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Related Experiment Video

Updated: Mar 1, 2026

Directed Protein Packaging within Outer Membrane Vesicles from Escherichia coli: Design, Production and Purification

Directed Protein Packaging within Outer Membrane Vesicles from Escherichia coli: Design, Production and Purification

Published on: November 16, 2016

Packing in protein cores.

J C Gaines¹, A H Clark, L Regan

¹Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, United States of America. Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, CT 06520, United States of America.

Journal of Physics. Condensed Matter : an Institute of Physics Journal

|May 31, 2017

Summary

This summary is machine-generated.

Accurate modeling of protein cores requires calibrated atom sizes and explicit hydrogen atoms. This reveals protein cores pack densely, similar to jammed particles, impacting protein stability and design.

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Last Updated: Mar 1, 2026

Directed Protein Packaging within Outer Membrane Vesicles from Escherichia coli: Design, Production and Purification

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Directed Assembly of Elastin-like Proteins into defined Supramolecular Structures and Cargo Encapsulation In Vitro

Published on: April 8, 2020

Area of Science:

Biophysics
Structural Biology
Computational Biology

Background:

Proteins are essential biological polymers with structure crucial for function.
Protein stability is significantly influenced by the hydrophobic effect within the protein core.
Understanding protein core packing is key to predicting structure and stability.

Purpose of the Study:

To investigate optimal modeling strategies for amino acid packing in protein cores.
To determine the packing fraction and arrangement of residues within protein cores.
To compare protein core packing to physical models of particle packing.

Main Methods:

Utilized calibrated atom sizes and explicit inclusion of hydrogen atoms for amino acid representation.
Calculated the packing fraction of protein cores.
Compared protein core packing to discrete element simulations of jammed particle systems.

Main Results:

Protein cores exhibit a packing fraction significantly lower than previously estimated using extended atom representations.
Amino acids in protein cores pack as densely as disordered jammed packings of similarly shaped particles.
Accurate modeling necessitates specific atom sizes and explicit hydrogen representation.

Conclusions:

Proper modeling of protein cores requires precise atomic representations, including hydrogen atoms.
Protein core packing density is comparable to that of jammed granular materials.
These findings are crucial for assessing mutation effects on protein stability and for protein design.