WO2017118494A1

WO2017118494A1 - Method and apparatus for imaging single molecules

Info

Publication number: WO2017118494A1
Application number: PCT/EP2016/065222
Authority: WO
Inventors: Jean-Nicolas LONGCHAMP; Hans-Werner Fink; Conrad Escher
Original assignee: Zurich Universitaet Institut fuer Medizinische Virologie
Current assignee: Zurich Universitaet Institut fuer Medizinische Virologie
Priority date: 2016-01-08
Filing date: 2016-06-29
Publication date: 2017-07-13
Anticipated expiration: 2018-07-08
Also published as: JP2021170015A; DE212016000262U1; US10515791B2; US20190035616A1; JP2019504318A

Abstract

A method of imaging single molecules, comprises the steps of: a) providing an assembly comprising a carrier substrate having a substrate face with an aperture, the aperture being covered with a receiving layer attached to the substrate face, the receiving layer being substantially transparent for low-energy electrons with a kinetic energy of 5 to 1'000 eV; b) depositing single molecules onto said receiving layer by means of soft-landing electrospray ion deposition, whereby a single molecule loaded receiving layer is formed; c) acquiring an in-line low-energy electron transmission pattern of said single molecule loaded receiving layer; and d) applying a reconstruction procedure to said electron transmission pattern to obtain at least one image of a single molecule on said single molecule loaded receiving layer. The above steps a) to c) are conducted under vacuum conditions.

Description

Method and apparatus for imaging single molecules

Field of the invention

The present invention relates to a method and an apparatus for imaging single molecules, particularly single protein molecules.

Background of the invention

Most of the protein structural information available today has been obtained from either X-ray crystallography experiments or cryo-electron microscopy investiga- tions by means of averaging over many molecules assembled into a crystal or over a large ensemble selected from low signal-to-noise ratio electron micrographs respectively¹⁰. Despite the impressive amount of available data, a strong desire for acquiring structural data from just one individual molecule is emerging for good reasons. Most of the biologically relevant molecules exhibit different conformations; the associated structural details however, remain undiscovered when averaging is involved. Moreover, a large subset of the entirety of proteins, in particular out of the important category of membrane proteins, does not crys- talize at all. If just one individual protein or protein complex can be analysed in sufficient detail, also those objects become finally accessible.

For a meaningful contribution to structural biology, a tool for single molecule imaging has to allow for observing an individual protein long enough to acquire a sufficient amount of data for revealing its structure, ideally without destroying it. The strong inelastic scattering cross-section for both, X-rays and high-energy electrons as employed in the state-of-the-art aberration corrected TEMs, inhibits accumulation of sufficient elastic scattering events required in order to reveal high-resolution reconstruction of just one molecule. Future X-ray Free Electron Lasers (XFELs) with drastically enhanced brightness and reduced pulse duration might eventually achieve the goal of single molecule imaging. Yet, the current and foreseeable state-of-the-art in XFEL performance still requires averaging over at least 1 million molecules¹'^11-13. Apart from protein molecules, there are also many other types of other molecules for which single molecule imaging would be desirable. These comprise molecules with a variety of molecular sizes. In view of the above, it is an object of the present invention to provide a method and an apparatus for imaging single molecules.

Summary of the invention

It has now been found that the above object can be achieved by means of a method as defined in claim 1 .

Therefore, according to one aspect of the invention, a method of imaging single molecules comprises the steps of:

a) providing an assembly comprising a carrier substrate having a substrate face with an aperture, the aperture being covered with a receiving layer attached to the substrate face, the receiving layer being substantially transparent for low-energy electrons with a kinetic energy of 5 to 1 Ό00 eV;

b) depositing single molecules onto said receiving layer by means of soft- landing electrospray ion deposition, whereby a single molecule loaded re- ceiving layer is formed;

c) acquiring an in-line low-energy electron transmission pattern of said single molecule loaded receiving layer; and

d) applying a reconstruction procedure to said electron transmission pattern to obtain at least one image of a single molecule on said single molecule loaded receiving layer;

the above steps a) to c) being conducted under vacuum conditions.

