Article
Biochemistry & Molecular Biology
Zsofia Lengyel-Zhand, Liam R. Marshall, Maximilian Jung, Megha Jayachandran, Min-Chul Kim, Austin Kriews, Olga Makhlynets, H. Christopher Fry, Armin Geyer, Ivan Korendovych
Summary: The self-assembly of short peptides into catalytic amyloid-like nanomaterials is a powerful tool for understanding the evolution of early proteins and identifying new catalysts. This study demonstrates that different arrangements of beta-sheets can accommodate metal ions for catalysis, and synergistic relationships in catalytic amyloid mixtures can be found in various species offering faster rates of assembly.
Article
Chemistry, Multidisciplinary
Oleksii Zozulia, Liam R. Marshall, Inhye Kim, Eric M. Kohn, Ivan V. Korendovych
Summary: Self-assembly of short peptides can produce versatile nanomaterials with efficient catalytic activity, showing practical utility and evolutionary connection.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Review
Chemistry, Multidisciplinary
Verity Baltutis, Paul D. O'Leary, Lisandra L. Martin
Summary: Antimicrobial peptides are a crucial defense mechanism of hosts against microbial assailants. They undergo a structural transition upon contact with membrane surfaces, leading to the destruction of microbes through detergent-like binding or formation of trans-membrane pores. Recent findings also suggest a potential link between self-assembled antimicrobial peptides and diseases like Alzheimer's disease. This review highlights the importance of studying the self-assembly of antimicrobial peptides into amyloid and its synergistic effect with the antimicrobial peptide response.
Article
Chemistry, Multidisciplinary
Filip Hasecke, Chamani Niyangoda, Gustavo Borjas, Jianjun Pan, Garrett Matthews, Martin Muschol, Wolfgang Hoyer
Summary: The study found that in the assembly of A beta and lysozyme, protofibrils bind to the lateral surfaces of amyloid fibrils, inhibiting the self-proliferation of amyloid fibrils. This suggests that metastable oligomers counteract the replacement by amyloid fibrils through competing for monomers and blocking secondary nucleation sites.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Biochemistry & Molecular Biology
Torsten John, Lisandra L. L. Martin, Bernd Abel
Summary: This review discusses the impact of surface interfaces on the structure and aggregation mechanisms of peptides and proteins, particularly their association with amyloid fibril formation and neurodegenerative diseases. Research findings demonstrate that surface interfaces can both accelerate and inhibit peptide self-assembly, with adsorption typically promoting aggregation. The review introduces experimental and theoretical models for better understanding peptide self-assembly at hard and soft matter interfaces, and proposes relationships between biological interfaces and amyloid fibril formation.
MACROMOLECULAR BIOSCIENCE
(2023)
Article
Microbiology
Lauren K. Nicastro, Jaime de Anda, Neha Jain, Kaitlyn C. M. Grando, Amanda L. Miller, Shingo Bessho, Stefania Gallucci, Gerard C. L. Wong, Cagla Tukel
Summary: Deposition of human amyloids is associated with complex human diseases such as Alzheimer's and Parkinson's. Amyloid proteins are also produced by bacteria, and the bacterial amyloid curli, when forming complexes with extracellular DNA, can trigger an autoimmune response in the host immune system. Different stages of curli fibrils formed during biofilm development have varying structural and pathogenic properties, with mature curli fibrils being the most pathogenic.
Review
Chemistry, Multidisciplinary
Rodrigo Diaz-Espinoza
Summary: Peptides and proteins can form highly ordered amyloid structures that have unique mechanical properties and catalytic activities. Recent advances in the design of amyloids have focused on the development of catalytic activities, such as hydrolysis, as well as novel types of activities. These catalytically active amyloids have great potential for the development of future bionanomaterials aimed at specific applications.
Article
Chemistry, Multidisciplinary
Chandranath Ghosh, Sneha Menon, Subhajit Bal, Surashree Goswami, Jagannath Mondal, Dibyendu Das
Summary: Through evolution, modern enzymes in metabolic pathways have become specialized, unlike their early ancestors which had broader substrate specificities. However, it is still unclear how these early enzymes displayed catalytic versatility without complex three-dimensional structures. This study reports the emergence of promiscuous catalytic triads in short amyloid peptide-based nanofibers that access paracrystalline folds of beta-sheets, allowing them to simultaneously catalyze multiple reactions and contribute to protometabolism and early evolutionary processes.
