REVIEWS

Emerging applications of small angle
solution scattering in structural biology

Barnali N. Chaudhuri*
Faculty of Life Sciences and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, India

Received 22 August 2014; Accepted 5 December 2014
DOI: 10.1002/pro.2624
Published online 16 December 2014 proteinscience.org

Abstract: Small angle solution X-ray and neutron scattering recently resurfaced as powerful tools to
address an array of biological problems including folding, intrinsic disorder, conformational transitions,
macromolecular crowding, and self or hetero-assembling of biomacromolecules. In addition, small
angle solution scattering complements crystallography, nuclear magnetic resonance spectroscopy,
and other structural methods to aid in the structure determinations of multidomain or multicomponent
proteins or nucleoprotein assemblies. Neutron scattering with hydrogen/deuterium contrast variation,
or X-ray scattering with sucrose contrast variation to a certain extent, is a convenient tool for charac-
terizing the organizations of two-component systems such as a nucleoprotein or a lipid-protein assem-
bly. Time-resolved small and wide-angle solution scattering to study biological processes in real time,
and the use of localized heavy-atom labeling and anomalous solution scattering for applications as
FRET-like molecular rulers, are amongst promising newer developments. Despite the challenges in
data analysis and interpretation, these X-ray/neutron solution scattering based approaches hold great
promise for understanding a wide variety of complex processes prevalent in the biological milieu.
Keywords: small angle X-ray scattering; anomalous solution scattering; solution neutron scattering;
solution structure determination

Introduction acterizations of protein/RNA folding, intrinsic disor-
Modern biological applications of small angle X-ray der, conformational transitions, and protein-protein
and neutron solution scattering (SAXS/SANS) or protein-nucleic acid assembling processes (Fig.
include low-resolution shape modeling, and the char- 1).1–5 Even though small angle solution scattering
(SAS) typically requires very pure and mono-
Abbreviations: ASAX, anomalous solution X-ray scattering; disperse sample, no specialized sample treatments
FRET, Fo €rster resonance energy transfer; IDP, Intrinsically like chemical fixation or crystallization are neces-
disordered protein; NMR, Nuclear magnetic resonance; sary, making the use of a range of physiologically
SANS, small angle neutron scattering; SAS, small angle
relevant buffer conditions possible. Furthermore,
scattering; SAXS, small angle X-ray scattering; SAXS-SEC,
small angle X-ray scattering–size exclusion chromatography; small sample volume at 1 to 10 mg/mL concentra-
WAXS, wide angle X-ray scattering. tion, rapid data collection at the synchrotron sites
*Correspondence to: Barnali Chaudhuri, Faculty of Life Sciences (0.5–5 s), practically no size-limitation (depending
and Biotechnology, South Asian University, Akbar Bhawan, upon the experimental setup), several dedicated
Chanakyapuri, New Delhi, India 110021. E-mail: barnalichaud- beam-lines at the synchrotron facilities including
huri1@gmail.com those with options for automated high-throughput
Barnali Chaudhuri current address is GN Ramachandran protein
center, CSIR Institute of Microbial Technology, Chandigarh-
data collection and the availability of user-friendly,
160036, India. automated software for data analysis makes SAXS a

Published by Wiley-Blackwell. V
C 2014 The Protein Society PROTEIN SCIENCE 2015 VOL 24:267—276 267

25. Despite the tremendous methodological advan- age molecular shape of a mono-disperse. SAXS ing component within the structure.22. While X-ray crystallography is a routine tool for the wise distance distribution profile computed from atomic resolution structure determinations of bio- SAS data are useful for testing various structural molecules held in crystal lattices.ORG Biological Applications of Small-Angle Solution Scattering . low-resolution shape model. aid in small angle scattering. globular mac.40 provides a quick way to compute a low-resolution. SAXS at ultra-low scattering angles can aid in ary or quaternary organizations. very popular technique.16 On the other the existing substructures to model their overall terti- hand.24 Recently.12 Comparisons of the SAS-derived shape models with corresponding known structures indicated Size and shape of a macromolecule excellent agreements for a number of cases. higher-order struc.13–15 These quantities and the pair. endorsed.27–32 In addition to ab initio at higher scattering angles contains information shape modeling. SAS can be used in conjunction with about its finer structural features. such as the nucleosome fiber. con- actively discussed in the research community.1.13 In ture prediction algorithms.2. cross-sectional size and linear mass density (mass per unit length) of a rod-shaped filament and SAS as a complementary technique in structural thickness of a disk-shaped particle can be estimated biology from SAS data. and multiple ab For the theoretical basis and technical details of initio shape computations with consistent results. guidelines for publications are Impositions of anticipated point-group symmetry. A schematic diagram showing various biological applications of small angle solution scattering technique. radius of gyration. Analysis of SAS data allows ready estimations of methods were developed to model RNA structures using mass. While small angle X-ray/neutron tions in solution.17 structures can help to predict the location of a miss- When a crystal structure is not available.18–21 ularity of SAXS. SAS can readily hypotheses and can be used as restraints for struc. recently published text-book.10.2 Solution scattering profiles are scattering1–4 provides information about the global computed from the atomic co-ordinates of available size and shape of the macromolecule in solution. the elucidation of large-scale.12 In this Due to the inherent ambiguity of SAS-based shape mod- review.26 addition. aver.11 nectivity and compactness conditions. crystal structures for comparisons with the experi- wide-angle X-ray scattering (WAXS) data obtained mental SAXS/WAXS data.2.1. and maximum diameter of experimental SAXS data in conjunction with the struc- a monodisperse macromolecule in solution. mental data that are “not seen by the model” are lems in structural biology. ces in structure determination techniques. reveal their oligomeric states and domain organiza- tural modeling. validations of the model using additional experi- applications of SAXS and SANS in a variety of prob. we refer the readers to an obtaining an average. we will focus our attention on the modern eling.23 excellent.Figure 1. romolecule from its scattering profile.1.5–9 Due to the immense pop.33–39 Furthermore. many 268 PROTEINSCIENCE. SAS-based shape computations with known partial tures.

