Name: directed assembly of elastin-like proteins into defined supramolecular structures and cargo encapsulation in vitro
Uploaded: 2020-04-08T14:00:00
Description: Watch this Scientific Journal Video about Directed Assembly of Elastin-like Proteins into defined Supramolecular Structures and Cargo Encapsulation In Vitro at JoVE.com

The authors thank the BMBF for financial support and the Center for Biological Systems Analysis (ZBSA) for providing the research facility. We are grateful to P. G. Schultz, TSRI, La Jolla, California, USA for providing the plasmid pEVOL-pAzF. We thank the staff of the Life Imaging Center (LIC) in the Center for Biological Systems Analysis (ZBSA) of the Albert-Ludwigs-University Freiburg for help with their confocal microscopy resources, and the excellent support in image recording.

1. Design and cloning of amphiphilic elastin-like proteins (ELPs)
<ol>
	<li>Clone and design the constructs as described elsewhere8,20. Plasmids are available upon request.</li>
</ol>
2. Protein expression, purification and preparation
<ol>
	<li>Expression of F20E20-mEGFP and F20E20-mCherry
	<ol>
		<li>Inoculate main expression culture from overnight pre-culture to an OD600 of 0.3. Incubate at 37 &#176;C, 200 rpm in sterile ...

<ol>
	<li>Elzoghby, A. O., Samy, W. M., Elgindy, N. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein-based+nanocarriers+as+promising+drug+and+gene+delivery+systems.">Protein-based nanocarriers as promising drug and gene delivery systems.</a> Journal of Controlled Release. 161 (1), 38-49 (2012).</li><li>Jang, Y., Champion, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Self-Assembled+Materials+Made+from+Functional+Recombinant+Proteins.">Self-Assembled Materials Made from Functional Recombinant Proteins.</a> Accounts of Chemical Research. 49 (10), 2188-2198 (2016).</li><li>Timmermans, S. B. P. E., van Hest, J. C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Self-assembled+nanoreactors+based+on+peptides+and+proteins.">Self-assembled nanoreactors based on peptides and proteins.</a> Current Opinion in Colloid &amp; Interface Science. 35, 26-35 (2018).</li><li>Dreher, M. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Temperature+Triggered+Self-Assembly+of+Polypeptides+into+Multivalent+Spherical+Micelles.">Temperature Triggered Self-Assembly of Polypeptides into Multivalent Spherical Micelles.</a> Journal of the American Chemical Society. 130 (2), 687-694 (2008).</li><li>Huber, M. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Designer+amphiphilic+proteins+as+building+blocks+for+the+intracellular+formation+of+organelle-like+compartments.">Designer amphiphilic proteins as building blocks for the intracellular formation of organelle-like compartments.</a> Nature Materials. 14 (1), 125-132 (2014).</li><li>Matsuurua, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rational+design+of+self-assembled+proteins+and+peptides+for+nano-+and+micro-sized+architectures.">Rational design of self-assembled proteins and peptides for nano- and micro-sized architectures.</a> RSC Advances. 4 (6), 2942-2953 (2013).</li><li>Rocklin, G. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Global+analysis+of+protein+folding+using+massively+parallel+design,+synthesis,+and+testing.">Global analysis of protein folding using massively parallel design, synthesis, and testing.</a> Science. 357 (6347), 168-175 (2017).</li><li>Schreiber, A., St&#252;hn, L. G., Huber, M. C., Geissinger, S. E., Rao, A., Schiller, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Self-Assembly+Toolbox+of+Tailored+Supramolecular+Architectures+Based+on+an+Amphiphilic+Protein+Library.">Self-Assembly Toolbox of Tailored Supramolecular Architectures Based on an Amphiphilic Protein Library.</a> Small. 15 (30), 1900163 (2019).</li><li>Jang, Y., Hsieh, M. -. C., Dautel, D., Guo, S., Grover, M. A., Champion, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Understanding+the+Coacervate-to-Vesicle+Transition+of+Globular+Fusion+Proteins+to+Engineer+Protein+Vesicle+Size+and+Membrane+Heterogeneity.">Understanding the Coacervate-to-Vesicle Transition of Globular Fusion Proteins to Engineer Protein Vesicle Size and Membrane Heterogeneity.</a> Biomacromolecules. 20 (9), 3494-3503 (2019).</li><li>Vargo, K. B., Sood, N., Moeller, T. D., Heiney, P. A., Hammer, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spherical+micelles+assembled+from+variants+of+recombinant+oleosin.">Spherical micelles assembled from variants of recombinant oleosin.</a> Langmuir: the ACS journal of surfaces and colloids. 30 (38), 11292-11300 (2014).</li><li>Bellomo, E. G., Wyrsta, M. D., Pakstis, L., Pochan, D. J., Deming, T. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stimuli-responsive+polypeptide+vesicles+by+conformation-specific+assembly.">Stimuli-responsive polypeptide vesicles by conformation-specific assembly.</a> Nature Materials. 3 (4), 244-248 (2004).</li><li>Mart&#237;n, L., Castro, E., Ribeiro, A., Alonso, M., Rodr&#237;guez-Cabello, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Temperature-Triggered+Self-Assembly+of+Elastin-Like+Block+Co-Recombinamers:The+Controlled+Formation+of+Micelles+and+Vesicles+in+an+Aqueous+Medium.">Temperature-Triggered Self-Assembly of Elastin-Like Block Co-Recombinamers:The Controlled Formation of Micelles and Vesicles in an Aqueous Medium.</a> Biomacromolecules. 13 (2), 293-298 (2012).</li><li>Li, Y., Rodriguez-Cabello, J. C., Aparicio, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intrafibrillar+Mineralization+of+Self-Assembled+Elastin-Like+Recombinamer+Fibrils.">Intrafibrillar Mineralization of Self-Assembled Elastin-Like Recombinamer Fibrils.