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Szefczyk M, Szulc N, Gąsior-Głogowska M, Bystranowska D, Żak A, Sikora A, Polańska O, Ożyhar A, Berlicki Ł. The application of the hierarchical approach for the construction of foldameric peptide self-assembled nanostructures. SOFT MATTER 2023; 19:3828-3840. [PMID: 37191235 DOI: 10.1039/d3sm00005b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
In this paper, we show that a hierarchical approach for the construction of nanofibrils based on α,β-peptide foldamers is a rational method for the design of novel self-assembled nanomaterials based on peptides. Incorporation of a trans-(1S,2S)-2-aminocyclopentanecarboxylic acid residue into the outer positions of the model coiled-coil peptide led to the formation of helical foldamers, which was determined by circular dichroism (CD) and vibrational spectroscopy. The oligomerization state of the obtained peptides in water was established by analytical ultracentrifugation (AUC). The thioflavin T assay and Congo red methods showed that the obtained α,β-peptides possess a strong tendency to aggregate, leading to the formation of self-assembled nanostructures, which were assessed by microscopic techniques. The location of the β-amino acid in the heptad repeat of the coiled-coil structure proved to have an influence on the secondary structure of the obtained peptides and on the morphology of the self-assembled nanostructures.
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Affiliation(s)
- Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Natalia Szulc
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
- Department of Physics and Biophysics, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland
| | - Marlena Gąsior-Głogowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Dominika Bystranowska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Andrzej Żak
- Electron Microscopy Laboratory, Faculty of Mechanical Engineering, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Andrzej Sikora
- Faculty of Electronics, Photonics and Microsystems, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Oliwia Polańska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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Matiiv AB, Trubitsina NP, Matveenko AG, Barbitoff YA, Zhouravleva GA, Bondarev SA. Structure and Polymorphism of Amyloid and Amyloid-Like Aggregates. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:450-463. [PMID: 35790379 DOI: 10.1134/s0006297922050066] [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: 09/28/2021] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 06/15/2023]
Abstract
Amyloids are protein aggregates with the cross-β structure. The interest in amyloids is explained, on the one hand, by their role in the development of socially significant human neurodegenerative diseases, and on the other hand, by the discovery of functional amyloids, whose formation is an integral part of cellular processes. To date, more than a hundred proteins with the amyloid or amyloid-like properties have been identified. Studying the structure of amyloid aggregates has revealed a wide variety of protein conformations. In the review, we discuss the diversity of protein folds in the amyloid-like aggregates and the characteristic features of amyloid aggregates that determine their unusual properties, including stability and interaction with amyloid-specific dyes. The review also describes the diversity of amyloid aggregates and its significance for living organisms.
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Affiliation(s)
- Anton B Matiiv
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Nina P Trubitsina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Yury A Barbitoff
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- Bioinformatics Institute, Saint Petersburg, 197342, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia.
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
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Arghavani P, Badiei A, Ghadami SA, Habibi-Rezaei M, Moosavi-Movahedi F, Delphi L, Moosavi-Movahedi AA. Inhibiting mTTR Aggregation/Fibrillation by a Chaperone-like Hydrophobic Amino Acid-Conjugated SPION. J Phys Chem B 2022; 126:1640-1654. [PMID: 35090112 DOI: 10.1021/acs.jpcb.1c08796] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transthyretin (TTR) aggregation via misfolding of a mutant or wild-type protein leads to systemic or partial amyloidosis (ATTR). Here, we utilized variable biophysical assays to characterize two distinct aggregation pathways for mTTR (a synthesized monomer TTR incapable of association into a tetramer) at pH 4.3 and also pH 7.4 with agitation, referred to as mTTR aggregation and fibrillation, respectively. The findings suggest that early-stage conformational changes termed monomer activation here determine the aggregation pathway, resulting in developing either amorphous aggregates or well-organized fibrils. Less packed partially unfolded monomers consisting of more non-regular secondary structures that were rapidly produced via a mildly acidic condition form amorphous aggregates. Meanwhile, more hydrophobic and packed monomers consisting of rearranged β sheets and increased helical content developed well-organized fibrils. Conjugating superparamagnetic iron oxide nanoparticles (SPIONs) with leucine and glutamine (L-SPIONs and G-SPIONs in order) via a trimethoxysilane linker provided the chance to study the effect of hydrophobic/hydrophilic surfaces on mTTR aggregation. The results indicated a powerful inhibitory effect of hydrophobic L-SPIONs on both mTTR aggregation and fibrillation. Monomer depletion was introduced as the governing mechanism for inhibiting mTTR aggregation, while a chaperone-like property of L-SPIONs by maintaining an mTTR native structure and adsorbing oligomers suppressed the progression of further fibril formation.
