Modeling and minimizing CAPRI round 30 symmetrical protein complexes from CASP-11 structural models.

Area of Science:

• Structural Biology
• Computational Biology
• Biophysics

Background:

• Many protein complexes in the CASP-11/CAPRI-30 experiment were symmetrical homo-dimers and homo-tetramers.
• Accurate modeling of these symmetrical protein assemblies is crucial for understanding their biological functions.

Purpose of the Study:

• To retrospectively analyze the performance of a symmetry docking algorithm (SAM) on published CAPRI Round 30 targets.
• To evaluate the quality of CASP structural models from a docking perspective.
• To establish an economical and effective strategy for modeling symmetrical protein complexes.

Main Methods:

• Utilized the 'SAM' polar Fourier symmetry docking algorithm for protein complex modeling.
• Combined SAM docking with NAMD energy minimization for refining 3D models.
• Performed docking analysis on CASP 'stage-2' fold prediction models and CASP 'center' structures.

Main Results:

• The SAM algorithm, coupled with NAMD minimization, frequently produced acceptable or superior 3D models of symmetrical protein complexes.
• Docking only CASP 'center' structures proved to be an efficient and cost-effective modeling strategy.
• A significant proportion of CASP models were found to be 'dockable', yielding acceptable symmetrical complex models.

Conclusions:

• The SAM docking algorithm offers a powerful tool for modeling symmetrical protein complexes.
• The developed docking protocol, when applied to CASP-quality models, can routinely generate accurate 3D structures.
• Future application on computer clusters is expected to enhance the routine modeling of symmetrical protein assemblies.