1
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Brightwell DF, Samanta K, Watts JA, Fay MW, Palma A. Sequence-controlled divergent supramolecular assembly of polyproline helices into metallo-peptide nanoparticles. NANOSCALE ADVANCES 2024; 7:94-98. [PMID: 39659764 PMCID: PMC11626207 DOI: 10.1039/d4na00762j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Accepted: 12/02/2024] [Indexed: 12/12/2024]
Abstract
The field of peptide based supramolecular biomaterials is fast evolving. These types of constructs have been shown to find applications in the fields of bioimaging, drug delivery and scaffolds for chemical reactions. However, the community typically focuses on the use of two specific classes of structured peptides: α-helices and β-sheets, clearly neglecting a unique peptide secondary structure: the polyproline helix. Herein, we report the first design, synthesis and characterization of polyproline based metallo-peptide nanoparticles. We demonstrate that rationally engineered polyproline helices can assemble in a divergent manner, into two types of nanoparticles. We also demonstrate that the primary sequence of the functionalised polyproline peptide is crucial to ensure a controlled assembly. This work clearly demonstrates that polyproline helices can be a powerful tool to achieve supramolecular assemblies of complex and responsive bioinspired nanomaterials.
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Affiliation(s)
- Dominic F Brightwell
- School of Chemistry and Forensic Science, Supramolecular and Interfacial Chemistry, Ingram Building, The University of Kent Canterbury CT2 7NZ Kent UK
| | - Kushal Samanta
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Julie A Watts
- Nanoscale and Microscale Research Centre, University of Nottingham Nottingham NG7 2RD UK
- School of Pharmacy, University of Nottingham Nottingham NG7 2RD UK
| | - Michael W Fay
- Nanoscale and Microscale Research Centre, University of Nottingham Nottingham NG7 2RD UK
- Faculty of Engineering, University of Nottingham Nottingham NG7 2RD UK
| | - Aniello Palma
- School of Chemistry, University College Dublin Belfield Dublin 4 Ireland
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2
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Leclercq L. Law and Order of Colloidal Tectonics: From Molecules to Self-Assembled Colloids. Molecules 2024; 29:5657. [PMID: 39683815 DOI: 10.3390/molecules29235657] [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: 10/31/2024] [Revised: 11/20/2024] [Accepted: 11/22/2024] [Indexed: 12/18/2024] Open
Abstract
Since biochemists and biologists have progressed in understanding the mechanisms involved in living organisms, biological systems have become a source of inspiration for chemists. In this context, the concept of colloidal tectonics, describing the spontaneous formation of colloidal particles or supracolloidal structures in which the building blocks are called "tectons", has emerged. Therefore, a bottom-up edification of tectons towards (supra) colloidal structures is allowed. Each (supra) colloidal system has at least one of the following properties: amphiphilicity, predictability, versatility, commutability, and reversibility. However, for these systems to perform even more interesting functions, it is necessary for tectons to have very precise chemical and physical properties so that new properties emerge in (supra) colloidal systems. In this way, colloidal tectonics enables engineering at the nano- and micrometric level and contributes to the development of smart bioinspired systems with applications in catalysis, drug delivery, etc. In this review, an overview of the concept of colloidal tectonics is illustrated by some biotic systems. The design of abiotic (supra) colloidal systems and their applications in various fields are also addressed (notably Pickering emulsions for catalysis or drug delivery). Finally, theoretical directions for the design of novel self-assembled (supra) colloidal systems are discussed.
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Affiliation(s)
- Loïc Leclercq
- Univ. Lille, CNRS, Centrale Lille, Univ. Artois, UMR 8181-UCCS, Unité de Catalyse et Chimie du Solide, Lille 59000, France
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3
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Zhai XJ, Luo MY, Luo XM, Dong XY, Si Y, Zhang C, Han Z, Han R, Zang SQ, Mak TCW. Hierarchical assembly of Ag 40 nanowheel ranging from building blocks to diverse superstructure regulation. Nat Commun 2024; 15:9155. [PMID: 39443465 PMCID: PMC11500184 DOI: 10.1038/s41467-024-53471-3] [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: 05/17/2024] [Accepted: 10/09/2024] [Indexed: 10/25/2024] Open
Abstract
Achieving precise and controllable hierarchical self-assembly of functional nanoclusters within crystal lattices to create distinct architectures is of immense significance, yet it creates considerable challenges. Here we successfully synthesized a silver nanowheel Ag40, along with its optically pure enantiomers S-/R-Ag40. Each species possesses an internal nanospace and exhibits host-guest interactions. These structures are constructed from primary building blocks (Ag9). By manipulating the surface anions and guest molecules, the nanowheels function as secondary building blocks, spontaneously organizing into complex double- and triple-helical crystalline superstructures or one-dimensional chains {Ag41}n through conformational matching and diverse noncovalent interactions. Moreover, we demonstrate that the water-mediated complex specifically assembled with uridine monophosphate nucleotides, resulting in chiral assemblies of Ag40 that exhibit chiroptical activity for specific recognition. Our findings provide insights into the efficient construction of assemblies with hollow frameworks and propose strategies for superstructure engineering by manipulating surface motifs.
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Affiliation(s)
- Xue-Jing Zhai
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Meng-Yu Luo
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Xi-Ming Luo
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China.
| | - Xi-Yan Dong
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
- College of Chemistry and Chemical Engineering, Henan Polytechnic University, Jiaozuo, 454003, China
| | - Yubing Si
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Chong Zhang
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Zhen Han
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Runping Han
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Shuang-Quan Zang
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China.
| | - Thomas C W Mak
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, SAR, China
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4
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Grizel AV, Gorsheneva NA, Stevenson JB, Pflaum J, Wilfling F, Rubel AA, Chernoff YO. Osmotic stress induces formation of both liquid condensates and amyloids by a yeast prion domain. J Biol Chem 2024; 300:107766. [PMID: 39276934 DOI: 10.1016/j.jbc.2024.107766] [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: 03/14/2024] [Revised: 07/30/2024] [Accepted: 08/21/2024] [Indexed: 09/17/2024] Open
Abstract
Liquid protein condensates produced by phase separation are involved in the spatiotemporal control of cellular functions, while solid fibrous aggregates (amyloids) are associated with diseases and/or manifest as infectious or heritable elements (prions). Relationships between these assemblies are poorly understood. The Saccharomyces cerevisiae release factor Sup35 can produce both fluid liquid-like condensates (e.g., at acidic pH) and amyloids (typically cross-seeded by other prions). We observed acidification-independent formation of Sup35-based liquid condensates in response to hyperosmotic shock in the absence of other prions, both at increased and physiological expression levels. The Sup35 prion domain, Sup35N, is both necessary and sufficient for condensate formation, while the middle domain, Sup35M antagonizes this process. Formation of liquid condensates in response to osmotic stress is conserved within yeast evolution. Notably, condensates of Sup35N/NM protein originated from the distantly related yeast Ogataea methanolica can directly convert to amyloids in osmotically stressed S. cerevisiae cells, providing a unique opportunity for real-time monitoring of condensate-to-fibril transition in vivo by fluorescence microscopy. Thus, cellular fate of stress-induced condensates depends on protein properties and/or intracellular environment.
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Affiliation(s)
- Anastasia V Grizel
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Natalia A Gorsheneva
- Laboratory of Amyloid Biology and Department of Genetics and Biotechnology, St Petersburg State University, St Petersburg, Russia
| | - Jonathan B Stevenson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jeremy Pflaum
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Florian Wilfling
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Aleksandr A Rubel
- Laboratory of Amyloid Biology and Department of Genetics and Biotechnology, St Petersburg State University, St Petersburg, Russia
| | - Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.
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5
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Niblo JK, Swartley JR, Zhang Z, DuBay KH. 2D capsid formation within an oscillatory energy landscape: orderly self-assembly depends on the interplay between a dynamic potential and intrinsic relaxation times. SOFT MATTER 2024; 20:6702-6713. [PMID: 39046256 DOI: 10.1039/d4sm00455h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Multiple dissipative self-assembly protocols designed to create novel structures or to reduce kinetic traps have recently emerged. Specifically, temporal oscillations of particle interactions have been shown effective at both aims, but investigations thus far have focused on systems of simple colloids or their binary mixtures. In this work, we expand our understanding of the effect of temporally oscillating interactions to a two-dimensional coarse-grained viral capsid-like model that undergoes a self-limited assembly. This model includes multiple intrinsic relaxation times due to the internal structure of the capsid subunits and, under certain interaction regimes, proceeds via a two-step nucleation mechanism. We find that oscillations much faster than the local intrinsic relaxation times can be described via a time averaged inter-particle potential across a wide range of interaction strengths, while oscillations much slower than these relaxation times result in structures that adapt to the attraction strength of the current half-cycle. Interestingly, oscillation periods similar to these relaxation times shift the interaction window over which orderly assembly occurs by enabling error correction during the half-cycles with weaker attractions. Our results provide fundamental insights to non-equilibrium self-assembly on temporally variant energy landscapes.
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Affiliation(s)
- Jessica K Niblo
- Department of Chemistry, University of Virginia, McCormick Road, PO Box 400319, Charlottesville, VA 22903-4319, USA.
| | - Jacob R Swartley
- Department of Chemistry, University of Virginia, McCormick Road, PO Box 400319, Charlottesville, VA 22903-4319, USA.
| | - Zhongmin Zhang
- Department of Chemistry, University of North Carolina at Chapel Hill, Campus Box 3290, Chapel Hill, NC 27599-3290, USA
| | - Kateri H DuBay
- Department of Chemistry, University of Virginia, McCormick Road, PO Box 400319, Charlottesville, VA 22903-4319, USA.
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6
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Sarma S, Sudarshan TR, Nguyen V, Robang AS, Xiao X, Le JV, Helmicki ME, Paravastu AK, Hall CK. Design of parallel 𝛽-sheet nanofibrils using Monte Carlo search, coarse-grained simulations, and experimental testing. Protein Sci 2024; 33:e5102. [PMID: 39037281 PMCID: PMC11261811 DOI: 10.1002/pro.5102] [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: 11/10/2023] [Revised: 06/20/2024] [Accepted: 06/22/2024] [Indexed: 07/23/2024]
Abstract
Peptide self-assembly into amyloid fibrils provides numerous applications in drug delivery and biomedical engineering applications. We augment our previously-established computational screening technique along with experimental biophysical characterization to discover 7-mer peptides that self-assemble into "parallel β-sheets", that is, β-sheets with N-terminus-to-C-terminus 𝛽-strand vectors oriented in parallel. To accomplish the desired β-strand organization, we applied the PepAD amino acid sequence design software to the Class-1 cross-β spine defined by Sawaya et al. This molecular configuration includes two layers of parallel β-sheets stacked such that N-terminus-to-C-terminus vectors are oriented antiparallel for molecules on adjacent β-sheets. The first cohort of PepAD identified peptides were examined for their fibrillation behavior in DMD/PRIME20 simulations, and the top performing sequence was selected as a prototype for a subsequent round of sequence refinement. The two rounds of design resulted in a library of eight 7-mer peptides. In DMD/PRIME20 simulations, five of these peptides spontaneously formed fibril-like structures with a predominantly parallel 𝛽-sheet arrangement, two formed fibril-like structure with <50% in parallel 𝛽-sheet arrangement and one remained a random coil. Among the eight candidate peptides produced by PepAD and DMD/PRIME20, five were synthesized and purified. All five assembled into amyloid fibrils composed of parallel β-sheets based on Fourier transform infrared spectroscopy, circular dichroism, electron microscopy, and thioflavin-T fluorescence spectroscopy measurements.
