Abstract
Supramolecular chemistry is the quintessential backbone of all biological processes. It encompasses a wide range from the metabolic network to the self-assembled cytoskeletal network. Combining the chemical diversity with the plethora of functional depth that biological systems possess is a daunting task for synthetic chemists to emulate. The only route for approaching such a challenge lies in understanding the complex and dynamic systems through advanced analytical techniques. The supramolecular complexity that can be successfully generated and analyzed is directly dependent on the analytical treatment of the system parameters. In this review, we illustrate advanced analytical techniques that have been used to investigate various supramolecular systems including complex mixtures, dynamic self-assembly, and functional nanomaterials. The underlying theme of such an overview is not only the exceeding detail with which traditional experiments can be probed but also the fact that complex experiments can now be attempted owing to the analytical techniques that can resolve an ensemble in astounding detail. Furthermore, the review critically analyzes the current state of the art analytical techniques and suggests the direction of future development. Finally, we envision that integrating multiple analytical methods into a common platform will open completely new possibilities for developing functional chemical systems.
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Aida T, Meijer EW, Stupp SI. Functional supramolecular polymers. Science. 2012;335(6070):813–7. https://doi.org/10.1126/science.1205962.
Du X, Zhou J, Shi J, Xu B. Supramolecular hydrogelators and hydrogels: from soft matter to molecular biomaterials. Chem Rev. 2015;115(24):13165–307. https://doi.org/10.1021/acs.chemrev.5b00299.
Singh N, Kumar M, Miravet JF, Ulijn RV, Escuder B. Peptide-based molecular hydrogels as supramolecular protein mimics. Chem Eur J. 2017;23(5):981–93. https://doi.org/10.1002/chem.201602624.
De Greef TF, Smulders MM, Wolffs M, Schenning AP, Sijbesma RP, Meijer EW. Supramolecular polymerization. Chem Rev. 2009;109(11):5687–754. https://doi.org/10.1021/cr900181u.
Mattia E, Otto S. Supramolecular systems chemistry. Nat Nanotechnol. 2015;10(2):111–9. https://doi.org/10.1038/nnano.2014.337.
Ashkenasy G, Hermans TM, Otto S, Taylor AF. Systems chemistry. Chem Soc Rev. 2017;46(9):2543–54. https://doi.org/10.1039/c7cs00117g.
Das K, Gabrielli L, Prins LJ. Chemically fueled self-assembly in biology and chemistry. Angew Chem Int Ed Engl. 2021;60(37):20120–43. https://doi.org/10.1002/anie.202100274.
Sheehan F, Sementa D, Jain A, Kumar M, Tayarani-Najjaran M, Kroiss D, Ulijn RV. Peptide-based supramolecular systems chemistry. Chem Rev. 2021. https://doi.org/10.1021/acs.chemrev.1c00089.
De S, Klajn R. Dissipative self-assembly driven by the consumption of chemical fuels. Adv Mater. 2018;30(41):e1706750. https://doi.org/10.1002/adma.201706750.
Forsythe JG, Petrov AS, Millar WC, Yu S-S, Krishnamurthy R, Grover MA, Hud NV, Fernández FM. Surveying the sequence diversity of model prebiotic peptides by mass spectrometry. Proc Natl Acad Sci USA. 2017;114(37):E7652. https://doi.org/10.1073/pnas.1711631114.
Surman AJ, Rodriguez-Garcia M, Abul-Haija YM, Cooper GJT, Gromski PS, Turk-MacLeod R, Mullin M, Mathis C, Walker SI, Cronin L. Environmental control programs the emergence of distinct functional ensembles from unconstrained chemical reactions. Proc Natl Acad Sci USA. 2019;116(12):5387. https://doi.org/10.1073/pnas.1813987116.
Valdivielso AM, Puig-Castellví F, Atcher J, Solà J, Tauler R, Alfonso I. Unraveling the multistimuli responses of a complex dynamic system of pseudopeptidic macrocycles. Chem Eur J. 2017;23(45):10789–99. https://doi.org/10.1002/chem.201701294.
Perez-Lopez C, Ginebreda A, Carrascal M, Barcelò D, Abian J, Tauler R. Non-target protein analysis of samples from wastewater treatment plants using the regions of interest-multivariate curve resolution (ROIMCR) chemometrics method. J Environ Chem Eng. 2021;9(4):105752. https://doi.org/10.1016/j.jece.2021.105752.
Leitão JM, Tauler R, da Silva JC. Chemometric analysis of excitation emission matrices of fluorescent nanocomposites. J Fluoresc. 2011;21(5):1987–96. https://doi.org/10.1007/s10895-011-0899-y.
Tauler R, Parastar H. Big (bio)chemical data mining using chemometric methods: a need for chemists. Angew Chem Int Ed Engl. 2018. https://doi.org/10.1002/anie.201801134.
