title: Classification of dynamical diffusion states in single molecule tracking microscopy.
abstract: Single molecule tracking of membrane proteins by fluorescence microscopy is a promising method to investigate dynamic processes in live cells. Translating the trajectories of proteins to biological implications, such as protein interactions, requires the classification of protein motion within the trajectories. Spatial information of protein motion may reveal where the protein interacts with cellular structures, because binding of proteins to such structures often alters their diffusion speed. For dynamic diffusion systems, we provide an analytical framework to determine in which diffusion state a molecule is residing during the course of its trajectory. We compare different methods for the quantification of motion to utilize this framework for the classification of two diffusion states (two populations with different diffusion speed). We found that a gyration quantification method and a Bayesian statistics-based method are the most accurate in diffusion-state classification for realistic experimentally obtained datasets, of which the gyration method is much less computationally demanding. After classification of the diffusion, the lifetime of the states can be determined, and images of the diffusion states can be reconstructed at high resolution. Simulations validate these applications. We apply the classification and its applications to experimental data to demonstrate the potential of this approach to obtain further insights into the dynamics of cell membrane proteins.
authors.affiliation: Nanobiophysics, MESA+ Institute for Nanotechnology, University of Twente, The Netherlands.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Bosch
authors.affiliation: MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, The Netherlands.
authors.forename: Johannes S
authors.initials: JS
authors.lastname: Kanger
authors.affiliation: Nanobiophysics, MESA+ Institute for Nanotechnology, University of Twente, The Netherlands; MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, The Netherlands. Electronic address: subramaniam@amolf.nl.
authors.forename: Vinod
authors.initials: V
authors.lastname: Subramaniam
mesh_terms: D003627:Data Interpretation, Statistical; D004058:Diffusion; D008565:Membrane Proteins / Q000378:metabolism*; D008856:Microscopy, Fluorescence / Q000379:methods; D057054:Molecular Imaging / Q000379:methods*; D009038:Motion; D021381:Protein Transport
chemical_list: D008565:Membrane Proteins
references.citation: Nat Struct Mol Biol. 2011 Oct 23;18(11):1244-9
references.pmid: 22020299
references.citation: Nat Methods. 2010 May;7(5):373-5
references.pmid: 20364146
references.citation: Biophys J. 2007 Jan 15;92(2):613-21
references.pmid: 17085496
references.citation: Methods. 2008 Oct;46(2):131-40
references.pmid: 18634880
references.citation: Cell. 2011 Aug 19;146(4):593-606
references.pmid: 21854984
references.citation: Nat Methods. 2008 Aug;5(8):687-94
references.pmid: 18604216
references.citation: Biophys J. 1991 Oct;60(4):910-21
references.pmid: 1742458
references.citation: Biophys J. 1997 Aug;73(2):1073-80
references.pmid: 9251823
references.citation: J Phys Chem B. 2013 Oct 24;117(42):13308-21
references.pmid: 23915358
references.citation: Biophys J. 2011 Apr 6;100(7):1810-8
references.pmid: 21463595
references.citation: Biophys J. 1993 Jun;64(6):1766-80
references.pmid: 8369407
references.citation: Nat Rev Mol Cell Biol. 2001 Jun;2(6):444-56
references.pmid: 11389468
references.citation: J Cell Sci. 2010 Feb 1;123(Pt 3):309-20
references.pmid: 20130139
references.citation: Biophys J. 1997 Apr;72(4):1744-53
references.pmid: 9083678
references.citation: Biophys J. 1993 Nov;65(5):2021-40
references.pmid: 8298032
references.citation: Nature. 2005 Dec 1;438(7068):578-80
references.pmid: 16319876
references.citation: Annu Rev Biophys Biomol Struct. 2005;34:351-78
references.pmid: 15869394
references.citation: Annu Rev Biophys Biomol Struct. 1997;26:373-99
references.pmid: 9241424
references.citation: Biophys J. 2000 Oct;79(4):2188-98
references.pmid: 11023923
references.citation: Cell Cycle. 2008 Jan 15;7(2):127-34
references.pmid: 18212529
references.citation: Nat Immunol. 2006 Nov;7(11):1139-42
references.pmid: 17053798
references.citation: Biophys J. 2007 Jan 15;92(2):654-60
references.pmid: 17071660
references.citation: Nat Biotechnol. 2004 Sep;22(9):1177-8
references.pmid: 15340486
references.citation: Nat Rev Mol Cell Biol. 2011 Sep 23;12(10):656-68
references.pmid: 21941275
references.citation: Biophys J. 1995 Sep;69(3):989-93
references.pmid: 8519998
references.citation: Nat Rev Mol Cell Biol. 2010 Jun;11(6):414-26
references.pmid: 20495582
references.citation: ACS Chem Biol. 2012 Jan 20;7(1):139-49
references.pmid: 22004174
references.citation: Cell. 2010 Jun 25;141(7):1117-34
references.pmid: 20602996
references.citation: J Phys Chem B. 2006 Oct 12;110(40):19763-70
references.pmid: 17020359
references.citation: Nat Rev Mol Cell Biol. 2003 Sep;Suppl:SS1-5
references.pmid: 14587519
references.citation: Nat Rev Mol Cell Biol. 2006 Jul;7(7):505-16
references.pmid: 16829981
references.citation: Nat Biotechnol. 2004 Feb;22(2):198-203
references.pmid: 14704683
references.citation: Ann Biomed Eng. 2012 Nov;40(11):2307-18
references.pmid: 22669501
references.citation: Science. 2006 Apr 14;312(5771):217-24
references.pmid: 16614209
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Oct;82(4 Pt 1):041914
references.pmid: 21230320
references.citation: Biophys J. 2008 Dec 15;95(12):5988-6001
references.pmid: 18805933
references.citation: Nat Methods. 2008 Feb;5(2):155-7
references.pmid: 18193054
references.citation: Trends Biochem Sci. 2009 May;34(5):234-43
references.pmid: 19362843
references.citation: Nat Cell Biol. 2000 Mar;2(3):168-72
references.pmid: 10707088
references.citation: J Struct Biol. 2007 Sep;159(3):347-58
references.pmid: 17532228
references.citation: PLoS One. 2012;7(3):e34175
references.pmid: 22470534
references.citation: Biochem Biophys Res Commun. 2008 May 2;369(2):730-4
references.pmid: 18313398
references.citation: Biophys J. 2002 Jan;82(1 Pt 1):274-84
references.pmid: 11751315
references.citation: Biophys J. 2005 Aug;89(2):1362-73
references.pmid: 15908575
references.citation: J Cell Sci. 2008 May 15;121(Pt 10):1750-7
references.pmid: 18469015
references.citation: Trends Cell Biol. 2008 Aug;18(8):364-71
references.pmid: 18620858
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jan;73(1 Pt 1):011915
references.pmid: 16486193
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Jul;82(1 Pt 1):011917
references.pmid: 20866658
references.citation: Phys Chem Chem Phys. 2011 Mar 14;13(10):4326-34
references.pmid: 21258684
references.citation: Nat Methods. 2013 Mar;10(3):265-9
references.pmid: 23396281
references.citation: Nat Cell Biol. 2007 Jan;9(1):7-14
references.pmid: 17199125