Ruoyi Qiu

Works (8)

Updated: July 5th, 2023 15:45

2021 article

Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25

Saikia, N., Yanez-Orozco, I. S., Qiu, R., Hao, P., Milikisiyants, S., Ou, E., … Ding, F. (2021, October 19). Cell Reports Physical Science, Vol. 11.

By: N. Saikia *, I. Yanez-Orozco*, R. Qiu n, P. Hao n, S. Milikisiyants n, E. Ou n, G. Hamilton *, K. Weninger n  ...

topics (OpenAlex): Protein Structure and Dynamics; Advanced Fluorescence Microscopy Techniques; Photosynthetic Processes and Mechanisms
TL;DR: An integrative method is reported to probe the structural dynamics of SNAP-25 by combining replica-exchange discrete molecular dynamics simulations and label-based experiments at ensemble and single-molecule levels and it is expected that this integrative approach may help further the understanding of IDPs. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: March 14, 2022

2018 article

Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study

Hellenkamp, B., Schmid, S., Doroshenko, O., Opanasyuk, O., Kühnemuth, R., Adariani, S. R., … Hugel, T. (2018, August 24). Nature Methods, Vol. 15, p. 669-.

By: B. Hellenkamp *, S. Schmid *, O. Doroshenko*, O. Opanasyuk *, R. Kühnemuth*, S. Adariani *, B. Ambrose *, M. Aznauryan * ...

MeSH headings : Fluorescence Resonance Energy Transfer / methods; Laboratories / standards; Reproducibility of Results
topics (OpenAlex): Advanced Fluorescence Microscopy Techniques; DNA and Nucleic Acid Chemistry; Advanced biosensing and bioanalysis techniques
TL;DR: A multi-laboratory study finds that single-molecule FRET is a reproducible and reliable approach for determining accurate distances in dye-labeled DNA duplexes. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: October 19, 2018

2016 journal article

Single-molecule FRET to measure conformational dynamics of DNA mismatch repair proteins

Single-Molecule Enzymology: Fluorescence-Based and High-Throughput Methods, 581, 285–315.

By: J. Gauer, S. LeBlanc, P. Hao, R. Qiu, B. Case, M. Sakato, M. Hingorani, D. Erie, K. Weninger 

Source: NC State University Libraries
Added: August 6, 2018

2015 article

MutL traps MutS at a DNA mismatch

Qiu, R., Sakato, M., Sacho, E. J., Wilkins, H., Zhang, X., Modrich, P., … Weninger, K. R. (2015, August 17). Proceedings of the National Academy of Sciences, Vol. 112, pp. 10914–10919.

By: R. Qiu n, M. Sakato*, E. Sacho n, H. Wilkins*, X. Zhang*, P. Modrich *, M. Hingorani *, D. Erie *, K. Weninger n 

author keywords: DNA mismatch repair; MutS; MutL; FRET
MeSH headings : Bacterial Proteins / genetics; Base Pair Mismatch; Genes, Bacterial; Thermus / genetics
topics (OpenAlex): Genetic factors in colorectal cancer; RNA Research and Splicing; RNA and protein synthesis mechanisms
TL;DR: It is discovered that MutL fundamentally changes the properties of mismatch-bound MutS by preventing it from sliding away from the mismatch, which it normally does when isolated, and suggests a mechanism for localizing the activity of repair proteins near the mismatch. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2014 article

Cancer/Testis Antigen PAGE4, a Regulator of c-Jun Transactivation, Is Phosphorylated by Homeodomain-Interacting Protein Kinase 1, a Component of the Stress-Response Pathway

Mooney, S. M., Qiu, R., Kim, J. J., Sacho, E. J., Rajagopalan, K., Johng, D., … Weninger, K. R. (2014, February 23). Biochemistry, Vol. 53, pp. 1670–1679.

By: S. Mooney *, R. Qiu n, J. Kim *, E. Sacho n, K. Rajagopalan *, D. Johng, T. Shiraishi*, P. Kulkarni, K. Weninger n 

MeSH headings : Amino Acid Motifs; Antigens, Neoplasm / chemistry; Antigens, Neoplasm / genetics; Antigens, Neoplasm / metabolism; Cell Line, Tumor; Humans; Male; Phosphorylation; Prostatic Neoplasms / enzymology; Prostatic Neoplasms / genetics; Prostatic Neoplasms / metabolism; Prostatic Neoplasms / physiopathology; Protein Binding; Protein Serine-Threonine Kinases / genetics; Protein Serine-Threonine Kinases / metabolism; Proto-Oncogene Proteins c-jun / genetics; Proto-Oncogene Proteins c-jun / metabolism; Signal Transduction; Stress, Physiological; Testis / metabolism; Transcriptional Activation
topics (OpenAlex): Sperm and Testicular Function; Immunotherapy and Immune Responses; Prostate Cancer Treatment and Research
TL;DR: The present results clearly implicate PAGE4 as a component of the stress-response pathway and uncover a novel link between components of this pathway and prostatic development and disease. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2014 article

Dynamics of MutS–Mismatched DNA Complexes Are Predictive of Their Repair Phenotypes

DeRocco, V. C., Sass, L. E., Qiu, R., Weninger, K. R., & Erie, D. A. (2014, March 4). Biochemistry, Vol. 53, pp. 2043–2052.