Payne EM, Holland-Moritz DA, Sun S, Kennedy RT. High-throughput screening by droplet microfluidics: perspective into key challenges and future prospects. Lab Chip. 2020;20(13):2247–62. https://doi.org/10.1039/D0LC00347F.
Zhuo Y, Wang X, Chen S, Chen H, Ouyang J, Yang L, Wang X, You L, Utz M, Tian Z, Cao X. Quantification and prediction of imine formation kinetics in aqueous solution by microfluidic NMR spectroscopy. Chem Eur J. 2021;27(37):9508–13. https://doi.org/10.1002/chem.202100874.
Bortolini C, Kartanas T, Copic D, Condado Morales I, Zhang Y, Challa PK, Peter Q, Jávorfi T, Hussain R, Dong M, Siligardi G, Knowles TPJ, Charmet J. Resolving protein mixtures using microfluidic diffusional sizing combined with synchrotron radiation circular dichroism. Lab Chip. 2019;19(1):50–8. https://doi.org/10.1039/C8LC00757H.
Carbajo D, Pérez Y, Bujons J, Alfonso I. Live-cell-templated dynamic combinatorial chemistry. Angew Chem Int Ed. 2020;59(39):17202–6. https://doi.org/10.1002/anie.202004745.
Boekhoven J, Brizard AM, Kowlgi KNK, Koper GJM, Eelkema R, van Esch JH. Dissipative self-assembly of a molecular gelator by using a chemical fuel. Angew Chem Int Ed. 2010;49(28):4825–8. https://doi.org/10.1002/anie.201001511.
Boekhoven J, Hendriksen WE, Koper GJM, Eelkema R, van Esch JH. Transient assembly of active materials fueled by a chemical reaction. Science. 2015;349(6252):1075–9. https://doi.org/10.1126/science.aac6103.
Sorrenti A, Leira-Iglesias J, Sato A, Hermans TM. Non-equilibrium steady states in supramolecular polymerization. Nat Commun. 2017;8:15899. https://doi.org/10.1038/ncomms15899.
Albertazzi L, van der Zwaag D, Leenders CMA, Fitzner R, van der Hofstad RW, Meijer EW. Probing exchange pathways in one-dimensional aggregates with super-resolution microscopy. Science. 2014;344(6183):491. https://doi.org/10.1126/science.1250945.
Sarkar A, Sasmal R, Empereur-mot C, Bochicchio D, Kompella SVK, Sharma K, Dhiman S, Sundaram B, Agasti SS, Pavan GM, George SJ. Self-sorted, random, and block supramolecular copolymers via sequence controlled, multicomponent self-assembly. J Am Chem Soc. 2020;142(16):7606–17. https://doi.org/10.1021/jacs.0c01822.
Sarkar A, Behera T, Sasmal R, Capelli R, Empereur-mot C, Mahato J, Agasti SS, Pavan GM, Chowdhury A, George SJ. Cooperative supramolecular block copolymerization for the synthesis of functional axial organic heterostructures. J Am Chem Soc. 2020;142(26):11528–39. https://doi.org/10.1021/jacs.0c04404.
Onogi S, Shigemitsu H, Yoshii T, Tanida T, Ikeda M, Kubota R, Hamachi I. In situ real-time imaging of self-sorted supramolecular nanofibres. Nat Chem. 2016;8(8):743–52. https://doi.org/10.1038/nchem.2526.
Westphal V, Rizzoli SO, Lauterbach MA, Kamin D, Jahn R, Hell SW. Video-rate far-field optical nanoscopy dissects synaptic vesicle movement. Science. 2008;320(5873):246–9. https://doi.org/10.1126/science.1154228.
Shao L, Kner P, Rego EH, Gustafsson MGL. Super-resolution 3D microscopy of live whole cells using structured illumination. Nat Methods. 2011;8(12):1044–6. https://doi.org/10.1038/nmeth.1734.
Godin Antoine G, Lounis B, Cognet L. Super-resolution microscopy approaches for live cell imaging. Biophys J. 2014;107(8):1777–84. https://doi.org/10.1016/j.bpj.2014.08.028.
Wang C, Taki M, Sato Y, Tamura Y, Yaginuma H, Okada Y, Yamaguchi S. A photostable fluorescent marker for the superresolution live imaging of the dynamic structure of the mitochondrial cristae. Proc Natl Acad Sci USA. 2019;116(32):15817–22. https://doi.org/10.1073/pnas.1905924116.
Jing Y, Zhang C, Yu B, Lin D, Qu J. Super-resolution microscopy: shedding new light on in vivo imaging. Front Chem. 2021;9:746900. https://doi.org/10.3389/fchem.2021.746900.
