Abstract
Integrative structure modeling is an emerging method for structural determination of protein-protein complexes that are challenging for conventional structural techniques. Here, we provide a practical protocol for implementing our integrated iSPOT platform by integrating three different biophysical techniques: small-angle X-ray scattering (SAXS), hydroxyl radical footprinting, and computational docking simulations. Specifically, individual techniques are described from experimental and/or computational perspectives, and complementary structural information from these different techniques are integrated for accurate characterization of the structures of large protein-protein complexes.
References
Bernado P, Blackledge M (2010) Structural biology: proteins in dynamic equilibrium. Nature 468:1046–1048
Blanchet CE, Svergun DI (2013) Small-angle X-ray scattering on biological macromolecules and nanocomposites in solution. Annu Rev Phys Chem 64:37–54
Chen R, Li L, Weng Z (2003) ZDOCK: an initial-stage protein-docking algorithm. Proteins 52:80–87
Comeau SR, Gatchell DW, Vajda S, Camacho CJ (2004) ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res 32:W96–W99
Dominguez C, Boelens R, Bonvin AM (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125:1731–1737
Gabb HA, Jackson RM, Sternberg MJE (1997) Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 272:106–120
Huang W, Ravikumar KM, Yang S (2014) A newfound cancer-activating mutation reshapes the energy landscape of estrogen-binding domain. J Chem Theory Comput 10:2897–2900
Huang W, Ravikumar KM, Chance MR, Yang S (2015) Quantitative mapping of protein structure by hydroxyl radical footprinting mediated structural mass spectrometry: a protection factor analysis. Biophys J 108:1–9
Huang W, Ravikumar KM, Parisien M, Yang S (2016) Theoretical modeling of multiprotein complexes by iSPOT: integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking. J Struct Biol 196:340
Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ, Critical Assessment of, P.I (2003) CAPRI: a critical assessment of predicted interactions. Proteins 52:2–9
Jeffries CM, Graewert MA, Blanchet CE, Langley DB, Whitten AE, Svergun DI (2016) Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments. Nat Protoc 11:2122–2153
Kaur P, Kiselar J, Yang S, Chance MR (2015) Quantitative protein topography analysis and high-resolution structure prediction using hydroxyl radical labeling and tandem-ion mass spectrometry. Mol Cell Proteomics (in press)
Kikhney AG, Svergun DI (2015) A practical guide to small angle X-ray scattering (SAXS) of flexible and intrinsically disordered proteins. FEBS Lett 589:2570–2577
Pierce BG, Wiehe K, Hwang H, Kim BH, Vreven T, Weng Z (2014) ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics 30:1771–1773
Putnam CD, Hammel M, Hura GL, Tainer JA (2007) X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys 40:191–285
Ravikumar KM, Huang W, Yang S (2012) Coarse-grained simulations of protein-protein association: an energy landscape perspective. Biophys J 103:837–845
Ravikumar KM, Huang W, Yang S (2013) Fast-SAXS-pro: a unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes. J Chem Phys 138:024112
Skou S, Gillilan RE, Ando N (2014) Synchrotron-based small-angle X-ray scattering of proteins in solution. Nat Protoc 9:1727–1739
Svergun D, Barberato C, Koch MHJ (1995) CRYSOL – a program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates. J Appl Crystallogr 28:768–773
Tong D, Yang S, Lu L (2016) Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures. J Appl Crystallogr 49:1148–1161
Tovchigrechko A, Vakser IA (2006) GRAMM-X public web server for protein-protein docking. Nucleic Acids Res 34:W310–W314
Xu G, Chance MR (2007) Hydroxyl radical-mediated modification of proteins as probes for structural proteomics. Chem Rev 107:3514–3543
Yang S (2014) Methods for SAXS-based structure determination of biomolecular complexes. Adv Mater 26:7902–7910
Yang S, Park S, Makowski L, Roux B (2009) A rapid coarse residue-based computational method for x-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes. Biophys J 96:4449–4463
Yang S, Blachowicz L, Makowski L, Roux B (2010a) Multidomain assembled states of Hck tyrosine kinase in solution. Proc Natl Acad Sci U S A 107:15757–15762
Yang S, Parisien M, Major F, Roux B (2010b) RNA structure determination using SAXS data. J Phys Chem B 114:10039–10048
Acknowledgements
This work was supported by the NIH (R01GM114056 and P30EB009998), the DoD (W81XWH-11-1033), and by the Ministry of Education of Singapore (2014-T2-1-065). Beamtime access was supported via the BioCAT at the Advanced Photo Source and the LiX beamline at the NSLS-II by the DoE (DE-AC02-06CH11357 and KP1605010) and by the NIH (9P41GM103622 and P41GM111244). Additional support was provided by the Ohio Supercomputer Center and the Clinical and Translational Science Collaborative of Cleveland (4UL1TR000439). The content is solely the responsibility of the authors and does not necessarily reflect the official views of the National Institute of General Medical Sciences or the National Institutes of Health.
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Hsieh, A., Lu, L., Chance, M.R., Yang, S. (2017). A Practical Guide to iSPOT Modeling: An Integrative Structural Biology Platform. In: Chaudhuri, B., Muñoz, I., Qian, S., Urban, V. (eds) Biological Small Angle Scattering: Techniques, Strategies and Tips. Advances in Experimental Medicine and Biology, vol 1009. Springer, Singapore. https://doi.org/10.1007/978-981-10-6038-0_14
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