title: Simulating the distance distribution between spin-labels attached to proteins.
abstract: EPR/DEER spectroscopy is playing an increasingly important role in the characterization of the conformational states of proteins. In this study, force field parameters for the bifunctional spin-label (RX) used in EPR/DEER are parametrized and tested with molecular dynamics (MD) simulations. The dihedral angles connecting the Cα atom of the backbone to the nitroxide ring moiety of the RX spin-label attached to i and i + 4 positions in a polyalanine α-helix agree very well with those observed in the X-ray crystallography. Both RXi,i+4 and RXi,i+3 are more rigid than the monofunctional spin-label (R1) commonly used in EPR/DEER, while RXi,i+4 is more rigid and causes less distortion in a protein backbone than RXi,i+3. Simplified dummy spin-label models with a single effective particle representing the RXi,i+3 and RXi,i+4 are also developed and parametrized from the all-atom simulations. MD simulations with dummy spin-labels (MDDS) provide distance distributions that can be directly compared to distance distributions obtained from EPR/DEER to rapidly assess if a hypothetical three-dimensional (3D) structural model is consistent with experiment. The dummy spin-labels can also be used in the restrained-ensemble MD (re-MD) simulations to carry out structural refinement of 3D models. Applications of this methodology to T4 lysozyme, KCNE1, and LeuT are shown to provide important insights about their conformational dynamics.
authors: Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, University of Chicago , Chicago, Illinois 60637, United States.
authors: Shahidul M
authors: SM
authors: Islam
authors: Benoît
authors: B
authors: Roux
mesh_terms: D017122:Bacteriophage T4 / Q000201:enzymology; D018360:Crystallography, X-Ray; D004578:Electron Spin Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry*; D024642:Potassium Channels, Voltage-Gated / Q000737:chemistry*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013113:Spin Labels
chemical_list: D024642:Potassium Channels, Voltage-Gated; D013113:Spin Labels; D009113:Muramidase
references: J Chem Theory Comput. 2012 Sep 11;8(9):3257-3273
references: 23341755
references: J Phys Chem B. 2008 Sep 4;112(35):11014-27
references: 18698714
references: Biochemistry. 2008 Aug 5;47(31):7999-8006
references: 18611041
references: Nature. 2012 Jan 26;481(7382):469-74
references: 22230955
references: J Comput Chem. 2008 Aug;29(11):1859-65
references: 18351591
references: J Biol Chem. 2006 Sep 8;281(36):26444-54
references: 16798738
references: Biochemistry. 2013 Sep 24;52(38):6627-32
references: 23984855
references: Nature. 2009 May 21;459(7245):347-55
references: 19458710
references: Science. 2008 Dec 12;322(5908):1655-61
references: 19074341
references: J Comput Chem. 2009 Jul 30;30(10):1545-614
references: 19444816
references: Proteins. 2008 Dec;73(4):851-63
references: 18536011
references: Proc Natl Acad Sci U S A. 2011 Sep 27;108(39):16241-6
references: 21911399
references: Proc Natl Acad Sci U S A. 2014 Feb 4;111(5):1831-6
references: 24429344
references: J Am Chem Soc. 2008 Aug 6;130(31):10141-9
references: 18620390
references: J Mol Biol. 1987 Jan 5;193(1):189-99
references: 3586019
references: Philos Trans R Soc Lond B Biol Sci. 2009 Jan 27;364(1514):149-54
references: 18977735
references: Phys Chem Chem Phys. 2011 Feb 14;13(6):2356-66
references: 21116569
references: Annu Rev Phys Chem. 2012;63:419-46
references: 22404592
references: J Phys Chem B. 2013 May 2;117(17):4740-54
references: 23510103
references: J Comput Chem. 2005 Dec;26(16):1781-802
references: 16222654
references: J Phys Chem B. 2006 Dec 28;110(51):26260-71
references: 17181284
references: Science. 2005 Dec 2;310(5753):1461-5
references: 16322449
references: J Mol Biol. 2008 Mar 28;377(3):804-18
references: 18280500
references: J Phys Chem B. 2006 Dec 28;110(51):26248-59
references: 17181283
references: Drug Alcohol Depend. 1998 Jun-Jul;51(1-2):87-96
references: 9716932
references: J Phys Chem B. 2013 May 2;117(17):4733-9
references: 23510121
references: Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9816-21
references: 24958877
references: Nature. 2005 Sep 8;437(7056):215-23
references: 16041361
references: Biopolymers. 2012 Jan;97(1):35-44
references: 21792846
references: J Phys Chem B. 2008 May 8;112(18):5755-67
references: 18412413
references: Proc Natl Acad Sci U S A. 2008 Jul 29;105(30):10338-43
references: 18647834
references: Nat Struct Mol Biol. 2014 May;21(5):472-9
references: 24747939
references: Structure. 1996 Jul 15;4(7):779-83
references: 8805569
references: J Chem Phys. 2013 Feb 28;138(8):084107
references: 23464140
references: J Phys Chem B. 2011 Jan 20;115(2):397-405
references: 21162593
references: Biophys J. 2008 Mar 1;94(5):1600-12
references: 18024499
references: Appl Magn Reson. 2012 Apr;42(3):377-391
references: 22448103