49–52 Thus.57 In addition.72 High salt conditions are scattering macromolecule. to learn about the structural organizations membrane proteins. q. component.12 ful approach to elucidate the structural organiza. from which individ. The “matching with the changes in sizes and pair-distribution func- out” conditions for lipids. are used to track folding-unfolding DNA/RNA are at about 10 to 14%. unaddressed issues such as bly.multicomponent or multidomain biological entities Scattering with contrast variation aided in elu- continue to pose considerable challenge to structure cidating the organizations of many two-component determination. acids.73 However. which can be changed by tal conditions.57 Neutron scattering with contrast pair-distributions functions are model-free indicators matching is an exceptional tool for observing a selected of large-scale conformational changes in folded. a large amount of sample requirement particular.13. possible to achieve solely based on SAXS.68–72 Moreover.q2 neutron scattering contribution from one of the compo.74 Furthermore. and q is nents can be selectively “matched out” or abolished by the momentum transfer).46–49 In facilities.1. a renewed assembly as well as the cross-term describing their search for additional contrast variation agents for relative orientations in a two-component assembly SAXS that are suitable for biological samples will be can be retrieved. ods are developed to integrate SAS data with other Due to a limited number of neutron scattering experimental data for structural modeling.74 Kratky plots. Thus. and tion profiles.72 Due to the relative ease of obtaining ual scattering profile for each component in the SAXS data in comparison to SANS. and behaviors of biomolecules under varying experimen- 65 to 72% D2O. conformational flexibility. respectively. 47%. Folding.53–57 A typical contrast var.66 Recently. shape or structural modeling. A global indication of “folded-ness” of the bio- In an alternative contrast matching experiment.13. problems. noisier data due to in-coherent scattering and long tions of various biological entities. SANS is useful for studying and SAS. and intrinsic SANS with H/D contrast variation is very well suited disorder for analyzing relative positioning of the components SAS is a powerful global sensor of the folding states within an assembly and an induced-fit or a mutual and conformational changes in proteins and nucleic induced fit mode of molecular recognition. such as crystallography. An effective way to tackle this chal. ing densities between proteins and lipids as well as transmission electron microscopy. SAXS ques can be an effective tool to address structural typically requires only 20 to 30 mL of sample and a problems that are not easily amenable to a single few seconds of exposure at a powerful synchrotron technique.. where I is the scattering intensity. but have limited applicability in biological a number of different H/D ratio. carbohydrates. together adjusting the H/D ratio of the buffer.44 Hybrid meth. NMR with SAS has emerged as a power.4. SAS data collection times (a few hours). which can be combined with ponent in a heteromeric assembly. Although less potent than SANS with H/D contrast variation.67 information about overall shape. 40 to 45%. protein-protein assemblies with a deuterated protein plementary methods. changes in sizes and deuteration.58–64 Owing to the differences in scatter- nuclear magnetic resonance spectroscopy (NMR).4.44. resurgence of in combination with other complementary techni. ces. proteins. sucrose can reduce the effect of iation experiments reveal the relative dispositions of radiation damage at the powerful synchrotron sour- components within a multicomponent assem. a range of two-component assemblies. centers of mass of the two components can be esti- mated from SANS contrast variation dataset. Although the Chaudhuri PROTEIN SCIENCE VOL 24:267—276 269 . distance between the rewarding to the SAS research community. (150 mL or more at 5–10 mg/mL concentration). In comparison. source.57 Thus. mass spectrometry proteins and detergents.53–56 A difference in the neutron scattering enhanced viscosity at higher sucrose concentration length density of hydrogen (H) and deuterium (D) is may limit the utility of these SAXS-based contrast exploited in a SANS contrast variation experiment to variation experiments and care should be taken to vary the excess scattering density or contrast of the account for these effects. relative orienta. romolecules for changing contrasts and the power of interface residues obtained from SAXS. NMR and H/D contrast variation allows SANS to characterize mass spectrometric data to learn about the oligo. such as nucleoprotein assemblies and lenge is to combine information obtained from com. non- component in the presence of another “invisible” com. tion. used by combining SAXS and SANS data was described. effective for SAXS-based contrast variation experi- iation dataset is obtained by collecting SANS data at ments. a hybrid strategy of proteins and their assemblies at data-dependent to model membrane proteins in lipidic environment levels of details. Wang et al. neutron scattering is gradual.41–45 For example. vs. molecule can be obtained from the Kratky plot (I. assemblies.65. aggregated proteins.1. the feasibility of deuterium-labeling the mac- tions of the components and the footprints of buried. which is not meric states of a chemokine CCL5. SAXS with varying amounts of Neutron and X-ray scattering with contrast sucrose provides another avenue to protein contrast variation matching and a limited range of contrast varia- Small angle neutron scattering or SANS contrast var.

and their complexes.96 Furthermore.105 Grishaev et al.81 proteins. SANS study on the intrinsically disordered. both folded tion function or a Porod-Debye plot. other hydrodynamic data analyses. when possible. concentrated conditions inhibit breathing motions in tude structural changes in proteins.99. the SAS data. quaternary structures of certain modular enzymes ordered regions often fold in the presence of a bind. esses and multimeric organizations. particularly in combi. a number of SANS in the presence of these “invisible” contrast- different computational methods were developed to matched.91 Synergy determined the structural organization of lead- between NMR and SAS were exploited in numerous substituted calmodulin-peptide complex using a com- studies of IDPs. SAS was found to be a suit- A large number of naturally occurring proteins able tool to study the effects of crowding on RNA are either disordered or contain long stretches of folding. structural components. of the available donor-acceptor pairs. as the scattering profile different un-labeled proteins as crowding agents represents an ensemble of conformations of the IDP under their “contrast matching” conditions indicated in solution.ORG Biological Applications of Small-Angle Solution Scattering . SAXS-based nation with NMR. which is a tal as a probe was successfully used to measure the clear advantage over crystallography. its function in solution. and are generally classified as crowding promotes compactions in the tertiary and intrinsically disordered proteins (IDP).82.100 On the other hand. which was critical for the correct positioning of tive SAXS and NMR based ensemble analyses.102. a left-skewed pair-distribu.82 An IDP or a flexible protein can be minimal effect of crowding on the protein N.97.75–79 WAXS can sense small ampli.105 Under a sensible approach. However. can be obtained from In addition to the global analysis.80.applications of SAXS are limited to detections of crowding on proteins. SAS provides global information on size and shape ble modeling with SAS data yielded structural but no local structural information on a particular information on the spatial occupancy of glycans in site can be generally obtained. ers that are restricted around the F€orster distance degenerative disorder. SAS analysis of the experimental conditions of low concentrations.84.93 In a recent article.104 In Due to the low information content of SAS and another recent SAXS study.86–89 Ensem.94 SAS. gold cluster-labeled a large number of parameters required for an DNA was used to track conformational changes exhaustive description of an IDP. scattering from the electron-dense gold-component circular dichroism. length of DNA using scattering interference. which is recently reviewed else. remarkable structure. nucleic acids and deuterated proteins. such site-specific details can crystallize.95 WAXS data suggested that large movements. protein parts was contrast matched by sucrose. deuterium-labeled protein N in the presence of two ble for studying these IDPs. SAS in combination with suitable be very instructive. use of labeled samples for SAXS analyses of localized Macromolecular crowding conformational changes.98 SAXS-based studies indicated that unstructured regions. well-defined ity. a much larger range of distances.101 Valu- identified from the global features in the SAS data.103 DNA coupled to gold nanocrys- ble proteins under different conditions. dynamic light scattering and dominated the total scattering.104 270 PROTEINSCIENCE. used SAXS with NMR on SAXS/WAXS and NMR residual dipolar coupling lanthanide-labeled proteins to determine the most measurements. for certain glycosylated proteins that are notoriously difficult to biological applications. able new insights on the effects of crowding on such as the Kratky plot. IDPs is typically complemented with solution NMR. exhaus.86–89 These methods typically involve computational generations of multiple conformers followed by their selections based on their compati. a recent. especially tant but often neglected effect of macromolecular coupled with time-resolved SAXS experiments.70 Unlike the F€orster reso- together with extensive cross-validations. rich elements.92 Bertini et al. were used nance energy transfer or FRET-based molecular rul- to predict conformations of IDPs relevant to neuro. SAXS-based molecular ruler bility with the experimental SAS data. One way to obtain local informa- computational methods can provide potentially unre. will continue to play a pivotal molecular rulers can be potentially used to measure role in providing key structural descriptions of IDPs. bination of sucrose contrast matching. lenge to structural biologists.83 The dis. this ing partners(s) and play crucial role in molecular compaction correlates with higher enzymatic activ- recognition.100 Quite significantly.83 Due to a lack of rigid. molecular recognition proc- SAS provides an elegant way to examine the impor. tion from SAXS is to label the protein with electron- stricted access to the conformational spaces of flexi. characterization of the IDPs pose a chal.99.90 Thus. combining SAS induced by a DNA mismatch repair protein. leading with additional complementary experimental data is to new insights into the repair mechanism.85 and intrinsically disordered. lead- which might be needed for a better explanation of ing to the heavy-atom dominated scattering profile.104 Therefore. conventional where.70 Scattering contribution from the abundant conformers of highly flexible calmodulin.82. SAS is naturally suita.82. unlabeled protein crowding agents that generate an ensemble of protein conformers from realistically mimics the intracellular environment.