According to another aspect of the invention, an apparatus for carrying out the method for imaging single molecules comprises:

a) a vacuum chamber containing a carrier substrate having a substrate face with an aperture, the aperture being covered with a receiving layer attached to the substrate face, the receiving layer being substantially transparent for low-energy electrons with a kinetic energy of 5 to 1 Ό00 eV;

b) means for depositing single molecules onto said receiving layer by means of soft-landing electrospray ion deposition to form a single molecule loaded receiving layer; and

c) means for acquiring an in-line low-energy electron transmission pattern of said single molecule loaded receiving layer.

In the present context, the term "low-energy electrons" shall be understood to refer to electrons having a kinetic energy in the range of 5 to 1 Ό00 eV with respect to the receiving layer onto which they are directed.

In principle, the method of the present invention can be applied to a large variety of molecules ranging from small inorganic or organic molecules all the way to very large biomolecules. It is also applicable to assemblies of molecules such as dimers, oligomers and clusters.

It will be understood that in case of very small, comparatively volatile molecules such as triatomics Oder even diatomics, it may be necessary to cool the receiving layer to temperatures well below ambient temperature in order to achieve a sufficiently stable arrangement of single molecule on the receiving layer.

The term "soft-landing electrospray ion deposition" shall be understood as an implementation of the generally known methodology of electrospray ion deposi- tion wherein "soft-landing" shall refer to a deposition conducted with an ion impact energy that is small enough to avoid any undesired effects. The corresponding energy threshold depends on the particular application. In many cases the impact energy shall be low enough to avoid dissociation of molecular bonds. Clearly, however, the study of weakly bound molecular assemblies will require particularly soft deposition conditions. Advantageous embodiments are defined in the dependent claims and in the description further below.

According to one embodiment (claims 2 and 10), the deposition of single mole- cules comprises ionization of single molecules to form single molecular ions, electrostatic extraction and mass filtering of said single molecular ions and electrostatic guidance of mass filtered single molecular ions onto said receiving layer.

According to one embodiment (claims 3 and 1 1 ), the single molecules are pro- tein molecules.

According to an advantageous embodiment (claims 4 and 12), the receiving layer is a graphene monolayer. Ultraclean freestanding graphene can be prepared by the Pt-metal catalysis method described in detail elsewhere⁶ (see also: WO 2014/064057 A2).

In principle, various types of electron transmission pattern can be used to obtain the desired information of the single molecules of interest. For example, one can use a low-energy electron diffraction pattern technique. According to an advan- tageous embodiment (claims 5 and 9), the electron transmission pattern is a hologram.

According to a further favorable embodiment (claims 6 and 13), the substrate face consists of a platinum metal selected from the group consisting of Pt, Pd and Rh, preferably Pt.

According to an advantageous embodiment, the apparatus of the present invention further comprises means for applying a reconstruction procedure to said electron transmission pattern to obtain at least one image of a single molecule on said single molecule loaded receiving layer. Brief description of the drawings

The above mentioned and other features and objects of this invention and the manner of achieving them will become more apparent and this invention itself will be better understood by reference to the following description of various embodiments of this invention taken in conjunction with the accompanying drawings, wherein are shown:

Fig. 1 : Schematic workflow for imaging a single protein. From top to bottom:

Preparation and characterisation of ultraclean freestanding graphene. Deposition of proteins onto freestanding graphene in a m/z filtered ES-IBD system. Imaging of the proteins within the previously characterised region by means of low-energy electron holography. During the whole experimental workflow, the sample is kept under strict UHV conditions with the help of a UHV suitcase for the transfer between the two experimental chambers (see Supplementary Information for more details).

Fig. 2: Images of individual BSA proteins deposited onto freestanding graphene. a, Mass spectrum of the BSA ion beam. Ion beams of mainly unfolded BSA (Sigma A4919) were prepared by electrospraying solutions of 0.4mg/ml_ BSA dissolved in a 1 :1 mixture of water and ethanol to which 2% formic acid is added. At a flow rate of 30 L/hr, an ion current of 2nA is measured at the TOF-MS. The mass spectrum above 1000u/e shows the characteristic peak group of multiply charged proteins (z = +35 ... +60). The low m/z range (<1000u/e) as well as the high m/z range (>2000 u/e) is free of any peaks indicating a pure beam free of contamination and unspecific agglomerations, b, Survey image of the deposited high-charge state BSA proteins on graphene. As expected from the mass spectrum the vast majority of proteins are in an unfolded state. Two high magnification images of BSA in a folded structure are presented in c and d. The scale bars correspond to 50nm in b and 5nm in c and d. The atomic model of BSA from the protein data bank (pdb id: 3V03) in the corresponding orientations is displayed in e and f for comparison. Fig. 3: Low-energy electron holograms of cytochrome C and their reconstructions, a, Three holograms of CytC recorded at kinetic electron energies of 142eV (left), 132eV (middle), and 1 17eV (right), b, Numerical reconstructions showing the protein in different orientations on gra- phene. The scale bars correspond to 2nm. c, Suggestions for possible orientations based on the averaged protein structure derived from X- ray crystallography data and documented in the protein data bank (pdb id:1 HRC).

