Patent Application
20220380486
The present invention is concerned with the general field of protein crystallisation.
The invention relates to a method for self-assembling proteins on a substrate into a three-dimensional honeycomb structure.
The invention is particularly interesting since it makes it possible to obtain a stable nanostructured material, the patterns of which are very regular.
The invention also relates to the thus obtained assembly, formed by the substrate and the protein structure. Such an assembly forms a grafting platform for a wide variety of molecules.
The invention also relates to a use of such an assembly. The invention finds applications in many industrial fields, especially in the fields of photolithography, catalysis, optics, or even for membrane manufacture.
The invention also relates to a method for manufacturing nanopillars from such an assembly.
Currently, to generate protein self-assembly on a surface, two approaches are used: the so-called “top-down” approach and “bottom-up” approach.
The top-down type approach consists in locally modifying the surface of a substrate in order to create binding sites that can interact with proteins. The self-assembly of proteins is then conditioned by their attachment to these binding sites. However, such an approach requires structuring the substrate at the nano- or micrometre scale, which requires additional steps and makes the method more time-consuming and expensive.
The “bottom-up” type approach relies on intrinsic properties of proteins to interact with each other. Several types of “bottom-up” methods have been reported. These include, especially:
For example, in Gonen et al (“Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces”, Science (2015), 348, 6241, 1365-1368), the computer-aided design of protein interfaces allowed the definition of different 2D array architectures. Protein crystals up to 1 μm long and 8 nm thick are obtained.
In the paper of Sayou et al (“A SAM oligomerisation domain shapes the genomic binding landscape of the LEAFY transcription factor”, Nature Communications (2016), 7, 11222), the crystal structure of the oligomerisation domain of Ginkgo biloba has been studied in solution. The authors have shown that the head-tail oligomerisation of the monomers leads to the formation of a helix.
The different architectures obtained are 2D architectures, formed by single or double layers. However, these protein architectures do not have a large stability.
One purpose of the present invention is therefore to provide a method for making a protein self-assembly that is stable over time and/or solvent-resistant.
For this, the present invention provides a method for self-assembling a protein into a three-dimensional honeycomb structure comprising the following successive steps of:
The invention differs fundamentally from prior art in that a tag is used which allows growth perpendicular to the substrate surface (i.e. growth upwards and not along the substrate) and thus a three dimensional architecture is obtained. The primary helices form regularly spaced cells, which can advantageously be functionalised, within the protein structure. Such an architecture has very good stability. Such a method is relatively simple to implement since the protein structure self-assembles spontaneously upon evaporating the solvent.
Advantageously, the method includes an additional step in which another protein corresponding to the oligomerisation domain of the tag-free LEAFY protein is added to the already formed honeycomb structure, whereby the height of the honeycomb structure is increased perpendicular to the substrate.
Advantageously, the substrate is made of a material selected from a metal, a metalloid or a carbonaceous material. The choice of the substrate material and especially its hydrophilic/hydrophobic properties affects the substrate/tag affinity. This will influence the surface area of the self-assembled structure and the coverage rate of the structure with the substrate.
The invention also relates to an assembly obtained by such a method, the assembly comprising a substrate covered with a protein self-assembly in a three-dimensional honeycomb structure,
the protein comprising an amino acid sequence corresponding to an oligomerisation domain of a LEAFY protein, for example the oligomerisation domain of Ginkgo biloba, fused to a tag,
the oligomerisation domain being crystallised as a primary helix, each primary helix interacting with six other primary helices, the structure being bound perpendicular to the substrate through the tag.
Advantageously, the pitch between each primary helix is less than 10 nm. By pitch, it is meant the distance between the centre of the lumen of two adjacent primary helices.
Advantageously, the internal diameter of a primary helix ranges from 4 nm to 6 nm, for example 5 nm.
Advantageously, the self-assembly covers an area of at least 50 μm2.
Advantageously, the substrate is porous. This embodiment is particularly advantageous, especially for making membranes whose pore size is defined by the honeycomb structure cells.
