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Bhargava S, Kulkarni R, Dewangan B, Kulkarni N, Jiaswar C, Kumar K, Kumar A, Bodhe PR, Kumar H, Sahu B. Microtubule stabilising peptides: new paradigm towards management of neuronal disorders. RSC Med Chem 2023; 14:2192-2205. [PMID: 37974959 PMCID: PMC10650357 DOI: 10.1039/d3md00012e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 08/09/2023] [Indexed: 11/19/2023] Open
Abstract
Neuronal cells made of soma, axon, and dendrites are highly compartmentalized and possess a specialized transport system that can convey long-distance electrical signals for the cross-talk. The transport system is made up of microtubule (MT) polymers and MT-binding proteins. MTs play vital and diverse roles in various cellular processes. Therefore, defects and dysregulation of MTs and their binding proteins lead to many neurological disorders as exemplified by Parkinson's disease, Alzheimer's disease, amyotrophic lateral sclerosis, Huntington's disease, and many others. MT-stabilising agents (MSAs) altering the MT-associated protein connections have shown great potential for several neurodegenerative disorders. Peptides are an important class of molecules with high specificity, biocompatibility and are devoid of side effects. In the past, peptides have been explored in various neuronal disorders as therapeutics. Davunetide, a MT-stabilising octapeptide, has entered into phase II clinical trials for schizophrenia. Numerous examples of peptides emerging as MSAs reflect the emergence of a new paradigm for peptides which can be explored further as drug candidates for neuronal disorders. Although small molecule-based MSAs have been reviewed in the past, there is no systematic review in recent years focusing on peptides as MSAs apart from davunetide in 2013. Therefore, a systematic updated review on MT stabilising peptides may shed light on many hidden aspects and enable researchers to develop new therapies for diseases related to the CNS. In this review we have summarised the recent examples of peptides as MSAs.
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Affiliation(s)
- Shubhangi Bhargava
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad India
| | - Riya Kulkarni
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research Ahmedabad India
| | - Bhaskar Dewangan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad India
| | - Neeraj Kulkarni
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad India
| | - Chirag Jiaswar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad India
| | - Kunal Kumar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad India
| | - Amit Kumar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad India
| | - Praveen Reddy Bodhe
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad India
| | - Hemant Kumar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research Ahmedabad India
| | - Bichismita Sahu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad India
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2
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Inaba H, Oikawa K, Ishikawa K, Kodama Y, Matsuura K, Numata K. Binding of Tau-derived peptide-fused GFP to plant microtubules in Arabidopsis thaliana. PLoS One 2023; 18:e0286421. [PMID: 37267323 DOI: 10.1371/journal.pone.0286421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/16/2023] [Indexed: 06/04/2023] Open
Abstract
Studies on how exogenous molecules modulate properties of plant microtubules, such as their stability, structure, and dynamics, are important for understanding and modulating microtubule functions in plants. We have developed a Tau-derived peptide (TP) that binds to microtubules and modulates their properties by binding of TP-conjugated molecules in vitro. However, there was no investigation of TPs on microtubules in planta. Here, we generated transgenic Arabidopsis thaliana plants stably expressing TP-fused superfolder GFP (sfGFP-TP) and explored the binding properties and effects of sfGFP-TP on plant microtubules. Our results indicate that the expressed sfGFP-TP binds to the plant microtubules without inhibiting plant growth. A transgenic line strongly expressing sfGFP-TP produced thick fibrous structures that were stable under conditions where microtubules normally depolymerize. This study generates a new tool for analyzing and modulating plant microtubules.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan
| | - Kazusato Oikawa
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kazuya Ishikawa
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
| | - Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan
| | - Keiji Numata
