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Related Experiment Video

Updated: Jul 6, 2026

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

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

Published on: July 14, 2015

Statistically enhanced promiscuity of structurally correlated patterns.

D B Lukatsky¹, E I Shakhnovich

¹Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics

|March 21, 2008

Summary

Correlated atomic surface density patterns enhance protein binding promiscuity. This principle applies to designing highly connected proteins (hubs) in biological networks.

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Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

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Last Updated: Jul 6, 2026

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

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

Published on: July 14, 2015

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

Area of Science:

Computational chemistry
Structural biology
Network science

Background:

Protein interaction networks are crucial for cellular functions.
Highly connected proteins (hubs) play significant roles in these networks.
Understanding the structural basis of protein promiscuity is key to network design.

Purpose of the Study:

To investigate the relationship between atomic surface density patterns and protein promiscuity.
To propose a design principle for enhancing protein connectivity.
To develop a theoretical framework for this phenomenon.

Main Methods:

Development of an analytical theory.
Statistical analysis of atomic surface density patterns.
Modeling of interatomic interactions.

Main Results:

Statistically higher promiscuity observed in correlated surface density patterns compared to noncorrelated ones.
The effect is independent of the specific interatomic interaction potential form (finite range).
Key predictions derived from the analytical theory.

Conclusions:

Correlated atomic surface density is a generic design principle for highly connected proteins.
This finding offers insights into the architecture of protein interaction networks.
The theoretical framework provides a basis for predicting and designing protein interactions.