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

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

Published on: July 16, 2017

Random close packing in protein cores.

Jennifer C Gaines^1,2, W Wendell Smith³, Lynne Regan^1,2,4,5

¹Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.

Physical Review. E

|April 15, 2016

Summary

This summary is machine-generated.

New research using the explicit hydrogen model reveals protein cores have a packing fraction of approximately 0.56. This finding, unlike previous estimates, offers a more accurate understanding of protein structure and mutation effects.

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Area of Science:

Structural Biology
Biophysics
Computational Biology

Background:

Early protein structure analyses reported core packing fractions (ϕ) around 0.75, similar to close-packed spheres.
These early studies used extended atom models, which were less physically accurate than explicit hydrogen models.

Purpose of the Study:

To recalculate protein core packing fractions using the physically accurate explicit hydrogen model.
To provide a more precise understanding of the physical basis of protein structure.

Main Methods:

Employed the explicit hydrogen model for analysis.
Calculated packing fractions for the cores of over 200 high-resolution protein structures.

Main Results:

Protein cores exhibit a packing fraction (ϕ) of approximately 0.56.
This value aligns with simulations of random amino acid packings, differing significantly from previous estimates.

Conclusions:

The explicit hydrogen model provides a more accurate representation of protein core packing.
This improved understanding facilitates predictions regarding amino acid mutations' effects on protein cores and interfaces.