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
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3
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Úsuga-Acevedo B, García Y, Díaz CF, Jiménez VA. Rational Discovery of Microtubule-Stabilizing Peptides. J Chem Inf Model 2022; 62:6844-6856. [PMID: 36074453 DOI: 10.1021/acs.jcim.2c00849] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Microtubule (MT) stabilization is an attractive pharmacological strategy to hamper the progress of neurodegenerative diseases. In this regard, seeking peptides with MT-stabilizing properties has awoken great interest. This work reports the rational discovery of two structurally related MT-stabilizing octapeptides using a combination of protein-peptide docking, conventional molecular dynamics, Gaussian accelerated molecular dynamics (GaMD), and tubulin polymerization assays. FASTA sequences for ∼1000 peptides were crafted from single and double mutants of davunetide (NAP) and docked against the Taxol (TX) site on an octameric MT model representing a portion of the MT wall. Docked peptides were rescored after MM minimization and binding free energy refinement through single-point MM/GBSA calculations. The 60 best-ranked peptides were subjected to 50 ns MD simulations on peptide-MT complexes at the terminal TX site in the octameric Tau-MT model resulting in 11 complexes with occupancies greater than 99% and peptide-protein binding free energies less than -40 kcal/mol. Selected peptides were then examined through 300 ns GaMD simulations in complexes containing two identical ligands at the terminal and intermediate TX sites in the Tau-MT model to account for the differential association of MT-binding peptides to different regions of the MT structure. Six candidates showed a favorable MT-binding potential based on the analysis of interaction frequencies and relative mobilities of the complex components, suggesting a pivotal role of Arg278, Gln281, and Arg369 residues for peptides recognition. Four candidates were predicted to preserve an adequate balance of longitudinal and lateral interactions between tubulin dimers in peptide-MT complexes such that MT-stabilizing effects could be expected. MT polymerization experiments confirmed that four peptides (HAPVSIHQ, NYPVSIHQ, NWPVSIWQ, HAPVSIIQ) exhibit MT-stabilizing activity in vitro with NWPVSIWQ (P43) and HAPVSIIQ (P52) being the most active. Tryptophan quenching assays verified that P43 and P52 bind to nonpolymeric tubulin, whereas viability experiments on HEK cells confirmed their safety to pursue future pharmacological studies. The results herein presented are valuable to making progress in the rational design of MT-stabilizing peptides.
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Affiliation(s)
- Brandon Úsuga-Acevedo
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Autopista Concepción-Talcahuano 7100, Talcahuano, Chile 4300866
| | - Yadiris García
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Autopista Concepción-Talcahuano 7100, Talcahuano, Chile 4300866
| | - Carola F Díaz
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Autopista Concepción-Talcahuano 7100, Talcahuano, Chile 4300866
| | - Verónica A Jiménez
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Autopista Concepción-Talcahuano 7100, Talcahuano, Chile 4300866
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4
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Tsuji C, Dodding MP. Lumenal components of cytoplasmic microtubules. Biochem Soc Trans 2022; 50:1953-1962. [PMID: 36524962 DOI: 10.1042/bst20220851] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 07/30/2023]
Abstract
The lumen of cytoplasmic microtubules is a poorly explored expanse of intracellular space. Although typically represented in textbooks as a hollow tube, studies over several decades have shown that the microtubule lumen is occupied by a range of morphologically diverse components. These are predominantly globular particles of varying sizes which appear to exist either in isolation, bind to the microtubule wall, or form discontinuous columns that extend through the lumenal space. Actin filaments with morphologies distinct from the canonical cytoplasmic forms have also now been found within the microtubule lumen. In this review, we examine the historic literature that observed these lumenal components in tissues from diverse species and integrate it with recent cryo-electron tomography studies that have begun to identify lumenal proteins. We consider their cell and tissue distribution, possible mechanisms of incorporation, and potential functions. It is likely that continuing work in this area will open a new frontier in cytoskeletal biology.