111.112 In an ray laser pulses are opening up the first-time possi- extension of this coupled approach. recently published a tallographic results.116 and the protein segment is usable.electron microscopy.12 In recent times. which might one component from the mixture. nated by each of the constituents. such as a “protein-quake. ditional means. while effectively excluding any biological processes.120–124 SANS provides another avenue for time-resolved studies.115 However. models as well as the association constants and ing sites within parvalbumin and the center of mass assembling pathway from the same experi- of the protein. valuable tool for investigating a range of processes For a separable mixture.127 measured using SAXS-SEC in a buffer saturated with Time-resolved SAS is suitable for probing many this peptide ligand. SAXS at a powerful synchrotron source time-scale) as well as fast folding kinetics (second to coupled with in-line size-exclusion column chromatog. 10 to 100 fs X- individual entities while being eluted.104 and contrast matching. may alleviate a biological reaction/process in terms of its constitu- this problem for ASAXS studies. which was consistent with the crys. Computational approaches were developed for which are routinely exploited in multiwavelength extracting individual scattering profiles of the con- anomalous dispersion phasing methods in macromo. cess can be initiated by a number of ways. observe the time progressions of SAXS/WAXS pro- lar recognition processes may become routine. SAXS is the nature and time-scale of the process under one of the very few structural techniques available investigation.114 Sokolova fibrillation pathways that are difficult to study by tra- et al.116–118 Petoukhov et al. 100 ms) and ultra-fast protein movements in the sub- raphy (SAXS-SEC) allows an elegant way to study nanosecond region. powerful syn. which can be judi- Sample heterogeneity pose challenges to routine ciously combined with contrast matching for a two- SAS data analysis that generally assumes stable component system. and WAXS studies can Theoretical calculations predict that the use of metal provide direct mechanistic insights on the course of clusters. However. Above computational approaches involving urements at a tunable-wavelength. and concomitant development of theories.106–109 Strong anomalous solution homo.119 However.”124. Mixed systems albeit at a longer time scale. has been used to a limited set obtained from mixed systems involving weak extent in SAXS. of oligomeric assemblies from condition-dependent tion scattering data at the Fe K edge to determine scattering curves for a variety of user-defined mixed the distance between centers of mass of hemoglobin/ system scenarios. such as ing solution state. powerful synchrotron ces.110 sources equipped with better detectors and better applications of ASAXS-based molecular rulers to methods to trigger an event make it possible to probe intricate conformational changes and molecu. Examples include movements in Chaudhuri PROTEIN SCIENCE VOL 24:267—276 271 . requiring very careful meas. stituents from concentration-dependent SAXS data- lecular crystallography. Data collection capability up to about 100 ps atomic clusters as labels to measure specific distan. such as a monomer with including the slow assembling (second or longer a stable dimer. noninteract. light-triggered proc- low-affinity complex of actin with a peptide ligand was esses.or hetero-oligomers co-existing with mono- X-ray scattering (ASAXS) of terbeium at the LIII mers. scattering from a bility to observe even faster. ment.126 The target biological pro- molecular species of one kind in dilute. such as capsid maturation and scattering from the higher aggregates.125. equilibrium mixtures can be potentially used in con- chrotron X-ray source. modeled intermediate filament assembling path.120–124 Thus. Anomalous scattering properties of metal ions.113.109 Time-resolved SAXS.70 will way from SAXS data by finding out conditions domi- almost certainly become more common in future. files of a variety of evolving systems. such as a gold nanocrystal.107 Makowski et al. time-resolved SAS is a to study these mixed systems. changes upon binding can make simple interpreta- bution due to the metal label to the total scattering tions of SAS data obtained from mixed systems diffi- is typically quite small. Although small anomalous junction with time series of SAXS to provide a rich contribution due to the cross-term between the label variety of information on the mixed system. conformational myoglobin and the metal ion. separation of individual entities in a mixture may not Anomalous solution X-ray scattering be possible or desirable in all cases. recently method for composition analysis and shape modeling used anomalous contribution from iron in the solu. depending upon include weak and transient interactions. scattering contri- bution due to the interference within the anomalous Time-resolved SAS to track biological processes scattering metal component itself is negligible. including the pathway intermedi- explorations of dissimilar anomalous scattering ates. SANS. many interesting biolog.109 Anomalous contri.110 With further ent components. time resolution at the modern. laser light for a light-initiated process (pump-probe) ical phenomena take place in a mixture of or by using a mixing device or by quickly removing interacting particles in solution. cult.116–118 These approaches are original in a sense edge was exploited to measure the mean distance that they allow derivations of low-resolution shape between the terbiums substituting the calcium bind.

