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Protein and Protein Structure02:15

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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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From Infinite Helices to β Sheets: Structural Insights from Electronic Structure Calculations.

Francisco Adasme-Carreño1,2, Camila Muñoz-Gutiérrez1,2, Mauricio Bedoya1,2

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Protein folding depends on helical and sheet structures. Periodic density functional theory (DFT) reveals that while helices dominate single chains, beta sheets become more stable with more strands, especially in water, impacting protein misfolding.

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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Protein Science

Background:

  • Protein folding and aggregation involve helical and sheet conformations.
  • The intrinsic energetics governing these structures are not fully understood.

Purpose of the Study:

  • To characterize the conformational landscape of polyalanine using periodic density functional theory (DFT).
  • To investigate the energetic balance between alpha-helices and beta-sheets in gas and aqueous phases.
  • To understand the role of hydrogen bonding and solvation in protein secondary structure stability.

Main Methods:

  • Periodic density functional theory (DFT) calculations at 0 K.
  • Utilized infinite one- and two-dimensional models for polyalanine.
  • Simulated both gas-phase and aqueous environments.

Main Results:

  • Alpha-helices are favored in isolated polyalanine chains.
  • Beta-sheet stability increases with the number of strands due to hydrogen-bond saturation.
  • Solvation lowers energy barriers for helix-to-sheet transitions.

Conclusions:

  • Beta sheets can be more stable than alpha-helices in extended structures, explaining their prevalence in amyloid and fibrous proteins.
  • Periodic DFT is a valuable tool for studying protein secondary structure energetics in condensed phases.
  • Findings provide insights into protein folding and misfolding mechanisms.