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Protein Folding

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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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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The function of proteins depends on their native three-dimensional structure, which is dictated by the amino acid sequence of the specific protein. Folding of the polypeptide chain takes place under specific conditions that energetically favor the folded conformation. In contrast, protein denaturation occurs spontaneously under unfavorable conditions that disrupt the integrity of the folded conformation. Thus, the chemical and physical environment of a protein, such as significant changes in pH...

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Studying DNA Looping by Single-Molecule FRET

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Shortening a loop can increase protein native state entropy.

Yulian Gavrilov¹, Shlomi Dagan¹, Yaakov Levy¹

¹Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel.

|September 16, 2015

Summary

This summary is machine-generated.

Shortening protein loops can increase native state entropy, enhancing protein stability. This effect varies, not being a universal rule for all proteins or loops.

Keywords:

coarse-grained model conformational entropy molecular dynamics native state dynamics protein folding

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Area of Science:

Biochemistry
Structural Biology
Computational Biology

Background:

Protein loops are crucial for protein structure, function, stability, and folding.
Shortening loops may increase native state conformational entropy, potentially stabilizing proteins more than predicted by polymer models.
The impact of loop length on native state dynamics and stability requires further investigation across different protein systems.

Purpose of the Study:

To generalize the effect of loop length shortening on native state dynamics.
To investigate how gradual shortening of long or solvent-exposed loops in four different proteins affects their stability.
To determine if increased native state entropy upon loop shortening is a general phenomenon or protein-specific.

Main Methods:

All-atom molecular dynamics simulations were employed.
Gradual shortening of loop regions in four distinct proteins was simulated.
Analysis focused on changes in native state and unfolded state entropy.

Main Results:

For AcP and Ubc7 proteins, loop shortening increased native state entropy, alongside effects on unfolded state entropy.
For two SH3 domain permutants, loop shortening only altered unfolded state entropy, consistent with experimental stabilization.
An increase in native state entropy due to loop shortening is not unique to AcP but is not a universal outcome for all proteins.

Conclusions:

Loop shortening can increase native state entropy, contributing to protein stabilization, but this is not a universal effect.
The impact of loop length modification on both folded and unfolded states influences overall protein stability.
Findings highlight the nuanced relationship between loop length, conformational entropy, and protein stability.