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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Published on: July 14, 2015

Mutational robustness and geometrical form in protein structures.

Julia Hartling¹, Junhyong Kim

¹Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.

Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution

|November 2, 2007

Summary

Mutationally robust proteins exhibit enhanced symmetry and compactness, aligning with theoretical predictions. This geometric regularity is linked to protein folding stability and landscape characteristics.

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Area of Science:

Structural biology
Biophysics
Computational biology

Background:

Theoretical models suggest mutationally robust (designable) phenotypes possess specific geometric features like compactness and regularity.
These geometric properties are hypothesized to influence protein folding speed, stability, and mutational robustness.

Purpose of the Study:

To empirically test the theoretical link between protein structure geometry and mutational robustness.
To investigate the relationship between protein compactness, geometric regularity, and stability.

Main Methods:

Analysis of 2,660 experimentally determined protein structures from the Protein Data Bank (PDB) and Class Architecture Topology Homologous superfamily (CATH) databases.
Development of a geometric regularity index to quantify structural features.
Statistical analysis to correlate geometric properties with mutational robustness.

Main Results:

Empirical data supports theoretical predictions: mutationally robust proteins are indeed more symmetric and compact.
The observed relationship between compactness and robustness is not solely due to amino acid packing but reflects system-level properties and folding landscape characteristics.
A strong correlation was found between geometric regularity and protein stability.

Conclusions:

Protein structure geometry, specifically symmetry and compactness, is a significant factor in mutational robustness.
The folding landscape and system-level properties, rather than just local packing, mediate the link between protein form and robustness.
A general triplet relationship between mutational robustness, stability, and form is hypothesized for systems optimizing sequence-structure relationships.