</a> ACS Applied Materials &amp; Interfaces. , (2017).</li><li>Vargo, K. B., Parthasarathy, R., Hammer, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Self-assembly+of+tunable+protein+suprastructures+from+recombinant+oleosin.">Self-assembly of tunable protein suprastructures from recombinant oleosin.</a> Proceedings of the National Academy of Sciences of the United States of America. 109 (29), 11657-11662 (2012).</li><li>Park, W. M., Champion, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thermally+Triggered+Self-Assembly+of+Folded+Proteins+into+Vesicles.">Thermally Triggered Self-Assembly of Folded Proteins into Vesicles.</a> Journal of the American Chemical Society. 136 (52), 17906-17909 (2014).</li><li>Vogele, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Towards+synthetic+cells+using+peptide-based+reaction+compartments.">Towards synthetic cells using peptide-based reaction compartments.</a> Nature Communications. 9 (1), 3862 (2018).</li><li>Vogele, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+Vesiculo+Synthesis+of+Peptide+Membrane+Precursors+for+Autonomous+Vesicle+Growth.">In Vesiculo Synthesis of Peptide Membrane Precursors for Autonomous Vesicle Growth.</a> Journal of Visualized Experiments. (148), e59831 (2019).</li><li>Huber, M. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Designer+amphiphilic+proteins+as+building+blocks+for+the+intracellular+formation+of+organelle-like+compartments.">Designer amphiphilic proteins as building blocks for the intracellular formation of organelle-like compartments.</a> Nature Materials. 14 (1), 125-132 (2015).</li><li>Urry, D. W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Elastin:+a+representative+ideal+protein+elastomer.">Elastin: a representative ideal protein elastomer.</a> Philosophical Transactions of the Royal Society B: Biological Sciences. 357 (1418), 169-184 (2002).</li><li>Huber, M. C., Schreiber, A., Wild, W., Benz, K., Schiller, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Introducing+a+combinatorial+DNA-toolbox+platform+constituting+defined+protein-based+biohybrid-materials.">Introducing a combinatorial DNA-toolbox platform constituting defined protein-based biohybrid-materials.</a> Biomaterials. 35 (31), 8767-8779 (2014).</li><li>Schreiber, A., Huber, M. C., Schiller, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Prebiotic+Protocell+Model+Based+on+Dynamic+Protein+Membranes+Accommodating+Anabolic+Reactions.">Prebiotic Protocell Model Based on Dynamic Protein Membranes Accommodating Anabolic Reactions.</a> Langmuir. 35 (29), 9593-9610 (2019).</li><li>Chin, J. W., Santoro, S. W., Martin, A. B., King, D. S., Wang, L., Schultz, P. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Addition+of+p-Azido-l-phenylalanine+to+the+Genetic+Code+of+Escherichia+coli.">Addition of p-Azido-l-phenylalanine to the Genetic Code of Escherichia coli.</a> Journal of the American Chemical Society. 124 (31), 9026-9027 (2002).</li><li>Sonnino, S., Prinetti, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Membrane+domains+and+the+"lipid+raft"+concept.">Membrane domains and the "lipid raft" concept.</a> Current Medicinal Chemistry. 20 (1), 4-21 (2013).</li><li>Br&#228;se, S., Gil, C., Knepper, K., Zimmermann, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Organische+Azide+-+explodierende+Vielfalt+bei+einer+einzigartigen+Substanzklasse.">Organische Azide - explodierende Vielfalt bei einer einzigartigen Substanzklasse.</a> Angewandte Chemie. 117 (33), 5320-5374 (2005).</li><li>Li, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Large-Scale+Structures+in+Tetrahydrofuran&#8211;Water+Mixture+with+a+Trace+Amount+of+Antioxidant+Butylhydroxytoluene+(BHT).">Large-Scale Structures in Tetrahydrofuran&#8211;Water Mixture with a Trace Amount of Antioxidant Butylhydroxytoluene (BHT).</a> The Journal of Physical Chemistry B. 115 (24), 7887-7895 (2011).</li><li>Huber, M. C., Schreiber, A., Schiller, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Minimalist+Protocell+Design:+A+Molecular+System+Based+Solely+on+Proteins+that+Form+Dynamic+Vesicular+Membranes+Embedding+Enzymatic+Functions.">Minimalist Protocell Design: A Molecular System Based Solely on Proteins that Form Dynamic Vesicular Membranes Embedding Enzymatic Functions.</a> ChemBioChem. 20 (20), 2618-2632 (2019).</li><li>Raghunathan, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+comparative+study+on+the+stability+and+structure+of+two+different+green+fluorescent+proteins+in+organic+co-solvent+systems.">A comparative study on the stability and structure of two different green fluorescent proteins in organic co-solvent systems.</a> Biotechnology and Bioprocess Engineering. 18 (2), 342-349 (2013).</li><li>Sallach, R. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Long-term+biostability+of+self-assembling+protein+polymers+in+the+absence+of+covalent+crosslinking.">Long-term biostability of self-assembling protein polymers in the absence of covalent crosslinking.</a> Biomaterials. 31 (4), 779-791 (2010).</li></ol>

A fault while following the described protocols for&#160;the assembly of defined supramolecular structures mainly leads either to the formation of unspecific aggregates (Figure 2, IV) or to homogeneously distributed ELP-amphiphiles. Critical steps of the protocol are discussed below:
For high expression yield of the amphiphilic ELP, a relatively low temperature of 20&#176;C is optimal. For successful affinity based purification of the amphiphilic ELP an urea conce...

