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Related Concept Videos

Protein Folding01:25

Protein Folding

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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
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Native proteins trap high-energy transit conformations.

Andrew E Brereton1, P Andrew Karplus1

  • 1Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.

Science Advances
|November 25, 2015
PubMed
Summary
This summary is machine-generated.

High-energy protein conformations, typically transient, are found stably trapped in native protein structures. Analysis reveals peptide bond angle distortions during these crucial folding and function transitions.

Keywords:
conformational transitiondipeptide conformationdisallowed conformationpeptide geometryprotein foldingprotein stabilityramachandran plotstraintransition state

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Area of Science:

  • Biophysics
  • Structural Biology
  • Protein Dynamics

Background:

  • Protein folding involves overcoming high-energy barriers between stable conformations.
  • Transitions between left (ϕ < 0°) and right (ϕ > 0°) sides of the Ramachandran plot are critical for protein function.
  • The precise mechanisms of peptide geometry distortions during these transitions remain unclear.

Purpose of the Study:

  • To investigate the occurrence and nature of high-energy peptide conformations in native proteins.
  • To map experimentally the bond angle distortions during barrier-crossing transitions.
  • To provide a foundation for theoretical studies on protein folding and function.

Main Methods:

  • Analysis of highly resolved native protein structures.
  • Identification and characterization of stably trapped high-energy conformations (ϕ ~ 0°).
  • Detailed examination of peptide bond angle distortions in these unique residues.

Main Results:

  • High-energy conformations with ϕ ~ 0° are stably trapped in native protein structures, not just transient states.
  • Experimentally derived maps of bond angle distortions along transition pathways were obtained.
  • Unfavorable interactions were observed even in designed, highly stable proteins.

Conclusions:

  • The study confirms the possibility and mechanism of non-glycine residue transitions across the Ramachandran plot.
  • Provides experimental evidence for peptide geometry distortions enabling barrier crossing.
  • Establishes a basis for improved theoretical models of protein folding and function.