Articles - 3q06 mentioned but not cited (7)
- An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity. Petty TJ, Emamzadah S, Costantino L, Petkova I, Stavridi ES, Saven JG, Vauthey E, Halazonetis TD. EMBO J 30 2167-2176 (2011)
- Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes. Kribelbauer JF, Laptenko O, Chen S, Martini GD, Freed-Pastor WA, Prives C, Mann RS, Bussemaker HJ. Cell Rep 19 2383-2395 (2017)
- Mapping the structural and dynamical features of multiple p53 DNA binding domains: insights into loop 1 intrinsic dynamics. Lukman S, Lane DP, Verma CS. PLoS One 8 e80221 (2013)
- DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions. Lambrughi M, De Gioia L, Gervasio FL, Lindorff-Larsen K, Nussinov R, Urani C, Bruschi M, Papaleo E. Nucleic Acids Res 44 9096-9109 (2016)
- The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins. Chakraborty S, Rendón-Ramírez A, Ásgeirsson B, Dutta M, Ghosh AS, Oda M, Venkatramani R, Rao BJ, Dandekar AM, Goñi FM. F1000Res 2 286 (2013)
- Physicochemical models of protein-DNA binding with standard and modified base pairs. Chiu TP, Rao S, Rohs R. Proc Natl Acad Sci U S A 120 e2205796120 (2023)
- Quercetin Induces Apoptosis in HepG2 Cells via Directly Interacting with YY1 to Disrupt YY1-p53 Interaction. Guan H, Zhang W, Liu H, Jiang Y, Li F, Wu M, Waterhouse GIN, Sun-Waterhouse D, Li D. Metabolites 13 229 (2023)
Reviews citing this publication (9)
- The p53 Pathway: Origins, Inactivation in Cancer, and Emerging Therapeutic Approaches. Joerger AC, Fersht AR. Annu Rev Biochem 85 375-404 (2016)
- Surf the post-translational modification network of p53 regulation. Gu B, Zhu WG. Int J Biol Sci 8 672-684 (2012)
- The Tail That Wags the Dog: How the Disordered C-Terminal Domain Controls the Transcriptional Activities of the p53 Tumor-Suppressor Protein. Laptenko O, Tong DR, Manfredi J, Prives C. Trends Biochem Sci 41 1022-1034 (2016)
- Structural Evolution and Dynamics of the p53 Proteins. Chillemi G, Kehrloesser S, Bernassola F, Desideri A, Dötsch V, Levine AJ, Melino G. Cold Spring Harb Perspect Med 7 a028308 (2017)
- Detecting and interpreting DNA methylation marks. Ren R, Horton JR, Zhang X, Blumenthal RM, Cheng X. Curr Opin Struct Biol 53 88-99 (2018)
- Recognition of Local DNA Structures by p53 Protein. Brázda V, Coufal J. Int J Mol Sci 18 E375 (2017)
- Dying to Survive-The p53 Paradox. Lees A, Sessler T, McDade S. Cancers (Basel) 13 3257 (2021)
- Understanding the core of RNA interference: The dynamic aspects of Argonaute-mediated processes. Zhu L, Jiang H, Sheong FK, Cui X, Wang Y, Gao X, Huang X. Prog Biophys Mol Biol 128 39-46 (2017)
- Targeting p53 pathways: mechanisms, structures, and advances in therapy. Wang H, Guo M, Wei H, Chen Y. Signal Transduct Target Ther 8 92 (2023)
Articles citing this publication (55)
- Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53. Wassman CD, Baronio R, Demir Ö, Wallentine BD, Chen CK, Hall LV, Salehi F, Lin DW, Chung BP, Hatfield GW, Richard Chamberlin A, Luecke H, Lathrop RH, Kaiser P, Amaro RE. Nat Commun 4 1407 (2013)
- The p53 C terminus controls site-specific DNA binding and promotes structural changes within the central DNA binding domain. Laptenko O, Shiff I, Freed-Pastor W, Zupnick A, Mattia M, Freulich E, Shamir I, Kadouri N, Kahan T, Manfredi J, Simon I, Prives C. Mol Cell 57 1034-1046 (2015)