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Affiliation(s)
- Chisato Tsuji
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, U.K
| | - Mark P Dodding
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, U.K
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5
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Inaba H, Sueki Y, Ichikawa M, Kabir AMR, Iwasaki T, Shigematsu H, Kakugo A, Sada K, Tsukazaki T, Matsuura K. Generation of stable microtubule superstructures by binding of peptide-fused tetrameric proteins to inside and outside. SCIENCE ADVANCES 2022; 8:eabq3817. [PMID: 36070375 PMCID: PMC9451167 DOI: 10.1126/sciadv.abq3817] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/22/2022] [Indexed: 05/24/2023]
Abstract
Microtubules play important roles in biological functions by forming superstructures, such as doublets and branched structures, in vivo. Despite the importance, it is challenging to construct these superstructures in vitro. Here, we designed a tetrameric fluorescent protein Azami-Green (AG) fused with His-tag and Tau-derived peptide (TP), TP-AG, to generate the superstructures. Main binding sites of TP-AG can be controlled to the inside and outside of microtubules by changing the polymerization conditions. The binding of TP-AG to the inside promoted microtubule formation and generated rigid and stable microtubules. The binding of TP-AG to the outside induced various microtubule superstructures, including doublets, multiplets, branched structures, and extremely long microtubules by recruiting tubulins to microtubules. Motile microtubule aster structures were also constructed by TP-AG. The generation of various microtubule superstructures by a single type of exogenous protein is a new concept for understanding the functions of microtubules and constructing microtubule-based nanomaterials.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
| | - Yurina Sueki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Muneyoshi Ichikawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | | | - Takashi Iwasaki
- Department of Bioresources Science, Graduate School of Agricultural Sciences, Tottori University, Tottori 680-8553, Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Kazuki Sada
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Tomoya Tsukazaki
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
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6
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Watari S, Inaba H, Tamura T, Kabir AMR, Kakugo A, Sada K, Hamachi I, Matsuura K. Light-induced stabilization of microtubules by photo-crosslinking of a Tau-derived peptide. Chem Commun (Camb) 2022; 58:9190-9193. [PMID: 35929838 DOI: 10.1039/d2cc01890j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For light-induced stabilization of microtubules (MTs) to manipulate cells, a photo-reactive diazirine group was conjugated to a Tau-derived peptide, a motif binding on the inside of MTs. Ultraviolet (UV) light irradiation induced significant stabilization of MTs via the formation of a covalent bond of the peptide and showed toxicity.
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Affiliation(s)
- Soei Watari
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan.
| | - Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan. .,Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.,Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Kazuki Sada
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.,Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.,JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Nishikyo-ku, Kyoto 615-8530, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan. .,Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
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7
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Lam NT, McCluskey JB, Glover DJ. Harnessing the Structural and Functional Diversity of Protein Filaments as Biomaterial Scaffolds. ACS APPLIED BIO MATERIALS 2022; 5:4668-4686. [PMID: 35766918 DOI: 10.1021/acsabm.2c00275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The natural ability of many proteins to polymerize into highly structured filaments has been harnessed as scaffolds to align functional molecules in a diverse range of biomaterials. Protein-engineering methodologies also enable the structural and physical properties of filaments to be tailored for specific biomaterial applications through genetic engineering or filaments built from the ground up using advances in the computational prediction of protein folding and assembly. Using these approaches, protein filament-based biomaterials have been engineered to accelerate enzymatic catalysis, provide routes for the biomineralization of inorganic materials, facilitate energy production and transfer, and provide support for mammalian cells for tissue engineering. In this review, we describe how the unique structural and functional diversity in natural and computationally designed protein filaments can be harnessed in biomaterials. In addition, we detail applications of these protein assemblies as material scaffolds with a particular emphasis on applications that exploit unique properties of specific filaments. Through the diversity of protein filaments, the biomaterial engineer's toolbox contains many modular protein filaments that will likely be incorporated as the main structural component of future biomaterials.
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Affiliation(s)
- Nga T Lam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Joshua B McCluskey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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8
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Joshi FM, Viar GA, Pigino G, Drechsler H, Diez S. Fabrication of High Aspect Ratio Gold Nanowires within the Microtubule Lumen. NANO LETTERS 2022; 22:3659-3667. [PMID: 35446032 DOI: 10.1021/acs.nanolett.2c00255] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gold nanowires have great potential use as interconnects in electronic, photonic, and optoelectronic devices. To date, there are various fabrication strategies for gold nanowires, each one associated with particular drawbacks as they utilize high temperatures, toxic chemicals, or expensive compounds to produce nanowires of suboptimal quality. Inspired by nanowire fabrication strategies that used higher-order biopolymer structures as molds for electroless deposition of gold, we here report a strategy for the growth of gold nanowires from seed nanoparticles within the lumen of microtubules. Luminal targeting of seed particles occurs through covalently linked Fab fragments of an antibody recognizing the acetylated lysine 40 on the luminal side of α-tubulin. Gold nanowires grown by electroless deposition within the microtubule lumen exhibit a homogeneous morphology and high aspect ratios with a mean diameter of 20 nm. Our approach is fast, simple, and inexpensive and does not require toxic chemicals or other harsh conditions.