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Affiliation(s)
- Sudeep Sarma
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Tarunya Rao Sudarshan
- Department of Chemical and Biomolecular EngineeringGeorgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Van Nguyen
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Alicia S. Robang
- Department of Chemical and Biomolecular EngineeringGeorgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Xingqing Xiao
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Present address:
Department of Chemistry, School of Chemistry and Chemical EngineeringHainan UniversityHaikou CityHainan ProvincePeople's Republic of China
| | - Justin V. Le
- Department of Chemical and Biomolecular EngineeringGeorgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Michael E. Helmicki
- Department of Chemical and Biomolecular EngineeringGeorgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Anant K. Paravastu
- Department of Chemical and Biomolecular EngineeringGeorgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Carol K. Hall
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNorth CarolinaUSA
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7
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Zhang J, Zhao D, Lu K, Yuan L, Du H. Gelation Behavior and Drug Sustained-Release Properties of a Helix Peptide Organohydrogel with pH Responsiveness. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:8568-8579. [PMID: 38591865 DOI: 10.1021/acs.langmuir.4c00266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Based on the typical similar repeat units (abcdefg)n of α-helical structure, the peptide H was designed to self-assemble into an organohydrogel in response to pH. Depending on the different pH, the proportions of secondary structure, microstructure, and mechanical properties of the gel were investigated. Circular dichroism (CD) and Fourier transform infrared (FT-IR) showed that the proportion of α-helical structure gradually increased to become dominant with the increase of pH. Combining transmission electron microscopy (TEM) and atomic force microscopy (AFM), it was found that the increase of the ordered α-helix structure promoted fiber formation. The further increase in pH changed the intermolecular forces, resulting in an increase in the α-helix content and the enhancement of helix-helix interaction, causing the gel fibers to converge into thicker and more dense ones. The temperature test showed the stable rheological properties of the organohydrogel between 20-60 °C. Drug release and cytotoxicity showed that the DOX-loaded organohydrogel could have a better release in an acidic environment, indicating its potential application as a drug local delivery carrier.
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Affiliation(s)
- Jiahui Zhang
- School of Chemistry and Chemical Engineering, Henan University of Technology Locus street, High-Tech Industry Development Zone, Zhengzhou 450001, China
| | - Dongxin Zhao
- School of Chemistry and Chemical Engineering, Henan University of Technology Locus street, High-Tech Industry Development Zone, Zhengzhou 450001, China
| | - Kui Lu
- School of Chemistry and Chemical Engineering, Henan University of Technology Locus street, High-Tech Industry Development Zone, Zhengzhou 450001, China
- School of Chemical Engineering and Food Science, Zhengzhou University of Technology, Yingcai Road 18, Zhengzhou 450044, Henan Province, China
| | - Libo Yuan
- School of Chemistry and Chemical Engineering, Henan University of Technology Locus street, High-Tech Industry Development Zone, Zhengzhou 450001, China
| | - Heng Du
- School of Food Science and Engineering, Henan University of Technology Locus street, High-Tech Industry Development Zone, Zhengzhou 450001, China
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8
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Xia X, Li H, Zang J, Cheng S, Du M. Advancements of the Molecular Directed Design and Structure-Activity Relationship of Ferritin Nanocage. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7629-7654. [PMID: 38518374 DOI: 10.1021/acs.jafc.3c09903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
Ferritin nanocages possess remarkable structural properties and biological functions, making them highly attractive for applications in functional materials and biomedicine. This comprehensive review presents an overview of the molecular characteristics, extraction and identification of ferritin, ferritin receptors, as well as the advancements in the directional design of high-order assemblies of ferritin and the applications based on its unique structural properties. Specifically, this Review focuses on the regulation of ferritin assembly from one to three dimensions, leveraging the symmetry of ferritin and modifications on key interfaces. Furthermore, it discusses targeted delivery of nutrition and drugs through facile loading and functional modification of ferritin. The aim of this Review is to inspire the design of micro/nano functional materials using ferritin and the development of nanodelivery vehicles for nutritional fortification and disease treatment.
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Affiliation(s)
- Xiaoyu Xia
- SKL of Marine Food Processing & Safety Control, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
- National Engineering Research Center of Seafood, Collaborative Innovation Centre of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Han Li
- SKL of Marine Food Processing & Safety Control, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
- National Engineering Research Center of Seafood, Collaborative Innovation Centre of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Jiachen Zang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Shuzhen Cheng
- SKL of Marine Food Processing & Safety Control, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
- National Engineering Research Center of Seafood, Collaborative Innovation Centre of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Ming Du
- SKL of Marine Food Processing & Safety Control, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
- National Engineering Research Center of Seafood, Collaborative Innovation Centre of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
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9
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Robang A, Roy A, Dodd-o JB, He D, Le JV, McShan AC, Hu Y, Kumar VA, Paravastu AK. Structural Consequences of Introducing Bioactive Domains to Designer β-Sheet Peptide Self-Assemblies. Biomacromolecules 2024; 25:1429-1438. [PMID: 38408372 PMCID: PMC10934295 DOI: 10.1021/acs.biomac.3c00962] [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: 09/11/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
We applied solid- and solution-state nuclear magnetic resonance spectroscopy to examine the structure of multidomain peptides composed of self-assembling β-sheet domains linked to bioactive domains. Bioactive domains can be selected to stimulate specific biological responses (e.g., via receptor binding), while the β-sheets provide the desirable nanoscale properties. Although previous work has established the efficacy of multidomain peptides, molecular-level characterization is lacking. The bioactive domains are intended to remain solvent-accessible without being incorporated into the β-sheet structure. We tested for three possible anticipated molecular-level consequences of introducing bioactive domains to β-sheet-forming peptides: (1) the bioactive domain has no effect on the self-assembling peptide structure; (2) the bioactive domain is incorporated into the β-sheet nanofiber; and (3) the bioactive domain interferes with self-assembly such that nanofibers are not formed. The peptides involved in this study incorporated self-assembling domains based on the (SL)6 motif and bioactive domains including a VEGF-A mimic (QK), an IGF-mimic (IGF-1c), and a de novo SARS-CoV-2 binding peptide (SBP3). We observed all three of the anticipated outcomes from our examination of peptides, illustrating the unintended structural effects that could adversely affect the desired biofunctionality and biomaterial properties of the resulting peptide hydrogel. This work is the first attempt to evaluate the structural effects of incorporating bioactive domains into a set of peptides unified by a similar self-assembling peptide domain. These structural insights reveal unmet challenges in the design of highly tunable bioactive self-assembling peptide hydrogels.
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Affiliation(s)
- Alicia
S. Robang
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Abhishek Roy
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Joseph B. Dodd-o
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Dongjing He
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Justin V. Le
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Andrew C. McShan
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Yuhang Hu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Vivek A. Kumar
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
- Department
of Chemicals and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department
of Biology, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Anant K. Paravastu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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10
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Lu Q, Xu Y, Poppleton E, Zhou K, Sulc P, Stephanopoulos N, Ke Y. DNA-Nanostructure-Guided Assembly of Proteins into Programmable Shapes. NANO LETTERS 2024; 24:1703-1709. [PMID: 38278134 PMCID: PMC10853956 DOI: 10.1021/acs.nanolett.3c04497] [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: 11/20/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
The development of methods to synthesize artificial protein complexes with precisely controlled configurations will enable diverse biological and medical applications. Using DNA to link proteins provides programmability that can be difficult to achieve with other methods. Here, we use DNA origami as an "assembler" to guide the linking of protein-DNA conjugates using a series of oligonucleotide hybridization and displacement operations. We constructed several isomeric protein nanostructures, including a dimer, two types of trimer structures, and three types of tetramer assemblies, on a DNA origami platform by using a C3-symmetric building block composed of a protein trimer modified with DNA handles. Our approach expands the scope for the precise assembly of protein-based nanostructures and will enable the formulation of functional protein complexes with stoichiometric and geometric control.
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Affiliation(s)
- Qinyi Lu
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Yang Xu
- Biodesign
Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Erik Poppleton
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Kun Zhou
- Department
of Biomedical Engineering, Georgia Institute
of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Petr Sulc
- Biodesign
Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Nicholas Stephanopoulos
- Biodesign
Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yonggang Ke
- Department
of Biomedical Engineering, Georgia Institute
of Technology and Emory University, Atlanta, Georgia 30322, United States
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11
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Min J, Rong X, Zhang J, Su R, Wang Y, Qi W. Computational Design of Peptide Assemblies. J Chem Theory Comput 2024; 20:532-550. [PMID: 38206800 DOI: 10.1021/acs.jctc.3c01054] [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: 01/13/2024]
Abstract
With the ongoing development of peptide self-assembling materials, there is growing interest in exploring novel functional peptide sequences. From short peptides to long polypeptides, as the functionality increases, the sequence space is also expanding exponentially. Consequently, attempting to explore all functional sequences comprehensively through experience and experiments alone has become impractical. By utilizing computational methods, especially artificial intelligence enhanced molecular dynamics (MD) simulation and de novo peptide design, there has been a significant expansion in the exploration of sequence space. Through these methods, a variety of supramolecular functional materials, including fibers, two-dimensional arrays, nanocages, etc., have been designed by meticulously controlling the inter- and intramolecular interactions. In this review, we first provide a brief overview of the current main computational methods and then focus on the computational design methods for various self-assembled peptide materials. Additionally, we introduce some representative protein self-assemblies to offer guidance for the design of self-assembling peptides.
