scholarly journals Revealing −1 Programmed Ribosomal Frameshifting Mechanisms by Single-Molecule Techniques and Computational Methods

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Kai-Chun Chang
Keyword(s):  
Computational Modeling ◽  
Single Molecule ◽  
Thermodynamic Stability ◽  
Translational Regulation ◽  
Regulation Mechanism ◽  
Viral Mrnas ◽  
Single Molecule Force Spectroscopy ◽  
Ribosomal Frameshifting ◽  
Antiviral Therapies ◽  
The Relationship

Programmed ribosomal frameshifting (PRF) serves as an intrinsic translational regulation mechanism employed by some viruses to control the ratio between structural and enzymatic proteins. Most viral mRNAs which use PRF adapt an H-type pseudoknot to stimulate −1 PRF. The relationship between the thermodynamic stability and the frameshifting efficiency of pseudoknots has not been fully understood. Recently, single-molecule force spectroscopy has revealed that the frequency of −1 PRF correlates with the unwinding forces required for disrupting pseudoknots, and that some of the unwinding work dissipates irreversibly due to the torsional restraint of pseudoknots. Complementary to single-molecule techniques, computational modeling provides insights into global motions of the ribosome, whose structural transitions during frameshifting have not yet been elucidated in atomic detail. Taken together, recent advances in biophysical tools may help to develop antiviral therapies that target the ubiquitous −1 PRF mechanism among viruses.

scholarly journals Modeling the structure of the frameshift stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers

2020 ◽  
Author(s):  
Sara Ibrahim Omar ◽  
Meng Zhao ◽  
Rohith Vedhthaanth Sekar ◽  
Sahar Arbabi Moghadam ◽  
Jack A. Tuszynski ◽  
...  
Keyword(s):  
Single Molecule ◽  
Structural Models ◽  
Viral Proteins ◽  
Single Molecule Force Spectroscopy ◽  
Ribosomal Frameshifting ◽  
Structural Prediction ◽  
Prediction Tools ◽  
Dynamics Simulations ◽  
Rna Pseudoknot ◽  
Stem Structure

The coronavirus causing the COVID-19 pandemic, SARS-CoV-2, uses −1 programmed ribosomal frameshifting (−1 PRF) to control the relative expression of viral proteins. As modulating −1 PRF can inhibit viral replication, the RNA pseudoknot stimulating −1 PRF may be a fruitful target for therapeutics treating COVID-19. We modeled the unusual 3-stem structure of the stimulatory pseudoknot of SARS-CoV-2 computationally, using multiple blind structural prediction tools followed by μs-long molecular dynamics simulations. The results were compared for consistency with nuclease-protection assays and single-molecule force spectroscopy measurements of the SARS-CoV-1 pseudoknot, to determine the most likely conformations. We found several possible conformations for the SARS-CoV-2 pseudoknot, all having an extended stem 3 but with different packing of stems 1 and 2. Several conformations featured rarely-seen threading of a single strand through the junction formed between two helices. These structural models may help interpret future experiments and support efforts to discover ligands inhibiting −1 PRF in SARS-CoV-2.

scholarly journals Decoding the mechanical fingerprints of biomolecules

2015 ◽  
Vol 49 ◽  
Author(s):  
Olga K. Dudko
Keyword(s):  
Single Molecule ◽  
Conformational Transition ◽  
Conformational Transitions ◽  
Applied Force ◽  
Biological Macromolecules ◽  
Force Extension ◽  
Single Molecule Force Spectroscopy ◽  
Unifying Principles ◽  
The Relationship ◽  
Analytical Expressions

AbstractThe capacity of biological macromolecules to act as exceedingly sophisticated and highly efficient cellular machines – switches, assembly factors, pumps, or motors – is realized through their conformational transitions, that is, their folding into distinct shapes and selective binding to other molecules. Conformational transitions can be induced, monitored, and manipulated by pulling individual macromolecules apart with an applied force. Pulling experiments reveal, for a given biomolecule, the relationship between applied force and molecular extension. Distinct signatures in the force–extension relationship identify a given biomolecule and thus serve as the molecule's ‘mechanical fingerprints’. But, how can these fingerprints be decoded to uncover the energy barriers crossed by the molecule in the course of its conformational transition, as well as the associated timescales? This review summarizes a powerful class of approaches to interpreting single-molecule force spectroscopy measurements – namely, analytically tractable approaches. On the fundamental side, analytical theories have the power to reveal the unifying principles underneath the bewildering diversity of biomolecules and their behaviors. On the practical side, analytical expressions that result from these theories are particularly well suited for a direct fit to experimental data, yielding the important parameters that govern biological processes at the molecular level.

scholarly journals Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers

2021 ◽  
Vol 17 (1) ◽  
pp. e1008603
Author(s):  
Sara Ibrahim Omar ◽  
Meng Zhao ◽  
Rohith Vedhthaanth Sekar ◽  
Sahar Arbabi Moghadam ◽  
Jack A. Tuszynski ◽  
...  
Keyword(s):  
Single Molecule ◽  
Structural Models ◽  
Viral Proteins ◽  
Single Molecule Force Spectroscopy ◽  
Ribosomal Frameshifting ◽  
Structural Prediction ◽  
Prediction Tools ◽  
Dynamics Simulations ◽  
Rna Pseudoknot ◽  
Stem Structure

