Publications:

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Rational design of phase separating peptides based on phase separating protein sequence of p53.

Scientific Reports

Kamagata, Kiyoto K; Hando, Atsumi A; Ariefai, Maulana M; Iwaki, Nanako N; Kanbayashi, Saori S; Koike, Ryotaro R; Ikeda, Keisuke K

Publication Date: 2023-04-06

Variant appearance in text: p53: Y236F

PubMed Link: 37024567

Variant Present in the following documents:

• Main text
• 41598_2023_Article_32632.pdf

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CTCF DNA-binding domain undergoes dynamic and selective protein-protein interactions.

Iscience

Zhou, Rong R; Tian, Kai K; Huang, Jie J; Duan, Wenjia W; Fu, Hongye H; Feng, Ying Y; Wang, Hui H; Jiang, Yongpeng Y; Li, Yuanjun Y; Wang, Rui R; Hu, Jiazhi J; Ma, Hanhui H; Qi, Zhi Z; Ji, Xiong X

Publication Date: 2022-09-16

Variant appearance in text: p53: 707A>T

PubMed Link: 36117989

Variant Present in the following documents:

• mmc4.xlsx, sheet 1

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Rational peptide design for regulating liquid-liquid phase separation on the basis of residue-residue contact energy.

Scientific Reports

Kamagata, Kiyoto K; Ariefai, Maulana M; Takahashi, Hiroto H; Hando, Atsumi A; Subekti, Dwiky Rendra Graha DRG; Ikeda, Keisuke K; Hirano, Atsushi A; Kameda, Tomoshi T

Publication Date: 2022-08-12

Variant appearance in text: p53: Y236F

PubMed Link: 35962177

Variant Present in the following documents:

• Main text
• 41598_2022_Article_17829.pdf

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Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery.

Nature Communications

Havugimana, Pierre C PC; Goel, Raghuveera Kumar RK; Phanse, Sadhna S; Youssef, Ahmed A; Padhorny, Dzmitry D; Kotelnikov, Sergei S; Kozakov, Dima D; Emili, Andrew A

Publication Date: 2022-07-13

Variant appearance in text: TP53: 707A>T

PubMed Link: 35831314

Variant Present in the following documents:

• 41467_2022_31809_MOESM8_ESM.xlsx, sheet 3

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Structure-dependent recruitment and diffusion of guest proteins in liquid droplets of FUS.

Scientific Reports

Kamagata, Kiyoto K; Iwaki, Nanako N; Kanbayashi, Saori S; Banerjee, Trishit T; Chiba, Rika R; Gaudon, Virginie V; Castaing, Bertrand B; Sakomoto, Seiji S

Publication Date: 2022-05-02

Variant appearance in text: p53: Y236F

PubMed Link: 35501371

Variant Present in the following documents:

• Main text
• 41598_2022_Article_11177.pdf

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Evolutionary history of the p53 family DNA-binding domain: insights from an Alvinella pompejana homolog.

Cell Death & Disease

Zhang, Qiang Q; Balourdas, Dimitrios-Ilias DI; Baron, Bruno B; Senitzki, Alon A; Haran, Tali E TE; Wiman, Klas G KG; Soussi, Thierry T; Joerger, Andreas C AC

Publication Date: 2022-03-07

Variant appearance in text: p53: Y236F

PubMed Link: 35256607

Variant Present in the following documents:

• Main text
• 41419_2022_Article_4653.pdf

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Molecular principles of recruitment and dynamics of guest proteins in liquid droplets.

Scientific Reports

Kamagata, Kiyoto K; Iwaki, Nanako N; Hazra, Milan Kumar MK; Kanbayashi, Saori S; Banerjee, Trishit T; Chiba, Rika R; Sakomoto, Seiji S; Gaudon, Virginie V; Castaing, Bertrand B; Takahashi, Hiroto H; Kimura, Michiko M; Oikawa, Hiroyuki H; Takahashi, Satoshi S; Levy, Yaakov Y

Publication Date: 2021-09-29

Variant appearance in text: p53: Y236F

PubMed Link: 34588591

Variant Present in the following documents:

• Main text
• 41598_2021_Article_98955.pdf

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Comparison of two targeted ultra-deep sequencing technologies for analysis of plasma circulating tumour DNA in endocrine-therapy-resistant breast cancer patients.

