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Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Protein Folding Quality Check in the RER

Protein Folding Quality Check in the RER

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...

Intrinsically Disordered Proteins

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...

Conservation of Protein Domains

Conservation of Protein Domains

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...

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Related Experiment Video

Updated: Mar 13, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Predicting Real-Valued Protein Residue Fluctuation Using FlexPred.

Lenna Peterson¹, Michal Jamroz², Andrzej Kolinski²

¹Department of Biological Sciences, College of Science, Purdue University, 915 W. State Street, West Lafayette, IN, 47907-2054, USA.

Methods in Molecular Biology (Clifton, N.J.)

|October 28, 2016

Summary

This summary is machine-generated.

FlexPred rapidly predicts protein residue fluctuation from 3D structures, offering a faster alternative to resource-intensive methods. This tool aids in understanding protein dynamics crucial for function and design.

Keywords:

Bioinformatics Computational biology Molecular dynamics Protein conformational flexibility Protein design Protein flexibility Protein residue fluctuation Protein structure Support vector machine Support vector regression

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Structural Biology
Computational Biology
Biophysics

Background:

Protein structure is conventionally viewed as static, but dynamics are increasingly recognized as vital for protein function, including interactions with other molecules.
Understanding protein flexibility is crucial for applications like computational protein docking and protein design.
Experimental methods (X-ray crystallography B-factors, NMR spectroscopy) and molecular dynamics (MD) simulations provide insights into residue flexibility but are resource-intensive.

Purpose of the Study:

To introduce FlexPred, a web server and stand-alone tool for rapid prediction of absolute per-residue fluctuation from 3D protein structures.
To provide a computationally efficient method for assessing protein dynamics.

Main Methods:

Development of the FlexPred web server and stand-alone software.
Prediction of absolute per-residue fluctuation from input 3D protein structures.

Main Results:

FlexPred demonstrated strong performance in predicting protein residue fluctuations.
Comparison with MD simulations on 592 nonredundant structures yielded an average correlation coefficient of 0.669.
The average root mean square error between predicted and observed fluctuations was 1.07 Å.

Conclusions:

FlexPred offers a rapid and accurate method for predicting protein residue fluctuations.
The tool provides a valuable resource for researchers studying protein dynamics, function, and design.
FlexPred is accessible via a web server at http://kiharalab.org/flexPred/.