- Revealing a human p53 universe. Nguyen TT, Grimm SA, Bushel PR, Li J, Li Y, Bennett BD, Lavender CA, Ward JM, Fargo DC, Anderson CW, Li L, Resnick MA, Menendez D. Nucleic Acids Res 46 8153-8167 (2018)
- Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion. Chen Y, Zhang X, Dantas Machado AC, Ding Y, Chen Z, Qin PZ, Rohs R, Chen L. Nucleic Acids Res 41 8368-8376 (2013)
- Long-range regulation of p53 DNA binding by its intrinsically disordered N-terminal transactivation domain. Krois AS, Dyson HJ, Wright PE. Proc Natl Acad Sci U S A 115 E11302-E11310 (2018)
- Protein domain-level landscape of cancer-type-specific somatic mutations. Yang F, Petsalaki E, Rolland T, Hill DE, Vidal M, Roth FP. PLoS Comput Biol 11 e1004147 (2015)
- Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions. Eldar A, Rozenberg H, Diskin-Posner Y, Rohs R, Shakked Z. Nucleic Acids Res 41 8748-8759 (2013)
- Structure of p73 DNA-binding domain tetramer modulates p73 transactivation. Ethayathulla AS, Tse PW, Monti P, Nguyen S, Inga A, Fronza G, Viadiu H. Proc Natl Acad Sci U S A 109 6066-6071 (2012)
- Vinylsulfonamide and acrylamide modification of DNA for cross-linking with proteins. Dadová J, Orság P, Pohl R, Brázdová M, Fojta M, Hocek M. Angew Chem Int Ed Engl 52 10515-10518 (2013)
- The p53 tetramer shows an induced-fit interaction of the C-terminal domain with the DNA-binding domain. D'Abramo M, Bešker N, Desideri A, Levine AJ, Melino G, Chillemi G. Oncogene 35 3272-3281 (2016)
- Constitutive p53 heightens mitochondrial apoptotic priming and favors cell death induction by BH3 mimetic inhibitors of BCL-xL. Le Pen J, Maillet L, Sarosiek K, Vuillier C, Gautier F, Montessuit S, Martinou JC, Letaï A, Braun F, Juin PP. Cell Death Dis 7 e2083 (2016)
- One-Dimensional Sliding of p53 Along DNA Is Accelerated in the Presence of Ca(2+) or Mg(2+) at Millimolar Concentrations. Murata A, Ito Y, Kashima R, Kanbayashi S, Nanatani K, Igarashi C, Okumura M, Inaba K, Tokino T, Takahashi S, Kamagata K. J Mol Biol 427 2663-2678 (2015)
- Reversal of the DNA-binding-induced loop L1 conformational switch in an engineered human p53 protein. Emamzadah S, Tropia L, Vincenti I, Falquet B, Halazonetis TD. J Mol Biol 426 936-944 (2014)
- Structure and Function of p53-DNA Complexes with Inactivation and Rescue Mutations: A Molecular Dynamics Simulation Study. Kamaraj B, Bogaerts A. PLoS One 10 e0134638 (2015)
- Transactivation specificity is conserved among p53 family proteins and depends on a response element sequence code. Ciribilli Y, Monti P, Bisio A, Nguyen HT, Ethayathulla AS, Ramos A, Foggetti G, Menichini P, Menendez D, Resnick MA, Viadiu H, Fronza G, Inga A. Nucleic Acids Res 41 8637-8653 (2013)
- Functional details of the Mycobacterium tuberculosis VapBC26 toxin-antitoxin system based on a structural study: insights into unique binding and antibiotic peptides. Kang SM, Kim DH, Lee KY, Park SJ, Yoon HJ, Lee SJ, Im H, Lee BJ. Nucleic Acids Res 45 8564-8580 (2017)
- Low-level p53 expression changes transactivation rules and reveals superactivating sequences. Jordan JJ, Menendez D, Sharav J, Beno I, Rosenthal K, Resnick MA, Haran TE. Proc Natl Acad Sci U S A 109 14387-14392 (2012)
- Y-family polymerase conformation is a major determinant of fidelity and translesion specificity. Wilson RC, Jackson MA, Pata JD. Structure 21 20-31 (2013)
- Conformational changes in DNA-binding proteins: relationships with precomplex features and contributions to specificity and stability. Andrabi M, Mizuguchi K, Ahmad S, Ahmad S. Proteins 82 841-857 (2014)
