Physical investigation and understanding of biomineralisation proteins and their use for the synthesis of new nanomaterials

Lead Research Organisation: University of Leeds
Department Name: Physics and Astronomy

Abstract

Scientific and economic interest in nanotechnology has grown in recent years. Within this the quest to produce tiny and highly tailored magnetic particles, or nanomagnets is crucial. Nanomagnets have a range of practical uses. Historically they have been used for information storage such as tapes and hard drives. Recently this has expanded, with the development of 3D information storage systems providing high density data storage. There is also much interest in the medical applications of nanomagnets. Magnetic particles are being developed to provide targeted medicine within the body. For example, if drugs are tied to nanomagnets at the molecular level then they can be directed by a magnet to specific sites within the patient. This allows a drug to be delivered to a specific area, without harming the rest of the body. Similarly, nanomagnets can be used in hyperthermic therapies. This is where, after being directed to specific tumour sites, magnetic particles are heated to either destroy a tumour or activate a drug. However, as nanotechnology grows, so too does the need to develop precisely engineered nanomagnets. Different applications demand different shapes and sizes of particles and different magnetic properties. Controlling the composition and dimensions of nanomagnets has therefore become a key goal of researchers. Biomineralisation is the process that occurs in living organisms to produce minerals such as bones. Because genetics control biomineralisation processes the materials produced exhibit very precise, uniform and intricate formations down to the nano-scale. Furthermore, if the genetics are understood it may be possible to change with precision the nature of biomineralised materials. Magnetotactic bacteria biomineralise high quality and uniform nanoparticles of the iron-oxide magnetite within biological fatty shells (or vesicles) within the bacterial cell (termed magnetosomes). Because magnetosomes exhibit considerable uniformity and precision they present a novel and attractive route to produce high quality nanoparticles. However, the biomineralisation method can be inefficient for commercial production and is restricted to the specifications imposed by the bacterial cell leaving little flexibility for further modifications. A protein found to be involved in making nanomagnets in the bacteria has previously been extracted, and mass produced (expressed) and used in a chemical precipitation of magnetic particles. The protein was found to control the particle's size and shape even in this chemical production outside the bacterial cell. This research will identify biomineralisation proteins from the genetic information we have about magnetic bacteria, and investigate these proteins individually by expressing then and using them in a chemical formation of nanoparticles similar to the previous study. From this we will study in detail how the protein physically controls the size and shape of the particles using microscopy, spectroscopy and diffraction techniques. These will study the proteins while they are making the particles, so we can identify which parts of the proteins are responsible for the control over formation. With this information we will develop a combined chemical/biological method of making nanomagnetic particles. The new method will combine the benefits of the precision offered by biomineralisation, with the higher yields and more malleable system with respect to variation, offered by chemical synthesis. Furthermore, once the specific role of each protein has been ascertained, particles can be designed and custom-made with the addition of a recipe of the specific proteins and metal ions. This will offer more control over the particles' characteristics than the biological system. This biomimetic synthetic method will allow for the production of particles on a larger, and more commercially viable, scale than if the bacteria alone were used.

Technical Summary

Magnetic nanoparticles have many uses in nanotechnology (information storage, advanced electronics, targeted healthcare and medicine) and as these technologies increase in sophistication, so does the demand for more customised precision particles. I propose a novel route for magnetic nanoparticle production by utilising biomineralisation proteins that synthesise high quality and uniform particles in magnetic bacteria. Specifically I intend to exploit the precise genetic control biomineralisation offers to develop an in vitro biomimetic system to produce large yields of tailor-made nanomagnets for commercial nanotechnological and biomedical applications. The addition of biomineralisation proteins into an in vitro chemical precipitation of nanoparticles of magnetite has been shown to improve particle regularity and yield. I thus propose to expand on this work to identify novel candidate biomineralisation using comparative bioinformatics, particularly specific shape defining proteins. We will then express and purify these proteins and study their affect on the in vitro precipitation of nanomagnets. We will study in detail how the protein physically controls this process using microscopy, spectroscopy and diffraction techniques. These will study the protein and genetically mutated proteins while they control the particle precipitation, so we can identify the protein motifs responsible for the control over formation. With this information we will develop this combined chemical/biological method of making nanomagnetic particles. The new method will combine the benefits of the precision offered by biomineralisation, with the higher yields and more malleable system with respect to variation, offered by chemical synthesis. Furthermore, once the specific role of each protein has been ascertained, particles can be designed and custom-made with the addition of a recipe of the specific proteins and metal ions, producing high yields of superior nanomagnets.