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Affiliation(s)
- Foram M Joshi
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany
| | - Gonzalo Alvarez Viar
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Gaia Pigino
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Human Technopole, 20157 Milan, Italy
| | - Hauke Drechsler
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01307 Dresden, Germany
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9
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Inaba H, Kabir AMR, Kakugo A, Sada K, Matsuura K. Structural Changes of Microtubules by Encapsulation of Gold Nanoparticles Using a Tau-Derived Peptide. CHEM LETT 2022. [DOI: 10.1246/cl.210761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552 Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552 Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, 060-0810 Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810 Japan
| | - Kazuki Sada
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, 060-0810 Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810 Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552 Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552 Japan
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10
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Inaba H, Matsuura K. Encapsulation of Nanomaterials Inside Microtubules by Using a Tau-Derived Peptide. Methods Mol Biol 2022; 2430:243-260. [PMID: 35476337 DOI: 10.1007/978-1-0716-1983-4_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Microtubules (MTs) are tubular cytoskeletons, which are used for the various applications such as active matters and therapeutic targets. Although modification of the exterior surface of MTs is frequently used for functionalization of MTs, there was no approach to introduce molecules inside MTs. We previously developed a unique peptide binding to the inner surface of MT, which is derived from a MT-associated protein, Tau. The Tau-derived peptide (TP) can be used to introduce various nanomaterials inside MTs. Here we describe the TP-based encapsulation of fluorescent dye, gold nanoparticle, green fluorescent protein, and magnetic CoPt nanoparticles inside MTs.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan.
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan.
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan.
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan.
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11
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Abstract
Preserving the integrity of neuronal microtubules (MTs) has emerged as a promising strategy to inhibit the progression of neurodegenerative disorders such as Alzheimer's disease. Such a goal could be achieved by peptides that mimic the functional role of Tau, an MT-associated protein that stabilizes MTs by dynamically binding to their outer surface. This work examines the binding properties and MT-stabilizing potential of a 27-amino acid Tau oligopeptide from 300 ns Gaussian-accelerated molecular dynamics simulations and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) calculations on octameric MT models bound to two equivalent and independent Tau peptides. Bound peptides adopted extended conformations that are highly consistent with cryo-electron microscopy reports for full-length Tau bound to MTs. Anchoring points in three consecutive tubulin subunits were identified, with a relevant contribution of the Ser419-Val435 region to α-tubulin. Tau peptides strengthen the longitudinal protein-protein contacts within the MT lattice and exert a cooperative MT-stabilizing effect in MT complexes simultaneously bonded to taxol or peloruside A. Ser phosphorylation results in a larger peptide mobility, altered interaction profiles, and MT destabilization, which are in line with the loss of MT integrity resulting from the post-translational hyperphosphorylation of Tau. Our results shed light on the MT-stabilizing potential of Tau-mimetic peptides to act as novel neuroprotective agents targeting MTs.
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Affiliation(s)
- Verónica A Jiménez
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Autopista Concepción-Talcahuano, Talcahuano 7100, Chile
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12
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Inaba H, Matsuura K. Modulation of Microtubule Properties and Functions by Encapsulation of Nanomaterials Using a Tau-Derived Peptide. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210202] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-Minami, Tottori 680-8552, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-Minami, Tottori 680-8552, Japan
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13
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Inaba H, Matsuura K. Live-Cell Fluorescence Imaging of Microtubules by Using a Tau-Derived Peptide. Methods Mol Biol 2021; 2274:169-179. [PMID: 34050471 DOI: 10.1007/978-1-0716-1258-3_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Microtubules (MTs) are important targets for imaging in living cells because of their vital roles in cellular processes. The dynamics (polymerization/depolymerization) of MTs has been imaged in living cells by utilizing MT-targeted drugs as scaffolds. We previously developed a unique MT-binding motif derived from a MT-associated protein, Tau. The Tau-derived peptide (TP) binds to the inner surface of MTs without inhibiting the dynamics of MTs. We introduce a new protocol for live-cell imaging of MTs by using fluorescently labeled TP. We exemplify that tetramethylrhodamine (TMR)-labeled TP (TP-TMR) is spontaneously internalized into HepG2 cells and binds to intracellular MTs, enabling visualization of MTs in living cells. TP-TMR shows no apparent effects on polymerization/depolymerization of MTs and no cytotoxicity. Thus, the peptide-based approach is useful for long-term imaging of MTs.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan.
