Abstract
Small-angle X-ray scattering (SAXS) is an increasingly common and useful technique for structural characterization of molecules in solution. A SAXS experiment determines the scattering intensity of a molecule as a function of spatial frequency, termed SAXS profile. SAXS profiles can be utilized in a variety of molecular modeling applications, such as comparing solution and crystal structures, structural characterization of flexible proteins, assembly of multi-protein complexes, and modeling of missing regions in the high-resolution structure. Here, we describe protocols for modeling atomic structures based on SAXS profiles. The first protocol is for comparing solution and crystal structures including modeling of missing regions and determination of the oligomeric state. The second protocol performs multi-state modeling by finding a set of conformations and their weights that fit the SAXS profile starting from a single-input structure. The third protocol is for protein-protein docking based on the SAXS profile of the complex. We describe the underlying software, followed by demonstrating their application on interleukin 33 (IL33) with its primary receptor ST2 and DNA ligase IV-XRCC4 complex.
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References
Hura GL, Menon AL, Hammel M, Rambo RP, Poole FL 2nd, Tsutakawa SE, Jenney FE Jr, Classen S, Frankel KA, Hopkins RC, Yang SJ, Scott JW, Dillard BD, Adams MW, Tainer JA (2009) Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat Methods 6(8):606–612. https://doi.org/10.1038/nmeth.1353. nmeth.1353 [pii]
Hura GL, Budworth H, Dyer KN, Rambo RP, Hammel M, McMurray CT, Tainer JA (2013) Comprehensive macromolecular conformations mapped by quantitative SAXS analyses. Nat Methods 10(6):453–454. https://doi.org/10.1038/nmeth.2453
Dyer KN, Hammel M, Rambo RP, Tsutakawa SE, Rodic I, Classen S, Tainer JA, Hura GL (2014) High-throughput SAXS for the characterization of biomolecules in solution: a practical approach. Methods Mol Biol 1091:245–258. https://doi.org/10.1007/978-1-62703-691-7_18
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(3):191–285. https://doi.org/10.1017/S0033583507004635. S0033583507004635 [pii]
Rambo RP, Tainer JA (2013) Super-resolution in solution x-ray scattering and its applications to structural systems biology. Annu Rev Biophys 42:415–441. https://doi.org/10.1146/annurev-biophys-083012-130301
Chacon P, Moran F, Diaz JF, Pantos E, Andreu JM (1998) Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm. Biophys J 74(6):2760–2775. https://doi.org/10.1016/S0006-3495(98)77984-6. S0006-3495(98)77984-6 [pii]
Svergun DI (1999) Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J 76(6):2879–2886. https://doi.org/10.1016/S0006-3495(99)77443-6. S0006-3495(99)77443-6 [pii]
Svergun DI, Petoukhov MV, Koch MH (2001) Determination of domain structure of proteins from X-ray solution scattering. Biophys J 80(6):2946–2953. https://doi.org/10.1016/S0006-3495(01)76260-1. S0006-3495(01)76260-1 [pii]
Petoukhov MV, Svergun DI (2005) Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys J 89(2):1237–1250. https://doi.org/10.1529/biophysj.105.064154. S0006-3495(05)72771-5 [pii]
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28(1):235–242
Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234(3):779–815. https://doi.org/10.1006/jmbi.1993.1626. S0022-2836(83)71626-8 [pii]
Förster F, Webb B, Krukenberg KA, Tsuruta H, Agard DA, Sali A (2008) Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies. J Mol Biol 382(4):1089–1106. https://doi.org/10.1016/j.jmb.2008.07.074. S0022-2836(08)00943-1 [pii]
Schneidman-Duhovny D, Hammel M, Sali A (2010) FoXS: a web server for rapid computation and fitting of SAXS profiles. Nucleic Acids Res 38(Suppl):W540–W544. https://doi.org/10.1093/nar/gkq461. gkq461 [pii]
