Long-Range Changes in Neurolysin Dynamics Upon Inhibitor Binding

Abstract

Crystal structures of neurolysin, a zinc metallopeptidase, do not show a significant conformational change upon the binding of an allosteric inhibitor. Neurolysin has a deep channel where it hydrolyzes a short neuropeptide neurotensin to create inactive fragments and thus controls its level in the tissue. Neurolysin is of interest as a therapeutic target since changes in neurotensin level have been implicated in cardiovascular disorders, neurological disorders, and cancer, and inhibitors of neurolysin have been developed. An understanding of the dynamical and structural differences between apo and inhibitor-bound neurolysin will aid in further design of potent inhibitors and activators. For this purpose, we performed several molecular dynamics (MD) simulations for both apo and inhibitor-bound neurolysin. A machine learning method (Linear Discriminant Analysis) is applied to reveal differences between the apo and inhibitor-bound ensembles in an automated way, and large differences are observed on residues that are far from both the active site and the inhibitor binding site. The effects of inhibitor binding on the collective motions of neurolysin are extensively analyzed and compared using both Principal Component Analysis and Elastic Network Model calculations. We find that inhibitor binding induces additional low-frequency motions that are not observed in the apo form. ENM also reveals changes in inter- and intradomain communication upon binding. Furthermore, differences are observed in the inhibitor-bound neurolysin contact network that are far from the active site, revealing long-range allosteric behavior. This study also provides insight into the allosteric modulation of other neuropeptidases with similar folds.

Tuning the “violin” of protein kinases: The role of dynamics‐based allostery

“…Recently, our violin model has been used to understand dynamics‐based allostery in protein families other than kinases. Examples include exploration of red light–sensing bacteriophytochromes associated with cyclic dimeric guanosine monophosphate–producing diguanylyl cyclases and the zinc metallopeptidase neurolysin .…”

Perturbation of ACE2 Structural Ensembles by SARS-CoV-2 Spike Protein Binding

“…LDA yields a classification vector—analogous to collective variables in principal component analysis—that results in the largest differences between the classes, while maintaining small differences within the classes. 51 , 52 This has been recently used to analyze molecular simulations, 33 , 53 including to determine collective variables for enhanced sampling simulations. 54 , 55 As there are only two classes during training here (“apo” and “complex”), the analysis yields only one LDA vector.…”

“…The extracellular domain of ACE2 is homologous to other metallo-peptidases such as ACE, 30 carboxypeptidase Pfu, 31 and neurolysin, 32 which all share the characteristic “clam shell” structure. Neurolysin dynamics were studied in detail in our previous work 33 using MD simulations and the linear discriminant analysis (LDA) machine learning method. Our findings compared contact networks of the apo neurolysin and neurolysin bound to an allosteric inhibitor and pinpointed several differences that were far from the inhibitor-binding site, which suggests long-range allosteric behavior in metallo-peptidases.…”

Identification and Characterization of Two Structurally Related Dipeptides that Enhance Catalytic Efficiency of Neurolysin

“…The search for a modulatory site was carried out in the hinge region because crystal structures of both Nln and ACE2 demonstrate that catalysis is accompanied by large hinge-bending motions (Brown et al, 2001;Towler et al, 2004). The hinge region in both peptidases can affect the distance between the two structural domains and by that modulate substrate binding and catalysis (Ray et al, 2004;Towler et al, 2004;Uyar et al, 2018). Several surface pockets with adequate solvent accessible volumes (DSSP (Kabsch and Sander, 1983) and castP (Dundas et al, 2006)) were identified in the hinge region of Nln.…”