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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

Mechanical Protein Functions

Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical forces and proteins that are subjected to mechanical forces. Proteins providing mechanical support to the structure of the cell, such as keratin, are subjected to mechanical force, whereas proteins involved in cell movement and transport of molecules across cell membranes, such as an ion pump, are examples of generating mechanical force.

Protein Folding Quality Check in the RER

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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

Protein-Protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

Protein and Protein Structure

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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

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Related Experiment Video

Updated: May 31, 2026

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

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

Published on: July 16, 2017

KINARI-Web: a server for protein rigidity analysis.

Naomi Fox¹, Filip Jagodzinski, Yang Li

¹Department of Computer Science, 140 Governors Drive, University of Massachusetts, Amherst, MA 01003, USA.

Nucleic Acids Research

|June 23, 2011

Summary

This summary is machine-generated.

KINARI-Web provides an interactive platform for protein rigidity analysis and visualization. This web server aids researchers in exploring molecular structures and stabilizing interactions, offering customizable features for all user levels.

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

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

Area of Science:

Computational Biology
Structural Biology
Bioinformatics

Background:

Protein structure-stability relationships are crucial for understanding molecular function.
Rigidity analysis offers insights into protein dynamics and stability.
Existing tools may lack comprehensive visualization or user-friendly features.

Purpose of the Study:

To introduce KINARI-Web, an interactive web server for protein rigidity analysis.
To provide tools for data pre-processing and visualization of rigidity properties.
To cater to both novice and expert users with customizable features.

Main Methods:

Development of an interactive web server (KINARI-Web).
Implementation of data pre-processing tools (chain selection, hydrogen addition, interaction identification).
Integration of a Jmol-based visualizer for exploring rigidity properties.

Main Results:

KINARI-Web enables interactive rigidity analysis of protein structures.
Users can customize analysis by selecting/modifying components and interactions.
Enhanced visualization allows detailed investigation of calculated rigidity properties.

Conclusions:

KINARI-Web offers a valuable resource for studying protein rigidity and stability.
The platform facilitates exploration and understanding of molecular mechanics.
It is freely accessible, promoting wider use in structural biology research.