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Affiliation(s)
- Jiwei Min
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Xi Rong
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Jiaxing Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
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12
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Gupta P, Sharma A, Mittal V. Polymeric Vehicles for Nucleic Acid Delivery: Enhancing the Therapeutic Efficacy and Cellular Uptake. RECENT ADVANCES IN DRUG DELIVERY AND FORMULATION 2024; 18:276-293. [PMID: 39356099 DOI: 10.2174/0126673878324536240805060143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/19/2024] [Accepted: 07/02/2024] [Indexed: 10/03/2024]
Abstract
BACKGROUND Therapeutic gene delivery may be facilitated by the use of polymeric carriers. When combined with nucleic acids to form nanoparticles or polyplexes, a variety of polymers may shield the cargo from in vivo breakdown and clearance while also making it easier for it to enter intracellular compartments. AIM AND OBJECTIVES Polymer synthesis design choices result in a wide variety of compounds and vehicle compositions. Depending on the application, these characteristics may be changed to provide enhanced endosomal escape, longer-lasting distribution, or stronger connection with nucleic acid cargo and cells. Here, we outline current methods for delivering genes in preclinical and clinical settings using polymers. METHODOLOGY Significant therapeutic outcomes have previously been attained using genetic material- delivering polymer vehicles in both in-vitro and animal models. When combined with nucleic acids to form nanoparticles or polyplexes, a variety of polymers may shield the cargo from in vivo breakdown and clearance while also making it easier for it to enter intracellular compartments. Many innovative diagnoses for nucleic acids have been investigated and put through clinical assessment in the past 20 years. RESULTS Polymer-based carriers have additional delivery issues due to their changes in method and place of biological action, as well as variances in biophysical characteristics. We cover recent custom polymeric carrier architectures that were tuned for nucleic acid payloads such genomemodifying nucleic acids, siRNA, microRNA, and plasmid DNA. CONCLUSION In conclusion, the development of polymeric carriers for gene delivery holds promise for therapeutic applications. Through careful design and optimization, these carriers can overcome various challenges associated with nucleic acid delivery, offering new avenues for treating a wide range of diseases.
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Affiliation(s)
- Parul Gupta
- Department of Pharmaceutics, Guru Gobind Singh College of Pharmacy, Yamunanagar, Haryana, 135001, India
| | - Anjali Sharma
- Department of Pharmaceutics, Guru Gobind Singh College of Pharmacy, Yamunanagar, Haryana, 135001, India
| | - Vishnu Mittal
- Department of Pharmaceutics, Guru Gobind Singh College of Pharmacy, Yamunanagar, Haryana, 135001, India
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13
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Chen X, Zhang T, Liu H, Zang J, Lv C, Du M, Zhao G. Shape-Anisotropic Assembly of Protein Nanocages with Identical Building Blocks by Designed Intermolecular π-π Interactions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2305398. [PMID: 37870198 PMCID: PMC10724428 DOI: 10.1002/advs.202305398] [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: 08/04/2023] [Revised: 09/12/2023] [Indexed: 10/24/2023]
Abstract
Protein lattices that shift the structure and shape anisotropy in response to environmental cues are closely coupled to potential functionality. However, to design and construct shape-anisotropic protein arrays from the same building blocks in response to different external stimuli remains challenging. Here, by a combination of the multiple, symmetric interaction sites on the outer surface of protein nanocages and the tunable features of phenylalanine-phenylalanine interactions, a protein engineering approach is reported to construct a variety of superstructures with shape anisotropy, including 3D cubic, 2D hexagonal layered, and 1D rod-like crystalline protein nanocage arrays by using one single protein building block. Notably, the assembly of these crystalline protein arrays is reversible, which can be tuned by external stimuli (pH and ionic strength). The anisotropic morphologies of the fabricated macroscopic crystals can be correlated with the Å-to-nm scale protein arrangement details by crystallographic elucidation. These results enhance the understanding of the freedom offered by an object's symmetry and inter-object π-π stacking interactions for protein building blocks to assemble into direction- and shape-anisotropic biomaterials.
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Affiliation(s)
- Xuemin Chen
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
| | - Tuo Zhang
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
| | - Hanxiong Liu
- School of Food Science and TechnologyNational Engineering Research Center of SeafoodDalian Polytechnic UniversityDalian116034China
| | - Jiachen Zang
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
| | - Chenyan Lv
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
| | - Ming Du
- School of Food Science and TechnologyNational Engineering Research Center of SeafoodDalian Polytechnic UniversityDalian116034China
| | - Guanghua Zhao
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
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Semchonok DA, Kyrilis FL, Hamdi F, Kastritis PL. Cryo-EM of a heterogeneous biochemical fraction elucidates multiple protein complexes from a multicellular thermophilic eukaryote. J Struct Biol X 2023; 8:100094. [PMID: 37638207 PMCID: PMC10451023 DOI: 10.1016/j.yjsbx.2023.100094] [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: 09/05/2022] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/29/2023] Open
Abstract
Biomolecular complexes and their interactions govern cellular structure and function. Understanding their architecture is a prerequisite for dissecting the cell's inner workings, but their higher-order assembly is often transient and challenging for structural analysis. Here, we performed cryo-EM on a single, highly heterogeneous biochemical fraction derived from Chaetomium thermophilum cell extracts to visualize the biomolecular content of the multicellular eukaryote. After cryo-EM single-particle image processing, results showed that a simultaneous three-dimensional structural characterization of multiple chemically diverse biomacromolecules is feasible. Namely, the thermophilic, eukaryotic complexes of (a) ATP citrate-lyase, (b) Hsp90, (c) 20S proteasome, (d) Hsp60 and (e) UDP-glucose pyrophosphorylase were characterized. In total, all five complexes have been structurally dissected in a thermophilic eukaryote in a total imaged sample area of 190.64 μm2, and two, in particular, 20S proteasome and Hsp60, exhibit side-chain resolution features. The C. thermophilum Hsp60 near-atomic model was resolved at 3.46 Å (FSC = 0.143) and shows a hinge-like conformational change of its equatorial domain, highly similar to the one previously shown for its bacterial orthologue, GroEL. This work demonstrates that cryo-EM of cell extracts will greatly accelerate the structural analysis of cellular complexes and provide unprecedented opportunities to annotate architectures of biomolecules in a holistic approach.
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Affiliation(s)
- Dmitry A. Semchonok
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Fotis L. Kyrilis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Farzad Hamdi
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Panagiotis L. Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, Halle/Saale, Germany
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15
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Chen Z, Xiao X, Yang L, Lian C, Xu S, Liu H. Prion-like Aggregation of the Heptapeptide GNNQQNY into Amyloid Nanofiber Is Governed by Configuration Entropy. J Chem Inf Model 2023; 63:6423-6435. [PMID: 37782627 DOI: 10.1021/acs.jcim.3c00370] [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: 10/04/2023]
Abstract
A major cause of prion infectivity is the early formation of small, fibril-like aggregates consisting of the heptapeptide GNNQQNY. The prion aggregates exhibit a unique stacking mode in which the hydrophobic tyrosine (Y) is exposed outward, forming a bilayer β-sheet-stacking zipper structure. This stacking mode of the prion peptides, termed "Y-outward" structure for convenience, goes against the common understanding that, for other amyloid-forming peptides, the hydrophobic residues should be hidden within the peptide fibril, referred to as "Y-inward" structure. To explore the extraordinary stacking behaviors of the prion GNNQQNY peptides, two fibril models are constructed in a fashion of "Y-outward" and "Y-inward" stackings and then studied in silico to examine their thermodynamic stabilities and disaggregation pathways. The "Y-inward" structure indeed exhibits stronger thermodynamic stability than the "Y-outward" structure, according to potential energy and stacking energy calculations. To show how the peptide fibrils dissociate, we illustrated two disaggregation pathways. A dihedral-based free energy landscape was then calculated to examine the conformational degrees of freedom of the GNNQQNY chains in the "Y-outward" and "Y-inward" structures. Peptide chains lose more configurational entropy in the "Y-inward" structure than in the "Y-outward" structure, indicating that the prion peptides are prone to aggregate in a fashion of "Y-outward" stacking pattern due to its low conformational constraints. The prion-like aggregation of the GNNQQNY peptides into amyloid fibrils is primarily governed by the configuration entropy.
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Affiliation(s)
- Zhangyang Chen
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xingqing Xiao
- Department of Chemistry, School of Chemistry and Chemical Engineering, Hainan University, Haikou City, Hainan Province 570228, P. R. China
| | - Li Yang
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, P. R. China
| | - Cheng Lian
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Shouhong Xu
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Honglai Liu
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
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16
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Zhang J, Zhao D, Lu K. Mechanisms and influencing factors of peptide hydrogel formation and biomedicine applications of hydrogels. SOFT MATTER 2023; 19:7479-7493. [PMID: 37756117 DOI: 10.1039/d3sm01057k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Self-assembled peptide-based hydrogels have shown great potential in bio-related applications due to their porous structure, strong mechanical stability, high biocompatibility, and easy functionalization. Herein, the structure and characteristics of hydrogels and the mechanism of action of several regular secondary structures during gelation are investigated. The factors influencing the formation of peptide hydrogels, especially the pH responsiveness and salt ion induction are analyzed and summarized. Finally, the biomedical applications of peptide hydrogels, such as bone tissue engineering, cell culture, antigen presentation, antibacterial materials, and drug delivery are reviewed.
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Affiliation(s)
- Jiahui Zhang
- School of Chemistry and Chemical Engineering, Henan University of Technology, Locus Street, High-Tech Industry Development Zone, Zhengzhou 450001, China.
| | - Dongxin Zhao
- School of Chemistry and Chemical Engineering, Henan University of Technology, Locus Street, High-Tech Industry Development Zone, Zhengzhou 450001, China.
| | - Kui Lu
- School of Chemistry and Chemical Engineering, Henan University of Technology, Locus Street, High-Tech Industry Development Zone, Zhengzhou 450001, China.
- School of Chemical Engineering and Food Science, Zhengzhou University of Technology, Yingcai Road 18, Zhengzhou, 450044, Henan Province, China.
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17
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Ghosh C, Ghosh S, Chatterjee A, Bera P, Mampallil D, Ghosh P, Das D. Dual enzyme-powered chemotactic cross β amyloid based functional nanomotors. Nat Commun 2023; 14:5903. [PMID: 37737223 PMCID: PMC10516904 DOI: 10.1038/s41467-023-41301-x] [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: 04/25/2022] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
Nanomotor chassis constructed from biological precursors and powered by biocatalytic transformations can offer important applications in the future, specifically in emergent biomedical techniques. Herein, cross β amyloid peptide-based nanomotors (amylobots) were prepared from short amyloid peptides. Owing to their remarkable binding capabilities, these soft constructs are able to host dedicated enzymes to catalyze orthogonal substrates for motility and navigation. Urease helps in powering the self-diffusiophoretic motion, while cytochrome C helps in providing navigation control. Supported by the simulation model, the design principle demonstrates the utilization of two distinct transport behaviours for two different types of enzymes, firstly enhanced diffusivity of urease with increasing fuel (urea) concentration and secondly, chemotactic motility of cytochrome C towards its substrate (pyrogallol). Dual catalytic engines allow the amylobots to be utilized for enhanced catalysis in organic solvent and can thus complement the technological applications of enzymes.
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Affiliation(s)
- Chandranath Ghosh
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, 741246, India
| | - Souvik Ghosh
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, 741246, India
| | - Ayan Chatterjee
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, 741246, India
| | - Palash Bera
- Tata Institute of Fundamental Research (TIFR), Hyderabad, Telangana, 500046, India
| | - Dileep Mampallil
- Department of Physics, Indian Institute of Science Education and Research (IISER) Tirupati, Mangalam, Andhra Pradesh, 517507, India
| | - Pushpita Ghosh
- School of Chemistry, Indian Institute of Science Education and Research (IISER), Thiruvananthapuram, Kerala, 695551, India
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, 741246, India.
