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Proline/sidechain C-H/O interactions stabilize cis-proline.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Chemistry

Background:

  • The cis-proline conformation is crucial for protein structure and function.
  • Understanding the factors stabilizing cis-proline is essential for protein engineering and drug design.

Purpose of the Study:

  • To identify local protein structures that stabilize the cis-proline conformation.
  • To investigate the role of C-H/O interactions in stabilizing cis-proline.

Main Methods:

  • Bioinformatics analysis of protein data bank (PDB) structures.
  • Density Functional Theory (DFT) calculations.

Main Results:

  • C-H/O interactions were identified between sidechain oxygen and Pro C-Hα in cis-proline conformations.
  • These interactions are most stabilizing in Glu-Pro sequences, showing a high frequency of cis-proline.
  • DFT calculations confirmed the stabilizing role of C-H/O interactions, especially with anionic residues like Glu and Asp.
  • C-H/O interactions also stabilize cis-proline at phosphoserine-proline and phosphothreonine-proline, with stronger interactions in their dianionic forms.

Conclusions:

  • C-H/O interactions are a key stabilizing factor for cis-proline conformations.
  • The findings explain the higher activation barrier for amide bond isomerism in phosphoserine-proline and phosphothreonine-proline sequences.
  • These interactions may also stabilize other cis amide bonds, highlighting their functional importance.