The coronavirus causing the COVID-19 pandemic, SARS-CoV-2, uses −1 programmed ribosomal frameshifting (−1 PRF) to control the relative expression of viral proteins. As modulating −1 PRF can inhibit viral replication, the RNA pseudoknot stimulating −1 PRF may be a fruitful target for therapeutics treating COVID-19. We modeled the unusual 3-stem structure of the stimulatory pseudoknot of SARS-CoV-2 computationally, using multiple blind structural prediction tools followed by μs-long molecular dynamics simulations. The results were compared for consistency with nuclease-protection assays and single-molecule force spectroscopy measurements of the SARS-CoV-1 pseudoknot, to determine the most likely conformations. We found several possible conformations for the SARS-CoV-2 pseudoknot, all having an extended stem 3 but with different packing of stems 1 and 2. Several conformations featured rarely-seen threading of a single strand through junctions formed between two helices. These structural models may help interpret future experiments and support efforts to discover ligands inhibiting −1 PRF in SARS-CoV-2.

scholarly journals Single Molecule Force Spectroscopy of Siloxanes

2021 ◽  
Vol 714 (3) ◽  
pp. 032023
Author(s):  
Ling Chen ◽  
Liya Yang ◽  
Chunxia Wang ◽  
Ting Zhu
Keyword(s):  
Single Molecule ◽  
Force Spectroscopy ◽  
Single Molecule Force Spectroscopy

CSF chitinase 3-like 1 is associated with iron rims in patients with a first demyelinating event

2021 ◽  
pp. 135245852110100
Author(s):  
Manuel Comabella ◽  
Margareta A Clarke ◽  
Sabine Schaedelin ◽  
Mar Tintoré ◽  
Deborah Pareto ◽  
...  
Keyword(s):  
Single Molecule ◽  
Multivariable Analysis ◽  
Enzyme Linked Immunosorbent Assay ◽  
Lesion Volume ◽  
Univariable Analysis ◽  
Neurofilament Light Chain ◽  
Neurofilament Light ◽  
Multivariable Analyses ◽  
Prognostic Implications ◽  
The Relationship

Background: Chronic active lesions with iron rims have prognostic implications in patients with multiple sclerosis. Objective: To assess the relationship between iron rims and levels of chitinase 3-like 1 (CHI3L1), neurofilament light chain (NfL) and glial fibrillary acidic protein (GFAP) in patients with a first demyelinating event. Methods: Iron rims were identified using 3T susceptibility-weighted imaging. Serum NfL and GFAP levels were measured by single-molecule array assays. CSF (cerebrospinal fluid) CHI3L1 levels were measured by enzyme-linked immunosorbent assay (ELISA). Results: Sixty-one patients were included in the study. The presence of iron rims was associated with higher T2 lesion volume and higher number of gadolinium-enhancing lesions. In univariable analysis, having ⩾2 iron rims (vs 0) was associated with increased CSF CHI3L1 levels (β = 1.41; 95% confidence interval (CI) = 1.10–1.79; p < 0.01) and serum NfL levels (β = 2.30; 95% CI = 1.47–3.60; p < 0.01). In multivariable analysis, however, only CSF CHI3L1 levels remained significantly associated with the presence of iron rim lesions (β = 1.45; 95% CI = 1.11–1.90; p < 0.01). The presence of ⩾2 iron rims was not associated with increased serum GFAP levels in univariable or multivariable analyses. Conclusion: These findings support an important contribution of activated microglia/macrophages to the pathophysiology of chronic active lesions with iron rims in patients with a first demyelinating event.

Pulling Genetic RNA out of Tobacco Mosaic Virus Using Single-Molecule Force Spectroscopy

2010 ◽  
Vol 132 (32) ◽  
pp. 11036-11038 ◽  
Author(s):  
Ningning Liu ◽  
Bo Peng ◽  
Yuan Lin ◽  
Zhaohui Su ◽  
Zhongwei Niu ◽  
...  
Keyword(s):  
Tobacco Mosaic Virus ◽  
Mosaic Virus ◽  
Single Molecule ◽  
Force Spectroscopy ◽  
Single Molecule Force Spectroscopy

The Nature of the Force-Induced Conformation Transition of dsDNA Studied by Using Single Molecule Force Spectroscopy

Langmuir ◽  
2010 ◽  
Vol 26 (12) ◽  
pp. 9491-9496 ◽  
Author(s):  
Ningning Liu ◽  
Tianjia Bu ◽  
Yu Song ◽  
Wei Zhang ◽  
Jinjing Li ◽  
...  
Keyword(s):  
Single Molecule ◽  
Force Spectroscopy ◽  
Single Molecule Force Spectroscopy ◽  
Conformation Transition
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