Ruoyi Qiu

Works (8)

Updated: July 5th, 2023 15:45

2021 journal article

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

CELL REPORTS PHYSICAL SCIENCE, 2(11).

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

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 journal article

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

NATURE METHODS, 15(9), 669-+.

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

MeSH headings : Fluorescence Resonance Energy Transfer / methods; Laboratories / standards; Reproducibility of Results
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 journal article

MutL traps MutS at a DNA mismatch

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112(35), 10914–10919.

By: R. Qiu n, M. Sakato*, E. Sacho n, H. Wilkins*, X. Zhang*, P. Modrichd, 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
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 journal 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

BIOCHEMISTRY, 53(10), 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
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 journal article

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

BIOCHEMISTRY, 53(12), 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
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 journal article

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

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE, 1842(2), 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
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 journal article

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

EMBO JOURNAL, 31(11), 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
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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7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

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