Breast Cancer Research And Treatment

Nteliopoulos, Georgios G; Page, Karen K; Hills, Allison A; Howarth, Karen K; Emmett, Warren W; Green, Emma E; Martinson, Luke J LJ; Fernadez-Garcia, Daniel D; Hastings, Robert R; Guttery, David S DS; Kenny, Laura L; Stebbing, Justin J; Cleator, Susan S; Rehman, Farah F; Gleason, Kelly L T KLT; Sanela, Andrijac A; Ion, Charlotte C; Rushton, Amelia J AJ; Rosenfeld, Nitzan N; Coombes, R Charles RC; Shaw, Jacqueline A JA

Publication Date: 2021-07

Variant appearance in text: TP53: Y236F

PubMed Link: 34097174

Variant Present in the following documents:

• 10549_2021_6220_MOESM2_ESM.xlsx, sheet 1
• 10549_2021_6220_MOESM2_ESM.xlsx, sheet 2

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Transient binding and jumping dynamics of p53 along DNA revealed by sub-millisecond resolved single-molecule fluorescence tracking.

Scientific Reports

Subekti, Dwiky Rendra Graha DRG; Murata, Agato A; Itoh, Yuji Y; Takahashi, Satoshi S; Kamagata, Kiyoto K

Publication Date: 2020-08-13

Variant appearance in text: p53: Y236F

PubMed Link: 32792545

Variant Present in the following documents:

• Main text
• 41598_2020_Article_70763.pdf

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Liquid-like droplet formation by tumor suppressor p53 induced by multivalent electrostatic interactions between two disordered domains.

Scientific Reports

Kamagata, Kiyoto K; Kanbayashi, Saori S; Honda, Masaya M; Itoh, Yuji Y; Takahashi, Hiroto H; Kameda, Tomoshi T; Nagatsugi, Fumi F; Takahashi, Satoshi S

Publication Date: 2020-01-17

Variant appearance in text: p53: Y236F

PubMed Link: 31953488

Variant Present in the following documents:

• Main text
• 41598_2020_Article_57521.pdf

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Rational design using sequence information only produces a peptide that binds to the intrinsically disordered region of p53.

Scientific Reports

Kamagata, Kiyoto K; Mano, Eriko E; Itoh, Yuji Y; Wakamoto, Takuro T; Kitahara, Ryo R; Kanbayashi, Saori S; Takahashi, Hiroto H; Murata, Agato A; Kameda, Tomoshi T

Publication Date: 2019-06-28

Variant appearance in text: p53: Y236F

PubMed Link: 31253862

Variant Present in the following documents:

• Main text

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Finding driver mutations in cancer: Elucidating the role of background mutational processes.

Plos Computational Biology

Brown, Anna-Leigh AL; Li, Minghui M; Goncearenco, Alexander A; Panchenko, Anna R AR

Publication Date: 2019-04

Variant appearance in text: TP53: Y236F

PubMed Link: 31034466

Variant Present in the following documents:

• Main text
• pcbi.1006981.pdf
• pcbi.1006981.s010.xlsx, sheet 1

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Incidence and distribution of UroSEEK gene panel in a multi-institutional cohort of bladder urothelial carcinoma.

Modern Pathology : An Official Journal Of The United States And Canadian Academy Of Pathology, Inc

Eich, Marie-Lisa ML; Rodriguez Pena, Maria Del Carmen MDC; Springer, Simeon U SU; Taheri, Diana D; Tregnago, Aline C AC; Salles, Daniela C DC; Bezerra, Stephania Martins SM; Cunha, Isabela W IW; Fujita, Kazutoshi K; Ertoy, Dilek D; Bivalacqua, Trinity J TJ; Tomasetti, Cristian C; Papadopoulos, Nickolas N; Kinzler, Ken W KW; Vogelstein, Bert B; Netto, George J GJ

Publication Date: 2019-10

Variant appearance in text: TP53: Y236F

PubMed Link: 31028363

Variant Present in the following documents:

• NIHMS1525315-supplement-2.xlsx, sheet 1

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One-Dimensional Search Dynamics of Tumor Suppressor p53 Regulated by a Disordered C-Terminal Domain.

Biophysical Journal

Murata, Agato A; Itoh, Yuji Y; Mano, Eriko E; Kanbayashi, Saori S; Igarashi, Chihiro C; Takahashi, Hiroto H; Takahashi, Satoshi S; Kamagata, Kiyoto K

Publication Date: 2017-06-06

Variant appearance in text: p53: Y236F

PubMed Link: 28591603

Variant Present in the following documents:

• Main text

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p53 Proteoforms and Intrinsic Disorder: An Illustration of the Protein Structure-Function Continuum Concept.

International Journal Of Molecular Sciences

Uversky, Vladimir N VN

Publication Date: 2016-11-10

Variant appearance in text: p53: Y236F

PubMed Link: 27834926

Variant Present in the following documents:

• ijms-17-01874-s001.pdf

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iFish: predicting the pathogenicity of human nonsynonymous variants using gene-specific/family-specific attributes and classifiers.

