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)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
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)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
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)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
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)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
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)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 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)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
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)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

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