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event with high precision (Fig. 1D and fig. S3).
iomolecular interactions and assemblies of interactions of biomolecules with the required These data revealed clear signatures of different
are central to a wide range of physiolog- spatiotemporal accuracy and resolution. oligomeric states of BSA, with relative abundances
ical and pathological processes spanning Given sufficient sensitivity, light scattering is for monomer to tetramer of 88.63, 9.94, 1.18, and
length scales from small complexes (1) to an ideal means for detecting and characterizing 0.25% of the detected particles. For nonspecific
the mesoscale (2, 3). Despite considerable molecules in low-scattering in vitro conditions binding to an unfunctionalized microscope
developments in techniques capable of providing because of its universal applicability. In an in- coverslip, surface attachment was effectively
high-resolution structural information (4), such terferometric detection scheme (Fig. 1A), the irreversible (12,209 binding versus 372 unbind-
techniques are typically static, involve averaging scattering signal scales with the polarizability, ing events). As a result, we could determine
over many molecules in the sample, and there-
fore often do not fully capture the diversity of A Fig. 1. Concept of interfero-
structures and interactions. Solution-based en- metric scattering mass
semble methods enable dynamic studies but lack spectrometry (iSCAMS).
the resolution of separation required to distin- (A) Schematic of the experi-
guish different species (5–7). Single-molecule mental approach relying
methods offer a means to circumvent heteroge- Incident light Scattered light Reflected light on immobilization of individual
neity in both structure and dynamics, and prog- molecules near a refractive index
ress has been made in terms of characterizing B D interface. Oligomeric states
200
interactions (8) and mechanisms (9, 10). So far, 3000 are colored differently for clarity.
150
Incidences
(bulk) binding rate constants, which generally and figs. S5B and S7), we did not find measur- agreement with the range of masses spanning
exhibited only small variations with oligomeric able differences in the apparent molecular mass 124 to 158 kDa reported from other methods
state. These could be accommodated to obtain beyond the increase expected for the addition (Fig. 2B and fig. S5D). Replacing MSP1D1 with
minor corrections to the recorded mass spectra of glutaraldehyde molecules used to cross-link the smaller MSP1DH5 reduced the nanodisc di-
and yield the solution distribution (fig. S4). Our myosin into the folded conformation (extended, ameter and the lipid content by ~20%, after ac-
results, including the detection and quantifica- 528.4 ± 16.2 kDa; folded, 579.4 ± 14.8 kDa; fig. S5B). counting for the thickness of the protein belt (19).
tion of rare complexes such as BSA tetramers, The resolution, as defined by the full width at Given the masses of MSP1D1 and MSP1DH5 (47
demonstrate the ability of interferometric scat- half-maximum of the measured contrast, reached and 42 kDa, respectively), we predicted a mass
tering mass spectrometry (iSCAMS) to char- 19 kDa for streptavidin. In all cases, the resolution for the MSP1DH5 nanodisc of 113.6 kDa, in ex-
acterize solution distributions of oligomeric was limited by photon shot noise and influenced cellent agreement with our measurement (114.1 ±
species and molecular complexes at high dy- by molecular mass, increasing from 19 kDa for 1.9 kDa). Mass shifts associated with changes
namic range. streptavidin to 102 kDa for thyroglobulin (fig. S6, in lipid composition, such as those introduced
The regular spacing in the contrast histogram B and C). The <0.5% deviation from sequence by partially unsaturated lipids and cholesterol,
of BSA tentatively confirms the expected linear mass for species of >100 kDa compares well with matched those predicted from the assembly
scaling between mass and interferometric con- native mass spectrometry (17) and demonstrates ratios (Fig. 2B and tables S2 to S6).