Kumar M, Son J, Huang RH, Sementa D, Lee M, O’Brien S, Ulijn RV. In situ, noncovalent labeling and stimulated emission depletion-based super-resolution imaging of supramolecular peptide nanostructures. ACS Nano. 2020;14(11):15056–63. https://doi.org/10.1021/acsnano.0c05029.
Parent LR, Bakalis E, Ramírez-Hernández A, Kammeyer JK, Park C, de Pablo J, Zerbetto F, Patterson JP, Gianneschi NC. Directly observing micelle fusion and growth in solution by liquid-cell transmission electron microscopy. J Am Chem Soc. 2017;139(47):17140–51. https://doi.org/10.1021/jacs.7b09060.
Touve MA, Carlini AS, Gianneschi NC. Self-assembling peptides imaged by correlated liquid cell transmission electron microscopy and MALDI-imaging mass spectrometry. Nat Commun. 2019;10(1):4837. https://doi.org/10.1038/s41467-019-12660-1.
Liao H-G, Zheng H. Liquid cell transmission electron microscopy. Annu Rev Phys Chem. 2016;67(1):719–47. https://doi.org/10.1146/annurev-physchem-040215-112501.
Marchello G, De Pace C, Duro-Castano A, Battaglia G, Ruiz PL. End-to-end image analysis pipeline for liquid-phase electron microscopy. J Microsc. 2020;279(3):242–8. https://doi.org/10.1111/jmi.12889.
Park J, Park H, Ercius P, Pegoraro AF, Xu C, Kim JW, Han SH, Weitz DA. Direct observation of wet biological samples by graphene liquid cell transmission electron microscopy. Nano Lett. 2015;15(7):4737–44. https://doi.org/10.1021/acs.nanolett.5b01636.
Dahmke IN, Verch A, Hermannsdörfer J, Peckys DB, Weatherup RS, Hofmann S, de Jonge N. Graphene liquid enclosure for single-molecule analysis of membrane proteins in whole cells using electron microscopy. ACS Nano. 2017;11(11):11108–17. https://doi.org/10.1021/acsnano.7b05258.
Fukui T, Uchihashi T, Sasaki N, Watanabe H, Takeuchi M, Sugiyasu K. Direct observation and manipulation of supramolecular polymerization by high-speed atomic force microscopy. Angew Chem Int Ed Engl. 2018;57(47):15465–70. https://doi.org/10.1002/anie.201809165.
Jin H, Jiao F, Daily MD, Chen Y, Yan F, Ding YH, Zhang X, Robertson EJ, Baer MD, Chen CL. Highly stable and self-repairing membrane-mimetic 2D nanomaterials assembled from lipid-like peptoids. Nat Commun. 2016;7:12252. https://doi.org/10.1038/ncomms12252.
Aratsu K, Takeya R, Pauw BR, Hollamby MJ, Kitamoto Y, Shimizu N, Takagi H, Haruki R, Adachi SI, Yagai S. Supramolecular copolymerization driven by integrative self-sorting of hydrogen-bonded rosettes. Nat Commun. 2020;11(1):1623. https://doi.org/10.1038/s41467-020-15422-6.
Ando T, Uchihashi T, Scheuring S. Filming biomolecular processes by high-speed atomic force microscopy. Chem Rev. 2014;114(6):3120–88. https://doi.org/10.1021/cr4003837.
Ando T, Kodera N, Takai E, Maruyama D, Saito K, Toda A. A high-speed atomic force microscope for studying biological macromolecules. Proc Natl Acad Sci USA. 2001;98(22):12468–72. https://doi.org/10.1073/pnas.211400898.
Fantner GE, Schitter G, Kindt JH, Ivanov T, Ivanova K, Patel R, Holten-Andersen N, Adams J, Thurner PJ, Rangelow IW, Hansma PK. Components for high speed atomic force microscopy. Ultramicroscopy. 2006;106(8):881–7. https://doi.org/10.1016/j.ultramic.2006.01.015.
Korevaar PA, George SJ, Markvoort AJ, Smulders MMJ, Hilbers PAJ, Schenning APHJ, De Greef TFA, Meijer EW. Pathway complexity in supramolecular polymerization. Nature. 2012;481(7382):492–6. https://doi.org/10.1038/nature10720.
Ogi S, Sugiyasu K, Manna S, Samitsu S, Takeuchi M. Living supramolecular polymerization realized through a biomimetic approach. Nat Chem. 2014;6(3):188–95. https://doi.org/10.1038/nchem.1849.
Maity S, Ottele J, Santiago GM, Frederix P, Kroon P, Markovitch O, Stuart MCA, Marrink SJ, Otto S, Roos WH. Caught in the act: mechanistic insight into supramolecular polymerization-driven self-replication from real-time visualization. J Am Chem Soc. 2020;142(32):13709–17. https://doi.org/10.1021/jacs.0c02635.
