Abstract
We present a Monte Carlo simulation environment for modelling complex biological molecular interaction networks and for the design, validation, and quantitative analysis of FRAP assays to study these. The program is straightforward in its implementation and can be instructed through an intuitive script language. The simulation tool fits very well in a systems biology research setting that aims to maintain an interactive cycle of experiment-driven modelling and model-driven experimentation: the model and the experiment are in the same simulation. The full program can be obtained by request to the authors.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Aldridge BB, Burke JM, Lauffenburger DA et al (2006) Physicochemical modelling of cell signalling pathways. Nat Cell Biol 8:1195–1203
van Royen ME, Dinant C, Farla P et al (2009) FRAP and FRET methods to study nuclear receptors in living cells. In: McEwan IJ (ed) Nuclear receptor superfamily, vol 505, Methods Mol Biol. Springer, Totowa, pp 69–96
van Royen ME, Farla P, Mattern KA et al (2009) Fluorescence recovery after photobleaching (FRAP) to study nuclear protein dynamics in living cells. In: Hancock R (ed) The nucleus, vol 464, Methods Mol Biol. Springer, Totowa, pp 363–385
Chen WW, Niepel M, Sorger PK (2010) Classic and contemporary approaches to modeling biochemical reactions. Genes Dev 24:1861–1875
Alves R, Antunes F, Salvador A (2006) Tools for kinetic modeling of biochemical networks. Nat Biotechnol 24:667–672
Beaudouin J, Mora-Bermudez F, Klee T et al (2006) Dissecting the contribution of diffusion and interactions to the mobility of nuclear proteins. Biophys J 90:1878–1894
Braga J, Desterro JM, Carmo-Fonseca M (2004) Intracellular macromolecular mobility measured by fluorescence recovery after photobleaching with confocal laser scanning microscopes. Mol Biol Cell 15:4749–4760
McNally JG (2008) Quantitative FRAP in analysis of molecular binding dynamics in vivo. Methods Cell Biol 85:329–351
Phair RD, Scaffidi P, Elbi C et al (2004) Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins. Mol Cell Biol 24:6393–6402
van Royen ME, Cunha SM, Brink MC et al (2007) Compartmentalization of androgen receptor protein-protein interactions in living cells. J Cell Biol 177:63–72
Farla P, Hersmus R, Trapman J et al (2005) Antiandrogens prevent stable DNA-binding of the androgen receptor. J Cell Sci 118:4187–4198
Mueller F, Mazza D, Stasevich TJ et al (2010) FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know? Curr Opin Cell Biol 22:403–411
Carrero G, McDonald D, Crawford E et al (2003) Using FRAP and mathematical modeling to determine the in vivo kinetics of nuclear proteins. Methods 29:14–28
Braeckmans K, Peeters L, Sanders NN et al (2003) Three-dimensional fluorescence recovery after photobleaching with the confocal scanning laser microscope. Biophys J 85:2240–2252
Kang M, Kenworthy AK (2008) A closed-form analytic expression for FRAP formula for the binding diffusion model. Biophys J 95:L13–L15
Tsibidis GD (2009) Quantitative interpretation of binding reactions of rapidly diffusing species using fluorescence recovery after photobleaching. J Microsc 233:384–390
Tsibidis GD, Ripoll J (2008) Investigation of binding mechanisms of nuclear proteins using confocal scanning laser microscopy and FRAP. J Theor Biol 253:755–768
Braeckmans K, Remaut K, Vandenbroucke RE et al (2007) Line FRAP with the confocal laser scanning microscope for diffusion measurements in small regions of 3-D samples. Biophys J 92:2172–2183
Hallen MA, Layton AT (2010) Expanding the scope of quantitative FRAP analysis. J Theor Biol 262:295–305
Mazza D, Braeckmans K, Cella F et al (2008) A new FRAP/FRAPa method for three-dimensional diffusion measurements based on multiphoton excitation microscopy. Biophys J 95:3457–3469