The assembly of supramolecular structures for biotechnological applications is becoming increasingly important1,2,3,4,5. For the assembly of functional architectures such as coacervates, vesicles, and fibers with desired physicochemical properties it is important to understand and control the physicochemical and conformational properties of the components. Due to the molecular precision of molecules found in nature, building blocks for supramolecular structures are increasingly based on lipids, nucleic acids or proteins. Compared to synthetic polymers, proteinaceous building blocks allow for precise control over emergent supramolecular structures6 on the genetic level. The primary amino acid (aa) sequence of the individual protein building blocks intrinsically encodes the information for their assembly potential from the molecular up to the macroscopic level as well as the three dimensional shape and physical properties of the final supramolecular structure7.
Reported methods for the assembly of different supramolecular structures often involve amphiphilic proteins such as temperature sensitive elastin-like proteins (ELP)5,8,9, recombinant oleosin10 and artificial protein amphiphiles11. Temperature triggered methods have led to the assembly of micelles4,10,12, fibers13, sheets14 and vesicles9,15,16. Methods involving organic solvents have been applied for the formation of dynamic protein based vesicles8,11,14. So far, applied protocols for vesicle formation often lack assembly control over micrometer sized assemblies16,17 or have limited assembly yield5. In addition, some reported ELP based vesicles have impaired encapsulation potential12 or limited stability over time9. Addressing these drawbacks, the presented protocols enable the self-assembly of micrometer and sub micrometer sized supramolecular structures with distinct physiochemical properties, good encapsulation potential and long-time stability. Tailored amphiphilic ELPs assemble into supramolecular structures, spanning the range from spherical coacervates and highly ordered twisted fiber bundles to unilamellar vesicles depending on the applied protocol and associated environmental conditions. Large vesicular Protein Membrane-Based Compartments (PMBC) reveal all main phenotypes such as membrane fusion and phase separation behaviour analogous to liposomes. PMBCs efficiently encapsulate chemically diverse fluorescent cargo molecules which can be monitored using simple epifluorescence microscopy. The repetitive ELP domains used in this study are attractive building blocks for protein based supramolecular architectures18. The ELP pentapeptide repeat unit (VPGVG) is known to tolerate different aa besides proline at the fourth position (valine, V), while preserving its structural and functional properties19. The design of amphiphilic ELPs containing distinctive hydrophilic and hydrophobic domains was realized by inserting aa guest residues (X) in the VPGXG repeat with distinct hydrophobicity, polarity, and charge20. Amphiphilic ELP domains where equipped with hydrophobic phenylalanine (F) or isoleucine (I) while the hydrophilic domain contained charged glutamic acid (E) or arginine (R) as guest residues. A list of eligible amphiphilic ELP constructs and corresponding aa sequences can be found in the supplementary information and references8,21. All building blocks where equipped either with small fluorescent dyes or fluorescent proteins for visualization via fluorescence microscopy. mEGFP and other fluorescent proteins were N-terminally fused to the hydrophilic domains of the ELP amphiphiles . Organic dyes were conjugated via copper-free strain promoted alkyne&#8211;azide cycloaddition (SPAAC) to a co-translationally introduced unnatural amino acid (UAA). The co-translational incorporation of the UAA para-azidophenylalanine (pAzF)22 permits the N-terminal modification of the hydrophilic ELP domain. In this way the green fluorescent dye BDP-FL-PEG4-DBCO (BDP) or any small fluorescent molecule with a strained cyclooctyne can be used as fluorescent probe. Successful incorporation of the UAA pAzF and cycloaddition of the dye via SPAAC can be easily confirmed via LC-MS/MS due to efficient ionization of the corresponding tryptic peptides8. This small organic dye was applied to broaden the solvent choice for assembly protocols, since fluorescent proteins are incompatible with most organic solvents. The two most efficient assembly protocols for supramolecular structures developed in our lab are described below. The THF swelling method is only compatible with organic dye modified amphiphilic ELP. In contrast, the 1-butanol (BuOH) extrusion method is compatible with many proteins as fluorescent probe e.g. mEGFP, since the described method fully preserves the fluorescence of these fusion proteins. In addition, the encapsulation of small molecules and vesicular fusion behavior works best by employing the BuOH extrusion method.

