RNA fragment assembly with experimental restraints

Chojnowski, Grzegorz; Zaborowski, Rafał; Magnus, Marcin; Bujnicki, Janusz

doi:10.1101/2021.02.08.430198

Cited by 8 publications

(4 citation statements)

References 32 publications

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“…Hence, high-resolution experiments are complemented with computational models. For example, computational approaches were used to refine 3D RNA reconstructions with additional restraints on tertiary contacts given by SAXS experiments [153,148]. Furthermore, based on chemical probing and CryoEM, it was possible to reconstruct the frameshift stimulating element from SARS-CoV-2 all the way down to atomistic resolution [24].…”

Section: Discussion and Prospective Methodsmentioning

confidence: 99%

RNA multiscale simulations as an interplay of electrostatic, mechanical properties, and structures inside viruses

Cruz-León

Assenza

Poblete

et al. 2023

Preprint

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Multiscale simulations have broadened our understanding of RNA structure and function. Various methodologies have enabled the quantification of electrostatic and mechanical interactions of RNA at the nanometer scale. Atom-by-atom simulations, coarse-grained strategies, and continuum models of RNA and its environment provide physical insight and allow to interpret diverse experiments in a systematic way. In this chapter, we present and discuss recent advances in a set of methods to study nucleic acids at different scales. In particular, we introduce details of their parameterization, recent applications, and current limitations. We discuss the interaction of the proteinacous virus capsid, RNA with substrates, compare the properties of RNA and DNA and their interaction with the environment, and analyze the application of these methods to reconstruct the structure of the virus genome structure. Finally, the last lines are dedicated to future developments and challenges ahead.

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Section: Discussion and Prospective Methodsmentioning

confidence: 99%

RNA multiscale simulations as an interplay of electrostatic, mechanical properties, and structures inside viruses

Cruz-León

Assenza

Poblete

et al. 2023

Preprint

View full text Add to dashboard Cite

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“…Nonetheless, many subdomains of such encapsidated RNA lie within the ’dynamic structures’, which are commonly difficult to efficiently sample by pure experiments. Hence, the field appeals to computational models, which have been used, for example, to refine 3D RNA reconstructions with additional restraints on tertiary contacts given by SAXS experiments [ 51 ], or the reconstruction of the frameshift stimulating element from SARS-CoV-2 all the way down to atomistic resolution. Such studies were based on chemical probing and CryoEM [ 52 ].…”

Section: Discussionmentioning

confidence: 99%

Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models

Poblete

Guzman

2021

Viruses

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Three-dimensional RNA domain reconstruction is important for the assembly, disassembly and delivery functionalities of a packed proteinaceus capsid. However, to date, the self-association of RNA molecules is still an open problem. Recent chemical probing reports provide, with high reliability, the secondary structure of diverse RNA ensembles, such as those of viral genomes. Here, we present a method for reconstructing the complete 3D structure of RNA genomes, which combines a coarse-grained model with a subdomain composition scheme to obtain the entire genome inside proteinaceus capsids based on secondary structures from experimental techniques. Despite the amount of sampling involved in the folded and also unfolded RNA molecules, advanced microscope techniques can provide points of anchoring, which enhance our model to include interactions between capsid pentamers and RNA subdomains. To test our method, we tackle the satellite tobacco mosaic virus (STMV) genome, which has been widely studied by both experimental and computational communities. We provide not only a methodology to structurally analyze the tertiary conformations of the RNA genome inside capsids, but a flexible platform that allows the easy implementation of features/descriptors coming from both theoretical and experimental approaches.

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“…We next refined secondary structure-based models of the RNAs including SAXS data as a restraint for the overall geometry and base pairing with RNAmasonry 52 . For SL2+3, we found the stem-loops in an atomic model would only fulfill experimental SAXS data in a non-coupled arrangement (Fig.…”

Section: Particular Structural/functional Features Of the Sl2+3 And S...mentioning

confidence: 99%

The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5’-genomic RNA elements

Korn

Dhamotharan

Schlundt

2022

Preprint

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The nucleocapsid protein (N) of SARS-CoV-2 plays a pivotal role during the viral life cycle. It is involved in RNA transcription and accounts for packaging of the large genome into virus particles. N manages the enigmatic balance of bulk RNA-coating versus precise RNA-binding to designated cis-regulatory elements. Numerous studies report the involvement of its disordered segments in non-selective RNA-recognition, but how N organizes the inevitable recognition of specific motifs remains unanswered. We here use NMR spectroscopy to systematically analyze the interactions of N’s N-terminal RNA-binding domain (NTD) with individual cis RNA elements clustering in the SARS-CoV-2 regulatory 5’-genomic end. Supported by broad solution-based biophysical data, we unravel the NTD RNA-binding preferences in the natural genome context. We show that the domain uses a set of flexible sensory residues to read the intrinsic signature of preferred RNA elements for selective and stable complex formation within the large pool of available motifs.

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RNA fragment assembly with experimental restraints

Cited by 8 publications

References 32 publications

RNA multiscale simulations as an interplay of electrostatic, mechanical properties, and structures inside viruses

RNA multiscale simulations as an interplay of electrostatic, mechanical properties, and structures inside viruses

Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models

The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5’-genomic RNA elements

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