SAS with complementary techniques can circumvent 15. which will be a giant step forward.130 fibrillation pathway in insulin amyloid and X-ray solution scattering (SAXS) combined with crys- alpha-synuclein. Frangakis AS. Chaudhuri BN (2012) The this limitation in many cases. 12. Curr Opin Struct Biol 23:748–754. acquisition. while simultaneously mon. 13.131 In another study. Q Rev Biophys 36:147–227. Mirza A. 3. glycopro. intrinsically disordered proteins.147. Biopolymers 95:517–530. Doniach S (2007) Small-angle X-ray scatter- ing from RNA. Weiss TM. Poole unrestricted movements of label-free biomolecules in FL. of beam dose on protein integrity. Q Rev Biophys 40:191–285. Dean R. Burkoth TS. Guss JM. Nishino Y. Meredith SC. Tsutakawa SE. Svergun DI. Nat Methods 6:606–612.136–138 and RNA folding. 9.. Yang SJ. Petoukhov MV. Classen S. Tainer JA (2009) Robust. Hura GL. Grant TD. Liu P.47–50 However. suitable for studying membrane-associated proteins Benzinger TLS. Takata H. Fischetti RF. structural changes of biological macromolecules in solu- tion. Makowski L (2003) High-resolution the coming years. shape. Chen et al. Irving TC. Montelione GT.140 In a molecular structures. biomacromolecules. Wolfley JR.1. chem J 254:313–327. mation from a helical nucleus. Feasibility of time. Svergun DI (2003) Small-angle of biological macromolecules from solution scattering scattering: a view on the properties.131. conformations and assemblies in seminal study by Vestergaard et al. J Synchrotron Radiat 19:431–434.128 microtubule forma. Seifert S. 2. much internal organization of mycobacterial partition assembly: work remains in method developments for data does the DNA wrap a protein core? PLoS One 7:e52690. insulin fibrillation solution. Jacques DA. combining J Appl Crystallogr 33:535–539. Jenney FE. Urban VS. Thiyagarajan P. Putnam CD. Protein Sci 19:642–657. J Synchrotron Radiat dented ways to reconstruct solution structures of 10:398–404. angle scattering data from biomolecules in solution. Svergun DI (1999) Restoring low resolution structure 1. essentially a low-information technique.142 structural studies. in near-natural environment. 11. Methods Mol Biol 544:307–323. Lipfert J. proteins. used to track local changes. Rambo RP. Acta Crystallogr D 68:620–626. UK: Oxford Univer- appropriate combinations of above are some of the sity Press. Hopkins RC. Perkins. Svergun DI time-resolved SAXS under protein contrast matching (2006) ATSAS 2.120. Niebuhr M. Jacques DA. accessibility data from time-resolved hydroxyl radical 5. a program package for small-angle conditions to track salt-induced DNA unwrapping in scattering data analysis. Martel A.ORG Biological Applications of Small-Angle Solution Scattering . rec. Urban V. folding pathway. Koch MH. Biophys J 76:2879–2886. Furthermore. Hammel M. 18. Timmins PA. teins with site-specific heavy atom labeling can be 8. Joti Y. and will conceivably reveal 17. Menon AL. Graewert MA. Takahashi Y. Kondrashkina E. ing (SAXS). Trewhella J (2010) Small-angle scattering for structural biology–expanding the frontier while resolved SAXS/WAXS studies of biological processes. opportunities to learn about size. process was modeled using time-resolved SAXS data. SJ (1988) Structural studies of proteins by key advantages and future promises of SAS tech- high-flux X-ray and neutron solution scattering. Morgan DM. Luft JR. performed 6. Hammel M. 4.129 allostery and structural dynamics in hemoglo. Adams near-physiological conditions at a wide range of tempo- MW. Trewhella J (2009) Small-angle scattering global size information obtained from time-resolved and neutron contrast variation for studying bio- SAS was effectively complemented with local solvent molecular complexes.141 Recently. membrane proteins.143 Although SAS is Lynn DG (2000) pH dependent self assembly of b- amyloid (10–35) and b-amyloid(10–35)-PEG3000. flexibility and disorder of soluble single/ Publication guidelines for structural modeling of small- multidomain proteins. tion.132 viral capsid maturation. Qian S. folding. Furthermore. 272 PROTEINSCIENCE. May RP (2013) convenient applications of SAXS or ASAXS on Small angle X-ray and neutron scattering from solu- heavy-atom labeled samples as molecular rulers and tions of biological macromolecules. avoiding the pitfalls. Trewhella J (2012) ognition. J Appl Crystrallogr 39:277–286. Hihara S.114. Volkov VV. unforeseen wealth of information on protein motion. Koch MHJ. Whitten AE. Dillard BD.light-driven proton pumps. DNA/RNA.133–135 tallography and computation: defining accurate macro- protein folding. Svergun DI (2013) Impact and progress footprinting to provide unique insights into the RNA in small and wide angle X-ray scattering (SAXS and WAXS). modern X-ray sources and meth- wide-angle X-ray scattering of protein solutions: effect odological advances will probably open up unprece. Hura GL. Tainer JA (2007) bin.139. Eltsov M. Tsuruta H. contrast variation for multicomponent assemblies. and protein complexes.72 An ability to probe 7. Martel A. Gordon D. Vachette P. Tsuruta H Concluding remarks (2012) An integrated high-throughput data acquisition Advances in SAS methods opened up the exciting system for biological solution X-ray scattering studies. grazing incidence solution scat. Ito K.124. Scott JW. structures and using simulated annealing. Svergun DI. Bio- nique. 10.148 Ishikawa T.144–146 In 16. high-throughput solu- ral resolutions is a huge advantage of time-resolved tion structural analyses by small angle X-ray scatter- SAS. Imamoto N. Annu leading to an elongation pathway for amyloid fibril for- Rev Biophys Biomol Struct 36:307–327. Konarev PV. Maeshima K (2012) Human mitotic chro- mosomes consist predominantly of irregularly folded nucleosome fibres without a 30-nm chromatin struc- References ture. Frankel KA. EMBO J 31:1644–1653. tering and related reflectivity techniques are 14. 1). time-resolved SAXS/WAXS on pro. the nucleosome core particle. and their assemblies (Fig. Snell EH (2011) Small angle X-ray scattering as a complementary tool for high-throughput itoring the global changes in the protein. analysis and model validation. teins. Rodi DJ.

