Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

Research output: Contribution to journalJournal articleResearchpeer-review

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Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics. / Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael; Boomsma, Wouter Krogh; Lindorff-Larsen, Kresten; Hamelryck, Thomas Wim; Jensen, Jan Halborg.

In: PLoS ONE, Vol. 8, No. 12, e84123, 2013.

Research output: Contribution to journalJournal articleResearchpeer-review

Harvard

Christensen, AS, Linnet, TE, Borg, M, Boomsma, WK, Lindorff-Larsen, K, Hamelryck, TW & Jensen, JH 2013, 'Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics', PLoS ONE, vol. 8, no. 12, e84123. https://doi.org/10.1371/journal.pone.0084123

APA

Christensen, A. S., Linnet, T. E., Borg, M., Boomsma, W. K., Lindorff-Larsen, K., Hamelryck, T. W., & Jensen, J. H. (2013). Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics. PLoS ONE, 8(12), [e84123]. https://doi.org/10.1371/journal.pone.0084123

Vancouver

Christensen AS, Linnet TE, Borg M, Boomsma WK, Lindorff-Larsen K, Hamelryck TW et al. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics. PLoS ONE. 2013;8(12). e84123. https://doi.org/10.1371/journal.pone.0084123

Author

Christensen, Anders Steen ; Linnet, Troels Emtekær ; Borg, Mikael ; Boomsma, Wouter Krogh ; Lindorff-Larsen, Kresten ; Hamelryck, Thomas Wim ; Jensen, Jan Halborg. / Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics. In: PLoS ONE. 2013 ; Vol. 8, No. 12.

Bibtex

@article{bbc95dd9bf1843bb8503cd2a4fc59542,
title = "Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics",
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) JNC' ) 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.",
author = "Christensen, {Anders Steen} and Linnet, {Troels Emtek{\ae}r} and Mikael Borg and Boomsma, {Wouter Krogh} and Kresten Lindorff-Larsen and Hamelryck, {Thomas Wim} and Jensen, {Jan Halborg}",
note = "O.A.",
year = "2013",
doi = "10.1371/journal.pone.0084123",
language = "English",
volume = "8",
journal = "P L o S One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "12",

}

RIS

TY - JOUR

T1 - Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

AU - Christensen, Anders Steen

AU - Linnet, Troels Emtekær

AU - Borg, Mikael

AU - Boomsma, Wouter Krogh

AU - Lindorff-Larsen, Kresten

AU - Hamelryck, Thomas Wim

AU - Jensen, Jan Halborg

N1 - O.A.

PY - 2013

Y1 - 2013

N2 - 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) JNC' ) 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.

AB - 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) JNC' ) 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.

U2 - 10.1371/journal.pone.0084123

DO - 10.1371/journal.pone.0084123

M3 - Journal article

VL - 8

JO - P L o S One

JF - P L o S One

SN - 1932-6203

IS - 12

M1 - e84123

ER -

ID: 99353055