Pengyu Hao

Works (8)

Updated: July 5th, 2023 21:21

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

2021 article

Structure, dynamics, and regulation of TRF1-TIN2-mediated trans- and cis-interactions on telomeric DNA

Pan, H., Kaur, P., Barnes, R., Detwiler, A. C., Sanford, S. L., Liu, M., … Wang, H. (2021, August 14). Journal of Biological Chemistry, Vol. 9.

By: H. Pan n, P. Kaur n, R. Barnes *, A. Detwiler *, S. Sanford *, M. Liu  n, P. Xu n, C. Mahn n ...

MeSH headings : Cell Adhesion Molecules / metabolism; Cell Adhesion Molecules / physiology; DNA / metabolism; DNA-Binding Proteins / metabolism; Humans; Microscopy, Atomic Force / methods; Models, Molecular; Multiprotein Complexes / metabolism; Protein Binding; Protein Isoforms / metabolism; Shelterin Complex / metabolism; Shelterin Complex / physiology; Telomere / metabolism; Telomere-Binding Proteins / metabolism; Telomere-Binding Proteins / physiology; Telomeric Repeat Binding Protein 1 / metabolism; Telomeric Repeat Binding Protein 1 / physiology; Telomeric Repeat Binding Protein 2 / metabolism; Telomeric Repeat Binding Protein 2 / physiology
topics (OpenAlex): Telomeres, Telomerase, and Senescence; DNA Repair Mechanisms; Genomics and Chromatin Dynamics
TL;DR: Analysis of DNA molecular structures promoted by TRF1-TIN2 interaction supports a molecular model in which protein assemblies at telomeres are heterogeneous with distinct subcomplexes and full shelterin complexes playing distinct roles in telomere protection and elongation. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: October 26, 2021

2020 article

Dynamic human MutSα–MutLα complexes compact mismatched DNA

Bradford, K. C., Wilkins, H., Hao, P., Li, Z. M., Wang, B., Burke, D., … Erie, D. A. (2020, June 25). Proceedings of the National Academy of Sciences, Vol. 117, pp. 16302–16312.

By: K. Bradford *, H. Wilkins*, P. Hao n, Z. Li *, B. Wang *, D. Burke*, D. Wu *, A. Smith * ...

author keywords: DNA repair; AFM; MutS; MutL; DREEM
MeSH headings : Adenosine Triphosphate / metabolism; DNA / chemistry; DNA / genetics; DNA / metabolism; DNA Mismatch Repair; DNA-Binding Proteins / chemistry; DNA-Binding Proteins / metabolism; Humans; Multiprotein Complexes / metabolism; MutL Proteins / chemistry; MutL Proteins / metabolism; MutS Homolog 2 Protein / chemistry; MutS Homolog 2 Protein / metabolism; Nucleic Acid Conformation; Nucleosomes / metabolism; Protein Folding; Protein Multimerization
topics (OpenAlex): Genetic factors in colorectal cancer; Cancer Genomics and Diagnostics; RNA and protein synthesis mechanisms
TL;DR: Atomic force microscopy is utilized coupled with other methods to reveal time- and concentration-dependent stoichiometries and conformations of assembling human MutSα–MutLα–DNA complexes, and it is found that they assemble into multimeric complexes comprising three to eight proteins around a mismatch on DNA. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 17, 2020

2020 article

Recurrent mismatch binding by MutS mobile clamps on DNA localizes repair complexes nearby

Hao, P., LeBlanc, S. J., Case, B. C., Elston, T. C., Hingorani, M. M., Erie, D. A., & Weninger, K. R. (2020, July 15). Proceedings of the National Academy of Sciences, Vol. 117, pp. 17775–17784.