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Affiliation(s)
- Payam Arghavani
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417466191, Iran
| | - Alireza Badiei
- School of Chemistry, College of Science, University of Tehran, Tehran 1417614411, Iran
| | - Seyyed Abolghasem Ghadami
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran 1993893973, Iran
| | - Mehran Habibi-Rezaei
- School of Biology, College of Science, University of Tehran, Tehran 1417614411, Iran
| | | | - Ladan Delphi
- Department of Animal Biology, College of Science, University of Tehran, Tehran 1417614411, Iran
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Scherpelz KP, Wang S, Pytel P, Madhurapantula RS, Srivastava AK, Sachleben JR, Orgel J, Ishii Y, Meredith SC. Atomic-level differences between brain parenchymal- and cerebrovascular-seeded Aβ fibrils. Sci Rep 2021; 11:247. [PMID: 33420184 PMCID: PMC7794565 DOI: 10.1038/s41598-020-80042-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 12/02/2020] [Indexed: 11/24/2022] Open
Abstract
Alzheimer's disease is characterized by neuritic plaques, the main protein components of which are β-amyloid (Aβ) peptides deposited as β-sheet-rich amyloid fibrils. Cerebral Amyloid Angiopathy (CAA) consists of cerebrovascular deposits of Aβ peptides; it usually accompanies Alzheimer's disease, though it sometimes occurs in the absence of neuritic plaques, as AD also occurs without accompanying CAA. Although neuritic plaques and vascular deposits have similar protein compositions, one of the characteristic features of amyloids is polymorphism, i.e., the ability of a single pure peptide to adopt multiple conformations in fibrils, depending on fibrillization conditions. For this reason, we asked whether the Aβ fibrils in neuritic plaques differed structurally from those in cerebral blood vessels. To address this question, we used seeding techniques, starting with amyloid-enriched material from either brain parenchyma or cerebral blood vessels (using meninges as the source). These amyloid-enriched preparations were then added to fresh, disaggregated solutions of Aβ to make replicate fibrils, as described elsewhere. Such fibrils were then studied by solid-state NMR, fiber X-ray diffraction, and other biophysical techniques. We observed chemical shift differences between parenchymal vs. vascular-seeded replicate fibrils in select sites (in particular, Ala2, Phe4, Val12, and Gln15 side chains) in two-dimensional 13C-13C correlation solid-state NMR spectra, strongly indicating structural differences at these sites. X-ray diffraction studies also indicated that vascular-seeded fibrils displayed greater order than parenchyma-seeded fibrils in the "side-chain dimension" (~ 10 Å reflection), though the "hydrogen-bond dimensions" (~ 5 Å reflection) were alike. These results indicate that the different nucleation conditions at two sites in the brain, parenchyma and blood vessels, affect the fibril products that get formed at each site, possibly leading to distinct pathophysiological outcomes.
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Affiliation(s)
| | - Songlin Wang
- Department of Chemistry, University of Illinois At Chicago, Chicago, IL, 60607, USA
| | - Peter Pytel
- Department of Pathology, The University of Chicago, Chicago, IL, 60637, USA
| | - Rama S Madhurapantula
- Department of Biology and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Atul K Srivastava
- Department of Pathology, The University of Chicago, Chicago, IL, 60637, USA
| | - Joseph R Sachleben
- Biomolecular NMR Facility, The University of Chicago, Chicago, IL, 60637, USA
| | - Joseph Orgel
- Department of Biology and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Yoshitaka Ishii
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Stephen C Meredith
- Department of Pathology, The University of Chicago, Chicago, IL, 60637, USA.
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.