<table border="0" cellpadding="0" cellspacing="0" style="width:1191px;" width="1191">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">1 &#181;m and 0.2 &#181;m Steril Filter</td>
			<td style="width:411px;">VWR</td>
			<td style="width:119px;"></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">1,4-Dithiothreitol</td>
			<td style="width:411px;">Merck</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">1-butanol. &#62;99.5% p.a.</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">2log DNA ladder</td>
			<td style="width:411px;">NEB</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">2-Mercaptoethanol</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">50 mL Falcon tubes</td>
			<td style="width:411px;">VWR</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">79249 Alkyne Mega Stokes dye</td>
			<td style="width:411px;">Sigma Aldrich</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Acetic acid glacial</td>
			<td style="width:411px;">VWR</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Acetonitrile, anhydrous, 99.8%</td>
			<td style="width:411px;">Sigma-Aldrich</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Ampicillin sodium-salt, 99%</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">BDP-FL-PEG4-DBCO</td>
			<td style="width:411px;">Jena Bioscience</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Biofuge</td>
			<td style="width:411px;">Heraeus</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Bottle Top Filter with PES membrane (45 &#181;m, 22 &#181;m)</td>
			<td style="width:411px;">Thermo Scientific</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Brillant Blue G250 (Coomassie)</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">BspQI</td>
			<td style="width:411px;">NEB</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Camera DS Qi1</td>
			<td style="width:411px;">Nikon</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Centrifuge 5417r</td>
			<td style="width:411px;">Eppendorf</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Centrifuge 5810r</td>
			<td style="width:411px;">Eppendorf</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">CF-400-Cu square mesh copper grid</td>
			<td style="width:411px;">EMS</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Chloramphenicol</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">CompactStar CS 4</td>
			<td style="width:411px;">VWR</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Dextran, Texas Red, 3000 MW, neutral</td>
			<td style="width:411px;">Life Technologies</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Digital sonifier</td>
			<td style="width:411px;">Branson</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Dimethylsulfoxide (DMSO)</td>
			<td style="width:411px;">Applichem</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Dnase I</td>
			<td style="width:411px;">Applichem</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">EarI</td>
			<td style="width:411px;">NEB</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">EcoRI-HF</td>
			<td style="width:411px;">NEB</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Environmental shaker incubator ES-20</td>
			<td style="width:411px;">Biosan</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Ethanol absolute</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Ethidium bromide solution</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Filter supports</td>
			<td style="width:411px;">Avanti</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Glass plates</td>
			<td style="width:411px;">Bio-Rad</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Glycerol Proteomics Grade</td>
			<td style="width:411px;">Amresco</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Glycin</td>
			<td style="width:411px;">Applichem</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">H4-Azido-Phe-OH</td>
			<td style="width:411px;">Bachhem</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Heat plate MR HeiTec</td>
			<td style="width:411px;">Heidolph</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">HindIII</td>
			<td style="width:411px;">NEB</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">HisTrap FF crude column</td>
			<td style="width:411px;">GE Life Sciences</td>
			<td style="width:119px;"></td>
			<td>Nickel column</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Hydrochloride acid fuming, 37%, p.a.</td>
			<td style="width:411px;">Merck</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Illuminator ix 20</td>
			<td style="width:411px;">INTAS</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Illuminator LAS-4000</td>
			<td style="width:411px;">Fujifilm</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Imidazole</td>
			<td style="width:411px;">Merck</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Immersions oil for microscopy</td>
			<td style="width:411px;">Merck</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Incubators shakers Unimax 1010</td>
			<td style="width:411px;">Heidolph</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Inkubator 1000</td>
			<td style="width:411px;">Heidolph</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">IPTG, &#62;99%</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Kanamycinsulfate</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">L(+)-Arabinose</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Laboratory scales Extend ed2202s/224s-OCE</td>
			<td style="width:411px;">Sartorius</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">LB-Medium</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Lyophilizer Alpha 2-4 LSC</td>
			<td style="width:411px;">Christ</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Lysozyme, 20000 U/mg</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Microscope CM 100</td>
			<td style="width:411px;">Philips</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Microscope Eclipse TS 100</td>
			<td style="width:411px;">Nikon</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Microscopy cover glasses (15 x 15 mm)</td>
			<td style="width:411px;">VWR</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Microscopy slides</td>
			<td style="width:411px;">VWR</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Microwave</td>
			<td style="width:411px;">Studio</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Mini-Extruder Set</td>
			<td style="width:411px;">Avanti Polar Lipids</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">NaCl, &#62;99.5%, p.a.</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Natriumhydroxid pellets</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Ni-NTA Agarose, PerfectPro</td>
			<td style="width:411px;">5 Prime</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Nucleopore Track-Etch Membrane</td>
			<td style="width:411px;">Avanti</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">PH meter 766 calimatic</td>
			<td style="width:411px;">Knick</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Phenylmethylsulfonylflourid (PMSF)</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Polypropylene Columns (1 mL)</td>
			<td style="width:411px;">Qiagen</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">PowerPac basic</td>
			<td style="width:411px;">BioRad</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Propanol-2-ol</td>
			<td style="width:411px;">Emplura</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Protein ladder 10-250 kDa</td>
			<td style="width:411px;">NEB</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Recirculating cooler F12</td>
			<td style="width:411px;">Julabo</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Reinforcement rings</td>
			<td style="width:411px;">Herma</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">SacI HF</td>
			<td style="width:411px;">NEB</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">SDS Pellets</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Sodiumdihydrogen phosphate dihydrate, NaH2PO4</td>
			<td style="width:411px;">VWR</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Sterile syringe filter 0.2 mm Cellulose Acetate</td>
			<td style="width:411px;">VWR</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">T4 DNA Ligase</td>
			<td style="width:411px;">NEB</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">TEMED</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">TexasRed Dextran-Conjugate</td>
			<td style="width:411px;">MolecularProbes</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Thermomix comfort</td>
			<td style="width:411px;">Eppendorf</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">THF, &#62;99.5% p.a.</td>
			<td style="width:411px;">Acros</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Triton X 100</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Trypton/Pepton from Casein</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Ultrasonic cleaner</td>
			<td style="width:411px;">VWR</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Urea p.a.</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">Vacuum pump 2.5</td>
			<td style="width:411px;">Vacuubrand</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">XbaI</td>
			<td style="width:411px;">NEB</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">XhoI</td>
			<td style="width:411px;">NEB</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:495px;">ZelluTrans regenerated cellulose tubular membrane (12.0 S/ 3.5 S/ 1.0 V)</td>
			<td style="width:411px;">Roth</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
	</tbody>
</table>

directed assembly of elastin-like proteins into defined supramolecular structures and cargo encapsulation in vitro

Tailored proteinaceous building blocks are versatile candidates for the assembly of supramolecular structures such as minimal cells, drug delivery vehicles and enzyme scaffolds. Due to their biocompatibility and tunability on the genetic level, Elastin-like proteins (ELP) are ideal building blocks for biotechnological and biomedical applications. Nevertheless, the assembly of protein based supramolecular structures with distinct physiochemical properties and good encapsulation potential remains challenging.
Here we provide two efficient protocols for guided self-assembly of amphiphilic ELPs into supramolecular protein architectures such as spherical coacervates, fibers and stable vesicles. The presented assembly protocols generate Protein Membrane-Based Compartments (PMBCs) based on ELPs with adaptable physicochemical properties. PMBCs demonstrate phase separation behavior and reveal method dependent membrane fusion and are able to encapsulate chemically diverse fluorescent cargo molecules. The resulting PMBCs have a high application potential as a drug formulation and delivery platform, artificial cell, and compartmentalized reaction space.

Protocol development for vesicle production 
Figure 1 outlines the two different vesicle preparation methods. The THF swelling method on the left side is composed of three successive steps and results in different supramolecular assemblies of the ELP depending on the temperature. In Figure 1A epifluorescence microscopy images show vesicles assembled from BDP-R20F20 and fibrillary structures assembled from BDP-R4...

Watch this Scientific Journal Video about Directed Assembly of Elastin-like Proteins into defined Supramolecular Structures and Cargo Encapsulation In Vitro at JoVE.com

Directed Assembly of Elastin-like Proteins into defined Supramolecular Structures and Cargo Encapsulation In Vitro

At the interface of organic and aqueous solvents, tailored amphiphilic elastin-like proteins assemble into complex supramolecular structures such as vesicles, fibers and coacervates triggered by environmental parameters. The described assembly protocols yield Protein Membrane-Based Compartments (PMBCs) with tunable properties, enabling the encapsulation of various cargo.

Tailored proteinaceous building blocks are versatile candidates for the assembly of supramolecular structures such as minimal cells, drug delivery ...