By: P. Hao n, S. LeBlanc n , B. Case *, T. Elston *, M. Hingorani *, D. Erie *, K. Weninger n 

author keywords: smFRET; MMR; mismatch repair; MutS
MeSH headings : Adenosine Triphosphatases / metabolism; Adenosine Triphosphate / metabolism; Base Pair Mismatch; DNA / chemistry; DNA / genetics; DNA / metabolism; DNA Mismatch Repair; Hydrolysis; Models, Molecular; Multiprotein Complexes / metabolism; MutL Proteins / chemistry; MutL Proteins / metabolism; MutS DNA Mismatch-Binding Protein / chemistry; MutS DNA Mismatch-Binding Protein / metabolism; Structure-Activity Relationship
topics (OpenAlex): Genetic factors in colorectal cancer; DNA Repair Mechanisms; RNA and protein synthesis mechanisms
TL;DR: It is revealed that after the initial mobile clamp formation event, MutS undergoes frequent cycles of mismatch rebinding and mobile clamp reformation without releasing DNA, and mechanisms that localize repair complexes to the vicinity of the mismatch are supported. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 17, 2020

2018 article

Coordinated protein and DNA conformational changes govern mismatch repair initiation by MutS

LeBlanc, S. J., Gauer, J. W., Hao, P., Case, B. C., Hingorani, M. M., Weninger, K. R., & Erie, D. A. (2018, September 27). Nucleic Acids Research, Vol. 10, pp. 10782–10795.

By: S. LeBlanc n , J. Gauer*, P. Hao n, B. Case *, M. Hingorani *, K. Weninger n , D. Erie *

MeSH headings : Base Pair Mismatch / genetics; Base Pairing / physiology; DNA / chemistry; DNA Mismatch Repair / genetics; Escherichia coli; Fluorescence Resonance Energy Transfer; Genomic Instability / genetics; Models, Molecular; MutS DNA Mismatch-Binding Protein / chemistry; MutS DNA Mismatch-Binding Protein / genetics; MutS DNA Mismatch-Binding Protein / metabolism; Mutant Proteins / chemistry; Mutant Proteins / metabolism; Nucleic Acid Conformation; Protein Binding / physiology; Protein Conformation; Protein Domains / genetics; Protein Isoforms / chemistry; Protein Isoforms / genetics; Protein Isoforms / metabolism
topics (OpenAlex): Genetic factors in colorectal cancer; DNA Repair Mechanisms; Genomics and Chromatin Dynamics
TL;DR: A unified model of coordinated MutS and DNA conformational changes wherein initiation of mismatch repair is governed by a balance of DNA bending/unbending energetics and MutS conformationalChanges coupled to its nucleotide binding properties is proposed. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries, ORCID
Added: February 11, 2019

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

2017 article

Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and potential role in phenotypic heterogeneity

Kulkarni, P., Jolly, M. K., Jia, D., Mooney, S. M., Bhargava, A., Kagohara, L. T., … Orban, J. (2017, March 13). Proceedings of the National Academy of Sciences, Vol. 114, pp. E2644–2653.

By: P. Kulkarni *, M. Jolly *, D. Jia *, S. Mooney *, A. Bhargava, L. Kagohara *, Y. Chen *, P. Hao n ...

author keywords: intrinsic disorder; androgen resistance; prostate cancer; PAGE-4; phenotypic heterogeneity
MeSH headings : Antigens, Neoplasm / chemistry; Antigens, Neoplasm / metabolism; Humans; Intrinsically Disordered Proteins / chemistry; Intrinsically Disordered Proteins / metabolism; Models, Molecular; Phenotype; Phosphorylation; Protein Conformation; Protein Serine-Threonine Kinases / genetics; Protein Serine-Threonine Kinases / metabolism; Protein Serine-Threonine Kinases / physiology; Protein-Tyrosine Kinases / genetics; Protein-Tyrosine Kinases / metabolism; Protein-Tyrosine Kinases / physiology; Proteome
topics (OpenAlex): Protein Structure and Dynamics; Mass Spectrometry Techniques and Applications; Advanced Proteomics Techniques and Applications
TL;DR: Multiple biophysical approaches that report conformational preferences of the intrinsically disordered protein (IDP) Prostate-Associated Gene 4 with human cancer biology and nonlinear dynamics suggest that the phosphorylation-induced conformational dynamics of PAGE4 may play a role in modulating changes between PCa cell phenotypes. (via Semantic Scholar)
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3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 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

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