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Li J, Zhao Y, Zhou P, Hu X, Wang D, King SM, Rogers SE, Wang J, Lu JR, Xu H. Ordered Nanofibers Fabricated from Hierarchical Self-Assembling Processes of Designed α-Helical Peptides. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2003945. [PMID: 33015967 DOI: 10.1002/smll.202003945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/15/2020] [Indexed: 06/11/2023]
Abstract
Peptide self-assembly is fast evolving into a powerful method for the development of bio-inspired nanomaterials with great potential for many applications, but it remains challenging to control the self-assembling processes and nanostrucutres because of the intricate interplay of various non-covalent interactions. A group of 28-residue α-helical peptides is designed including NN, NK, and HH that display distinct hierarchical events. The key of the design lies in the incorporation of two asparagine (Asn) or histidine (His) residues at the a positions of the second and fourth heptads, which allow one sequence to pack into homodimers with sticky ends through specific interhelical Asn-Asn or metal complexation interactions, followed by their longitudinal association into ordered nanofibers. This is in contrast to classical self-assembling helical peptide systems consisting of two complementary peptides. The collaborative roles played by the four main non-covalent interactions, including hydrogen-bonding, hydrophobic interactions, electrostatic interactions, and metal ion coordination, are well demonstrated during the hierarchical self-assembling processes of these peptides. Different nanostructures, for example, long and short nanofibers, thin and thick fibers, uniform metal ion-entrapped nanofibers, and polydisperse globular stacks, can be prepared by harnessing these interactions at different levels of hierarchy.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Yurong Zhao
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Peng Zhou
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Xuzhi Hu
- Biological Physics Group, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
| | - Dong Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Stephen M King
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Didcot, Oxon, OX11 0QX, UK
| | - Sarah E Rogers
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Didcot, Oxon, OX11 0QX, UK
| | - Jiqian Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Jian R Lu
- Biological Physics Group, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
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Han H, Zeng W, Zhang G, Zhou J. Active tyrosine phenol-lyase aggregates induced by terminally attached functional peptides in Escherichia coli. J Ind Microbiol Biotechnol 2020; 47:563-571. [PMID: 32737623 PMCID: PMC7508748 DOI: 10.1007/s10295-020-02294-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022]
Abstract
The formation of inclusion bodies (IBs) without enzyme activity in bacterial research is generally undesirable. Researchers have attempted to recovery the enzyme activities of IBs, which are commonly known as active IBs. Tyrosine phenol-lyase (TPL) is an important enzyme that can convert pyruvate and phenol into 3,4-dihydroxyphenyl-L-alanine (L-DOPA) and IBs of TPL can commonly occur. To induce the correct folding and recover the enzyme activity of the IBs, peptides, such as ELK16, DKL6, L6KD, ELP10, ELP20, L6K2, EAK16, 18A, and GFIL16, were fused to the carboxyl terminus of TPL. The results showed that aggregate particles of TPL-DKL6, TPL-ELP10, TPL-EAK16, TPL-18A, and TPL-GFIL16 improved the enzyme activity by 40.9%, 50.7%, 48.9%, 86.6%, and 97.9%, respectively. The peptides TPL-DKL6, TPL-EAK16, TPL-18A, and TPL-GFIL16 displayed significantly improved thermostability compared with TPL. L-DOPA titer of TPL-ELP10, TPL-EAK16, TPL-18A, and TPL-GFIL16, with cells reaching 37.8 g/L, 53.8 g/L, 37.5 g/L, and 29.1 g/L, had an improvement of 111%, 201%, 109%, and 63%, respectively. A higher activity and L-DOPA titer of the TPL-EAK16 could be valuable for its industrial application to biosynthesize L-DOPA.
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Affiliation(s)
- Hongmei Han
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Guoqiang Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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Iadanza MG, Jackson MP, Hewitt EW, Ranson NA, Radford SE. A new era for understanding amyloid structures and disease. Nat Rev Mol Cell Biol 2019; 19:755-773. [PMID: 30237470 DOI: 10.1038/s41580-018-0060-8] [Citation(s) in RCA: 569] [Impact Index Per Article: 113.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The aggregation of proteins into amyloid fibrils and their deposition into plaques and intracellular inclusions is the hallmark of amyloid disease. The accumulation and deposition of amyloid fibrils, collectively known as amyloidosis, is associated with many pathological conditions that can be associated with ageing, such as Alzheimer disease, Parkinson disease, type II diabetes and dialysis-related amyloidosis. However, elucidation of the atomic structure of amyloid fibrils formed from their intact protein precursors and how fibril formation relates to disease has remained elusive. Recent advances in structural biology techniques, including cryo-electron microscopy and solid-state NMR spectroscopy, have finally broken this impasse. The first near-atomic-resolution structures of amyloid fibrils formed in vitro, seeded from plaque material and analysed directly ex vivo are now available. The results reveal cross-β structures that are far more intricate than anticipated. Here, we describe these structures, highlighting their similarities and differences, and the basis for their toxicity. We discuss how amyloid structure may affect the ability of fibrils to spread to different sites in the cell and between organisms in a prion-like manner, along with their roles in disease. These molecular insights will aid in understanding the development and spread of amyloid diseases and are inspiring new strategies for therapeutic intervention.