The efficient assembly of supramolecular structures for minimal cell design and drug delivery remains challenging. Here, we demonstrate efficient protocols that yield supramolecular structures based on amphiphilic elastin-like proteins. The presented assembly protocols generate versatile supramolecular structures with adaptable physicochemical properties, such as vesicles, fibers, and coacervates.Protein membrane-based compartments demonstrate phase separation behavior and allow for the encapsulation of chemically diverse fluorescent cargo molecules. For expression of F20E20-mEGFP and F20E20-mCherry, inoculate the main expression culture from the overnight pre-culture to an OD600 of 0.3. Incubate it in 400 milliliters of sterile LB medium supplemented with appropriate antibiotics at 37 degrees Celsius and 200 rpm.When the expression culture reaches OD600 of 0.5 to 0.8, add IPTG to a final concentration of one millimolar, and reduce the incubation temperature to 20 degrees Celsius. For expression of amphiphilic ELP with the unnatural amino acid, inoculate the main expression culture from overnight E.coli pre-culture containing the appropriate plasmids to an OD of 0.3. Incubate it in 400 milliliters of sterile LB medium supplemented with kanamycin and chloramphenicol at 37 degrees Celsius and 200 rpm.To prepare the 100-millimolar unnatural amino acid stock, add 206.2 milligrams of unnatural amino acid to eight milliliters of ultrapure water. Raise the pH of the solution with three-molar sodium hydroxide, and mix vigorously. When the unnatural amino acid is dissolved, lower the pH to approximately 10.5, and add ultrapure water to a volume of 10 milliliters.Filter the solution with a sterile 0.22-micrometer filter, and aliquot it in two-milliliter reaction tubes. When the expression culture reaches OD600 of 0.5 to 0.8, add the unnatural amino acid to a final concentration of two millimolar. Incubate it for 10 more minutes.Then induce expression of the target protein and the necessary tRNA synthetase via simultaneous addition of IPTG and arabinose. Reduce the incubation temperature to 20 degrees Celsius, and allow expression to continue for approximately 20 hours. After the incubation, harvest the cells by centrifugation at four degrees Celsius and 4, 000 times g for 40 minutes.Resuspend the cell pellet in lysis buffer with lysozyme and PMSF. Incubate the solution for 30 minutes on ice. Then freeze and thaw it twice by submerging in liquid nitrogen.Sonicate the suspension, and clear the lysate by centrifugation at 10, 000 times g and four degrees Celsius for 40 minutes. Then purify the protein using affinity chromatography. After protein elution, store it at four degrees Celsius until further use.Add one microliter of fluorescent dye to 500 microliters of ELP solution, and incubate the reaction for about 10 hours at 15 degrees Celsius while shaking in a ThermoMixer, making sure to protect it from light. To remove excessive fluorescent dye, equilibrate a dialysis membrane in ultrapure water for 10 minutes. Cut the membrane into the correct size to be placed on top of the opening of the reaction tube with the clicked ELP solution.Then fix the membrane to the opening by closing the tube with a lid that has no core. Fill the space between lid and membrane with buffer to prevent trapping of air. Then place the reaction tube in the chosen buffer, push it below the surface, and turn it upside down.Perform dialysis for at least three hours at four degrees Celsius, allowing dialysis to continue for at least three more hours after each buffer change. For THF swelling, dialyze the homogenous ELP solution against phosphate or Tris buffer with stable pH 7.5. Prepare the lyophilizer, and cool it to starting temperature for freeze-drying.Aliquot the dialyzed protein solution in 1.5-milliliter reaction tubes, and seal with caps with a small hole to avoid losing the solid sample due to pressure changes in the course of freeze-drying. Shock-freeze the samples in liquid nitrogen. Take the frozen protein samples out of the liquid nitrogen, and immediately place them in the lyophilizer to start freeze-drying.After the sample is completely dry, ventilate it with dry nitrogen, and immediately close the reaction tube lids to avoid contact with air moisture. Add pure THF to the lyophilized samples, and place the solution in a water bath sonicator with ice water for 15 minutes. Preheat a thermocycler to 30 to 60 degrees Celsius for vesicle formation or up to 90 degrees Celsius for fiber formation, and prepare new reaction tubes with either ultrapure water or buffer.After sonication, place the ELP/THF solution and the prepared water or buffer in the thermocycler for five minutes. Then stratify the ELP solution on top of the water or buffer, making sure that the separation of the two phases and a distinct interphase is visible, and place the mixture back in the thermocycler. Let the sample cool down at room temperature for 10 minutes, and proceed with dialysis against water or buffer or with fluorescence microscopy.Prepare a one-to 50-micromolar ELP solution, and add 10 to 20%1-butanol. Immediately mix the solution by pipetting up and down. The turbidity of the solution should increase during mixing, indicating vesicle formation.To achieve a narrow size distribution, extrude vesicles with a mini extruder through a membrane with a pore size of one micrometer. For dye encapsulation, mix approximately 40 microliters of ELP solution in 10-millimolar Tris-HCl with one microliter of Dextran Texas Red stock solution in DMSO. Add 10 microliters of 1-butanol, and extrude five to 10 times through a syringe equipped with a 0.25-by-25-millimeter needle.The THF swelling method is composed of three successive steps and results in different supramolecular assemblies of the ELP depending on the temperature. The epifluorescence microscopy images show vesicles assembled from BDP-R20F20 and fibrillary structures assembled from BDP-R40F20. The 1-butanol extrusion method leads exclusively to the formation of ELP vesicles.About two orders of magnitude more vesicles are produced compared to the THF swelling method. BDP-R40F20 was mixed with 10 to 15%butanol, and vesicles were prepared via extrusion of the mixture. Different supramolecular structures were assembled from BDP-R40F20 via the THF swelling protocol.The pH of the buffer and the temperature of the assembly process was adjusted to form either coacervates, fibrils, or vesicles. Small mistakes in the assembly protocol can lead to the formation of aggregates. Positively charged dye ATTO Rho 13 and the polysaccharide dextran red 3000 were encapsulated into the lumen of vesicles assembled from F20R20-mEGFP via the 1-butanol extrusion method.Confocal microscopy images show the vesicles in the green channel, the cargo in the red channel, and the successful encapsulation in the resulting merged channel. The phase separation and fusion behavior of ELP amphiphiles upon mixing of single PMBC building blocks versus assembled PMBC populations was also demonstrated. Mixing prior to PMBC assembly leads to homogenously distributed molecules within the assembled PMBC membrane, while mixing assembled vesicle populations leads to membrane patches of red or green fluorescence that are visible for at least 20 minutes.When attempting this procedure, it is important to pay attention to the correct step order and for the differences between the THF swelling method and the butanol extrusion method. Following this protocol, the ELP vesicles can be used as drug delivery shuttles, as platform for enzymatic reactions, such as in vitro transcription and translation, or in the formation of synthetic minimal cells.

