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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Mapping monomeric threading to protein-protein structure prediction.

Aysam Guerler1, Brandon Govindarajoo, Yang Zhang

  • 1Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan, 48109, United States.

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Summary

We developed SPRING, a novel strategy for protein complex identification that bypasses laborious library construction. This method efficiently recognizes quaternary structures, improving protein-protein interaction modeling.

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Area of Science:

  • Computational biology
  • Structural biology
  • Bioinformatics

Background:

  • Template-based protein-protein structure prediction relies on recognizing similar quaternary folds from experimental libraries.
  • Maintaining monomer and dimer structure libraries is labor-intensive and can limit template recognition.
  • Inappropriate library construction can negatively impact the accuracy of protein complex prediction.

Purpose of the Study:

  • To introduce a novel strategy, SPRING, for efficient and accurate protein complex identification.
  • To overcome the limitations of traditional library-dependent methods in template recognition.
  • To enhance the quality and coverage of quaternary structure recognition for protein-protein interactions.

Main Methods:

  • SPRING maps monomeric threading alignments to protein-protein interactions using original Protein Data Bank (PDB) oligomer entries.
  • The method avoids the need for constructing and maintaining separate monomer and dimer structure libraries.
  • SPRING was evaluated on 1838 nonhomologous protein complexes and benchmarked against ZDOCK.

Main Results:

  • SPRING successfully recognized correct quaternary template structures (TM-score >0.5) in 1115 out of 1838 cases.
  • SPRING achieved a 60% and 17% higher average TM-score for the first model compared to HHsearch and COTH, respectively.
  • SPRING demonstrated a 134% and 167% higher success rate for interface RMSD <2.5 Å compared to HHsearch and COTH.

Conclusions:

  • SPRING offers an efficient and accurate approach to quaternary structure recognition, bypassing the need for library construction.
  • The method significantly improves upon existing tools like HHsearch and COTH in identifying protein complexes.
  • SPRING's speed and accuracy make it suitable for genome-scale modeling of protein-protein interactions, especially when combined with docking methods like ZDOCK.