Planned Impact

The research proposed will investigate how proteins biomineralise nanomagnetic particles in magnetic bacteria, with the future long-term goal of using this knowledge to develop new commercial biomimetic methods, presenting an immediate and vastly improved solution to the synthesis of highly uniform magnetic nanoparticles for nanotechnological and biomedical applications. The biomimetic additives (proteins, peptides or molecules) identified and created here will potentially offer an ambient conditioned synthetic method of producing high yields of high-quality morphologically controlled nanoparticles. It can therefore be seen that the study proposed here has considerable long-term commercial implications, potentially benefiting industries producing nanomagnets for recording and information storage media, advanced electronics and healthcare nanotechnologies. By presenting a commercially viable route to high yields of precision particles this research could be further developed to make advanced technologies more cost efficient, thus more widely available, benefiting industries as well as governmental bodies such as the NHS and thus the general public with respect to quality of life. With this in mind I have planned a commercial exploitation strategy which will look to patent successful biomineralisation additives and to seek partnerships to exploit innovative industrial development of this biomimetic nanoparticle production. This will be done in consultation with the University of Leeds enterprise and innovations office and 'TechTran' and by seeking follow-on funding in the form of CASE and Industrial partnership awards. I also plan to work closely with other academics that have experience and expertise in this field of research and have developed this research commercially with spin-out companies. The project is inherently multidisciplinary and as such it aligns well with the BBSRC's roadmap and it specifically addresses the BBSRC strategic priority areas of 'synthetic biology' and 'nanoscience through engineering to application: bionanotechnology'. The multidisciplinary nature of the project also provides excellent cross-disciplinary training for both the PDRA and the technician. Furthermore the project offers additional interdisciplinary networking and knowledge transfer, not only for the PDRA and technician, but also for all the collaborators. I plan to increase the impact of this project through a wide range of dissemination methods. I have a strong track-record in publishing my results in the best high-profile journals and in gaining wide media coverage of my research to give my research maximum impact. I plan to follow a similar strategy for this project, disseminating my results promptly in the form of journal articles and conference papers, while simultaneously working with the press office to gain media coverage. The skills and methodologies developed in the work will also be disseminated to students in the form of material in advanced undergraduate courses and project based laboratory skills training. Further hands-on dissemination to the public will take the form of interactive workshops in the discovery zone of the Leeds science festival.

Publications

10 25 50
 
Description Please not that this is the same grant and same work as BB/H005412/2 so the summary below will be identical in both entries.
Summary of project
Magnetic nanoparticles have many uses in nanotechnology (information storage, advanced electronics, targeted healthcare and medicine) and as these technologies increase in sophistication, so does the demand for more customised precision particles.
I propose a novel route for magnetic nanoparticle production by utilising biomineralisation proteins that synthesise high quality and uniform particles in magnetic bacteria. Specifically I intend to exploit the precise genetic control biomineralisation offers to develop an in vitro biomimetic system to produce large yields of tailor-made nanomagnets for commercial nanotechnological and biomedical applications.
The addition of biomineralisation proteins into an in vitro chemical precipitation of nanoparticles of magnetite has been shown to improve particle regularity and yield. I thus propose to expand on this work to identify novel candidate biomineralisation using comparative bioinformatics, particularly specific shape defining proteins. We will then express and purify these proteins and study their effect on the in vitro precipitation of nanomagnets. We will study in detail how the protein physically controls this process using microscopy, spectroscopy and diffraction techniques. These will study the protein and genetically mutated proteins while they control the particle precipitation, so we can identify the protein motifs responsible for the control over formation. With this information we will develop this combined chemical/biological method of making nanomagnetic particles. The new method will combine the benefits of the precision offered by biomineralisation, with the higher yields and more malleable system with respect to variation, offered by chemical synthesis. Furthermore, once the specific role of each protein has been ascertained, particles can be designed and custom-made with the addition of a recipe of the specific proteins and metal ions, producing high yields of superior nanomagnets.

