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Protein Dynamics in Living Cells

Protein Dynamics in Living Cells

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...

Mechanical Protein Functions

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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...

Adaptability of Cytoskeletal Filaments

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Conservation of Protein Domains Over Different Proteins

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

A General, Adaptive, Roadmap-Based Algorithm for Protein Motion Computation.

Kevin Molloy, Amarda Shehu

IEEE Transactions on Nanobioscience

|February 11, 2016

Summary

This summary is machine-generated.

This study introduces a novel algorithm inspired by robotics to map protein dynamics across vast time scales. It efficiently identifies transition pathways between protein structures, advancing our understanding of protein function.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

Computational Biology
Biophysics
Structural Biology

Background:

Protein function is intrinsically linked to its dynamic equilibrium.
Characterizing protein transitions between stable and meta-stable states is challenging due to disparate time scales.
Current methods struggle to efficiently map the complex conformational landscape of proteins.

Purpose of the Study:

To develop a novel algorithm for characterizing protein equilibrium dynamics.
To overcome time-scale limitations in analyzing protein conformational transitions.
To provide a method for identifying and prioritizing transition paths between protein structures.

Main Methods:

A robotics-inspired algorithm adapting roadmap-based frameworks for protein conformation space.
Handling rugged energy surfaces by drawing analogies between protein and robot motion.
Balancing global and local searches for comprehensive and physically realistic path generation.

Main Results:

The algorithm generates time- and energy-prioritized lists of transition paths between known protein structures.
Paths are represented as series of intermediate protein conformations.
Demonstrated utility across various proteins, improving upon existing state-of-the-art methods.

Conclusions:

The proposed algorithm effectively addresses time-scale challenges in protein dynamics analysis.
It offers a generalizable approach to mapping protein conformational landscapes.
This method enhances the study of protein function through detailed characterization of equilibrium dynamics.