1
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Mondal S, Sauer MA, Heyden M. Exploring Conformational Landscapes Along Anharmonic Low-Frequency Vibrations. J Phys Chem B 2024; 128:7112-7120. [PMID: 38986052 DOI: 10.1021/acs.jpcb.4c02743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
We aim to automatize the identification of collective variables to simplify and speed up enhanced sampling simulations of conformational dynamics in biomolecules. We focus on anharmonic low-frequency vibrations that exhibit fluctuations on time scales faster than conformational transitions but describe a path of least resistance toward structural change. A key challenge is that harmonic approximations are ill-suited to characterize these vibrations, which are observed at far-infrared frequencies and are easily excited by thermal collisions at room temperature. Here, we approached this problem with a frequency-selective anharmonic (FRESEAN) mode analysis that does not rely on harmonic approximations and successfully isolates anharmonic low-frequency vibrations from short molecular dynamics simulation trajectories. We applied FRESEAN mode analysis to simulations of alanine dipeptide, a common test system for enhanced sampling simulation protocols, and compared the performance of isolated low-frequency vibrations to conventional user-defined collective variables (here backbone dihedral angles) in enhanced sampling simulations. The comparison shows that enhanced sampling along anharmonic low-frequency vibrations not only reproduces known conformational dynamics but can even further improve the sampling of slow transitions compared to user-defined collective variables. Notably, free energy surfaces spanned by low-frequency anharmonic vibrational modes exhibit lower barriers associated with conformational transitions relative to representations in backbone dihedral space. We thus conclude that anharmonic low-frequency vibrations provide a promising path for highly effective and fully automated enhanced sampling simulations of conformational dynamics in biomolecules.
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Affiliation(s)
- Souvik Mondal
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Michael A Sauer
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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2
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Surfaro F, Zhang F, Schreiber F, Roth R. The ion-activated attractive patchy particle model and its application to the liquid-vapor phase transitions. J Chem Phys 2024; 161:034901. [PMID: 39007873 DOI: 10.1063/5.0215920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Patchy particles are an intriguing subject of study and indeed a model system in the field of soft matter physics. In recent years, patchy particle models have been applied to describe a wide variety of systems, including colloidal crystals, macromolecular interactions, liquid crystals, and nanoparticle assemblies. Given the importance of the topic, rationalizing and capturing the basic features of these models is crucial to their correct application in specific systems. In this study, we extend the ion-activated attractive patchy particles model previously employed to elucidate the phase behavior of protein solutions in the presence of trivalent salts. Our extension incorporates the effect of repulsion between unoccupied and occupied binding sites, depicted as patches. Furthermore, we examine the influence of model parameters on the liquid-vapor coexistence region within the phase diagram, employing numerical methods. A deeper understanding of this model will facilitate a better comprehension of the effects observed in experiments.
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Affiliation(s)
- Furio Surfaro
- Institute of Applied Physics, University of Tübingen, 72076 Tübingen, Germany
| | - Fajun Zhang
- Institute of Applied Physics, University of Tübingen, 72076 Tübingen, Germany
| | - Frank Schreiber
- Institute of Applied Physics, University of Tübingen, 72076 Tübingen, Germany
| | - Roland Roth
- Institute of Theoretical Physics, University of Tübingen, 72076 Tübingen, Germany
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3
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Ikeda T, Kobayashi Y, Yamakawa M. Structure and dynamics of amphiphilic patchy cubes in a nanoslit under shear. J Chem Phys 2024; 161:024901. [PMID: 38973760 DOI: 10.1063/5.0216550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/17/2024] [Indexed: 07/09/2024] Open
Abstract
Patchy nanocubes are intriguing materials with simple shapes and space-filling and multidirectional bonding properties. Previous studies have revealed various mesoscopic structures such as colloidal crystals in the solid regime and rod-like or fractal-like aggregates in the liquid regime of the phase diagram. Recent studies have also shown that mesoscopic structural properties, such as an average cluster size M and orientational order, in amphiphilic nanocube suspensions are associated with macroscopic viscosity changes, mainly owing to differences in cluster shape among patch arrangements. Although many studies have been conducted on the self-assembled structures of nanocubes in bulk, little is known about their self-assembly in nanoscale spaces or structural changes under shear. In this study, we investigated mixtures of one- and two-patch amphiphilic nanocubes confined in two flat parallel plates at rest and under shear using molecular dynamics simulations coupled with multiparticle collision dynamics. We considered two different patch arrangements for the two-patch particles and two different slit widths H to determine the degree of confinement in constant volume fractions in the liquid regime of the phase diagram. We revealed two unique cluster morphologies that have not been previously observed under bulk conditions. At rest, the size of the rod-like aggregates increased with decreasing H, whereas that of the fractal-like aggregates remained constant. Under weak shear with strong confinement, the rod-like aggregates maintained a larger M than the fractal-like aggregates, which were more rigid and maintained a larger M than the rod-like aggregates under bulk conditions.
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Affiliation(s)
- Takahiro Ikeda
- Faculty of Mechanical Engineering, Kyoto Institute of Technology, Goshokaido-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Yusei Kobayashi
- Faculty of Mechanical Engineering, Kyoto Institute of Technology, Goshokaido-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Masashi Yamakawa
- Faculty of Mechanical Engineering, Kyoto Institute of Technology, Goshokaido-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
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4
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Müller L, Salman S, Hoppe T. Chemical cross-linking to study protein self-assembly in cellulo. STAR Protoc 2024; 5:103032. [PMID: 38652664 PMCID: PMC11059278 DOI: 10.1016/j.xpro.2024.103032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/22/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024] Open
Abstract
Many proteins self-assemble into dimers and higher-order oligomers. Therefore, the goal of this protocol is to characterize the conformational states of an endogenous protein of interest. Here, we present a protocol for assessing protein self-assembly in cell lysates using chemical cross-linking. We describe steps for chemical cross-linking with recombinant proteins as well as steps for cell culture and cell lysate preparation, chemical cross-linking, SDS-PAGE, and western blotting for the detection of endogenous proteins. For complete details on the use and execution of this protocol, please refer to Balaji et al.1.
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Affiliation(s)
- Leonie Müller
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, 50931 Cologne, Germany
| | - Sirin Salman
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Thorsten Hoppe
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, 50931 Cologne, Germany.
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5
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Yu Z, Gao Y, Shang Z, Wang T, He X, Lei J, Tai F, Zhang L, Chen Y. A stable delivery system for curcumin: Fabrication and characterization of self-assembling acylated kidney bean protein isolate nanogels. Food Chem 2024; 443:138526. [PMID: 38290298 DOI: 10.1016/j.foodchem.2024.138526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/27/2023] [Accepted: 01/18/2024] [Indexed: 02/01/2024]
Abstract
The construction of protein-based nano-gels as curcumin delivery system effectively enhances the stability and bioavailability of curcumin. In this study, acylation modification and self-assembly techniques were jointly employed to construct acylated kidney bean protein isolate (AKBPI)-nanogels. Optimal conditions for AKBPI-nanogels were determined to be pH 7, concentration of 2 mg/mL, and temperature at 90℃ for 30 min. The optimized AKBPI-nanogels exhibited excellent uniformity as evidenced by decreasing average particle size (137.35 nm) and polydispersity index (0.38). Acylation enhanced the intermolecular interactions within the nanogel by reducing the polarity of tyrosine microenvironment and free sulfhydryl groups. AKBPI-nanogels demonstrated remarkable characteristics in terms of pH sensitivity, salt concentration, and storage tolerance. The curcumin-loaded AKBPI-nanogels exhibited an encapsulation efficiency of 92.30 % and maintained high antioxidant activity. In simulated gastrointestinal digestion, AKBPI-nanogels facilitated the controlled release and higher bioavailability of curcumin. Therefore, AKBPI-nanogels can be a stable tool for delivering curcumin.
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Affiliation(s)
- Zhihui Yu
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China; Houji Laboratory in Shanxi Province, Taiyuan 030031, Shanxi, China; Food Nutrition and Safety Institute, Shanxi Agricultural University, Taiyuan 030031, Shanxi, China
| | - Yating Gao
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Ziqi Shang
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Tengfei Wang
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Xuli He
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Jian Lei
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Fei Tai
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Lixin Zhang
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China; Food Nutrition and Safety Institute, Shanxi Agricultural University, Taiyuan 030031, Shanxi, China.
| | - Yisheng Chen
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China; Houji Laboratory in Shanxi Province, Taiyuan 030031, Shanxi, China; Food Nutrition and Safety Institute, Shanxi Agricultural University, Taiyuan 030031, Shanxi, China.
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6
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Karabulut G, Feng H. Enhancing techno-functional attributes of plant protein and curcumin complexation: A comparative examination of Maillard conjugation induced by manothermosonication and ultrasonication. Food Chem 2024; 442:138488. [PMID: 38244438 DOI: 10.1016/j.foodchem.2024.138488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/30/2023] [Accepted: 01/15/2024] [Indexed: 01/22/2024]
Abstract
The Maillard conjugation of hemp protein with d-xylose was studied, focusing on the influence of ultrasonic waves, processing time, and pressure. Cavitation-driven processes, including ultrasonication (US) and manothermosonication (MTS), were found to impact the degree of grafting, functional characteristics, and structural alterations, affecting conjugation efficiency. The glycation of hemp protein with xylose assisted with US and MTS was investigated under varying pressures. MTS- and US-assisted glycation processes result in 4.22- and 1.64-fold higher degrees of grafting compared to the classical method within a short time frame. The MTS procedures also improved solubility (+3.6-fold), emulsion (+15-fold), and foaming (+1.7-fold) properties, especially at optimized pressure levels, compared to classical conjugates. Furthermore, the complexation of MTS-assisted conjugates with curcumin (Cur) enhanced Cur stability by more than 1.4-fold compared to the classical procedure during 20-day storage at 4 oC. The findings suggest potential applications in the pharmaceutical industry, active dairy/meat analog development, and gel formulation.
