No abstract

Inactive rhodopsin can absorb photons, which induces different structural transitions that finally activate rhodopsin. We have examined the change in spatial configurations and physicochemical factors that result during the transition mechanism from the inactive to the active rhodopsin state via intermediates. During the activation process, many existing atomic contacts are disrupted, and new ones are formed. This is related to the movement of Helix 5, which tilts away from Helix 3 in the intermediate state in lumirhodopsin and moves closer to Helix 3 again in the active state. Similar patterns of changing atomic contacts are observed between Helices 3 and 5 of the adenosine and neurotensin receptors. In addition, residues 220–238 of rhodopsin, which are disordered in the inactive state, fold in the active state before binding to the Gα, where it catalyzes GDP/GTP exchange on the Gα subunit. Finally, molecular dynamics simulations in the membrane environment revealed that the arrestin binding region adopts a more flexible extended conformation upon phosphorylation, likely promoting arrestin binding and inactivation. In summary, our results provide additional structural understanding of specific rhodopsin activation which might be relevant to other Class A G protein‐coupled receptor proteins.

No abstract

The 14-3-3ζ protein acts as a molecular switch in regulating the TGF-β pathway, which alters from a tumor suppressor in the early stage of breast cancer to a promoter of metastasis in the late stage. This change is due to the binding of 14-3-3ζ with YAP1 and β-TRCP in premalignant and cancer cells, respectively. Owing to this inappropriate role of 14-3-3ζ when involved in cancer and metastasis, we predicted that Gln15, Glu17, Tyr211, and Gln219 are hotspot residues of 14-3-3ζ during its interaction with YAP1 protein. Similarly, we identified Gln15, Tyr211, Leu216, and Leu220 as hotspot residues of 14-3-3ζ during its interaction with β-TRCP protein. Targeting these residues of 14-3-3ζ can prevent cancer and metastasis caused by malfunctioning of the TGF-β pathway. In this work, we also predicted that YAP1 is an intrinsically disordered protein (IDP), and such proteins bind with other proteins via either an induced fit or a conformational selection mechanism. Intuitively, we found that 14-3-3ζ has high affinity towards phosphorylated YAP1 at Ser127 rather than unphosphorylated YAP1, which is in close agreement with previously reported experimental works. Thus, we performed an analysis by molecular dynamics simulations to reveal the conformational changes in YAP1 after phosphorylation at the atomistic level. Our work clearly illustrates the effect of phosphorylation on YAP1 in terms of conformational changes and the regulation of its function.

Drugs targeting transcriptional cofactors (TcoFs) function well in mouse models but fail to replicate their efficacy in human beings. Thus, we performed a comparative study on the TcoFs of humans and mice to find the similarity and dissimilarity between them. We observed high similarity in protein sequence and interacting domains between humans and mice. At the same time, dissimilarity was gradually increased in terms of interacting motifs, post-translational modifications, and molecular switches. Indeed, some of the post-translational modifications and molecular switches present in human beings are preferentially exempted in mice. Thus, structure-specific drugs designed to target TcoFs are functional in mice but fail in human beings, because the absence of some molecular switches in mice offers a particular conformation on the interacting motifs, which might facilitate drug binding. But in humans, owing to the presence of molecular switches, drug binding is not possible. From molecular dynamics simulation analysis, we inferred 8 different molecular switches on 3 proteins and found that 5 molecular switches influenced structural change in interacting motifs and revealed the reason for the functioning of drug in mice but not in human beings. From protein interaction network analysis, we find that a few interacting partners in mice are exempted in humans, and in both the cases the interacting partners are high when the domains are highly structured and the interacting partners are low when the domains are highly disordered. Hence, we are sure that our investigations will provide a promising support in future for designing drugs with high translational efficiency from mice models to human clinical trials.