Summary of outcomes from the grant, original objective by objective

Due to the ambitious multidisciplinary nature of the project, a lot of early time on the grant was spent on training in new techniques. A collaborative Japanese visit was also carried out in the early months. Both PDRA developed new insight and expertise in areas of science outside their comfort zones, and how to proceed with the Matsunaga group (ensuring we did not replicate research) was achieved. With respect to the Japanese group we agreed that the Mms structural determination work would be split up so that the Japanese group would concentrate on crystallising the proteins while we would investigate using NMR for structure determination (paper due to be published soon). Due to the fact that I had two periods on maternity over this grant a six month extension has been applied for and granted. Over my second period of maternity leave (July 2013-Oct 2013) the group also moved institutions from Leeds to Sheffield (hence new grant code). The group found the new research environment both stimulating and productive for the project.
Even with these unanticipated events the project delivered all of its objectives, along with additional interesting research which has seeded new ideas which are the subject of this new application. There are currently 23 papers detailing the result from this grant ranging from those that have been published (15), under review (4), completed and approaching submission (1), in preparation (3). These will be discussed as this report goes through each objective one by one outlining the progress, results and key findings, as well as additional work pursued.

Objective [1] Expression and purification of candidate biomineralisation proteins
We have developed an optimal method of producing Mms6 protein. This has been very difficult due to its hydrophobic nature. We developed soluble SUMO and MBP fusion constructs to aid in solubility. Our improved protocol is now well used and increased quantities of protein can be produced. This work will be written up as a methods paper. Other candidate Mms proteins discussed in the proposal (Mms5 and 13) have also been expressed and the protocol optimised. Interestingly, Mms13 is a much more hydrophobic protein than the others and although we have obtained the pure protein, it does not work well with our aquatic precipitation reactions. As such, as an extra work package we have pursued displaying the acidic binding section of this protein as a loop between an intramolecular coiled coil scaffold protein. This is working well and we have been able to purified the pure ccMms13 and use it in precipitation reaction. This work is being pursued by a PhD students and the PDRA on this grant. An additional candidate Mms protein, MmsF, which was identified as a morphological regulator in vivo in 2012, has also been expressed and purified. This should be very hydrophobic (3 trans-membrane regions) but expresses very well as soluble aggregates. MmsF has had a marked effect on the morphology of formed MNP on its addition to a precipitation reaction. This is a very exciting result that has been published in PNAS (2014). Similarly, a coiled-coil construct of the MmsF acidic region has also been produced. A paper on the coiled-coil constructs has been written up and is ready for submission. Finally, different magnetic bacteria produce different shaped particles. We have collaborated with C. Lefevre who works on a strain that produce bullet shaped particles. We have identified via bioinformatics target genes, expressed and purified these proteins and will be performing precipitation reactions with these in the near future (results will form another publication).
Objective [2] Investigation of Mms protein function using an in vitro magnetite nanoparticle precipitation assay. It can clearly be seen in the previous section we have many proteins to test in vitro but the precipitation step, has proved to be not quite as established as first thought. Iron oxides are very difficult to work with and it proved very difficult to obtain even reproducible controls. Thus we have had to strip this precipitation assay right back to first principles to understand the process properly by performing numerous titrations. This has been completed and we have performed the precipitation reaction in the presence of Mms6 with compelling results (paper under review in Chemistry a European journal). Now this rigorous methodology is fully established, other proteins can move quickly down this pipeline. While investigating reproducibility we have additional research of performing precipitations in a macrofluidic device. We can now introduce protein at precise points in this reaction. This work has been continued by Masters project students and the first paper on this is under preparation.
Objective [3] Identify specific protein motifs involved in the biomineralisation process using site-directed mutagenesis in combination with in vitro magnetite nanoparticle precipitation assays.
Very early on in the project mutagenesis was performed on the SUMO-Mms6 construct to give a range of mutants. Iron binding assays were performed on these and yielded very interesting results. We found that certain glutamate residues in the C-terminus are critical for Fe binding whereas the aspartate residues seem to have negligible effect. Two key glutamate to alanine mutations have allowed us to postulate an iron binding site. We are currently performing correction for this paper for the journal of inorganic biochemistry. Furthermore we have supported all this data with a structureal NMR study of Mms6 peptide with and without iron ions. Interstingly there is a marked structural shift with ferrous ions and not with ferric ions showing a more specific interaction with ferrous ions. this (along with the pH experiments above) and with molecular modelling in collaboration with D. Cooke have being incorporated into a joint publication (Chemistry a European journal paper), along with data from objective 7.
Objective [4] Protein/mineral interaction analysis