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Affiliation(s)
- Gulsah Karabulut
- Department of Food Engineering, Sakarya University, 54187 Sakarya, Turkey.
| | - Hao Feng
- Department of Family and Consumer Sciences, North Carolina A&T State University, Greensboro, NC 27401, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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7
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Mukherjee S, Poudyal M, Dave K, Kadu P, Maji SK. Protein misfolding and amyloid nucleation through liquid-liquid phase separation. Chem Soc Rev 2024; 53:4976-5013. [PMID: 38597222 DOI: 10.1039/d3cs01065a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Liquid-liquid phase separation (LLPS) is an emerging phenomenon in cell physiology and diseases. The weak multivalent interaction prerequisite for LLPS is believed to be facilitated through intrinsically disordered regions, which are prevalent in neurodegenerative disease-associated proteins. These aggregation-prone proteins also exhibit an inherent property for phase separation, resulting in protein-rich liquid-like droplets. The very high local protein concentration in the water-deficient confined microenvironment not only drives the viscoelastic transition from the liquid to solid-like state but also most often nucleate amyloid fibril formation. Indeed, protein misfolding, oligomerization, and amyloid aggregation are observed to be initiated from the LLPS of various neurodegeneration-related proteins. Moreover, in these cases, neurodegeneration-promoting genetic and environmental factors play a direct role in amyloid aggregation preceded by the phase separation. These cumulative recent observations ignite the possibility of LLPS being a prominent nucleation mechanism associated with aberrant protein aggregation. The present review elaborates on the nucleation mechanism of the amyloid aggregation pathway and the possible early molecular events associated with amyloid-related protein phase separation. It also summarizes the recent advancement in understanding the aberrant phase transition of major proteins contributing to neurodegeneration focusing on the common disease-associated factors. Overall, this review proposes a generic LLPS-mediated multistep nucleation mechanism for amyloid aggregation and its implication in neurodegeneration.
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Affiliation(s)
- Semanti Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Manisha Poudyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Kritika Dave
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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8
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DeLuca M, Duke D, Ye T, Poirier M, Ke Y, Castro C, Arya G. Mechanism of DNA origami folding elucidated by mesoscopic simulations. Nat Commun 2024; 15:3015. [PMID: 38589344 PMCID: PMC11001925 DOI: 10.1038/s41467-024-46998-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the behavior of single- and double-stranded DNA motifs and transitions between them, allowing us to simulate the folding of DNA origami up to several kilobases in size. Brownian dynamics simulations of small structures reveal a hierarchical folding process involving zipping into a partially folded precursor followed by crystallization into the final structure. We elucidate the effects of various design choices on folding order and kinetics. Larger structures are found to exhibit heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to more accessible structures which exhibit first-order kinetics and virtually defect-free folding. This model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.
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Affiliation(s)
- Marcello DeLuca
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27705, USA
| | - Daniel Duke
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27705, USA
| | - Tao Ye
- Department of Chemistry & Biochemistry, University of California, Merced, CA, 95343, USA
- Department of Materials and Biomaterials Science & Engineering, University of California, Merced, CA, 95343, USA
| | - Michael Poirier
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Yonggang Ke
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
| | - Carlos Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Gaurav Arya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27705, USA.
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9
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Solomonov A, Kozell A, Shimanovich U. Designing Multifunctional Biomaterials via Protein Self-Assembly. Angew Chem Int Ed Engl 2024; 63:e202318365. [PMID: 38206201 DOI: 10.1002/anie.202318365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/27/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
Protein self-assembly is a fundamental biological process where proteins spontaneously organize into complex and functional structures without external direction. This process is crucial for the formation of various biological functionalities. However, when protein self-assembly fails, it can trigger the development of multiple disorders, thus making understanding this phenomenon extremely important. Up until recently, protein self-assembly has been solely linked either to biological function or malfunction; however, in the past decade or two it has also been found to hold promising potential as an alternative route for fabricating materials for biomedical applications. It is therefore necessary and timely to summarize the key aspects of protein self-assembly: how the protein structure and self-assembly conditions (chemical environments, kinetics, and the physicochemical characteristics of protein complexes) can be utilized to design biomaterials. This minireview focuses on the basic concepts of forming supramolecular structures, and the existing routes for modifications. We then compare the applicability of different approaches, including compartmentalization and self-assembly monitoring. Finally, based on the cutting-edge progress made during the last years, we summarize the current knowledge about tailoring a final function by introducing changes in self-assembly and link it to biomaterials' performance.
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Affiliation(s)
- Aleksei Solomonov
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 234 Herzl st., Rehovot, 76100, Israel
| | - Anna Kozell
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 234 Herzl st., Rehovot, 76100, Israel
| | - Ulyana Shimanovich
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 234 Herzl st., Rehovot, 76100, Israel
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10
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De Virgiliis A, Meyra A, Ciach A. Lattice Model Results for Pattern Formation in a Mixture with Competing Interactions. Molecules 2024; 29:1512. [PMID: 38611792 PMCID: PMC11013164 DOI: 10.3390/molecules29071512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
A monolayer consisting of two types of particles, with energetically favored alternating stripes of the two components, is studied by Monte Carlo simulations and within a mesoscopic theory. We consider a triangular lattice model and assume short-range attraction and long-range repulsion between particles of the same kind, as well as short-range repulsion and long-range attraction for the cross-interaction. The structural evolution of the model upon increasing temperature is studied for equal chemical potentials of the two species. We determine the structure factor, the chemical potential-density isotherms, the specific heat, and the compressibility, and show how these thermodynamic functions are associated with the spontaneous formation of stripes with varying degrees of order.
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Affiliation(s)
- Andres De Virgiliis
- Instituto de Física de Líquidos y Sistemas Biológicos, Facultad de Ciencias Exactas-UNLP-CONICET, La Plata 1900, Argentina; (A.D.V.); (A.M.)
- Departamento de Ciencias Básicas, Facultad de Ingeniería, Universidad Nacional de La Plata, La Plata 1900, Argentina
| | - Ariel Meyra
- Instituto de Física de Líquidos y Sistemas Biológicos, Facultad de Ciencias Exactas-UNLP-CONICET, La Plata 1900, Argentina; (A.D.V.); (A.M.)
- Departamento de Ingeniería Mecánica, Facultad Regional La Plata, Universidad Tecnológica Nacional, La Plata 1900, Argentina
| | - Alina Ciach
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
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11
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Mougkogiannis P, Adamatzky A. On interaction of proteinoids with simulated neural networks. Biosystems 2024; 237:105175. [PMID: 38460836 DOI: 10.1016/j.biosystems.2024.105175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024]
Abstract
Proteinoid-neuron networks combine biological neurons with spiking proteinoid microspheres, which are generated by thermal condensation of amino acids. Complex and dynamic spiking patterns in response to varied stimuli make these networks suitable for unconventional computing. This research examines the interaction of proteinoid-neuron networks with function-generator-artificial neural networks (ANN) that may create distinct electrical waveforms. Function-generator- artificial neural network (ANN) stimulates and modulates proteinoid-neuron network spiking activity and synchronisation to encode and decode information. We employ function-generator-ANN to study proteinoid-neuron network nonlinear dynamics and chaos and optimise their performance and energy efficiency. Function-generator-ANN improves proteinoid-neuron networks' computational capacities and robustness and creates unique hybrid systems with electrical devices. We address the benefits as well as the drawbacks of employing proteinoid-neuron networks for unconventional computing with function-generator-ANN.
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Fu C, Wang Z, Zhou X, Hu B, Li C, Yang P. Protein-based bioactive coatings: from nanoarchitectonics to applications. Chem Soc Rev 2024; 53:1514-1551. [PMID: 38167899 DOI: 10.1039/d3cs00786c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Protein-based bioactive coatings have emerged as a versatile and promising strategy for enhancing the performance and biocompatibility of diverse biomedical materials and devices. Through surface modification, these coatings confer novel biofunctional attributes, rendering the material highly bioactive. Their widespread adoption across various domains in recent years underscores their importance. This review systematically elucidates the behavior of protein-based bioactive coatings in organisms and expounds on their underlying mechanisms. Furthermore, it highlights notable advancements in artificial synthesis methodologies and their functional applications in vitro. A focal point is the delineation of assembly strategies employed in crafting protein-based bioactive coatings, which provides a guide for their expansion and sustained implementation. Finally, the current trends, challenges, and future directions of protein-based bioactive coatings are discussed.
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Affiliation(s)
- Chengyu Fu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Zhengge Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Xingyu Zhou
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Bowen Hu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Chen Li
- School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Eastern HuaLan Avenue, Xinxiang, Henan 453003, China
| | - Peng Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
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13
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Ross JL. Self-assembling synthetic polymer forms liquid-like droplets. Nature 2024; 626:957-958. [PMID: 38418908 DOI: 10.1038/d41586-024-00421-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
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14
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Nagar N, Naidu G, Mishra A, Poluri KM. Protein-Based Nanocarriers and Nanotherapeutics for Infection and Inflammation. J Pharmacol Exp Ther 2024; 388:91-109. [PMID: 37699711 DOI: 10.1124/jpet.123.001673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 08/04/2023] [Accepted: 08/21/2023] [Indexed: 09/14/2023] Open
Abstract
Infectious and inflammatory diseases are one of the leading causes of death globally. The status quo has become more prominent with the onset of the coronavirus disease 2019 (COVID-19) pandemic. To combat these potential crises, proteins have been proven as highly efficacious drugs, drug targets, and biomarkers. On the other hand, advancements in nanotechnology have aided efficient and sustained drug delivery due to their nano-dimension-acquired advantages. Combining both strategies together, the protein nanoplatforms are equipped with the advantageous intrinsic properties of proteins as well as nanoformulations, eloquently changing the field of nanomedicine. Proteins can act as carriers, therapeutics, diagnostics, and theranostics in their nanoform as fusion proteins or as composites with other organic/inorganic materials. Protein-based nanoplatforms have been extensively explored to target the major infectious and inflammatory diseases of clinical concern. The current review comprehensively deliberated proteins as nanocarriers for drugs and nanotherapeutics for inflammatory and infectious agents, with special emphasis on cancer and viral diseases. A plethora of proteins from diverse organisms have aided in the synthesis of protein-based nanoformulations. The current study specifically presented the proteins of human and pathogenic origin to dwell upon the field of protein nanotechnology, emphasizing their pharmacological advantages. Further, the successful clinical translation and current bottlenecks of the protein-based nanoformulations associated with the infection-inflammation paradigm have also been discussed comprehensively. SIGNIFICANCE STATEMENT: This review discusses the plethora of promising protein-based nanocarriers and nanotherapeutics explored for infectious and inflammatory ailments, with particular emphasis on protein nanoparticles of human and pathogenic origin with reference to the advantages, ADME (absorption, distribution, metabolism, and excretion parameters), and current bottlenecks in development of protein-based nanotherapeutic interventions.
