Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Negative Regulator Molecules01:23

Negative Regulator Molecules

35.2K
Positive regulators allow a cell to advance through cell cycle checkpoints. Negative regulators have an equally important role as they terminate a cell’s progression through the cell cycle—or pause it—until the cell meets specific criteria.
35.2K
Abnormal Proliferation02:23

Abnormal Proliferation

4.5K
Under normal conditions, most adult cells remain in a non-proliferative state unless stimulated by internal or external factors to replace lost cells. Abnormal cell proliferation is a condition in which the cell's growth exceeds and is uncoordinated with normal cells. In such situations, cell division persists in the same excessive manner even after cessation of the stimuli, leading to persistent tumors. The tumor arises from the damaged cells that replicate to pass the damage to the...
4.5K
DNA Damage can Stall the Cell Cycle02:37

DNA Damage can Stall the Cell Cycle

9.1K
In response to DNA damage, cells can pause the cell cycle to assess and repair the breaks. However, the cell must check the DNA at certain critical stages during the cell cycle. If the cell cycle pauses before DNA replication, the cells will contain twice the amount of DNA. On the other hand, if cells arrest after DNA replication but before mitosis, they will contain four times the normal amount of DNA. With a host of specialized proteins at their disposal,cells must use the right protein at...
9.1K
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

6.8K
Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....
6.8K
Molecular Factors Affecting Cell Division01:27

Molecular Factors Affecting Cell Division

3.0K
Several external and internal factors influence the initiation and inhibition of cell division. For instance, the death of nearby cells or the release of human growth hormone (hGH) promotes cell division. In contrast, lack of hGH or crowding of cells can inhibit cell division.
Several proteins function as internal regulators to ensure each cell cycle stage is completed faithfully before proceeding to the next. Regulator molecules may act directly or influence the activity or production of other...
3.0K
Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

6.2K
Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
6.2K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Nucleosome spacing across cell types, diseases, and ages.

Nucleic acids research·2026
Same author

From Molecules to Mechanisms: Integrating MD and Stochastic Modeling to Decipher RXR-RAR Gene Regulation.

The journal of physical chemistry. B·2025
Same author

CTCF binding landscape is shaped by the epigenetic state of the N-terminal nucleosome in relation to CTCF motif orientation.

Nucleic acids research·2025
Same author

A general, robust framework for determining the key species that forewarns sudden transitions in biological circuits.

Physical chemistry chemical physics : PCCP·2025
Same author

Predicting the Electrophoretic Mobility of Charged Particles in an Aqueous Medium.

Langmuir : the ACS journal of surfaces and colloids·2024
Same author

Genomic alterations and transcriptional phenotypes in circulating tumor DNA and matched metastatic tumor.

bioRxiv : the preprint server for biology·2024
Same journal

A data-driven modeling study on the accurate identification of Doppler-free saturated absorption spectra in diatomic tellurium (130Te2).

The Journal of chemical physics·2026
Same journal

Anharmonic phonons via quantum thermal bath simulations.

The Journal of chemical physics·2026
Same journal

Quantum simulation of alignment dependent differential cross sections in co-propagating molecular beams at cold collision energies.

The Journal of chemical physics·2026
Same journal

Non-additive ion effects on the coil-globule equilibrium of a generic polymer in aqueous salt solutions.

The Journal of chemical physics·2026
Same journal

Insights into the unexpected small reduction of the temperature of maximum density of water by lithium chloride addition.

The Journal of chemical physics·2026
Same journal

Optical frequency comb double-resonance spectroscopy of the 9030-9175 cm-1 states of ethylene.

The Journal of chemical physics·2026
See all related articles

Related Experiment Video

Updated: Jun 11, 2025

Yeast As a Chassis for Developing Functional Assays to Study Human P53
14:57

Yeast As a Chassis for Developing Functional Assays to Study Human P53

Published on: August 4, 2019

9.5K

Predicting p53-dependent cell transitions from thermodynamic models.

Pankaj Gautam1, Isabella Ciuta2, Vladimir B Teif2

  • 1Theoretical and Computational Biophysical Chemistry Group, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India.

The Journal of Chemical Physics
|October 2, 2024
PubMed
Summary
This summary is machine-generated.

This study models how the p53 signaling network and 3D genome organization influence malignant cell fate transitions. Thermodynamic models reveal that p53 binding to gene promoters can act as a phase transition, impacting cancer cell states.

More Related Videos

Through the Looking Glass: Time-lapse Microscopy and Longitudinal Tracking of Single Cells to Study Anti-cancer Therapeutics
06:00

Through the Looking Glass: Time-lapse Microscopy and Longitudinal Tracking of Single Cells to Study Anti-cancer Therapeutics

Published on: May 14, 2016

11.0K
Procedure and Key Optimization Strategies for an Automated Capillary Electrophoretic-based Immunoassay Method
09:32

Procedure and Key Optimization Strategies for an Automated Capillary Electrophoretic-based Immunoassay Method

Published on: September 10, 2017

10.9K

Related Experiment Videos

Last Updated: Jun 11, 2025

Yeast As a Chassis for Developing Functional Assays to Study Human P53
14:57

Yeast As a Chassis for Developing Functional Assays to Study Human P53

Published on: August 4, 2019

9.5K
Through the Looking Glass: Time-lapse Microscopy and Longitudinal Tracking of Single Cells to Study Anti-cancer Therapeutics
06:00

Through the Looking Glass: Time-lapse Microscopy and Longitudinal Tracking of Single Cells to Study Anti-cancer Therapeutics

Published on: May 14, 2016

11.0K
Procedure and Key Optimization Strategies for an Automated Capillary Electrophoretic-based Immunoassay Method
09:32

Procedure and Key Optimization Strategies for an Automated Capillary Electrophoretic-based Immunoassay Method

Published on: September 10, 2017

10.9K

Area of Science:

  • Systems Biology
  • Genomics
  • Biophysics

Background:

  • Cell fate is determined by gene expression profiles, influenced by gene regulatory networks and 3D genome organization.
  • The tumor suppressor p53 signaling network plays a critical role in stress response and cell fate decisions.
  • Understanding the interplay between network topology, genome organization, and cell fate is crucial for cancer research.

Purpose of the Study:

  • To develop thermodynamic models for predicting malignant cell fate based on the p53 signaling network.
  • To incorporate long-range chromatin interactions and network topology into cell fate determination models.
  • To investigate the role of p53 dynamics, including phosphorylation and DNA binding, in regulating cell fate.

Main Methods:

  • Development of thermodynamic models based on network topology and equilibrium thermodynamics.
  • Application of the mean-field approximation to account for long-range chromatin interactions.
  • Analysis of minimum free energy as a determinant of biological network states.
  • Modeling of p53 binding to target gene promoters as a potential first-order phase transition.

Main Results:

  • The study demonstrates that the binding of phosphorylated p53 to target gene promoters can exhibit first-order phase transition properties.
  • The developed models successfully link network topology to cell fate determination in various cancer cell lines (MCF-7, HCT116, K562).
  • Results highlight the significance of p53 signaling dynamics, including phosphorylation and DNA binding, in modulating cell fate decisions.

Conclusions:

  • The findings clarify the biological relevance of p53 network dynamics and 3D genome organization in cell fate determination.
  • The study suggests that these mechanisms represent flexible network designs enabling switches between developmental decisions.
  • The developed thermodynamic framework provides insights into cancer cell plasticity and potential therapeutic targets.