System Maintenance Notice

Please note that maintenance work is scheduled between 4 AM and 5 AM - CET. During this time, you may experience reduced performance. Thanks for your patience.

Publications

Journal Article Epublish 4 citations

PubMed: 34641789 DOI: 10.1186/s12859-021-04403-1

CirPred, the first structure modeling and linker design system for circularly permuted proteins.

BMC Bioinformatics 22(Suppl 10):494

Authors: Teng-Ruei Chen, Yen-Cheng Lin, Yu-Wei Huang, Chih-Chieh Chen, Wei-Cheng Lo

Affiliations

  • Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.
  • Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.
  • Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.
  • Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.
  • Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan.
  • Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.
  • Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.
  • Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.
  • Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.
  • The Center for Bioinformatics Research, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.

Abstract

BACKGROUND

This work aims to help develop new protein engineering techniques based on a structural rearrangement phenomenon called circular permutation (CP), equivalent to connecting the native termini of a protein followed by creating new termini at another site. Although CP has been applied in many fields, its implementation is still costly because of inevitable trials and errors.

RESULTS

Here we present CirPred, a structure modeling and termini linker design method for circularly permuted proteins. Compared with state-of-the-art protein structure modeling methods, CirPred is the only one fully capable of both circularly-permuted modeling and traditional co-linear modeling. CirPred performs well when the permutant shares low sequence identity with the native protein and even when the permutant adopts a different conformation from the native protein because of three-dimensional (3D) domain swapping. Linker redesign experiments demonstrated that the linker design algorithm of CirPred achieved subangstrom accuracy.

CONCLUSIONS

The CirPred system is capable of (1) predicting the structure of circular permutants, (2) designing termini linkers, (3) performing traditional co-linear protein structure modeling, and (4) identifying the CP-induced occurrence of 3D domain swapping. This method is supposed helpful for broadening the application of CP, and its web server is available at http://10.life.nctu.edu.tw/CirPred/ and http://lo.life.nctu.edu.tw/CirPred/ .

MeSH

Computational Biology

Cited by