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DCI profiles for the unbound symmetric and bound asymmetric wildtype MS2 coat protein dimers. (a) DCI profile for the unbound symmetric dimer. The FG-loops are symmetrically coupled, where a perturbation at one end of the dimer produces a strong response at the other end. (b) DCI profile for the bound asymmetric dimer. The symmetric coupling of the two FG-loops is broken, such that FG-loop A now drives the communication to FG-loop B. All cartoon structures are colored with DCI for perturbations at residue 74 (shown as a sphere).
Source publication
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
... further investigate how the RNA-induced conformational change facilitates successful capsid assembly, we examined the DCI profiles of the wildtype unbound symmetric dimer and the wildtype bound asymmetric dimer, as shown in Fig. 3 (see Fig. S2 for DCI analysis of the mutant dimer). In the unbound symmetric dimer [ Fig. 3(a)], the FGloops and the binding interface are strongly coupled to each other. Conversely, in the bound asymmetric dimer [ Fig. 3(b)], while FG-loops A/B are still highly coupled to the binding interface, only FG-loop A (in the flexible conformation) is highly coupled to FG-loop B (in the rigid conformation). Hence, the RNA-induced ...
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... we examined the DCI profiles of the wildtype unbound symmetric dimer and the wildtype bound asymmetric dimer, as shown in Fig. 3 (see Fig. S2 for DCI analysis of the mutant dimer). In the unbound symmetric dimer [ Fig. 3(a)], the FGloops and the binding interface are strongly coupled to each other. Conversely, in the bound asymmetric dimer [ Fig. 3(b)], while FG-loops A/B are still highly coupled to the binding interface, only FG-loop A (in the flexible conformation) is highly coupled to FG-loop B (in the rigid conformation). Hence, the RNA-induced conformational change results in unidirectional asymmetric communication between the FGloops, which propagates from FG-loop A to FG-loop ...
Context 3
... Fig. 5(a)]. Additionally, for the threefold ring and the fivefold ring, perturbations at any of the three or five outer FG-loops, respectively, result in a strong response everywhere in the structure, reflecting their rotational symmetry (see Fig. S3). In contrast, perturbations at inner FG-loops, where interdimer contacts are fully saturated, do not propagate beyond their immediate neighbors, indicating a region of high stability at the center of the threefold and fivefold axes during ...
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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.