According to a first advantageous alternative, the protein is functionalised with a metal (metal nanoparticles), a metal salt, an inorganic complex or an organic molecule. This embodiment is particularly advantageous for making metal nanopillars, nanocatalysts or nanophosphors.
The organic molecule may be, for example, a chromophore or a fluorophore. According to one particularly advantageous embodiment, the organic molecule is a peptide that can interact with metals (such as gold for example) and/or can reduce metal salts to make metal nanopillars.
According to another advantageous alternative, the protein is functionalised with quantum boxes (also called quantum dots QDs).
According to another advantageous alternative, the honeycomb structure is metallised, for example with gold. This embodiment is particularly advantageous for forming regularly spaced metal rings with nanometre dimensions, for optical applications.
According to one particularly advantageous embodiment, the C-terminal sequence of the protein is modified with a peptide sequence that can interact with metals (such as gold, for example) and/or can reduce metal salts, for example, to make metal nanopillars.
Such a structure has many advantages:
The invention also relates to a use of an assembly as defined above, to develop applications in nanotechnology, for example as a photolithography mask, as a signal amplifier of an optical sensor, as a membrane, or as a catalyst.
The invention also relates to a method for manufacturing metal nanopillars comprising the following successive steps of:
Further characteristics and advantages of the invention will become apparent from the following further description.
No need to say this further description is given only by way of illustration of the object of the invention and should in no way be construed as a limitation of that object.
The present invention will be better understood upon reading the description of exemplary embodiments given purely by way of illustrating and in no way limiting purposes, with reference to the appended drawings in which:
The different parts represented in the figures are not necessarily represented on a uniform scale, to make the figures more legible.
The various possibilities (alternatives and embodiments) are to be understood as not being exclusive of each other and may be combined with one another.
Further, in the following description, terms that depend on the orientation, such as “on”, “over”, “below”, “under”, etc. of a structure are applied assuming that the structure is oriented as illustrated in the figures.
Here and hereafter, the self-assembly method is described for a protein. However, the invention is applicable to peptides, polypeptides and more generally to amino acid sequences homologous to the amino acid sequence of the oligomerisation domain of the LEAFY protein.
The self-assembly method for obtaining a three-dimensional honeycomb protein structure comprises the following successive steps of:
a) providing a solution containing a protein of interest,
b) contacting the solution with the surface of a substrate,
c) crystallising the protein, whereby a three-dimensional self-assembly of the protein into a honeycomb structure is obtained, perpendicular to the surface of the substrate.
In step a), the protein of interest used to form the three-dimensional honeycomb protein structure on the substrate has a primary amino acid sequence comprising:
By oligomerisation domain, it is intended an amino acid sequence that allows proteins to assemble in sequence into small chains.
The oligomerisation domain is that of the LEAFY protein. The LEAFY transcription factor (also known as LFY) is involved in developmental processes in plants, especially flower formation. The oligomerisation of the LEAFY protein is a head-tail oligomerisation (
By way of illustrating and not limiting purposes, the oligomerisation domain can be that of Arabidopsis thaliana (AtLFY), Ginkgo biloba (GbLFY), Ceratopteris richardii (CrLFY) or Physcomitrella patens (PpLFY).
For example, the oligomerisation domain of the Ginkgo biloba LEAFY protein is (here and hereafter all amino acid sequences are noted from N-terminal to C-terminal):
The orientation of the self-assembly is determined by the addition of a tag. Generally, the tag is a short amino acid sequence (typically having 6 to 30 amino acids).
In the absence of this tag, self-assembly grows parallel to the surface, that is in the plane of the substrate surface in contact with the protein of interest solution in step b) (
Several types of tags can be used, such as
The tag starts with an initiator methionine (M).
The tag may end with a sequence of, for example, 2-20 residues acting as a linker, for example GA.