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Affiliation(s)
- Nupur Nagar
- Department of Biosciences and Bioengineering (N.N., G.N., K.M.P.) and Centre for Nanotechnology (K.M.P.), Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; and Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India (A.M.)
| | - Goutami Naidu
- Department of Biosciences and Bioengineering (N.N., G.N., K.M.P.) and Centre for Nanotechnology (K.M.P.), Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; and Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India (A.M.)
| | - Amit Mishra
- Department of Biosciences and Bioengineering (N.N., G.N., K.M.P.) and Centre for Nanotechnology (K.M.P.), Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; and Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India (A.M.)
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering (N.N., G.N., K.M.P.) and Centre for Nanotechnology (K.M.P.), Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; and Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India (A.M.)
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15
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Hilditch AT, Romanyuk A, Cross SJ, Obexer R, McManus JJ, Woolfson DN. Assembling membraneless organelles from de novo designed proteins. Nat Chem 2024; 16:89-97. [PMID: 37710047 PMCID: PMC10774119 DOI: 10.1038/s41557-023-01321-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 08/09/2023] [Indexed: 09/16/2023]
Abstract
Recent advances in de novo protein design have delivered a diversity of discrete de novo protein structures and complexes. A new challenge for the field is to use these designs directly in cells to intervene in biological processes and augment natural systems. The bottom-up design of self-assembled objects such as microcompartments and membraneless organelles is one such challenge. Here we describe the design of genetically encoded polypeptides that form membraneless organelles in Escherichia coli. To do this, we combine de novo α-helical sequences, intrinsically disordered linkers and client proteins in single-polypeptide constructs. We tailor the properties of the helical regions to shift protein assembly from arrested assemblies to dynamic condensates. The designs are characterized in cells and in vitro using biophysical methods and soft-matter physics. Finally, we use the designed polypeptide to co-compartmentalize a functional enzyme pair in E. coli, improving product formation close to the theoretical limit.
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Affiliation(s)
- Alexander T Hilditch
- School of Chemistry, University of Bristol, Bristol, UK
- School of Biochemistry, University of Bristol, Bristol, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK
| | - Andrey Romanyuk
- School of Chemistry, University of Bristol, Bristol, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK
| | - Stephen J Cross
- Wolfson Bioimaging Facility, University of Bristol, Bristol, UK
| | - Richard Obexer
- School of Chemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK.
- Department of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Jennifer J McManus
- HH Wills Physics Laboratory, School of Physics, University of Bristol, Bristol, UK.
- Bristol BioDesign Institute, School of Chemistry, University of Bristol, Bristol, UK.
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, UK.
- School of Biochemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK.
- Bristol BioDesign Institute, School of Chemistry, University of Bristol, Bristol, UK.
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16
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Morariu S, Avadanei M, Nita LE. Effect of pH on the Poly(acrylic acid)/Poly(vinyl alcohol)/Lysozyme Complexes Formation. Molecules 2023; 29:208. [PMID: 38202791 PMCID: PMC10780248 DOI: 10.3390/molecules29010208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/20/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
The interactions between poly(acrylic acid) (PAA), poly(vinyl alcohol) (PVA), and lysozyme (Lys) in an aqueous environment at pHs of 2, 4, and 7.4 were discussed considering the experimental data obtained by turbidimetry, electrokinetic and rheological measurements, and FTIR analysis. It was found that the increase in PAA amount reduces the coacervation zone by shifting the critical pHcr1to higher values while the critical pHcr2 remains unchanged. The coacervation zone extended from 3.1-4.2 to 2.9-4.7 increasing the Lys concentration from 0.2% to 0.5%. The zeta potential measurements showed that the PAA-PVA-Lys mixture in water is the most stable in the pH range of 4.5-8. Zero shear viscosity exhibited deviations from additivity at both investigated pHs, and a maximum value corresponding to a maximum hydrodynamic volume was revealed at PAA weight fractions of 0.4 and 0.5 for pHs of 4 and 7.4, respectively. The binding affinity to Lys of PAA, established by molecular dynamics simulation, was slightly higher than that of PVA. The more stable complex was PAA-Lys formed in a very acidic environment; for that, a binding affinity of -7.1 kcal/mol was determined.
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Affiliation(s)
- Simona Morariu
- “Petru Poni” Institute of Macromolecular Chemistry, 41-A Grigore Ghica Voda Alley, 700487 Iasi, Romania; (M.A.); (L.E.N.)
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17
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Prestipino S, Pini D, Costa D, Malescio G, Munaò G. A density functional theory and simulation study of stripe phases in symmetric colloidal mixtures. J Chem Phys 2023; 159:204902. [PMID: 38010334 DOI: 10.1063/5.0177209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023] Open
Abstract
In a binary mixture, stripes refer to a one-dimensional periodicity of the composition, namely, a regular alternation of layers filled with particles of mostly one species. We have recently introduced [Munaò et al., Phys. Chem. Chem. Phys. 25, 16227 (2023)] a model that possibly provides the simplest binary mixture endowed with stripe order. The model consists of two species of identical hard spheres with equal concentration, which mutually interact through a square-well potential. In that paper, we have numerically shown that stripes are present in both liquid and solid phases when the attraction range is rather long. Here, we study the phase behavior of the model in terms of a density functional theory capable to account for the existence of stripes in the dense mixture. Our theory is accurate in reproducing the phases of the model, at least insofar as the composition inhomogeneities occur on length scales quite larger than the particle size. Then, using Monte Carlo simulations, we prove the existence of solid stripes even when the square well is much thinner than the particle diameter, making our model more similar to a real colloidal mixture. Finally, when the width of the attractive well is equal to the particle diameter, we observe a different and more complex form of compositional order in the solid, where each species of particle forms a regular porous matrix holding in its holes the other species, witnessing a surprising variety of emergent behaviors for a very basic model of interaction.
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Affiliation(s)
- Santi Prestipino
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Davide Pini
- Dipartimento di Fisica "A. Pontremoli," Università di Milano, Via Celoria 16, 20133 Milano, Italy
| | - Dino Costa
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Gianpietro Malescio
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Gianmarco Munaò
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
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18
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Vlachy V, Kalyuzhnyi YV, Hribar-Lee B, Dill KA. Protein Association in Solution: Statistical Mechanical Modeling. Biomolecules 2023; 13:1703. [PMID: 38136574 PMCID: PMC10742237 DOI: 10.3390/biom13121703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Protein molecules associate in solution, often in clusters beyond pairwise, leading to liquid phase separations and high viscosities. It is often impractical to study these multi-protein systems by atomistic computer simulations, particularly in multi-component solvents. Instead, their forces and states can be studied by liquid state statistical mechanics. However, past such approaches, such as the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, were limited to modeling proteins as spheres, and contained no microscopic structure-property relations. Recently, this limitation has been partly overcome by bringing the powerful Wertheim theory of associating molecules to bear on protein association equilibria. Here, we review these developments.
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Affiliation(s)
- Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | | | - Barbara Hribar-Lee
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Ken A. Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, New York, NY 11794, USA;
- Department of Chemistry, Physics and Astronomy, Stony Brook University, New York, NY 11790, USA
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19
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Aftahy K, Arrasate P, Bashkirov PV, Kuzmin PI, Maurizot V, Huc I, Frolov VA. Molecular Sensing and Manipulation of Protein Oligomerization in Membrane Nanotubes with Bolaamphiphilic Foldamers. J Am Chem Soc 2023; 145:25150-25159. [PMID: 37948300 PMCID: PMC10682987 DOI: 10.1021/jacs.3c05753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 11/12/2023]
Abstract
Adaptive and reversible self-assembly of supramolecular protein structures is a fundamental characteristic of dynamic living matter. However, the quantitative detection and assessment of the emergence of mesoscale protein complexes from small and dynamic oligomeric precursors remains highly challenging. Here, we present a novel approach utilizing a short membrane nanotube (sNT) pulled from a planar membrane reservoir as nanotemplates for molecular reconstruction, manipulation, and sensing of protein oligomerization and self-assembly at the mesoscale. The sNT reports changes in membrane shape and rigidity caused by membrane-bound proteins as variations of the ionic conductivity of the sNT lumen. To confine oligomerization to the sNT, we have designed and synthesized rigid oligoamide foldamer tapes (ROFTs). Charged ROFTs incorporate into the planar and sNT membranes, mediate protein binding to the membranes, and, driven by the luminal electric field, shuttle the bound proteins between the sNT and planar membranes. Using Annexin-V (AnV) as a prototype, we show that the sNT detects AnV oligomers shuttled into the nanotube by ROFTs. Accumulation of AnV on the sNT induces its self-assembly into a curved lattice, restricting the sNT geometry and inhibiting the material uptake from the reservoir during the sNT extension, leading to the sNT fission. By comparing the spontaneous and ROFT-mediated entry of AnV into the sNT, we reveal how intricate membrane curvature sensing by small AnV oligomers controls the lattice self-assembly. These results establish sNT-ROFT as a powerful tool for molecular reconstruction and functional analyses of protein oligomerization and self-assembly, with broad application to various membrane processes.
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Affiliation(s)
- Kathrin Aftahy
- Department
of Pharmacy, Ludwig-Maximilians-Universität
München, Munich 81377, Germany
| | - Pedro Arrasate
- Biofisika
Institute (CSIC, UPV/EHU), University of
the Basque Country, Leioa 48940, Spain
- Department
of Biochemistry and Molecular Biology, University
of the Basque Country, Leioa 48940, Spain
| | - Pavel V. Bashkirov
- Research
Institute for Systems Biology and Medicine, Moscow 117246, Russia
| | - Petr I. Kuzmin
- A.N.
