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Wang H, Wang K, Bai S, Wei L, Gao Y, Zhi K, Guo X, Wang Y. Spatiotemporal control over self-assembly of supramolecular hydrogels through reaction-diffusion. J Colloid Interface Sci 2024; 664:938-945. [PMID: 38503079 DOI: 10.1016/j.jcis.2024.03.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/21/2024]
Abstract
Supramolecular self-assembly is ubiquitous in living system and is usually controlled to proceed in time and space through sophisticated reaction-diffusion processes, underpinning various vital cellular functions. In this contribution, we demonstrate how spatiotemporal self-assembly of supramolecular hydrogels can be realized through a simple reaction-diffusion-mediated transient transduction of pH signal. In the reaction-diffusion system, a relatively faster diffusion of acid followed by delayed enzymatic production and diffusion of base from the opposite site enables a transient transduction of pH signal in the substrate. By coupling such reaction-diffusion system with pH-sensitive gelators, dynamic supramolecular hydrogels with tunable lifetimes are formed at defined locations. The hydrogel fibers show interesting dynamic growing behaviors under the regulation of transient pH signal, reminiscent of their biological counterpart. We further demonstrate a proof-of-concept application of the developed methodology for dynamic information encoding in a soft substrate. We envision that this work may provide a potent approach to enable transient transduction of various chemical signals for the construction of new colloidal materials with the capability to evolve their structures and functionalities in time and space.
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Affiliation(s)
- Hucheng Wang
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Kainan Wang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Shengyu Bai
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lai Wei
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yuliang Gao
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Kangkang Zhi
- Department of Vascular Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China.
| | - Xuhong Guo
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yiming Wang
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Key Laboratory for Intelligent Sensing and Detection Technology, East China University of Science and Technology, Shanghai 200237, China.
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2
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Edenharter K, Jaworek MW, Engelbrecht V, Winter R, Happe T. H 2 production under stress: [FeFe]‑hydrogenases reveal strong stability in high pressure environments. Biophys Chem 2024; 308:107217. [PMID: 38490110 DOI: 10.1016/j.bpc.2024.107217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 03/10/2024] [Indexed: 03/17/2024]
Abstract
Hydrogenases are a diverse group of metalloenzymes that catalyze the conversion of H2 into protons and electrons and the reverse reaction. A subgroup is formed by the [FeFe]‑hydrogenases, which are the most efficient enzymes of microbes for catalytic H2 conversion. We have determined the stability and activity of two [FeFe]‑hydrogenases under high temperature and pressure conditions employing FTIR spectroscopy and the high-pressure stopped-flow methodology in combination with fast UV/Vis detection. Our data show high temperature stability and an increase in activity up to the unfolding temperatures of the enzymes. Remarkably, both enzymes reveal a very high pressure stability of their structure, even up to pressures of several kbars. Their high pressure-stability enables high enzymatic activity up to 2 kbar, which largely exceeds the pressure limit encountered by organisms in the deep sea and sub-seafloor on Earth.
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Affiliation(s)
- Kristina Edenharter
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Michel W Jaworek
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Vera Engelbrecht
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
| | - Thomas Happe
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr-University Bochum, 44801 Bochum, Germany.
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3
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Kalita K, Zeng B, You JB, Li Y, Moyo A, Xu BB, Zhang X. Spontaneous Rise of Hydrogen Microbubbles in Interfacial Gas Evolution Reaction. Small 2024:e2400849. [PMID: 38644168 DOI: 10.1002/smll.202400849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/08/2024] [Indexed: 04/23/2024]
Abstract
Liquid organic hydrogen carrier is a promising option for the transport and storage of hydrogen as a clean energy source. This study examines the stability and behavior of organic drops immobilized on a substrate during an interfacial hydrogen-evolution reaction (HER) at the drop surface and its surrounding aqueous solution. Hydrogen microbubbles form within the drop and rise to the drop apex. The growth rate of the hydrogen in-drop bubble increases with the concentration of the reactant in the surrounding medium. The drop remains stable till the buoyancy acting on the in-drop bubble is large enough to overcome the capillary force and the external viscous drag. The bubble spontaneously rises and carries a portion drop liquid to the solution surface. These spontaneous rising in-drop bubbles are detected in measurements using a high-precision sensor placed on the upper surface of the aqueous solution, reversing the settling phase from phase separation in the reactive emulsion. The finding from this work provides new insights into the behaviors of drops and bubbles in many interfacial gas evolution reactions in clean technologies.
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Affiliation(s)
- Kangkana Kalita
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, T6G 1H9, Canada
| | - Binglin Zeng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, T6G 1H9, Canada
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, 999077, China
| | - Jae Bem You
- Department of Chemical Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea
| | - Yifan Li
- Department of Mechanical and Construction Engineering, Faculty of Engineering and Environment, Northumbria University, Newcastle Upon Tyne, NE1 8ST, UK
| | - Anotidaishe Moyo
- Department of Mechanical and Construction Engineering, Faculty of Engineering and Environment, Northumbria University, Newcastle Upon Tyne, NE1 8ST, UK
| | - Ben Bin Xu
- Department of Mechanical and Construction Engineering, Faculty of Engineering and Environment, Northumbria University, Newcastle Upon Tyne, NE1 8ST, UK
| | - Xuehua Zhang
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, T6G 1H9, Canada
- Physics of Fluids Group and Max Planck Center for Complex Fluid Dynamics, University of Twente, 7500 AE, Enschede, The Netherlands
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4
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Harris R, Veretnik S, Dewan S, Baruch Leshem A, Lampel A. Regulation of enzymatic reactions by chemical composition of peptide biomolecular condensates. Commun Chem 2024; 7:90. [PMID: 38643237 PMCID: PMC11032315 DOI: 10.1038/s42004-024-01174-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 04/09/2024] [Indexed: 04/22/2024] Open
Abstract
Biomolecular condensates are condensed intracellular phases that are formed by liquid-liquid phase separation (LLPS) of proteins, either in the absence or presence of nucleic acids. These condensed phases regulate various biochemical reactions by recruitment of enzymes and substrates. Developments in the field of LLPS facilitated new insights on the regulation of compartmentalized enzymatic reactions. Yet, the influence of condensate chemical composition on enzymatic reactions is still poorly understood. Here, by using peptides as minimalistic condensate building blocks and β-galactosidase as a simple enzymatic model we show that the reaction is restricted in homotypic peptide condensates, while product formation is enhanced in peptide-RNA condensates. Our findings also show that condensate composition affects the recruitment of substrate, the spatial distribution, and the kinetics of the reaction. Thus, these findings can be further employed for the development of microreactors for biotechnological applications.
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Affiliation(s)
- Rif Harris
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shirel Veretnik
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Simran Dewan
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Avigail Baruch Leshem
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ayala Lampel
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
- Center for Nanoscience and Nanotechnology Tel Aviv University, Tel Aviv, 69978, Israel.
- Sagol Center for Regenerative Biotechnology Tel Aviv University, Tel Aviv, 69978, Israel.
- Center for the Physics and Chemistry of Living Systems Tel Aviv University, Tel Aviv, 69978, Israel.
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5
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Rothschild LJ, Averesch NJH, Strychalski EA, Moser F, Glass JI, Cruz Perez R, Yekinni IO, Rothschild-Mancinelli B, Roberts Kingman GA, Wu F, Waeterschoot J, Ioannou IA, Jewett MC, Liu AP, Noireaux V, Sorenson C, Adamala KP. Building Synthetic Cells─From the Technology Infrastructure to Cellular Entities. ACS Synth Biol 2024; 13:974-997. [PMID: 38530077 DOI: 10.1021/acssynbio.3c00724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The de novo construction of a living organism is a compelling vision. Despite the astonishing technologies developed to modify living cells, building a functioning cell "from scratch" has yet to be accomplished. The pursuit of this goal alone has─and will─yield scientific insights affecting fields as diverse as cell biology, biotechnology, medicine, and astrobiology. Multiple approaches have aimed to create biochemical systems manifesting common characteristics of life, such as compartmentalization, metabolism, and replication and the derived features, evolution, responsiveness to stimuli, and directed movement. Significant achievements in synthesizing each of these criteria have been made, individually and in limited combinations. Here, we review these efforts, distinguish different approaches, and highlight bottlenecks in the current research. We look ahead at what work remains to be accomplished and propose a "roadmap" with key milestones to achieve the vision of building cells from molecular parts.
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Affiliation(s)
- Lynn J Rothschild
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California 94035-1000, United States
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Nils J H Averesch
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | | | - Felix Moser
- Synlife, One Kendall Square, Cambridge, Massachusetts 02139-1661, United States
| | - John I Glass
- J. Craig Venter Institute, La Jolla, California 92037, United States
| | - Rolando Cruz Perez
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
- Blue Marble Space Institute of Science at NASA Ames Research Center, Moffett Field, California 94035-1000, United States
| | - Ibrahim O Yekinni
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brooke Rothschild-Mancinelli
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0150, United States
| | - Garrett A Roberts Kingman
- NASA Postdoctoral Program, Ames Research Center, Moffett Field, California 94035-1000, United States
| | - Feilun Wu
- J. Craig Venter Institute, Rockville, Maryland 20850, United States
| | - Jorik Waeterschoot
- Mechatronics, Biostatistics and Sensors (MeBioS), KU Leuven, 3000 Leuven Belgium
| | - Ion A Ioannou
- Department of Chemistry, MSRH, Imperial College London, London W12 0BZ, U.K
| | - Michael C Jewett
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Allen P Liu
- Mechanical Engineering & Biomedical Engineering, Cellular and Molecular Biology, Biophysics, Applied Physics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent Noireaux
- Physics and Nanotechnology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carlise Sorenson
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Gil-Garcia M, Benítez-Mateos AI, Papp M, Stoffel F, Morelli C, Normak K, Makasewicz K, Faltova L, Paradisi F, Arosio P. Local environment in biomolecular condensates modulates enzymatic activity across length scales. Nat Commun 2024; 15:3322. [PMID: 38637545 PMCID: PMC11026464 DOI: 10.1038/s41467-024-47435-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 03/28/2024] [Indexed: 04/20/2024] Open
Abstract
The mechanisms that underlie the regulation of enzymatic reactions by biomolecular condensates and how they scale with compartment size remain poorly understood. Here we use intrinsically disordered domains as building blocks to generate programmable enzymatic condensates of NADH-oxidase (NOX) with different sizes spanning from nanometers to microns. These disordered domains, derived from three distinct RNA-binding proteins, each possessing different net charge, result in the formation of condensates characterized by a comparable high local concentration of the enzyme yet within distinct environments. We show that only condensates with the highest recruitment of substrate and cofactor exhibit an increase in enzymatic activity. Notably, we observe an enhancement in enzymatic rate across a wide range of condensate sizes, from nanometers to microns, indicating that emergent properties of condensates can arise within assemblies as small as nanometers. Furthermore, we show a larger rate enhancement in smaller condensates. Our findings demonstrate the ability of condensates to modulate enzymatic reactions by creating distinct effective solvent environments compared to the surrounding solution, with implications for the design of protein-based heterogeneous biocatalysts.
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Affiliation(s)
- Marcos Gil-Garcia
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Ana I Benítez-Mateos
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Marcell Papp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Florence Stoffel
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Chiara Morelli
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Karl Normak
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Katarzyna Makasewicz
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Francesca Paradisi
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland.