Schneidman-Duhovny D, Hammel M, Sali A (2011) Macromolecular docking restrained by a small angle X-ray scattering profile. J Struct Biol 173(3):461–471. https://doi.org/10.1016/j.jsb.2010.09.023. S1047-8477(10)00292-3 [pii]
Schneidman-Duhovny D, Rossi A, Avila-Sakar A, Kim SJ, Velazquez-Muriel J, Strop P, Liang H, Krukenberg KA, Liao M, Kim HM, Sobhanifar S, Dotsch V, Rajpal A, Pons J, Agard DA, Cheng Y, Sali A (2012) A method for integrative structure determination of protein-protein complexes. Bioinformatics 28(24):3282–3289. https://doi.org/10.1093/bioinformatics/bts628
Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A (2013) Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophys J 105(4):962–974. https://doi.org/10.1016/j.bpj.2013.07.020
Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A (2016) FoXS, FoXSDock and MultiFoXS: single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles. Nucleic Acids Res 44(W1):W424–W429. https://doi.org/10.1093/nar/gkw389
Hammel M (2012) Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS). Eur Biophys J 41(10):789–799. https://doi.org/10.1007/s00249-012-0820-x
Schneidman-Duhovny D, Kim SJ, Sali A (2012) Integrative structural modeling with small angle X-ray scattering profiles. BMC Struct Biol 12(1):17. https://doi.org/10.1186/1472-6807-12-17
Rambo RP, Tainer JA (2011) Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law. Biopolymers 95(8):559–571. https://doi.org/10.1002/bip.21638
Petoukhov MV, Franke D, Shkumatov AV, Tria G, Kikhney AG, Gajda M, Gorba C, Mertens HDT, Konarev PV, Svergun DI (2012) New developments in the ATSAS program package for small-angle scattering data analysis. J Appl Crystallogr 45(2):342–350. https://doi.org/10.1107/S0021889812007662
Pons C, D'Abramo M, Svergun DI, Orozco M, Bernado P, Fernandez-Recio J (2010) Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data. J Mol Biol 403(2):217–230. https://doi.org/10.1016/j.jmb.2010.08.029. S0022-2836(10)00891-0 [pii]
Jimenez-Garcia B, Pons C, Svergun DI, Bernado P, Fernandez-Recio J (2015) pyDockSAXS: protein-protein complex structure by SAXS and computational docking. Nucleic Acids Res 43(W1):W356–W361. https://doi.org/10.1093/nar/gkv368
Liu X, Hammel M, He Y, Tainer JA, Jeng US, Zhang L, Wang S, Wang X (2013) Structural insights into the interaction of IL-33 with its receptors. Proc Natl Acad Sci U S A 110(37):14918–14923. https://doi.org/10.1073/pnas.1308651110
Debye P (1915) Zerstreuung von Röntgenstrahlen. Ann Phys 351(6):809–823
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(6):768–773
Fraser RDB, MacRae TP, Suzuki E (1978) An improved method for calculating the contribution of solvent to the X-ray diffraction pattern of biological molecules. J Appl Crystallogr 11(6):693–694
Connolly ML (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science 221(4612):709–713
Rambo RP, Tainer JA (2013) Accurate assessment of mass, models and resolution by small-angle scattering. Nature 496(7446):477–481. https://doi.org/10.1038/nature12070
LaValle SM, Kuffner JJ (2001) Rapidly-exploring random trees: progress and prospects. In: Algorithmic and computational robotics: New Directions, pp. 293–308
Amato NM, Song G (2002) Using motion planning to study protein folding pathways. J Comput Biol 9(2):149–168
Cortes J, Simeon T, Ruiz de Angulo V, Guieysse D, Remaud-Simeon M, Tran V (2005) A path planning approach for computing large-amplitude motions of flexible molecules. Bioinformatics 21(Suppl 1):i116–i125. https://doi.org/10.1093/bioinformatics/bti1017
Raveh B, London N, Schueler-Furman O (2010) Sub-angstrom modeling of complexes between flexible peptides and globular proteins. Proteins 78(9):2029–2040. https://doi.org/10.1002/prot.22716
Suhre K, Sanejouand YH (2004) On the potential of normal-mode analysis for solving difficult molecular-replacement problems. Acta Crystallogr D Biol Crystallogr 60:796
Ma JP (2005) Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure 13:373