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18
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Wang Y, Geng Q, Zhang Y, Adler-Abramovich L, Fan X, Mei D, Gazit E, Tao K. Fmoc-diphenylalanine gelating nanoarchitectonics: A simplistic peptide self-assembly to meet complex applications. J Colloid Interface Sci 2023; 636:113-133. [PMID: 36623365 DOI: 10.1016/j.jcis.2022.12.166] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/19/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023]
Abstract
9-fluorenylmethoxycarbonyl-diphenylalanine (Fmoc-FF), has been has been extensively explored due to its ultrafast self-assembly kinetics, inherent biocompatibility, tunable physicochemical properties, and especially, the capability of forming self-sustained gels under physiological conditions. Consequently, various methodologies to develop Fmoc-FF gels and their corresponding applications in biomedical and industrial fields have been extensively studied. Herein, we systemically summarize the mechanisms underlying Fmoc-FF self-assembly, discuss the preparation methodologies of Fmoc-FF hydrogels, and then deliberate the properties as well as the diverse applications of Fmoc-FF self-assemblies. Finally, the contemporary shortcomings which limit the development of Fmoc-FF self-assembly are raised and the alternative solutions are proposed, along with future research perspectives.
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Affiliation(s)
- Yunxiao Wang
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China; Zhejiang-Israel Joint Laboratory of Self-Assembling Functional Materials, Hangzhou 311200, China
| | - Qiang Geng
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Yan Zhang
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel; Zhejiang-Israel Joint Laboratory of Self-Assembling Functional Materials, Hangzhou 311200, China.
| | - Xinyuan Fan
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou 310027, China; Key Laboratory of Advanced Manufacturing Technology of Zhejiang Province, School of Mechanical Engineering, Zhejiang University, Hangzhou 310027, China; Zhejiang-Israel Joint Laboratory of Self-Assembling Functional Materials, Hangzhou 311200, China
| | - Deqing Mei
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou 310027, China; Key Laboratory of Advanced Manufacturing Technology of Zhejiang Province, School of Mechanical Engineering, Zhejiang University, Hangzhou 310027, China
| | - Ehud Gazit
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel; Department of Materials Science and Engineering, Iby and Aladar Fleischman, Tel Aviv University, 6997801 Tel Aviv, Israel; Zhejiang-Israel Joint Laboratory of Self-Assembling Functional Materials, Hangzhou 311200, China.
| | - Kai Tao
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China; Key Laboratory of Advanced Manufacturing Technology of Zhejiang Province, School of Mechanical Engineering, Zhejiang University, Hangzhou 310027, China; Zhejiang-Israel Joint Laboratory of Self-Assembling Functional Materials, Hangzhou 311200, China.
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19
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Zheng W, Oki K, Saha R, Hijikata Y, Yashima E, Ikai T. One-Handed Helical Tubular Ladder Polymers for Chromatographic Enantioseparation. Angew Chem Int Ed Engl 2023; 62:e202218297. [PMID: 36680515 DOI: 10.1002/anie.202218297] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023]
Abstract
Defect-free one-handed contracted helical tubular ladder polymers with a π-electron-rich cylindrical helical cavity were synthesized by alkyne benzannulations of the random-coil precursor polymers containing 6,6'-linked-1,1'-spirobiindane-7,7'-diol-based chiral monomer units. The resulting tightly-twisted helical tubular ladder polymers showed remarkably high enantioseparation abilities toward a variety of chiral hydrophobic aromatics with point, axial, and planar chiralities. The random-coil precursor polymer and analogous rigid-rod extended helical ribbon-like ladder polymer with no internal helical cavity exhibited no resolution abilities. The molecular dynamics simulations suggested that the π-electron-rich cylindrical helical cavity formed in the tightly-twisted tubular helical ladder structures is of key importance for producing the highly-enantioseparation ability, by which chiral aromatics can be enantioselectively encapsulated by specific π-π and/or hydrophobic interactions.
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Affiliation(s)
- Wei Zheng
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Kosuke Oki
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Ranajit Saha
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Yuh Hijikata
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Eiji Yashima
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Tomoyuki Ikai
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, 464-8603, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, Saitama, 332-0012, Japan
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20
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Amphipathic peptide-phospholipid nanofibers: Kinetics of fiber formation and molecular transfer between assemblies. Biophys Chem 2023; 296:106985. [PMID: 36863073 DOI: 10.1016/j.bpc.2023.106985] [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: 12/06/2022] [Revised: 02/13/2023] [Accepted: 02/23/2023] [Indexed: 02/27/2023]
Abstract
Understanding the kinetics of nano-assembly formation is important to elucidate the biological processes involved and develop novel nanomaterials with biological functions. In the present study, we report the kinetic mechanisms of nanofiber formation from a mixture of phospholipids and the amphipathic peptide 18A[A11C], carrying cysteine substitution of the apolipoprotein A-I-derived peptide 18A at residue 11. 18A[A11C] with acetylated N-terminus and amidated C-terminus can associate with phosphatidylcholine to form fibrous aggregates at neutral pH and lipid-to-peptide molar ratio of ∼1, although the reaction pathways of self-assembly remain unclear. Here, the peptide was added to giant 1-palmitoyl-2-oleoyl phosphatidylcholine vesicles to monitor nanofiber formation under fluorescence microscopy. The peptide initially solubilized the lipid vesicles into particles smaller than the resolution of optical microscope, and fibrous aggregates appeared subsequently. Transmission electron microscopy and dynamic light scattering analyses revealed that the vesicle-solubilized particles were spherical or circular, measuring ∼10-20 nm in diameter. The rate of nanofiber formation of 18A with 1,2-dipalmitoyl phosphatidylcholine from the particles was proportional to the square of lipid-peptide concentration in the system, suggesting that the association of particles, accompanied by conformational changes, was the rate-limiting step. Moreover, molecules in the nanofibers could be transferred between aggregates faster than those in the lipid vesicles. These findings provide useful information for the development and control of nano-assembling structures using peptides and phospholipids.
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21
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Yan J, Yang G, Zhu B, Zheng R, Cheng S, He K, Yin J. Deformable and Disintegrable Multifunctional Integrated Polyprodrug Amphiphiles for Synergistic Phototherapy and Chemotherapy. Biomacromolecules 2023; 24:400-412. [PMID: 36475673 DOI: 10.1021/acs.biomac.2c01215] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multimodal collaborative therapy has been recognized as one of the more effective means to eliminate tumors in the current biomedicine research field as compared with monotherapy. Among them, by taking advantage of its high-precision and controllability, phototherapy has become a mainstay of treatment. However, physical encapsulation of free photosensitive units within nanocarriers was one of the main implementations, which might inevitably result in the photosensitizer leakage and side effect. For this purpose, a kind of multifunctional integrated polyprodrug amphiphiles, P(PFO-IG-CPT)-PEG, were prepared by reversible addition-fragmentation chain transfer polymerization from polymerizable pentadecafluorooctan monomers, indocyanine green monomers, reduction-responsive camptothecin monomers, and acid-responsive PEG based methacrylate monomers (GMA(-OH/-PEG)). The resultant copolymers could self-assemble into spherical nanoparticles in water, performing size-deformability in acidic conditions and subsequent disintegration in reduction environment as demonstrated by in vitro experiments. Furthermore, an enhanced CPT release ratio and rate from nanoparticles could be achieved by a NIR irradiation due to the hyperthermia induced by the covalently linked IG moieties. Not only that, because of the sufficient O2 content brought by PFO, the NIR light-triggered generation of 1O2 was also detected in cells. With the combination of CPT-guided chemotherapy as well as NIR light-guided photo-thermal and photodynamic therapies, fatal and irreversible damage to cancer cells was observed by cell experiments; the implanted tumor size in the mouse model was obviously shrunk upon receiving multimodal collaborative therapy. We speculate that such fabricated nanodiagnosis and treatment systems could meet the growing emergency for effective drug delivery, programmed and on-demand drug release, and multimodal integrated therapy.
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Affiliation(s)
- Jinhao Yan
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology and Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, Hefei, Anhui 230009, P. R. China
| | - Guangwei Yang
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology and Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, Hefei, Anhui 230009, P. R. China
| | - Benshun Zhu
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology and Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, Hefei, Anhui 230009, P. R. China
| | - Ruifu Zheng
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology and Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, Hefei, Anhui 230009, P. R. China
| | - Sheng Cheng
- Instrumental Analysis Center, Hefei University of Technology Hefei, Anhui 230009, P. R. China
| | - Kewu He
- Imaging Center of the Third Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230031, P. R. China
| | - Jun Yin
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology and Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, Hefei, Anhui 230009, P. R. China
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22
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Xiao X, Robang AS, Sarma S, Le JV, Helmicki ME, Lambert MJ, Guerrero-Ferreira R, Arboleda-Echavarria J, Paravastu AK, Hall CK. Sequence patterns and signatures: Computational and experimental discovery of amyloid-forming peptides. PNAS NEXUS 2022; 1:pgac263. [PMID: 36712347 PMCID: PMC9802472 DOI: 10.1093/pnasnexus/pgac263] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
Screening amino acid sequence space via experiments to discover peptides that self-assemble into amyloid fibrils is challenging. We have developed a computational peptide assembly design (PepAD) algorithm that enables the discovery of amyloid-forming peptides. Discontinuous molecular dynamics (DMD) simulation with the PRIME20 force field combined with the FoldAmyloid tool is used to examine the fibrilization kinetics of PepAD-generated peptides. PepAD screening of ∼10,000 7-mer peptides resulted in twelve top-scoring peptides with two distinct hydration properties. Our studies revealed that eight of the twelve in silico discovered peptides spontaneously form amyloid fibrils in the DMD simulations and that all eight have at least five residues that the FoldAmyloid tool classifies as being aggregation-prone. Based on these observations, we re-examined the PepAD-generated peptides in the sequence pool returned by PepAD and extracted five sequence patterns as well as associated sequence signatures for the 7-mer amyloid-forming peptides. Experimental results from Fourier transform infrared spectroscopy (FTIR), thioflavin T (ThT) fluorescence, circular dichroism (CD), and transmission electron microscopy (TEM) indicate that all the peptides predicted to assemble in silico assemble into antiparallel β-sheet nanofibers in a concentration-dependent manner. This is the first attempt to use a computational approach to search for amyloid-forming peptides based on customized settings. Our efforts facilitate the identification of β-sheet-based self-assembling peptides, and contribute insights towards answering a fundamental scientific question: "What does it take, sequence-wise, for a peptide to self-assemble?".