trast. Repeating these measurements for eight the intrinsic utility of iSCAMS for the accurate To see whether our approach also applies to
different proteins, spanning 53 to 803 kDa, vali- mass measurement of biomolecules with oligo- solvent-exposed moieties that experience a dif-
dates the linear relationship (Fig. 2A and fig. S5A). meric resolution. ferent dielectric environment from those buried
The deviation between measured and sequence Moving beyond species composed solely of within a protein, we selected the HIV envelope
mass was <5 kDa, resulting in an average error of amino acids, lipid nanodiscs are an ideal system glycoprotein complex (Env), which is a trimer
1.9%, and this deviation showed no detectable for testing the broad applicability of iSCAMS of gp41-gp120 heterodimers. Env is extensively
correlation with refractivity in relation to the owing to their flexibility in terms of polypeptide N-glycosylated, with the carbohydrates contribut-
A B
Mass error /10-2
4 DLS
MSP1D1
0 DMPC
0.95 SEC MS NMR
Expected contrast change
-4
-8 0.90
MSP1D1
6 DMPC/PC14:1/Chol
0.85
MSP1D1
PC14:1/Chol
0.80 MSP1ΔH5
DMPC Lipid nanodiscs
Contrast /10-2
0.55 Streptavidin-biotin
2.5
Expected contrast change
+ Kifunensine
0.50
2.3 0 12 24 36 48 60 72 84
2 Number of glycans
0 12 24 36 48 60 72 84 + Biotin + Biotin•ACTH
2.1 0.45
- Kifunensine
+ Biotin•DSG3
1.9 0.40
Env glycosylation
0
0 200 400 600 800 240 280 320 360 50 60 70
Sequence mass /kDa Mass /kDa
Fig. 2. Characterization of iSCAMS accuracy, precision, and the contrast measured and the thick bars representing the measurement
dependence on molecular shape and identity. (A) Contrast versus uncertainty in terms of the standard error of the mean (SEM) for repeated
molecular mass, including for proteins used for mass calibration (black), experiments. For each sample, the upper text denotes the membrane
characterization of shape dependence (yellow), protein-ligand binding scaffold protein (MSP) used, and the lower text indicates the lipids in the
(green), lipid nanodisc composition (red), and glycosylation (blue). Mass nanodisc. (C) Recorded differential contrast for Env expressed in the
error (upper panel) is given as a percentage of the sequence mass relative presence or absence of kifunensine and associated mass ranges expected
to the given linear fit. (B) Nanodisc mass measurement for different for different glycosylation levels. (D) Mass-sensitive detection of ligand
lipid compositions and protein belts. Masses obtained by alternative binding in the biotin-streptavidin system, according to the sequence mass
methodologies for MSP1D1/DMPC are marked and extrapolated to the of streptavidin and the masses of biotin and two biotinylated peptides
other compositions. The horizontal bars indicate the expected mass range relative to the calibration obtained from (A). Abbreviations are defined in
as a function of characterization technique, with the thin bars indicating table S8. In (A) and (D), error bars represent SEM.
mannose; GlcNAc, N-acetylglucosamine) (fig. S8), systems that are difficult to assess quantitatively a result, we could show that binding of Env to
we recorded a mass of 350.0 ± 5.7 kDa. Making with existing techniques as a consequence of het- BanLec that is already bound to Env (KEnv) is
the crude approximation that glycans and amino erogeneity and multistep assembly mechanisms much stronger than to free BanLec (KBanLec), a
acids have similar polarizabilities, this corre- (Fig. 3). In addition, we aimed to monitor nuclea- key characteristic of cooperative behavior. More-
sponds to a glycan occupancy of 74 ± 3 out of 84 tion and polymerization dynamics of mesoscopic over, the mass resolution of our approach enabled
possible sites (Fig. 2C and fig. S5E), consistent structures down to the single-molecule level, us to quantify the number of BanLecs bound per
with recent observations of high occupancy for which is challenging because of the simulta- dimer (one to two), trimer (two to three), and
gp120 expressed with kifunensine (21). For Env neous requirement for high dynamic range, high tetramer (three to four) of Env, demonstrating
expressed without kifunensine, we recorded a imaging speed, and direct correlation between bivalent binding. These results are directly rel-
lower mass of 315.3 ± 10.5 kDa. The mass differ- the observed signals and the associated molec- evant to the characterization and optimization of
ence can be attributed only in part to the lower ular events. The biotin-streptavidin system exhib- antiretrovirals, given that multivalency and ag-
average mass of the processed glycans (fig. S8) its nearly covalent binding, raising the question gregation have been proposed to be linked to
and yields a total N-glycan occupancy of 61 ± 6. of whether iSCAMS is capable not only of de- neutralization potency (25). We anticipate sim-
Although the exact values for occupancy are be- termining mass distributions, but also of quanti- ilar quantitative insights to be achievable for
holden to our calibration (Fig. 2A), the presence fying weaker equilibria, as are often encountered other therapeutic target proteins and protein-
of unoccupied sites is consistent with their ob- for protein-protein interactions. protein interactions in general.
