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Proteins with selected sequences: a heteropolymeric study.

J Wilder1, E I Shakhnovich

  • 1Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA. juergen@chasma.harvard.edu

Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics
|December 2, 2000
PubMed
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This study models protein sequence optimization for stable native structures using selective temperature. Advanced replica calculations reveal crucial phase diagram changes beyond quadratic approximations, ensuring kinetic accessibility.

Area of Science:

  • Protein folding and biophysics
  • Statistical mechanics of polymers

Background:

  • Protein sequences are not random; they encode stable, kinetically accessible native structures.
  • Optimizing sequences for specific conformations is essential for understanding protein function.

Purpose of the Study:

  • To develop a model incorporating selective temperature to statistically optimize protein sequences for target conformations.
  • To investigate phase transitions to the native state (frozen globule) using advanced replica calculations.

Main Methods:

  • Utilizing a selective temperature in sequence space to optimize sequences.
  • Performing replica calculations that extend beyond quadratic approximations in the field-theoretical Hamiltonian.
  • Analyzing the sequence correlation function along the chain for short-ranged monomer potentials.

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Main Results:

  • A phase diagram was obtained, showing transitions to the native state at specific temperatures and selective temperatures.
  • Going beyond quadratic approximations significantly alters the phase diagram.
  • A one-step replica permutation symmetry scheme is proposed as sufficient for model solution.
  • The sequence correlation function for native contacts was derived.

Conclusions:

  • The model provides insights into the statistical selection of protein sequences for stable structures.
  • Advanced theoretical approximations are critical for accurately predicting protein folding phase diagrams.
  • The proposed symmetry scheme simplifies the analysis of such complex systems.