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Affiliation(s)
- Matthew G Iadanza
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Matthew P Jackson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Eric W Hewitt
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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Miyawaki S, Uemura Y, Hongo K, Kawata Y, Mizobata T. Acid-denatured small heat shock protein HdeA from Escherichia coli forms reversible fibrils with an atypical secondary structure. J Biol Chem 2018; 294:1590-1601. [PMID: 30530490 DOI: 10.1074/jbc.ra118.005611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 12/06/2018] [Indexed: 12/13/2022] Open
Abstract
The periplasmic small heat shock protein HdeA from Escherichia coli is inactive under normal growth conditions (at pH 7) and activated only when E. coli cells are subjected to a sudden decrease in pH, converting HdeA into an acid-denatured active state. Here, using in vitro fibrillation assays, transmission EM, atomic-force microscopy, and CD analyses, we found that when HdeA is active as a molecular chaperone, it is also capable of forming inactive aggregates that, at first glance, resemble amyloid fibrils. We noted that the molecular chaperone activity of HdeA takes precedence over fibrillogenesis under acidic conditions, as the presence of denatured substrate protein was sufficient to suppress HdeA fibril formation. Further experiments suggested that the secondary structure of HdeA fibrils deviates somewhat from typical amyloid fibrils and contains α-helices. Strikingly, HdeA fibrils that formed at pH 2 were immediately resolubilized by a simple shift to pH 7 and from there could regain molecular chaperone activity upon a return to pH 1. HdeA, therefore, provides an unusual example of a "reversible" form of protein fibrillation with an atypical secondary structure composition. The competition between active assistance of denatured polypeptides (its "molecular chaperone" activity) and the formation of inactive fibrillary deposits (its "fibrillogenic" activity) provides a unique opportunity to probe the relationship among protein function, structure, and aggregation in detail.
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Affiliation(s)
- Shiori Miyawaki
- Graduate School of Sustainability Science, Tottori University, Tottori 680-8552, Japan
| | - Yumi Uemura
- Department of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Kunihiro Hongo
- Graduate School of Sustainability Science, Tottori University, Tottori 680-8552, Japan; Department of Engineering, Tottori University, Tottori 680-8552, Japan; Center for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
| | - Yasushi Kawata
- Graduate School of Sustainability Science, Tottori University, Tottori 680-8552, Japan; Department of Engineering, Tottori University, Tottori 680-8552, Japan; Center for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
| | - Tomohiro Mizobata
- Graduate School of Sustainability Science, Tottori University, Tottori 680-8552, Japan; Department of Engineering, Tottori University, Tottori 680-8552, Japan; Center for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan.