According to one particularly advantageous embodiment, the tag is a histidine tag (also called a polyhistidine tag or histidine tag). The histidine tag comprises at least six histidine amino acids. It may include more than six histidine amino acids. It may also comprise other amino acids. By way of illustrating and not limiting purposes, one of the following sequences may be chosen:
All these sequences have been tested and allow anchoring of the honeycomb structure perpendicular to the substrate surface.
Other constructs including a poly-Lysine, poly-Glutamate, poly-Glutamate/Lysine and poly-Proline tag have also been obtained:
Hereafter, a histidine tag will be described. Any other tag, especially one with equivalent size, which non-specifically or specifically links to a substrate, and allows the protein structure to grow perpendicular to the substrate, may be used.
The amino acid sequence also includes a portion for lining the cells of the honeycomb. For example, this portion corresponds to the sequence:
This part is fully adjustable. It can be removed. It can also be modified by deletion, substitution, or insertion. Modifications to this part do not affect the self-assembly ability of the protein. Advantageously, it is modified by substitution or insertion so as to introduce one or more specific amino acids capable of being functionalised by a metal ion, a metal or an organic molecule. For example, a cysteine (also called cysteine (C) residue) is chosen as the specific amino acid, for specifically grafting molecules carrying a maleimide or iodoacetamide group or metal salts.
The sequence of the portion lining the cells modified by substitution can be for example: CKLDLFVDVDGKRKADENALDTLSQ (SEQ ID NO: 13 in the appended sequence listing).
By way of illustrating and not limiting purposes, the following table lists different amino acid sequences of the protein that can be used: a primary sequence and mutant sequences. The mutant sequences are obtained by modifying the tag and/or the C-terminal sequence lining the cells of the primary sequence. These mutants have been tested and self-assemble into honeycombs perpendicular to the surface. In the examples given, the C-terminal can be shortened or replaced by combinations of amino acids (Cysteine, Histidine, Lysine; Glutamate, Glycine) capable of interacting with molecules and preceded by a shorter or longer spacer. The spacer can be comprised of the amino acids Glycine and Serine. For example, the spacer can be GGSGGS (SEQ ID NO: 14 in the appended sequence listing), GGS and G.
MKHHHHHHPMSDYDIPTTENLYFQGAMARK
TLSQ
MKHHHHHHPMSDYDIPTTENLYFQGAMARK
TLSQ
MKHHHHHHPMSDYDIPTTENLYFQGAMARK
MHHHHHHGAMARKELSSLEELFRHYGVRYMT
MKHHHHHHPMSDYDIPTTENLYFQGAMARK
MKHHHHHHPMSDYDIPTTENLYFQGAMARK
MKHHHHHHPMSDYDIPTTENLYFQGAMARK
MKHHHHHHPMSDYDIPTTENLYFQGAMARK
MKHHHHHHPMSDYDIPTTENLYFQGAMARK
MKHHHHHHPMSDYDIPTTENLYFQGAMARK
MKHHHHHHPMSDYDIPTTENLYFQGAMARK
MHHHHHHGAMARKELSSLEELFRHYGVRYMT
MHHHHHHGAMARKELSSLEELFRHYGVRYMT
HHHHH
According to a first alternative, the protein of interest can be synthesised by synthetic biology.
According to a second preferred alternative, the protein of interest is produced by a bacterium. For this, the protein of interest can be expressed in a commercial strain, advantageously by a strain of E. coli bacteria. The protein of interest is then purified from the soluble extract of the bacteria that produced it. The purification consists, for example, in collecting the bacteria by centrifugation, breaking their membrane by sonication and then separating the soluble proteins containing the protein of interest by centrifugation. The protein of interest is then purified one or more times.
This can be an affinity purification on a Nickel-containing resin (for example Nickel-Sepharose type) and/or on a permeation gel (for example Superdex 200 type, marketed by GE Healthcare). Only proteins with the histidine tag are retained on the nickel-containing resin.
The protein is soluble in an aqueous buffer, preferably Tris-HCl (pH between 7.0 and 9.0 at a concentration between 10 and 100 mM) containing a thiol function reducer (DTT (Dithiothreitol) or TCEP (Tris(2-carboxyethyl)phosphine hydrochloride) at a concentration of 1 mM) to form a protein solution.
