Abstract
Odorant-binding proteins (OBPs) play a pivotal role in transporting odorants through the sensillar lymph of insect chemosensory sensilla and increasing the sensitivity of the olfactory system. To address the ligand binding, activation, and release mechanisms of OBPs, we performed a set of conventional molecular dynamics simulations for binding of the odorant-binding protein DhelOBP21 from Dastarcus helophoroides with 18 ligands (1-NPN and 17 volatiles), as well as four constant-pH molecular dynamics simulations. We found that the open pocket DhelOBP21 at pH 5.0 could bind volatiles and form a closed pocket complex via transformation of its N-terminus into regular Helix at pH 7.0 and vice versa. Moreover, the discrimination of volatiles (selectivity and promiscuity) was determined by the characteristics of both the volatiles and the ‘essential’ and ‘selective’ amino acid residues in OBP binding pockets, rather than the binding affinity of the volatiles. This study put forward a new hypothesis that during the binding of volatiles there are two transitions for the DhelOBP21 amino-terminus: pH- and odorant binding-dependent random-coil-to-helix. Another important finding is providing a framework for the exploration of the complete coil-to-helix transition process and theoretically analyzing its underlying causes at molecular level.
Highlights
The same mechanisms have been proposed based on the structures of several Odorant-binding proteins (OBPs) with a long C-terminus, e.g., ApolPBP from Antheraea Polyphemus[10] and AtraPBP1 from Amyelois transitella[21]
The basis of the complex sensory system that discriminates thousands of volatile substances at low concentrations[25] remains a big challenge. To address these issues and gain more insight into the odorant binding mechanism, here we conducted all-atom conventional molecular dynamics (CMD) simulations for the binding of 18 ligands to DhelOBP21, an OBP characterized by our group from Dastarcus helophoroides, which is the most important natural enemy of the forest pest Monochamus alternatus[26]
According to the Root-mean-square Deviations (RMSDs) plots of protein main chain in all the 19 systems (Fig. S1), it was apparent that DhelOBP21 underwent remarkable conformational shifts ranging from 3 and 6 Å at the beginning of the simulation, mostly in the first 40 ns, eliminating the spatial conflicts
Summary
The same mechanisms have been proposed based on the structures of several OBPs with a long C-terminus, e.g., ApolPBP from Antheraea Polyphemus[10] and AtraPBP1 from Amyelois transitella[21]. The basis of the complex sensory system that discriminates thousands of volatile substances at low concentrations[25] remains a big challenge. To address these issues and gain more insight into the odorant binding mechanism, here we conducted all-atom conventional molecular dynamics (CMD) simulations for the binding of 18 ligands to DhelOBP21, an OBP characterized by our group from Dastarcus helophoroides, which is the most important natural enemy of the forest pest Monochamus alternatus[26]. The results showed that the N-terminus underwent a random coil-to-helix transition during binding We hypothesized that both pH and odorant binding might contribute to this secondary structural transition.
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