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Protein as evolvable functionally constrained amorphous matter.

Madhusmita Tripathy1, Anand Srivastava, Srikanth Sastry

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Proteins can be modeled as amorphous materials using graphs to predict function and stability. This approach reveals how protein structure enables specific functions and resistance to mutations.

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Area of Science:

  • Computational biology
  • Biophysics
  • Structural biology

Background:

  • Proteins function through conformational changes.
  • Understanding protein structure-function relationships is key to drug discovery and protein engineering.

Purpose of the Study:

  • To represent proteins as amorphous materials using graph theory.
  • To establish a genotype-phenotype map for protein evolution.
  • To investigate the emergence of functional features in proteins.

Main Methods:

  • Representing proteins as graphs G with edges weighted by elastic stiffnesses.
  • Embedding graphs in physical space to analyze conformational fluctuations.
  • Evolving amorphous materials to select for fitness using a genotype-phenotype map.

Main Results:

  • Observed emergence of allosteric interactions, hinge joints, crack formation, and slide bolts in proteins like adenylate kinase, HSP90, calmodulin, and GPCRs.
  • Identified specific geometries and mode spectra of floppy/liquid-like regions associated with emergent features.
  • Demonstrated a link between protein architecture, function, and stability against mutations.

Conclusions:

  • Protein architecture dictates function and stability.
  • Floppy or liquid-like regions play a crucial role in emergent functional properties.
  • This graph-based approach offers insights into protein design and mutation effects.