Frumkin Institute of Physical Chemistry and Electrochemistry, Moscow 119071, Russia
| | - Victor Maurizot
- Univ. Bordeaux,
CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Pessac 33600, France
| | - Ivan Huc
- Department
of Pharmacy, Ludwig-Maximilians-Universität
München, Munich 81377, Germany
| | - Vadim A. Frolov
- Biofisika
Institute (CSIC, UPV/EHU), University of
the Basque Country, Leioa 48940, Spain
- Department
of Biochemistry and Molecular Biology, University
of the Basque Country, Leioa 48940, Spain
- Ikerbasque,
Basque Foundation for Science, Bilbao 48009, Spain
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20
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Fedorov D, Roas-Escalona N, Tolmachev D, Harmat AL, Scacchi A, Sammalkorpi M, Aranko AS, Linder MB. Triblock Proteins with Weakly Dimerizing Terminal Blocks and an Intrinsically Disordered Region for Rational Design of Condensate Properties. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2306817. [PMID: 37964343 DOI: 10.1002/smll.202306817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/20/2023] [Indexed: 11/16/2023]
Abstract
Condensates are molecular assemblies that are formed through liquid-liquid phase separation and play important roles in many biological processes. The rational design of condensate formation and their properties is central to applications, such as biosynthetic materials, synthetic biology, and for understanding cell biology. Protein engineering is used to make a triblock structure with varying terminal blocks of folded proteins on both sides of an intrinsically disordered mid-region. Dissociation constants are determined in the range of micromolar to millimolar for a set of proteins suitable for use as terminal blocks. Varying the weak dimerization of terminal blocks leads to an adjustable tendency for condensate formation while keeping the intrinsically disordered region constant. The dissociation constants of the terminal domains correlate directly with the tendency to undergo liquid-liquid phase separation. Differences in physical properties, such as diffusion rate are not directly correlated with the strength of dimerization but can be understood from the properties and interplay of the constituent blocks. The work demonstrates the importance of weak interactions in condensate formation and shows a principle for protein design that will help in fabricating functional condensates in a predictable and rational way.
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Affiliation(s)
- Dmitrii Fedorov
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - Nelmary Roas-Escalona
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - Dmitry Tolmachev
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - Adam L Harmat
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - Alberto Scacchi
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Department of Applied Physics, Aalto University, P.O. Box 11000, Aalto, FI-00076, Finland
| | - Maria Sammalkorpi
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - A Sesilja Aranko
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - Markus B Linder
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
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21
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Thijssen K, Liverpool TB, Royall CP, Jack RL. Necking and failure of a particulate gel strand: signatures of yielding on different length scales. SOFT MATTER 2023; 19:7412-7428. [PMID: 37743690 DOI: 10.1039/d3sm00681f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
"Sticky" spheres with a short-ranged attraction are a basic model of a wide range of materials from the atomic to the granular length scale. Among the complex phenomena exhibited by sticky spheres is the formation of far-from-equilibrium dynamically arrested networks which comprise "strands" of densely packed particles. The aging and failure of such gels under load is a remarkably challenging problem, given the simplicity of the model, as it involves multiple length- and time-scales, making a single approach ineffective. Here we tackle this challenge by addressing the failure of a single strand with a combination of methods. We study the mechanical response of a single strand of a model gel-former to deformation, both numerically and analytically. Under elongation, the strand breaks by a necking instability. We analyse this behaviour at three different length scales: a rheological continuum model of the whole strand; a microscopic analysis of the particle structure and dynamics; and the local stress tensor. Combining these different approaches gives a coherent picture of the necking and failure. The strand has an amorphous local structure and has large residual stresses from its initialisation. We find that neck formation is associated with increased plastic flow, a reduction in the stability of the local structure, and a reduction in the residual stresses; this indicates that the system loses its solid character and starts to behave more like a viscous fluid. These results will inform the development of more detailed models that incorporate the heterogeneous network structure of particulate gels.
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Affiliation(s)
- Kristian Thijssen
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen 2100, Denmark
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | | | - C Patrick Royall
- H.H. Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
| | - Robert L Jack
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- DAMTP, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK.
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22
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Yokoyama T, Kobayashi Y, Arai N, Nikoubashman A. Aggregation of amphiphilic nanocubes in equilibrium and under shear. SOFT MATTER 2023; 19:6480-6489. [PMID: 37575055 DOI: 10.1039/d3sm00671a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
We investigate the self-assembly of amphiphilic nanocubes into finite-sized aggregates in equilibrium and under shear, using molecular dynamics (MD) simulations and kinetic Monte Carlo (KMC) calculations. These patchy nanoparticles combine both interaction and shape anisotropy, making them valuable models for studying folded proteins and DNA-functionalized nanoparticles. The nanocubes can self-assemble into various finite-sized aggregates ranging from rods to self-avoiding random walks, depending on the number and placement of the hydrophobic faces. Our study focuses on suspensions containing multi- and one-patch cubes, with their ratio systematically varied. When the binding energy is comparable to the thermal energy, the aggregates consist of only few cubes that spontaneously associate/dissociate. However, highly stable aggregates emerge when the binding energy exceeds the thermal energy. Generally, the mean aggregation number of the self-assembled clusters increases with the number of hydrophobic faces and decreases with increasing fraction of one-patch cubes. In sheared suspensions, the more frequent collisions between nanocube clusters lead to faster aggregation dynamics but also to smaller terminal steady-state mean cluster sizes. The results from the MD and KMC simulations are in excellent agreement for all investigated two-patch cases, whereas the three-patch cubes form systematically smaller clusters in the MD simulations compared to the KMC calculations due to finite-size effects and slow aggregation kinetics. By analyzing the rate kernels, we are able to identify the primary mechanisms responsible for (shear-induced) cluster growth and breakup. This understanding allows us to tune nanoparticle and process parameters to achieve desired cluster sizes and shapes.
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Affiliation(s)
- Takahiro Yokoyama
- Department of Mechanical Engineering, Keio University, 223-8522 Yokohama, Japan.
| | - Yusei Kobayashi
- Faculty of Mechanical Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Noriyoshi Arai
- Department of Mechanical Engineering, Keio University, 223-8522 Yokohama, Japan.
| | - Arash Nikoubashman
- Department of Mechanical Engineering, Keio University, 223-8522 Yokohama, Japan.
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, 01069 Dresden, Germany
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23
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Toledo PL, Gianotti AR, Vazquez DS, Ermácora MR. Protein nanocondensates: the next frontier. Biophys Rev 2023; 15:515-530. [PMID: 37681092 PMCID: PMC10480383 DOI: 10.1007/s12551-023-01105-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/21/2023] [Indexed: 09/09/2023] Open
Abstract
Over the past decade, myriads of studies have highlighted the central role of protein condensation in subcellular compartmentalization and spatiotemporal organization of biological processes. Conceptually, protein condensation stands at the highest level in protein structure hierarchy, accounting for the assembly of bodies ranging from thousands to billions of molecules and for densities ranging from dense liquids to solid materials. In size, protein condensates range from nanocondensates of hundreds of nanometers (mesoscopic clusters) to phase-separated micron-sized condensates. In this review, we focus on protein nanocondensation, a process that can occur in subsaturated solutions and can nucleate dense liquid phases, crystals, amorphous aggregates, and fibers. We discuss the nanocondensation of proteins in the light of general physical principles and examine the biophysical properties of several outstanding examples of nanocondensation. We conclude that protein nanocondensation cannot be fully explained by the conceptual framework of micron-scale biomolecular condensation. The evolution of nanocondensates through changes in density and order is currently under intense investigation, and this should lead to the development of a general theoretical framework, capable of encompassing the full range of sizes and densities found in protein condensates.
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Affiliation(s)
- Pamela L. Toledo
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Alejo R. Gianotti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Diego S. Vazquez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Mario R. Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
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24
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Deng D, Chang Y, Liu W, Ren M, Xia N, Hao Y. Advancements in Biosensors Based on the Assembles of Small Organic Molecules and Peptides. BIOSENSORS 2023; 13:773. [PMID: 37622859 PMCID: PMC10452798 DOI: 10.3390/bios13080773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023]
Abstract
Over the past few decades, molecular self-assembly has witnessed tremendous progress in a variety of biosensing and biomedical applications. In particular, self-assembled nanostructures of small organic molecules and peptides with intriguing characteristics (e.g., structure tailoring, facile processability, and excellent biocompatibility) have shown outstanding potential in the development of various biosensors. In this review, we introduced the unique properties of self-assembled nanostructures with small organic molecules and peptides for biosensing applications. We first discussed the applications of such nanostructures in electrochemical biosensors as electrode supports for enzymes and cells and as signal labels with a large number of electroactive units for signal amplification. Secondly, the utilization of fluorescent nanomaterials by self-assembled dyes or peptides was introduced. Thereinto, typical examples based on target-responsive aggregation-induced emission and decomposition-induced fluorescent enhancement were discussed. Finally, the applications of self-assembled nanomaterials in the colorimetric assays were summarized. We also briefly addressed the challenges and future prospects of biosensors based on self-assembled nanostructures.
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Affiliation(s)
- Dehua Deng
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China
| | - Yong Chang
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China
| | - Wenjing Liu
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China
| | - Mingwei Ren
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China
| | - Ning Xia
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China
| | - Yuanqiang Hao
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
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25
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He X, Qu Y, Xiong S, Jiang Z, Tang Y, Yan F, Deng Y, Sun Y. Functional L-Arginine Derivative as an Efficient Vector for Intracellular Protein Delivery for Potential Cancer Therapy. J Funct Biomater 2023; 14:301. [PMID: 37367265 DOI: 10.3390/jfb14060301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
The utilization of cytosolic protein delivery is a promising approach for treating various diseases by replacing dysfunctional proteins. Despite the development of various nanoparticle-based intracellular protein delivery methods, the complicated chemical synthesis of the vector, loading efficiency and endosomal escape efficiency of proteins remain a great challenge. Recently, 9-fluorenylmethyloxycarbonyl (Fmoc)-modified amino acid derivatives have been used to self-assemble into supramolecular nanomaterials for drug delivery. However, the instability of the Fmoc group in aqueous medium restricts its application. To address this issue, the Fmoc ligand neighboring arginine was substituted for dibenzocyclooctyne (DBCO) with a similar structure to Fmoc to obtain stable DBCO-functionalized L-arginine derivative (DR). Azide-modified triethylamine (crosslinker C) was combined with DR to construct self-assembled DRC via a click chemical reaction for delivering various proteins, such as BSA and saporin (SA), into the cytosol of cells. The hyaluronic-acid-coated DRC/SA was able to not only shield the cationic toxicity, but also enhance the intracellular delivery efficiency of proteins by targeting CD44 overexpression on the cell membrane. The DRC/SA/HA exhibited higher growth inhibition efficiency and lower IC50 compared to DRC/SA toward various cancer cell lines. In conclusion, DBCO-functionalized L-arginine derivative represents an excellent potential vector for protein-based cancer therapy.
