Full-atomistic molecular dynamics analysis of p53 active tetramer

Zhou Han; Geng Yi-Zhao; Yan Shi-Wei

doi:10.7498/aps.73.20231515

Abstract

p53 is a tumor suppressor protein that plays a crucial role in inhibiting cancer development and maintaining the genetic integrity. Within the cell nucleus, four p53 molecules constitute a stable tetrameric active structure through highly cooperative interactions, bind to DNA via its DNA-binding domain, and transcriptionally activate or inhibit their target genes. However, in most human tumor cells, there are numerous p53 mutations. The majority of these mutations are formed in the p53 DNA-binding domain, importantly, the p53 DNA-binding domain is critical for p53 to form the tetrameric active structures and to regulate the transcription of its downstream target genes. In this work, the all-atom molecular dynamics simulation is conducted to investigate the mechanism of interaction within the wild-type p53 tetramers. This study indicates that the symmetric dimers on either side of the DNA are stable ones, keeping stable structures before and after DNA binding. The binding of two monomers on the same side of the DNA depends on protein-protein interaction provided by two contact surfaces. DNA scaffold stabilizes the tetrameric active structure. Such interactions crucially contribute to the tetramer formation. This study clarifies the internal interactions and key residues within the p53 tetramer in dynamic process, as well as the critical sites at various interaction interfaces. The findings of this study may provide a significant foundation for us to further understand the p53’s anticancer mechanisms, to explore the effective cancer treatment strategies, and in near future, to develop the effective anti-cancer drugs.

Keywords:

Authors and contacts

1.
Department of Physics, Beijing Normal University, Beijing 100875, China
2.
Faculty of Science, Hebei University of Technology, Tianjin 300131, China
3.
Faculty of Arts and Sciences, Beijing Normal University, Zhuhai 519085, China

Corresponding author: Yan Shi-Wei, yansw@bnu.edu.cn

Funds: Project supported by the National Natural Science Foundation of China (Grant Nos. 11675018, 11735005).

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References

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[14]	Cho Y, Gorina S, Jeffrey P D, Pavletich N P 1994 Science 265 346 Google Scholar
[15]	Liu X, Tian W, Cheng J, Li D, Liu T, Zhang L 2020 Comput. Biol. Chem. 84 107194 Google Scholar
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Cited By

图 1 p53 核心结合域四聚体结构: A链(蓝色); B链(红色); C链(绿色); D链(橙色). 蓝线表示对称二聚体界面, 红线表示二聚体-二聚体界面

Figure 1. The p53 core binding domain tetramer structure: Chain A (blue); Chain B (red); Chain C (green); Chain D (orange). Blue lines represent symmetric dimer interfaces, while red lines represent dimer-dimer interfaces.

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图 2 p53对称二聚体与DNA复合物的初始结构　(a)由A, B链和DNA组成的p53对称二聚体结构; (b) Zn离子的配位结构; (c) DNA轴垂直于图平面的对称二聚体

Figure 2. Initial structure of the p53 symmetric dimer-DNA complex: (a) The p53 symmetric dimer structure composed of chains A, B and DNA; (b) coordination structure of Zn ions; (c) symmetric dimer with the DNA axis perpendicular to the plane of the figure

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图 3 “无”DNA的p53对称二聚体初始结构

Figure 3. Initial structure of the p53 symmetric dimer without DNA.

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图 4 对称二聚体在“有”和“无”DNA结合时的RMSD演化

Figure 4. Evolution of RMSD for the symmetric dimer with and without DNA.

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图 5 A-B单体间的相互作用残基　(a) A-B单体间形成盐桥的残基; (b) A-B单体间参与范德瓦耳斯作用的残基

Figure 5. Residues involved in interactions between A and B monomers: (a) Residues forming salt bridges between A and B monomers; (b) residues involved in van der Waals interaction between A and B monomers.

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图 6 与DNA结合前(a)后(b)对称二聚体的残基能量贡献分布

Figure 6. Residue energy contribution distribution of symmetric dimers with (a) and without (b) DNA.

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图 7 对称二聚体与DNA结合的关键残基. 黄色残基表示A, B单体与DNA结合的一致残基, 绿色表示与DNA结合不一致的残基

Figure 7. Key residues involved in the binding of the symmetric dimer to DNA. Yellow residues represent consistent residues between monomers A and B and DNA binding, while green residues represent inconsistent residues with DNA binding.

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图 8 由 A, D和DNA组成的复合物初始结构

Figure 8. Initial structure of composite molecule including A, D and DNA.

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图 9 有/无DNA结合时, A-D二聚体构象上的差别　(a) A, D两个单体质心间距的概率密度分布; (b) A, D分子间接触面积的概率密度分布; (c)有DNA的A, D分子间二聚接触面; (d)无DNA的A, D分子间二聚接触面

Figure 9. Differences in the A-D dimer conformation with/without DNA binding: (a) Probability density distribution of the distance between the centers of mass of A and D monomers; (b) probability density distribution of the interfacial contact area between A and D molecules; (c) dimeric contact area between A and D molecules in the presence of DNA; (d) dimeric contact area between A and D molecules in the absence of DNA.