- Molecular dynamics of the full-length p53 monomer. Chillemi G, Davidovich P, D'Abramo M, Mametnabiev T, Garabadzhiu AV, Desideri A, Melino G. Cell Cycle 12 3098-3108 (2013)
- Full-length p53 tetramer bound to DNA and its quaternary dynamics. Demir Ö, Ieong PU, Amaro RE. Oncogene 36 1451-1460 (2017)
- Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Degtjarik O, Golovenko D, Diskin-Posner Y, Abrahmsén L, Rozenberg H, Shakked Z. Nat Commun 12 7057 (2021)
- A phosphorylation-dependent switch in the disordered p53 transactivation domain regulates DNA binding. Sun X, Dyson HJ, Wright PE. Proc Natl Acad Sci U S A 118 e2021456118 (2021)
- Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling. Zhang X, Dantas Machado AC, Ding Y, Chen Y, Lu Y, Duan Y, Tham KW, Chen L, Rohs R, Qin PZ. Nucleic Acids Res 42 2789-2797 (2014)
- Structural Basis for p53 Lys120-Acetylation-Dependent DNA-Binding Mode. Vainer R, Cohen S, Shahar A, Zarivach R, Arbely E. J Mol Biol 428 3013-3025 (2016)
- Decreased GLUT2 and glucose uptake contribute to insulin secretion defects in MODY3/HNF1A hiPSC-derived mutant β cells. Low BSJ, Lim CS, Ding SSL, Tan YS, Ng NHJ, Krishnan VG, Ang SF, Neo CWY, Verma CS, Hoon S, Lim SC, Tai ES, Teo AKK. Nat Commun 12 3133 (2021)
- Two-step mechanism involving active-site conformational changes regulates human telomerase DNA binding. Tomlinson CG, Moye AL, Holien JK, Parker MW, Cohen SB, Bryan TM. Biochem J 465 347-357 (2015)
- Interactions of p53 with poly(ADP-ribose) and DNA induce distinct changes in protein structure as revealed by ATR-FTIR spectroscopy. Krüger A, Stier A, Fischbach A, Bürkle A, Hauser K, Mangerich A. Nucleic Acids Res 47 4843-4858 (2019)
- One-Dimensional Search Dynamics of Tumor Suppressor p53 Regulated by a Disordered C-Terminal Domain. Murata A, Itoh Y, Mano E, Kanbayashi S, Igarashi C, Takahashi H, Takahashi S, Kamagata K. Biophys J 112 2301-2314 (2017)
- Azidopropylvinylsulfonamide as a New Bifunctional Click Reagent for Bioorthogonal Conjugations: Application for DNA-Protein Cross-Linking. Dadová J, Vrábel M, Adámik M, Brázdová M, Pohl R, Fojta M, Hocek M. Chemistry 21 16091-16102 (2015)
- Quantifying the two-state facilitated diffusion model of protein-DNA interactions. Leven I, Levy Y. Nucleic Acids Res 47 5530-5538 (2019)
- Solution structure and binding specificity of the p63 DNA binding domain. Enthart A, Klein C, Dehner A, Coles M, Gemmecker G, Kessler H, Hagn F. Sci Rep 6 26707 (2016)
- Crystal structures of the DNA-binding domain tetramer of the p53 tumor suppressor family member p73 bound to different full-site response elements. Ethayathulla AS, Nguyen HT, Viadiu H. J Biol Chem 288 4744-4754 (2013)
- Distinct mechanisms control genome recognition by p53 at its target genes linked to different cell fates. Farkas M, Hashimoto H, Bi Y, Davuluri RV, Resnick-Silverman L, Manfredi JJ, Debler EW, McMahon SB. Nat Commun 12 484 (2021)
- On the origin of the stereoselective affinity of Nutlin-3 geometrical isomers for the MDM2 protein. ElSawy KM, Verma CS, Lane DP, Caves LS. Cell Cycle 12 3727-3735 (2013)
- iASPP mediates p53 selectivity through a modular mechanism fine-tuning DNA recognition. Chen S, Wu J, Zhong S, Li Y, Zhang P, Ma J, Ren J, Tan Y, Wang Y, Au KF, Siebold C, Bond GL, Chen Z, Lu M, Jones EY, Lu X. Proc Natl Acad Sci U S A 116 17470-17479 (2019)