The protein solution is advantageously mixed with a crystallisation solution (consisting of a buffer and a salt). This may be a 50/50 volume mixture. The crystallisation solution comprises, for example, Tris-HCl (the buffer) and ammonium sulphate (the salt). More generally, a so-called Good buffer (for example ADA, HEPES, CAPS) may also be used at concentrations between 25 and 200 mM and a pH between 6.5 and 8.5. Other salts such as lithium sulphate may also be used.
The concentration of the protein in the solution used in step a) can range from 0.5 mg/mL to 5 mg/mL.
In step b), a volume V1 of the solution containing the protein of interest is contacted with the substrate. The substrate can be of different kinds. For example, it may be metallic, made of a metalloid element or of a carbonaceous material. By way of illustration, it may be silicon or carbon. For example, a silicon wafer or a silicon or carbon microscopy grid may be chosen. The substrate may be transparent. By transparent, it is meant that the substrate has a transmittance greater than 50% in the visible range, i.e. from 350 nm to 750 nm, and preferably greater than 70% in the visible range.
Advantageously, the substrate is hydrophilic in order to favour its covering by the solution containing the protein of interest and/or the interactions with the histidine tag.
The surface area of the substrate to be functionalised may be greater than 50 μm2, or even greater than 1 mm2. It can be, for example, about 7 mm2.
A drop of solution containing the protein of interest, or a larger volume of such solution, may be deposited onto the surface to be treated or the surface to be treated may be deposited onto the solution containing the protein of interest.
In step b), the protein solution may advantageously locally cover the substrate. According to one particularly advantageous alternative embodiment, a step during which a so-called protective layer is formed locally on the substrate, for example during a photolithography step through a mask, can be carried out prior to step b). The substrate then comprises parts covered with the protective layer and parts not covered with the protective layer. This makes it possible to delimit zones on the substrate to be functionalised with the protein structure. The protein solution is in contact with the surface of the substrate at parts not covered with the protective layer. Walls of the protective layer act as a guide upon growing the protein structure.
In step c), the protein is crystallised to form the protein structure. Crystallisation consists in making the protein change from a soluble state to a solid, ordered state. The solution containing the protein is gradually evaporated to increase concentration of the protein until it crystallises.
Self-assembly of the protein on the surface of the substrate is advantageously carried out in a closed chamber, for example in a crystallisation chamber.
The enclosure contains, advantageously, a crystallisation tank with a volume V2 containing the crystallisation buffer solution. A volume V2 greater than the volume V1 will be chosen. The volume V2 ranges, for example, from 500 μL to 5 mL. Once the enclosure is sealed, vapour diffusion from the drop containing the protein solution to the reservoir is initiated and results in slow evaporation of the solvent from the protein solution allowing the protein to self-assemble on the surface.
The crystallisation is advantageously carried out at room temperature (i.e. 20 to 25° C.) and at room pressure (in the order of 1 bar). The duration of step c) ranges, advantageously, from 4 h to 48 h. This duration depends on the surface area of the substrate to be functionalised as well as the solution volume. The self-assembly is visible from 4 hours and reaches an optimum after 24 hours.
At the end of the method, an assembly is obtained comprising a substrate covered with the crystallised and self-assembled protein in a three-dimensional honeycomb structure perpendicular to the surface of the substrate. It has a controlled height corresponding to the stack of the different monomers. The height of the protein structure averages 18 nm with the protein containing the histidine tag but may be higher using a second growth step in the presence of the protein without the histidine tag. The internal diameter of the honeycomb cells ranges, for example, from 4 nm to 6 nm. The pitch between primary helices is less than 10 nm. It ranges, for example, from 8 nm to 10 nm.
By way of illustration, the protein architecture obtained with the oligomerisation domain of the Ginkgo biloba LEAFY protein has the following characteristics (
These characteristics can be measured by atomic force microscopy (AFM) or transmission electron microscopy (STEM), for example STEM, TEM after a standard protein structure staining step using uranyl acetate.