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7
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Maity S, Pahari S, Santra S, Jana M. Interfacial Glucose to Regulate Hydrated Lipid Bilayer Properties: Influence of Concentrations. J Chem Inf Model 2024. [PMID: 38635679 DOI: 10.1021/acs.jcim.3c01991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
A series of atomistic molecular dynamics (MD) simulations were carried out with a hydrated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayer with the variation of glucose concentrations from 0 to 30 wt % in the presence of 0.3 M NaCl. The study suggested that although the thickness of the lipid bilayer dropped significantly with the increase in glucose concentration, it expanded laterally at high glucose levels due to the intercalation of glucose between the headgroups of adjacent lipids. We adopted the surface assessment via the grid evaluation method to compute the deviation of the bilayer's key structural features for the different amounts of glucose present. This suggested that the accumulation of glucose molecules near the headgroups influences the local lipid bilayer undulation and crimping of the lipid tails. We find that the area compressibility modulus increases with the glucose level, causing enhanced bilayer rigidity arising from the slow lateral diffusion of lipids. The restricted lipid motion at high glucose concentrations controls the sustainability of the curved bilayer surface. Calculations revealed that certain orientations of CO → of interfacial glucose with the PN → of lipid headgroups are preferred, which helps the glucose to form direct hydrogen bonds (HBs) with the lipid headgroups. Such lipid-glucose (LG) HBs relax slowly at low glucose concentrations and exhibit a higher lifetime, whereas fast structural relaxation of LG HBs with a shorter lifetime was noticed at a higher glucose level. In contrast, lipid-water (LW) HBs exhibited a higher lifetime at a higher glucose level, which gradually decreased with the glucose level lowering. The study interprets that the glucose concentration-driven LW and LG interactions are mutually inclusive. Our detailed analysis will exemplify small saccharide concentration-driven membrane stabilizing efficiency, which is, in general, helpful for drug delivery study.
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Affiliation(s)
- Sankar Maity
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Somdev Pahari
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Santanu Santra
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
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8
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Sarkar A, Dúzs B, Walther A. Fuel-Driven Enzymatic Reaction Networks to Program Autonomous Thiol/Disulfide Redox Systems. J Am Chem Soc 2024; 146:10281-10285. [PMID: 38569008 DOI: 10.1021/jacs.4c02680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Fuel-driven dissipative formation of disulfide bonds using competing oxidative activation and reductive deactivation presents a possibly very versatile avenue for autonomous materials design. However, this is challenging to realize because of the direct annihilation of oxidizing fuel and a deactivating reducing agent. We overcome this challenge by introducing a redox-based enzymatic reaction network (ERN), enabling the dissipative disulfide formation for molecularly dissolved thiols in a fully autonomous manner. Moreover, the ERN allows for programming hydrogel lifetimes by utilizing thiol-terminated star polymers (sPEG-SH). The ERN can be customized to operate with aliphatic and aromatic thiols and should thus be broadly applicable to functional thiols.
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Affiliation(s)
- Aritra Sarkar
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Brigitta Dúzs
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Andreas Walther
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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9
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Pansuriya R, Patel T, Kumar S, Aswal VK, Raje N, Hoskins C, Kailasa SK, Malek NI. Multifunctional Ionic Hydrogel-Based Transdermal Delivery of 5-Fluorouracil for the Breast Cancer Treatment. ACS Appl Bio Mater 2024. [PMID: 38620030 DOI: 10.1021/acsabm.4c00152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Transdermal drug delivery systems (TDDS) are a promising and innovative approach for breast cancer treatment, offering advantages such as noninvasiveness, potential for localized and prolonged drug delivery while minimizing systemic side effects through avoiding first-pass metabolism. Utilizing the distinctive characteristics of hydrogels, such as their biocompatibility, versatility, and higher drug loading capabilities, in the present work, we prepared ionic hydrogels through synergistic interaction between ionic liquids (ILs), choline alanine ([Cho][Ala]), and choline proline ([Cho][Pro]) with oleic acid (OA). ILs used in the study are biocompatible and enhance the solubility of 5-fluorouracil (5-FU), whereas OA is a known chemical penetration enhancer. The concentration-dependent (OA) change in morphological aggregates, that is, from cylindrical micelles to worm-like micelles to hydrogels was formed with both ILs and was characterized by SANS measurement, whereas the interactions involved were confirmed by FTIR spectroscopy. The hydrogels have excellent mechanical properties, which studied by rheology and their morphology through FE-SEM analysis. The in vitro skin permeation study revealed that both hydrogels penetrated 255 times ([Cho][Ala]) and 250 times ([Cho][Pro]) more as compared to PBS after 48 h. Those ionic hydrogels exhibited the capability to change the lipid and keratin arrangements within the skin layer, thereby enhancing the transdermal permeation of the 5-FU. Both ionic hydrogels exhibit excellent biocompatibility with normal cell lines (L-132 cells) as well as cancerous cell lines (MCF-7 cells), demonstrating over 92% cell viability after 48 h in both cell lines. In vitro, the cytotoxicity of the 5-FU-loaded hydrogels was evaluated on MCF-7 and HeLa cell lines. These results indicate that the investigated biocompatible and nontoxic ionic hydrogels enable the transdermal delivery of hydrophilic drugs, making them a viable option for effectively treating breast cancer.
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Affiliation(s)
- Raviraj Pansuriya
- Ionic Liquids Research Laboratory, Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat395007, Gujarat ,India
| | - Tapas Patel
- Ionic Liquids Research Laboratory, Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat395007, Gujarat ,India
| | - Sugam Kumar
- Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai400085, India
| | - Vinod K Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai400085, India
| | - Naina Raje
- Analytical Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai400085, India
| | - Clare Hoskins
- Technology and Innovation Centre, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1RD, U.K
| | - Suresh Kumar Kailasa
- Ionic Liquids Research Laboratory, Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat395007, Gujarat ,India
| | - Naved I Malek
- Ionic Liquids Research Laboratory, Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat395007, Gujarat ,India
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10
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Chandrasekaran A, Graham K, Stachowiak JC, Rangamani P. Kinetic trapping organizes actin filaments within liquid-like protein droplets. Nat Commun 2024; 15:3139. [PMID: 38605007 PMCID: PMC11009352 DOI: 10.1038/s41467-024-46726-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 03/07/2024] [Indexed: 04/13/2024] Open
Abstract
Several actin-binding proteins (ABPs) phase separate to form condensates capable of curating the actin network shapes. Here, we use computational modeling to understand the principles of actin network organization within VASP condensate droplets. Our simulations reveal that the different actin shapes, namely shells, rings, and mixture states are highly dependent on the kinetics of VASP-actin interactions, suggesting that they arise from kinetic trapping. Specifically, we show that reducing the residence time of VASP on actin filaments reduces degree of bundling, thereby promoting assembly of shells rather than rings. We validate the model predictions experimentally using a VASP-mutant with decreased bundling capability. Finally, we investigate the ring opening within deformed droplets and found that the sphere-to-ellipsoid transition is favored under a wide range of filament lengths while the ellipsoid-to-rod transition is only permitted when filaments have a specific range of lengths. Our findings highlight key mechanisms of actin organization within phase-separated ABPs.
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Affiliation(s)
- Aravind Chandrasekaran
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, 92093-0411, USA
| | - Kristin Graham
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, 92093-0411, USA.
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11
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Wan L, Zhu Y, Zhang W, Mu W. Recent advances in design and application of synthetic membraneless organelles. Biotechnol Adv 2024; 73:108355. [PMID: 38588907 DOI: 10.1016/j.biotechadv.2024.108355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 02/26/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Membraneless organelles (MLOs) formed by liquid-liquid phase separation (LLPS) have been extensively studied due to their spatiotemporal control of biochemical and cellular processes in living cells. These findings have provided valuable insights into the physicochemical principles underlying the formation and functionalization of biomolecular condensates, which paves the way for the development of versatile phase-separating systems capable of addressing a variety of application scenarios. Here, we highlight the potential of constructing synthetic MLOs with programmable and functional properties. Notably, we organize how these synthetic membraneless compartments have been capitalized to manipulate enzymatic activities and metabolic reactions. The aim of this review is to inspire readerships to deeply comprehend the widespread roles of synthetic MLOs in the regulation enzymatic reactions and control of metabolic processes, and to encourage the rational design of controllable and functional membraneless compartments for a broad range of bioengineering applications.
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Affiliation(s)
- Li Wan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China.
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12
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Qi Y, Zhang Z, Wu Z, Qin Z, Zhou Y, Yang X. Composite System of Lauryl Glucoside and Lauryl Glycoside Sulfosuccinate: Properties and Applications in Vitamin E Nanoemulsions. Chempluschem 2024:e202400058. [PMID: 38578659 DOI: 10.1002/cplu.202400058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/06/2024]
Abstract
The synergistic effect of surfactant compounding on performance can be leveraged to enhance product application performance. An investigation of the surface tension and emulsification properties revealed the complex synergistic effect of the composite system comprising lauryl glucoside (LG) and lauryl glycoside sulfosuccinate (LG-SS). The composite system was used as an emulsifier for vitamin E (VE) emulsification. VE nanoemulsions with high VE content were successfully prepared. The nanoemulsion appears homogeneous and transparent and has an average size of approximately 200 nm. It has better temperature and centrifugal stability, an antioxidant capacity 2.89 times that of untreated VE, and is not easily oxidized and deactivated. In this study, we successfully constructed a complex system of LG and its derivatives and applied it to VE emulsification - this is a step toward expanding the effective application of glycosides and their derivative composite systems in food, pharmaceutics, and other industries.
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Affiliation(s)
- Yunqin Qi
- Department Bio-based Functional Surfactant Research Department, Institution 1 China Research Institute of Daily Chemical Industry, Institution 2 Shanxi Key Laboratory of Functional Surfactants, Address 34 Wenyuan Street, Taiyuan, Shanxi Province, 030001, P.R. China
| | - Zhihui Zhang
- Department Bio-based Functional Surfactant Research Department, Institution 1 China Research Institute of Daily Chemical Industry, Institution 2 Shanxi Key Laboratory of Functional Surfactants, Address 34 Wenyuan Street, Taiyuan, Shanxi Province, 030001, P.R. China
| | - Zhiyu Wu
- Department Bio-based Functional Surfactant Research Department, Institution 1 China Research Institute of Daily Chemical Industry, Institution 2 Shanxi Key Laboratory of Functional Surfactants, Address 34 Wenyuan Street, Taiyuan, Shanxi Province, 030001, P.R. China
| | - Ziyu Qin
- Department Bio-based Functional Surfactant Research Department, Institution 1 China Research Institute of Daily Chemical Industry, Institution 2 Shanxi Key Laboratory of Functional Surfactants, Address 34 Wenyuan Street, Taiyuan, Shanxi Province, 030001, P.R. China
| | - Yuan Zhou
- Department Bio-based Functional Surfactant Research Department, Institution 1 China Research Institute of Daily Chemical Industry, Institution 2 Shanxi Key Laboratory of Functional Surfactants, Address 34 Wenyuan Street, Taiyuan, Shanxi Province, 030001, P.R. China
| | - Xiuquan Yang
- Department Bio-based Functional Surfactant Research Department, Institution 1 China Research Institute of Daily Chemical Industry, Institution 2 Shanxi Key Laboratory of Functional Surfactants, Address 34 Wenyuan Street, Taiyuan, Shanxi Province, 030001, P.R. China
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13
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Calaça Serrão A, Wunnava S, Dass AV, Ufer L, Schwintek P, Mast CB, Braun D. High-Fidelity RNA Copying via 2',3'-Cyclic Phosphate Ligation. J Am Chem Soc 2024; 146:8887-8894. [PMID: 38503430 PMCID: PMC10995993 DOI: 10.1021/jacs.3c10813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/21/2024]
Abstract
Templated ligation offers an efficient approach to replicate long strands in an RNA world. The 2',3'-cyclic phosphate (>P) is a prebiotically available activation that also forms during RNA hydrolysis. Using gel electrophoresis and high-performance liquid chromatography, we found that the templated ligation of RNA with >P proceeds in simple low-salt aqueous solutions with 1 mM MgCl2 under alkaline pH ranging from 9 to 11 and temperatures from -20 to 25 °C. No additional catalysts were required. In contrast to previous reports, we found an increase in the number of canonical linkages to 50%. The reaction proceeds in a sequence-specific manner, with an experimentally determined ligation fidelity of 82% at the 3' end and 91% at the 5' end of the ligation site. With splinted oligomers, five ligations created a 96-mer strand, demonstrating a pathway for the ribozyme assembly. Due to the low salt requirements, the ligation conditions will be compatible with strand separation. Templated ligation mediated by 2',3'-cyclic phosphate in alkaline conditions therefore offers a performant replication and elongation reaction for RNA on early Earth.