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Affiliation(s)
- Xiao He
- Department of Geriatrics, Peking University Shenzhen Hospital, Shenzhen 518036, China
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yannv Qu
- Department of Geriatrics, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Su Xiong
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China
| | - Zhiru Jiang
- Department of Geriatrics, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Yaqin Tang
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China
| | - Fei Yan
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuanfei Deng
- Department of Geriatrics, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Yansun Sun
- Department of Geriatrics, Peking University Shenzhen Hospital, Shenzhen 518036, China
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Shao C, Bapat RA, Su J, Moradian-Oldak J. Regulation of Hydroxyapatite Nucleation In Vitro through Ameloblastin-Amelogenin Interactions. ACS Biomater Sci Eng 2023; 9:1834-1842. [PMID: 35068157 PMCID: PMC9308824 DOI: 10.1021/acsbiomaterials.1c01113] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Amelogenin (Amel) and ameloblastin (Ambn) are two primary extracellular enamel matrix proteins that play crucial roles for proper thickness, prismatic structure, and robust mechanical properties. Previous studies have shown that Amel and Ambn bind to each other, but the effect of their coassembly on the nucleation of hydroxyapatite (HAP) is unclear. Here, we systematically investigated the coassembly of recombinant mouse Amel and Ambn in various ratios using in situ atomic force microscopy, dynamic light scattering, and transmission electron microscopy. The size of protein particles decreased as the Ambn:Amel ratio increased. To define the coassembly domain on Ambn, we used Ambn-derived peptides and Ambn variants to examine their effects on the amelogenin particle size distribution. We found that the peptide sequence encoded by exon 5 of Ambn affected Amel self-assembly but the variant lacking this sequence did not have any effect on Amel self-assembly. Furthermore, through monitoring the pH change in bulk mineralization solution, we tracked the nucleation behavior of HAP in the presence of Ambn and Amel and found that their coassemblies at different ratios showed varying abilities to stabilize amorphous calcium phosphate. These results demonstrated that Ambn and Amel coassemble with each other via a motif within the sequence encoded by exon 5 of Ambn and cooperate in regulating the nucleation of HAP crystals, enhancing our understanding of the important role of enamel matrix proteins in amelogenesis.
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Affiliation(s)
- Changyu Shao
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, 2250 Alcazar Street, Los Angeles, California 90033, United States
| | - Rucha Arun Bapat
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, 2250 Alcazar Street, Los Angeles, California 90033, United States
| | - Jingtan Su
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, 2250 Alcazar Street, Los Angeles, California 90033, United States
| | - Janet Moradian-Oldak
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, 2250 Alcazar Street, Los Angeles, California 90033, United States
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Fang T, Han M, Wang Y, Xiang X, Chen L, Yang H, Kang Z, Huang F, Fan X, Han M, Xu X, Zhou G, Ullah N, Feng X. Effects of heating rates on the self-assembly behavior and gelling properties of beef myosin. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:2473-2482. [PMID: 36658470 DOI: 10.1002/jsfa.12456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/02/2023] [Accepted: 01/20/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Myosin is the most important component of myofibrillar protein, with excellent gelling properties. To date, heating treatment remains the mainstream method for forming gel in meat products, and it has the most extensive application in the field of meat industry. However, at present, there are few reports on the effects of heating rates on myosin self-assembly and aggregation behavior during heating treatment. RESULTS The present study aimed to investigate the effects of different heating rates (1, 2, 3 and 5 °C min-1 ) on the self-assembly behavior, physicochemical, structural and gelling properties of myosin. At the lowest heating rate of 1 °C min-1 , the myosin gel had a dense microstructure, the highest elastic modulus (G') and water holding capacity compared to higher heating rates (2, 3 and 5 °C min-1 ). At higher temperatures (40, 45 °C), the surface hydrophobicity, turbidity, particle size distribution and self-assembly behavior of myosin in pre-gelling solutions showed that myosin had sufficient time to denature, underwent full structure unfolding before aggregation at the heating rate of 1°C min-1 , and formed regular and homogeneous spherical aggregates. Therefore, the myosin gel also had a better three-dimensional network. CONCLUSION The heating rates had an important effect on the quality of myosin gels, and had theoretical implications for improving the quality of meat gel products. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Tian Fang
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Xi'an, China
| | - Mengfan Han
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Xi'an, China
| | - Yue Wang
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Xi'an, China
| | - Xiaomei Xiang
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Xi'an, China
| | - Lin Chen
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Xi'an, China
| | - Huijuan Yang
- College of Standardization, China Jiliang University, Zhejiang, China
| | - Zhuangli Kang
- School of Food Science, Henan Institute of Science and Technology, Xinxiang, China
| | - Feng Huang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, China
| | - Xiaojing Fan
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Xi'an, China
| | - Minyi Han
- Lab of Meat Processing and Quality Control of EDU, Synergetic Innovation Center of Food Safety and Nutrition, Nanjing, China
| | - Xinglian Xu
- Lab of Meat Processing and Quality Control of EDU, Synergetic Innovation Center of Food Safety and Nutrition, Nanjing, China
| | - Guanghong Zhou
- Lab of Meat Processing and Quality Control of EDU, Synergetic Innovation Center of Food Safety and Nutrition, Nanjing, China
| | - Niamat Ullah
- Department of Human Nutrition, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Xianchao Feng
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Xi'an, China
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Gomez Melo S, Wörthmüller D, Gönczy P, Banterle N, Schwarz US. Grand canonical Brownian dynamics simulations of adsorption and self-assembly of SAS-6 rings on a surface. J Chem Phys 2023; 158:085102. [PMID: 36859084 DOI: 10.1063/5.0135349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
The Spindle Assembly Abnormal Protein 6 (SAS-6) forms dimers, which then self-assemble into rings that are critical for the nine-fold symmetry of the centriole organelle. It has recently been shown experimentally that the self-assembly of SAS-6 rings is strongly facilitated on a surface, shifting the reaction equilibrium by four orders of magnitude compared to the bulk. Moreover, a fraction of non-canonical symmetries (i.e., different from nine) was observed. In order to understand which aspects of the system are relevant to ensure efficient self-assembly and selection of the nine-fold symmetry, we have performed Brownian dynamics computer simulation with patchy particles and then compared our results with the experimental ones. Adsorption onto the surface was simulated by a grand canonical Monte Carlo procedure and random sequential adsorption kinetics. Furthermore, self-assembly was described by Langevin equations with hydrodynamic mobility matrices. We find that as long as the interaction energies are weak, the assembly kinetics can be described well by coagulation-fragmentation equations in the reaction-limited approximation. By contrast, larger interaction energies lead to kinetic trapping and diffusion-limited assembly. We find that the selection of nine-fold symmetry requires a small value for the angular interaction range. These predictions are confirmed by the experimentally observed reaction constant and angle fluctuations. Overall, our simulations suggest that the SAS-6 system works at the crossover between a relatively weak binding energy that avoids kinetic trapping and a small angular range that favors the nine-fold symmetry.
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Affiliation(s)
- Santiago Gomez Melo
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120 Heidelberg, Germany
| | - Dennis Wörthmüller
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120 Heidelberg, Germany
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Niccolo Banterle
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Ulrich S Schwarz
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120 Heidelberg, Germany
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29
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Hisamatsu Y, Cheng F, Yamamoto K, Takase H, Umezawa N, Higuchi T. Control of the stepwise self-assembly process of a pH-responsive amphiphilic 4-aminoquinoline-tetraphenylethene conjugate. NANOSCALE 2023; 15:3177-3187. [PMID: 36655765 DOI: 10.1039/d2nr05756e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Controlling the kinetic processes of self-assembly and switching their kinetic properties according to the changes in external environments are crucial concepts in the field of supramolecular polymers in water for biological and biomedical applications. Here we report a new self-assembling amphiphilic 4-aminoquinoline (4-AQ)-tetraphenylethene (TPE) conjugate that exhibits kinetically controllable stepwise self-assembly and has the ability of switching its kinetic nature in response to pH. The self-assembly process of the 4-AQ amphiphile comprises the formation of sphere-like nanoparticles, a transition to short nanofibers, and their growth to long nanofibers with ∼1 μm length scale at room temperature (RT). The timescale of the self-assembly process differs according to the pH-responsivity of the 4-AQ moiety in a weakly acidic to neutral pH range. Therefore, after aging for 24 h at RT, the 4-AQ amphiphile forms metastable short nanofibers at pH 5.5, while it forms thermodynamically favored long nanofibers at pH 7.4. Moreover, the modulation of nanofiber growth proceeding spontaneously at RT was achieved by switching the kinetic pathway through changing the pH between 7.4 and 5.5.
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Affiliation(s)
- Yosuke Hisamatsu
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.
| | - Fangzhou Cheng
- Faculty of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Katsuhiro Yamamoto
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Hiroshi Takase
- Graduate School of Medical Sciences, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.
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Hiew SH, Lu Y, Han H, Gonçalves RA, Alfarano SR, Mezzenga R, Parikh AN, Mu Y, Miserez A. Modulation of Mechanical Properties of Short Bioinspired Peptide Materials by Single Amino-Acid Mutations. J Am Chem Soc 2023; 145:3382-3393. [PMID: 36730942 DOI: 10.1021/jacs.2c09853] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The occurrence of modular peptide repeats in load-bearing (structural) proteins is common in nature, with distinctive peptide sequences that often remain conserved across different phylogenetic lineages. These highly conserved peptide sequences endow specific mechanical properties to the material, such as toughness or elasticity. Here, using bioinformatic tools and phylogenetic analysis, we have identified the GX8 peptide with the sequence GLYGGYGX (where X can be any residue) in a wide range of organisms. By simple mutation of the X residue, we demonstrate that GX8 can be self-assembled into various supramolecular structures, exhibiting vastly different physicochemical and viscoelastic properties, from liquid-like coacervate microdroplets to hydrogels to stiff solid materials. A combination of spectroscopic, electron microscopy, mechanical, and molecular dynamics studies is employed to obtain insights into molecular scale interactions driving self-assembly of GX8 peptides, underscoring that π-π stacking and hydrophobic interactions are the drivers of peptide self-assembly, whereas the X residue determines the extent of hydrogen bonding that regulates the macroscopic mechanical response. This study highlights the ability of single amino-acid polymorphism to tune the supramolecular assembly and bulk material properties of GX8 peptides, enabling us to cover a broad range of potential biomedical applications such as hydrogels for tissue engineering or coacervates for drug delivery.