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9
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Castelletto V, Hamley IW, Seitsonen J, Ruokolainen J, Harris G, Bellmann-Sickert K, Beck-Sickinger AG. Conformation and Aggregation of Selectively PEGylated and Lipidated Gastric Peptide Hormone Human PYY3–36. Biomacromolecules 2018; 19:4320-4332. [DOI: 10.1021/acs.biomac.8b01209] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Valeria Castelletto
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| | - Ian W. Hamley
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| | - Jani Seitsonen
- Department of Applied Physics, Aalto University School of Science,
P.O. Box 15100, FI-00076 Aalto, Finland
| | - Janne Ruokolainen
- Department of Applied Physics, Aalto University School of Science,
P.O. Box 15100, FI-00076 Aalto, Finland
| | - Gemma Harris
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, United Kingdom
| | - Kathrin Bellmann-Sickert
- Institute of Biochemistry, Faculty of Life Science, Leipzig University, Brüderstrasse 3, D 04103 Leipzig, Germany
| | - Annette G. Beck-Sickinger
- Institute of Biochemistry, Faculty of Life Science, Leipzig University, Brüderstrasse 3, D 04103 Leipzig, Germany
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Cieślik-Boczula K. Alpha-helix to beta-sheet transition in long-chain poly-l-lysine: Formation of alpha-helical fibrils by poly-l-lysine. Biochimie 2017; 137:106-114. [PMID: 28315381 DOI: 10.1016/j.biochi.2017.03.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/12/2017] [Indexed: 01/06/2023]
Abstract
The temperature-induced α-helix to β-sheet transition in long-chain poly-l-lysine (PLL), accompanied by the gauche-to-trans isomerization of CH2 groups in the hydrocarbon side chains of Lys amino acid residues, and formation of β-sheet as well as α-helix fibrillar aggregates of PLL have been studied using Fourier-transform infrared (FT-IR) and vibrational circular dichroism (VCD) spectroscopy, and transmission electron microscopy (TEM). In a low-temperature alkaline water solution or in a methanol-rich water mixture, the secondary structure of PLL is represented by α-helical conformations with unordered and gauche-rich hydrocarbon side chains. Under these conditions, PLL molecules aggregate into α-helical fibrils. PLLs dominated by extended antiparallel β-sheet structures with highly ordered trans-rich hydrocarbon side chains are formed in a high-temperature range at alkaline pD and aggregate into fibrillar, protofibrillar, and spherical forms. Presented data support the idea that fibrillar aggregation is a varied phenomenon possible in repetitive structural elements with not only a β-sheet-rich conformation, but also an α-helical-rich conformation.
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11
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Kim B, Do TD, Hayden EY, Teplow DB, Bowers MT, Shea JE. Aggregation of Chameleon Peptides: Implications of α-Helicity in Fibril Formation. J Phys Chem B 2016; 120:5874-83. [PMID: 27001160 DOI: 10.1021/acs.jpcb.6b00830] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigate the relationship between the inherent secondary structure and aggregation propensity of peptides containing chameleon sequences (i.e., sequences that can adopt either α or β structure depending on context) using a combination of replica exchange molecular dynamics simulations, ion-mobility mass spectrometry, circular dichroism, and transmission electron microscopy. We focus on an eight-residue long chameleon sequence that can adopt an α-helical structure in the context of the iron-binding protein from Bacillus anthracis (PDB id 1JIG ) and a β-strand in the context of the baculovirus P35 protein (PDB id 1P35 ). We show that the isolated chameleon sequence is intrinsically disordered, interconverting between α-helical and β-rich conformations. The inherent conformational plasticity of the sequence can be constrained by addition of flanking residues with a given secondary structure propensity. Intriguingly, we show that the chameleon sequence with helical flanking residues aggregates rapidly into fibrils, whereas the chameleon sequence with flanking residues that favor β-conformations has weak aggregation propensity. This work sheds new insights into the possible role of α-helical intermediates in fibril formation.
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Affiliation(s)
| | | | - Eric Y Hayden
- Department of Neurology, David Geffen School of Medicine at UCLA, Mary S. Easton Center for Alzheimer's Disease Research at UCLA, and Brain Research Institute and Molecular Biology Institute, University of California , 635 Charles Young Drive South, Los Angeles, California 90095, United States
| | - David B Teplow
- Department of Neurology, David Geffen School of Medicine at UCLA, Mary S. Easton Center for Alzheimer's Disease Research at UCLA, and Brain Research Institute and Molecular Biology Institute, University of California , 635 Charles Young Drive South, Los Angeles, California 90095, United States
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12
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Do TD, Chamas A, Zheng X, Barnes A, Chang D, Veldstra T, Takhar H, Dressler N, Trapp B, Miller K, McMahon A, Meredith SC, Shea JE, Lazar Cantrell K, Bowers MT. Elucidation of the Aggregation Pathways of Helix-Turn-Helix Peptides: Stabilization at the Turn Region Is Critical for Fibril Formation. Biochemistry 2015; 54:4050-62. [PMID: 26070092 DOI: 10.1021/acs.biochem.5b00414] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Aggregation of proteins to fiberlike aggregates often involves a transformation of native monomers to β-sheet-rich oligomers. This general observation underestimates the importance of α-helical segments in the aggregation cascade. Here, using a combination of experimental techniques and accelerated molecular dynamics simulations, we investigate the aggregation of a 43-residue, apolipoprotein A-I mimetic peptide and its E21Q and D26N mutants. Our study indicates a strong propensity of helical segments not to adopt cross-β-fibrils. The helix-turn-helix monomeric conformation of the peptides is preserved in the mature fibrils. Furthermore, we reveal opposite effects of mutations on and near the turn region in the self-assembly of these peptides. We show that the E21-R24 salt bridge is a major contributor to helix-turn-helix folding, subsequently leading to abundant fibril formation. On the other hand, the K19-D26 interaction is not required to fold the native helix-turn-helix peptide. However, removal of the charged D26 residue decreases the stability of the helix-turn-helix monomer and consequently reduces the level of aggregation. Finally, we provide a more refined assembly model for the helix-turn-helix peptides from apolipoprotein A-I based on the parallel stacking of helix-turn-helix dimers.
