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Quantum mechanical NMR simulation algorithm for protein-size spin systems

Quantum mechanical NMR simulation algorithm for protein-size spin systems
Quantum mechanical NMR simulation algorithm for protein-size spin systems
Nuclear magnetic resonance spectroscopy is one of the few remaining areas of physical chemistry for which polynomially scaling quantum mechanical simulation methods have not so far been available. In this communication we adapt the restricted state space approximation to protein NMR spectroscopy and illustrate its performance by simulating common 2D and 3D liquid state NMR experiments (including accurate description of relaxation processes using Bloch–Redfield–Wangsness theory) on isotopically enriched human ubiquitin – a protein containing over a thousand nuclear spins forming an irregular polycyclic three-dimensional coupling lattice. The algorithm uses careful tailoring of the density operator space to only include nuclear spin states that are populated to a significant extent. The reduced state space is generated by analysing spin connectivity and decoherence properties: rapidly relaxing states as well as correlations between topologically remote spins are dropped from the basis set.
nuclear magnetic resonance, protein, simulation
107-113
Edwards, Luke J.
fc858f09-2669-4a26-9b25-6a00364954cd
Savostyanov, D.V.
e96cbd06-e7b0-4712-8cb6-d786e34bf796
Welderufael, Z.T.
b8cd955d-dc28-46aa-8841-4a5e65ac69a8
Lee, Donghan
4c6de539-1a1c-4c68-aea7-235116338f28
Kuprov, Ilya
bb07f28a-5038-4524-8146-e3fc8344c065
Edwards, Luke J.
fc858f09-2669-4a26-9b25-6a00364954cd
Savostyanov, D.V.
e96cbd06-e7b0-4712-8cb6-d786e34bf796
Welderufael, Z.T.
b8cd955d-dc28-46aa-8841-4a5e65ac69a8
Lee, Donghan
4c6de539-1a1c-4c68-aea7-235116338f28
Kuprov, Ilya
bb07f28a-5038-4524-8146-e3fc8344c065

Edwards, Luke J., Savostyanov, D.V., Welderufael, Z.T., Lee, Donghan and Kuprov, Ilya (2014) Quantum mechanical NMR simulation algorithm for protein-size spin systems. Journal of Magnetic Resonance, 243, 107-113. (doi:10.1016/j.jmr.2014.04.002).

Record type: Article

Abstract

Nuclear magnetic resonance spectroscopy is one of the few remaining areas of physical chemistry for which polynomially scaling quantum mechanical simulation methods have not so far been available. In this communication we adapt the restricted state space approximation to protein NMR spectroscopy and illustrate its performance by simulating common 2D and 3D liquid state NMR experiments (including accurate description of relaxation processes using Bloch–Redfield–Wangsness theory) on isotopically enriched human ubiquitin – a protein containing over a thousand nuclear spins forming an irregular polycyclic three-dimensional coupling lattice. The algorithm uses careful tailoring of the density operator space to only include nuclear spin states that are populated to a significant extent. The reduced state space is generated by analysing spin connectivity and decoherence properties: rapidly relaxing states as well as correlations between topologically remote spins are dropped from the basis set.

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More information

e-pub ahead of print date: 18 April 2014
Published date: 18 April 2014
Additional Information: Funded by EPSRC: Spin Dynamics - from quantum theory to cancer diagnostics (EP/H003789/1)
Keywords: nuclear magnetic resonance, protein, simulation
Organisations: Computational Systems Chemistry

Identifiers

Local EPrints ID: 369179
URI: http://eprints.soton.ac.uk/id/eprint/369179
PURE UUID: 92ef650d-feed-4801-be2c-357b71d3281b
ORCID for Ilya Kuprov: ORCID iD orcid.org/0000-0003-0430-2682

Catalogue record

Date deposited: 29 Sep 2014 11:37
Last modified: 10 Sep 2019 00:37

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