Shuting Yan
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View article: Conformational Analysis and Structure-Altering Mutations of the HIV-1 Frameshifting Element
Conformational Analysis and Structure-Altering Mutations of the HIV-1 Frameshifting Element Open
Human immunodeficiency virus (HIV) continues to be a threat to public health. An emerging technique with promise in the context of fighting HIV type 1 (HIV-1) focuses on targeting ribosomal frameshifting. A crucial –1 programmed ribosomal …
View article: To Knot or Not to Knot: Multiple Conformations of the SARS-CoV‑2 Frameshifting RNA Element
To Knot or Not to Knot: Multiple Conformations of the SARS-CoV‑2 Frameshifting RNA Element Open
The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open R…
View article: A Cascade of Conformational Switches in SARS-CoV‑2 Frameshifting: Coregulation by Upstream and Downstream Elements
A Cascade of Conformational Switches in SARS-CoV‑2 Frameshifting: Coregulation by Upstream and Downstream Elements Open
Targeting ribosomal frameshifting has emerged as a potential therapeutic intervention strategy against COVID-19. In this process, a -1 shift in the ribosomal reading frame encodes alternative viral proteins. Any interference with this proc…
View article: A Cascade of Conformational Switches in SARS-CoV-2 Frameshifting: Coregulation by Upstream and Downstream Elements
A Cascade of Conformational Switches in SARS-CoV-2 Frameshifting: Coregulation by Upstream and Downstream Elements Open
Targeting ribosomal frameshifting has emerged as a potential therapeutic intervention strategy against COVID-19. In this process, a -1 shift in the ribosomal reading frame encodes alternative viral proteins. Any interference with this proc…
View article: Heterogeneous and multiple conformational transition pathways between pseudoknots of the SARS-CoV-2 frameshift element
Heterogeneous and multiple conformational transition pathways between pseudoknots of the SARS-CoV-2 frameshift element Open
Frameshifting is an essential mechanism employed by many viruses including coronaviruses to produce viral proteins from a compact RNA genome. It is facilitated by specific RNA folds in the frameshift element (FSE), which has emerged as an …
View article: Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: Implications to alternative conformations and their statistical structural analyses
Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: Implications to alternative conformations and their statistical structural analyses Open
The SARS-CoV-2 frameshifting element (FSE) has been intensely studied and explored as a therapeutic target for coronavirus diseases including COVID-19. Besides the intriguing virology, this small RNA is known to adopt many length-dependent…
View article: Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: implications to alternative conformations and their statistical structural analyses
Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: implications to alternative conformations and their statistical structural analyses Open
The SARS-CoV-2 frameshifting element (FSE) has been intensely studied and explored as a therapeutic target for coronavirus diseases, including COVID-19. Besides the intriguing virology, this small RNA is known to adopt many length-dependen…
View article: An intricate balancing act: Upstream and downstream frameshift co-regulatory elements
An intricate balancing act: Upstream and downstream frameshift co-regulatory elements Open
Targeting ribosomal frameshifting has emerged as a potential therapeutic intervention strategy against Covid-19. During ribosomal translation, a fraction of elongating ribosomes slips by one base in the 5 ′ direction and enters a new readi…
View article: Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: Implications to alternative conformations and their statistical structural analyses
Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: Implications to alternative conformations and their statistical structural analyses Open
The SARS-CoV-2 frameshifting element (FSE) has been intensely studied and explored as a therapeutic target for coronavirus diseases including COVID-19. Besides the intriguing virology, this small RNA is known to adopt many length-dependent…
View article: Evolution of coronavirus frameshifting elements: Competing stem networks explain conservation and variability
Evolution of coronavirus frameshifting elements: Competing stem networks explain conservation and variability Open
The frameshifting RNA element (FSE) in coronaviruses (CoVs) regulates the programmed −1 ribosomal frameshift (−1 PRF) mechanism common to many viruses. The FSE is of particular interest as a promising drug candidate. Its associated pseudok…
View article: Evolutionarily distinct and sperm-specific supersized chromatin loops are marked by Helitron transposons in Xenopus tropicalis
