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The proposed assembly pathway for bacteriophage MS2 capsid. Higher-order capsid intermediates are formed by the alternating 1:1 association of asymmetric-symmetric dimers. Threefold rings and fivefold rings form independently, with an RNA-bound asymmetric dimer acting as the nucleation site of capsid assembly. Crescent and horseshoe conformations are two possible intermediates that arise during the formation of the fivefold ring structure. In the full T = 3 capsid, five threefold rings converge at one fivefold ring.
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Understanding the mechanisms by which single-stranded RNA viruses regulate capsid assembly around their RNA genomes has become increasingly important for the development of both antiviral treatments and drug delivery systems. In this study, we investigate the effects of RNA-induced allostery in a single-stranded RNA virus—Levivirus bacteriophage MS...
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Context 1
... are several higher-order structures proposed for the assembly pathway of the bacteriophage MS2 capsid (Fig. 4). Although detecting protein complex intermediates can be challenging due to their short lifespan, two significant intermediates, namely the threefold and fivefold rings, have been identified on the MS2 capsid assembly pathway via mass spectrometry [40][41][42]. While crescent and horseshoe structures have not been experimentally ...
Context 2
... the analysis of MS2 capsid with its cognate RNA, we used coarse-grained models comprised of alpha carbons (CA) for the viral coat protein, and the phosphate/ribose sugar backbone atoms (P, C, and O) for the RNA-hairpin, ignoring the nitrogenous bases to avoid any sequence-specific interactions. For a comparison of coarsegrained RNA models, see Fig. ...
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Withdrawal Statement
The authors have withdrawn their manuscript owing to a conflict of interest. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author, Soumendranath Bhakat.
Citations
... Among these, allosteric regulation [1][2][3] is particularly notable for its ability to modulate the activity of one site on a molecule in response to changes at another, often distant, site [4,5]. This non-local influence is fundamental to processes such as enzyme activation [6][7][8][9], assembly [10][11][12][13][14][15] and signalling [16][17][18], where precise control over interactions is crucial for maintaining functionality. Due to its ubiquitous presence in biological systems, allosteric regulation has also proved an important consideration in disease and drug development [19][20][21][22]. ...
Allosteric effects, where interactions at one part of a complex affect interactions at another part, offer a high degree of control in multi-species processes. These interactions play a crucial role in many natural biological contexts and have also been utilised in artificial nanotechnology systems. Leveraging allosteric principles in synthetic systems holds great potential for designing materials and systems that can autonomously adapt, reconfigure or replicate. In this work, using a simple allosteric model, we design systems to exhibit four different complex behaviours: shape-shifting, fibre growth, sorting and self-replication. As well as showing the design of each behaviour we also calculate and measure key length and time scales, in order to verify that the systems evolve according to the pathways we have developed. Our findings demonstrate that with minimal interaction rules, allosteric systems can be engineered to achieve sophisticated emergent behaviours, opening new avenues for the design of responsive and adaptive materials.
A newly uncovered mechanism for the assembly of viral protein shells could help scientists develop antiviral treatments and drug-delivery systems.