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Affiliation(s)
- Adriana Calaça Serrão
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Sreekar Wunnava
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Avinash V. Dass
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
- Department
of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4M1, Canada
| | - Lennard Ufer
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Philipp Schwintek
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Christof B. Mast
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Dieter Braun
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
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14
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Markovitch O, Wu J, Otto S. Binding of Precursors to Replicator Assemblies Can Improve Replication Fidelity and Mediate Error Correction. Angew Chem Int Ed Engl 2024; 63:e202317997. [PMID: 38380789 DOI: 10.1002/anie.202317997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/06/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024]
Abstract
Copying information is vital for life's propagation. Current life forms maintain a low error rate in replication, using complex machinery to prevent and correct errors. However, primitive life had to deal with higher error rates, limiting its ability to evolve. Discovering mechanisms to reduce errors would alleviate this constraint. Here, we introduce a new mechanism that decreases error rates and corrects errors in synthetic self-replicating systems driven by self-assembly. Previous work showed that macrocycle replication occurs through the accumulation of precursor material on the sides of the fibrous replicator assemblies. Stochastic simulations now reveal that selective precursor binding to the fiber surface enhances replication fidelity and error correction. Centrifugation experiments show that replicator fibers can exhibit the necessary selectivity in precursor binding. Our results suggest that synthetic replicator systems are more evolvable than previously thought, encouraging further evolution-focused experiments.
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Affiliation(s)
- Omer Markovitch
- Stratingh Institute, Centre for Systems Chemistry, University of Groningen, Groningen, The Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Juntian Wu
- Stratingh Institute, Centre for Systems Chemistry, University of Groningen, Groningen, The Netherlands
| | - Sijbren Otto
- Stratingh Institute, Centre for Systems Chemistry, University of Groningen, Groningen, The Netherlands
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15
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Ranganath VA, Maity I. Artificial Homeostasis Systems Based on Feedback Reaction Networks: Design Principles and Future Promises. Angew Chem Int Ed Engl 2024; 63:e202318134. [PMID: 38226567 DOI: 10.1002/anie.202318134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/17/2024]
Abstract
Feedback-controlled chemical reaction networks (FCRNs) are indispensable for various biological processes, such as cellular mechanisms, patterns, and signaling pathways. Through the intricate interplay of many feedback loops (FLs), FCRNs maintain a stable internal cellular environment. Currently, creating minimalistic synthetic cells is the long-term objective of systems chemistry, which is motivated by such natural integrity. The design, kinetic optimization, and analysis of FCRNs to exhibit functions akin to those of a cell still pose significant challenges. Indeed, reaching synthetic homeostasis is essential for engineering synthetic cell components. However, maintaining homeostasis in artificial systems against various agitations is a difficult task. Several biological events can provide us with guidelines for a conceptual understanding of homeostasis, which can be further applicable in designing artificial synthetic systems. In this regard, we organize our review with artificial homeostasis systems driven by FCRNs at different length scales, including homogeneous, compartmentalized, and soft material systems. First, we stretch a quick overview of FCRNs in different molecular and supramolecular systems, which are the essential toolbox for engineering different nonlinear functions and homeostatic systems. Moreover, the existing history of synthetic homeostasis in chemical and material systems and their advanced functions with self-correcting, and regulating properties are also emphasized.
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Affiliation(s)
- Vinay Ambekar Ranganath
- Centre for Nano and Material Sciences, Jain (Deemed-to-be University), Jain Global Campus, Bangalore, 562112, Karnataka, India
| | - Indrajit Maity
- Centre for Nano and Material Sciences, Jain (Deemed-to-be University), Jain Global Campus, Bangalore, 562112, Karnataka, India
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16
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Lim S, Clark DS. Phase-separated biomolecular condensates for biocatalysis. Trends Biotechnol 2024; 42:496-509. [PMID: 37925283 DOI: 10.1016/j.tibtech.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/06/2023]
Abstract
Nature often uses dynamically assembling multienzymatic complexes called metabolons to achieve spatiotemporal control of complex metabolic reactions. Researchers are aiming to mimic this strategy of organizing enzymes to enhance the performance of artificial biocatalytic systems. Biomolecular condensates formed through liquid-liquid phase separation (LLPS) can serve as a powerful tool to drive controlled assembly of enzymes. Diverse enzymatic pathways have been reconstituted within catalytic condensates in vitro as well as synthetic membraneless organelles in living cells. Furthermore, in vivo condensates have been engineered to regulate metabolic pathways by selectively sequestering enzymes. Thus, harnessing LLPS for controlled organization of enzymes provides an opportunity to dynamically regulate biocatalytic processes.
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Affiliation(s)
- Samuel Lim
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA..
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17
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Matreux T, Aikkila P, Scheu B, Braun D, Mast CB. Heat flows enrich prebiotic building blocks and enhance their reactivity. Nature 2024; 628:110-116. [PMID: 38570715 PMCID: PMC10990939 DOI: 10.1038/s41586-024-07193-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/09/2024] [Indexed: 04/05/2024]
Abstract
The emergence of biopolymer building blocks is a crucial step during the origins of life1-6. However, all known formation pathways rely on rare pure feedstocks and demand successive purification and mixing steps to suppress unwanted side reactions and enable high product yields. Here we show that heat flows through thin, crack-like geo-compartments could have provided a widely available yet selective mechanism that separates more than 50 prebiotically relevant building blocks from complex mixtures of amino acids, nucleobases, nucleotides, polyphosphates and 2-aminoazoles. Using measured thermophoretic properties7,8, we numerically model and experimentally prove the advantageous effect of geological networks of interconnected cracks9,10 that purify the previously mixed compounds, boosting their concentration ratios by up to three orders of magnitude. The importance for prebiotic chemistry is shown by the dimerization of glycine11,12, in which the selective purification of trimetaphosphate (TMP)13,14 increased reaction yields by five orders of magnitude. The observed effect is robust under various crack sizes, pH values, solvents and temperatures. Our results demonstrate how geologically driven non-equilibria could have explored highly parallelized reaction conditions to foster prebiotic chemistry.
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Affiliation(s)
- Thomas Matreux
- Systems Biophysics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paula Aikkila
- Systems Biophysics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Bettina Scheu
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dieter Braun
- Systems Biophysics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christof B Mast
- Systems Biophysics, Ludwig-Maximilians-Universität München, Munich, Germany.
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18
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Li L, Zheng R, Sun R. Understanding multicomponent low molecular weight gels from gelators to networks. J Adv Res 2024:S2090-1232(24)00126-7. [PMID: 38570015 DOI: 10.1016/j.jare.2024.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 02/11/2024] [Accepted: 03/29/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND The construction of gels from low molecular weight gelators (LMWG) has been extensively studied in the fields of bio-nanotechnology and other fields. However, the understanding gaps still prevent the prediction of LMWG from the full design of those gel systems. Gels with multicomponent become even more complicated because of the multiple interference effects coexist in the composite gel systems. AIM OF REVIEW This review emphasizes systems view on the understanding of multicomponent low molecular weight gels (MLMWGs), and summarizes recent progress on the construction of desired networks of MLMWGs, including self-sorting and co-assembly, as well as the challenges and approaches to understanding MLMWGs, with the hope that the opportunities from natural products and peptides can speed up the understanding process and close the gaps between the design and prediction of structures. KEY SCIENTIFIC CONCEPTS OF REVIEW This review is focused on three key concepts. Firstly, understanding the complicated multicomponent gels systems requires a systems perspective on MLMWGs. Secondly, several protocols can be applied to control self-sorting and co-assembly behaviors in those multicomponent gels system, including the certain complementary structures, chirality inducing and dynamic control. Thirdly, the discussion is anchored in challenges and strategies of understanding MLMWGs, and some examples are provided for the understanding of multicomponent gels constructed from small natural products and subtle designed short peptides.
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Affiliation(s)
- Liangchun Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China.
| | - Renlin Zheng
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Rongqin Sun
- School of Materials Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
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19
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Alfano C, Fichou Y, Huber K, Weiss M, Spruijt E, Ebbinghaus S, De Luca G, Morando MA, Vetri V, Temussi PA, Pastore A. Molecular Crowding: The History and Development of a Scientific Paradigm. Chem Rev 2024; 124:3186-3219. [PMID: 38466779 PMCID: PMC10979406 DOI: 10.1021/acs.chemrev.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.
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Affiliation(s)
- Caterina Alfano
- Structural
Biology and Biophysics Unit, Fondazione
Ri.MED, 90100 Palermo, Italy
| | - Yann Fichou
- CNRS,
Bordeaux INP, CBMN UMR 5248, IECB, University
of Bordeaux, F-33600 Pessac, France
| | - Klaus Huber
- Department
of Chemistry, University of Paderborn, 33098 Paderborn, Germany
| | - Matthias Weiss
- Experimental
Physics I, Physics of Living Matter, University
of Bayreuth, 95440 Bayreuth, Germany
| | - Evan Spruijt
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Simon Ebbinghaus
- Lehrstuhl
für Biophysikalische Chemie and Research Center Chemical Sciences
and Sustainability, Research Alliance Ruhr, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Giuseppe De Luca
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Valeria Vetri
- Dipartimento
di Fisica e Chimica − Emilio Segrè, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Annalisa Pastore
- King’s
College London, Denmark
Hill Campus, SE5 9RT London, United Kingdom
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20
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Asatryan R, Hudzik J, Swihart M. Intramolecular Catalytic Hydrogen Atom Transfer (CHAT). J Phys Chem A 2024; 128:2169-2190. [PMID: 38451855 DOI: 10.1021/acs.jpca.3c06794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Intramolecular catalysis (IntraCat) is the acceleration of a process at one site of a molecule catalyzed by a functional group in the same molecule; an external agent such as a solvent typically facilitates it. Here, we report a general first-principles-based IntraCat mechanism, which strictly occurs within a single molecule with no coreagent being involved─we call it intramolecular catalytic transfer of hydrogen atoms (CHAT). A reactive part of a molecule (chat catalyst moiety or chat agent, represented by -OOH, -COOH, -SH, -CH2OH, -HPO4, or another bifunctional H-donor/acceptor group) catalyzes an interconversion process, such as keto-enol or amino-imino tautomerization, and cyclization in the same molecule, while being regenerated in the process. It can thus be regarded as an intramolecular version of the intermolecular H atom transfer processes mediated by an external molecular catalyst, e.g., dihydrogen, water, or a carboxylic acid. Earlier, we proposed a general mechanistic systematization of intermolecular processes, illustrated in the simplest case of the H2-mediated reactions classified as dihydrogen catalysis [Asatryan, R.; et al. Catal. Rev.: Sci. Eng., 2014, 56, 403-475]. Following this systematization, the CHAT catalysis belongs to the category of relay transfer of H atoms, albeit in an intramolecular manner. A broader class of intramolecular processes includes all types of H-transfer reactions stimulated by an H-migration, which we call self-catalyzed H atom transfer (SC-HAT). The CHAT mechanism comprises a subset of SC-HAT in which the catalytic moiety is regenerated (i.e., acts as a true catalyst and not a reagent). We provide several characteristic examples of CHAT mechanism based on detailed analysis of the corresponding potential energy surfaces. All such cases showed a dramatically reduced activation barrier relative to the corresponding uncatalyzed H-transfer reactions. For example, we show that CHAT can facilitate long-range H-migration in larger molecules and can occur multiple times in one molecule with multiple interconverting groups. It also facilitates amino-imino tautomerization of unsaturated GABA-analogues and peptides, as well as intramolecular cyclization processes to form heterocycles, e.g., oxygenated rings. CHAT pathways may also explain the pH-dependent increase of mutarotation rate of glucose-6-phosphate demonstrated in pioneering experiments that introduced the classical IntraCat concept. In addition, we identify a ground electronic state CHAT pathway as an alternative to the UV-promoted long-range molecular crane keto-enol conversion with a remarkably low activation energy. To initially assess the possible impact of the new keto-enol conversion pathway on combustion of n-alkanes, we present a detailed kinetic analysis of isomerization and decomposition of pentane-2,4-ketohydroperoxide (2,4-KHP). The results are compared with key alternative reactions, including direct dissociation and Korcek channels (for which a new alkyl group migration channel is also identified), revealing the competitiveness of the CHAT pathway across a range of conditions. Taken together, this work provides insight into a general class of reaction pathways that has not previously being systematically considered and that may occur in a broad range of contexts from combustion to atmospheric chemistry to biochemistry.
