ArticlePloS one2013
Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- UCBShift 2.0: Bridging the Gap from Backbone to Side Chain Protein Chemical Shift Prediction for Protein Structures.Journal of the American Chemical Society · 2024Article
- Accurate prediction of chemical shifts for aqueous protein structure on "Real World" data.Chemical science · 2020Article
- Structural Characterization of N-WASP Domain V Using MD Simulations with NMR and SAXS Data.Biophysical journal · 2019Article
- Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes.Frontiers in chemistry · 2018Article
- Toward Closing the Gap: Quantum Mechanical Calculations and Experimentally Measured Chemical Shifts of a Microcrystalline Lectin.The journal of physical chemistry. B · 2017Article
- Protein structure refinement using a quantum mechanics-based chemical shielding predictor.Chemical science · 2017Article
- Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods.International journal of molecular sciences · 2016Review
- Article
- Article
- FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models.PeerJ · 2014Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts--sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond ((h3)J(NC')) spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding.
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