Spinozzi F. Tsuruta H.dimensional Zernike polynomials. PLoS Biol 10:e1001244. CCL5/RANTES from NMR. Bernad o box C/D enzyme reveals regulation of RNA methyla- P. Garcia AE (2001) (2002) Addition of missing loops and domains to pro- Functional dynamics of the hydrophobic cleft in the N. Matsudaira P. Acta Crystallogr D 69:683–694. Sobhanifar S. Prestegard 27. mobility mass spectrometry and SAXS data in scoring 32. Hexemer A. Volkov VV. J Mol Biol 396:153–165. Petoukhov. 44. 611. D€ otsch V.19. Delarue M 46. Grossmann JG. MV. Bonvin AM (2013) On the usefulness of ion- Crystallogr A 68:278–285. Grandison S. data for biomolecules. Watson C. Webb B. Lapinaite A. 40. Hazelwood L. Biophys J 103:511–521. Svergun DI. Marcaida MJ. Liu H. structure determination using SAXS data. Grishaev A. applications to small. of solution small-angle X-ray scattering and NMR 34. Pons J. J Mol Biol 299:1289–1302. Biophys J 101:2061–2069. Orland H. Handel TM. Avila-Sakar A. Doniach S pressor p53 and a specific p53 DNA complex. Shkumatov AV. Biophys J 101:2981–2991. Kobe B. 3113–3125. Valle M. tion of modular proteins with small angle neutron scat- 38. Bax A (2005) Refine- modelling of macromolecular complexes against small. EMBO J 27:458–469. Roux B (2010) RNA 43. Liao M. Matthews S. M. Svergun DI (2012) New developments in struction of protein form with X-ray solution scattering the ATSAS program package for small-angle scattering and a genetic algorithm. Schneidman-Duhovny D. Sali A (2012) A method 30. 22. S. Krukenberg KA. K. Chaudhuri PROTEIN SCIENCE VOL 24:267—276 273 . Moulin M. Petoukhov MV. Crystallogr 28:768–773. Sali A docking decoys. Hennig J. DI 21.and wide-angle X-ray scattering. Seifert S. Goult BT. Mor an F. Ross I. King G. A (2012) Putting the pieces 31. (2013) Combining NMR and small angle X-ray and 35. tein models by x-ray solution scattering. Gabel F. Tekpinar M (2011) Accurate flexible fitting of 54. Melero R. Konarev PV. Cowieson NP. 28. Haertlein M. Biophys solution scattering data in Xplor-NIH structure calcu- J 105:962–974. J Mol Biol 403:217–230. scattering data using a coarse-grained model with Timmins P (2008) Complementing structural informa- implicit hydration shell. Ali M. Putz NS. Velazquez-Muriel. Schneidman. Gorba C. (2013) Accurate SAXS profile computation and its 49. Carazo JM. Gingras AR. Freund SM. Nucleic Acids Res 39:W184–W189. Beltramini M (2012) Quafit: a novel method of low-resolution three-dimensional density maps from for the quaternary structure determination from small- one-dimensional small-angle X-ray solution scattering angle scattering data. Annu Rev Biophys Bioeng 4:219–241. tering and contrast variation. Lasker. 29. Fersht AR (2007) Quaternary structures of tumor sup- 26. 45. Mertens HDT. Liang H. analysis using small-angle scattering in solution. Curry data. Krukenberg fitting of SAXS profiles with non-uniformally hydrated KA. Hammel M. tering data into structural modeling of proteins and 52. Wu J. Canestrelli I. Parisien M. J Appl Chiu W (1999) Scaling structure factor amplitudes in Crystallogr 36:860–864. Russel. Proc Natl (2010) The ligand-free state of the TPP riboswitch: a Acad Sci USA 104:12324–12329. Yang S. Franke D. Roberts 24. 33. ternary structure by small angle neutron scattering. Vigil D. J Struct Biol 128:51–57. nary protein-RNA complex. Tsuruta H. Rossi A. Critchley protein models obtained by small-angle X-ray scattering DR (2008) The structure of the C-terminal actin-bind- and crystallography. Agard DA. Rakwalska-Bange their assemblies. Doniach S. Biophys J 80:2082–2092. Svergun DI (2005) Global rigid body 50. electron cryomicroscopy using X-ray solution scatter- 23. 25. Tidow H. of SAXS profiles. F€orster F. Strop P. Acta 48. J Phys Grossmann JG. Callaghan AJ. Pons C. 20. Hammel M. Agard neutron scattering in the structural analysis of a ter- DA. Tokatlidis K. Chacon P. Walther D. 47. Rajpal atomic models. Doniach S (2000) Reconstruction 39. Major F. Petoukhov MV. J Appl ture 19:1138–1148. Gajda M. Barsukov IL. 37. high-resolution protein structures to small-angle X-ray Alcock FH. J Biomol NMR 56:17–30. Kim HM. Freed KF for integrative structure determination of protein- (2011) Modeling the hydration layer around proteins: protein complexes. Karaca E. J Appl Crystallogr 33:350–363. D. J Appl Crystallogr 45:342–350. Orozco M. Luisi BF. Gabel F. Chem B 114:10039–10048. Andreu JM (2000) Recon. Svergun DI. Herschlag D. Sali. D’Abramo M. Clore GM (2014) Using small angle assessment by contrast variation experiments. Mylonas E. Brown. Schmid MF. Cheng Y. Grossmann JG. Zipper P. Webb. Cohen FE. ing domain of talin. Bate N. Koehl P. Monie TP. Tria G. ment of multidomain protein structures by combination angle scattering data. Schneidman-Duhovny D. JH (2011) Oligomeric structure of the chemokine a program to evaluate X-ray solution scattering of bio. Biophys J 89:1237–1250. AA (2007) Comparison of GC. Sharp JS. KA. Velazquez-Muriel J. Koch MH (2002) Advances in structure ing. Opin Struct Biol 12:654–660. Huber T. Curr 42. Wang X. Morris RJ. Sosnick Tobin R. Virtanen J. Prog Nucl Magn Reson Spectrosc 80:1–11. Zwart PH together: integrative structure determination of macro- (2012) Computation of small-angle scattering profiles molecular assemblies. Kim (2011) AQUASAXS: a web server for computation and SJ. Wang I. Eady. Skjaerven L. 53. Schneidman-Duhovny D. Nucleic Acids Res 38:W540–W544. MS. NA. Eur Biophys J 37:603– Kikhney AG. Simon B. Sonntag M. data analysis. J Appl Crystallogr 40:1123–1134. Petoukhov MV. with three. Poitevin F. J Am Chem Soc 127:16621–16628. Allain FH. Krebs. and SAXS data. Koch MHJ (1995) CRYSOL . D. shape determination in small-angle scattering. Svergun. Zheng W. Struc- logical macromolecules from atomic coordinates. Dıaz JF. Tainer JA. Hanein D. Svergun DI (2006) Conformation of polypyrimidine 51. Gallagher SC. Trewhella J. lations. Nature 502:519–523. Barberato C. J Mol Biol 382:1089–1106. Schwieters CD. partially folded RNA structure. Svergun DI (2003) Uniqueness of ab-initio 41. Durchschlag H. Bioinformatics 28:3282–3289. Lipfert J. Cookson D. Sattler M tract binding protein in solution. Trewhella J. J. tion of protein-protein complexes by integrating compu. Engelman DM. Sherman MB. Moore PB (1975) Determination of qua- tational docking with small-angle scattering data. Sali A (2008) Integration of small-angle X-ray scat. B. Structure 14:1021–1027. A. Svergun DI. Sali A (2010) Hume DA. tion. Svergun DI. Fern andez-Recio J (2010) Structural characteriza. Biophys J 83: domain of calmodulin. Volkmann N. J Biol Chem 283:16187–16193. Carlomagno T (2013) The structure of the 36. Makowski L. Martin JL (2008) Cortactin adopts FoXS: A web server for rapid computation and fitting a globular conformation and bundles actin into sheets. Liu H.