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Affiliation(s)
| | | | | | - Aaron Barnes
- §Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Dayna Chang
- §Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Tjitske Veldstra
- §Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Harmeet Takhar
- §Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Nicolette Dressler
- §Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Benjamin Trapp
- §Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Kylie Miller
- §Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Audrene McMahon
- §Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | | | | | - Kristi Lazar Cantrell
- §Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
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13
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Enhancement of thermo-stability and product tolerance of Pseudomonas putida nitrile hydratase by fusing with self-assembling peptide. J Biosci Bioeng 2014; 118:249-52. [DOI: 10.1016/j.jbiosc.2014.02.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/13/2014] [Accepted: 02/14/2014] [Indexed: 10/25/2022]
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14
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Han R, Li J, Shin HD, Chen RR, Liu L, Du G, Chen J. Fusion of self-assembling amphipathic oligopeptides with cyclodextrin glycosyltransferase improves 2-O-D-glucopyranosyl-L-ascorbic acid synthesis with soluble starch as the glycosyl donor. Appl Environ Microbiol 2014; 80:4717-24. [PMID: 24858090 PMCID: PMC4148807 DOI: 10.1128/aem.01249-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/13/2014] [Indexed: 11/20/2022] Open
Abstract
In this study, we fused six self-assembling amphipathic peptides (SAPs) with cyclodextrin glycosyltransferase (CGTase) from Paenibacillus macerans to catalyze 2-O-D-glucopyranosyl-L-ascorbic acid (AA-2G) production with cheap substrates, including maltose, maltodextrin, and soluble starch as glycosyl donors. The results showed that two fusion enzymes, SAP5-CGTase and SAP6-CGTase, increased AA-2G yields to 2.33- and 3.36-fold that of wild-type CGTase when soluble starch was used as a substrate. The cyclization activities of these enzymes decreased, while disproportionation activities increased. Enzymatic characterization of the two fusion enzymes was performed, and kinetics analysis of AA-2G synthesis confirmed the enhanced soluble starch specificity of SAP5-CGTase and SAP6-CGTase compared to that in the wild-type CGTase. As revealed by structure modeling of the fusion and wild-type CGTases, enhanced substrate-binding capacity may result from the increased number of hydrogen bonds present after fusion. This study demonstrates an effective protein fusion approach to improving the substrate specificity of CGTase for AA-2G synthesis. Fusion enzymes, especially SAP6-CGTase, are promising starting points for further development through protein engineering.