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Affiliation(s)
- Rubik Asatryan
- Department of Chemical and Biological Engineering, and Center for Hybrid Rocket Exascale Simulation Technology (CHREST), University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Jason Hudzik
- Department of Chemical and Biological Engineering, and Center for Hybrid Rocket Exascale Simulation Technology (CHREST), University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Mark Swihart
- Department of Chemical and Biological Engineering, and Center for Hybrid Rocket Exascale Simulation Technology (CHREST), University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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21
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Baretta R, Frasconi M. Electrically Powered Dissipative Hydrogel Networks Reveal Transient Stiffness Properties for Out-of-Equilibrium Operations. J Am Chem Soc 2024; 146:7408-7418. [PMID: 38440849 DOI: 10.1021/jacs.3c12653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Living systems use dissipative processes to enable precise spatiotemporal control over various functions, including the transient modulation of the stiffness of tissues, which, however, is challenging to achieve in soft materials. Here, we report a new platform to program hydrogel films with tunable, time-dependent mechanical properties under out-of-equilibrium conditions, powered by electricity. We show that the lifetime of the transient network of a surface-confined hydrogel film can be effectively controlled by programming the generation of an electrochemically oxidized mediator in the presence of a chemical or photoreducing agent in solution. It is, therefore, electrically possible to direct the transient stiffening or softening of the hydrogel film, enabling high modularity of the material functions with precise spatiotemporal control. Temporally controlled operations of the hydrogel films are demonstrated for the on-demand, dose-controlled release of multiple model protein payloads from electrode arrays using the present electrically powered dissipative system. This demonstration of electrically driven transient modulation of the stiffness properties of hydrogel films represents an important step toward the engineering of dissipative materials for developing future biomedical applications that can harness the temporal, adaptive properties of this new class of materials.
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Affiliation(s)
- Roberto Baretta
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Marco Frasconi
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
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22
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Hazra B, Mandal R, Sahu J, Das S, Prasad M, Tarafdar PK. Self-immolation Assisted Morphology Transformation of Prebiotic Lipidated-cationic Amino Acids: Electro-droplet Mediated C-C Coupling Reaction to Synthesize Macromolecules. Chemistry 2024; 30:e202303555. [PMID: 38205907 DOI: 10.1002/chem.202303555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 01/12/2024]
Abstract
Compartmentalization protected biomolecules from the fluctuating environments of early Earth. Although contemporary cells mostly use phospholipid-based bilayer membranes, the utility of non-bilayer compartments was not ruled out during the prebiotic and modern eras. In the present study, we demonstrated the prebiotic synthesis of lipidated cationic amino acid-based amphiphiles [lauryl ester of lysine (LysL); ornithine (OrnL); and 2,4-diamino butyric acid (DabL)] using model dry-down reaction. These amphiphiles self-assemble into micellar membranes. However, the OrnL and DabL-based micelles undergo pH-responsive transformation to lipid droplet-like morphologies, a modelcompartment in the prebiotic Earth. These cationic droplets encapsulated prebiotic molecules (isoprene) and assisted electron transfer reaction to synthesize isoprenoid derivatives at primitive Earth conditions. The self-assembly of prebiotic amphiphiles, their transformation to droplet compartments, and droplet-assisted C-C bond formation reaction might have helped the evolution to synthesize various biomolecules required for the origin of life.
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Affiliation(s)
- Bibhas Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, 741 246, Mohanpur, Nadia, West Bengal, India
| | - Raki Mandal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, 741 246, Mohanpur, Nadia, West Bengal, India
| | - Jayati Sahu
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, 741 246, Mohanpur, Nadia, West Bengal, India
| | - Subrata Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, 741 246, Mohanpur, Nadia, West Bengal, India
| | - Mahesh Prasad
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, 741 246, Mohanpur, Nadia, West Bengal, India
| | - Pradip K Tarafdar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, 741 246, Mohanpur, Nadia, West Bengal, India
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23
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Ghosh S, Baltussen MG, Ivanov NM, Haije R, Jakštaitė M, Zhou T, Huck WTS. Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems. Chem Rev 2024; 124:2553-2582. [PMID: 38476077 PMCID: PMC10941194 DOI: 10.1021/acs.chemrev.3c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
The intricate and complex features of enzymatic reaction networks (ERNs) play a key role in the emergence and sustenance of life. Constructing such networks in vitro enables stepwise build up in complexity and introduces the opportunity to control enzymatic activity using physicochemical stimuli. Rational design and modulation of network motifs enable the engineering of artificial systems with emergent functionalities. Such functional systems are useful for a variety of reasons such as creating new-to-nature dynamic materials, producing value-added chemicals, constructing metabolic modules for synthetic cells, and even enabling molecular computation. In this review, we offer insights into the chemical characteristics of ERNs while also delving into their potential applications and associated challenges.
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Affiliation(s)
- Souvik Ghosh
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Mathieu G. Baltussen
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Nikita M. Ivanov
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Rianne Haije
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Miglė Jakštaitė
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Tao Zhou
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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24
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Morelli C, Faltova L, Capasso Palmiero U, Makasewicz K, Papp M, Jacquat RPB, Pinotsi D, Arosio P. RNA modulates hnRNPA1A amyloid formation mediated by biomolecular condensates. Nat Chem 2024:10.1038/s41557-024-01467-3. [PMID: 38472406 DOI: 10.1038/s41557-024-01467-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
Several RNA binding proteins involved in membraneless organelles can form pathological amyloids associated with neurodegenerative diseases, but the mechanisms of how this aggregation is modulated remain elusive. Here we investigate how heterotypic protein-RNA interactions modulate the condensation and the liquid to amyloid transition of hnRNPA1A, a protein involved in amyothropic lateral sclerosis. In the absence of RNA, formation of condensates promotes hnRNPA1A aggregation and fibrils are localized at the interface of the condensates. Addition of RNA modulates the soluble to amyloid transition of hnRNPA1A according to different pathways depending on RNA/protein stoichiometry. At low RNA concentrations, RNA promotes both condensation and amyloid formation, and the catalytic effect of RNA adds to the role of the interface between the dense and dilute phases. At higher RNA concentrations, condensation is suppressed according to re-entrant phase behaviour but formation of hnRNPA1A amyloids is observed over longer incubation times. Our findings show how heterotypic nucleic acid-protein interactions affect the kinetics and molecular pathways of amyloid formation.
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Affiliation(s)
- Chiara Morelli
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Katarzyna Makasewicz
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Marcell Papp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Raphaël P B Jacquat
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Dorothea Pinotsi
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, Zürich, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland.
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25
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Jaworek MW, Oliva R, Winter R. Enabling High Activation of Glucose-6-Phosphate Dehydrogenase Activity Through Liquid Condensate Formation and Compression. Chemistry 2024:e202400690. [PMID: 38471074 DOI: 10.1002/chem.202400690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/14/2024]
Abstract
Droplet formation via liquid-liquid phase separation is thought to be involved in the regulation of various biological processes, including enzymatic reactions. We investigated a glycolytic enzymatic reaction, the conversion of glucose-6-phosphate to 6-phospho-D-glucono-1,5-lactone with concomitant reduction of NADP+ to NADPH both in the absence and presence of dynamically controlled liquid droplet formation. Here, the nucleotide serves as substrate as well as the scaffold required for the formation of liquid droplets. To further expand the process parameter space, temperature and pressure dependent measurements were performed. Incorporation of the reactants in the liquid droplet phase led to a boost in enzymatic activity, which was most pronounced at medium-high pressures. The crowded environment of the droplet phase induced a marked increase of the affinity of the enzyme and substrate. An increase in turnover number in the droplet phase at high pressure contributed to a further strong increase in catalytic efficiency. Enzyme systems that are dynamically coupled to liquid condensate formation may be the key to deciphering many biochemical reactions. Expanding the process parameter space by adjusting temperature and pressure conditions can be a means to further increase the efficiency of industrial enzyme utilization and help uncover regulatory mechanisms adopted by extremophiles.
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Affiliation(s)
- Michel W Jaworek
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126, Napoli, Italy
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
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26
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Ray S, Buell AK. Emerging experimental methods to study the thermodynamics of biomolecular condensate formation. J Chem Phys 2024; 160:091001. [PMID: 38445729 DOI: 10.1063/5.0190160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024] Open
Abstract
The formation of biomolecular condensates in vivo is increasingly recognized to underlie a multitude of crucial cellular functions. Furthermore, the evolution of highly dynamic protein condensates into progressively less reversible assemblies is thought to be involved in a variety of disorders, from cancer over neurodegeneration to rare genetic disorders. There is an increasing need for efficient experimental methods to characterize the thermodynamics of condensate formation and that can be used in screening campaigns to identify and rationally design condensate modifying compounds. Theoretical advances in the field are also identifying the key parameters that need to be measured in order to obtain a comprehensive understanding of the underlying interactions and driving forces. Here, we review recent progress in the development of efficient and quantitative experimental methods to study the driving forces behind and the temporal evolution of biomolecular condensates.
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Affiliation(s)
- Soumik Ray
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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27
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Williams ER, Ruff CX, Stefik M. Unimer suppression enables supersaturated homopolymer swollen micelles with long-term stability after glassy entrapment. Soft Matter 2024; 20:2288-2300. [PMID: 38358107 DOI: 10.1039/d3sm01754k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Micelle sizes are critical for a range of applications where the simple ability to adjust and lock in specific stable sizes has remained largely elusive. While micelle swelling agents are well-known, their dynamic re-equilibration in solution implies limited stability. Here, a non-equilibrium processing sequence is studied where supersaturated homopolymer swelling is combined with glassy-core ("persistent") micelles. This path-dependent process was found to sensitively depend on unimer concentration as revealed by DLS, SAXS, and TEM analysis. Here, lower-selectivity solvent combinations led to the formation of unimer-homopolymer aggregates and eventual precipitation, reminiscent of anomalous micellization. In contrast, higher-selectivity solvents enabled supersaturated homopolymer loadings favored by rapid homopolymer insertion. The demonstrated ∼40-130 nm core-size tuning exceeded prior equilibrium demonstrations and subsequent core-vitrification enabled size persistence beyond 6 months. Lastly, the linear change in micelle diameter with homopolymer addition was found to correlate with a plateau in the interfacial area per copolymer chain.
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Affiliation(s)
- Eric R Williams
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208.
| | - Christian X Ruff
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208.
| | - Morgan Stefik
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208.
