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Contact-assisted protein structure modeling by global optimization in CASP11.

Keehyoung Joo1,2, InSuk Joung1,3, Qianyi Cheng1,3

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|December 18, 2015
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Summary

This study improved protein structure modeling using contact information in CASP11. While direct contact data offered minor gains, Nuclear Overhauser Effect restraints enabled accurate 3D protein modeling, outperforming other methods.

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NMR structure determinationcaspcontact-assisted modelingglobal optimizationprotein structure modelingsparse and ambiguous NOE restrainttwo-tier optimization

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Protein structure modeling is crucial for understanding biological function.
  • CASP (Critical Assessment of protein Structure Prediction) provides a benchmark for protein structure prediction methods.
  • Contact information, such as residue-residue contacts and Nuclear Overhauser Effect (NOE) restraints, can aid in protein structure prediction.

Purpose of the Study:

  • To evaluate the effectiveness of contact-assisted protein structure modeling using the conformational space annealing method in CASP11.
  • To assess the impact of predicted residue-residue contacts (Tp targets) and ambiguous NOE restraints (Ts targets) on protein model accuracy.
  • To explore the potential of brute-force optimization for accurate 3D protein model generation from NOE restraints.

Main Methods:

  • Applied the conformational space annealing method for protein structure modeling.
  • Incorporated a Lorentzian function for contact energy terms in template-free modeling for Tp targets.
  • Formulated a two-tier optimization problem for Ts targets, involving NOE peak assignment and 3D model generation.

Main Results:

  • Limited structural improvement was observed for Tp models due to inaccurate contact information (only ~18% correct).
  • Remarkably accurate protein 3D models (3.6 Å Cα accuracy) were generated for Ts targets using brute-force optimization of NOE restraints.
  • Significant structural improvement was achieved for Tc targets, with generated structures outperforming other CASP11 groups in GDT-TS for 20 out of 24 targets.

Conclusions:

  • Contact-assisted protein modeling shows promise, particularly when utilizing reliable NOE restraints.
  • Brute-force optimization of energy functions is a viable strategy for accurate protein structure prediction from NOE data.
  • The applied methods demonstrated competitive performance in CASP11, especially for targets with ambiguous NOE information.