Neylon C (2008) Small angle neutron and X-ray scat. Vives C. Biochemis. Nat Struct Mol Biol 81. 78. Makowski L. Lavery LA. of nuclear receptor heterodimers on DNA direct repeat Chem Biol 11:1431–1443. Hura GL.ORG Biological Applications of Small-Angle Solution Scattering . Bernad o P. Tokuda JM. Jeffries CM. Pebay- Biol 368:407–420. synaptic arrangement. Bardhan J. Rambo RP. Fujiwara S. J Biol Chem 275:14432–14439. transient structures of nucleosomes as DNA unwinds. scale DNA-induced compaction in the mycobacterial D’Mello R. Topping T. DiCapua E. Timmins PA (1989) The loca. Roux B (2009) A rapid plex. Boone CD. Contreras LM. Engelman DM (1999) A method for determining Svergun DI (2007) Structural characterization of flexi- transmembrane helix association and orientation in ble proteins using small-angle X-ray scattering. Ueki T (1992) X. rRNA distribution in the 70 S Escherichia coli ribo. Svergun DI. Eur Biophys J 37:531–541. Garg R. Uversky VN (2013) A decade and a half of protein lar modeling. 69. Ho NT. Cannella D. Trewhella J (2007) Small-angle solution scat. Gabel F.55. 76. Nierhaus KH (2000) A map of protein. Whitten AE. Rodi DJ. Park S. scattering reveals information on conformational 60. Callow P. Biopolymers environment. Neylon C. Petoukhov MV. Hanley T. Doniach S (2001) Changes in biomolecular conforma- try 28:3287–3292. Clantin B. 68. intrinsic disorder: biology still waits for physics. tion of DNA in complexes of recA protein with double. A neutron scattering study. Whitten AE. Whitten AE. Smith L. 75. Belfort M. Nucleic Acids Res 42: literature. Anthis NJ. Ebel C (2014) Probing the conformation of scattering. Acta Crystallogr A 64:181–191. Smith D. Van Duyne GD multiple conformational states of large protein com- (2014) Quaternary arrangement of an active. Gloss LM. global and local approach to elucidate spatial organiza. J Biochem 111:310–316. 86. Yamamoto M. (2011) Substrate tion of the Mycobacterial ParB-parS partition assem. Stuhrmann HB (2008) Small-angle scattering and its 72. 274 PROTEINSCIENCE. Fujisawa TJ (2004) Radia- variation data from biomolecular complexes. SR. Peyroula E. Roessle M. J Am Chem Soc 134:14686–14689. Biophys J 107:185–196. ric mechanism of histidine kinase inhibition. Langley DB (2007) The within the soluble domains of the CD4 receptor is structure of the Sda-KinA complex suggests an alloste. 88. Schweins R. Tainer JA (2011) Characterizing flexible (2014) Small-angle scattering gives direct structural and intrinsically unstructured biological macromole- information about a membrane protein inside a lipid cules by SAS using the Porod-Debye law. 87. Street TO. elements with different spacings. Chaudhuri BN. coarse residue-based computational method for X-ray 71. Mol Biosyst 8:151–167. Trewhella J. Inoko Y. Sutton JL. Krueger JK (2002) Small-angle solution some. angle X-ray scattering. interactions with regulatory targets. cation to a lead-substituted calmodulin-peptide com. Urban VS. contrast variation in SP. in solution. J Mol 77. Dean R (2011) The evidence of large- 63. Acta Crystallogr D 70:371–383. Lal J. native plexes. Clifton LA. Agard DA. Biophys J 77:1064–1073. binding drives large-scale conformational changes in bly. considerations and suppression by cryoprotectants. Pelikan M. Vachette P. Biochemistry 50:1799–1807. Ashish. Jacques DA. J Mol Biol 413:901–907. Bernado P. solution scattering characterization of protein folds and Spruce LA. Pedersen MC. Mortensen K. Pabit SA. Hamouda B. Comoletti D. 82. Kynde SA. Chance MR. 95:559–571. Gore D. Lyons K. stranded DNA. Nucleic Acids Res 42:8767–8776. Moman E. Ciesielski F. tron X-ray small-angle scattering: dose-related 58. Mandava S. Trewhella J. solution: a practical guide. 61. 56. Harris SP. dynamics in calcium-binding proteins and in their Taylor P. 85. Gee J (2011) A combined chromosomal ParB. detected by synchro- Crystallogr 41:222–226. flexibility within proteins as identified through small matched small-angle X-ray scattering from a heavy. Meisburger interplay with crystallography. Durand D. Blackledge M. Fischetti RF (2011) 65. J Am detergent micelles using small angle x-ray scattering. Ho C. Chen Y. Tsigelny I. 5347–5360. Seeholzer SH. Clore GM (2012) Contrast. Jacob-Dubuisson F. 80. J Mol Biol 408:909–921. Gore DB. Huang T. Haertlein M. Rochel N. Arleth L 84. Perez J. Sci USA 105:18360–18365. Midtgaard tein Sci 22:693–724. Kuwamoto S. Simonsen JB. ligand-specific. 79. Moras D (2011) Common architecture ligand-induced conformational changes in proteins. 101:1763–1778. 83. Proc Natl Acad Biol 169:45–53. Skar-Gislinge N. Methods Mol Biol 896:123–135. tion seen by small angle X-ray scattering. Mol Cell 42:96–105. Mylonas E. 18:564–570. Makowski L. 189. Pro- 67. Godet J. Pollack L (2014) Revealing SAXS and SANS. M ely Wide-angle X-ray solution scattering as a probe of Y. Cai S. Synchrotron Radiat 11:462–468. group II intron ribonucleoprotein complex revealed by tering in structural biology: recent examples from the small-angle X-ray scattering. J Appl tion damage to a protein solution. 57. Hammel M (2009) Structure and 70. Whitten AH. Anguita J. FhaC with small-angle neutron scattering and molecu. Methods Mol Biol tering of the neuroligin/b-neurexin complex reveals its 173:137–159. Svergun DI (2012) Structural analysis of 66. tidomain protein with semi-flexible linkers. Trewhella J (2008) MULCh: Mod. Park S. J Struct actin: implications for cardiac function. Lakey JH (2013) Examining WAXS studies of the structural diversity of hemoglobin protein-lipid complexes using neutron scattering. Methods Mol Biol 974:119–150. Fischetti RF. Bu Z. J Biol Chem 283:2761–2772. Lensink MF. Chem Rev 59. ULes for the analysis of small-angle neutron contrast 73. Makowski L (2004) Peluso-Iltis C. Schnarr M. Moulin M. Yang SC. Biophys J 96:4449–4463. the Hsp90 molecular chaperone. Gen Physiol Biophys 28:174– atom-labeled protein in structure determination: appli. intrinsically disordered proteins by small-angle X-ray Villeret V. Chaudhuri BN. Gupta K. Chem Soc 129:5656–5664. Fieschi F (2010) NADPH oxi- 62. 64. Grishaev A. Svergun DI. Guss MJ. Qu G. Rodi DJ. Gabel F (2012) Small angle neutron scattering for the ray scattering study of the shape of the DNA region in structural study of intrinsically disordered proteins in nucleosome core particle with synchrotron radiation. Akiyama S. King Krueger JK (2008) Conformational rearrangement GF. Juncadella IJ. Structure 15:693–705. Grishaev A. Gupta S. 74. Trewhella J dase activator p67(phox) behaves in solution as a mul- (2008) Cardiac myosin-binding protein C decorates F.

