Study of the conformational dynamics of prolyl oligopeptidase

Abstract

Prolyl oligopeptidase (POP) is an 81-KDa bidomain enzyme which hydrolyses short proline-containing peptides. This enzyme is involved in mnemonic and cognitive processes, and the dysregulation of POP activity is related to mental diseases. Probably, POP modulates the phosphoinositide signalling pathway through protein-protein interactions (PPI). Hence, the development of POP inhibitors is an area of great interest for the treatment of cognitive deficits associated with mental and neurodegenerative diseases. Recently, it has been found that the administration of POP inhibitors increases the clearance of a-synuclein aggregates in vivo, indicating that POP can be related to some extend with the pathogenic conditions of Parkinson’s disease (PD). Probably, this increase in the a-synuclein catabolism might be a consequence of a direct interaction between the two proteins. For this reason, POP inhibitors might be drug candidates for the preventive treatment of PD. Although the X-ray structure of POP is well studied, it is not clear which are the conformational fluctuations responsible for the circulation of substrates and products during the catalytic cycle. Several studies suggest that loops surrounding the active site are involved in a gating mechanism, while others postulate that interdomain separation might expose the active site. Moreover, such conformational transitions might be essential for the recognition events of POP. The elucidation of the conformational landscape of POP is a challenging task due to the high molecular weight of the enzyme.

In this PhD thesis we have used a combination of robust biophysical tools (in particular, NMR and SAXS) together with molecular dynamics simulations (MD) in order to decipher the conformational dynamics of POP in solution. In addition, POP was also analysed by ion mobility mass spectrometry, an emerging biophysical tool in structural biology. Finally, we performed preliminary studies of the interaction between POP and a-synuclein by NMR.

The results obtained in this PhD thesis demonstrated that POP exists in solution in a slow conformational exchange between open and closed conformations. The conformational transitions involved the periodic separation of the two domains in a hinge-type motion. Relaxation dispersion experiments showed that this long range conformational transition was better described by several independent motions of different amplitudes, stressing the highly dynamic behaviour of POP. Moreover, the analysis of SAXS data complemented by MD simulations found that the interdomain separation caused the inactive arrangement of the active site. This suggests that the separation between domains might be critical for substrate recruitment and product release. Of interest, inhibitors caused the total displacement of this equilibrium towards the stabilized closed conformation, therefore quenching dynamics and the catalytic activity.

The study of the interaction between POP and a-synuclein by NMR disclosed that both proteins might be involved in a weak and transient interaction. Of interest, this interaction showed more affinity in the case of POP bound to inhibitors. In this case, interaction specially affected a broad segment of the C-terminal region of a-synuclein. This result suggested that the recognition between the two proteins depends on the conformational state of POP. Therefore, modulating the conformational landscape of POP by inhibitors might control this interaction. In summary, the results obtained in this PhD thesis demonstrated that POP undergo slow exchange between open and closed conformations in solution, and found that inhibitors have deep effects in the native conformational landscape of POP. Of interest, these conformational transitions might be essential for regulating the PPI necessary for the biological function of POP. Hence, the in vivo effects of POP inhibitors might result as a consequence of the alterations in the recognition events of POP.

La prolil oligopeptidasa (POP) es un enzim de 81 KDa que hidrolitza pèptids curts amb contingut en prolina. La POP actua en el sistema nerviós central mitjançant interaccions proteïna-proteïna (IPP), i la seva funció biològica està relacionada amb la memòria i els processos cognitius. Per aquesta raó, els inhibidors de la POP són compostos d’interès terapèutic per al tractament dels dèficits cognitius. Recentment, s’ha descobert que els inhibidors de la POP poden prevenir la patogènesis de la malaltia de Pàrkinson, probablement a través d’una interacció directa entre la POP i l’a-sinucleïna (la principal proteïna causant dels processos neurodegeneratius de la malaltia de Parkinson). Tot i que l’estructura cristal·logràfica de la POP està ben definida, no es sap quines són les transicions conformacionals que permeten completar el cicle catalític de la POP. Probablement, aquesta riquesa conformacional també té un paper rellevant en el control de les IPP. Malauradament, l’estudi conformacional complet de la POP és tot un repte degut al seu elevat pes molecular.

En aquesta tesis doctoral s’ha emprat una combinació de tècniques biofísiques avançades (en concret, la resonància magnètica nuclear, la dispersió de raigs X de baix angle, i l’espectrometria de masses de mobilitat iònica) conjuntament amb simulacions de dinàmica molecular, per tal d’analitzar la dinàmica conformacional de la POP en solució. A més, s’ha estudiat la possible interacció entre la POP i l’a-sinucleïna mitjançant experiments de RMN.

Els resultats obtinguts en aquesta tesi doctoral han demostrat que la POP es troba en solució en un equilibri conformacional lent entre conformacions obertes i tancades, originades a partir de la separació entre dos dominis. Els inhibidors de la POP causen una gran estabilització de la conformació tancada, amb la qual cosa l’equilibri dinàmic es desplaça totalment cap a aquesta conformació. A més, es va poder detectar una interacció dèbil i transitòria entre la POP i l’a-sinucleïna, que esdevenia especialment afavorida en la presència d’inhibidors. Així, els nostres resultats suggereixen que la diversitat conformacional de la POP es necessària per a la seva funció, i que els inhibidors poden desencadenar la seva funció biològica desplaçant l’equilibri conformacional.