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图 10 (a)无DNA结合时A-D二聚体的RMSD演化; (b) 120 ns前后A-D二聚体的构象重叠, 两单体的构象发生了明显的偏移, 使得A-D之间的相互作用增加. 120 ns前后的构象分别用银色和橙色表示

Figure 10. (a) RMSD evolution of the A-D dimer in the absence of DNA binding; (b) at around 120 ns, there is an overlap in the conformation of the A-D dimer, with noticeable deviations in the conformations of the two monomers, leading to an increased interaction between A and D. Conformations before and after 120 ns are represented in silver and orange, respectively.

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图 11 无DNA时的A-D二聚体不能与DNA结合

Figure 11. A-D dimer can’t bind to DNA in the absence of DNA.

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图 12 (a)二聚体上的弹性应力; (b)稳定后, 弹性应力作用下A-D二聚体的结构

Figure 12. (a) Elastic stress on the dimer; (b) structure of the A-D dimer under the action of elastic stress after stabilization.

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图 13 有DNA时, A-D二聚体的稳定性　(a) RMSD; (b) RMSF

Figure 13. Stability of A-D dimer in the presence of DNA: (a) RMSD; (b) RMSF.

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图 14 与DNA结合的A-D二聚体间的(a)接触面和(b)相互作用残基

Figure 14. Contact surface (a) and residues involved in the interaction (b) between the A-D dimer bound to DNA.

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图 15 单体A, D与DNA间相互作用的关键残基. 黄色残基表示A, D单体与DNA结合的一致残基, 绿色表示与DNA结合不一致的残基

Figure 15. Key residues involved in the interaction between monomers A and D with DNA. Yellow residues represent consistent residues between monomers A and D and DNA binding, while green residues represent inconsistent residues with DNA binding.

DownLoad: Full-Size Img PowerPoint

图 16 与DNA结合的A-D二聚体的能量分解

Figure 16. Energy decomposition of the A-D dimer binding to DNA.

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图 17 结构域之间的动态互相关图

Figure 17. Dynamic cross-correlation map between domains.

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表 1 氢键、盐桥稳定性

Table 1. Hydrogen bond and salt bridge stability.

单体A	单体D	占有率/%
S94	L201	88.9
N210	D228	55.5
S94	G199	54.7
L264	V225	54.3
S99	D228	35.1, 30.0
S96	T231	33.1
N263	V225	31.8, 26.1
N210	S227	25.1
R267	D228	78.83 (盐桥)
R209	E224	35.88 (盐桥)

DownLoad: CSV

表 2 与DNA结合时A-D二聚体间的氢键、盐桥稳定性

Table 2. Stability of hydrogen bonds and salt bridges between A-D dimers when binding to DNA.

单体A	单体D	持续度/%
T170	G199	49.3
K101	P222	19.9
K101	P223	13.0
Q100	P223	16.9
P92	D186	12.6, 12.8
K101	E224	45.89 (盐桥)

