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Related Concept Videos

Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

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Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
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Protein Diffusion in the Membrane01:24

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Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
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Efficient Sampling of Short Protein Trajectories with Conditional Diffusion Models.

Chuanye Xiong1,2,3, Palanisamy Kandhan1,2,3, Dongyang Chen1,2,3

  • 1Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States.

Journal of Chemical Theory and Computation
|January 2, 2026
PubMed
Summary
This summary is machine-generated.

TSS-Pro, a new diffusion framework, efficiently samples protein conformational trajectories. It aids in understanding protein dynamics and exploring complex protein landscapes, advancing structural biology.

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Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Protein structure dictates biological function, a key challenge in structural biology.
  • Advances like AlphaFold predict static protein structures but exploring dynamics requires new methods.
  • Efficient sampling of protein conformational space is crucial for understanding function.

Purpose of the Study:

  • To introduce TSS-Pro, a conditional generative diffusion framework for efficient protein conformational trajectory sampling.
  • To enable exploration of protein dynamics and conformational landscapes.
  • To provide a tool for high-throughput analysis of large and complex protein systems.

Main Methods:

  • Developed TSS-Pro, a conditional generative diffusion framework.
  • Implemented two sampling strategies: consecutive sampling for temporal coherence and parallel sampling for diversity.
  • Validated TSS-Pro on alanine dipeptide, ubiquitin, and Drosophila cryptochrome (dCRY).

Main Results:

  • TSS-Pro successfully reproduced the free energy landscape of alanine dipeptide.
  • Consecutive sampling with TSS-Pro identified distinct conformational states in ubiquitin.
  • Parallel sampling with TSS-Pro efficiently explored the conformational dynamics of the large dCRY protein.

Conclusions:

  • TSS-Pro enables efficient sampling of protein conformational trajectories.
  • The framework facilitates high-throughput exploration of protein dynamics for complex systems.
  • TSS-Pro advances the study of protein structure-function relationships by exploring conformational space.