title: Quantum mechanical NMR simulation algorithm for protein-size spin systems.
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.
authors.affiliation: Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK; School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK.
authors.forename: Luke J
authors.initials: LJ
authors.lastname: Edwards
authors.affiliation: School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK.
authors.forename: D V
authors.initials: DV
authors.lastname: Savostyanov
authors.affiliation: School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK.
authors.forename: Z T
authors.initials: ZT
authors.lastname: Welderufael
authors.affiliation: Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Goettingen, Germany.
authors.forename: Donghan
authors.initials: D
authors.lastname: Lee
authors.affiliation: School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK. Electronic address: i.kuprov@soton.ac.uk.
authors.forename: Ilya
authors.initials: I
authors.lastname: Kuprov
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D006801:Humans; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008956:Models, Chemical; D011789:Quantum Theory; D013113:Spin Labels; D025801:Ubiquitin / Q000032:analysis* / Q000737:chemistry*
chemical_list: D013113:Spin Labels; D025801:Ubiquitin
keywords: Nuclear magnetic resonance; Protein; Simulation