Fig. 4: Freestanding graphene before (a) and after (b) the deposition of

30pA/h native CytC. In b individual globular objects of a size of 2-5nm or agglomerates thereof are observed. Such agglomeration has previously been observed on a Au(1 1 1 ) surface after deposition of native CytC in low charge states¹⁴, c, After moving the electron point source closer to the globular objects, their dimensions can be measured and correspond to the size of individual folded CytC molecules. The scale bars correspond to 50nm in a and b and to 5nm in c.

Low-energy electron holograms of two individual haemoglobin and their reconstructions, a, Two holograms of haemoglobin recorded at kinetic electron energies of 71 eV (left) and 69eV (right) respectively, b, Numerical reconstructions showing the protein complex in two different orientations on graphene. The scale bars correspond to 5nm. The diffuse rings around the object are due to the presence of the out- of-focus twin image inherent to in-line holography, c, Suggestions for possible orientations based on the averaged protein structure derived from X-ray crystallography data and documented in the protein data bank (pdb id: 2QSS ).

Time evolution of the orientation of CytC complexes. The time lapse between subsequent observations amounts to 30sec. From these images it is evident that at least some of the deposited proteins are mobile on freestanding graphene. Low-energy electron holography appears to be a method for also studying diffusion of proteins on surfaces. This observation suggests that a low-energy electron holographic microscope operating at cryogenic temperatures might be needed in order to fix the protein in space and attain atomic resolution. The scale bars correspond to 5nm.

Mass spectra of Cytochrome C (left) and Haemoglobin (right). Top: the m/z spectra before mass filtering are displayed. Bottom: the corresponding mass-filtered spectra.

UHV Vacuum Suitcase and its performance, a, Three-dimensional rendering of the transport suitcase enabling UHV transfer of ultraclean freestanding graphene between the low-energy electron microscope and the ES-IBD chamber. Low-energy electron projection images before (b) and after (c) a complete transfer and travel cycle without protein deposition. During the course of the transfer procedure between the two vacuum chambers no relevant contamination of the graphene built up.

UHV Vacuum Suitcase and its performance, a, Three-dimensional rendering of the transport suitcase enabling UHV transfer of ultraclean freestanding graphene between the low-energy electron microscope and the ES-IBD chamber. Low-energy electron projection images before (b) and after (c) a complete transfer and travel cycle without pro- tein deposition. During the course of the transfer procedure between the two vacuum chambers no relevant contamination of the graphene built up. Detailed description of the invention Experimental studies

Ultraclean freestanding graphene was prepared by the Pt-metal catalysis method described in detail elsewhere⁶. Prior to the transfer of the ultraclean substrate from the UHV chamber of the low-energy electron holographic microscope to the UHV chamber of the ES-IBD device, the cleanliness of the substrate is characterized and reference images are recorded for comparing the very same region of freestanding graphene before and after protein deposition. During the whole experimental workflow, the samples are kept under strict UHV conditions with the help of a UHV suitcase for transfer between the two experimental chambers.