Evolutionarily distinct and sperm-specific supersized chromatin loops are marked by Helitron transposons in Xenopus tropicalis Open
Transposable elements (TEs) are abundant in metazoan genomes and have multifaceted effects on host fitness. However, the mechanisms underlying the functions of TEs are still not fully understood. Here, we combine Hi-C, ATAC-seq, and ChIP-s…
View article: Computational Modeling of RNA Aptamers: Structure Prediction of the Apo State
Computational Modeling of RNA Aptamers: Structure Prediction of the Apo State Open
RNA aptamers are single-stranded oligonucleotides that bind to specific molecular targets with high affinity and specificity. To design aptamers for new applications, it is critical to understand the ligand binding mechanism in terms of th…
View article: Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression
Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression Open
The SARS-CoV-2 frameshifting element (FSE), a highly conserved mRNA region required for correct translation of viral polyproteins, defines an excellent therapeutic target against Covid-19. As discovered by our prior graph-theory analysis w…
View article: Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression
Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression Open
Supplementary dataset for manuscript "Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression"
View article: Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression
Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression Open
Supplementary dataset for manuscript "Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression"
View article: Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression
Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression Open
Conserved SARS-CoV-2 RNA regions of critical biological functions define excellent targets for anti-viral therapeutics against Covid-19 variants. One such region is the frameshifting element (FSE), responsible for correct translation of vi…
View article: To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element
To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element Open
The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open R…
View article: To Knot\nor Not to Knot: Multiple Conformations of\nthe SARS-CoV‑2 Frameshifting RNA Element
To Knot\nor Not to Knot: Multiple Conformations of\nthe SARS-CoV‑2 Frameshifting RNA Element Open
The SARS-CoV-2 frameshifting RNA\nelement (FSE) is an excellent\ntarget for therapeutic intervention against Covid-19. This small gene\nelement employs a shifting mechanism to pause and backtrack the ribosome\nduring translation between Op…
View article: Adjusting COVID-19 seroprevalence survey results to account for test sensitivity and specificity
Adjusting COVID-19 seroprevalence survey results to account for test sensitivity and specificity Open
Population-based seroprevalence surveys can provide useful estimates of the number of individuals previously infected with SARS-CoV-2 and still susceptible as well as contribute to better estimates of the case fatality rate and other measu…
View article: Structure-Altering Mutations of the SARS-CoV-2 Frame Shifting RNA Element
Structure-Altering Mutations of the SARS-CoV-2 Frame Shifting RNA Element Open
With the rapid rate of Covid-19 infections and deaths, treatments and cures besides hand washing, social distancing, masks, isolation, and quarantines are urgently needed. The treatments and vaccines rely on the basic biophysics of the com…
View article: Sampling Performance of Multiple Independent Molecular Dynamics Simulations of an RNA Aptamer
Sampling Performance of Multiple Independent Molecular Dynamics Simulations of an RNA Aptamer Open
Using multiple independent simulations instead of one long simulation has been shown to improve the sampling performance attained with the molecular dynamics (MD) simulation method. However, it is generally not known how long each independ…
View article: Common Secondary and Tertiary Structural Features of Aptamer–Ligand Interaction Shared by RNA Aptamers with Different Primary Sequences
Common Secondary and Tertiary Structural Features of Aptamer–Ligand Interaction Shared by RNA Aptamers with Different Primary Sequences Open
Aptamer selection can yield many oligonucleotides with different sequences and affinities for the target molecule. Here, we have combined computational and experimental approaches to understand if aptamers with different sequences but the …
View article: Approaches for studying RNA aptamers with molecular dynamics simulation
Approaches for studying RNA aptamers with molecular dynamics simulation Open
The objective of this dissertation is to study RNA aptamers with molecular dynamics simulation. It addresses fundamental challenges associated with RNA aptamers that can be investigated via molecular dynamics simulation, including the unav…