title: Direct NOE simulation from long MD trajectories.
abstract: A software package, MD2NOE, is presented which calculates Nuclear Overhauser Effect (NOE) build-up curves directly from molecular dynamics (MD) trajectories. It differs from traditional approaches in that it calculates correlation functions directly from the trajectory instead of extracting inverse sixth power distance terms as an intermediate step in calculating NOEs. This is particularly important for molecules that sample conformational states on a timescale similar to molecular reorientation. The package is tested on sucrose and results are shown to differ in small but significant ways from those calculated using an inverse sixth power assumption. Results are also compared to experiment and found to be in reasonable agreement despite an expected underestimation of water viscosity by the water model selected.
authors.affiliation: Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States.
authors.forename: G
authors.initials: G
authors.lastname: Chalmers
authors.affiliation: Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States.
authors.forename: J N
authors.initials: JN
authors.lastname: Glushka
authors.affiliation: Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States.
authors.forename: B L
authors.initials: BL
authors.lastname: Foley
authors.affiliation: Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States.
authors.forename: R J
authors.initials: RJ
authors.lastname: Woods
authors.affiliation: Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States. Electronic address: jpresteg@ccrc.uga.edu.
authors.forename: J H
authors.initials: JH
authors.lastname: Prestegard
mesh_terms: D000465:Algorithms; D002236:Carbohydrate Conformation; D003198:Computer Simulation; D009682:Magnetic Resonance Spectroscopy / Q000379:methods* / Q000706:statistics & numerical data*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D012984:Software; D013395:Sucrose / Q000737:chemistry*; D014783:Viscosity; D014867:Water / Q000737:chemistry
chemical_list: D014867:Water; D013395:Sucrose
keywords: Molecular dynamics; Nuclear Overhauser Effect; Simulation; Spin relaxation; Sucrose
references.citation: Prog Nucl Magn Reson Spectrosc. 2014 Apr;78:1-46
references.pmid: 24534087
references.citation: Curr Opin Struct Biol. 2009 Feb;19(1):23-30
references.pmid: 19162471
references.citation: Biopolymers. 2012 May;97(5):276-88
references.pmid: 22189655
references.citation: Nat Rev Mol Cell Biol. 2015 Jan;16(1):18-29
references.pmid: 25531225
references.citation: Molecules. 2013;18(9):10802-28
references.pmid: 24008243
references.citation: Prog Nucl Magn Reson Spectrosc. 2014 May;79:48-68
references.pmid: 24815364
references.citation: J Comput Chem. 2008 Mar;29(4):622-55
references.pmid: 17849372
references.citation: Biochemistry. 1986 Nov 4;25(22):6854-65
references.pmid: 3801398
references.citation: Biopolymers. 2012 May;97(5):289-302
references.pmid: 22058066
references.citation: J Am Chem Soc. 2001 May 23;123(20):4792-802
references.pmid: 11457289
references.citation: J Chem Theory Comput. 2014 Jun 10;10(6):2599-607
references.pmid: 26580780
references.citation: Magn Reson Chem. 2012 Dec;50 Suppl 1:S80-5
references.pmid: 23280664
references.citation: Glycobiology. 2008 Jun;18(6):426-40
references.pmid: 18390826
references.citation: Nucleic Acids Res. 2012 Feb;40(3):1345-55
references.pmid: 22009676
references.citation: J Magn Reson. 2001 Jan;148(1):31-4
references.pmid: 11133273
references.citation: J Am Chem Soc. 2002 Apr 24;124(16):4522-34
references.pmid: 11960483
references.citation: Bioorg Med Chem. 2013 Sep 1;21(17):4976-87
references.pmid: 23886813
references.citation: Glycobiology. 2000 Nov;10(11):1147-56
references.pmid: 11087707
references.citation: Chem Rev. 2014 Jul 9;114(13):6632-60
references.pmid: 24725176
references.citation: J Phys Chem B. 2013 May 2;117(17):4860-9
references.pmid: 23531151
references.citation: RNA. 2014 Jun;20(6):782-91
references.pmid: 24742933
references.citation: PLoS One. 2012;7(6):e39605
references.pmid: 22768096
references.citation: Acc Chem Res. 2002 Jun;35(6):325-31
references.pmid: 12069616
references.citation: J Am Chem Soc. 2005 Sep 21;127(37):12764-5
references.pmid: 16159246
references.citation: FEBS Lett. 1988 Aug 15;236(1):71-6
references.pmid: 2841170
references.citation: J Magn Reson. 2015 May;254:19-26
references.pmid: 25771525
references.citation: J Biomol NMR. 2001 Aug;20(4):297-310
references.pmid: 11563554