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan.
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan.
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan.
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14
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A new approach to explore the mechanoresponsiveness of microtubules and its application in studying dynamic soft interfaces. Polym J 2020. [DOI: 10.1038/s41428-020-00415-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Inaba H, Yamada M, Rashid MR, Kabir AMR, Kakugo A, Sada K, Matsuura K. Magnetic Force-Induced Alignment of Microtubules by Encapsulation of CoPt Nanoparticles Using a Tau-Derived Peptide. NANO LETTERS 2020; 20:5251-5258. [PMID: 32525681 DOI: 10.1021/acs.nanolett.0c01573] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Construction of magnetotactic materials is a significant challenge in nanotechnology applications such as nanodevices and nanotransportation. Artificial magnetotactic materials can be designed from magnetotactic bacteria because these bacteria use magnetic nanoparticles for aligning with and moving within magnetic fields. Microtubules are attractive scaffolds to construct magnetotactic materials because of their intrinsic motility. Nonetheless, it is challenging to magnetically control their orientation while retaining their motility by conjugating magnetic nanoparticles on their outer surface. Here we solve the issue by encapsulating magnetic cobalt-platinum nanoparticles inside microtubules using our developed Tau-derived peptide that binds to their internal pockets. The in situ growth of cobalt-platinum nanoparticles resulted in the formation of a linear-chain assembly of nanoparticles inside the microtubules. The magnetic microtubules significantly aligned with a high order parameter (0.71) along the weak magnetic field (0.37 T) and showed increased motility. This work provides a new concept for designing magnetotactic materials.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori 680-8552, Japan
| | - Mayuki Yamada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori 680-8552, Japan
| | - Mst Rubaya Rashid
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Arif Md Rashedul Kabir
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori 680-8552, Japan
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16
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Kabir AMR, Inoue D, Kakugo A. Molecular swarm robots: recent progress and future challenges. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2020; 21:323-332. [PMID: 32939158 PMCID: PMC7476543 DOI: 10.1080/14686996.2020.1761761] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Recent advancements in molecular robotics have been greatly contributed by the progress in various fields of science and technology, particularly in supramolecular chemistry, bio- and nanotechnology, and informatics. Yet one of the biggest challenges in molecular robotics has been controlling a large number of robots at a time and employing the robots for any specific task as flocks in order to harness emergent functions. Swarming of molecular robots has emerged as a new paradigm with potentials to overcome this hurdle in molecular robotics. In this review article, we comprehensively discuss the latest developments in swarm molecular robotics, particularly emphasizing the effective utilization of bio- and nanotechnology in swarming of molecular robots. Importance of tuning the mutual interaction among the molecular robots in regulation of their swarming is introduced. Successful utilization of DNA, photoresponsive molecules, and natural molecular machines in swarming of molecular robots to provide them with processing, sensing, and actuating ability is highlighted. The potentials of molecular swarm robots for practical applications by means of their ability to participate in logical operations and molecular computations are also discussed. Prospects of the molecular swarm robots in utilizing the emergent functions through swarming are also emphasized together with their future perspectives.