servation in proteomics data (22). We therefore investigated the interaction of An advantage of our imaging-based approach
The high precision of 1.8 ± 0.5% with respect Env with the antiviral lectin BanLec, which is its ability to time-resolve mass changes in a
to the protein mass (Fig. 2A) indicates the po- neutralizes HIV by binding to surface N-glycans position- and local concentration–sensitive man-
tential for direct detection of small-molecule (23, 24) through an unknown mechanism. We ner. This enables us to examine surface-catalyzed
binding. To probe the current limits of iSCAMS were able to monitor the interactions and short- nucleation events that may eventually lead to
in terms of precision, we therefore examined the lived complexes before aggregation, with the ad- amyloid formation (26). Previous studies using
0.5
[BanLec] /nM
40
self-assembly, molecule by molecule. In an actin
0.50 polymerization assay, subtraction of the con-
stant background revealed the growth of surface-
immobilized filaments. In contrast to a-synuclein,
where the growth of interest took place within
0.25
a diffraction-limited spot, in this case we could
quantify length changes of filaments larger than
the diffraction limit upon the attachment and
0 detachment of actin subunits (Fig. 4C, fig. S10C,
500 1000 1500 0.1 1 10 and movie S3). We observed distinct, stepwise
Mass /kDa [BanLec] /nM changes in the filament length (Fig. 4D; fig. S10,
D to F; and movie S4), the most frequent forward
Fig. 3. Single-molecule mass analysis of heterogeneous protein assembly. (A) Mass distributions and backward step sizes in the traces being 3.0 ±
for Env in the presence of 0.5 to 40 nM BanLec monomer, alongside expected positions for 0.8 and 2.7 ± 0.7 nm, respectively—very close to
multiples of bound BanLec tetramers. Inset, a zoomed-in view of the region for larger species. the expected length increase of 2.7 nm upon
(B) Oligomeric fractions colored according to (A) versus BanLec concentration, including predictions binding of a single actin subunit to a filament
(curves) using the model shown. (Fig. 4E). Detection of larger step sizes represents
-12 -6
0s 1s 2s 0s 5s 10 s
Contrast /10-2
Contrast /10-2
8 3
B D
15
20 nm
Contrast /10-2
100 10 1s
Aggregation rate /MDa·s-1
5
Step size /nm
E -5 0 5 10
200
0
10 0 0.5 1.0 1.5
Time /s
Incidences 100
50
0
1 10 -100 -50 0 50 100 150
[α-synuclein] /µM Mass increment /kDa
Fig. 4. Mass imaging of mesoscopic dynamics. (A) Schematic and (D) Representative traces of actin filament tip position (gray) and
iSCAMS images of a-synuclein (1 mM) aggregation on a negatively charged corresponding detected steps (black). (E) Step and mass histogram from
bilayer membrane. (B) Initial growth rate versus a-synuclein concentration, 1523 steps and 33 filaments, including a fit to a Gaussian mixture model
shown with the best fit assuming first-order kinetics. Error bars denote (black) and individual contributions (colored according to fig. S10G). Scale
SEM for different particles. Inset, individual (gray) and average (black) bars, 1 mm. In these experiments, background correction involved removal
growth trajectories for 21 particles from (A). (C) Schematic and iSCAMS of the static background before acquisition, rather than continuous differential
images of actin polymerization. The arrow highlights a growing filament. imaging as in Figs. 2 and 3 (supplementary materials).
