions. The high energy barrier found between the two major substates leads to transitions that are slow on the timescale of the diffusional encounter of noninteracting FAS2 and AChE. The more stable of the two apo substates may not be the one observed in the complex with AChE. It seems likely that the more stable apo form binds rapidly to AChE and conformational readjustments then occur in the resulting encounter complex.

Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism

“…2, conformations in FAS2a states have lower energy than those in FAS2b states. It is of interest to note that FAS2a is a stable and predominant state in solution, consistent with the previous study (9). The energy barrier between the two states is remarkably high.…”

“…Interestingly, all TMD trajectories appear to sample conformations with q Ϸ8-10 Å more frequently. A careful analysis of an average structure of snapshots with q in a range of 9-10 Å shows that the FAS2:T9 side chain no longer packs against the hydrophobic pocket, as other hydrophobic residues such as AChE:V73 compete for the pocket (9,11,12). AChE:P78 at the tip of the long omega loop (AChE:C69-C96) also moves toward the hydrophobic pocket from a distance of Ϸ10 Å (measuring from the AChE:P78CG and FAS2:A12CA) to Ϸ5 Å for the FAS2a͞AChE and FAS2b͞AChE conformations, respectively (see Fig.…”

“…Two major conformational states of FAS2 were identified in the previous MD simulations (9), namely unbound and liganded forms. Ten snapshots of each submicrosecond MD trajectory of apo-FAS2a and apo-FAS2b were chosen as reference structures for TMD simulations (9). That study also showed that the encounter complex of FAS2a͞AChE is reasonably stable, relative to the separated proteins.…”

Molecular dynamics simulations of the conformational changes in signal transducers and activators of transcription, Stat1 and Stat3

“…k-mean clustering algorithm has been used to identify the structural representations of conformation families that are most populated during MD simulations [27,28]. This analysis would offer insight into the nature of the large-scale conformational changes, if any in Stat3 and Stat1 dimers.…”

“…This analysis would offer insight into the nature of the large-scale conformational changes, if any in Stat3 and Stat1 dimers. With the projections of MD snapshots onto the essential space [29], we calculated the distribution of the conformer density in the essential space, r, and the corresponding molecular potential given by [28] E ¼ ÀRT lnðrÞ (2) where R is the gas constant and T is temperature. The adaptation of k-means clustering algorithm available in ''Weka'' [30] was applied to projections of MD snapshots in the essential space to identify the conformation clusters.…”