We have encountered many problems obtaining single plane surfaces of magnetite to perform this experiment with. Our collaborators in York were unable to do this so we tried to make them ourselves in- house in Leeds but could not achieve the precision necessary. Recently we have sourced surfaces from the company PiKem, which are very high purity, so can now proceed with confidence. We have recently developed a methodology using an AFM pulling strategy were the protein is attached to the tip via a cysteine and then pulled from the magnetite surface to obtain the binding energy. The feasibility experiments have been performed. However, while the grant has now finished we are still trying to finish off this work with our collaborator (Lorna Dougan) in Leeds, as we already have the computational data from our collaborators to form a paper. This exciting novel method will be further utilised in a further grant application.
Objective [5] Analysis of nanoparticle formation in situ
We have performed several exploratory experiments to investigate the best way to do this both in vivo and in vitro. For in vivo: We originally looked into using soft X-rays at the German facility BESSY, but need to develop a non-trivial sample preparation. This is till in mind if this can be achieved. We have recently pursued an alternative and exciting method using a fluid cell TEM with collaborators in York (R. Kröger). Preliminary studies have been performed but then PDRA staff left leaving this collaboration in viable. Recently we have formed a collaboration with N. Sommerdijk and will again run this in vivo TEM experiement with him and his PhD studetns in the near future. This should provide high quality images and X-ray analysis of magnetite forming within the bacteria, potentially making a great paper. Additionally, we applied for and received time on the XMCD at the Diamond central facility to analyse the magnetic structure of MNP produced both with and without Mms6 and MmsF. This data was used in on of our patterned surfaces papers (see below)
Objective [6] To exploit information from objectives [3-5] to identify small molecule substitutes for biomineralisation proteins.
This objective has been changed slightly to more robust smaller protein/peptide mimics, rather than small molecules, in keeping with the biological nature of the technique. To this end the coiled coil scaffold forms the first model mimicking system and the second is the adhiron scaffold we have been using to biopan with in collaboration with the University of Leeds. Briefly, in order to identify protein sequences that bind to magnetite on a stable adhiron protein scaffold (forming a biomineralsiaiton protein mimic), a phage display biopanning approach was used. We hypothesised that sequences similar to Mms proteins would be identified. However, interestingly, this has not been the case. The selected binding proteins have shown remarkable control over the size and homogeneity of particles when mediating their synthesis. This work is very exciting nad has been published (chemical science 2015),there is much more work to follow-on in this area and as such we have applied for a BBSRC NIBBs POC which was awarded and is currently running and a follow-on funding grant that we will resubmit once we have data from the POC. Furthermore we have written another grant using this methodology to further this work. This work is being continued by a PhD students and has resulting in one paper (chemical science) one coiled coli paper written up ready to submit, and grant applications as outlined. Update 2020, The coiled coil paper is now published in Nature communications.
Objective [7] To investigate the structural basis of biomineralisation protein-mineral interaction.
We have performed extensive work in this area using both protein/peptide NMR (with our collaborators in Leeds NMR facility and in Sheffeild) and computational modelling (in collaboration with D. Cooke, Huddersfield). We have tried to obtain the structure on Mms6 but have found difficulty due to its solubility. Data has been collected for the SUMO-Mms6 but it seems the SUMO may influence the structure of Mms6. Therefore the whole protein aspect of the NMR work was halted in favour of Fe binding NMR. Here we probed the structure of the acidic Mms6 peptide when Fe bound and unbound states. We also have computational modelling for this system. All this data was added to the Chemistry a European journal paper described in objective [3]. Additionally we have computational modelling data for the acidic C-terminus Mms6 region's interaction with magnetite surfaces and this data will support the experimental data described in objective 4 and will be added to the paper described there.
Additional work.
• Our group is interested in doping MNPs and thus we have combined the insights from the BBSRC project and other work to investigate if Mms6 can mediate the controlled precipitation of cobalt-doped MNP. This was a success and has resulted in a publication.
• I have had 2 completed PhD project working on the Mms6 protein and its attachment to surfaces and how this protein mineralises when attached to surfaces. This has resulted in 7 published research papers (and 3 highlight/review/opinion pieces). One of which (Small 2012) attracted extensive publicity.
• As mentioned in [2], a macro-fluidics platform has been developed for precise MNP precipitation. Future work is planned for this system by introducing proteins at exact points in MNP formation. Update 2020. The paper on fluidic system has been published in 2019
• The BBSRC NIBBs POC was very successful and has resulted in the submission of a strong BBSRC follow-on funding application to commercialise this work as a biotechnology and chemical industry platform as well as a method to decorate nanoparticles for nanomedicine and recycling.
Exploitation Route See above where this is detailed. Briefly, two additional grants have been written and submitted (EPSRC and BBSRC) and while both were unsuccessful last time, both have been invited for re-submission. Since then both have now been resubmitted and we await a funding descision. Finally, another manufacturing grant has been awarded by the EPSRC to scale up these biomimetic methods of nanoparticle production. We expect results to come after the research in this aspects begins in Oct 2017.
Sectors Chemicals,Digital/Communication/Information Technologies (including Software),Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