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Affiliation(s)
- Shu Hui Hiew
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Yang Lu
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Hao Han
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Rui A Gonçalves
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Serena Rosa Alfarano
- Department of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Atul N Parikh
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore.,Departments of Biomedical Engineering and Materials Science & Engineering, University of California, Davis, California 95616, United States
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Ali Miserez
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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Hansen J, Egelhaaf SU, Platten F. Protein solutions close to liquid-liquid phase separation exhibit a universal osmotic equation of state and dynamical behavior. Phys Chem Chem Phys 2023; 25:3031-3041. [PMID: 36607608 DOI: 10.1039/d2cp04553b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Liquid-liquid phase separation (LLPS) of protein solutions is governed by highly complex protein-protein interactions. Nevertheless, it has been suggested that based on the extended law of corresponding states (ELCS), as proposed for colloids with short-range attractions, one can rationalize not only the thermodynamics, but also the structure and dynamics of such systems. This claim is systematically and comprehensively tested here by static and dynamic light scattering experiments. Spinodal lines, the isothermal osmotic compressibility κT and the relaxation rate of concentration fluctuations Γ are determined for protein solutions in the vicinity of LLPS. All these quantities are found to exhibit a corresponding-states behavior. This means that, for different solution conditions, these quantities are essentially the same if considered at similar reduced temperature or second virial coefficient. For moderately concentrated solutions, the volume fraction ϕ dependence of κT and Γ can be consistently described by Baxter's model of adhesive hard spheres. The off-critical, asymptotic T behavior of κT and Γ close to LLPS is consistent with the scaling laws predicted by mean-field theory. Thus, the present work aims at a comprehensive experimental test of the applicability of the ELCS to structural and dynamical properties of concentrated protein solutions.
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Affiliation(s)
- Jan Hansen
- Condensed Matter Physics Laboratory, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany.
| | - Stefan U Egelhaaf
- Condensed Matter Physics Laboratory, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany.
| | - Florian Platten
- Condensed Matter Physics Laboratory, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany.
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32
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Protein-Based High Internal Phase Pickering Emulsions: A Review of Their Fabrication, Composition and Future Perspectives in the Food Industry. Foods 2023; 12:foods12030482. [PMID: 36766011 PMCID: PMC9914728 DOI: 10.3390/foods12030482] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/05/2023] [Accepted: 01/12/2023] [Indexed: 01/22/2023] Open
Abstract
Protein-based high internal phase Pickering emulsions (HIPEs) are emulsions using protein particles as a stabilizer in which the volume fraction of the dispersed phase exceeds 74%. Stabilizers are irreversibly adsorbed at the interface of the oil phase and water phase to maintain the droplet structure. Protein-based HIPEs have shown great potential for a variety of fields, including foods, due to the wide range of materials, simple preparation, and good biocompatibility. This review introduces the preparation routes of protein-based HIPEs and summarizes and classifies the preparation methods of protein stabilizers according to their formation mechanism. Further outlined are the types and properties of protein stabilizers used in the present studies, the composition of the oil phase, the encapsulating substances, and the properties of the constituted protein-based HIPEs. Finally, future development of protein-based HIPEs was explored, such as the development of protein-based stabilizers, the improvement of emulsification technology, and the quality control of stabilizers and protein-based HIPEs.
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Strofaldi A, Quinn MK, Seddon AM, McManus JJ. Polymorphic protein phase transitions driven by surface anisotropy. J Chem Phys 2023; 158:014905. [PMID: 36610968 DOI: 10.1063/5.0125452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Phase transitions of proteins are strongly influenced by surface chemical modifications or mutations. Human γD-crystallin (HGD) single-mutants have been extensively studied because they are associated with the onset of juvenile cataract. However, they have also provided a rich library of molecules to examine how specific inter-protein interactions direct protein assembly, providing new insights and valuable experimental data for coarse-grained patchy-particle models. Here, we demonstrate that the addition of new inter-protein interactions by mutagenesis is additive and increases the number and variety of condensed phases formed by proteins. When double mutations incorporating two specific single point mutations are made, the properties of both single mutations are retained in addition to the formation of a new condensed phase. We find that the HGD double-mutant P23VC110M self-assembles into spherical particles with retrograde solubility, orthorhombic crystals, and needle/plate shape crystals, while retaining the ability to undergo liquid-liquid phase separation. This rich polymorphism is only partially predicted by the experimental data on the constituent single mutants. We also report a previously un-characterized amorphous protein particle, with unique properties that differ from those of protein spherulites, protein particulates previously described. The particles we observe are amorphous, reversible with temperature, tens of microns in size, and perfectly spherical. When they are grown on pristine surfaces, they appear to form by homogeneous nucleation, making them unique, and we believe a new form of protein condensate. This work highlights the challenges in predicting protein behavior, which has frustrated rational assembly and crystallization but also provides rich data to develop new coarse-grained models to explain the observed polymorphism.
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Affiliation(s)
| | - Michelle K Quinn
- Department of Chemistry Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Annela M Seddon
- HH Wills Physics Laboratory, School of Physics, University of Bristol, Bristol BS8 1TL, United Kingdom
| | - Jennifer J McManus
- HH Wills Physics Laboratory, School of Physics, University of Bristol, Bristol BS8 1TL, United Kingdom
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BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions. Int J Mol Sci 2022; 23:ijms232315371. [PMID: 36499696 PMCID: PMC9741033 DOI: 10.3390/ijms232315371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
We present here a freely available web-based database, called BioMThermDB 1.0, of thermophysical and dynamic properties of various proteins and their aqueous solutions. It contains the hydrodynamic radius, electrophoretic mobility, zeta potential, self-diffusion coefficient, solution viscosity, and cloud-point temperature, as well as the conditions for those determinations and details of the experimental method. It can facilitate the meta-analysis and visualization of data, can enable comparisons, and may be useful for comparing theoretical model predictions with experiments.
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35
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Wijesundara YH, Herbert FC, Kumari S, Howlett T, Koirala S, Trashi O, Trashi I, Al-Kharji NM, Gassensmith JJ. Rip it, stitch it, click it: A Chemist's guide to VLP manipulation. Virology 2022; 577:105-123. [PMID: 36343470 DOI: 10.1016/j.virol.2022.10.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/09/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
Viruses are some of nature's most ubiquitous self-assembled molecular containers. Evolutionary pressures have created some incredibly robust, thermally, and enzymatically resistant carriers to transport delicate genetic information safely. Virus-like particles (VLPs) are human-engineered non-infectious systems that inherit the parent virus' ability to self-assemble under controlled conditions while being non-infectious. VLPs and plant-based viral nanoparticles are becoming increasingly popular in medicine as their self-assembly properties are exploitable for applications ranging from diagnostic tools to targeted drug delivery. Understanding the basic structure and principles underlying the assembly of higher-order structures has allowed researchers to disassemble (rip it), reassemble (stitch it), and functionalize (click it) these systems on demand. This review focuses on the current toolbox of strategies developed to manipulate these systems by ripping, stitching, and clicking to create new technologies in the biomedical space.
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Affiliation(s)
- Yalini H Wijesundara
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Rd. Richardson, TX, 75080, USA
| | - Fabian C Herbert
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Rd. Richardson, TX, 75080, USA
| | - Sneha Kumari
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Rd. Richardson, TX, 75080, USA
| | - Thomas Howlett
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Rd. Richardson, TX, 75080, USA
| | - Shailendra Koirala
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Rd. Richardson, TX, 75080, USA
| | - Orikeda Trashi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Rd. Richardson, TX, 75080, USA
| | - Ikeda Trashi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Rd. Richardson, TX, 75080, USA
| | - Noora M Al-Kharji
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Rd. Richardson, TX, 75080, USA
| | - Jeremiah J Gassensmith
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Rd. Richardson, TX, 75080, USA; Department of Biomedical Engineering, The University of Texas at Dallas, 800 West Campbell Rd. Richardson, TX, 75080, USA.
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36
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Noll GA, Furch ACU, Rose J, Visser F, Prüfer D. Guardians of the phloem - forisomes and beyond. THE NEW PHYTOLOGIST 2022; 236:1245-1260. [PMID: 36089886 DOI: 10.1111/nph.18476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
The phloem is a highly specialized vascular tissue that forms a fundamentally important transport and signaling pathway in plants. It is therefore a system worth protecting. The main function of the phloem is to transport the products of photosynthesis throughout the whole plant, but it also transports soluble signaling molecules and propagates electrophysiological signals. The phloem is constantly threatened by mechanical injuries, phloem-sucking pests and parasites, and the spread of pathogens, which has led to the evolution of efficient defense mechanisms. One such mechanism involves structural phloem proteins, which are thought to facilitate sieve element occlusion following injury and to defend the plant against pathogens. In leguminous plants, specialized structural phloem proteins known as forisomes form unique mechanoproteins via sophisticated molecular interaction and assembly mechanisms, thus enabling reversible sieve element occlusion. By understanding the structure and function of forisomes and other structural phloem proteins, we can develop a toolbox for biotechnological applications in material science and medicine. Furthermore, understanding the involvement of structural phloem proteins in plant defense mechanisms will allow phloem engineering as a new strategy for the development of crop varieties that are resistant to pests, pathogens and parasites.
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Affiliation(s)
- Gundula A Noll
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 8, 48143, Muenster, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143, Muenster, Germany
| | - Alexandra C U Furch
- Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Dornburger Straße 159, 07743, Jena, Germany
| | - Judith Rose
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 8, 48143, Muenster, Germany
| | - Franziska Visser
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 8, 48143, Muenster, Germany
| | - Dirk Prüfer
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 8, 48143, Muenster, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143, Muenster, Germany
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37
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Ionic liquids as protein stabilizers for biological and biomedical applications: A review. Biotechnol Adv 2022; 61:108055. [DOI: 10.1016/j.biotechadv.2022.108055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/13/2022] [Accepted: 10/23/2022] [Indexed: 11/22/2022]
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38
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Collard Y, Piñan Basualdo FN, Bolopion A, Gauthier M, Lambert P, Vandewalle N. Controlled transitions between metastable states of 2D magnetocapillary crystals. Sci Rep 2022; 12:16027. [PMID: 36163481 PMCID: PMC9513081 DOI: 10.1038/s41598-022-20035-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/07/2022] [Indexed: 11/22/2022] Open
Abstract
Magnetocapillary interactions between particles allow to self-assemble floating crystals along liquid interfaces. For a fixed number of particles, different states possessing different symmetrical features, known as metastable states, coexist. In this paper, we demonstrate how to trigger the transition from one state to another, either by rearranging the crystal, or by controlling its growth. First, we show that externally controlled magnetic fields can squeeze the entire crystal to induce structural modifications, that upon relaxation can lead to a modified state. Second, we propose localized laser-induced thermocapillary flows that can be used to guide new particles towards an existing crystal in a desired direction, thus favoring a particular resulting state. The control of the formation of metastable states is a key ingredient to functionalize such assemblies, paving the way to self-assembled microrobots.