Details of the ES-IBD procedure and of the low-energy electron holography ex- perimental scheme are described in the supplementary information

The workflow for imaging a single protein involves several steps as illustrated in Fig. 1 . An ultraclean freestanding graphene sample is prepared using the recently developed platinum metal catalysis method⁶ and characterized in the low- energy electron holographic microscope (Fig. 1 top). Such sample is subsequently transferred to an ES-IBD system (Fig. 1 middle) under permanent UHV conditions by means of a UHV suitcase operating in the 10^"11 mbar regime (see Supplementary Information for more details). Native cytochrome C (CytC), and haemoglobin (HG) ion beams are generated by electrospray ionization and mass filtering. For CytC the charge states z=5-7 are selected¹⁵. In the case of HG the charge states z=16 or z=17 of the intact complex are known to be of native con- formation¹⁶ and hence the corresponding m/z region is selected (the corresponding mass spectra are displayed in the Supplementary Information). In a third experiment, bovine serum albumin (BSA) in the high-charge states z=35-60 is chosen for deposition (see Fig. 2). In all three cases, the ions land with a kinetic en- ergy of 2-5eV per charge¹⁴ on ultraclean freestanding graphene covering 500x500nm² apertures milled in a 100nm thick SiN membrane⁶.

After deposition, the samples are transferred again under preserved UHV conditions from the ES-IBD system back to the low-energy electron holographic mi- croscope, where low-energy electron holograms of individual proteins are recorded¹³. In this experimental scheme inspired by Dennis Gabor's original idea of holography, the samples are presented to a highly coherent beam of low-energy electrons generated by an atomically sharp field emitter tip placed as close as 100nm in front of the sample (Fig.1 bottom). The interference pattern formed by the scattered and the un-scattered electron waves, the so-called hologram, is recorded at a several centimetres distant electron detector (for more details see supplementary information). Subsequent numerical hologram reconstruction involving back propagation of the wave front from the hologram to the sample plane^17-19 finally reveals the protein structure.

Holograms of individual CytC proteins and their respective reconstructions are presented in Fig. 3(a-b). Survey images of freestanding graphene before and after deposition of CytC is presented in Fig. 4. The shapes of the imaged proteins are compared with the structural data information obtained from X-ray crys- tallography investigations and available from the protein data bank (pdb id: 1 HRC). The overall size of the imaged CytC corresponds to the expected dimensions and the low-energy electron images can be associated with proteins in several distinct orientations. The resolution in the electron images is sufficient to identify individual CytC as well as agglomerates thereof (Fig. 3b). As demon- strated previously with DNA⁸, no sign of decomposition of the protein during electron exposure is observed. From the data displayed in the right column of Fig. 3, it remains unsettled whether the agglomerate formed by several CytC has assembled prior or past deposition. On the other hand, in Fig. 5 two holograms and their respective reconstruc- tions of individual haemoglobin are presented demonstrating that with our method it is not only possible to image individual proteins but also to deposit and image entire biologically relevant protein complexes. As apparent from the high contrast images of individual haemoglobin, not just the globular structure with the correct overall dimensions of the protein complex is revealed, but also details of its shape in different orientations. In Fig. 5(b right), structural features of 0.7- 0.8nm in size can clearly be identified and may serve as a rough resolution estimate for the low-energy electron images. In a hologram the spacing between consecutive interference fringes gradually decreases towards higher orders. Hence, high-order interference fringes and consequently high-resolution struc- tural details are most susceptible to mechanical vibrations. The latter are currently limiting the resolution and intense efforts are ongoing to increase the mechanical stability of the low-energy electron holographic microscope in order to overcome this limitation and approach atomic resolution. At this stage, the comparison with the protein data bank structure has the character of a control experiment. However, the future goal is to directly uncover the structure of unknown proteins and all their possible conformations that might differ in the position of a small number of atoms only. Nevertheless, on the road towards this ambition, additional fundamental questions remain to be addressed as for instance: the influence of the substrate, the possibility to add a hydration shell under UHV conditions, as well as issues related to transport, like diffusion of proteins and subsequent association into protein complexes. First observations of diffusion of folded proteins on freestanding graphene by means of low- energy electron holography are presented in Fig. 6 illustrating that our method described here is also capable of accessing dynamical processes. To conclude, we have shown how to image a single protein by combining the ES-IBD technology with low-energy electron holography. This has led to the first tool ever for revealing structural details of native single proteins and protein complexes without destroying them. With the recent advances in electrospray ionization of large protein complexes²⁰ and in particular membrane proteins²¹'²², even the structure of these biologically important but reluctant to readily crystal- ize entities will possibly become accessible in the near future.