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Affiliation(s)
| | - Daisuke Inoue
- Faculty of Design, Department of Human Science, Kyushu University, Fukuoka, Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
- CONTACT Akira Kakugo Hokkaido University, Sapporo shi, Kita ku, Kita 10, Nishi 8, Science building-7, Room-215, Sapporo060-0810, Japan
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17
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Inaba H, Nagata M, Miyake KJ, Kabir AMR, Kakugo A, Sada K, Matsuura K. Cyclic Tau-derived peptides for stabilization of microtubules. Polym J 2020. [DOI: 10.1038/s41428-020-0356-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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18
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Inaba H, Yamamoto T, Iwasaki T, Kabir AMR, Kakugo A, Sada K, Matsuura K. Fluorescent Tau-derived Peptide for Monitoring Microtubules in Living Cells. ACS OMEGA 2019; 4:11245-11250. [PMID: 31460226 PMCID: PMC6648849 DOI: 10.1021/acsomega.9b01089] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/18/2019] [Indexed: 06/04/2023]
Abstract
Microtubules (MTs) are key cytoskeletal components that modulate various cellular activities with their dynamic structural changes, including polymerization and depolymerization. To monitor the dynamics of MTs in living cells, many drug-based fluorescent probes have been developed; however, these also potentially disturb the polymerization/depolymerization of MTs. Here, we report nondrug, peptide-based fluorescent probes to monitor MTs in living cells. We employed a Tau-derived peptide (TP) that has been shown to bind MTs without inhibiting polymerization/depolymerization in vitro. We show that a tetramethylrhodamine (TMR)-labeled TP (TP-TMR) is internalized into HepG2 cells and binds to intracellular MTs, enabling visualization of MTs as clear, fibrous structures. The binding of TP-TMR shows no apparent effects on polymerization/depolymerization of MTs induced by MT-targeted drugs and temperature change. The main uptake mechanism of TP-TMR was elucidated as endocytosis, and partial endosomal escape resulted in the binding of TP-TMR to MTs. TP-TMR exhibited no cytotoxicity compared with MT-targeted drug scaffolds. These results indicate that TP scaffolds can be exploited as useful MT-targeted tools in living cells, such as in long-term imaging of MTs.
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Affiliation(s)
- Hiroshi Inaba
- Department
of Chemistry and Biotechnology, Graduate School of Engineering and Centre for Research
on Green Sustainable Chemistry, Tottori
University, Koyama-Minami 4-101, Tottori 680-8552, Japan
| | - Takahisa Yamamoto
- Department
of Chemistry and Biotechnology, Graduate School of Engineering and Centre for Research
on Green Sustainable Chemistry, Tottori
University, Koyama-Minami 4-101, Tottori 680-8552, Japan
| | - Takashi Iwasaki
- Department
of Bioresources Science, Graduate School of Agricultural Sciences, Tottori University, Koyama-Minami 4-101, Tottori 680-8553, Japan
| | - Arif Md. Rashedul Kabir
- Faculty of Science and Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Akira Kakugo
- Faculty of Science and Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazuki Sada
- Faculty of Science and Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazunori Matsuura
- Department
of Chemistry and Biotechnology, Graduate School of Engineering and Centre for Research
on Green Sustainable Chemistry, Tottori
University, Koyama-Minami 4-101, Tottori 680-8552, Japan
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19
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Lee ACL, Harris JL, Khanna KK, Hong JH. A Comprehensive Review on Current Advances in Peptide Drug Development and Design. Int J Mol Sci 2019; 20:ijms20102383. [PMID: 31091705 PMCID: PMC6566176 DOI: 10.3390/ijms20102383] [Citation(s) in RCA: 353] [Impact Index Per Article: 70.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 11/16/2022] Open
Abstract
Protein-protein interactions (PPIs) execute many fundamental cellular functions and have served as prime drug targets over the last two decades. Interfering intracellular PPIs with small molecules has been extremely difficult for larger or flat binding sites, as antibodies cannot cross the cell membrane to reach such target sites. In recent years, peptides smaller size and balance of conformational rigidity and flexibility have made them promising candidates for targeting challenging binding interfaces with satisfactory binding affinity and specificity. Deciphering and characterizing peptide-protein recognition mechanisms is thus central for the invention of peptide-based strategies to interfere with endogenous protein interactions, or improvement of the binding affinity and specificity of existing approaches. Importantly, a variety of computation-aided rational designs for peptide therapeutics have been developed, which aim to deliver comprehensive docking for peptide-protein interaction interfaces. Over 60 peptides have been approved and administrated globally in clinics. Despite this, advances in various docking models are only on the merge of making their contribution to peptide drug development. In this review, we provide (i) a holistic overview of peptide drug development and the fundamental technologies utilized to date, and (ii) an updated review on key developments of computational modeling of peptide-protein interactions (PepPIs) with an aim to assist experimental biologists exploit suitable docking methods to advance peptide interfering strategies against PPIs.
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Affiliation(s)
- Andy Chi-Lung Lee
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
- Radiation Biology Research Center, Institute for Radiological Research, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 333, Taiwan.
- Department of Radiation Oncology, Chang Gung Memorial Hospital, Linkou 333, Taiwan.
| | | | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
| | - Ji-Hong Hong
- Radiation Biology Research Center, Institute for Radiological Research, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 333, Taiwan.