Kodera N, Yamamoto D, Ishikawa R, Ando T. Video imaging of walking myosin V by high-speed atomic force microscopy. Nature. 2010;468(7320):72–6. https://doi.org/10.1038/nature09450.
Uchihashi T, Iino R, Ando T, Noji H. High-speed atomic force microscopy reveals rotary catalysis of rotorless F1-ATPase. Science. 2011;333(6043):755–8. https://doi.org/10.1126/science.1205510.
Scheuring S, Sturgis JN. Dynamics and diffusion in photosynthetic membranes from Rhodospirillum photometricum. Biophys J. 2006;91(10):3707–17. https://doi.org/10.1529/biophysj.106.083709.
Pfreundschuh M, Martinez-Martin D, Mulvihill E, Wegmann S, Muller DJ. Multiparametric high-resolution imaging of native proteins by force-distance curve–based AFM. Nat Protoc. 2014;9(5):1113–30. https://doi.org/10.1038/nprot.2014.070.
Calò A, Reguera D, Oncins G, Persuy M-A, Sanz G, Lobasso S, Corcelli A, Pajot-Augy E, Gomila G. Force measurements on natural membrane nanovesicles reveal a composition-independent, high Young’s modulus. Nanoscale. 2014;6(4):2275–85. https://doi.org/10.1039/C3NR05107B.
Calò A, Eleta-Lopez A, Stoliar P, De Sancho D, Santos S, Verdaguer A, Bittner AM. Multifrequency force microscopy of helical protein assembly on a virus. Sci Rep. 2016;6(1):21899. https://doi.org/10.1038/srep21899.
Millan-Solsona R, Checa M, Fumagalli L, Gomila G. Mapping the capacitance of self-assembled monolayers at metal/electrolyte interfaces at the nanoscale by in-liquid scanning dielectric microscopy. Nanoscale. 2020;12(40):20658–68. https://doi.org/10.1039/D0NR05723A.
Dols-Perez A, Gramse G, Calò A, Gomila G, Fumagalli L. Nanoscale electric polarizability of ultrathin biolayers on insulating substrates by electrostatic force microscopy. Nanoscale. 2015;7(43):18327–36. https://doi.org/10.1039/C5NR04983K.
Kumar M, Ing NL, Narang V, Wijerathne NK, Hochbaum AI, Ulijn RV. Amino-acid-encoded biocatalytic self-assembly enables the formation of transient conducting nanostructures. Nat Chem. 2018;10(7):696–703. https://doi.org/10.1038/s41557-018-0047-2.
Dal Molin M, Verolet Q, Colom A, Letrun R, Derivery E, Gonzalez-Gaitan M, Vauthey E, Roux A, Sakai N, Matile S. Fluorescent flippers for mechanosensitive membrane probes. J Am Chem Soc. 2015;137(2):568–71. https://doi.org/10.1021/ja5107018.
Goujon A, Colom A, Strakova K, Mercier V, Mahecic D, Manley S, Sakai N, Roux A, Matile S. Mechanosensitive fluorescent probes to image membrane tension in mitochondria, endoplasmic reticulum, and lysosomes. J Am Chem Soc. 2019;141(8):3380–4. https://doi.org/10.1021/jacs.8b13189.
Strakova K, Assies L, Goujon A, Piazzolla F, Humeniuk HV, Matile S. Dithienothiophenes at work: access to mechanosensitive fluorescent probes, chalcogen-bonding catalysis, and beyond. Chem Rev. 2019;119(19):10977–1005. https://doi.org/10.1021/acs.chemrev.9b00279.
Bal S, Ghosh C, Ghosh T, Vijayaraghavan RK, Das D. Non-equilibrium polymerization of cross-β amyloid peptides for temporal control of electronic properties. Angew Chem Int Ed. 2020;59(32):13506–10. https://doi.org/10.1002/anie.202003721.
Funding
This project was funded by a fellowship from “la Caixa” Foundation (ID 100010434) and from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 847648. The fellowship code is “LCF/BQ/PI21/11830035.” AC received the Ajut a la Recerca Transversal project from IN2UB (ART2020).
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Published in the topical collection featuring Promising Early-Career (Bio)Analytical Researchers with guest editors Antje J. Baeumner, María C. Moreno-Bondi, Sabine Szunerits, and Qiuquan Wang.
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Jain, A., Calò, A., Barceló, D. et al. Supramolecular systems chemistry through advanced analytical techniques. Anal Bioanal Chem 414, 5105–5119 (2022). https://doi.org/10.1007/s00216-021-03824-4
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DOI: https://doi.org/10.1007/s00216-021-03824-4