Article
Chemistry, Multidisciplinary
Soumili Roy, Ayan Chatterjee, Subhajit Bal, Dibyendu Das
Summary: In Darwin's warm pond, early protometabolism demonstrated catalytic diversity by catalyzing diverse biochemical transformations. The newly discovered amyloid-based short peptide assemblies exhibit catalytic promiscuity and can simultaneously catalyze three orthogonal metabolic reactions. These findings suggest a possible role for short peptides in promoting the protometabolic network on early Earth.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Chemistry, Multidisciplinary
Beom Jin Kim
Summary: Enzyme-instructed self-assembly, integrating enzymatic reaction and molecular self-assembly, has attracted attention for its potential applications. Recent advances allow for spatiotemporal control of peptide self-assembly in cellular milieu, broadening its applications in cancer therapy and subcellular delivery.
CHEMISTRY-AN ASIAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Kristian Le Vay, Emilie Yeonwha Song, Basusree Ghosh, T. -Y. Dora Tang, Hannes Mutschler
Summary: The study demonstrates that RNA catalysis efficiency can be significantly improved through charge-mediated phase separation with poly-L-lysine, shifting the reaction equilibrium towards RNA ligation in peptide-RNA coaggregates and coacervates. This compartmentalization enables robust isothermal RNA assembly under a broad range of conditions, bridging the gap between pools of short oligomers and functional RNAs by assembling long and complex RNAs from short fragments in mild conditions without the use of exogenous activation chemistry.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Nhan Dai Thien Tram, Jian Xu, Devika Mukherjee, Antonio Eduardo Obanel, Venkatesh Mayandi, Vanitha Selvarajan, Xiao Zhu, Jeanette Teo, Veluchamy Amutha Barathi, Rajamani Lakshminarayanan, Pui Lai Rachel Ee
Summary: Researchers have developed synthetic peptides that can self-assemble into nanonets in the presence of bacteria, trapping and killing microbial cells effectively. These bacteria-responsive peptide nanonets show promise as clinical anti-infective alternatives to combat antibiotic resistance.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Polymer Science
James P. Warren, Matthew P. Culbert, Danielle E. Miles, Steven Maude, Ruth K. Wilcox, Paul A. Beales
Summary: Self-assembling peptides are a versatile biomaterial that can form self-supporting hydrogels. Balancing attractive and repulsive forces through peptide charge and hydrogen bonding is crucial for successful hydrogel formation. A net peptide charge of +/-2 and modulating hydrogen bonding can optimize the assembly and viscoelastic properties of the hydrogel. These findings demonstrate the potential of controlling self-assembly mechanisms to create structures with desired properties.
Article
Chemistry, Multidisciplinary
Zili Li, Zhiqun Lin
Summary: The study presents a one-step synthesis of anionic bolaamphiphiles with a rational design, revealing the correlation between molecular structure and self-assemblies. By delicate regulation of interactions, 2D nanosheets are crafted, with the potential to serve as a substrate for a variety of applications including catalysis, optical devices, and photothermal therapy.
Article
Chemistry, Multidisciplinary
Si Sun, Hong-Wen Liang, Hao Wang, Quanming Zou
Summary: Controlled self-assembly is of great interest in biological and nanotechnological applications. We have demonstrated a light-triggered platform that allows precise control of self-assembly from nanoparticles into nanofibers in living cells. The process is biocompatible, fast, and can be applied for regulating molecular assembly in living cells.