Pons M 101. Kwok LW. Predictive atomic resolution descriptions of intrinsi. Bertini I. Curr Opin Struct Biol 22:670–678. Le Clainche C. Biochemistry Crystallogr 21:355–362. Mendillo ML. Ihee H (2008) quantitative distance distributions. Wagner G. Strelkov SV (2006) Monitor- 135:10055–10063. Gajda M. Weinkam P. Luchinat C. 110. Miake-Lye RC. Kim YC. M. 111. Guo L. ing intermediate filament assembly by small-angle x- ray scattering reveals the molecular architecture of 99. Mills TT. Cupane A. Vainshtein BK. Jaremko X-ray scattering simulations: Proof of concept for dis- L. Akabayov B. Pierattelli R. PLoS One 9:e95664. Makowski L. Guittet E. Mathew-Fenn RS. Schotte F. Mirza A. Canard min in solution. M€ ucke N. Choi J. Nakasako. J Am Chem Soc ing: from solution SAXS to achievements with coher- 132:8690–6896. as studied by anomalous dispersion. Akabayov B. Pinfield VJ. dered protein: a small-angle neutron scattering study. Smith tion using time-resolved wide-angle X-ray scattering. Minh DD. F (1988) Struc. Rodi DJ. Stuhrmann HB. Putnam CD. Mastroianni AJ. Zweckstetter M. Structure 22: ing proteins. Receveur-Br echot V. Kilburn D. Silverman JA. 120. Proc Natl Acad 90. Mandava S. Lvov YM. Maskel GS. Briber RM. Petoukhov MV. associating proteins by singular value decomposition Richardson CC (2013) Impact of macromolecular of solution scattering data. Walker PA. Gore D. Uversky VN. Parigi G. Nishino Y (2012) Advances in X-ray scatter- ture by the excluded volume effect. Graewert MA. Richardson CC. J Am Chem Soc 131:4378–4386. Ozenne V. Rozycki _ B. Ravera E. Takacs M. domains controls their functions in actin assembly. Proc Natl ments facilitated by online HPLC buffer exchange. Kondrashkina E. Svergun DI. Claridge SA. Herschlag D. Goldenberg DP. J Synchrotron Radiat 11:314–318. Hummer G (2011) SAXS ensemble 106. AM. J Appl small-angle x-ray scattering. Wedig T. Svergun DI (2010) Confor. Billas IM. Fischetti 93. Biernat J. B. Briber RM. Longhi S (2006) Assessing protein disorder and 108. Feigin LA. Akabayov SR. 118. Craig BA. Lee SJ. Biophys J 102:927–933. Sali A. Williams GJ. Biophys J 106:905–914. Williamson TE. Havelund S. Bibow S. Anfinrud PA. using medium-angle X-ray solution scattering (MAD- mational space of flexible biological macromolecules MAX). Menhart N (2004) Liquid-chroma- cally disordered hTau40 and a-synuclein in solution tography-coupled SAXS for accurate sizing of aggregat- from NMR and small angle scattering. 109. affinities of interacting proteins from concentration tion of the distance between heavy-atom markers in series of solution scattering data: decomposition by haemoglobin and histidine decarboxylase in solution by least squares and quadratic optimization. 119:2863–2869. Cantrelle FX. Guttman M. induced folding. Svergun energy landscapes to favor folding. Bardhan J. Kellogg C. AM. Sibille N. Makowski L. Toft KN. Akabayov SR. Williamson TE. Biophys J 41:287–292. Bourhis JM. Das R. Bailey- J Am Chem Soc 135:10040–10047. Jensen MH. Roh JH. Doniach S. Blackledge M (2014) cromolecules in solution. van Heijenoort C. 112. Sokolova AV. Crystallogr 47:899–914. 113. JM. Roh JH. Jaremko M. P erez J. Argyle B (2014) Minimal effects of (2009) Low-resolution structures of transient protein- macromolecular crowding on an intrinsically disor. 107. J Mol Biol a single residue in individual b-thymosin/WH2 375:529–546. protein complexes using small-angle X-ray scattering. Wulff M. Acad Sci USA 110:17308–17313. Blobel J. David G. Cammarata M. Friedman 102. from average data. Kolodner RD. Inoko Y (2009) Size-exclusion chromatog- 95. J Am Chem Soc 132:13553–13558. 52:6844–6855. Das R. Finkelstein KD. Levantino M. Proteins 62:24–45. Alivisatos AP. tural information on proteins obtainable from small. Hertzog M. 119. tance measurements for nanoparticle-labelled bioma- Mandelkow E. Perez J. J Synchrotron Radiat 17:769–773. J Chromatogr A 1216:7461–7465. 117. Renault L (2011) How molecular breathing motions in proteins. Structure 21:321–331. Woodson SA EMBO J 31:1000–1013. PLoS One 3:e3229. Svergun DI (2013) Reconstruction of quater- angle X-ray scattering with heavy-atom labeling. J Am Chem Soc DI. Petoukhov RF (2012) Multiwavelength anomalous diffraction MV. Chaudhuri PROTEIN SCIENCE VOL 24:267—276 275 . Tainer JA (2013) DNA 121. Chandola H. M. 104. ent beams. Proc Natl Acad Sci USA 103: (2013) Molecular crowding enhanced ATPase activity of 16206–16211. of NMR and SAXS. Lee KK (2013) All-atom Sci USA 78:6216–6220. Nat Methods 5:881–886. Structure 19:109–116. Hura GL. Giachetti A. Tauler R. Herrmann H. 97. Roblin P. Tracking the structural dynamics of proteins in solu- 105. 238–249. Tsai CL. Millett IS. Fischetti RF (2008) Molecular crowding inhibits intra- Carlier MF. Harbury PA (2008) A molecular ruler for measuring Ewald F. alous x-ray scattering from terbium-labeled parvalbu- 91. Gore DB. Notbohm H (1981) Configuration of refinement of ESCRT-III CHMP3 conformational tran. Bernado P (2012) Structural characterization (2003) Counterion distribution around DNA probed by of intrinsically disordered proteins by the combined use solution X-ray scattering. Scott DJ (2014) Anomalous small angle 94. Rodi DJ. Jensen MR. Mathew E. Friedman AM (2008) Analysis of self- 100. Moras D. Likhtenshtein GI (1980) Determina. Craig BA. Bernad o P. 103. Gvozdev RI. Hodgson KO (1983) Anom- ing of glycosylated proteins. Moorthy 96. Kilburn D. the RNA helicase eIF4A correlates with compaction of its quaternary structure and association with eIF4G. Becker S. nary structure from X-ray scattering by equilibrium Application to solubilized bacteriorhodopsin. Minton AP (2006) How can biochemical reactions raphy combined with small-angle X-ray scattering within cells differ from those in test tubes? J Cell Sci optics. crowding on DNA replication. Wagner G assembly intermediates. Kreplak L. Biochem Soc Trans 40:955–962. Biophys J 94:4906–4923. ensemble modeling to analyze small-angle x-ray scatter. Behrouzi R. Perez J. Nat Commun 4:1615. Doniach S. 116. conformations in mismatch repair probed in solution Vestergaard B (2010) Time-resolved SAXS measure- by X-ray scattering from gold nanocrystals. 98. Watanabe Y. J Appl mixtures of biological macromolecules. Husson C. (2010) Molecular crowding stabilizes folded RNA struc- 114. Schwalbe M. Pollack L 92. Bailey-Kellogg C (2014) Stoichiometries and Marakushev SA. Kataoka. FEBS Lett 116:107–110. Tokunaga. Woodson SA (2013) Crowders perturb the entropy of RNA 115. Aebi U. the four iron atoms in dissolved human hemoglobin sitions. Phys Rev Lett 90:188103. Didry D.89.