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28
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Bayram I, Parra-Escudero C, Decker EA, Lu J. Mathematical Modeling of Alpha-Tocopherol Early Degradation Kinetics to Predict the Shelf-Life of Bulk Oils. J Agric Food Chem 2024; 72:4939-4946. [PMID: 38401060 DOI: 10.1021/acs.jafc.3c08272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2024]
Abstract
The kinetics of lipid oxidation includes a lag phase followed by an exponential increase in oxidation products, which cause rancidity. Current models focus on the slope of this exponential curve for shelf-life estimation, which still requires the measurement of full oxidation kinetics. In this paper, we analyzed the formation of lipid oxidation products in stripped soybean oil containing different levels of α-tocopherol. The lag phases of lipid hydroperoxides and headspace hexanal formation were found to have a strong positive correlation with the α-tocopherol depletion time. We propose that the kinetics of antioxidant (α-tocopherol) depletion occur during the lag phase and could serve as an early shelf-life indicator. Our results showed that α-tocopherol degradation can be described by Weibull kinetics over a wide range of initial concentrations. Furthermore, we conducted in silico investigations using Monte Carlo simulations to critically evaluate the feasibility and sensitivity of the shelf-life prediction using early antioxidant degradation kinetics. Our results revealed that the shelf life of soybean oil may be accurately predicted as early as 20% of the overall shelf life. This innovative approach provides a more efficient and faster assessment of shelf life, ultimately reducing waste and enhancing product quality.
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Affiliation(s)
- Ipek Bayram
- Department of Food Science, University of Massachusetts, Chenoweth Laboratory, Amherst, 01003 Massachusetts, United States
| | - Carlos Parra-Escudero
- Department of Food Science, University of Massachusetts, Chenoweth Laboratory, Amherst, 01003 Massachusetts, United States
| | - Eric A Decker
- Department of Food Science, University of Massachusetts, Chenoweth Laboratory, Amherst, 01003 Massachusetts, United States
| | - Jiakai Lu
- Department of Food Science, University of Massachusetts, Chenoweth Laboratory, Amherst, 01003 Massachusetts, United States
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29
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Nguindjel AD, Franssen SCM, Korevaar PA. Reconfigurable Droplet-Droplet Communication Mediated by Photochemical Marangoni Flows. J Am Chem Soc 2024; 146:6006-6015. [PMID: 38391388 PMCID: PMC10921405 DOI: 10.1021/jacs.3c12882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/19/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Droplets are attractive building blocks for dynamic matter that organizes into adaptive structures. Communication among collectively operating droplets opens untapped potential in settings that vary from sensing, optics, protocells, computing, or adaptive matter. Inspired by the transmission of signals among decentralized units in slime mold Physarum polycephalum, we introduce a combination of surfactants, self-assembly, and photochemistry to establish chemical signal transfer among droplets. To connect droplets that float at an air-water interface, surfactant triethylene glycol monododecylether (C12E3) is used for its ability to self-assemble into wires called myelins. We show how the trajectory of these myelins can be directed toward selected photoactive droplets upon UV exposure. To this end, we developed a strategy for photocontrolled Marangoni flow, which comprises (1) the liquid crystalline coating formed at the surface of an oleic acid/sodium oleate (OA/NaO) droplet when in contact with water, (2) a photoacid generator that protonates sodium oleate upon UV exposure and therefore disintegrates the coating, and (3) the surface tension gradient that is generated upon depletion of the surfactant from the air-water interface by the uncoated droplet. Therefore, localized UV exposure of selected OA/NaO droplets results in attraction of the myelins such that they establish reconfigurable connections that self-organize among the C12E3 and OA/NaO droplets. As an example of communication, we demonstrate how the myelins transfer fluorescent dyes, which are selectively delivered in the droplet interior upon photochemical regulation of the liquid crystalline coating.
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Affiliation(s)
- Anne-Déborah
C. Nguindjel
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Stan C. M. Franssen
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Peter A. Korevaar
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
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30
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Green CM, Sementa D, Mathur D, Melinger JS, Deshpande P, Elbaum-Garfinkle S, Medintz IL, Ulijn RV, Díaz SA. Sequestration within peptide coacervates improves the fluorescence intensity, kinetics, and limits of detection of dye-based DNA biosensors. Commun Chem 2024; 7:49. [PMID: 38424154 PMCID: PMC10904739 DOI: 10.1038/s42004-024-01124-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Peptide-based liquid-liquid phase separated domains, or coacervates, are a biomaterial gaining new interest due to their exciting potential in fields ranging from biosensing to drug delivery. In this study, we demonstrate that coacervates provide a simple and biocompatible medium to improve nucleic acid biosensors through the sequestration of both the biosensor and target strands within the coacervate, thereby increasing their local concentration. Using the well-established polyarginine (R9) - ATP coacervate system and an energy transfer-based DNA molecular beacon we observed three key improvements: i) a greater than 20-fold reduction of the limit of detection within coacervates when compared to control buffer solutions; ii) an increase in the kinetics, equilibrium was reached more than 4-times faster in coacervates; and iii) enhancement in the dye fluorescent quantum yields within the coacervates, resulting in greater signal-to-noise. The observed benefits translate into coacervates greatly improving bioassay functionality.
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Affiliation(s)
- Christopher M Green
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Deborah Sementa
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, NY, 10031, USA
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Joseph S Melinger
- Electronics Sciences and Technology Division Code 6816, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Priyasha Deshpande
- Structural Biology Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, NY, 10031, USA
| | - Shana Elbaum-Garfinkle
- Structural Biology Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, NY, 10031, USA
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Rein V Ulijn
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, NY, 10031, USA
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
- Department of Chemistry Hunter College, City University of New York, New York, NY, 10065, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA.
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31
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Stan-Bernhardt A, Glinkina L, Hulm A, Ochsenfeld C. Exploring Chemical Space Using Ab Initio Hyperreactor Dynamics. ACS Cent Sci 2024; 10:302-314. [PMID: 38435517 PMCID: PMC10906254 DOI: 10.1021/acscentsci.3c01403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 03/05/2024]
Abstract
In recent years, first-principles exploration of chemical reaction space has provided valuable insights into intricate reaction networks. Here, we introduce ab initio hyperreactor dynamics, which enables rapid screening of the accessible chemical space from a given set of initial molecular species, predicting new synthetic routes that can potentially guide subsequent experimental studies. For this purpose, different hyperdynamics derived bias potentials are applied along with pressure-inducing spherical confinement of the molecular system in ab initio molecular dynamics simulations to efficiently enhance reactivity under mild conditions. To showcase the advantages and flexibility of the hyperreactor approach, we present a systematic study of the method's parameters on a HCN toy model and apply it to a recently introduced experimental model for the prebiotic formation of glycinal and acetamide in interstellar ices, which yields results in line with experimental findings. In addition, we show how the developed framework enables the study of complicated transitions like the first step of a nonenzymatic DNA nucleoside synthesis in an aqueous environment, where the molecular fragmentation problem of earlier nanoreactor approaches is avoided.
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Affiliation(s)
- Alexandra Stan-Bernhardt
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5, D-81377 München, Germany
| | - Liubov Glinkina
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5, D-81377 München, Germany
| | - Andreas Hulm
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5, D-81377 München, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
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32
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Wang T, Ménard-Moyon C, Bianco A. Structural Transformation of Coassembled Fmoc-Protected Aromatic Amino Acids to Nanoparticles. ACS Appl Mater Interfaces 2024; 16:10532-10544. [PMID: 38367060 DOI: 10.1021/acsami.3c18463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Materials made of assembled biomolecules such as amino acids have drawn much attention during the past decades. Nevertheless, research on the relationship between the chemical structure of building block molecules, supramolecular interactions, and self-assembled structures is still necessary. Herein, the self-assembly and the coassembly of fluorenylmethoxycarbonyl (Fmoc)-protected aromatic amino acids (tyrosine, tryptophan, and phenylalanine) were studied. The individual self-assembly of Fmoc-Tyr-OH and Fmoc-Phe-OH in water formed nanofibers, while Fmoc-Trp-OH self-assembled into nanoparticles. Moreover, when Fmoc-Tyr-OH or Fmoc-Phe-OH was coassembled with Fmoc-Trp-OH, the nanofibers were transformed into nanoparticles. UV-vis spectroscopy, Fourier transform infrared spectroscopy, and fluorescence spectroscopy were used to investigate the supramolecular interactions leading to the self-assembled architectures. π-π stacking and hydrogen bonding were the main driving forces leading to the self-assembly of Fmoc-Tyr-OH and Fmoc-Phe-OH forming nanofibers. Further, a mechanism involving a two-step coassembly process is proposed based on nucleation and elongation/growth to explain the structural transformation. Fmoc-Trp-OH acted as a fiber inhibitor to alter the molecular interactions in the Fmoc-Tyr-OH or Fmoc-Phe-OH self-assembled structures during the coassembly process, locking the coassembly in the nucleation step and preventing the formation of nanofibers. This structural transformation is useful for extending the application of amino acid self- or coassembled materials in different fields. For example, the amino acids forming nanofibers could be applied for tissue engineering, while they could be exploited as drug nanocarriers when they form nanoparticles.
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Affiliation(s)
- Tengfei Wang
- CNRS, Immunology, Immunopathology and Therapeutic Chemistry, UPR 3572, University of Strasbourg, ISIS, 67000 Strasbourg, France
| | - Cécilia Ménard-Moyon
- CNRS, Immunology, Immunopathology and Therapeutic Chemistry, UPR 3572, University of Strasbourg, ISIS, 67000 Strasbourg, France
| | - Alberto Bianco
- CNRS, Immunology, Immunopathology and Therapeutic Chemistry, UPR 3572, University of Strasbourg, ISIS, 67000 Strasbourg, France
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33
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Kojima T, Noguchi Y, Terasaka K, Asakura K, Banno T. Engineering pH-Responsive, Self-Healing Vesicle-Type Artificial Tissues with Higher-Order Cooperative Functionalities. Small 2024:e2311255. [PMID: 38415816 DOI: 10.1002/smll.202311255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/30/2024] [Indexed: 02/29/2024]
Abstract
Multicellular organisms demonstrate a hierarchical organization where multiple cells collectively form tissues, thereby enabling higher-order cooperative functionalities beyond the capabilities of individual cells. Drawing inspiration from this biological organization, assemblies of multiple protocells are developed to create novel functional materials with emergent higher-order cooperative functionalities. This paper presents new artificial tissues derived from multiple vesicles, which serve as protocellular models. These tissues are formed and manipulated through non-covalent interactions triggered by a salt bridge. Exhibiting pH-sensitive reversible formation and destruction under neutral conditions, these artificial vesicle tissues demonstrate three distinct higher-order cooperative functionalities: transportation of large cargoes, photo-induced contractions, and enhanced survivability against external threats. The rapid assembly and disassembly of these artificial tissues in response to pH variations enable controlled mechanical task performance. Additionally, the self-healing property of these artificial tissues indicates robustness against external mechanical damage. The research suggests that these vesicles can detect specific pH environments and spontaneously assemble into artificial tissues with advanced functionalities. This leads to the possibility of developing intelligent materials with high environmental specificity, particularly for applications in soft robotics.
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Affiliation(s)
- Tomoya Kojima
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Yutaro Noguchi
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Koichi Terasaka
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Kouichi Asakura
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Taisuke Banno
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
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34
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Sakref Y, Rivoire O. On the exclusion of exponential autocatalysts by sub-exponential autocatalysts. J Theor Biol 2024; 579:111714. [PMID: 38128753 DOI: 10.1016/j.jtbi.2023.111714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Selection among autocatalytic species fundamentally depends on their growth law: exponential species, whose number of copies grows exponentially, are mutually exclusive, while sub-exponential ones, whose number of copies grows polynomially, can coexist. Here we consider competitions between autocatalytic species with different growth laws and make the simple yet counterintuitive observation that sub-exponential species can exclude exponential ones while the reverse is, in principle, impossible. This observation has implications for scenarios pertaining to the emergence of natural selection.