the addition of multiple actin subunits within Specific functionalization and immobilization 7. S. I. A. Cohen, M. Vendruscolo, C. M. Dobson, T. P. J. Knowles,
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25. S. Lusvarghi et al., ACS Infect. Dis. 2, 882–891 (2016). Scholarship from St John’s College, University of Oxford, and P.S., R.R., M.R.G., W.B.S., J.L.P.B., and P.K. Visualization: G.Y.,
26. C. Galvagnion et al., Nat. Chem. Biol. 11, 229–234 (2015). an Engineering and Physical Sciences Research Council (EPSRC) N.H., J.L.P.B., and P.K. Supervision: P.K. Competing interests:
27. A. Iyer, N. Schilderink, M. M. A. E. Claessens, V. Subramaniam, Studentship. J.Al. and M.C. were supported by the National P.K. has filed a patent for the contrast enhancement methodology
Biophys. J. 111, 2440–2449 (2016). Institute of Allergy and Infectious Diseases (Center for HIV/AIDS and its application to mass measurement of single biomolecules.
28. M. Kasai, S. Asakura, F. Oosawa, Biochim. Biophys. Acta 57, Vaccine Immunology and Immunogen Discovery grant All other authors declare no competing interests. Data and
22–31 (1962). UM1AI100663). J.R.S. was supported by NHLBI intramural materials availability: All data necessary to support the
29. H. P. Erickson, J. Mol. Biol. 206, 465–474 (1989). program HL0001786. C.E. is supported by a Swiss National conclusions are available in the manuscript or supplementary
30. B. Hua et al., Nat. Methods 11, 1233–1236 (2014). Science Foundation advanced postdoctoral mobility fellowship materials and are deposited in the University of Oxford Research
(P300PA160979). P.S. is funded by a European Research Council Archive (DOI, 10.5287/bodleian:PmA5Va0a2).
ACKN OW LEDG MEN TS (ERC) Consolidator Grant (NeuroInCellNMR, 647474). J.L.P.B.
J.R.S. thanks F. Zhang for technical assistance and the NHLBI thanks the EPSRC for EP/J01835X/1. P.K. was supported by an
SUPPLEMENTARY MATERIALS
electron microscopy core facility. Funding: G.Y. was supported by ERC Starting Investigator Grant (Nanoscope, 337577). Author
a Zvi and Ofra Meitar Magdalen Graduate Scholarship. N.H. was contributions: Conceptualization: W.B.S., J.L.P.B., and P.K. www.sciencemag.org/content/360/6387/423/suppl/DC1
supported by a DFG (German Research Foundation) research Methodology: G.Y., N.H., D.C., J.An., E.G.M., C.E., P.S., M.R.G., Materials and Methods
fellowship (HU 2462/1-1). E.G.M. thanks the Swedish Research W.B.S., J.L.P.B., and P.K. Software: G.Y. and N.H. Validation: G.Y., Figs. S1 to S10
Council and the European Commission for a Marie Skłodowska Curie N.H., J.L.P.B., and P.K. Formal analysis: G.Y., N.H., A.T., A.A., Tables S1 to S8
International Career Grant (2015-00559). M.P.C. is a Clarendon A.O., J.An., E.G.M., and M.R.G. Investigation: G.Y., N.H., D.C., A.F., References (31–51)
Scholar supported by the Oxford University Press. S.A.C. is J.An., A.T., A.A., N.B., Y.T., and C.E. Resources: M.P.C., S.A.C., O.T.,
Movies S1 to S4
supported by the Biotechnology and Biological Sciences Research J.Al., M.C., N.B., Y.T., J.R.S., C.E., P.S., L.F., R.R., and W.B.S. Writing
Council and Waters Corp through the iCASE studentship of original draft: G.Y., J.L.P.B., and P.K. Revision and editing: 26 November 2017; accepted 26 March 2018
BB/L017067/1 to J.L.P.B. O.T. acknowledges a Lamb and Flag G.Y., N.H., A.F., A.O., E.G.M., M.P.C., S.A.C., O.T., M.C., J.R.S., C.E., 10.1126/science.aar5839
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