While bare freestanding graphene has already been imaged with 2 Angstrom resolution by coherent diffraction with low-energy electrons²³, it is now a chal- lenge of adopting the technologies described here for reaching atomic resolution in structural biology at the single protein level.

Supplementary Information ElectjrDSBia _Jon_BeamJDepos CES-_IBD)

Soft-landing electrospray ion beam deposition takes place in a home-built instrument⁴'⁵. The ion beam is generated by a nano electrospray source with an optimized hydrodynamic behaviour²⁴ at a flow rate of 20-30μΙ_/Ιπ and an emitter voltage of approximately 3kV. The positive ions enter the vacuum through a heated metal capillary and are collimated in an ion funnel and a collisional colli- mation quadrupole operated in ff-only mode. In the third pumping stage a mass filtering quadrupole selects the m/z region of interest, which is monitored by the time-of-flight mass spectrometer in the fourth pumping stage. Here, a retarding field energy analyser measures the kinetic energy of the ions. The beam is then guided by electrostatic lenses towards the target in the 6^th pumping stage being at 2x 1 0^"10mbar, where the protein deposition takes place. To ensure gentle landing, the collision energy is controlled by applying a bias voltage to the target and hence reducing the kinetic energy of the protein ions. To obtain ion beams of native CytC (bovine, Fluka 30398), a solution of 0.15mg/ml_ was prepared in aqueous 50mM ammonium acetate buffer. With a spray flow rate of 25pl_/hr, an ion current of 1 .1 nA is detected at the TOF-MS. Unfiltered mass spectra (Fig. 7 left/top) show low charge states of +5 to +7, corresponding to folded CytC. At lower m/z values peaks corresponding to highly charged (z>+8) unfolded CytC and peaks that relate to fragments or contamina- tion are found. Note that, due to the limited dynamic range of the TOF-MS, the detector amplification was set very high, such that the peaks of the native CytC are distorted. The m/z selective quadrupole was tuned to select a m/z-window from 1250u/e to approximately 3500u/e by setting a ff-amplitude of 700V with a differential dc-voltage of 5%. This results in a beam of predominantly native CytC (Fig. 7 left/bottom) from which unfolded proteins (low m/z) and undefined heavy aggregates (high m/z) are removed.

Haemoglobin (bovine, Sigma H2500) is a protein complex of four myoglobin subunits, two A and two B. Ion beams are generated from solutions of 0.3mg/ml_ HG prepared in 50mM ammonium acetate buffer. A current of 600pA is detected at the TOF-MS. The mass spectrum is very complex and is resolved only partially due to the limited performance concerning resolution and dynamic range of the home-built linear TOF-MS. Nevertheless, a comparison with literature spectra allows identifying characteristic peaks (Fig. 7 right/bottom), which become more pronounced after removal of the unspecific agglomeration in the high m/z range (>5000u/e) by mass filtering with the quadrupole. The beam transmitted for deposition contains native intact HG complexes (Q¹⁷⁺, Q¹⁶⁺) along with dimers (D) and monomers (HBA). Low_zEne_rgy_ Eject_rgn_ holography

In the low-energy electron holographic setup³ ((Fig. 8), inspired by Dennis Ga- bor's original idea of in-line holography²⁵'²⁶, a sharp (1 1 1 )-oriented tungsten tip acts as electron point source (EPS) providing a divergent beam of highly coherent electrons²⁷'²⁸. The atomic sized electron field emitter can be brought as close as 100nm to the sample with the help of a 3-axis nanopositioner. Part of the electron wave is elastically scattered off the object and hence is called the object wave, while the un-scattered part of the wave represents the reference wave. At a distant detector, the hologram, i.e. the pattern resulting from the interference of these two wave fronts is recorded. The magnification of the imaging system is given by the ratio between detector-to-source distance and sample-to-source distance and can be as high as 1 0⁵. A hologram, in contrast to a diffraction pattern, contains the phase information of the object wave, and the object structure can thus be reconstructed unambiguously. The numerical reconstruction from the hologram is essentially achieved by back propagation to the object plane, which corresponds to evaluating the Fresnel-Kirchhoff integral transformation^17-

UHV T ansfer

A vacuum suitcase, Fig. 9(a) {Ferrovac GmbH, Zurich), is used to transfer samples between the two UHV based experiments, electron holography on the one side, and electrospray ion beam deposition on the other side.