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Affiliation(s)
- Ylona Collard
- GRASP, Institute of Physics B5a, Université de Liège, 4000, Liège, Belgium.
| | - Franco N Piñan Basualdo
- TIPs, École Polytechnique de Bruxelles, Université Libre de Bruxelle, 1050, Brussels, Belgium. .,FEMTO-ST, CNRS, Université Bourgogne Franche-Comté, 25000, Besançon, France.
| | - Aude Bolopion
- FEMTO-ST, CNRS, Université Bourgogne Franche-Comté, 25000, Besançon, France
| | - Michaël Gauthier
- FEMTO-ST, CNRS, Université Bourgogne Franche-Comté, 25000, Besançon, France
| | - Pierre Lambert
- TIPs, École Polytechnique de Bruxelles, Université Libre de Bruxelle, 1050, Brussels, Belgium
| | - Nicolas Vandewalle
- GRASP, Institute of Physics B5a, Université de Liège, 4000, Liège, Belgium
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39
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Vazquez DS, Toledo PL, Gianotti AR, Ermácora MR. Protein conformation and biomolecular condensates. Curr Res Struct Biol 2022; 4:285-307. [PMID: 36164646 PMCID: PMC9508354 DOI: 10.1016/j.crstbi.2022.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 10/27/2022] Open
Abstract
Protein conformation and cell compartmentalization are fundamental concepts and subjects of vast scientific endeavors. In the last two decades, we have witnessed exciting advances that unveiled the conjunction of these concepts. An avalanche of studies highlighted the central role of biomolecular condensates in membraneless subcellular compartmentalization that permits the spatiotemporal organization and regulation of myriads of simultaneous biochemical reactions and macromolecular interactions. These studies have also shown that biomolecular condensation, driven by multivalent intermolecular interactions, is mediated by order-disorder transitions of protein conformation and by protein domain architecture. Conceptually, protein condensation is a distinct level in protein conformational landscape in which collective folding of large collections of molecules takes place. Biomolecular condensates arise by the physical process of phase separation and comprise a variety of bodies ranging from membraneless organelles to liquid condensates to solid-like conglomerates, spanning lengths from mesoscopic clusters (nanometers) to micrometer-sized objects. In this review, we summarize and discuss recent work on the assembly, composition, conformation, material properties, thermodynamics, regulation, and functions of these bodies. We also review the conceptual framework for future studies on the conformational dynamics of condensed proteins in the regulation of cellular processes.
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Affiliation(s)
- Diego S. Vazquez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Pamela L. Toledo
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Alejo R. Gianotti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Mario R. Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
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40
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Munaò G, Costa D, Malescio G, Bomont JM, Prestipino S. Competition between clustering and phase separation in binary mixtures containing SALR particles. SOFT MATTER 2022; 18:6453-6464. [PMID: 35984438 DOI: 10.1039/d2sm00944g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We investigate by Monte Carlo simulations a mixture of particles with competing interactions (hard-sphere two-Yukawa, HSTY) and hard spheres (HS), with same diameters σ and a square-well (SW) cross attraction. In a recent study [G. Munaò et al., J. Phys. Chem. B, 2022, 126, 2027-2039], we have analysed situations-in terms of relative concentration and attraction strength-where HS promote the formation of clusters involving particles of both species under thermodynamic conditions that would not allow for clustering of the pure HSTY fluid. Here, we focus on the role played by the range of cross attraction in determining the equilibrium structure of the mixture, starting from a homogeneous low-density state. When the width of the well exceeds approximately σ, clustering takes place in the system, with aggregates characterised by various sizes and shapes. Only for low HSTY concentrations (less than 10%) a single big cluster appears, anticipating the behaviour observed for a wider well, around 1.2σ. In the latter case, a spherical cluster encompassing almost all particles is the stable structure at equilibrium. We interpret this outcome as a macrophase, liquid-vapour separation where the spherical cluster is just the form taken at low density by the liquid phase inside the vapour phase: indeed, when the density takes larger values, periodic boundary conditions select liquid-vapour interfaces with other non-spherical shapes, similarly as found for a finite sample of simple fluid going through the liquid-vapour coexistence region. For still higher densities we document the existence of a solid phase characterized by the alternation of bilayers filled with particles of one species and bilayers of the other species, giving the solid a peculiar wafer structure.
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Affiliation(s)
- Gianmarco Munaò
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy.
| | - Dino Costa
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy.
| | - Gianpietro Malescio
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy.
| | | | - Santi Prestipino
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy.
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41
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Kobayashi Y, Nikoubashman A. Self-Assembly of Amphiphilic Cubes in Suspension. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:10642-10648. [PMID: 35972298 DOI: 10.1021/acs.langmuir.2c01614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We study the self-assembly of amphiphilic cubic colloids using molecular dynamics as well as rejection-free kinetic Monte Carlo simulations. We vary both the number and location of the solvophobic faces (patches) on the cubes at several colloid volume fractions and determine the resulting size and shape distributions of the self-assembled aggregates. When the binding energy is comparable to the thermal energy of the system, aggregates typically consist of only few spontaneously associating/dissociating colloids. Increasing the binding energy (or lowering the temperature) leads to the emergence of highly stable aggregates, e.g., small dimers in pure suspensions of one-patch cubes or large (system-spanning) aggregates in suspensions of multipatch colloids. In mixtures of one- and multipatch cubes, the average aggregation number increases with increasing number of solvophobic faces on the multipatch cubes as well with increasing fraction of multipatch cubes. The resulting aggregate shapes range from elongated rods over fractal objects to compact spheres, depending on the number and arrangement of solvophobic patches on the cubic colloids. Our findings establish the complex self-assembly pathways for a class of building blocks that combine both interaction and shape anisotropy, with the potential of forming hierarchically ordered superstructures.
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Affiliation(s)
- Yusei Kobayashi
- Department of Mechanical Engineering, Keio University, 223-8522 Yokohama, Japan
| | - Arash Nikoubashman
- Department of Mechanical Engineering, Keio University, 223-8522 Yokohama, Japan
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
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42
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Li Y, Dong L, Mu Z, Liu L, Yang J, Wu Z, Pan D, Liu L. Research Advances of Lactoferrin in Electrostatic Spinning, Nano Self-Assembly, and Immune and Gut Microbiota Regulation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10075-10089. [PMID: 35968926 DOI: 10.1021/acs.jafc.2c04241] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Lactoferrin (LF) is a naturally present iron-binding globulin with the structural properties of an N-lobe strongly positively charged terminus and a cage-like structure of nano self-assembly encapsulation. These unique structural properties give it potential for development in the fields of electrostatic spinning, targeted delivery systems, and the gut-brain axis. This review will provide an overview of LF's unique structure, encapsulation, and targeted transport capabilities, as well as its applications in immunity and gut microbiota regulation. First, the microstructure of LF is summarized and compared with its homologous ferritin, revealing both structural and functional similarities and differences between them. Second, the electrostatic interactions of LF and its application in electrostatic spinning are summarized. Its positive charge properties can be applied to functional environmental protection packaging materials and to improving drug stability and antiviral effects, while electrostatic spinning can promote bone regeneration and anti-inflammatory effects. Then the nano self-assembly behavior of LF is exploited as a cage-like protein to encapsulate bioactive substances to construct functional targeted delivery systems for applications such as contrast agents, antibacterial dressings, anti-cancer therapy, and gene delivery. In addition, some covalent and noncovalent interactions of LF in the Maillard reaction and protein interactions and other topics are briefly discussed. Finally, LF may affect immunological function via controlling the gut microbiota. In conclusion, this paper reviews the research advances of LF in electrostatic spinning, nano self-assembly, and immune and gut microbiota regulation, aiming to provide a reference for its application in the food and pharmaceutical fields.
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Affiliation(s)
- Ying Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Lezhen Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Zhishen Mu
- Inner Mongolia Enterprise Technology Center, Inner Mongolia Mengniu Dairy (Group) Co., Ltd., Huhhot 011500, PR China
| | - Lingyi Liu
- Department of Food Science and Technology, University of Nebraska─Lincoln, Lincoln, Nebraska 68588-6205, United States
| | - Junsi Yang
- Department of Food Science and Technology, University of Nebraska─Lincoln, Lincoln, Nebraska 68588-6205, United States
| | - Zufang Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Daodong Pan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Lianliang Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, PR China
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43
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Oppen D, Grossmann L, Weiss J. Insights into characterizing and producing anisotropic food structures. Crit Rev Food Sci Nutr 2022; 64:1158-1176. [PMID: 35997311 DOI: 10.1080/10408398.2022.2113365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Besides the flavor profile of food, texture plays a major role in terms of the acceptance and likeability of food products. In contrast to gel-like homogenous isotropic structures, where the characterization is established and structure-texture mechanisms are well understood, there is still a lack of knowledge in the field of anisotropic complex food matrices. Food systems that show anisotropic properties in terms of macroscopic mechanical anisotropy as in grown meat, or mixed complex systems where anisotropic shaped particles or fibers are embedded into an isotropic matrix are challenging to characterize, hence the structure-texture correlation is not trivial to understand. In this paper, we bring together the state of the art of different anisotropic structures as a source of food, their formation in terms of structured plant proteins, and consequently the structure-texture correlation of those. Characteristic terms and properties to differentiate between anisotropic systems are introduced with the purpose to facilitate characterization of those. Based on the here provided terms and characteristics, further studies toward understanding such systems and their perception can be conducted. Beyond that, a first opinion on crucial influencing factors on the perception of anisotropic systems and their mechanistic background is provided.
