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A peptide bond covalently attaches amino acids through a dehydration reaction. One amino acid's carboxyl group and another amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond. The products that such linkages form are peptides. As more amino acids join this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end has the N-terminal, or the amino-terminal, and the other end has a free...
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Elucidating Molecular Design Principles for Charge-Alternating Peptides.

Josh Smith1, Patrick McMullen1, Zhefan Yuan1

  • 1Department of Chemical Engineering , University of Washington , Seattle , Washington 98195-1750 , United States.

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|November 19, 2019
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Summary

Engineered fusion proteins can improve drug stability and delivery. This study found that glycine substitutions in alternating-charge peptides promote disorder, enhancing their potential for therapeutic applications.

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Area of Science:

  • Biochemistry and biophysics
  • Protein engineering
  • Computational biology

Background:

  • Protein drugs face challenges with stability and rapid clearance, limiting their therapeutic use.
  • Recombinant fusion proteins offer a platform to enhance biologic drug properties by appending polypeptide domains.
  • Existing fusion strategies use conformationally disordered or superhydrophilic peptides separately to improve drug half-life or stability.

Purpose of the Study:

  • To investigate the conformational ensemble of alternating-charge peptides and their glycine-substituted variants.
  • To determine if combining superhydrophilicity and conformational disorder in fusion peptides can address both stability and therapeutic lifetime concerns.
  • To develop a computational method for quantifying conformational disorder in polypeptides for *de novo* fusion protein design.

Main Methods:

  • Enhanced sampling molecular dynamics (MD) simulations to explore peptide conformational landscapes.
  • Circular dichroism (CD) spectroscopy to validate structural predictions from MD simulations.
  • Computational analysis to quantify conformational disorder in polypeptide sequences.

Main Results:

  • The (EK)15 peptide shows a propensity for forming stable antiparallel β-strand secondary structures.
  • Extensive salt bridging stabilizes the secondary structure of the (EK)15 peptide.
  • Limited glycine substitutions disrupt secondary structure, promoting disordered conformations at physiological temperatures.

Conclusions:

  • Alternating-charge peptides exhibit conformational disorder that is crucial for drug delivery applications.
  • Glycine substitutions can effectively modulate the conformational properties of alternating-charge peptides.
  • A validated computational approach is provided for designing effective fusion proteins by quantifying conformational disorder.