URL https://bionanomagnetic.wordpress.com/
 
Description We have been working on using the phage-display proteins developed that bind to magnetite for chemical and biotechnological industrial purification as well as to decorate magnetite nanoparticles with biomedical molecules and catalysts for nanomedicine and recycling respectively. We have had a NIBBs proof-of-concept award to develop this further with industry with very promising results and have since put in a BBSRC follow-on funding proposal to work this up into a commercial process. This was awarded last year and we are working with Biocat and other industries on commercializing MagTag. Update 2020: the final pieces of data have been obtianed to persue patenting and commericalisation. A PhD student is registered on lean launchpad to develop commercialisation
Sector Chemicals,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
Description David Cooke modelling 
Organisation University of Huddersfield
Department Department of Chemical and Biological Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Provide experimental data
Collaborator Contribution Modelling the experiment to see if correlates with experimental data
Impact several publications
Start Year 2009
 
Description Leeds Adhirons 
Organisation University of Leeds
Department School of Biology
Country United Kingdom 
Sector Academic/University 
PI Contribution we have designed and conducted the research project in question
Collaborator Contribution aided by the use of the adhirons and their biopanning capability
Impact one paper (chemical science 2015), and a further grant application
Start Year 2011
 
Description Matsunaga lab collaboration 
Organisation Tokyo University of Agriculture
Country Japan 
Sector Academic/University 
PI Contribution we collaborate academically with respect to magnetotactic bacteria
Collaborator Contribution we collaborate academically with respect to magnetotactic bacteria
Impact 5 research papers, I hosted a RS Newton fellow, we visit exchange students. etc.
Start Year 2006