Fonseca R, Pachov DV, Bernauer J, van den Bedem H (2014) Characterizing RNA ensembles from NMR data with kinematic models. Nucleic Acids Res 42(15):9562–9572. https://doi.org/10.1093/nar/gku707
Fonseca R, van den Bedem H, Bernauer J (2015) KGSrna: efficient 3D kinematics-based sampling for nucleic acids. In: Przytycka TM (ed) Research in computational molecular biology: 19th annual international conference, RECOMB 2015, Warsaw, Poland, April 12–15, 2015, Proceedings. Springer International Publishing, Cham, pp. 80–95. doi:https://doi.org/10.1007/978-3-319-16706-0_11
Emekli U, Schneidman-Duhovny D, Wolfson HJ, Nussinov R, Haliloglu T (2008) HingeProt: automated prediction of hinges in protein structures. Proteins 70(4):1219–1227. https://doi.org/10.1002/prot.21613
Bernado P, Mylonas E, Petoukhov MV, Blackledge M, Svergun DI (2007) Structural characterization of flexible proteins using small-angle X-ray scattering. J Am Chem Soc 129(17):5656–5664. https://doi.org/10.1021/ja069124n
Carter L, Kim SJ, Schneidman-Duhovny D, Stohr J, Poncet-Montange G, Weiss TM, Tsuruta H, Prusiner SB, Sali A (2015) Prion protein-antibody complexes characterized by chromatography-coupled small-angle X-ray scattering. Biophys J 109(4):793–805. https://doi.org/10.1016/j.bpj.2015.06.065
Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30(10):1545–1614. https://doi.org/10.1002/jcc.21287
Williams GJ, Hammel M, Radhakrishnan SK, Ramsden D, Lees-Miller SP, Tainer JA (2014) Structural insights into NHEJ: building up an integrated picture of the dynamic DSB repair super complex, one component and interaction at a time. DNA Repair (Amst) 17:110–120. https://doi.org/10.1016/j.dnarep.2014.02.009
Wu PY, Frit P, Meesala S, Dauvillier S, Modesti M, Andres SN, Huang Y, Sekiguchi J, Calsou P, Salles B, Junop MS (2009) Structural and functional interaction between the human DNA repair proteins DNA ligase IV and XRCC4. Mol Cell Biol 29(11):3163–3172. https://doi.org/10.1128/MCB.01895-08
Pascal JM, O'Brien PJ, Tomkinson AE, Ellenberger T (2004) Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 432(7016):473–478. https://doi.org/10.1038/nature03082
Cotner-Gohara E, Kim IK, Hammel M, Tainer JA, Tomkinson AE, Ellenberger T (2010) Human DNA ligase III recognizes DNA ends by dynamic switching between two DNA-bound states. Biochemistry 49(29):6165–6176. https://doi.org/10.1021/bi100503w
Duhovny D, Nussinov R, Wolfson HJ (2002) Efficient unbound docking of rigid molecules. In: Guigó R, Gusfield D (eds) Second International Workshop, WABI 2002, Rome, Italy. Lecture notes in computer science. Springer Berlin, Heidelberg, pp. 185–200. doi:https://doi.org/10.1007/3-540-45784-4
Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ (2005) PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res 33(Web Server issue):W363–W367. https://doi.org/10.1093/nar/gki481. 33/suppl_2/W363 [pii]
Dong GQ, Fan H, Schneidman-Duhovny D, Webb B, Sali A (2013) Optimized atomic statistical potentials: assessment of protein interfaces and loops. Bioinformatics 29(24):3158–3166. https://doi.org/10.1093/bioinformatics/btt560
Acknowledgments
We thank Drs. Andrej Sali, John Tainer, Ben Webb, David Agard, Friedrich Foerster, Seung Jong Kim, Hiro Tsuruta, Tsutomu Matsui, Lester Carter, Greg Hura, Riccardo Pellarin, Barak Raveh, Patrick Weinkam, and many others who contributed to our SAXS-based modeling efforts over the years. SAXS at the Advanced Light Source SIBYLS beamline in supported by National Institutes of Health (NIH) grants CA92584, DOE BER Integrated Diffraction Analysis Technologies (IDAT) program and NIGMS grant P30 GM124169-01, ALS-ENABLE.
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Schneidman-Duhovny, D., Hammel, M. (2018). Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles. In: Marsh, J. (eds) Protein Complex Assembly. Methods in Molecular Biology, vol 1764. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7759-8_29
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