The suitcase is equipped with a SAES getter/ion getter pump combination operated by a battery driven power supply. The pressure is kept below 2 x 1 0^"10mbar at all times, except for the short duration of the transfer (1 -2 minutes) where it rises into the 1 x 1 0^"9mbar regime. The performance of this suitcase, originally developed for STM experiments is well known from various surface science stud-

Each instrument is equipped with a load-lock to which the suitcase can be at- tached. The load-lock is pumped by a turbo molecular pump supported by a cryogenic active charcoal trap at LN₂ temperature. A pressure in the 1 0^"9 mbar range is established within a few hours, ensuring a contamination-free transfer of the samples. Fig. 9 shows low-energy electron projection images of the very same freestanding graphene region before (b) and after (c) the transfer from the low-energy electron holographic microscope located in Zurich to the ES-IBD chamber in Stuttgart and back to the microscope in Zurich. No relevant sign of contamination due to transfer and transport is observed.

Concluding remarks:

To achieve the goal of imaging single molecules, exemplified here for the case of single protein molecules, one needs to master and combine three requirements. At first, a method for isolating individual proteins for further inspection has to be at hand; quite the opposite to the current challenge of assembling proteins into a crystal for X-ray analysis¹'². Furthermore, technologies are required for keeping a single protein fixed in space long enough to accumulate sufficient structural information from a scattering experiment. Last but not least, gentle radiation with a wavelength small enough to uncover structural details while ensuring that radiation damage does not decompose the protein during observation as it is available by low-energy electron holography³ is vital for imaging. Here we show that soft-landing electrospray beam deposition⁴'⁵ allows for specific selection and sound deposition⁵ of individual proteins and protein complexes onto ultraclean freestanding graphene⁶ in an ultra-high vacuum environment. Due to the fact that graphene is transparent for low-energy electrons⁷ and since the latter do not damage biological molecules⁸'⁹, we were able to acquire high signal-to-noise ra- tio electron holograms of individual proteins (Cytochrome C and BSA) as well as of protein complexes (haemoglobin). The numerical hologram reconstructions reveal the overall shape of single proteins. With this, images of individual folded proteins and protein complexes, not being the result of an averaging process, have been obtained for the first time.

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Claims

A method of imaging single molecules, comprising the steps of:

b) depositing single molecules onto said receiving layer by means of soft- landing electrospray ion deposition, whereby a single molecule loaded receiving layer is formed;

the above steps a) to c) being conducted under vacuum conditions.

The method according to claim 1 , wherein step b) comprises ionization of single molecules to form single molecular ions, electrostatic extraction and mass filtering of said single molecular ions and electrostatic guidance of mass filtered single molecular ions onto said receiving layer.

The method according to claim 1 or 2, wherein said single molecules are protein molecules.

The method according to one of claims 1 to 3, wherein said receiving layer is a graphene monolayer.

The method according to one of claims 1 to 4, wherein said electron transmission pattern is a hologram.

6. The method according to one of claim 1 to 5, wherein said substrate face consists of a platinum metal selected from the group consisting of Pt, Pd and Rh, preferably Pt.

An apparatus for carrying out the method of claim 1 , comprising:

b) means for depositing single molecules onto said receiving layer by

means of soft-landing electrospray ion deposition to form a single molecule loaded receiving layer; and

The apparatus according to claim 7, further comprising means for applying a reconstruction procedure to said electron transmission pattern to obtain at least one image of a single molecule on said single molecule loaded receiving layer.

9. The apparatus according to claim 8, wherein said reconstructing means are configured to process a holographic electron transmission pattern.

The apparatus according to one of claims 7 to 9, wherein said depositing means comprise means for ionization of single molecules to form single molecular ions, means for electrostatic extraction and mass filtering of said single molecular ions and means for electrostatic guidance of mass filtered single molecular ions onto said receiving layer.

1 1 . The apparatus according to one of claims 7 to 10, wherein said depositing means are configured to deposit single protein molecules.

12. The apparatus according to one of claims 7 to 1 1 , wherein said receiving layer is a graphene monolayer.

13. The apparatus according to one of claims 7 to 12, wherein said substrate face consists of a platinum metal selected from the group consisting of Pt, Pd and Rh, preferably Pt.