Scientific Reports

Wang, Meng M; Wei, Liping L

Publication Date: 2016-08-16

Variant appearance in text: TP53: Y236F

PubMed Link: 27527004

Variant Present in the following documents:

• srep31321-s5.xls, sheet 1

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Solution structure and binding specificity of the p63 DNA binding domain.

Scientific Reports

Enthart, Andreas A; Klein, Christian C; Dehner, Alexander A; Coles, Murray M; Gemmecker, Gerd G; Kessler, Horst H; Hagn, Franz F

Publication Date: 2016-05-26

Variant appearance in text: p53: Y236F

PubMed Link: 27225672

Variant Present in the following documents:

• Main text
• srep26707.pdf

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GESPA: classifying nsSNPs to predict disease association.

Bmc Bioinformatics

Khurana, Jay K JK; Reeder, Jay E JE; Shrimpton, Antony E AE; Thakar, Juilee J

Publication Date: 2015-07-25

Variant appearance in text: TP53: Y236F

PubMed Link: 26206375

Variant Present in the following documents:

• 12859_2015_673_MOESM1_ESM.xls, sheet 1

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Oxidation of p53 through DNA charge transport involves a network of disulfides within the DNA-binding domain.

Biochemistry

Schaefer, Kathryn N KN; Geil, Wendy M WM; Sweredoski, Michael J MJ; Moradian, Annie A; Hess, Sonja S; Barton, Jacqueline K JK

Publication Date: 2015-01-27

Variant appearance in text: p53: Y236F

PubMed Link: 25584637

Variant Present in the following documents:

• Main text
• bi501424v.pdf

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Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations.

Genome Biology

Martelotto, Luciano G LG; Ng, Charlotte Ky CK; De Filippo, Maria R MR; Zhang, Yan Y; Piscuoglio, Salvatore S; Lim, Raymond S RS; Shen, Ronglai R; Norton, Larry L; Reis-Filho, Jorge S JS; Weigelt, Britta B

Publication Date: 2014-10-28

Variant appearance in text: TP53: Y236F

PubMed Link: 25348012

Variant Present in the following documents:

• 13059_2014_484_MOESM2_ESM.xlsx, sheet 1

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PZR coordinates Shp2 Noonan and LEOPARD syndrome signaling in zebrafish and mice.

Molecular And Cellular Biology

Paardekooper Overman, Jeroen J; Yi, Jae-Sung JS; Bonetti, Monica M; Soulsby, Matthew M; Preisinger, Christian C; Stokes, Matthew P MP; Hui, Li L; Silva, Jeffrey C JC; Overvoorde, John J; Giansanti, Piero P; Heck, Albert J R AJ; Kontaridis, Maria I MI; den Hertog, Jeroen J; Bennett, Anton M AM

Publication Date: 2014-08

Variant appearance in text: p53: Y236F

PubMed Link: 24865967

Variant Present in the following documents:

• Main text

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Effects of stability on the biological function of p53.

The Journal Of Biological Chemistry

Khoo, Kian Hoe KH; Mayer, Sebastian S; Fersht, Alan R AR

Publication Date: 2009-11-06

Variant appearance in text: p53: Y236F

PubMed Link: 19700401

Variant Present in the following documents:

• Main text

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Stabilising the DNA-binding domain of p53 by rational design of its hydrophobic core.

Protein Engineering, Design & Selection : Peds

Khoo, Kian Hoe KH; Joerger, Andreas C AC; Freund, Stefan M V SM; Fersht, Alan R AR

Publication Date: 2009-07

Variant appearance in text: p53: Y236F

PubMed Link: 19515728

Variant Present in the following documents:

• Main text

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Stability of the core domain of p53: insights from computer simulations.

Bmc Bioinformatics

Madhumalar, Arumugam A; Smith, Derek John DJ; Verma, Chandra C

Publication Date: 2008

Variant appearance in text: p53: Tyr236Phe

PubMed Link: 18315848

Variant Present in the following documents:

• Main text
• 1471-2105-9-S1-S17.pdf

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Solution structure of p53 core domain: structural basis for its instability.

Proceedings Of The National Academy Of Sciences Of The United States Of America

Cañadillas, José Manuel Pérez JM; Tidow, Henning H; Freund, Stefan M V SM; Rutherford, Trevor J TJ; Ang, Hwee Ching HC; Fersht, Alan R AR

Publication Date: 2006-02-14

Variant appearance in text: p53: Y236F

PubMed Link: 16461916

Variant Present in the following documents:

• Main text

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