Guo L. 143. Davidsson J. Mills TT. Barty A. Lurio L. Akiyama S. RA. Brenowitz M. Howells. Westenhoff S. 142. Wickstrand C. Wulff M. Matsui T. Biol 357:997–1008. formational change associated with maturation of view: structural insights into early folding events T 5 4 virus. 10 ms with pump. Boutet S. (2010) Beyond small-angle x-ray scattering: exploiting 133. Pande V. Proc Natl Acad Sci USA 99:4266–4271. Ikeda-Saito M. Pollack L. Malmerberg E. Kwok LW. Kirian. HN. Shoeman RL. the solution-scattering profiles of macromolecules. Neutze R (2008) A proposed time-resolved X-ray 129. Wang D. J. McWilliams-Koeppen 138. Canady MA. Kastrup JS. Kwok LW. 146. Matthews CR. VL. Kimura T. Poon BK. Pollack L (2002) Rapid compaction during Henning R. A. Groenhof G. Flink JM. Park HY. mutant alpha-synuclein form different fibril struc. Kosheleva I. 137. PLoS One 8:e67713. Das R. the radiation damage limit with Cryo-SAXS. Raccosta S. Sj€ ohamn J. Zatsepin NA. M. Vestergaard B. Spence JC. Groenning M. Rambo RP. Kirian RA.ORG Biological Applications of Small-Angle Solution Scattering . J Mol Biol 355:282–293. 125.probe X-ray solution scattering. HC. models and resolution by small-angle scatter- PLoS Biol 5:e134. Tanaka M (2012) Quantitative determination of 130. tion. Liang M. Duda RL. Tsuruta H. Biopolymers 95:550–558. Nobrega RP. Lee KK. Bari S. Smith H. Andersson M. ing. Millett IS. Manakovaa E. Kwok LW. Lamb JS. Berntsen P. Gajhede M. Liu H. Westenhoff S. Kathuria SV. Hendrix RW. Doniach S. Warkentin M. Uzawa T. Manno M. Malmerberg E. Austin RH. submillisecond intermediates of protein folding. Kimura T. J Mol Milathianaki D. Bogan M. Millett IS. Fromme P. Herschlag D (2003) The fastest Schlichting I. JE (2005) Cooperative reorganization of a 420 subunit ond time-resolved SAXS using a continuous-flow mixer virus capsid. Kyrsting A. J Am Chem Soc 134:7001–7008. Maskel GS. Doniach S. Pollack L. Spence. Grotjohann I. Curr Opin Struct Biol scattering. Martin AV. Holzingerb J. Ewald F. Johansson LC. 144. KE. Johnson JE (2010) Balanced 123. Kim KH. Vanataluc K. Katona K. Nielsen SB. Kjær KS. Bai Y. of rapid. Biophys J 98:1337–1343. large-scale protein quaternary structural 148. Katona G. Kim J. 132. Thorne RE (2013) Breaking 131. Graceffa R. 140. Kalidas C. ica B 276:532–533. Bilsel O. Bilsel O (2011) Minire. Roessle M. Kupitz C. van der Spoel D. Takahashi S. Heumanna H (2000) Time-resolved small. W€ ohri AB. Tate MW. Russell R. Hopkins JB. Oddershede L. van Driel TB. Neutze R (2009) and local perspectives. Cammarata M. James D. Meisburger SP. microsecond-resolved small-angle X-ray scattering. mational landscape of cytochrome c folding studied by angle neutron scattering of proteins in solution. Frokjaer S. Johansson LC. Johnson Chakravarthy S. scattering approach to track local and global confor- Bordas J (1996) Structural intermediates in the mational changes in membrane transport proteins. Adachi S. Tsuruta H. Herschlag D. Davidsson J. RNA folding. Koshihara SY. White TA. Tate MW. 22:651–659. exploration of the kinetics of RNA folding from global Eklund M. using continuous-flow time-resolved small-angle X-ray 136. Stanley CB. 124. investigation of the folding dynamics of heme oxygen- 127. Doak Gruner SM. Nielsen MM. Arnlund D. Chapman HN. Tsuruta H. Rowe EL. ase: implication of the scaling relationship for the Williams GJ. Takahashi S. 141. Aquila 139. Biophys van de Weert M. Vestergaard B. Hunter MS. Hartel A. Langkilde AE. Vincent J. Jones NG. Acta Crystallogr A 69:365–373. Biophys J 106:1489–1496. Messerschmidt M. Nishikawa Y. Spence JC. DePonte DP. Shneerson. using angular correlations from X-ray laser data. Frank M. J Mol Biol 352:723–735. Saldin DK. Weierstall U. 135. Nozawa the lateral density and intermolecular correlation S. Structural dynamics of light-driven proton pumps. Nielsen NC. J Chem dynamics of homodimeric hemoglobin from 100 ps to Phys 137:204907. Kathuria SV. Kosheleva I. Ihee H (2012) using grazing incidence small-angle X-ray scattering Direct observation of cooperative protein structural and grazing incidence X-ray fluorescence. Andresen 128. Stellato F. Kim TW. Johnson JE (2001) Analysis angular correlations. global events in RNA folding: electrostatic relaxation Neutze R (2014) Visualizing a protein quake with and tertiary collapse of the Tetrahymena ribozyme. Andreu JM. Abuillan W. Otzen DE (2013) Wildtype and A30P 147. Kim JG. time-resolved X-ray scattering at a free-electron laser. Muniyappan S. J 104:227–236. Oang KY. Graceffa R. Nakatani B. Fujisawa structural impact of the glutamine repeat in hunting. JCH tures. Moore PB (2014) The effects of thermal disorder on Giehm L. Schmidt. Trotter S. Towns-Andrews E. Nobrega electrostatic and structural forces guide the large con- RP. scattering. Mochrie SG (2001) Time resolved collapse studies at synchrotrons and X-ray free electron lasers: of a folding protein observed with small angle x-ray opportunities and challenges. Chen H. Biophys J 107:411–421. R€osslea M. Irving TC (2013) Sub-millisec. Chapman. Morishima I. Vorobiev A. Svane AS. and X-ray microbeam. M. Pollack L (2006) Concordant G. Diaz JF. Neutze R.122. Jacob J. Fujisawa T (2002) Confor- Mayb RP. Phys Rev B 81:174105. Akiyama S. 126. Ki between proteins anchored on the membrane surfaces H. mass. Thiyagarajan P. J Mol Biol 332:311–319. Zwart PH changes: time-resolved X-ray solution scattering of (2013) Three-dimensional single-particle imaging Nudaurelia capensis omega virus (NomegaV) matura. T (2006) Time-resolved small-angle X-ray scattering tin assembly. 276 PROTEINSCIENCE. Nat Methods 11:923–926. Ishimori K. Gillilan RE. Irving TC. Mochrie SG. Shcherbakova I. Macchi F. Fromme R. Barrea R. Phys. Sato T. Engstler Biophys J 70:2408–2420. Mochrie SG. Proc Natl Acad Sci USA 99:1329–1334. assembly of taxoid-induced microtubules and GDP. Structure 16:21–28. Pollack L. RB. Perevozchikova T. Phys Rev Lett 86:4962–4965. Diakun G. Christiansen G. Andersson M. Seibert MM. Henning R. Moffat K (2012) Time-resolved structural Gruner SM. Seifert S. Matsui HP. Finnefrock AC. Svergun DI (2007) A helical structural nucleus is the 145. Darnton NC. Berthelier V (2014) Investigating the T. Tainer JA (2013) Accurate assessment of primary elongating unit of insulin amyloid fibrils. J Synchrotron Radiat 20:820–825. tubulin double rings: time-resolved X-ray scattering. Barrea RA. Batt CA. Kim Y. Nature 496:477–481. J Mol Biol 311:803–814. Davidsson Structure 17:1265–1275. Ishimori K. Morishima I. Saldin DK. 134. Poon.