Parameters of the self-assembled protein structure, such as well diameter and well height can be easily modified.
For example, by increasing the number of amino acids lining the well wall, the well diameter can be reduced. Varying the number of amino acids lining the interior of the wells also allows the number of molecules grafted into the cells of the protein structure to be modulated.
The height of the self-assembled structure can be increased by the addition of the oligomerisation domain, which lacks the histidine tag, in other words by adding monomers of the oligomerisation domain to the self-assembly so as to grow the primary helices of the protein structure. This modification makes it possible, for example, to increase the number of grafted (inorganic, organic or mixed) molecules, to have a nanolithography mask with a greater thickness or even to increase the height of the pillars that can grow within the self-assembly.
The surface area of the self-assembled structure and the coverage rate of a substrate can be increased, for example, by varying affinity of the substrate for the histidine tag.
It is also possible to modify the shape, diameter and spacing of the wells by choosing different protein architectures. The identification of these protein architectures or protein domains capable of making head-tail interactions can be done in the Protein Data Bank (PDB) collecting all known protein structures.
The resulting three-dimensional self-assembled honeycomb structure is a biomaterial that can be used for many applications.
According to one particular embodiment, the structure can be used as a membrane, when the self-assembled structure is formed on a porous surface, the permeability threshold is determined by the internal diameter of the primary helices.
According to another embodiment, the self-assembled structure can be covered, totally or partially, by a metallic layer, for example of gold. It may be metallised by physical vapour deposition, chemical vapour deposition, chemical deposition or electrochemical deposition. Such a structure can be used to influence behaviour of a light wave at the surface of a substrate. This is of particular interest for amplifying the signal of an optical sensor, such as a sensor selected from among sensors based on surface plasmon resonance (SPR), surface-enhanced Raman scattering (SERS) sensors, or for surface-enhanced infrared spectroscopy (SEIRAS). It is, for example, possible to form regularly spaced gold rings by covering the upper part of the structure with gold.
According to another embodiment, the self-assembled structure can be used as a photolithography mask: as the self-assembly generates wells of regular diameter and spacing (for example 5 nm in diameter and 9 nm apart), it can be used as a photolithography mask to etch a support through the honeycomb cells. Etching could be, for example, of the chemical (HF) type on silicon support or with ultraviolet (UV) on a photosensitive surface.
According to another embodiment, the self-assembly can serve as a platform/support for grafting inorganic (metal ions, inorganic complexes, QDs or metal particles, for example) and organic (fluorophores or peptides, for example) molecules. For this, a protein with a sequence comprising one or more amino acids that can be functionalised by metal salts that can be reduced to metal nanoparticles, by inorganic complexes with some catalytic activity, by organic molecules or by QDs or nanoparticles will be chosen. Alternatively, the C-terminal part of the protein can be replaced by an amino acid sequence that allows both the attraction of metal salts and their reduction in situ without needing to add a reducer.
By way of illustration, on the basis of a self-assembly of 31 nm in height alone (that is a stack of 40 monomers per well) and approximately 12,000 wells per μm2, it is estimated that approximately 480,000 molecules/μm2 (that is 48,000 billion/cm2) are bound. Such a self-assembly has a high surface area and therefore allows a high quantity of molecules to be bound. The position and specificity of grafting can be controlled by the amino acid composition lining the lumen of the wells and the reactivity of the compounds to be grafted.
By way of example, functionalisation operations can be performed on naturally occurring or modified amino acids of the C-terminal end of the protein that are found in the lumen of the honeycombs. The molecule grafting chemistry is that developed for amino acids.
There can be mentioned, by way of example, grafting techniques involving:
This grafting platform can be used in the photovoltaic field or for the detection of molecules. It is possible to contemplate detection of single molecules. It is possible to graft molecules that act, for example, as catalysts. Immobilisation of catalysts increases their stability. It is thus possible to manufacture bio-hybrid materials, for example, for photo-catalysis.