- An indolylquinoline derivative promotes apoptosis in human lung cancer cells by impairing mitochondrial functions. Liu CY, Wu PT, Wang JP, Fan PW, Hsieh CH, Su CL, Chiu CC, Yao CF, Fang K. Apoptosis 20 1471-1482 (2015)
- Crystal structure of the DNA-binding domain of Myelin-gene Regulatory Factor. Zhen X, Li B, Hu F, Yan S, Meloni G, Li H, Shi N. Sci Rep 7 3696 (2017)
- The molecular mechanism of action of methylene quinuclidinone and its effects on the structure of p53 mutants. Omar SI, Tuszynski J. Oncotarget 9 37137-37156 (2018)
- Molecular basis for modulation of the p53 target selectivity by KLF4. Brandt T, Townsley FM, Teufel DP, Freund SM, Veprintsev DB. PLoS One 7 e48252 (2012)
- Markov state models and NMR uncover an overlooked allosteric loop in p53. Barros EP, Demir Ö, Soto J, Cocco MJ, Amaro RE. Chem Sci 12 1891-1900 (2020)
- The complex architecture of p53 binding sites. Senitzki A, Safieh J, Sharma V, Golovenko D, Danin-Poleg Y, Inga A, Haran TE. Nucleic Acids Res 49 1364-1382 (2021)
- Dynamics and Molecular Mechanisms of p53 Transcriptional Activation. Offutt TL, Ieong PU, Demir Ö, Amaro RE. Biochemistry 57 6528-6537 (2018)
- Reactivation of mutant p53: Constraints on mechanism highlighted by principal component analysis of the DNA binding domain. Ouaray Z, ElSawy KM, Lane DP, Essex JW, Verma C. Proteins 84 1443-1461 (2016)
- Association between Predicted Effects of TP53 Missense Variants on Protein Conformation and Their Phenotypic Presentation as Li-Fraumeni Syndrome or Hereditary Breast Cancer. Liu Y, Axell O, van Leeuwen T, Konrat R, Kharaziha P, Larsson C, Wright APH, Bajalica-Lagercrantz S. Int J Mol Sci 22 6345 (2021)
- Single molecule studies reveal that p53 tetramers dynamically bind response elements containing one or two half sites. Ly E, Kugel JF, Goodrich JA. Sci Rep 10 16176 (2020)
- Agathis robusta Bark Extract Protects from Renal Ischemia-Reperfusion Injury: Phytochemical, In Silico and In Vivo Studies. Mohamed ME, Tawfeek N, Elbaramawi SS, Elbatreek MH, Fikry E. Pharmaceuticals (Basel) 15 1270 (2022)
- P53 conformational switching for selectivity may reveal a general solution for specific DNA binding. Tubbs JL, Tainer JA. EMBO J 30 2099-2100 (2011)
- Cluster Analysis of p53 Binding Site Sequences Reveals Subsets with Different Functions. Lim JH, Latysheva NS, Iggo RD, Barker D. Cancer Inform 15 199-209 (2016)
- Differential salt-induced dissociation of the p53 protein complexes with circular and linear plasmid DNA substrates suggest involvement of a sliding mechanism. Šebest P, Brázdová M, Fojta M, Pivoňková H. Int J Mol Sci 16 3163-3177 (2015)
- Investigating Conformational Dynamics and Allostery in the p53 DNA-Binding Domain Using Molecular Simulations. Papaleo E. Methods Mol Biol 2253 221-244 (2021)
- Mapping Interactions of the Intrinsically Disordered C-Terminal Regions of Tetrameric p53 by Segmental Isotope Labeling and NMR. Krois AS, Park S, Martinez-Yamout MA, Dyson HJ, Wright PE. Biochemistry 61 2709-2719 (2022)
- Accurate prediction of protein-nucleic acid complexes using RoseTTAFoldNA. Baek M, McHugh R, Anishchenko I, Jiang H, Baker D, DiMaio F. Nat Methods (2023)
- Insights into Allosteric Mechanisms of the Lung-Enriched p53 Mutants V157F and R158L. Lei J, Li X, Cai M, Guo T, Lin D, Deng X, Li Y. Int J Mol Sci 23 10100 (2022)
- Single molecule studies characterize the kinetic mechanism of tetrameric p53 binding to different native response elements. Suwita JP, Voong CK, Ly E, Goodrich JA, Kugel JF. PLoS One 18 e0286193 (2023)