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Affiliation(s)
- Yann Sakref
- Gulliver, CNRS, ESPCI Paris, Université PSL, 75005 Paris, France.
| | - Olivier Rivoire
- Gulliver, CNRS, ESPCI Paris, Université PSL, 75005 Paris, France.
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35
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Nan M, Guo K, Jia T, Wang G, Liu S. Novel Acid-Driven Bioinspired Self-Resettable Bilayer Hydrogel Actuator Mimicking Natural Muscles. ACS Appl Mater Interfaces 2024; 16:9224-9230. [PMID: 38335011 DOI: 10.1021/acsami.3c16500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Soft robots have great potential applications in manufacturing, disaster rescue, medical treatment, etc. Artificial muscle is one of the most important components of a soft robot. In previous years, hydrogel actuators that can be controllably deformed by the stimuli of external signals have been developed as good candidates for muscle-like materials. In this article, we successfully prepared a chemical fuel-driven self-resettable bilayer hydrogel actuator mimicking natural muscles with the aid of a new negative feedback reaction network. The actuator can temporarily deform upon the addition of H+ (chemical fuel). Subsequently, H+ accelerated the reaction between BrO3- and Fe(CN)64-, which consume H+. It resulted in the spontaneous recovery of the pH as well as the shape of the actuator. Such an actuator exhibits a great similarity with natural muscles in actuation mechanisms and automaticity in the manipulation compared to the widely reported stimuli-responsive hydrogel actuators. This illustrates that fuel-driven self-resettable hydrogel is a promising dynamic material for mimicking the functions of living creatures.
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Affiliation(s)
- Mengmeng Nan
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, Heilongjiang 150040 People's Republic of China
| | - Kangle Guo
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, Heilongjiang 150040 People's Republic of China
| | - Tao Jia
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, Heilongjiang 150040 People's Republic of China
| | - Guangtong Wang
- School of Medicine and Health, Harbin Institute of Technology, Harbin, Heilongjiang 150080, People's Republic of China
| | - Shaoqin Liu
- School of Medicine and Health, Harbin Institute of Technology, Harbin, Heilongjiang 150080, People's Republic of China
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36
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Todd ZR, Wogan NF, Catling DC. Favorable Environments for the Formation of Ferrocyanide, a Potentially Critical Reagent for Origins of Life. ACS Earth Space Chem 2024; 8:221-229. [PMID: 38379837 PMCID: PMC10875668 DOI: 10.1021/acsearthspacechem.3c00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 02/22/2024]
Abstract
Cyanide and its derivatives play important roles in prebiotic chemistry through a variety of possible mechanisms. In particular, cyanide has been shown to allow for the synthesis of ribonucleotides and amino acids. Although dissolved hydrogen cyanide can be lost as a gas or undergo hydrolysis reactions, cyanide can also potentially be stored and stockpiled as ferrocyanide (Fe(CN)6-4), which is more stable. Furthermore, ferrocyanide aids in some prebiotic synthetic reactions. Here, we investigate the formation rates and yields of ferrocyanide as a function of various environmental parameters, such as the pH, temperature, and concentration. We find that ferrocyanide formation rates and yields are optimal at slightly alkaline conditions (pH 8-9) and moderate temperatures (≈20-30 °C). Given the wide range of possible lake environments likely available on early Earth, our results help to constrain the environmental conditions that would favor cyanide- and ferrocyanide-based prebiotic chemistries. We construct lake box models and find that ferrocyanide may be able to form and reach significant concentrations for prebiotic chemistry on the time scale of years under favorable conditions.
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Affiliation(s)
- Zoe R. Todd
- Department
of Earth and Space Sciences, University
of Washington, Seattle, Washington 98195, United States
- Departments
of Chemistry and Astronomy, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Nicholas F. Wogan
- Department
of Earth and Space Sciences, University
of Washington, Seattle, Washington 98195, United States
| | - David C. Catling
- Department
of Earth and Space Sciences, University
of Washington, Seattle, Washington 98195, United States
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37
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Sementilli A, Rengifo RF, Li W, Stewart AM, Stewart KL, Twahir U, Kim Y, Yue J, Mehta AK, Shearer J, Warncke K, Lynn DG. Engineering Synthetic Electron Transfer Chains from Metallopeptide Membranes. Inorg Chem 2024; 63:2899-2908. [PMID: 38127051 PMCID: PMC10865380 DOI: 10.1021/acs.inorgchem.3c02861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
The energetic and geometric features enabling redox chemistry across the copper cupredoxin fold contain key components of electron transfer chains (ETC), which have been extended here by templating the cross-β bilayer assembly of a synthetic nonapeptide, HHQALVFFA-NH2 (K16A), with copper ions. Similar to ETC cupredoxin plastocyanin, these assemblies contain copper sites with blue-shifted (λmax 573 nm) electronic transitions and strongly oxidizing reduction potentials. Electron spin echo envelope modulation and X-ray absorption spectroscopies define square planar Cu(II) sites containing a single His ligand. Restrained molecular dynamics of the cross-β peptide bilayer architecture support metal ion coordination stabilizing the leaflet interface and indicate that the relatively high reduction potential is not simply the result of distorted coordination geometry (entasis). Cyclic voltammetry (CV) supports a charge-hopping mechanism across multiple copper centers placed 10-12 Å apart within the assembled peptide leaflet interface. This metal-templated scaffold accordingly captures the electron shuttle and cupredoxin functionality in a peptide membrane-localized electron transport chain.
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Affiliation(s)
- Anthony Sementilli
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Rolando F. Rengifo
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Wei Li
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Andrew M. Stewart
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Katie L. Stewart
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Umar Twahir
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Youngsun Kim
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Jipeng Yue
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Anil K. Mehta
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Jason Shearer
- Department
of Chemistry, Trinity University, San Antonio, Texas 78212, United States
| | - Kurt Warncke
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - David G. Lynn
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
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38
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Sommerfeld IK, Malyaran H, Neuss S, Demco DE, Pich A. Multiresponsive Core-Shell Microgels Functionalized by Nitrilotriacetic Acid. Biomacromolecules 2024; 25:903-923. [PMID: 38170471 DOI: 10.1021/acs.biomac.3c01056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Stimuli-responsive microgels with ionizable functional groups offer versatile applications, e.g., by the uptake of oppositely charged metal ions or guest molecules such as drugs, dyes, or proteins. Furthermore, the incorporation of carboxylic groups enhances mucoadhesive properties, crucial for various drug delivery applications. In this work, we successfully synthesized poly{N-vinylcaprolactam-2,2'-[(5-acrylamido-1-carboxypentyl)azanediyl]diacetic acid} [p(VCL/NTAaa)] microgels containing varying amounts of nitrilotriacetic acid (NTA) using precipitation polymerization. We performed fundamental characterization by infrared (IR) spectroscopy and dynamic and electrophoretic light scattering. Despite their potential multiresponsiveness, prior studies on NTA-functionalized microgels lack in-depth analysis of their stimuli-responsive behavior. This work addresses this gap by assessing the microgel responsiveness to temperature, ionic strength, and pH. Morphological investigations were performed via NMR relaxometry, nanoscale imaging (AFM and SEM), and reaction calorimetry. Finally, we explored the potential application of the microgels by conducting cytocompatibility experiments and demonstrating the immobilization of the model protein cytochrome c in the microgels.
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Affiliation(s)
- Isabel K Sommerfeld
- Functional and Interactive Polymers, Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
- DWI─Leibniz-Institute for Interactive Materials e.V., Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Hanna Malyaran
- Interdisciplinary Center for Clinical Research (IZKF), RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany
- Helmholtz Institute for Biomedical Engineering, BioInterface Group, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany
- Department of Orthodontics, University Hospital of RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Sabine Neuss
- Helmholtz Institute for Biomedical Engineering, BioInterface Group, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany
- Institute of Pathology, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Dan E Demco
- DWI─Leibniz-Institute for Interactive Materials e.V., Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Andrij Pich
- Functional and Interactive Polymers, Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
- DWI─Leibniz-Institute for Interactive Materials e.V., Forckenbeckstraße 50, 52074 Aachen, Germany
- Aachen Maastricht Institute for Biobased Materials (AMIBM), Maastricht University, Brightlands Chemelot Campus, Urmonderbaan 22, 6167 RD Geleen, The Netherlands
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39
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Song Y, Selmani S, Freites JA, Guan Z, Tobias DJ. Multiscale Molecular Dynamics Simulations of an Active Self-Assembling Material. J Phys Chem B 2024; 128:1266-1274. [PMID: 38290526 DOI: 10.1021/acs.jpcb.3c06572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Inspired by the adaptability observed in biological materials, self-assembly processes have attracted significant interest for their potential to yield novel materials with unique properties. However, experimental methods have often fallen short in capturing the molecular details of the assembly process. In this study, we employ a multiscale molecular dynamics simulation approach, complemented by NMR quantification, to investigate the mechanism of self-assembly in a redox-fueled bioinspired system. Contrary to conventional assumptions, we have uncovered a significant role played by the monomer precursor in the assembly process, with its presence varying with concentration and the extent of conversion of the monomer to the dimer. Experimental confirmation through NMR quantification underscores the concentration-dependent incorporation of monomers into the fibrous structures. Furthermore, our simulations also shed light on the diverse intermolecular interactions, including T-shaped and parallel π stacking, as well as hydrogen bonds, in stabilizing the aggregates. Overall, the open conformation of the dimer is preferred within these aggregates. However, inside the aggregates, the distribution of conformations shifts slightly to the closed conformation compared to on the surface. These findings contribute to the growing field of bioinspired materials science by providing valuable mechanistic and structural insights to guide the design and development of self-assembling materials with biomimetic functionalities.
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Affiliation(s)
- Yuanming Song
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Center for Complex and Active Materials, University of California, Irvine, Irvine, California 92697, United States
| | - Serxho Selmani
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Center for Complex and Active Materials, University of California, Irvine, Irvine, California 92697, United States
| | - J Alfredo Freites
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Zhibin Guan
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Center for Complex and Active Materials, University of California, Irvine, Irvine, California 92697, United States
| | - Douglas J Tobias
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Center for Complex and Active Materials, University of California, Irvine, Irvine, California 92697, United States
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40
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Fu H, Cao N, Zeng W, Liao M, Yao S, Zhou J, Zhang W. Pumping Small Molecules Selectively through an Energy-Assisted Assembling Process at Nonequilibrium States. J Am Chem Soc 2024; 146:3323-3330. [PMID: 38273768 DOI: 10.1021/jacs.3c12228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
In living organisms, precise control over the spatial and temporal distribution of molecules, including pheromones, is crucial. This level of control is equally important for the development of artificial active materials. In this study, we successfully controlled the distribution of small molecules in the system at nonequilibrium states by actively transporting them, even against the apparent concentration gradient, with high selectivity. As a demonstration, in the aqueous solution of acid orange (AO7) and TMC10COOH, we found that AO7 molecules can coassemble with transient anhydride (TMC10CO)2O to form larger assemblies in the presence of chemical fuel 1-ethyl-3-(3-(dimethylamino)propyl) carbodiimide hydrochloride (EDC). This led to a decrease in local free AO7 concentration and caused AO7 molecules from other locations in the solution to move toward the assemblies. Consequently, AO7 accumulates at the location where EDC was injected. By continuously injecting EDC, we could maintain a stable high value of the apparent AO7 concentration at the injection point. We also observed that this process which operated at nonequilibrium states exhibited high selectivity.