directed-assembly-elastin-like-proteins-into-defined-supramolecular

Research

JoVE Journal

Chemistry

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

In nature, complex functional structures are formed by the self-assembly of biomolecules under mild conditions. Understanding the forces that control self-assembly and mimicking this process in vitro will bring about major advances in the areas of materials science and nanotechnology. Among the available biological building blocks, peptides have several advantages as they present substantial diversity, their synthesis in large scale is straightforward, and they can easily be modified with biological and chemical entities1,2. Several classes of designed peptides such as cyclic peptides, amphiphile peptides and peptide-conjugates self-assemble into ordered structures in solution. Homoaromatic dipeptides, are a class of short self-assembled peptides that contain all the molecular information needed to form ordered structures such as nanotubes, spheres and fibrils3-8. A large variety of these peptides is commercially available.
This paper presents a procedure that leads to the formation of ordered structures by the self-assembly of homoaromatic peptides. The protocol requires only commercial reagents and basic laboratory equipment. In addition, the paper describes some of the methods available for the characterization of peptide-based assemblies. These methods include electron and atomic force microscopy and Fourier-Transform Infrared Spectroscopy (FT-IR). Moreover, the manuscript demonstrates the blending of peptides (coassembly) and the formation of a &#34;beads on a string&#34;-like structure by this process.9 The protocols presented here can be adapted to other classes of peptides or biological building blocks and can potentially lead to the discovery of new peptide-based structures and to better control of their assembly.

This paper describes the formation of highly ordered peptide-based structures by the spontaneous process of self-assembly. The method utilizes commercially available peptides and common lab equipment. This technique can be applied to a large variety of peptides and may lead to the discovery of new peptide-based assemblies.

In nature, complex functional structures are formed by the self-assembly of biomolecules under mild conditions. Understanding the forces that control ...

In Situ SIMS and IR Spectroscopy of Well-defined Surfaces Prepared by Soft Landing of Mass-selected Ions

Soft landing of mass-selected ions onto surfaces is a powerful approach for the highly-controlled preparation of materials that are inaccessible using conventional synthesis techniques. Coupling soft landing with in situ characterization using secondary ion mass spectrometry (SIMS) and infrared reflection absorption spectroscopy (IRRAS) enables analysis of well-defined surfaces under clean vacuum conditions. The capabilities of three soft-landing instruments constructed in our laboratory are illustrated for the representative system of surface-bound organometallics prepared by soft landing of mass-selected ruthenium tris(bipyridine) dications, [Ru(bpy)3]2+ (bpy = bipyridine), onto carboxylic acid terminated self-assembled monolayer surfaces on gold (COOH-SAMs). In situ time-of-flight (TOF)-SIMS provides insight into the reactivity of the soft-landed ions. In addition, the kinetics of charge reduction, neutralization and desorption occurring on the COOH-SAM both during and after ion soft landing are studied using in situ Fourier transform ion cyclotron resonance (FT-ICR)-SIMS measurements. In situ IRRAS experiments provide insight into how the structure of organic ligands surrounding metal centers is perturbed through immobilization of organometallic ions on COOH-SAM surfaces by soft landing. Collectively, the three instruments provide complementary information about the chemical composition, reactivity and structure of well-defined species supported on surfaces.

In Situ SIMS and IR Spectroscopy of Well-defined Surfaces Prepared by Soft Landing of Mass-selected Ions

Soft landing of mass-selected ions onto surfaces is a powerful approach for the highly-controlled preparation of novel materials. Coupled with analysis by in situ secondary ion mass spectrometry (SIMS) and infrared reflection absorption spectroscopy (IRRAS), soft landing provides unprecedented insights into the interactions of well-defined species with surfaces.

Soft landing of mass-selected ions onto surfaces is a powerful approach for the highly-controlled preparation of materials that are inaccessible using ...

Atomically Defined Templates for Epitaxial Growth of Complex Oxide Thin Films

Atomically defined substrate surfaces are prerequisite for the epitaxial growth of complex oxide thin films. In this protocol, two approaches to obtain such surfaces are described. The first approach is the preparation of single terminated perovskite SrTiO3 (001) and DyScO3 (110) substrates. Wet etching was used to selectively remove one of the two possible surface terminations, while an annealing step was used to increase the smoothness of the surface. The resulting single terminated surfaces allow for the heteroepitaxial growth of perovskite oxide thin films with high crystalline quality and well-defined interfaces between substrate and film. In the second approach, seed layers for epitaxial film growth on arbitrary substrates were created by Langmuir-Blodgett (LB) deposition of nanosheets. As model system Ca2Nb3O10- nanosheets were used, prepared by delamination of their layered parent compound HCa2Nb3O10. A key advantage of creating seed layers with nanosheets is that relatively expensive and size-limited single crystalline substrates can be replaced by virtually any substrate material.

Various procedures are outlined to prepare atomically defined templates for epitaxial growth of complex oxide thin films. Chemical treatments of single crystalline SrTiO3 (001) and DyScO3 (110) substrates were performed to obtain atomically smooth, single terminated surfaces. Ca2 Nb3 O10- nanosheets were used to create atomically defined templates on arbitrary substrates.

Atomically defined substrate surfaces are prerequisite for the epitaxial growth of complex oxide thin films. In this protocol, two approaches to obtain ...