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Affiliation(s)
- Dominic Oppen
- Department of Food Material Science, Institute of Food Science and Biotechnology, University of Hohenheim, Stuttgart, Germany
| | - Lutz Grossmann
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Jochen Weiss
- Department of Food Material Science, Institute of Food Science and Biotechnology, University of Hohenheim, Stuttgart, Germany
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44
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Lu Q, Hu Y, Yin Li C, Kuang Y. Aptamer‐Array‐Guided Protein Assembly Enhances Synthetic mRNA Switch Performance. Angew Chem Int Ed Engl 2022; 61:e202207319. [PMID: 35703374 PMCID: PMC9544043 DOI: 10.1002/anie.202207319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Indexed: 11/17/2022]
Abstract
Synthetic messenger RNA (mRNA) switches are powerful synthetic biological tools that can sense cellular molecules to manipulate cell fate. However, their performances are limited by high output signal noise due to leaky output protein expression. Here, we designed a readout control module that disables protein leakage from generating signal. Aptamer array on the switch guides the inactive output protein to self‐assemble into functional assemblies that generate output signal. Leaky protein expression fails to saturate the array, thus produces marginal signal. In this study, we demonstrated that switches with this module exhibit substantially lower signal noise and, consequently, higher input sensitivity and wider output range. Such switches are applicable for different types of input molecules and output proteins. The work here demonstrates a new type of spatially guided protein self‐assembly, affording novel synthetic mRNA switches that promise accurate cell manipulation for biomedical applications.
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Affiliation(s)
- Qiuyu Lu
- Department of Chemical and Biological Engineering The Hong Kong University of Science and Technology Clear Water Bay, Kowloon, Hong Kong Hong Kong
| | - Yaxin Hu
- Department of Chemical and Biological Engineering The Hong Kong University of Science and Technology Clear Water Bay, Kowloon, Hong Kong Hong Kong
| | - Cheuk Yin Li
- Department of Chemical and Biological Engineering The Hong Kong University of Science and Technology Clear Water Bay, Kowloon, Hong Kong Hong Kong
| | - Yi Kuang
- Department of Chemical and Biological Engineering The Hong Kong University of Science and Technology Clear Water Bay, Kowloon, Hong Kong Hong Kong
- HKUST Shenzhen Research Institute Shenzhen Guangdong China
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45
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Scotti A, Gasser U, Petrunin AV, Fruhner L, Richtering W, Houston JE. Experimental determination of the bulk moduli of hollow nanogels. SOFT MATTER 2022; 18:5750-5758. [PMID: 35899831 DOI: 10.1039/d2sm00680d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The softness of an object can be quantified by one of the fundamental elastic moduli. The bulk modulus of the particle is most appropriate in the presence of isotropic compressions. Here, we use small-angle neutron scattering with contrast variation to directly access the bulk modulus of polymeric nanocapsules - pNIPAM-based hollow nanogels. We show that the size of the cavity is the most important quantity that determines the softness of hollow nanogels. During initial compression, the polymer collapses into the cavity and leads to a large change in the particle volume, resulting in a very small initial bulk modulus. Once the cavity is partially occupied by the polymer, the hollow nanogels become significantly stiffer since now the highly crosslinked network has to be compressed. Furthermore, we show that the larger the cavity, the softer the nanogel.
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Affiliation(s)
- Andrea Scotti
- Institute of Physical Chemistry, RWTH Aachen University, 52056 Aachen, Germany.
| | - Urs Gasser
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | | | - Lisa Fruhner
- Forschungszentrum Jülich GmbH Jülich Centre for Neutron Science (JCNS-1) and Institute for Biological Information processing (IBI-8), 52425 Jülich, Germany
| | - Walter Richtering
- Institute of Physical Chemistry, RWTH Aachen University, 52056 Aachen, Germany.
| | - Judith E Houston
- European Spallation Source ERIC, Box 176, SE-221 00 Lund, Sweden
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46
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In vitro investigation of protein assembly by combined microscopy and infrared spectroscopy at the nanometer scale. Proc Natl Acad Sci U S A 2022; 119:e2200019119. [PMID: 35914130 PMCID: PMC9371722 DOI: 10.1073/pnas.2200019119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The nanoscale structure and dynamics of proteins on surfaces has been extensively studied using various imaging techniques, such as transmission electron microscopy and atomic force microscopy (AFM) in liquid environments. These powerful imaging techniques, however, can potentially damage or perturb delicate biological material and do not provide chemical information, which prevents a fundamental understanding of the dynamic processes underlying their evolution under physiological conditions. Here, we use a platform developed in our laboratory that enables acquisition of infrared (IR) spectroscopy and AFM images of biological material in physiological liquids with nanometer resolution in a cell closed by atomically thin graphene membranes transparent to IR photons. In this work, we studied the self-assembly process of S-layer proteins at the graphene-aqueous solution interface. The graphene acts also as the membrane separating the solution containing the proteins and Ca2+ ions from the AFM tip, thus eliminating sample damage and contamination effects. The formation of S-layer protein lattices and their structural evolution was monitored by AFM and by recording the amide I and II IR absorption bands, which reveal the noncovalent interaction between proteins and their response to the environment, including ionic strength and solvation. Our measurement platform opens unique opportunities to study biological material and soft materials in general.
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47
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Zhang C, Liu W, Deng J, Ma S, Chang Z, Yang J. Structural Insights into the Interaction between Bacillus subtilis SepF Assembly and FtsZ by Solid-State NMR Spectroscopy. J Phys Chem B 2022; 126:5219-5230. [PMID: 35799411 DOI: 10.1021/acs.jpcb.2c02810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In many species of Gram-positive bacteria, SepF participated in the membrane tethering of FtsZ Z-ring during bacteria division. However, atomic-level details of interaction between SepF and FtsZ in an assembled state are lacking. Here, by combining solid-state NMR (SSNMR) with biochemical analyses, the interaction of Bacillus subtilis SepF and the C-terminal domain (CTD) of FtsZ was investigated. We obtained near complete chemical shift assignments of SepF and determined the structural model of the SepF monomer. Interaction with FtsZ-CTD caused further packing of SepF rings, and SSNMR experiments revealed the affected residues locating at α1, α2, β3, and β4 of SepF. Solution NMR experiments of dimeric SepF constructed by point mutation strategy proved a prerequisite role of α-α interface formation in SepF for FtsZ binding. Overall, our results provide structural insights into the mechanisms of SepF-FtsZ interaction for better understanding the function of SepF in bacteria.
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Affiliation(s)
- Chang Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P. R. China.,National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Wenjing Liu
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jing Deng
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Shaojie Ma
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P. R. China.,National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Ziwei Chang
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Jun Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P. R. China.,National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
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48
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Catalini S, Lutz-Bueno V, Usuelli M, Diener M, Taschin A, Bartolini P, Foggi P, Paolantoni M, Mezzenga R, Torre R. Multi-length scale structural investigation of lysozyme self-assembly. iScience 2022; 25:104586. [PMID: 35784788 PMCID: PMC9240868 DOI: 10.1016/j.isci.2022.104586] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/20/2022] [Accepted: 06/07/2022] [Indexed: 12/02/2022] Open
Abstract
Reactive amyloid oligomers are responsible for cytotoxicity in amyloid pathologies and because of their unstable nature characterizing their behavior is a challenge. The physics governing the self-assembly of proteins in crowded conditions is extremely complex and its comprehension, despite its paramount relevance to understanding molecular mechanisms inside cells and optimizing pharmaceutical processes, remains inconclusive. Here, we focus on the amyloid oligomerization process in self-crowded lysozyme aqueous solutions in acidic conditions. We reveal that the amyloid oligomers form at high protein concentration and low pH. Through multi-length scale spectroscopic investigations, we find that amyloid oligomers can further interconnect with each other by weak and non-specific interactions forming an extended network that leads to the percolation of the whole system. Our multi-length scale structural analysis follows the thermal history of amyloid oligomers from different perspectives and highlights the impact of hierarchical self-assembly of biological macromolecules on functional properties. Use of multi-length scale spectroscopies to characterize unstable amyloid oligomers Lysozyme form thermo-labile amyloid oligomers in self-crowded conditions Amyloid oligomers interact and form an extended hydrogel network Amyloid oligomers are responsible for the existence of the hydrogel matrix
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49
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Hansen J, Pedersen JN, Pedersen JS, Egelhaaf SU, Platten F. Universal effective interactions of globular proteins close to liquid–liquid phase separation: Corresponding-states behavior reflected in the structure factor. J Chem Phys 2022; 156:244903. [DOI: 10.1063/5.0088601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Intermolecular interactions in protein solutions, in general, contain many contributions. If short-range attractions dominate, the state diagram exhibits liquid–liquid phase separation (LLPS) that is metastable with respect to crystallization. In this case, the extended law of corresponding states (ELCS) suggests that thermodynamic properties are insensitive to details of the underlying interaction potential. Using lysozyme solutions, we investigate the applicability of the ELCS to the static structure factor and how far effective colloidal interaction models can help to rationalize the phase behavior and interactions of protein solutions in the vicinity of the LLPS binodal. The (effective) structure factor has been determined by small-angle x-ray scattering. It can be described by Baxter’s adhesive hard-sphere model, which implies a single fit parameter from which the normalized second virial coefficient b2 is inferred and found to quantitatively agree with previous results from static light scattering. The b2 values are independent of protein concentration but systematically vary with temperature and solution composition, i.e., salt and additive content. If plotted as a function of temperature normalized by the critical temperature, the values of b2 follow a universal behavior. These findings validate the applicability of the ELCS to globular protein solutions and indicate that the ELCS can also be reflected in the structure factor.
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Affiliation(s)
- Jan Hansen
- Heinrich Heine University, Condensed Matter Physics Laboratory, Düsseldorf, Germany
| | - Jannik N. Pedersen
- iNANO Interdisciplinary Nanoscience Center and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Jan Skov Pedersen
- iNANO Interdisciplinary Nanoscience Center and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Stefan U. Egelhaaf
- Heinrich Heine University, Condensed Matter Physics Laboratory, Düsseldorf, Germany
| | - Florian Platten
- Heinrich Heine University, Condensed Matter Physics Laboratory, Düsseldorf, Germany
- Forschungszentrum Jülich, Institute of Biological Information Processing IBI-4, Biomacromolecular Systems and Processes, Jülich, Germany
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50
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Lu Q, Hu Y, Li CY, Kuang Y. Aptamer‐Array‐Guided Protein Assembly Enhances Synthetic mRNA Switch Performance. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Qiuyu Lu
- Hong Kong University of Science and Technology School of Engineering Chemical and Biological Engineering HONG KONG
| | - Yaxin Hu
- Hong Kong University of Science and Technology School of Engineering Chemical and Biological Engineering HONG KONG
| | - Cheuk Yin Li
- Hong Kong University of Science and Technology School of Engineering Chemical and Biological Engineering HONG KONG
| | - Yi Kuang
- Hong Kong University of Science and Technology Chemical and Biological Engineering Room 5578, Academic Bldg,Clear Water Bay 000000 Kowloon HONG KONG
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