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Related Experiment Videos

Prediction of polyelectrolyte polypeptide structures using Monte Carlo conformational search methods with implicit

J S Evans1, S I Chan, W A Goddard

  • 1Arthur Amos Noyes Laboratory for Chemical Physics, California Institute of Technology, Pasadena 91125, USA.

Protein Science : a Publication of the Protein Society
|October 1, 1995
PubMed
Summary

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Computational methods predict protein structures for charged amino acid sequences. Polyelectrolyte peptides like poly-L-glutamic acid favor alpha-helices, while aspartic acid and phosphoserine sequences adopt beta-strand and beta-turn structures, forming unique folded conformations.

Area of Science:

  • Computational structural biology
  • Protein biophysics
  • Biochemistry

Background:

  • Many proteins contain negatively charged amino acid sequences crucial for function.
  • Experimental methods like X-ray crystallography and NMR struggle to determine structures for these charged domains.

Purpose of the Study:

  • To computationally predict the folded structures of polyelectrolyte peptides representing charged regions in proteins.
  • To investigate the correlation between amino acid sequence and global conformational minima.

Main Methods:

  • Applied the dihedral probability grid-Monte Carlo (DPG-MC) conformational search algorithm.
  • Used charge equilibration for atomic charges and DREIDING parameters.
  • Simulated solvation using sodium counterions and a distance-dependent dielectric constant.

Related Experiment Videos

  • Calculated solvation energies for lowest energy conformers using the protein dipole-Langevin dipole method.

    • Main Results:

    • Poly-L-glutamic acid (Poly-L-Glu20) showed a preference for right-handed alpha-helix (47% helicity), aligning with experimental data.
    • Aspartic acid (Aspn) and phosphoserine (PSer20) containing sequences exhibited low alpha-helix preference (<10%).
    • Aspn, PSer20, and (PSer-Asp)10 sequences showed significant percentages of beta-strand and beta-turn dihedrals, forming supercoils, collapsed bends, and C-shaped structures.

    Conclusions:

    • Amino acid sequence dictates the global folded conformation of charged polypeptide regions.
    • Computational modeling provides insights into the structures of intrinsically disordered or difficult-to-crystallize protein domains.
    • Predicted structures offer a basis for understanding the function of these charged sequences in proteins like sodium channels and parathymosin.