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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...

Intrinsically Disordered Proteins

Intrinsically Disordered Proteins

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 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....

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Related Experiment Video

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Controlling Structural Bias in Intrinsically Disordered Proteins Using Solution Space Scanning.

Alex S Holehouse^1,2, Shahar Sukenik³

¹Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States.

Journal of Chemical Theory and Computation

|January 31, 2020

Summary

This summary is machine-generated.

Intrinsically disordered proteins (IDPs) can change their shape and structure by altering the surrounding solution conditions. A new computational method, SolSpace Scanning, allows researchers to explore these changes and potentially control protein function.

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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:

Biochemistry
Computational Biology
Structural Biology

Background:

Intrinsically disordered proteins (IDPs) and regions (IDRs) lack stable tertiary structures, existing as dynamic conformational ensembles.
Their function is influenced by local residual structures and global conformational biases, which are affected by both amino acid sequence and solution environment.

Purpose of the Study:

To investigate how altering solution conditions can modulate the conformational ensemble of IDPs/IDRs.
To develop an efficient computational method for exploring these solution-protein interactions.

Main Methods:

Development and application of Solution Space (SolSpace) Scanning, an all-atom Monte Carlo simulation technique.
Systematic exploration of diverse solution conditions to alter protein-solution interactions.

Main Results:

SolSpace Scanning effectively modifies IDR global dimensions and local residual structures by tuning specific protein-solution interactions.
The method demonstrates that solution conditions can significantly impact the conformational ensemble of IDRs.

Conclusions:

SolSpace Scanning provides an alternative to traditional mutational studies for understanding sequence-to-ensemble relationships in IDRs.
The findings suggest the potential for solution-based regulation of IDR functions within cellular environments.