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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...

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

Protein Folding

Protein Folding

Induced-fit Model

Induced-fit Model

Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical...

Globular and Fibrous Proteins

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...

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...

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Related Experiment Video

Updated: Oct 7, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Recent Developments in Data-Assisted Modeling of Flexible Proteins.

Cezary Czaplewski¹, Zhou Gong², Emilia A Lubecka³

¹Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.

Frontiers in Molecular Biosciences

|January 10, 2022

Summary

This review covers methods for determining dynamic protein structures, focusing on intrinsically-disordered proteins (IDPs) and flexible peptides. Techniques like nuclear magnetic resonance (NMR) and small-angle X-ray scattering (SAXS) help analyze protein conformational ensembles.

Keywords:

chemical cross-linking coupled with mass spectroscopy coarse graining conformational ensembles data-assisted modeling molecular dynamics nuclear magnetic resonance proteins small-angle X-ray scattering

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Last Updated: Oct 7, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

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Published on: June 20, 2025

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

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

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

Published on: July 16, 2017

Area of Science:

Biochemistry and Structural Biology
Computational Biology

Background:

Proteins exhibit diverse conformational dynamics, including intrinsically-disordered proteins (IDPs) lacking fixed structures.
Conformational flexibility is crucial for protein function, leading to ensemble-averaged experimental observations.

Purpose of the Study:

To review recent advancements in determining dynamic structures of flexible peptides and proteins.
To highlight methods for analyzing protein conformational ensembles.

Main Methods:

Nuclear Magnetic Resonance (NMR) spectroscopy.
Small-Angle X-ray Scattering (SAXS).
Chemical Cross-linking coupled with Mass Spectrometry (XL-MS).

Main Results:

These techniques provide ensemble-averaged restraints for structural analysis.
Methods allow for re-weighting simulated conformational ensembles.
Information extraction from experimental data is key to understanding dynamic structures.

Conclusions:

Dynamic structure determination is essential for understanding protein function.
Integrated approaches using NMR, SAXS, and XL-MS advance the study of protein conformational ensembles.
These methods enable a more comprehensive view of protein dynamics.