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Affiliation(s)
| | | | | | - Justin V Le
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Michael E Helmicki
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Matthew J Lambert
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ricardo Guerrero-Ferreira
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Johana Arboleda-Echavarria
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University School of Medicine, Atlanta, GA 30322, USA
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23
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Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
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Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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24
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Li S, Xing R, van Hest JCM, Yan X. Peptide-based supramolecular assembly drugs toward cancer theranostics. Expert Opin Drug Deliv 2022; 19:847-860. [PMID: 35748126 DOI: 10.1080/17425247.2022.2093855] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION : Peptide-based supramolecular self-assembly has been demonstrated to be a flexible approach for the fabrication of programmable de novo nanodrugs by employing synergistic or reciprocal intermolecular non-covalent interactions; this class of nanomaterials holds significant promise for clinical translation, especially as cancer theranostics. AREAS COVERED : In this review, we describe the concept of cancer theranostic drug assembly by employing non-covalent interactions. That is, molecular drugs are formulated into nanoscale and even microscale architectures by peptide-modulated self-assembly. A series of peptide-based supramolecular assembly drugs are discussed, with an emphasis on the relation between structural feature and theranostic performance. EXPERT OPINION : Molecular design, manipulation of non-covalent interactions and elucidation of structure-function relationships not only facilitate the implementation of supramolecular self-assembly principles in drug development, but also provide a new means for advancing anticancer nanostructured drugs toward clinical application.
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Affiliation(s)
- Shukun Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Beijing 100190, China.,Bio-Organic Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, The Netherlands
| | - Ruirui Xing
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Beijing 100190, China.,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jan C M van Hest
- Bio-Organic Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, The Netherlands
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Beijing 100190, China.,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China.,Center for Mesoscience, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
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25
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Li J, Xue Y, Wang A, Tian S, Li Q, Bai S. Polyaniline Functionalized Peptide Self-Assembled Conductive Hydrogel for 3D Cell Culture. Gels 2022; 8:372. [PMID: 35735716 PMCID: PMC9222261 DOI: 10.3390/gels8060372] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/30/2022] [Accepted: 06/03/2022] [Indexed: 12/10/2022] Open
Abstract
The functionalization of self-assembled peptide hydrogel is of great importance to broaden its applications in the field of biomedicine. In this work, conductive hydrogel is fabricated by introducing conductive polymer polyaniline into peptide self-assembled hydrogel. Compared with pure peptide formed hydrogel, the conductive hydrogel exhibits enhanced conductivity, mechanical property and stability. In addition, the hydrogel is tested to be of great injectability and 3D bio-printability and could support the viability of encapsulated cells that are sensitive to electrical signals. It should have great application prospects in the preparation of tissue engineering scaffolds.
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Affiliation(s)
- Jieling Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No. 1 North 2nd Street, Zhongguancun, Beijing 100190, China; (J.L.); (Y.X.); (A.W.)
| | - Yan Xue
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No. 1 North 2nd Street, Zhongguancun, Beijing 100190, China; (J.L.); (Y.X.); (A.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anhe Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No. 1 North 2nd Street, Zhongguancun, Beijing 100190, China; (J.L.); (Y.X.); (A.W.)
| | - Shaonan Tian
- Modular Platform Public Instrument Center, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China;
| | - Qi Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No. 1 North 2nd Street, Zhongguancun, Beijing 100190, China; (J.L.); (Y.X.); (A.W.)
| | - Shuo Bai
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No. 1 North 2nd Street, Zhongguancun, Beijing 100190, China; (J.L.); (Y.X.); (A.W.)
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26
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Chatterjee A, Reja A, Pal S, Das D. Systems chemistry of peptide-assemblies for biochemical transformations. Chem Soc Rev 2022; 51:3047-3070. [PMID: 35316323 DOI: 10.1039/d1cs01178b] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
During the billions of years of the evolutionary journey, primitive polymers, involved in proto metabolic pathways with low catalytic activity, played critical roles in the emergence of modern enzymes with remarkable substrate specificity. The precise positioning of amino acid residues and the complex orchestrated interplay in the binding pockets of evolved enzymes promote covalent and non-covalent interactions to foster a diverse set of complex catalytic transformations. Recent efforts to emulate the structural and functional information of extant enzymes by minimal peptide based assemblies have attempted to provide a holistic approach that could help in discerning the prebiotic origins of catalytically active binding pockets of advanced proteins. In addition to the impressive sets of advanced biochemical transformations, catalytic promiscuity and cascade catalysis by such small molecule based dynamic systems can foreshadow the ancestral catalytic processes required for the onset of protometabolism. Looking beyond minimal systems that work close to equilibrium, catalytic systems and compartments under non-equilibrium conditions utilizing simple prebiotically relevant precursors have attempted to shed light on how bioenergetics played an essential role in chemical emergence of complex behaviour. Herein, we map out these recent works and progress where diverse sets of complex enzymatic transformations were demonstrated by utilizing minimal peptide based self-assembled systems. Further, we have attempted to cover the examples of peptide assemblies that could feature promiscuous activity and promote complex multistep cascade reaction networks. The review also covers a few recent examples of minimal transient catalytic assemblies under non-equilibrium conditions. This review attempts to provide a broad perspective for potentially programming functionality via rational selection of amino acid sequences leading towards minimal catalytic systems that resemble the traits of contemporary enzymes.
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Affiliation(s)
- Ayan Chatterjee
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Antara Reja
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Sumit Pal
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
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27
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Chen J, Pan S, Zhou J, Lin Z, Qu Y, Glab A, Han Y, Richardson JJ, Caruso F. Assembly of Bioactive Nanoparticles via Metal-Phenolic Complexation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2108624. [PMID: 34933398 DOI: 10.1002/adma.202108624] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/13/2021] [Indexed: 06/14/2023]
Abstract
The integration of bioactive materials (e.g., proteins and genes) into nanoparticles holds promise in fields ranging from catalysis to biomedicine. However, it is challenging to develop a simple and broadly applicable nanoparticle platform that can readily incorporate distinct biomacromolecules without affecting their intrinsic activity. Herein, a metal-phenolic assembly approach is presented whereby diverse functional nanoparticles can be readily assembled in water by combining various synthetic and natural building blocks, including poly(ethylene glycol), phenolic ligands, metal ions, and bioactive macromolecules. The assembly process is primarily mediated by metal-phenolic complexes through coordination and hydrophobic interactions, which yields uniform and spherical nanoparticles (mostly <200 nm), while preserving the function of the incorporated biomacromolecules (siRNA and five different proteins used). The functionality of the assembled nanoparticles is demonstrated through cancer cell apoptosis, RNA degradation, catalysis, and gene downregulation studies. Furthermore, the resulting nanoparticles can be used as building blocks for the secondary engineering of superstructures via templating and cross-linking with metal ions. The bioactivity and versatility of the platform can potentially be used for the streamlined and rational design of future bioactive materials.
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Affiliation(s)
- Jingqu Chen
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Shuaijun Pan
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Jiajing Zhou
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Zhixing Lin
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Yijiao Qu
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Agata Glab
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Yiyuan Han
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Joseph J Richardson
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Frank Caruso
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
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28
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Arghavani P, Pirhaghi M, Moosavi-Movahedi F, Mamashli F, Hosseini E, Moosavi-Movahedi AA. Amyloid management by chaperones: The mystery underlying protein oligomers’ dual functions. Curr Res Struct Biol 2022; 4:356-364. [DOI: 10.1016/j.crstbi.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
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Hu S, Yan J, Yang G, Ma C, Yin J. Self-Assembled Polymeric Materials: Design, Morphology, and Functional-Oriented Applications. Macromol Rapid Commun 2021; 43:e2100791. [PMID: 34967061 DOI: 10.1002/marc.202100791] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/15/2021] [Indexed: 11/10/2022]
Abstract
This Review focuses on the current research advances of the synthesis of various amphiphilic block copolymers (ABCs), such as conventional ABCs and newly-presented polyprodrug amphiphiles (PPAs), and the development of corresponding self-assemblies in selective solvents driven by the intermolecular interactions, like noncovalent hydrophobic interactions, π-π interactions, and hydrogen bonds, between ABCs or preformed small polymeric nanoparticles. The design of these assemblies is systematically introduced, and the diverse examples concerning the unique assembly structures along with the fast development of their exclusive properties and various applications in different fields were discussed. Possible perspectives on the existential challenges and glorious future were elucidated finally. We hope this review will provide a convenient way for readers to motivate more evolutional innovative concepts and methods to design next generation of novel polymeric nanoassemblies, and fill the gap between material design and practical applications. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Shoukui Hu
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology and Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering Hefei, Anhui, 230009, P. R. China
| | - Jinhao Yan
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology and Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering Hefei, Anhui, 230009, P. R. China
| | - Guangwei Yang
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology and Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering Hefei, Anhui, 230009, P. R. China
| | - Chao Ma
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology and Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering Hefei, Anhui, 230009, P. R. China
| | - Jun Yin
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology and Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering Hefei, Anhui, 230009, P. R. China
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30
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Dyakin VV, Dyakina-Fagnano NV, Mcintire LB, Uversky VN. Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology. Int J Mol Sci 2021; 23:ijms23010285. [PMID: 35008708 PMCID: PMC8745688 DOI: 10.3390/ijms23010285] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/24/2021] [Accepted: 12/22/2021] [Indexed: 12/23/2022] Open
Abstract
In humans, age-associated degrading changes, widely observed in molecular and cellular processes underly the time-dependent decline in spatial navigation, time perception, cognitive and psychological abilities, and memory. Cross-talk of biological, cognitive, and psychological clocks provides an integrative contribution to healthy and advanced aging. At the molecular level, genome, proteome, and lipidome instability are widely recognized as the primary causal factors in aging. We narrow attention to the roles of protein aging linked to prevalent amino acids chirality, enzymatic and spontaneous (non-enzymatic) post-translational modifications (PTMs SP), and non-equilibrium phase transitions. The homochirality of protein synthesis, resulting in the steady-state non-equilibrium condition of protein structure, makes them prone to multiple types of enzymatic and spontaneous PTMs, including racemization and isomerization. Spontaneous racemization leads to the loss of the balanced prevalent chirality. Advanced biological aging related to irreversible PTMs SP has been associated with the nontrivial interplay between somatic (molecular aging) and mental (psychological aging) health conditions. Through stress response systems (SRS), the environmental and psychological stressors contribute to the age-associated “collapse” of protein homochirality. The role of prevalent protein chirality and entropy of protein folding in biological aging is mainly overlooked. In a more generalized context, the time-dependent shift from enzymatic to the non-enzymatic transformation of biochirality might represent an important and yet underappreciated hallmark of aging. We provide the experimental arguments in support of the racemization theory of aging.
