The authors state no conflict of interest.
Exploring conformational changes coupled to ionization states using a hybrid Rosetta-MCCE protocol†
Article first published online: 30 AUG 2011
Copyright © 2011 Wiley-Liss, Inc.
Proteins: Structure, Function, and Bioinformatics
Special Issue: Protein Electrostatics Calculations: Critical Assessment of Progress and Problems
Volume 79, Issue 12, pages 3356–3363, December 2011
How to Cite
Song, Y. (2011), Exploring conformational changes coupled to ionization states using a hybrid Rosetta-MCCE protocol. Proteins, 79: 3356–3363. doi: 10.1002/prot.23146
- Issue published online: 10 NOV 2011
- Article first published online: 30 AUG 2011
- Accepted manuscript online: 2 AUG 2011 09:26AM EST
- Manuscript Accepted: 24 JUL 2011
- Manuscript Revised: 9 JUL 2011
- Manuscript Received: 11 JAN 2011
- pKa prediction;
- Rosetta refinement;
- reorganization energy
A hybrid protocol combining Rosetta fullatom refinement and Multi-Conformation Continuum Electrostatics (MCCE) to estimate pKa is applied to the blind prediction of 94 mutated residues in Staphylococcal nuclease (SNase), as part of the pKa-cooperative benchmark test. The standard MCCE method is limited to sidechain conformational changes. The Rosetta refinement protocol is used to add the backbone conformational changes in pKa calculations. The non-electrostatic energy component from Rosetta and the electrostatic energy from MCCE are combined to weight the calculated ionization states. Of 63 measured pKas, the root mean squared deviation (RMSD) between the calculated pKas and the measured values is 4.3, showing an improvement compared to the RMSD of 6.6 in the standard MCCE calculations, using a low protein dielectric constant of 4. The breakdown of pKa shift from the solution values (ΔpKa) shows that the desolvation energy contributes the most in the standard MCCE calculations. Lowering desolvation penalties and optimizing electrostatic interactions with the Rosetta/MCCE protocol reduces the ΔpKa to favor the charged states. Analysis also showed that the Rosetta/MCCE protocol samples conformations with pKas close to the solution values. The question remains whether the correct conformational changes coupled to the ionization changes are found here. Nevertheless, a challenge emerges to accurately estimate the reorganization energy, which is not directly measured from the electrostatic environment of the site of interest. Possible improvements to the protocol are also discussed. Proteins 2011; © 2011 Wiley-Liss, Inc.