Construction and Systematical Symmetric Studies of a Series of Supramolecular Clusters with Binary or Ternary Ammonium Triphenylacetates

Functions of clusters in nano or sub-nano scale significantly depend on not only kinds of their components but also arrangements, or symmetry, of their components. Therefore, the arrangements in the clusters have been precisely characterized, especially for metal complexes. Contrary to this, characterizations of molecular arrangements in supramolecular clusters composed of organic molecules are limited to a few cases. This is because construction of the supramolecular clusters, especially obtaining a series of the supramolecular clusters, is difficult due to low stability of non-covalent bonds compare to covalent bonds. From this viewpoint, utilization of organic salts is one of the most useful strategies. A series of the supramolecules could be constructed by combinations of a specific organic molecule with various counter ions. Especially, primary ammonium carboxylates are suitable as typical examples of supramolecules because various kinds of carboxylic acids and primary amines are commercially available, and it is easy to change their combinations. Previously, it was demonstrated that primary ammonium triphenylacetates using various kinds of primary amines specifically construct supramolecular clusters, which are composed of four ammoniums and four triphenylacetates assembled by charge-assisted hydrogen bonds, in crystals obtained from non-polar solvents. This study demonstrates an application of the specific construction of the supramolecular clusters as a strategy to conduct systematical symmetric study for clarification of correlations between molecular arrangements in supramolecules and kinds and numbers of their components. In the same way with binary salts composed of triphenylacetates and one kind of primary ammoniums, ternary organic salts composed of triphenylacetates and two kinds of ammoniums construct the supramolecular clusters, affording a series of the supramolecular clusters with various kinds and numbers of the components.

This article describes construction of a series of hydrogen-bonding supramolecular clusters in crystals using primary ammonium triphenylacetates, which are recrystallized from non-polar solvents. This selective construction of the supramolecular clusters leads to effective systematical symmetric studies about a correlation between the supramolecular clusters and their components.

Functions of clusters in nano or sub-nano scale significantly depend on not only kinds of their components but also arrangements, or symmetry, of their ...

Encapsulation of Cancer Therapeutic Agent Dacarbazine Using Nanostructured Lipid Carrier

The only formula of dacarbazine (Dac) in clinical use is intravenous infusion, presenting a poor therapeutic profile due to the low dispersity of the drug in aqueous solution. To overcome this, a nanostructured lipid carrier (NLC) consisting of glyceryl palmitostearate and isopropyl myristate was developed to encapsulate Dac. NLCs with controlled size were achieved using high shear dispersion (HSD) following solidification of oil-in-water emulsion. The synthesis parameters, including surfactant concentration, the speed and time of HSD were optimized to achieve the smallest NLC with size, polydispersion index and zeta potential of 155 &#177; 10 nm, 0.2 &#177; 0.01, and -43.4 &#177; 2 mV, respectively. The optimal parameters were also employed for Dac-loaded NLC preparation. The resultant NLC loaded with Dac possessed size, polydispersion index and zeta potential of 190 &#177; 10 nm, 0.2 &#177; 0.01, and -43.5 &#177; 1.2 mV, respectively. The drug encapsulation efficiency and drug loading reached 98% and 14%, respectively. This is the first report on encapsulation of Dac using NLC, implying that NLC could be a new potential candidate as drug carrier to improve the therapeutic profile of Dac.

The most commonly used method for nanostructured lipid carrier (NLC) synthesis involves oil-in-water emulsion, homogenization and solidification. This was modified here by applying high shear dispersion after solidification to achieve a NLC with desirable size, improved drug encapsulation and drug loading efficiency as a potential carrier for dacarbazine delivery.

The only formula of dacarbazine (Dac) in clinical use is intravenous infusion, presenting a poor therapeutic profile due to the low dispersity of the drug ...

Synthesis and Characterization of Supramolecular Colloids

Control over colloidal assembly is of utmost importance for the development of functional colloidal materials with tailored structural and mechanical properties for applications in photonics, drug delivery and coating technology. Here we present a new family of colloidal building blocks, coined supramolecular colloids, whose self-assembly is controlled through surface-functionalization with a benzene-1,3,5-tricarboxamide (BTA) derived supramolecular moiety. Such BTAs interact via directional, strong, yet reversible hydrogen-bonds with other identical BTAs. Herein, a protocol is presented that describes how to couple these BTAs to colloids and how to quantify the number of coupling sites, which determines the multivalency of the supramolecular colloids. Light scattering measurements show that the refractive index of the colloids is almost matched with that of the solvent, which strongly reduces the van der Waals forces between the colloids. Before photo-activation, the colloids remain well dispersed, as the BTAs are equipped with a photo-labile group that blocks the formation of hydrogen-bonds. Controlled deprotection with UV-light activates the short-range hydrogen-bonds between the BTAs, which triggers the colloidal self-assembly. The evolution from the dispersed state to the clustered state is monitored by confocal microscopy. These results are further quantified by image analysis with simple routines using ImageJ and Matlab. This merger of supramolecular chemistry and colloidal science offers a direct route towards light- and thermo-responsive colloidal assembly encoded in the surface-grafted monolayer.

A protocol for the synthesis and characterization of colloids coated with supramolecular moieties is described. These supramolecular colloids undergo self-assembly upon the activation of the hydrogen-bonds between the surface-anchored molecules by UV-light.

Control over colloidal assembly is of utmost importance for the development of functional colloidal materials with tailored structural and mechanical ...

Site Directed Spin Labeling and EPR Spectroscopic Studies of Pentameric Ligand-Gated Ion Channels

Ion channel gating is a stimulus-driven orchestration of protein motions that leads to transitions between closed, open, and desensitized states. Fundamental to these transitions is the intrinsic flexibility of the protein, which is critically modulated by membrane lipid-composition. To better understand the structural basis of channel function, it is necessary to study protein dynamics in a physiological membrane environment. Electron Paramagnetic Resonance (EPR) spectroscopy is an important tool to characterize conformational transitions between functional states. In comparison to NMR and X-ray crystallography, the information obtained from EPR is intrinsically of lower resolution. However, unlike in other techniques, in EPR there is no upper-limit to the molecular weight of the protein, the sample requirements are significantly lower, and more importantly the protein is not constrained by the crystal lattice forces. Therefore, EPR is uniquely suited for studying large protein complexes and proteins in reconstituted systems. In this article, we will discuss general protocols for site-directed spin labeling and membrane reconstitution using a prokaryotic proton-gated pentameric Ligand-Gated Ion Channel (pLGIC) from Gloeobacter violaceus (GLIC) as an example. A combination of steady-state Continuous Wave (CW) and Pulsed (Double Electron Electron Resonance-DEER) EPR approaches will be described that will enable a complete quantitative characterization of channel dynamics.