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Affiliation(s)
- Victor V. Dyakin
- The Nathan S. Kline Institute for Psychiatric Research (NKI), 140 Old Orangeburg Road, Bldg, 35, Bld. 35. Rom 201-C, Orangeburg, NY 10962, USA
- Correspondence: ; Tel.: +1-845-548-96-94; Fax: +1-845-398-5510
| | - Nuka V. Dyakina-Fagnano
- Child, Adolescent and Young Adult Psychiatry, 36 Franklin Turnpike, Waldwick, NJ 07463, USA;
| | - Laura B. Mcintire
- Department of Pathology and Cell Biology, Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA;
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA;
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31
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Bae J, Kim H, Kim G, Song J, Kim H. Dendrimer-Like Supramolecular Assembly of Proteins with a Tunable Size and Valency Through Stepwise Iterative Growth. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2102991. [PMID: 34719882 PMCID: PMC8693032 DOI: 10.1002/advs.202102991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/15/2021] [Indexed: 06/13/2023]
Abstract
The assembly of proteins in a programmable manner provides insight into the creation of novel functional nanomaterials for practical applications. Despite many advances, however, a rational protein assembly with an easy scalability in terms of size and valency remains a challenge. Here, a simple bottom-up approach to the supramolecular protein assembly with a tunable size and valency in a programmable manner is presented. The dendrimer-like protein assembly, simply called a "protein dendrimer," is constructed through a stepwise and alternate addition of a building block protein. Starting from zeroth-generation protein dendrimer (pG0 ) of 27 kDa, the protein dendrimer is sequentially grown to pG1 , pG2 , pG3 , to pG4 with a molecular mass of 94, 216, 483, and 959 kDa, respectively. The valency of the protein dendrimers at the periphery increases by a factor of two after each generation, allowing a tunable valency and easy functionalization. The protein dendrimers functionalizes with a targeting moiety and a cytotoxic protein cargo shows a typical feature of multi-valency in the avidity and a highly enhanced cellular cytotoxicity, exemplifying their utility as a protein delivery platform. The present approach can be effectively used in the creation of protein architectures with new functions for biotechnological and medical applications.
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Affiliation(s)
- Jin‐Ho Bae
- Department of Biological SciencesKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Korea
- Present address:
ProEn TherapeuticsSeongnam‐si13105Korea
| | - Hong‐Sik Kim
- Department of Biological SciencesKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Korea
| | - Gijeong Kim
- Department of Biological SciencesKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Korea
| | - Ji‐Joon Song
- Department of Biological SciencesKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Korea
| | - Hak‐Sung Kim
- Department of Biological SciencesKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Korea
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32
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Hirota S, Mashima T, Kobayashi N. Use of 3D domain swapping in constructing supramolecular metalloproteins. Chem Commun (Camb) 2021; 57:12074-12086. [PMID: 34714300 DOI: 10.1039/d1cc04608j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Supramolecules, which are formed by assembling multiple molecules by noncovalent intermolecular interactions instead of covalent bonds, often show additional properties that cannot be exhibited by a single molecule. Supramolecules have evolved into molecular machines in the field of chemistry, and various supramolecular proteins are responsible for life activities in the field of biology. The design and creation of supramolecular proteins will lead to development of new enzymes, functional biomaterials, drug delivery systems, etc.; thus, the number of studies on the regulation of supramolecular proteins is increasing year by year. Several methods, including disulfide bond, metal coordination, and surface-surface interaction, have been utilized to construct supramolecular proteins. In nature, proteins have been shown to form oligomers by 3D domain swapping (3D-DS), a phenomenon in which a structural region is exchanged between molecules of the same protein. We have been studying the mechanism of 3D-DS and utilizing 3D-DS to construct supramolecular metalloproteins. Cytochrome c forms cyclic oligomers and polymers by 3D-DS, whereas other metalloproteins, such as various c-type cytochromes and azurin form small oligomers and myoglobin forms a compact dimer. We have also utilized 3D-DS to construct heterodimers with different active sites, a protein nanocage encapsulating a Zn-SO4 cluster in the internal cavity, and a tetrahedron with a designed building block protein. Protein oligomer formation was controlled for the 3D-DS dimer of a dimer-monomer transition protein. This article reviews our research on supramolecular metalloproteins.
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Affiliation(s)
- Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
| | - Tsuyoshi Mashima
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
| | - Naoya Kobayashi
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
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33
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Zeng R, Lv C, Wang C, Zhao G. Bionanomaterials based on protein self-assembly: Design and applications in biotechnology. Biotechnol Adv 2021; 52:107835. [PMID: 34520791 DOI: 10.1016/j.biotechadv.2021.107835] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 01/13/2023]
Abstract
Elegant protein assembly to generate new biomaterials undergoes extremely rapid development for wide extension of biotechnology applications, which can be a powerful tool not only for creating nanomaterials but also for advancing understanding of the structure of life. Unique biological properties of proteins bestow these artificial biomaterials diverse functions that can permit them to be applied in encapsulation, bioimaging, biocatalysis, biosensors, photosynthetic apparatus, electron transport, magnetogenetic applications, vaccine development and antibodies design. This review gives a perspective view of the latest advances in the construction of protein-based nanomaterials. We initially start with distinguishable, specific interactions to construct sundry nanomaterials through protein self-assembly and concisely expound the assembly mechanism from the design strategy. And then, the design and construction of 0D, 1D, 2D, 3D protein assembled nanomaterials are especially highlighted. Furthermore, the potential applications have been discussed in detail. Overall, this review will illustrate how to fabricate highly sophisticated nanomaterials oriented toward applications in biotechnology based on the rules of supramolecular chemistry.
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Affiliation(s)
- Ruiqi Zeng
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China
| | - Chenyan Lv
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China
| | - Chengtao Wang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, No. 11 Fucheng Road, Haidian District, Beijing 100048, China
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China.
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34
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Chen G, Huang S, Shen Y, Kou X, Ma X, Huang S, Tong Q, Ma K, Chen W, Wang P, Shen J, Zhu F, Ouyang G. Protein-directed, hydrogen-bonded biohybrid framework. Chem 2021. [DOI: 10.1016/j.chempr.2021.07.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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35
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Xiao X, Wang Y, Seroski DT, Wong KM, Liu R, Paravastu AK, Hudalla GA, Hall CK. De novo design of peptides that coassemble into β sheet-based nanofibrils. SCIENCE ADVANCES 2021; 7:eabf7668. [PMID: 34516924 PMCID: PMC8442925 DOI: 10.1126/sciadv.abf7668] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Peptides’ hierarchical coassembly into nanostructures enables controllable fabrication of multicomponent biomaterials. In this work, we describe a computational and experimental approach to design pairs of charge-complementary peptides that selectively coassemble into β-sheet nanofibers when mixed together but remain unassembled when isolated separately. The key advance is a peptide coassembly design (PepCAD) algorithm that searches for pairs of coassembling peptides. Six peptide pairs are identified from a pool of ~106 candidates via the PepCAD algorithm and then subjected to DMD/PRIME20 simulations to examine their co-/self-association kinetics. The five pairs that spontaneously aggregate in kinetic simulations selectively coassemble in biophysical experiments, with four forming β-sheet nanofibers and one forming a stable nonfibrillar aggregate. Solid-state NMR, which is applied to characterize the coassembling pairs, suggests that the in silico peptides exhibit a higher degree of structural order than the previously reported CATCH(+/−) peptides.
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Affiliation(s)
- Xingqing Xiao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Dillon T. Seroski
- Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Kong M. Wong
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Renjie Liu
- Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Anant K. Paravastu
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gregory A. Hudalla
- Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Carol K. Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
- Corresponding author.
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Pal S, Goswami S, Das D. Cross β amyloid assemblies as complex catalytic machinery. Chem Commun (Camb) 2021; 57:7597-7609. [PMID: 34278403 DOI: 10.1039/d1cc02880d] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
How modern enzymes evolved as complex catalytic machineries to facilitate diverse chemical transformations is an open question for the emerging field of systems chemistry. Inspired by Nature's ingenuity in creating complex catalytic structures for exotic functions, short peptide-based cross β amyloid sequences have been shown to access intricate binding surfaces demonstrating the traits of extant enzymes and proteins. Based on their catalytic proficiencies reported recently, these amyloid assemblies have been argued as the earliest protein folds. Herein, we map out the recent progress made by our laboratory and other research groups that demonstrate the catalytic diversity of cross β amyloid assemblies. The important role of morphology and specific mutations in peptide sequences has been underpinned in this review. We have divided the feature article into different sections where examples from biology have been covered demonstrating the mechanism of extant biocatalysts and compared with recent works on cross β amyloid folds showing covalent catalysis, aldolase, hydrolase, peroxidase-like activities and complex cascade catalysis. Beyond equilibrium, we have extended our discussion towards transient catalytic amyloid phases mimicking the energy driven cytoskeleton polymerization. Finally, a future outlook has been provided on the way ahead for short peptide-based systems chemistry approaches that can lead to the development of robust catalytic networks with improved enzyme-like proficiencies and higher complexities. The discussed examples along with the rationale behind selecting specific amino acids sequence will benefit readers to design systems for achieving catalytic reactivity similar to natural complex enzymes.
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Affiliation(s)
- Sumit Pal
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Surashree Goswami
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
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Partridge BE, Winegar PH, Han Z, Mirkin CA. Redefining Protein Interfaces within Protein Single Crystals with DNA. J Am Chem Soc 2021; 143:8925-8934. [PMID: 34096291 PMCID: PMC8381744 DOI: 10.1021/jacs.1c04191] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Proteins are exquisite nanoscale building blocks: molecularly pure, chemically addressable, and inherently selective for their evolved function. The organization of proteins into single crystals with high positional, orientational, and translational order results in materials where the location of every atom can be known. However, controlling the organization of proteins is challenging due to the myriad interactions that define protein interfaces within native single crystals. Recently, we discovered that introducing a single DNA-DNA interaction between protein surfaces leads to changes in the packing of proteins within single crystals and the protein-protein interactions (PPIs) that arise. However, modifying specific PPIs to effect deliberate changes to protein packing is an unmet challenge. In this work, we hypothesized that disrupting and replacing a highly conserved PPI with a DNA-DNA interaction would enable protein packing to be modulated by exploiting the programmability of the introduced oligonucleotides. Using concanavalin A (ConA) as a model protein, we circumvent potentially deleterious mutagenesis and exploit the selective binding of ConA toward mannose to noncovalently attach DNA to the protein surface. We show that DNA association eliminates the major PPI responsible for crystallization of native ConA, thereby allowing subtle changes to DNA design (length, complementarity, and attachment position) to program distinct changes to ConA packing, including the realization of three novel crystal structures and the deliberate expansion of ConA packing along a single crystallographic axis. These findings significantly enhance our understanding of how DNA can supersede native PPIs to program protein packing within ordered materials.