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Affiliation(s)
- Huimin Fu
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, P. R. China
| | - Nengjie Cao
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, P. R. China
| | - Wang Zeng
- National Centre for Inorganic Mass Spectrometry in Shanghai, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050, P. R. China
| | - Min Liao
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, P. R. China
| | - Shenglin Yao
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, P. R. China
| | - Jiajia Zhou
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, P. R. China
| | - Wei Zhang
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, P. R. China
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41
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Kufner CL, Crucilla S, Ding D, Stadlbauer P, Šponer J, Szostak JW, Sasselov DD, Szabla R. Photoinduced charge separation and DNA self-repair depend on sequence directionality and stacking pattern. Chem Sci 2024; 15:2158-2166. [PMID: 38332835 PMCID: PMC10848779 DOI: 10.1039/d3sc04971j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/27/2023] [Indexed: 02/10/2024] Open
Abstract
Charge separation is one of the most common consequences of the absorption of UV light by DNA. Recently, it has been shown that this process can enable efficient self-repair of cyclobutane pyrimidine dimers (CPDs) in specific short DNA oligomers such as the GAT[double bond, length as m-dash]T sequence. The mechanism was characterized as sequential electron transfer through the nucleobase stack which is controlled by the redox potentials of nucleobases and their sequence. Here, we demonstrate that the inverse sequence T[double bond, length as m-dash]TAG promotes self-repair with higher quantum yields (0.58 ± 0.23%) than GAT[double bond, length as m-dash]T (0.44 ± 0.18%) in a comparative study involving UV-irradiation experiments. After extended exposure to UV irradiation, a photostationary equilibrium between self-repair and damage formation is reached at 33 ± 13% for GAT[double bond, length as m-dash]T and at 40 ± 16% for T[double bond, length as m-dash]TAG, which corresponds to the maximum total yield of self-repair. Molecular dynamics and quantum mechanics/molecular mechanics (QM/MM) simulations allowed us to assign this disparity to better stacking overlap between the G and A bases, which lowers the energies of the key A-˙G+˙ charge transfer state in the dominant conformers of the T[double bond, length as m-dash]TAG tetramer. These conformational differences also hinder alternative photorelaxation pathways of the T[double bond, length as m-dash]TAG tetranucleotide, which otherwise compete with the sequential electron transfer mechanism responsible for CPD self-repair. Overall, we demonstrate that photoinduced electron transfer is strongly dependent on conformation and the availability of alternative photodeactivation mechanisms. This knowledge can be used in the identification and prediction of canonical and modified DNA sequences exhibiting efficient electron transfer. It also further contributes to our understanding of DNA self-repair and its potential role in the photochemical selection of the most photostable sequences on the early Earth.
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Affiliation(s)
- Corinna L Kufner
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics 60 Garden Street Cambridge MA 02138 USA
| | - Sarah Crucilla
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics 60 Garden Street Cambridge MA 02138 USA
- Department of Earth and Planetary Sciences, Harvard University Cambridge Massachusetts 02138 USA
| | - Dian Ding
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital Boston Massachusetts 02114 USA
- Department of Chemistry and Chemical Biology, Harvard University Cambridge Massachusetts 02138 USA
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61200 Brno Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc Slechtitelu 241/27, 783 71, Olomouc - Holice Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61200 Brno Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc Slechtitelu 241/27, 783 71, Olomouc - Holice Czech Republic
| | - Jack W Szostak
- Howard Hughes Medical Institute, The University of Chicago Chicago IL 60637 USA
- Department of Chemistry, The University of Chicago Chicago Illinois 60637 USA
| | - Dimitar D Sasselov
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics 60 Garden Street Cambridge MA 02138 USA
| | - Rafał Szabla
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 Wrocław 50-370 Poland
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42
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Szyszka TN, Andreas MP, Lie F, Miller LM, Adamson LSR, Fatehi F, Twarock R, Draper BE, Jarrold MF, Giessen TW, Lau YH. Point mutation in a virus-like capsid drives symmetry reduction to form tetrahedral cages. bioRxiv 2024:2024.02.05.579038. [PMID: 38370832 PMCID: PMC10871247 DOI: 10.1101/2024.02.05.579038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Protein capsids are a widespread form of compartmentalisation in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximises the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of novel symmetry-reduced structures. Starting with the encapsulin from Myxococcus xanthus, a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryo-EM, we determine the structures of a precedented 60-mer icosahedral assembly and an unprecedented 36-mer tetrahedron that features significant geometric rearrangements around a novel interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple point mutation to various amino acids, and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent the first example of tetrahedral geometry across all characterised encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in protein sequence.
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Affiliation(s)
- Taylor N Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Felicia Lie
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Lohra M Miller
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Lachlan S R Adamson
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Farzad Fatehi
- Department of Mathematics, University of York, York, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Reidun Twarock
- Department of Mathematics, University of York, York, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - Benjamin E Draper
- Megadalton Solutions Inc., 3750 E Bluebird Ln, Bloomington, IN 47401, USA
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW 2006, Australia
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43
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Bistervels MH, Hoogendoorn NT, Kamp M, Schoenmaker H, Brouwer AM, Noorduin WL. Light-controlled morphological development of self-organizing bioinspired nanocomposites. Nanoscale 2024; 16:2310-2317. [PMID: 38230748 PMCID: PMC10832358 DOI: 10.1039/d3nr05828j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/09/2024] [Indexed: 01/18/2024]
Abstract
Nature's intricate biominerals inspire fundamental questions on self-organization and guide innovations towards functional materials. While advances in synthetic self-organization have enabled many levels of control, generating complex shapes remains difficult. Specifically, controlling morphologies during formation at the single micro/nanostructure level is the key challenge. Here, we steer the self-organization of barium carbonate nanocrystals and amorphous silica into complex nanocomposite morphologies by photogeneration of carbon dioxide (CO2) under ultraviolet (UV) light. Using modulations in the UV light intensity, we select the growth mode of the self-organization process inwards or outwards to form helical and coral-like morphologies respectively. The spatiotemporal control over CO2 photogeneration allows formation of different morphologies on pre-assigned locations, switching between different growth modes-to form for instance a coral on top of a helix or vice versa, and subtle sculpting and patterning of the nanocomposites during formation. These findings advance the understanding of these versatile self-organization processes and offer new prospects for tailored designs of functional materials using photochemically driven self-organization.
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Affiliation(s)
| | | | - Marko Kamp
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands.
| | | | - Albert M Brouwer
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam 1090 GD, The Netherlands
| | - Willem L Noorduin
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands.
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam 1090 GD, The Netherlands
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44
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Maffeis V, Heuberger L, Nikoletić A, Schoenenberger C, Palivan CG. Synthetic Cells Revisited: Artificial Cells Construction Using Polymeric Building Blocks. Adv Sci (Weinh) 2024; 11:e2305837. [PMID: 37984885 PMCID: PMC10885666 DOI: 10.1002/advs.202305837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/06/2023] [Indexed: 11/22/2023]
Abstract
The exponential growth of research on artificial cells and organelles underscores their potential as tools to advance the understanding of fundamental biological processes. The bottom-up construction from a variety of building blocks at the micro- and nanoscale, in combination with biomolecules is key to developing artificial cells. In this review, artificial cells are focused upon based on compartments where polymers are the main constituent of the assembly. Polymers are of particular interest due to their incredible chemical variety and the advantage of tuning the properties and functionality of their assemblies. First, the architectures of micro- and nanoscale polymer assemblies are introduced and then their usage as building blocks is elaborated upon. Different membrane-bound and membrane-less compartments and supramolecular structures and how they combine into advanced synthetic cells are presented. Then, the functional aspects are explored, addressing how artificial organelles in giant compartments mimic cellular processes. Finally, how artificial cells communicate with their surrounding and each other such as to adapt to an ever-changing environment and achieve collective behavior as a steppingstone toward artificial tissues, is taken a look at. Engineering artificial cells with highly controllable and programmable features open new avenues for the development of sophisticated multifunctional systems.
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Affiliation(s)
- Viviana Maffeis
- Department of ChemistryUniversity of BaselMattenstrasse 22BaselCH‐4002Switzerland
- NCCR‐Molecular Systems EngineeringBPR 1095, Mattenstrasse 24aBaselCH‐4058Switzerland
| | - Lukas Heuberger
- Department of ChemistryUniversity of BaselMattenstrasse 22BaselCH‐4002Switzerland
| | - Anamarija Nikoletić
- Department of ChemistryUniversity of BaselMattenstrasse 22BaselCH‐4002Switzerland
- Swiss Nanoscience InstituteUniversity of BaselKlingelbergstrasse 82BaselCH‐4056Switzerland
| | | | - Cornelia G. Palivan
- Department of ChemistryUniversity of BaselMattenstrasse 22BaselCH‐4002Switzerland
- NCCR‐Molecular Systems EngineeringBPR 1095, Mattenstrasse 24aBaselCH‐4058Switzerland
- Swiss Nanoscience InstituteUniversity of BaselKlingelbergstrasse 82BaselCH‐4056Switzerland
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45
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Puza F, Thiel MC, Wagner Y, Marx M, Motz C, Lienkamp K. Polymer Hydrogel Sheets with Perpendicular Cross-Linking Gradient: Non-Monotonic Actuation and Ion-Specific Effects on the Actuation Kinetics. Macromol Rapid Commun 2024; 45:e2300539. [PMID: 37985952 DOI: 10.1002/marc.202300539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/11/2023] [Indexed: 11/22/2023]
Abstract
Non-monotonous actuation, that is, different kinds of motion in response to a single stimulus, is observed in some natural materials but difficult to implement in synthetic systems. Herein, polymer hydrogel sheets made from polyacrylamide (PAAm) or poly(dimethylacrylamide) (PDMAA) with a cross-linking gradient along the sheet thickness are reported. These are obtained by thermally initiated free radical polymerization using a specially designed Teflon mold with a glass lid. The resulting PAAm hydrogels undergo non-monotonous actuation (rolling into a tube and re-opening) when exposed to aqueous media as a single external stimulus. Their actuation kinetics is tuned with anions that have specific ion effects in their interaction with the surrounding solvent and the polymer itself: structure-breaking chloride enhances the hydration of the polymer backbone, structure-making sulfate decreases it, and is thus slowing down the actuation kinetics of the PAAm hydrogels. The PDMAA gel rolls up instantaneously in aqueous NaCl and only re-opens after 24 h. PDMAA actuation in aqueous Na2 SO4 is only moderate as the gel did not swell in that solvent. Bilayer hydrogels made from PAAm and PDMAA (without gradient) show monotonic actuation, closing in NaCl solution and re-opening in Na2 SO4 .
