scholarly journals Clustering of Aromatic Residues in Prion-like Domains Can Tune the Formation, State, and Organization of Biomolecular Condensates

Biochemistry ◽  
2021 ◽  
Author(s):  
Alex S. Holehouse ◽  
Garrett M. Ginell ◽  
Daniel Griffith ◽  
Elvan Böke
Keyword(s):  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Youri Timsit ◽  
Grégoire Sergeant-Perthuis ◽  
Daniel Bennequin

AbstractTo perform an accurate protein synthesis, ribosomes accomplish complex tasks involving the long-range communication between its functional centres such as the peptidyl transfer centre, the tRNA bindings sites and the peptide exit tunnel. How information is transmitted between these sites remains one of the major challenges in current ribosome research. Many experimental studies have revealed that some r-proteins play essential roles in remote communication and the possible involvement of r-protein networks in these processes have been recently proposed. Our phylogenetic, structural and mathematical study reveals that of the three kingdom’s r-protein networks converged towards non-random graphs where r-proteins collectively coevolved to optimize interconnection between functional centres. The massive acquisition of conserved aromatic residues at the interfaces and along the extensions of the newly connected eukaryotic r-proteins also highlights that a strong selective pressure acts on their sequences probably for the formation of new allosteric pathways in the network.


2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Zhi-Yong Yan ◽  
Xiao-Jie Xu ◽  
Le Fang ◽  
Chao Geng ◽  
Yan-Ping Tian ◽  
...  

AbstractCoat protein (CP) is required for potyviruses to move and establish a systemic infection in plants. π-stackings formed by aromatic residues play critical roles in maintaining protein stability and functions. As we know, many aromatic residues located in the core region of potyvirus CPs are conserved. However, their roles in potyvirus infection remain largely unknown. Here, through analysis of the three-dimensional model of the tobacco vein banding mosaic virus (TVBMV; genus Potyvirus) CP, 16 aromatic residues were predicated to form π-stackings. The results of transient expression experiments demonstrated that deletion of any of these 16 aromatic residues reduced CP accumulation. Infectivity assays showed that deletion of any of these aromatic residues in the TVBMV infectious clone abolished cell-to-cell movement and reduced replication of the virus. Substitution of Y105 and Y147 individually with non-aromatic residues alanine or glycine reduced CP accumulation, virus replication, and abolished the ability of TVBMV to move intercellularly, while substitution of these two residues individually with aromatic residues phenylalanine or tryptophan, had no or little effect on CP accumulation and TVBMV systemic movement and replication. Similar results were obtained from the CP mutants of watermelon mosaic virus (WMV, genus Potyvirus). Taken together, our results demonstrate that multiple aromatic residues in CP are involved in potyvirus movement by forming π-stackings to maintain CP accumulation.


2021 ◽  
Vol 30 (5) ◽  
pp. 1022-1034
Author(s):  
Mikhail Makarov ◽  
Jingwei Meng ◽  
Vyacheslav Tretyachenko ◽  
Pavel Srb ◽  
Anna Březinová ◽  
...  

ChemPhysChem ◽  
2014 ◽  
Vol 15 (15) ◽  
pp. 3282-3290 ◽  
Author(s):  
Artur Nenov ◽  
Silvio a Beccara ◽  
Ivan Rivalta ◽  
Giulio Cerullo ◽  
Shaul Mukamel ◽  
...  

2013 ◽  
Vol 67 (7) ◽  
Author(s):  
Pavan GhattyVenkataKrishna ◽  
Neelima Chavali ◽  
Edward Uberbacher

AbstractThe presence of an unusually large number of aromatic residues in the active site gorge of acetylcholinesterase is a subject of great interest. Flexibility of these residues has been suspected to be a key player in controlling the ligand traversal in the gorge. This raises the question of whether the over-representation of aromatic residues in the gorge implies higher-than-normal flexibility of these residues. The current study suggests that it does not. Large changes in the hydrophobic cross-sectional area due to dihedral oscillations are probably the reason of their presence in the gorge.


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