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Updated: Jul 19, 2025
07:08
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
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Distance-based global analysis of consistent cis-bonds in protein backbones.
Tetsuji Okada1, Fumiaki Tomoike1
1Department of Life Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan.
Heliyon
|August 14, 2023
Summary
Biological polypeptides contain important cis-bonds. This study introduces a protein-wide analysis to identify consistent cis-bonds, revealing trends and limits in protein structures.
Area of Science:
- Structural biology
- Proteomics
- Biochemistry
Background:
- Biological polypeptides feature cis-linkages, impacting protein structure and function.
- Experimental evidence for cis-bonds is primarily from X-ray crystallography.
- Previous analyses of cis-bonds were entry-wise or residue-wise, lacking a global, protein-wide perspective.
Purpose of the Study:
- To develop a protein-wise analysis for detecting and confirming cis-bonds.
- To distinguish true cis-bonds from isomerizable or misassigned bonds.
- To investigate the consistency and trends of cis-bonds across multiple protein chains.
Main Methods:
- Utilized a computational approach on experimental Protein Data Bank (PDB) chains.
- Developed a procedure for detecting and confirming cis-bonds within protein structures.
- Analyzed cis-bond consistency across multiple chains of the same protein.
Main Results:
- Identified sets of consistent cis-bonds across multiple protein chains.
- Provided insights into proteins with high cis-bond content.
- Established an upper limit for consistent cis-bonds relative to polypeptide length.
Conclusions:
- Consistent cis-bond analysis offers a new perspective on protein structure.
- Findings aid in validating new structural data and understanding protein design limitations.
- Highlights the importance of cis-bonds in protein structural biology and design.
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