This article describes methods for site-directed spin labeling and reconstitution of pentameric ligand-gated channels for Electron Paramagnetic Resonance studies. This protocol can be adapted for any membrane protein. The reconstitution method described here can also be used for patch-clamp measurements of macroscopic and single-channel currents in a defined lipid system.

Ion channel gating is a stimulus-driven orchestration of protein motions that leads to transitions between closed, open, and desensitized states. ...

Highly Stable, Functional Hairy Nanoparticles and Biopolymers from Wood Fibers: Towards Sustainable Nanotechnology

Nanoparticles, as one of the key materials in nanotechnology and nanomedicine, have gained significant importance during the past decade. While metal-based nanoparticles are associated with synthetic and environmental hassles, cellulose introduces a green, sustainable alternative for nanoparticle synthesis. Here, we present the chemical synthesis and separation procedures to produce new classes of hairy nanoparticles (bearing both amorphous and crystalline regions) and biopolymers based on wood fibers. Through periodate oxidation of soft wood pulp, the glucose ring of cellulose is opened at the C2-C3 bond to form 2,3-dialdehyde groups. Further heating of the partially oxidized fibers (e.g., T = 80 &#176;C) results in three products, namely fibrous oxidized cellulose, sterically stabilized nanocrystalline cellulose (SNCC), and dissolved dialdehyde modified cellulose (DAMC), which are well separated by intermittent centrifugation and co-solvent addition. The partially oxidized fibers (without heating) were used as a highly reactive intermediate to react with chlorite for converting almost all aldehyde to carboxyl groups. Co-solvent precipitation and centrifugation resulted in electrosterically stabilized nanocrystalline cellulose (ENCC) and dicarboxylated cellulose (DCC). The aldehyde content of SNCC and consequently surface charge of ENCC (carboxyl content) were precisely controlled by controlling the periodate oxidation reaction time, resulting in highly stable nanoparticles bearing more than 7 mmol functional groups per gram of nanoparticles (e.g., as compared to conventional NCC bearing &#60;&#60; 1 mmol functional group/g). Atomic force microscopy (AFM), transmission electron microscopy (TEM), and scanning electron microscopy (SEM) attested to the rod-like morphology. Conductometric titration, Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR), dynamic light scattering (DLS), electrokinetic-sonic-amplitude (ESA) and acoustic attenuation spectroscopy shed light on the superior properties of these nanomaterials.

Synthesis schemes to prepare highly stable wood fiber-based hairy nanoparticles and functional cellulose-based biopolymers have been detailed.

Nanoparticles, as one of the key materials in nanotechnology and nanomedicine, have gained significant importance during the past decade. While ...

From Molecules to Materials: Engineering New Ionic Liquid Crystals Through Halogen Bonding

Herein, we demonstrate that a bottom-up approach, based on halogen bonding (XB), can be successfully applied for the design of a new type of ionic liquid crystals (ILCs). Taking advantages of the high specificity of XB for haloperfluorocarbons and the ability of anions to act as XB-acceptors, we obtained supramolecular complexes based on 1-alkyl-3-methylimidazolium iodides and iodoperfluorocarbons, overcoming the well-known immiscibility between hydrocarbons (HCs) and perfluorocarbons (PFCs). The high directionality of the XB combined with the fluorophobic effect, allowed us to obtain enantiotropic liquid crystals where a rigid, non-aromatic, XB supramolecular anion acts as mesogenic core.
X-ray structure analysis of the complex between 1-ethyl-3-methylimidazolium iodide and iodoperfluorooctane showed the presence of a layered structure, which is a manifestation of the well-known tendency to segregation of perfluoroalkyl chains. This is consistent with the observation of smectic mesophases. Moreover, all the reported complexes melt below 100 &#176;C, and most are mesomorphic even at room temperature, despite that the starting materials were non-mesomorphic in nature.
The supramolecular strategy reported here provides new design principles for mesogen design allowing a totally new class of functional materials.

A protocol for the synthesis of a new type of mesogens, based on the halogen-bonded supramolecular anion [CnF2n+1-I&#183;&#183;&#183;I&#183;&#183;&#183;I-CnF2n+1]&#8722;, is reported.

Herein, we demonstrate that a bottom-up approach, based on halogen bonding (XB), can be successfully applied for the design of a new type of ionic liquid ...

Assembly of Gold Nanorods into Chiral Plasmonic Metamolecules Using DNA Origami Templates

The inherent addressability of DNA origami structures makes them ideal templates for the arrangement of metal nanoparticles into complex plasmonic nanostructures. The high spatial precision of a DNA origami-templated assembly allows controlling the coupling between plasmonic resonances of individual particles and enables tailoring optical properties of the constructed nanostructures. Recently, chiral plasmonic systems attracted a lot of attention due to the strong correlation between the spatial configuration of plasmonic assemblies and their optical responses (e.g., circular dichroism [CD]). In this protocol, we describe the whole workflow for the generation of DNA origami-based chiral assemblies of gold nanorods (AuNRs). The protocol includes a detailed description of the design principles and experimental procedures for the fabrication of DNA origami templates, the synthesis of AuNRs, and the assembly of origami-AuNR structures. In addition, the characterization of structures using transmission electron microscopy (TEM) and CD spectroscopy is included. The described protocol is not limited to chiral configurations and can be adapted for the construction of various plasmonic architectures.

We describe the detailed protocol for the DNA origami-based assembly of gold nanorods into chiral plasmonic metamolecules with strong chiroptical responses. The protocol is not limited to chiral configurations and can be easily adapted for the fabrication of various plasmonic architectures.