scholarly journals Mechanistic insight into light-dependent recognition of Timeless by Drosophila cryptochrome

2021 ◽  
Author(s):  
Changfan Lin ◽  
Connor M. Schneps ◽  
Siddarth Chandrasekaran ◽  
Abir Ganguly ◽  
Brian R. Crane

SUMMARYCryptochrome (CRY) entrains the fly circadian clock by binding to Timeless (TIM) in light and triggering its degradation. Undocking of a helical C-terminal tail (CTT) in response to photoreduction of the CRY flavin cofactor gates TIM binding. A generally-applicable Select Western-blot-Free Tagged-protein Interaction (SWFTI) assay enables quantification of CRY binding to TIM in dark and light. The assay is utilized to study CRY variants with residue substitutions in the flavin pocket and correlate their TIM affinities with CTT undocking, as measured by pulse-dipolar ESR spectroscopy and evaluated by molecular dynamics simulations. CRY variants with the CTT removed or undocked bind TIM constitutively, whereas those incapable of photoreduction bind TIM weakly. In response to flavin redox state, two conserved histidine residues contribute to a robust on/off switch by mediating CTT interactions with the flavin pocket and TIM. Our approach provides an expeditious means to quantify protein-protein interactions and photoreceptor targeting.

2021 ◽  
Vol 17 (5) ◽  
pp. e1008988
Author(s):  
Nikolina ŠoŠtarić ◽  
Vera van Noort

Post-translational modifications (PTMs) play a vital, yet often overlooked role in the living cells through modulation of protein properties, such as localization and affinity towards their interactors, thereby enabling quick adaptation to changing environmental conditions. We have previously benchmarked a computational framework for the prediction of PTMs’ effects on the stability of protein-protein interactions, which has molecular dynamics simulations followed by free energy calculations at its core. In the present work, we apply this framework to publicly available data on Saccharomyces cerevisiae protein structures and PTM sites, identified in both normal and stress conditions. We predict proteome-wide effects of acetylations and phosphorylations on protein-protein interactions and find that acetylations more frequently have locally stabilizing roles in protein interactions, while the opposite is true for phosphorylations. However, the overall impact of PTMs on protein-protein interactions is more complex than a simple sum of local changes caused by the introduction of PTMs and adds to our understanding of PTM cross-talk. We further use the obtained data to calculate the conformational changes brought about by PTMs. Finally, conservation of the analyzed PTM residues in orthologues shows that some predictions for yeast proteins will be mirrored to other organisms, including human. This work, therefore, contributes to our overall understanding of the modulation of the cellular protein interaction networks in yeast and beyond.


ACS Catalysis ◽  
2020 ◽  
Vol 10 (15) ◽  
pp. 8904-8915 ◽  
Author(s):  
Stefan A. F. Nastase ◽  
Pieter Cnudde ◽  
Louis Vanduyfhuys ◽  
Kristof De Wispelaere ◽  
Veronique Van Speybroeck ◽  
...  

2016 ◽  
Vol 12 (4) ◽  
pp. 1378-1387 ◽  
Author(s):  
Meng-Chen Lu ◽  
Zhen-Wei Yuan ◽  
Yong-Lin Jiang ◽  
Zhi-Yun Chen ◽  
Qi-Dong You ◽  
...  

Protein–protein interactions (PPIs) as drug targets have been gaining growing interest, though developing drug-like small molecule PPI inhibitors remains challenging.


2020 ◽  
Vol 44 (45) ◽  
pp. 19450-19458
Author(s):  
Samima Khatun ◽  
Anamika Sindhu ◽  
Pannuru Venkatesu

Binding of stem bromelain to bovine serum albumin induced conformational changes, as shown by various biophysical techniques.


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