Performance of density functional models to reproduce observed 13Cα chemical shifts of proteins in solution
- 8 September 2008
- journal article
- research article
- Published by Wiley in Journal of Computational Chemistry
- Vol. 30 (6), 884-892
- https://doi.org/10.1002/jcc.21105
Abstract
The purpose of this work is to test several density functional models (namely, OPBE, O3LYP, OPW91, BPW91, OB98, BPBE, B971, OLYP, PBE1PBE, and B3LYP) to determine their accuracy and speed for computing 13Cα chemical shifts in proteins. The test is applied to 10 NMR-derived conformations of the 76-residue α/β protein ubiquitin (protein data bank id 1D3Z). With each functional, the 13Cα shielding was computed for 760 amino acid residues by using a combination of approaches that includes, but is not limited to, treating each amino acid X in the sequence as a terminally blocked tripeptide with the sequence Ac-GXG-NMe in the conformation of the regularized experimental protein structure. As computation of the 13Cα chemical shifts, not their shielding, is the main goal of this work, a computation of the 13Cα shielding of the reference, namely, tetramethylsilane, is investigated here and an effective and a computed tetramethylsilane shielding value for each of the functionals is provided. Despite observed small differences among all functionals tested, the results indicate that four of them, namely, OPBE, OPW91, OB98, and OLYP, provide the most accurate functionals with which to reproduce observed 13Cα chemical shifts of proteins in solution, and are among the faster ones. This study also provides evidence for the applicability of these functionals to proteins of any size or class, and for the validation of our previous results and conclusions, obtained from calculations with the slower B3LYP functional. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009Keywords
This publication has 64 references indexed in Scilit:
- Intrinsic apoptosis in mechanically ventilated human diaphragm: linkage to a novel Fos/FoxO1/Stat3‐Bim axisThe FASEB Journal, 2011
- FoxO Transcription Factors Promote Cardiomyocyte Survival upon Induction of Oxidative StressPublished by Elsevier BV ,2011
- Factors affecting the use of13Cα chemical shifts to determine, refine, and validate protein structuresProteins-Structure Function and Bioinformatics, 2007
- RNA regulons: coordination of post-transcriptional eventsNature Reviews Genetics, 2007
- Use of 13Cα Chemical Shifts in Protein Structure DeterminationThe Journal of Physical Chemistry B, 2007
- FoxOs Are Lineage-Restricted Redundant Tumor Suppressors and Regulate Endothelial Cell HomeostasisCell, 2007
- HuR and mRNA stabilityCellular and Molecular Life Sciences, 2001
- The Protein Data BankNucleic Acids Research, 2000
- 1H, 13C and 15N chemical shift referencing in biomolecular NMRJournal of Biomolecular NMR, 1995
- Structure of ubiquitin refined at 1.8 Å resolutionJournal of Molecular Biology, 1987