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Affiliation(s)
- Fatih Puza
- Professur für Polymerwerkstoffe, Fachrichtung Materialwissenschaft und Werkstofftechnik, Universität des Saarlandes, Campus, 66123, Saarbrücken, Germany
| | - Marc Christopher Thiel
- Professur für Polymerwerkstoffe, Fachrichtung Materialwissenschaft und Werkstofftechnik, Universität des Saarlandes, Campus, 66123, Saarbrücken, Germany
| | - Yannic Wagner
- Professur für Polymerwerkstoffe, Fachrichtung Materialwissenschaft und Werkstofftechnik, Universität des Saarlandes, Campus, 66123, Saarbrücken, Germany
| | - Michael Marx
- Professur für Experimentelle Methodik der Werkstoffwissenschaften, Fachrichtung Materialwissenschaft und Werkstofftechnik, Universität des Saarlandes, Campus, 66123, Saarbrücken, Germany
| | - Christian Motz
- Professur für Experimentelle Methodik der Werkstoffwissenschaften, Fachrichtung Materialwissenschaft und Werkstofftechnik, Universität des Saarlandes, Campus, 66123, Saarbrücken, Germany
| | - Karen Lienkamp
- Professur für Polymerwerkstoffe, Fachrichtung Materialwissenschaft und Werkstofftechnik, Universität des Saarlandes, Campus, 66123, Saarbrücken, Germany
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Fu H, Huang J, van der Tol JJB, Su L, Wang Y, Dey S, Zijlstra P, Fytas G, Vantomme G, Dankers PYW, Meijer EW. Supramolecular polymers form tactoids through liquid-liquid phase separation. Nature 2024; 626:1011-1018. [PMID: 38418913 PMCID: PMC10901743 DOI: 10.1038/s41586-024-07034-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 01/05/2024] [Indexed: 03/02/2024]
Abstract
Liquid-liquid phase separation (LLPS) of biopolymers has recently been shown to play a central role in the formation of membraneless organelles with a multitude of biological functions1-3. The interplay between LLPS and macromolecular condensation is part of continuing studies4,5. Synthetic supramolecular polymers are the non-covalent equivalent of macromolecules but they are not reported to undergo LLPS yet. Here we show that continuously growing fibrils, obtained from supramolecular polymerizations of synthetic components, are responsible for phase separation into highly anisotropic aqueous liquid droplets (tactoids) by means of an entropy-driven pathway. The crowding environment, regulated by dextran concentration, affects not only the kinetics of supramolecular polymerizations but also the properties of LLPS, including phase-separation kinetics, morphology, internal order, fluidity and mechanical properties of the final tactoids. In addition, substrate-liquid and liquid-liquid interfaces proved capable of accelerating LLPS of supramolecular polymers, allowing the generation of a myriad of three-dimensional-ordered structures, including highly ordered arrays of micrometre-long tactoids at surfaces. The generality and many possibilities of supramolecular polymerizations to control emerging morphologies are demonstrated with several supramolecular polymers, opening up a new field of matter ranging from highly structured aqueous solutions by means of stabilized LLPS to nanoscopic soft matter.
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Affiliation(s)
- Hailin Fu
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Department of Chemistry and Chemical Engineering and Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands.
| | - Jingyi Huang
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Biomedical Engineering and Laboratory of Chemical Biology, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Joost J B van der Tol
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Chemistry and Chemical Engineering and Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Lu Su
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Yuyang Wang
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Applied Physics and Science Education, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Swayandipta Dey
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Applied Physics and Science Education, Eindhoven University of Technology, Eindhoven, The Netherlands
- Eindhoven Hendrik Casimir Institute, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Peter Zijlstra
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Applied Physics and Science Education, Eindhoven University of Technology, Eindhoven, The Netherlands
- Eindhoven Hendrik Casimir Institute, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - George Fytas
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Max Planck Institute for Polymer Research, Mainz, Germany
- Institute of Electronic Structure and Laser, FO.R.T.H, Heraklion, Greece
| | - Ghislaine Vantomme
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Chemistry and Chemical Engineering and Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Patricia Y W Dankers
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Biomedical Engineering and Laboratory of Chemical Biology, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - E W Meijer
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Department of Chemistry and Chemical Engineering and Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands.
- School of Chemistry and RNA Institute, University of New South Wales, Sydney, New South Wales, Australia.
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Garg A, González-Foutel NS, Gielnik MB, Kjaergaard M. Design of functional intrinsically disordered proteins. Protein Eng Des Sel 2024; 37:gzae004. [PMID: 38431892 DOI: 10.1093/protein/gzae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/22/2023] [Indexed: 03/05/2024] Open
Abstract
Many proteins do not fold into a fixed three-dimensional structure, but rather function in a highly disordered state. These intrinsically disordered proteins pose a unique challenge to protein engineering and design: How can proteins be designed de novo if not by tailoring their structure? Here, we will review the nascent field of design of intrinsically disordered proteins with focus on applications in biotechnology and medicine. The design goals should not necessarily be the same as for de novo design of folded proteins as disordered proteins have unique functional strengths and limitations. We focus on functions where intrinsically disordered proteins are uniquely suited including disordered linkers, desiccation chaperones, sensors of the chemical environment, delivery of pharmaceuticals, and constituents of biomolecular condensates. Design of functional intrinsically disordered proteins relies on a combination of computational tools and heuristics gleaned from sequence-function studies. There are few cases where intrinsically disordered proteins have made it into industrial applications. However, we argue that disordered proteins can perform many roles currently performed by organic polymers, and that these proteins might be more designable due to their modularity.
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Affiliation(s)
- Ankush Garg
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | | | - Maciej B Gielnik
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
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48
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Zhang X, Mao L, He R, Shi Y, Li L, Li S, Zhu C, Zhang Y, Ma D. Tunable cyclic operation of dissipative molecular switches based on anion recognition. Chem Commun (Camb) 2024; 60:1180-1183. [PMID: 38193867 DOI: 10.1039/d3cc05912j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Artificial dissipative molecular switches based on anion recognition are of great importance to simulate biological functions and construct smart materials. Five activated carboxylic acids are used as chemical fuels for dissipative molecular switches, which consist of an imidazolium macrocyclic host and a carboxylate anionic guest. By choosing different types of chemical fuels and using varied fuel concentrations, the rates of cyclic operations are tunable. The operation is capable of undergoing at least three cycles.
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Affiliation(s)
- Xin Zhang
- School of Pharmaceutical Engineering and Institute for Advanced Studies, Taizhou University, Taizhou 318000, China.
| | - Lijun Mao
- School of Pharmaceutical Engineering and Institute for Advanced Studies, Taizhou University, Taizhou 318000, China.
| | - Rongjing He
- School of Pharmaceutical Engineering and Institute for Advanced Studies, Taizhou University, Taizhou 318000, China.
| | - Yanting Shi
- School of Pharmaceutical Engineering and Institute for Advanced Studies, Taizhou University, Taizhou 318000, China.
| | - Lingyi Li
- School of Pharmaceutical Engineering and Institute for Advanced Studies, Taizhou University, Taizhou 318000, China.
| | - Shuo Li
- School of Pharmaceutical Engineering and Institute for Advanced Studies, Taizhou University, Taizhou 318000, China.
| | - Chenghao Zhu
- School of Pharmaceutical Engineering and Institute for Advanced Studies, Taizhou University, Taizhou 318000, China.
| | - Yanjing Zhang
- School of Pharmaceutical Engineering and Institute for Advanced Studies, Taizhou University, Taizhou 318000, China.
| | - Da Ma
- School of Pharmaceutical Engineering and Institute for Advanced Studies, Taizhou University, Taizhou 318000, China.
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49
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Du C, Woolcott S, Wahba AS, Hamry SR, Odette WL, Thibodeaux CJ, Marchand P, Mauzeroll J. Evaluation of Quatsome Morphology, Composition, and Stability for Pseudomonas aeruginosa Biofilm Eradication. Langmuir 2024; 40:1623-1632. [PMID: 38194503 DOI: 10.1021/acs.langmuir.3c02491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Biofilm infections are a major cause of food poisoning and hospital-acquired infections. Quaternary ammonium compounds are a group of effective disinfectants widely used in industry and households, yet their efficacy is lessened when used as antibiofilm agents compared to that against planktonic bacteria. It is therefore necessary to identify alternative formulations of quaternary ammonium compounds to achieve an effective biofilm dispersal. Quaternary ammonium amphiphiles can form vesicular structures termed "quatsomes" in the presence of cholesterol. In addition to their intrinsic antimicrobial properties, quatsomes can also be used for the delivery of other types of antibiotics or biomarkers. In this study, quatsomes were prepared from binary mixtures of cholesterol and mono- or dialkyl-quaternary ammonium compounds; then, the integrity and stability of their vesicular structure were assessed and related to monomer chain number and chain length. The quatsomes were used to treat Pseudomonas aeruginosa biofilms, showing effective antibiofilm abilities comparable to those of their monomers. A systematic liquid chromatography-mass spectrometry method for quantifying quatsome vesicle components was also developed and used to establish the significance of cholesterol in the quatsome self-assembly processes.
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Affiliation(s)
- Changyue Du
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Sascha Woolcott
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | | | - Sally R Hamry
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - William L Odette
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | | | - Patrick Marchand
- Sani-Marc Group, 42 Rue De L'Artisan, Victoriaville, Quebec G6P 7E3, Canada
| | - Janine Mauzeroll
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
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50
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Hurst PJ, Mulvey JT, Bone RA, Selmani S, Hudson RF, Guan Z, Green JR, Patterson JP. CryoEM reveals the complex self-assembly of a chemically driven disulfide hydrogel. Chem Sci 2024; 15:1106-1116. [PMID: 38239701 PMCID: PMC10793653 DOI: 10.1039/d3sc05790a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/11/2023] [Indexed: 01/22/2024] Open
Abstract
Inspired by the adaptability of biological materials, a variety of synthetic, chemically driven self-assembly processes have been developed that result in the transient formation of supramolecular structures. These structures form through two simultaneous reactions, forward and backward, which generate and consume a molecule that undergoes self-assembly. The dynamics of these assembly processes have been shown to differ from conventional thermodynamically stable molecular assemblies. However, the evolution of nanoscale morphologies in chemically driven self-assembly and how they compare to conventional assemblies has not been resolved. Here, we use a chemically driven redox system to separately carry out the forward and backward reactions. We analyze the forward and backward reactions both sequentially and synchronously with time-resolved cryogenic transmission electron microscopy (cryoEM). Quantitative image analysis shows that the synchronous process is more complex and heterogeneous than the sequential process. Our key finding is that a thermodynamically unstable stacked nanorod phase, briefly observed in the backward reaction, is sustained for ∼6 hours in the synchronous process. Kinetic Monte Carlo modeling show that the synchronous process is driven by multiple cycles of assembly and disassembly. The collective data suggest that chemically driven self-assembly can create sustained morphologies not seen in thermodynamically stable assemblies by kinetically stabilizing transient intermediates. This finding provides plausible design principles to develop and optimize supramolecular materials with novel properties.
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Affiliation(s)
- Paul Joshua Hurst
- Department of Chemistry, University of California, Irvine Irvine California 92697 USA
- Center for Complex and Active Materials, University of California, Irvine Irvine California 92697 USA
| | - Justin T Mulvey
- Center for Complex and Active Materials, University of California, Irvine Irvine California 92697 USA
- Department of Materials Science and Engineering, University of California, Irvine Irvine California 92697 USA
| | - Rebecca A Bone
- Department of Chemistry, University of Massachusetts Boston Boston Massachusetts 02125 USA
| | - Serxho Selmani
- Department of Chemistry, University of California, Irvine Irvine California 92697 USA
- Center for Complex and Active Materials, University of California, Irvine Irvine California 92697 USA
| | - Redford F Hudson
- Department of Computer Science, University of California, Irvine Irvine California 92697 USA
| | - Zhibin Guan
- Department of Chemistry, University of California, Irvine Irvine California 92697 USA
- Center for Complex and Active Materials, University of California, Irvine Irvine California 92697 USA
- Department of Materials Science and Engineering, University of California, Irvine Irvine California 92697 USA
- Department of Chemical and Biomolecular Engineering, University of California, Irvine Irvine California 92697 USA
- Department of Biomedical Engineering, University of California, Irvine Irvine California 92697 USA
| | - Jason R Green
- Department of Chemistry, University of Massachusetts Boston Boston Massachusetts 02125 USA
- Department of Physics, University of Massachusetts Boston Boston Massachusetts 02125 USA
| | - Joseph P Patterson
- Department of Chemistry, University of California, Irvine Irvine California 92697 USA
- Center for Complex and Active Materials, University of California, Irvine Irvine California 92697 USA
- Department of Materials Science and Engineering, University of California, Irvine Irvine California 92697 USA
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