Article
Nanoscience & Nanotechnology
Areetha D'Souza, Jennifer H. Yoon, Henry Beaman, Pallavi Gosavi, Zsofia Lengyel-Zhand, Alex Sternisha, Garrick Centola, Liam R. Marshall, Matthew D. Wehrman, Kelly M. Schultz, Mary Beth Monroe, Olga V. Makhlynets
ACS APPLIED MATERIALS & INTERFACES
(2020)
Article
Neurosciences
Aladdin Riad, Zsofia Lengyel-Zhand, Chenbo Zeng, Chi-Chang Weng, Virginia M. -Y. Lee, John Q. Trojanowski, Robert H. Mach
MOLECULAR NEUROBIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Zsofia Lengyel-Zhand, Liam R. Marshall, Maximilian Jung, Megha Jayachandran, Min-Chul Kim, Austin Kriews, Olga Makhlynets, H. Christopher Fry, Armin Geyer, Ivan Korendovych
Summary: The self-assembly of short peptides into catalytic amyloid-like nanomaterials is a powerful tool for understanding the evolution of early proteins and identifying new catalysts. This study demonstrates that different arrangements of beta-sheets can accommodate metal ions for catalysis, and synergistic relationships in catalytic amyloid mixtures can be found in various species offering faster rates of assembly.
Article
Chemistry, Multidisciplinary
Oleksii Zozulia, Liam R. Marshall, Inhye Kim, Eric M. Kohn, Ivan V. Korendovych
Summary: Self-assembly of short peptides can produce versatile nanomaterials with efficient catalytic activity, showing practical utility and evolutionary connection.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Review
Biochemistry & Molecular Biology
Liam R. Marshall, Ivan Korendovych
Summary: Amyloids, originally considered as disease symptoms, have diverse functions including biologically beneficial ones. Instead of being seen as 'misfolding,' the aggregation of polypeptides into amyloid-like structures should be viewed as 'alternative folding,' with recent studies showing that these structures can be used to create highly efficient catalysts with specific catalytic efficiencies.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Sagar Bhattacharya, Eleonora G. Margheritis, Katsuya Takahashi, Alona Kulesha, Areetha D'Souza, Inhye Kim, Jennifer H. Yoon, Jeremy R. H. Tame, Alexander N. Volkov, Olga V. Makhlynets, Ivan V. Korendovych
Summary: Directed evolution is a powerful tool for improving protein properties and functionality. However, the vast number of possible amino acid sequences limits its potential. Current predictive methods rely on structural and bioinformatics information, which may not be available for all proteins, and they have limited ability to identify beneficial mutations outside of the active site. Machine learning methods show promise but require large training datasets. This study demonstrates the use of NMR spectroscopy to identify mutagenic hot spots in enzymes, providing a simple and a priori knowledge-free approach for directed enzyme evolution.
Article
Chemistry, Multidisciplinary
Rohit Batra, Troy D. Loeffler, Henry Chan, Srilok Srinivasan, Honggang Cui, Ivan Korendovych, Vikas Nanda, Liam C. Palmer, Lee A. Solomon, H. Christopher Fry, Subramanian K. R. S. Sankaranarayanan
Summary: Peptide materials have a wide range of functions, but increasing the sequence length leads to a larger number of candidate sequences. Traditional design methods guided by human expertise and intuition are not easily scalable or free from bias. This article introduces a machine learning-based computational search engine that efficiently discovers peptide sequences with high self-assembly potential, overcoming human bias and accelerating peptide discovery.
Article
Chemistry, Multidisciplinary
Liam R. Marshall, Sagar Bhattacharya, Ivan V. Korendovych
Summary: Directed evolution has revolutionized protein engineering by providing a way to quickly improve protein properties. However, the vast protein sequence search space limits its practical application, requiring the identification of mutagenic hot spots where mutations are likely to have a productive impact. This perspective categorizes and discusses recent progress in experimental approaches, such as structural, bioinformatic, and dynamic methods, for hot spot identification. Recent successes in utilizing protein dynamics and machine learning offer new opportunities for the field and will undoubtedly enhance the effectiveness of directed evolution.
Article
Chemistry, Multidisciplinary
Wei Luo, Hironaga Noguchi, Chen Chen, Yoshiki Nakamura, Chishu Homma, Oleksii Zozulia, Ivan Korendovych, Yuhei Hayamizu
Summary: Researchers demonstrate a novel nanoarchitecture based on self-assembled short peptides on a graphite surface, which exhibits catalytic activity comparable to natural enzymes and forms highly ordered and uniform structures. This new approach has the potential to create highly efficient and practical electrocatalysts.