This confinement is also particularly interesting for example for artificial photosynthesis or for carrying out redox reactions.
Particularly advantageously, the specific grafting of metals (or metal ions which are subsequently reduced) into the wells could be used to design metal nanopillars in the cells of the protein structure (wells), for example for nanoelectronics. Their lengths and diameters depend on the protein architecture. The nanopillars are oriented perpendicular to the substrate surface and are regularly spaced. For example, gold nanopillars can be made via a thiol function that binds to the cysteines of the protein's amino acid sequence. For binding metal salts, for example, histidines will be chosen.
The method for manufacturing the nanopillars advantageously comprises the following successive steps of:
An alternative way to grow nanopillars in the honeycomb lumen is to replace the C-terminal part of the protein with an amino acid sequence that allows both attraction of the metal salts and reduction in situ without the need to add a reducer. For example, one of the amino acid sequences listed in the following table can be used:
MKHHHHHHPMSDYDIPTTENLYFQGAMARK
MKHHHHHHPMSDYDIPTTENLYFQGAMARK
MKHHHHHHPGAMARKELSSLEELFRHYGVRY
GSTGTSVLIATPGV
MKHHHHHHPMSDYDIPTTENLYFQGAMARK
MKHHHHHHPGAMARKELSSLEELFRHYGVRY
GSWAGAKRLVLRRE
These proteins self-assemble in honeycombs perpendicular to the surface. The peptides GGSTGTSVLIATPGV (SEQ ID NO: 32 in the appended sequence listing) and GGSWAGAKRLVLRRE (SEQ ID NO: 33 in the appended sequence listing), coupled to the protein, make it possible to both attract and reduce metal salts.
According to this embodiment, a step could be subsequently carried out during which the protein structure is removed to leave only the nanopillars on the surface of the substrate. This step can be performed, depending on the nature of the substrate, by plasma, or by thermal annealing at a temperature higher than the decomposition temperature of the protein (typically at a temperature higher than 100° C.).
Illustrative and Non-Limiting Examples of One Embodiment:
In this example, the self-assembled protein architecture is obtained by performing the following successive steps of:
1) selecting and synthesising a sequence capable of oligomerising with head-tail interactions to ensure 3D growth of the self-assembly; the head-tail interactions leading to the formation of a primary helix having a groove with sufficient width to allow interlocking of the helices (as shown in
2) adding a histidine tag to this sequence at the N-terminal so as to position the self-assembly with a growth perpendicular to the surface.
3) using this construct or so-called mutant sequences to specifically functionalise the honeycomb lumen.
4) producing the protein of interest in bacteria.
5) purifying the protein of interest from the soluble extract of the bacteria that produced it, by performing the following steps of:
6) a volume of x μL of the protein of interest solution (with x ranging, for example, from 5 to 50 μL) is mixed with the same volume of a crystallisation solution so as to form a drop of protein which is then contacted with a surface to be treated. The crystallisation solution may comprise Tris-HCl with a pH of 7 to 9 and ammonium sulphate at a concentration ranging from 40 to 350 mM. The surface to be treated can be made hydrophilic, for example by plasma treatment (“glow-discharge”). A crystallisation tank with a volume ranging, for example, from 500 μL to 5 mL is filled with the crystallisation solution. Then the crystallisation chamber is sealed to initiate vapour diffusion of the drop into the tank. After a time ranging from 4 h to 48 h at room temperature, the surface treated is removed from the crystallisation chamber.
At the end of the method, the resulting material can be viewed by transmission electron microscopy (STEM, TEM) when the support is transparent to electrons. For this, the support is deposited onto an aqueous solution containing a stain (for example 2% uranyl acetate) for 2 minutes. Uranyl acetate will more specifically label the lumen of the honeycombs by interaction of the metal with negative amino acids (Glutamate and Aspartate) that line the lumen of the wells.
| Number | Date | Country | Kind |
|---|---|---|---|
| FR1908150 | Jul 2019 | FR | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/FR2020/050932 | 6/2/2020 | WO |
