The authors state no conflict of interest.
MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease†
Article first published online: 9 SEP 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 3306–3319, December 2011
How to Cite
Gunner, M. R., Zhu, X. and Klein, M. C. (2011), MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease. Proteins, 79: 3306–3319. doi: 10.1002/prot.23124
- Issue published online: 10 NOV 2011
- Article first published online: 9 SEP 2011
- Accepted manuscript online: 15 JUL 2011 11:13AM EST
- Manuscript Accepted: 19 MAY 2011
- Manuscript Revised: 12 MAY 2011
- Manuscript Received: 12 JAN 2011
- NSF. Grant Number: MCB-1022208
- NIH. Grant Number: 5G12 RR03060
- continuum electrostatics;
- staphylococcal nuclease;
The pKas of 96 acids and bases introduced into buried sites in the staphylococcal nuclease protein (SNase) were calculated using the multiconformation continuum electrostatics (MCCE) program and the results compared with experimental values. The pKas are obtained by Monte Carlo sampling of coupled side chain protonation and position as a function of pH. The dependence of the results on the protein dielectric constant (ϵprot) in the continuum electrostatics analysis and on the Lennard–Jones non-electrostatics parameters was evaluated. The pKas of the introduced residues have a clear dependence on ϵprot, whereas native ionizable residues do not. The native residues have electrostatic interactions with other residues in the protein favoring ionization, which are larger than the desolvation penalty favoring the neutral state. Increasing ϵprot scales both terms, which for these residues leads to small changes in pKa. The introduced residues have a larger desolvation penalty and negligible interactions with residues in the protein. For these residues, changing ϵprot has a large influence on the calculated pKa. An ϵprot of 8–10 and a Lennard–Jones scaling of 0.25 is best here. The X-ray crystal structures of the mutated proteins are found to provide somewhat better results than calculations carried out on mutations made in silico. Initial relaxation of the in silico mutations by Gromacs and extensive side chain rotamer sampling within MCCE can significantly improve the match with experiment. Proteins 2011; © 2011 Wiley-Liss, Inc.