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Affiliation(s)
- Benjamin E Partridge
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Peter H Winegar
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Zhenyu Han
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Chad A Mirkin
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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Raczyński K, Pihut A, Panek JJ, Jezierska A. Competition of Intra- and Intermolecular Forces in Anthraquinone and Its Selected Derivatives. Molecules 2021; 26:3448. [PMID: 34204133 PMCID: PMC8201066 DOI: 10.3390/molecules26113448] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 11/16/2022] Open
Abstract
Intra- and intermolecular forces competition was investigated in the 9,10-anthraquinone (1) and its derivatives both in vacuo and in the crystalline phase. The 1,8-dihydroxy-9,10-anthraquinone (2) and 1,8-dinitro-4,5-dihydroxy-anthraquinone (3) contain Resonance-Assisted Hydrogen Bonds (RAHBs). The intramolecular hydrogen bonds properties were studied in the electronic ground and excited states employing Møller-Plesset second-order perturbation theory (MP2), Density Functional Theory (DFT) method in its classical formulation as well as its time-dependent extension (TD-DFT). The proton potential functions were obtained via scanning the OH distance and the dihedral angle related to the OH group rotation. The topological analysis was carried out on the basis of theories of Atoms in Molecules (AIM-molecular topology, properties of critical points, AIM charges) and Electron Localization Function (ELF-2D maps showing bonding patterns, calculation of electron populations in the hydrogen bonds). The Symmetry-Adapted Perturbation Theory (SAPT) was applied for the energy decomposition in the dimers. Finally, Car-Parrinello molecular dynamics (CPMD) simulations were performed to shed light onto bridge protons dynamics upon environmental influence. The vibrational features of the OH stretching were revealed using Fourier transformation of the autocorrelation function of atomic velocity. It was found that the presence of OH and NO2 substituents influenced the geometric and electronic structure of the anthraquinone moiety. The AIM and ELF analyses showed that the quantitative differences between hydrogen bonds properties could be neglected. The bridged protons are localized on the donor side in the electronic ground state, but the Excited-State Intramolecular Proton Transfer (ESIPT) was noticed as a result of the TD-DFT calculations. The hierarchy of interactions determined by SAPT method indicated that weak hydrogen bonds play modifying role in the organization of these crystal structures, but primary ordering factor is dispersion. The CPMD crystalline phase results indicated bridged proton-sharing in the compound 2.
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Affiliation(s)
| | | | | | - Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland; (K.R.); (A.P.); (J.J.P.)
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Ozkan A, Sitharam M, Flores-Canales JC, Prabhu R, Kurnikova M. Baseline Comparisons of Complementary Sampling Methods for Assembly Driven by Short-Ranged Pair Potentials toward Fast and Flexible Hybridization. J Chem Theory Comput 2021; 17:1967-1987. [PMID: 33576635 DOI: 10.1021/acs.jctc.0c00945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This work measures baseline sampling characteristics that highlight fundamental differences between sampling methods for assembly driven by short-ranged pair potentials. Such granular comparison is essential for fast, flexible, and accurate hybridization of complementary methods. Besides sampling speed, efficiency, and accuracy of uniform grid coverage, other sampling characteristics measured are (i) accuracy of covering narrow low energy regions that have low effective dimension (ii) ability to localize sampling to specific basins, and (iii) flexibility in sampling distributions. As a proof of concept, we compare a recently developed geometric methodology EASAL (Efficient Atlasing and Search of Assembly Landscapes) and the traditional Monte Carlo (MC) method for sampling the energy landscape of two assembling trans-membrane helices, driven by short-range pair potentials. By measuring the above-mentioned sampling characteristics, we demonstrate that EASAL provides localized and accurate coverage of crucial regions of the energy landscape of low effective dimension, under flexible sampling distributions, with much fewer samples and computational resources than MC sampling. EASAL's empirically validated theoretical guarantees permit credible extrapolation of these measurements and comparisons to arbitrary number and size of assembling units. Promising avenues for hybridizing the complementary advantages of the two methods are discussed.
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Affiliation(s)
- Aysegul Ozkan
- CISE Department, University of Florida, Gainesville, Florida 32611-6120, United States
| | - Meera Sitharam
- CISE Department, University of Florida, Gainesville, Florida 32611-6120, United States
| | | | - Rahul Prabhu
- CISE Department, University of Florida, Gainesville, Florida 32611-6120, United States
| | - Maria Kurnikova
- Chemistry Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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Seo H, Lee H. Recent developments in microfluidic synthesis of artificial cell-like polymersomes and liposomes for functional bioreactors. BIOMICROFLUIDICS 2021; 15:021301. [PMID: 33833845 PMCID: PMC8012066 DOI: 10.1063/5.0048441] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/18/2021] [Indexed: 05/16/2023]
Abstract
Recent advances in droplet microfluidics have led to the fabrication of versatile vesicles with a structure that mimics the cellular membrane. These artificial cell-like vesicles including polymersomes and liposomes effectively enclose an aqueous core with well-defined size and composition from the surrounding environment to implement various biological reactions, serving as a diverse functional reactor. The advantage of realizing various biological phenomena within a compartment separated by a membrane that resembles a natural cell membrane is actively explored in the fields of synthetic biology as well as biomedical applications including drug delivery, biosensors, and bioreactors, to name a few. In this Perspective, we first summarize various methods utilized in producing these polymersomes and liposomes. Moreover, we will highlight some of the recent advances in the design of these artificial cell-like vesicles for functional bioreactors and discuss the current issues and future perspectives.
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Affiliation(s)
- Hanjin Seo
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Hyomin Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
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Galeb HA, Wilkinson EL, Stowell AF, Lin H, Murphy ST, Martin‐Hirsch PL, Mort RL, Taylor AM, Hardy JG. Melanins as Sustainable Resources for Advanced Biotechnological Applications. GLOBAL CHALLENGES (HOBOKEN, NJ) 2021; 5:2000102. [PMID: 33552556 PMCID: PMC7857133 DOI: 10.1002/gch2.202000102] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/04/2020] [Indexed: 05/17/2023]
Abstract
Melanins are a class of biopolymers that are widespread in nature and have diverse origins, chemical compositions, and functions. Their chemical, electrical, optical, and paramagnetic properties offer opportunities for applications in materials science, particularly for medical and technical uses. This review focuses on the application of analytical techniques to study melanins in multidisciplinary contexts with a view to their use as sustainable resources for advanced biotechnological applications, and how these may facilitate the achievement of the United Nations Sustainable Development Goals.
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Affiliation(s)
- Hanaa A. Galeb
- Department of ChemistryLancaster UniversityLancasterLA1 4YBUK
- Department of ChemistryScience and Arts CollegeRabigh CampusKing Abdulaziz UniversityJeddah21577Saudi Arabia
| | - Emma L. Wilkinson
- Department of Biomedical and Life SciencesLancaster UniversityLancasterLA1 4YGUK
| | - Alison F. Stowell
- Department of Organisation, Work and TechnologyLancaster University Management SchoolLancaster UniversityLancasterLA1 4YXUK
| | - Hungyen Lin
- Department of EngineeringLancaster UniversityLancasterLA1 4YWUK
| | - Samuel T. Murphy
- Department of EngineeringLancaster UniversityLancasterLA1 4YWUK
- Materials Science InstituteLancaster UniversityLancasterLA1 4YBUK
| | - Pierre L. Martin‐Hirsch
- Lancashire Teaching Hospitals NHS TrustRoyal Preston HospitalSharoe Green LanePrestonPR2 9HTUK
| | - Richard L. Mort
- Department of Biomedical and Life SciencesLancaster UniversityLancasterLA1 4YGUK
| | - Adam M. Taylor
- Lancaster Medical SchoolLancaster UniversityLancasterLA1 4YWUK
| | - John G. Hardy
- Department of ChemistryLancaster UniversityLancasterLA1 4YBUK
- Materials Science InstituteLancaster UniversityLancasterLA1 4YBUK
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Ikai T, Kawabata S, Mamiya F, Taura D, Ousaka N, Yashima E. Helix-Sense-Selective Encapsulation of Helical Poly(lactic acid)s within a Helical Cavity of Syndiotactic Poly(methyl methacrylate) with Helicity Memory. J Am Chem Soc 2020; 142:21913-21925. [PMID: 33315394 DOI: 10.1021/jacs.0c11204] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We report a highly enantio- and helix-sense-selective encapsulation of helical poly(lactic acid)s (PLAs) through a unique "helix-in-helix" superstructure formation within the helical cavity of syndiotactic poly(methyl methacrylate) (st-PMMA) with a one-handed helicity memory, which enables the separation of the enantiomeric helices of the left (M)- and right (P)-handed-PLAs. The M- and P-helical PLAs with different molar masses and a narrow molar mass distribution were prepared by the ring-opening living polymerization of the optically pure l- and d-lactides, respectively, followed by end-capping of the terminal residues of the PLAs with a 4-halobenzoate and then a C60 unit, giving the C60-free and C60-bound M- and P-PLAs. The C60-free and C60-bound M- and P-PLAs formed crystalline inclusion complexes with achiral st-PMMA accompanied by a preferred-handed helix induction in the st-PMMA backbone, thereby producing helix-in-helix superstructures with the same-handedness to each other. The induced helical st-PMMAs were retained after replacement with the achiral C60, indicating the memory of the induced helicity of the st-PMMAs. Both the C60-free and C60-bound helical PLAs were enantio- and helix-sense selectively encapsulated into the helical hollow space of the optically active M- and P-st-PMMAs with the helicity memory prepared using chiral amines. The M- and P-PLAs are preferentially encapsulated within the M- and P-st-PMMA helical cavity with the same-handedness to each other, respectively, independent of the terminal units. The C60-bound PLAs were more efficiently and enantioselectively trapped in the st-PMMA compared to the C60-free PLAs. The enantioselectivities were highly dependent on the molar mass of the C60-bound and C60-free PLAs and significantly increased as the molar mass of the PLAs increased.
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Affiliation(s)
- Tomoyuki Ikai
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Satoshi Kawabata
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Fumihiko Mamiya
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Daisuke Taura
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan.,Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Naoki Ousaka
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan.,Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Eiji Yashima
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan.,Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
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Chakraborty S, Khamrui R, Ghosh S. Redox responsive activity regulation in exceptionally stable supramolecular assembly and co-assembly of a protein. Chem Sci 2020; 12:1101-1108. [PMID: 34163877 PMCID: PMC8179030 DOI: 10.1039/d0sc05312k] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/14/2020] [Indexed: 11/23/2022] Open
Abstract
Supramolecular assembly of biomolecules/macromolecules stems from the desire to mimic complex biological structures and functions of living organisms. While DNA nanotechnology is already in an advanced stage, protein assembly is still in its infancy as it is a significantly difficult task due to their large molecular weight, conformational complexity and structural instability towards variation in temperature, pH or ionic strength. This article reports highly stable redox-responsive supramolecular assembly of a protein Bovine serum albumin (BSA) which is functionalized with a supramolecular structure directing unit (SSDU). The SSDU consists of a benzamide functionalized naphthalene-diimide (NDI) chromophore which is attached with the protein by a bio-reducible disulfide linker. The SSDU attached protein (NDI-BSA) exhibits spontaneous supramolecular assembly in water by off-set π-stacking among the NDI chromophores, leading to the formation of spherical nanoparticles (diameter: 150-200 nm). The same SSDU when connected with a small hydrophilic wedge (NDI-1) instead of the large globular protein, exhibits a different π-stacking mode with relatively less longitudinal displacement which results in a fibrillar network and hydrogelation. Supramolecular co-assembly of NDI-BSA and NDI-1 (3 : 7) produces similar π-stacking and an entangled 1D morphology. Both the spherical assembly of NDI-BSA or the fibrillar co-assembly of NDI-BSA + NDI-1 (3 : 7) provide sufficient thermal stability to the protein as its thermal denaturation could be completely surpassed while the secondary structure remained intact. However, the esterase like activity of the protein reduced significantly as a result of such supramolecular assembly indicating limited access by the substrate to the active site of the enzyme located in the confined environment. In the presence of glutathione (GSH), a biologically important tri-peptide, due to the cleavage of the disulfide bond, the protein became free and was released, resulting in fully regaining its enzymatic activity. Such supramolecular assembly provided excellent protection to the protein against enzymatic hydrolysis as the relative hydrolysis was estimated to be <30% for the co-assembled protein with respect to the free protein under identical conditions. Similar to bioactivity, the enzymatic hydrolysis also became prominent after GSH-treatment, confirming that the lack of hydrolysis in the supramolecularly assembled state is indeed related to the confinement of the protein in the nanostructure assembly.