By: V. DeRocco, L. Sass, R. Qiu n, K. Weninger n  & D. Erie

MeSH headings : Bacterial Proteins / chemistry; Bacterial Proteins / genetics; DNA Repair / genetics; Fluorescence Resonance Energy Transfer; INDEL Mutation; MutS DNA Mismatch-Binding Protein / chemistry; MutS DNA Mismatch-Binding Protein / genetics; Phenotype; Predictive Value of Tests; Signal Transduction / genetics; Thermus / enzymology; Thermus / genetics
topics (OpenAlex): DNA Repair Mechanisms; Genetic factors in colorectal cancer; Cancer Genomics and Diagnostics
TL;DR: Comparison of MutS and MutS-E41A dynamics on GT and the T-bulge suggests that hydrogen bonding to MutS facilitates the changes in base–base hydrogen bonding that are required to achieve the U state, which has been implicated in repair signaling. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2013 article

The Stress-response protein prostate-associated gene 4, interacts with c-Jun and potentiates its transactivation

Rajagopalan, K., Qiu, R. Y., Mooney, S. M., Rao, S., Shiraishi, T., Sacho, E., … al. (2013, November 21). Biochimica Et Biophysica Acta (BBA) - Molecular Basis of Disease, Vol. 1842, pp. 154–163.

By: K. Rajagopalan *, R. Qiu n, S. Mooney *, S. Rao*, T. Shiraishi*, E. Sacho n, H. Huang*, E. Shapiro* ...

author keywords: PAGE4; Cancer/Testis Antigen; c-Jun; smFRET; Prostate cancer; Intrinsically disordered protein
MeSH headings : 3' Untranslated Regions / genetics; Antigens, Neoplasm / chemistry; Antigens, Neoplasm / genetics; Antigens, Neoplasm / metabolism; Cell Line, Tumor; Cyclin-Dependent Kinase Inhibitor p27 / genetics; Cyclin-Dependent Kinase Inhibitor p27 / metabolism; Fluorescence Resonance Energy Transfer; Gene Expression Regulation, Neoplastic; Humans; Immunohistochemistry; Male; MicroRNAs / genetics; MicroRNAs / metabolism; Mutation; Prostate / embryology; Prostate / growth & development; Prostate / metabolism; Prostatic Neoplasms / genetics; Prostatic Neoplasms / metabolism; Prostatic Neoplasms / pathology; Protein Binding; Protein Conformation; Proto-Oncogene Mas; Proto-Oncogene Proteins c-jun / genetics; Proto-Oncogene Proteins c-jun / metabolism; Reverse Transcriptase Polymerase Chain Reaction; Stress, Physiological; Transcriptional Activation
topics (OpenAlex): Prostate Cancer Treatment and Research; Ubiquitin and proteasome pathways; Immunotherapy and Immune Responses
TL;DR: PAGE4 specifically interacts with c-Jun and that, conformational dynamics may account for its observed pleiotropic functions, the first report demonstrating crosstalk between a CTA and a proto-oncogene. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2012 article

Large conformational changes in MutS during DNA scanning, mismatch recognition and repair signalling

Qiu, R., DeRocco, V. C., Harris, C., Sharma, A., Hingorani, M. M., Erie, D. A., & Weninger, K. R. (2012, April 13). The EMBO Journal, Vol. 31, pp. 2528–2540.

By: R. Qiu n, V. DeRocco*, C. Harris*, A. Sharma*, M. Hingorani *, D. Erie *, K. Weninger n 

author keywords: DNA mismatch repair; MMR; MutS; protein conformational change; sliding clamp
MeSH headings : Adenosine Diphosphate / chemistry; Adenosine Triphosphate / chemistry; DNA Mismatch Repair / genetics; DNA Mismatch Repair / physiology; Fluorescence Resonance Energy Transfer; MutS DNA Mismatch-Binding Protein / chemistry; MutS DNA Mismatch-Binding Protein / genetics; MutS DNA Mismatch-Binding Protein / metabolism; Protein Conformation
topics (OpenAlex): Genetic factors in colorectal cancer; DNA Repair Mechanisms; RNA and protein synthesis mechanisms
TL;DR: It is found that the DNA‐binding domains of MutS dynamically interconvert among multiple conformations when the protein is free and while it scans homoduplex DNA. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

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