Mazza D, Cella F, Vicidomini G et al (2007) Role of three-dimensional bleach distribution in confocal and two-photon fluorescence recovery after photobleaching experiments. Appl Opt 46:7401–7411
Kang M, Day CA, Drake K et al (2009) A generalization of theory for two-dimensional fluorescence recovery after photobleaching applicable to confocal laser scanning microscopes. Biophys J 97:1501–1511
Mueller F, Wach P, McNally JG (2008) Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved quantitative fluorescence recovery after photobleaching. Biophys J 94:3323–3339
Agarwal S, van Cappellen WA, Guenole A et al (2011) ATP-dependent and independent functions of Rad54 in genome maintenance. J Cell Biol 192:735–750
de Graaf P, Mousson F, Geverts B et al (2010) Chromatin interaction of TATA-binding protein is dynamically regulated in human cells. J Cell Sci 123:2663–2671
Farla P, Hersmus R, Geverts B et al (2004) The androgen receptor ligand-binding domain stabilizes DNA binding in living cells. J Struct Biol 147:50–61
Luijsterburg MS, Goedhart J, Moser J et al (2007) Dynamic in vivo interaction of DDB2 E3 ubiquitin ligase with UV-damaged DNA is independent of damage-recognition protein XPC. J Cell Sci 120:2706–2716
Nicassio F, Corrado N, Vissers JH et al (2007) Human USP3 is a chromatin modifier required for S phase progression and genome stability. Curr Biol 17:1972–1977
Nishi R, Alekseev S, Dinant C et al (2009) UV-DDB-dependent regulation of nucleotide excision repair kinetics in living cells. DNA Repair (Amst) 8:767–776
Sabbioneda S, Gourdin AM, Green CM et al (2008) Effect of proliferating cell nuclear antigen ubiquitination and chromatin structure on the dynamic properties of the Y-family DNA polymerases. Mol Biol Cell 19:5193–5202
Tanner TM, Denayer S, Geverts B et al (2010) A 629RKLKK633 motif in the hinge region controls the androgen receptor at multiple levels. Cell Mol Life Sci 67:1919–1927
van den Boom V, Kooistra SM, Boesjes M et al (2007) UTF1 is a chromatin-associated protein involved in ES cell differentiation. J Cell Biol 178:913–924
Xouri G, Squire A, Dimaki M et al (2007) Cdt1 associates dynamically with chromatin throughout G1 and recruits Geminin onto chromatin. EMBO J 26:1303–1314
Zotter A, Luijsterburg MS, Warmerdam DO et al (2006) Recruitment of the nucleotide excision repair endonuclease XPG to sites of UV-induced dna damage depends on functional TFIIH. Mol Cell Biol 26:8868–8879
van Royen ME, van Cappellen WA, Geverts B et al (2014) Androgen receptor complexes probe DNA for recognition sequences by short random interactions. J Cell Sci 127(Pt 7):1406–1416
Houtsmuller AB, Rademakers S, Nigg AL et al (1999) Action of DNA repair endonuclease ERCC1/XPF in living cells. Science 284:958–961
Phair RD, Misteli T (2000) High mobility of proteins in the mammalian cell nucleus. Nature 404:604–609
Dinant C, van Royen ME, Vermeulen W et al (2008) Fluorescence resonance energy transfer of GFP and YFP by spectral imaging and quantitative acceptor photobleaching. J Microsc 231:97–104
Faraday M (2008) The correspondence of Michael Faraday, Vol 5. Institution of Engineering and Technology, Stevenage, pp 1855–1860
Tweney RD (2009) Mathematical representations in science: a cognitive-historical case history. Top Cogn Sci 1:758–776, 2010
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Geverts, B., van Royen, M.E., Houtsmuller, A.B. (2015). Analysis of Biomolecular Dynamics by FRAP and Computer Simulation. In: Verveer, P. (eds) Advanced Fluorescence Microscopy. Methods in Molecular Biology, vol 1251. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2080-8_7
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2080-8_7
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2079-2
Online ISBN: 978-1-4939-2080-8
eBook Packages: Springer Protocols