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Affiliation(s)
- Saptarshi Chakraborty
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science 2A and 2B Raja S. C. Mullick Road Kolkata India-700032
| | - Rajesh Khamrui
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science 2A and 2B Raja S. C. Mullick Road Kolkata India-700032
| | - Suhrit Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science 2A and 2B Raja S. C. Mullick Road Kolkata India-700032
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Paik B, Calero-Rubio C, Lee JY, Jia X, Kiick KL, Roberts CJ. Characterizing aggregate growth and morphology of alanine-rich polypeptides as a function of sequence chemistry and solution temperature from scattering, spectroscopy, and microscopy. Biophys Chem 2020; 267:106481. [PMID: 33035751 DOI: 10.1016/j.bpc.2020.106481] [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: 06/16/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 10/23/2022]
Abstract
The aggregation behavior and stability of a series of alanine-rich peptides, which are included as components of peptide-polymer conjugates, were characterized using a combination of biophysical techniques. Light scattering techniques were used to monitor changes in peptide morphology and size distributions as a function of time and temperature. The results show large particles immediately upon dissolution in buffer. At room temperature, these particles relaxed to reach a mostly monomeric peptide state, while at higher temperatures, they grew to form aggregates. Circular dichroism spectroscopy (CD) was used to monitor temperature- and time-dependent conformational changes as a function of peptide sequence and incubation time. CD measurements reveal that all of the sequences are helical at low temperatures with transitions to non-helical conformation with increased temperature. Samples incubated at room temperature were able to recover their original helicity. At increased temperature, the shorter and longer peptide sequences showed notable changes in conformation, and were not able to recover their original helicity after 72 h. After incubation for up to one week, β-sheet conformations were observed in these two cases, while only α-helical conformation loss was observed for the peptide of intermediate molecular weight. Transmission electron microscopy measurements reveal the formation of fibrils after 72 h of incubation at 60 °C for all samples, in agreement with the scattering measurements. Additional quenching experiments show that peptide aggregation can be stalled when solutions are cooled to room temperature.
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Affiliation(s)
- Bradford Paik
- Department of Material Science & Engineering Department, University of Delaware, Newark, DE 19716, United States of America
| | - Cesar Calero-Rubio
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States of America
| | - Jee Young Lee
- Department of Material Science & Engineering Department, University of Delaware, Newark, DE 19716, United States of America
| | - Xinqiao Jia
- Department of Material Science & Engineering Department, University of Delaware, Newark, DE 19716, United States of America
| | - Kristi L Kiick
- Department of Material Science & Engineering Department, University of Delaware, Newark, DE 19716, United States of America.
| | - Christopher J Roberts
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States of America.
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Functional Mammalian Amyloids and Amyloid-Like Proteins. Life (Basel) 2020; 10:life10090156. [PMID: 32825636 PMCID: PMC7555005 DOI: 10.3390/life10090156] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/12/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023] Open
Abstract
Amyloids are highly ordered fibrous cross-β protein aggregates that are notorious primarily because of association with a variety of incurable human and animal diseases (termed amyloidoses), including Alzheimer’s disease (AD), Parkinson’s disease (PD), type 2 diabetes (T2D), and prion diseases. Some amyloid-associated diseases, in particular T2D and AD, are widespread and affect hundreds of millions of people all over the world. However, recently it has become evident that many amyloids, termed “functional amyloids,” are involved in various activities that are beneficial to organisms. Functional amyloids were discovered in diverse taxa, ranging from bacteria to mammals. These amyloids are involved in vital biological functions such as long-term memory, storage of peptide hormones and scaffolding melanin polymerization in animals, substrate attachment, and biofilm formation in bacteria and fungi, etc. Thus, amyloids undoubtedly are playing important roles in biological and pathological processes. This review is focused on functional amyloids in mammals and summarizes approaches used for identifying new potentially amyloidogenic proteins and domains.
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46
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Engineering allosteric communication. Curr Opin Struct Biol 2020; 63:115-122. [DOI: 10.1016/j.sbi.2020.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 11/18/2022]
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Chernoff YO, Grizel AV, Rubel AA, Zelinsky AA, Chandramowlishwaran P, Chernova TA. Application of yeast to studying amyloid and prion diseases. ADVANCES IN GENETICS 2020; 105:293-380. [PMID: 32560789 PMCID: PMC7527210 DOI: 10.1016/bs.adgen.2020.01.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Amyloids are fibrous cross-β protein aggregates that are capable of proliferation via nucleated polymerization. Amyloid conformation likely represents an ancient protein fold and is linked to various biological or pathological manifestations. Self-perpetuating amyloid-based protein conformers provide a molecular basis for transmissible (infectious or heritable) protein isoforms, termed prions. Amyloids and prions, as well as other types of misfolded aggregated proteins are associated with a variety of devastating mammalian and human diseases, such as Alzheimer's, Parkinson's and Huntington's diseases, transmissible spongiform encephalopathies (TSEs), amyotrophic lateral sclerosis (ALS) and transthyretinopathies. In yeast and fungi, amyloid-based prions control phenotypically detectable heritable traits. Simplicity of cultivation requirements and availability of powerful genetic approaches makes yeast Saccharomyces cerevisiae an excellent model system for studying molecular and cellular mechanisms governing amyloid formation and propagation. Genetic techniques allowing for the expression of mammalian or human amyloidogenic and prionogenic proteins in yeast enable researchers to capitalize on yeast advantages for characterization of the properties of disease-related proteins. Chimeric constructs employing mammalian and human aggregation-prone proteins or domains, fused to fluorophores or to endogenous yeast proteins allow for cytological or phenotypic detection of disease-related protein aggregation in yeast cells. Yeast systems are amenable to high-throughput screening for antagonists of amyloid formation, propagation and/or toxicity. This review summarizes up to date achievements of yeast assays in application to studying mammalian and human disease-related aggregating proteins, and discusses both limitations and further perspectives of yeast-based strategies.
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Affiliation(s)
- Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States; Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia.
| | - Anastasia V Grizel
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Aleksandr A Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia; Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia; Sirius University of Science and Technology, Sochi, Russia
| | - Andrew A Zelinsky
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| | | | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
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Yang Z, Xu H, Zhao X. Designer Self-Assembling Peptide Hydrogels to Engineer 3D Cell Microenvironments for Cell Constructs Formation and Precise Oncology Remodeling in Ovarian Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903718. [PMID: 32382486 PMCID: PMC7201262 DOI: 10.1002/advs.201903718] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/08/2020] [Indexed: 02/05/2023]
Abstract
Designer self-assembling peptides form the entangled nanofiber networks in hydrogels by ionic-complementary self-assembly. This type of hydrogel has realistic biological and physiochemical properties to serve as biomimetic extracellular matrix (ECM) for biomedical applications. The advantages and benefits are distinct from natural hydrogels and other synthetic or semisynthetic hydrogels. Designer peptides provide diverse alternatives of main building blocks to form various functional nanostructures. The entangled nanofiber networks permit essential compositional complexity and heterogeneity of engineering cell microenvironments in comparison with other hydrogels, which may reconstruct the tumor microenvironments (TMEs) in 3D cell cultures and tissue-specific modeling in vitro. Either ovarian cancer progression or recurrence and relapse are involved in the multifaceted TMEs in addition to mesothelial cells, fibroblasts, endothelial cells, pericytes, immune cells, adipocytes, and the ECM. Based on the progress in common hydrogel products, this work focuses on the diverse designer self-assembling peptide hydrogels for instructive cell constructs in tissue-specific modeling and the precise oncology remodeling for ovarian cancer, which are issued by several research aspects in a 3D context. The advantages and significance of designer peptide hydrogels are discussed, and some common approaches and coming challenges are also addressed in current complex tumor diseases.
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Affiliation(s)
- Zehong Yang
- West China School of Basic Medical Sciences and Forensic MedicineSichuan UniversityChengduSichuan610041P. R. China
- Institute for Nanobiomedical Technology and Membrane BiologyWest China HospitalSichuan UniversityChengduSichuan610041P. R. China
| | - Hongyan Xu
- GL Biochem (Shanghai) Ltd.519 Ziyue Rd.Shanghai200241P. R. China
| | - Xiaojun Zhao
- Institute for Nanobiomedical Technology and Membrane BiologyWest China HospitalSichuan UniversityChengduSichuan610041P. R. China
- Wenzhou InstituteUniversity of Chinese Academy of Sciences (Wenzhou Institute of Biomaterials & Engineering)WenzhouZhejiang325001P. R. China
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49
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Abstract
The traditional view of protein aggregation as being strictly disease-related has been challenged by many examples of cellular aggregates that regulate beneficial biological functions. When coupled with the emerging view that many regulatory proteins undergo phase separation to form dynamic cellular compartments, it has become clear that supramolecular assembly plays wide-ranging and critical roles in cellular regulation. This presents opportunities to develop new tools to probe and illuminate this biology, and to harness the unique properties of these self-assembling systems for synthetic biology for the purposeful manipulation of biological function.
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Affiliation(s)
- Giulio Chiesa
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Szilvia Kiriakov
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA, 02215, USA. .,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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50
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Abstract
The use of proteins and peptides as nanoscale components to generate new-to-nature physical entities holds great promise in biocatalysis, therapeutic or diagnostic delivery, and materials templating. The majority of functionalized particles have been based on existing structures found in nature. Developing biomimetic particles in this way takes advantage of highly evolved platforms for organization or encapsulation of functional moieties, offering significant advantages in stoichiometry, multivalency, and sequestration. However, novel assembly paradigms for the modular construction of macromolecular structures are now greatly expanding the functional diversity of protein-based nanoparticles in health and manufacturing. In the February issue of ACS Nano, Kepiro et al. demonstrate the refinement of this concept, engineering the capacity for self-assembly such that it is integral to pore-forming peptide motifs, resulting in superior antibiotic activity of the self-assembled particle. Nature encodes multiple functions in proteins with exquisite efficiency, and emulating this multiplicity may be the ultimate goal of biomimetic nanotechnologies.
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Affiliation(s)
- Frank Sainsbury
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
- Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation, Brisbane, Queensland 4001, Australia
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