- Department of Radiation Oncology, Chang Gung Memorial Hospital, Linkou 333, Taiwan.
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20
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Inaba H, Yamamoto T, Iwasaki T, Kabir AMR, Kakugo A, Sada K, Matsuura K. Stabilization of microtubules by encapsulation of the GFP using a Tau-derived peptide. Chem Commun (Camb) 2019; 55:9072-9075. [DOI: 10.1039/c9cc04345d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Encapsulation of the GFP inside microtubules by using a Tau-derived peptide increased the stability, rigidity, and velocity of microtubules.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology
- Graduate School of Engineering, Tottori University
- Tottori 680-8552
- Japan
- Centre for Research on Green Sustainable Chemistry
| | - Takahisa Yamamoto
- Department of Chemistry and Biotechnology
- Graduate School of Engineering, Tottori University
- Tottori 680-8552
- Japan
| | - Takashi Iwasaki
- Department of Bioresources Science, Graduate School of Agricultural Sciences
- Tottori University
- Tottori 680-8553
- Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University
- Sapporo 060-0810
- Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University
- Sapporo 060-0810
| | - Kazuki Sada
- Faculty of Science, Hokkaido University
- Sapporo 060-0810
- Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University
- Sapporo 060-0810
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology
- Graduate School of Engineering, Tottori University
- Tottori 680-8552
- Japan
- Centre for Research on Green Sustainable Chemistry
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21
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Inaba H, Matsuura K. Peptide Nanomaterials Designed from Natural Supramolecular Systems. CHEM REC 2018; 19:843-858. [PMID: 30375148 DOI: 10.1002/tcr.201800149] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/07/2018] [Indexed: 12/22/2022]
Abstract
Natural supramolecular assemblies exhibit unique structural and functional properties that have been optimized over the course of evolution. Inspired by these natural systems, various bio-nanomaterials have been developed using peptides, proteins, and nucleic acids as components. Peptides are attractive building blocks because they enable the important domains of natural protein assemblies to be isolated and optimized while retaining the original structures and functions. Furthermore, the peptide subunits can be conjugated with exogenous molecules such as peptides, proteins, nucleic acids, and metal nanoparticles to generate advanced functions. In this personal account, we summarize recent progress in the construction of peptide-based nanomaterial designed from natural supramolecular systems, including (1) artificial viral capsids, (2) self-assembled nanofibers, and (3) protein-binding motifs. The peptides inspired by nature should provide new design principles for bio-nanomaterials.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan.,Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan.,Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan
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22
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Inaba H, Yamamoto T, Kabir AMR, Kakugo A, Sada K, Matsuura K. Molecular Encapsulation Inside Microtubules Based on Tau-Derived Peptides. Chemistry 2018; 24:14958-14967. [PMID: 30088680 PMCID: PMC6220817 DOI: 10.1002/chem.201802617] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Indexed: 11/20/2022]
Abstract
Microtubules are cytoskeletal filaments that serve as attractive scaffolds for developing nanomaterials and nanodevices because of their unique structural properties. The functionalization of the outer surface of microtubules has been established for this purpose. However, no attempts have been made to encapsulate molecules inside microtubules with 15 nm inner diameter. The encapsulation of various molecular cargos inside microtubules constitutes a new concept for nanodevice and nanocarrier applications of microtubules. Here, we developed peptide motifs for binding to the inner surface of microtubules, based on a repeat domain of the microtubule‐associated protein Tau. One of the four Tau‐derived peptides, 2N, binds to a taxol binding pocket of β‐tubulin located inside microtubules by preincubation with tubulin dimer and subsequent polymerization of the peptide‐tubulin complex. By conjugation of 2N to gold nanoparticles, encapsulation of gold nanoparticles inside microtubules was achieved. The methodology for molecular encapsulation inside microtubules by the Tau‐derived peptide is expected to advance the development of microtubule‐based nanomaterials and nanodevices.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan.,Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan
| | - Takahisa Yamamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan
| | - Arif Md Rashedul Kabir
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan.,Graduate School of Chemical Sciences and Engineering, Hokkaido University, Hokkaido, 060-0810, Japan
| | - Kazuki Sada
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan.,Graduate School of Chemical Sciences and Engineering, Hokkaido University, Hokkaido, 060-0810, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan.,Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan
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