DownLoad: CSV

[1]	Schuijer M, Berns E M 2003 Hum. Mutat. 21 285 Google Scholar
[2]	Funk W D, Pak D T, Karas R H, Wright W E, Shay J W 1992 Mol. Cell. Biol. 12 2866
[3]	Levine A J, Oren M 2009 Nat. Rev. Cancer 9 749 Google Scholar
[4]	Riley T, Sontag E, Chen P, Levine A 2008 Nat. Rev. Mol. Cell Biol. 9 402 Google Scholar
[5]	Petitjean A, Mathe E, Kato S, Ishioka C, Tavtigian S V, Hainaut P, Olivier M 2007 Hum. Mutat. 28 622 Google Scholar
[6]	Olivier M, Hollstein M, Hainaut P 2010 CSH Perspect Biol. 2 a001008 Google Scholar
[7]	Silva J L, Cino E A, Soares I N, Ferreira V F, de Oliveira G A P 2018 Acc. Chem. Res. 51 181 Google Scholar
[8]	Joerger A, Fersht A R 2007 Oncogene 26 2226 Google Scholar
[9]	张丽娟, 晏世伟, 卓益忠 2007 物理学报 56 2442 Google Scholar Zhang L J, Yan S W, Zhuo Y Z 2007 Acta Phys. Sin. 56 2442 Google Scholar
[10]	Liu S X, Geng Y Z, Yan S W 2017 Front. Phys. 12 1 Google Scholar
[11]	周晗, 耿轶钊, 晏世伟 2023 物理学报 72 068702 Google Scholar Zhou H, Geng Y Z, Yan S W 2023 Acta Phys. Sin. 72 068702 Google Scholar
[12]	Gomes A S, Ramos H, Inga A, Sousa E, Saraiva L 2021 Cancers 13 3344 Google Scholar
[13]	Wang H, Guo M, Wei H, Chen Y 2023 Signal Transduct Target Ther. 8 92 Google Scholar
[14]	Cho Y, Gorina S, Jeffrey P D, Pavletich N P 1994 Science 265 346 Google Scholar
[15]	Liu X, Tian W, Cheng J, Li D, Liu T, Zhang L 2020 Comput. Biol. Chem. 84 107194 Google Scholar
[16]	Tang Y, Yao Y, Wei G 2021 J. Phys. Chem. B 125 10138
[17]	Zhao K, Chai X, Johnston K, Clements A, Marmorstein R 2001 J. Biol. Chem. 276 12120 Google Scholar
[18]	Balagurumoorthy P, Sakamoto H, Lewis M S, Zambrano N, Clore G M, Gronenborn A M, Appella E, Harrington R E 1995 PNAS 92 8591 Google Scholar
[19]	Nicholls C D, McLure K G, Shields M A, Lee P W 2002 J. Biol. Chem. 277 12937 Google Scholar
[20]	Kitayner M, Rozenberg H, Kessler N, Rabinovich D, Shaulov L, Haran T E, Shakked Z 2006 Mol. Cell 22 741 Google Scholar
[21]	McLure K G, Lee P W 1998 EMBO J 17 3342 Google Scholar
[22]	Weinberg R L, Veprintsev D B, Fersht A R 2004 J. Mol. Biol. 341 1145 Google Scholar
[23]	Chen Y, Dey R, Chen L 2010 Structure 18 246 Google Scholar
[24]	Malecka K A, Ho W C, Marmorstein R 2009 Oncogene 28 325 Google Scholar
[25]	Nagaich A K, Zhurkin V B, Durell S R, Jernigan R L, Appella E, Harrington R E 1999 PNAS 96 1875 Google Scholar
[26]	Ho W C, Fitzgerald M X, Marmorstein R 2006 J. Biol. Chem. 281 20494 Google Scholar
[27]	Kamaraj B, Bogaerts A 2015 PLoS One 10 e0134638 Google Scholar
[28]	Pradhan M R, Siau J W, Kannan S, Nguyen M N, Ouaray Z, Kwoh C K, Lane D P, Ghadessy F, Verma C S 2019 Nucleic Acids Res. 47 1637 Google Scholar
[29]	Ma B, Pan Y, Gunasekaran K, Venkataraghavan R B, Levine A J, Nussinov R 2005 PNAS 102 3988 Google Scholar
[30]	Pan Y, Nussinov R 2007 J. Biol. Chem. 282 691 Google Scholar
[31]	Terakawa T, Takada S 2015 Sci. Rep. 5 17107 Google Scholar
[32]	Lu Q, Tan Y H, Luo R 2007 J. Phys. Chem. B 111 11538 Google Scholar
[33]	Abraham M J, Murtola T, Schulz R, Páll S, Smith J C, Hess B, Lindahl E 2015 SoftwareX 1 19
[34]	Humphrey W, Dalke A, Schulten K 1996 J. Mol. Graphics 14 33 Google Scholar
[35]	Arunan E, Desiraju G R, Klein R A, et al. 2011 Pure Appl. Chem. 83 1637 Google Scholar
[36]	Musafia B, Buchner V, Arad D 1995 J. Mol. Biol. 254 761 Google Scholar
[37]	Miller III B R, McGee Jr T D, Swails J M, Homeyer N, Gohlke H, Roitberg A E 2012 J. Chem. Theory Comput. 8 3314 Google Scholar
[38]	Wilcken R, Liu X, Zimmermann M O, Rutherford T J, Fersht A R, Joerger A C, Boeckler F M 2012 J. Am. Chem. Soc. 134 6810 Google Scholar
[39]	Klein C, Planker E, Diercks T, Kessler H, Kunkele K P, Lang K, Hansen S, Schwaiger M 2001 J. Biol. Chem. 276 49020 Google Scholar
[40]	Sabapathy K, Lane D P 2018 Nat. Rev. Clin. Oncol. 15 13 Google Scholar
[41]	Freed-Pastor W A, Prives C 2012 Genes Dev. 26 1268 Google Scholar
[42]	Dolma L, Muller P A 2022 Cancers 14 5091 Google Scholar
[43]	Wei H, Qu L, Dai S, et al. 2021 Nat. Commun. 12 2280 Google Scholar
[44]	Joo W S, Jeffrey P D, Cantor S B, Finnin M S, Livingston D M, Pavletich N P 2002 Genes Dev. 16 583 Google Scholar
[45]	Gorina S, Pavletich N P 1996 Science 274 1001 Google Scholar
[46]	Torrie G M, Valleau J P 1977 J. Comput. Phys. 23 187 Google Scholar Torrie G M, Valleau J P 1977 J. Comput. Phys. 23 187 Google Scholar
[47]	Klein C, Georges G, Kunkele K P, Huber R, Engh R A, Hansen S 2001 J. Biol. Chem. 276 37390 Google Scholar
[48]	McCammon J A, Harvey S C 1988 Dynamics of Proteins and Nucleic Acids (Cambridge: Cambridge University Press) pp289–302
[49]	McCammon J 1984 Rep. Prog. Phys. 47 1 Google Scholar
[50]	Joerger A C, Fersht A R 2008 Annu. Rev. Biochem. 77 557 Google Scholar

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