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Affiliation(s)
- Ruizhi Han
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Synergetic Innovation of Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Synergetic Innovation of Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China
| | - Hyun-dong Shin
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rachel R. Chen
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Synergetic Innovation of Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- National Engineering of Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
| | - Jian Chen
- Synergetic Innovation of Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China
- National Engineering of Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
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15
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Bocchinfuso G, Conflitti P, Raniolo S, Caruso M, Mazzuca C, Gatto E, Placidi E, Formaggio F, Toniolo C, Venanzi M, Palleschi A. Aggregation propensity of Aib homo-peptides of different length: an insight from molecular dynamics simulations. J Pept Sci 2014; 20:494-507. [DOI: 10.1002/psc.2648] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 04/16/2014] [Accepted: 04/16/2014] [Indexed: 12/18/2022]
Affiliation(s)
- Gianfranco Bocchinfuso
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Paolo Conflitti
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Stefano Raniolo
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Mario Caruso
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Claudia Mazzuca
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Emanuela Gatto
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Ernesto Placidi
- Department of Physics; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
- CNR-ISM; Via Fosso del Cavaliere 100 I-00133 Roma Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry; University of Padova; I-35131 Padua Italy
| | - Claudio Toniolo
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry; University of Padova; I-35131 Padua Italy
| | - Mariano Venanzi
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Antonio Palleschi
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
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16
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Lin Z, Zhou B, Wu W, Xing L, Zhao Q. Self-assembling amphipathic alpha-helical peptides induce the formation of active protein aggregates in vivo. Faraday Discuss 2014; 166:243-56. [PMID: 24611280 DOI: 10.1039/c3fd00068k] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We recently found that several self-assembling alpha, beta, or surfactant-like peptides, when terminally attached to proteins, can promote the in vivo assembly of active protein aggregates (or active inclusion bodies, AIBs) in Escherichia coil. In this work, we systematically examined the AIBs induced by an amphipathic alpha-helical peptide 18Awt (EWLKAFYEKVLEKLKELF) and its variants with altered ion pairs. Transmission electron microscopic and Fourier transform infrared spectroscopic analyses suggested that the AIBs appeared to adopt an amorphous mesh-like structure, and were likely induced by helical structures formed by the assembly of the 18A peptides. Confocal fluorescent micrographic analysis revealed that the AIBs resided around the periphery of the cell membrane or in the cytoplasm, depending on the distribution of ion pairs on the 18A peptides, which suggested that the association between the aggregates and the cell membrane was mediated by the lipid-18A interaction. Two of these 18A peptide variants were further used in constructing cleavable self-aggregating tags (cSAT) in conjunction with an intein molecule for protein purification, and verified using two model proteins. This extends the cSAT approach for laboratory and potentially industrial uses. Our study might also provide new insights into aggregation-related diseases.
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17
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Yang X, Huang A, Peng J, Wang J, Wang X, Lin Z, Li S. Self-assembly amphipathic peptides induce active enzyme aggregation that dramatically increases the operational stability of nitrilase. RSC Adv 2014; 4:60675-60684. [DOI: 10.1039/c4ra11236a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023] Open
Abstract
Dramatic improvements in the substrate tolerance, operational stability and recycle times were successfully achieved through coupling the fusion of an amphipathic self-assembly peptide 18A to the nitrilase with alginate entrapment.
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Affiliation(s)
- Xiaofeng Yang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou 510006, China
| | - An Huang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou 510006, China
| | - Jizong Peng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou 510006, China
| | - Jufang Wang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou 510006, China
| | - Xiaoning Wang
- State Key Laboratory of Kidney
- The Institute of Life Sciences
- Chinese PLA General Hospital
- Beijing 100853, China
| | - Zhanglin Lin
- Department of Chemical Engineering
- Tsinghua University
- Beijing 100084, China
| | - Shuang Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou 510006, China
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18
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Börner HG, Sütterlin RI, Theato P, Wiss KT. Topology-Dependent Swichability of Peptide Secondary Structures in Bioconjugates with Complex Architectures. Macromol Rapid Commun 2013; 35:180-185. [DOI: 10.1002/marc.201300808] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 11/06/2013] [Indexed: 12/27/2022]
Affiliation(s)
- Hans G. Börner
- Humboldt-Universität zu Berlin; Department of Chemistry, Laboratory for Organic Synthesis of Functional Systems; D-12489 Berlin Germany
| | - Romina I. Sütterlin
- Humboldt-Universität zu Berlin; Department of Chemistry, Laboratory for Organic Synthesis of Functional Systems; D-12489 Berlin Germany
| | - Patrick Theato
- University of Mainz; Institute of Organic Chemistry; Duesbergweg 10-14 D-55099 Mainz Germany
- University of Hamburg; Institute for Technical and Macromolecular Chemistry, Bundesstr 45; D-20146 Hamburg Germany
| | - Kerstin T. Wiss
- University of Mainz; Institute of Organic Chemistry; Duesbergweg 10-14 D-55099 Mainz Germany
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19
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Takei T, Hasegawa K, Imada K, Namba K, Tsumoto K, Kuriki Y, Yoshino M, Yazaki K, Kojima S, Takei T, Ueda T, Miura KI. Effects of chain length of an amphipathic polypeptide carrying the repeated amino acid sequence (LETLAKA)(n) on α-helix and fibrous assembly formation. Biochemistry 2013; 52:2810-20. [PMID: 23530905 DOI: 10.1021/bi400001c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Polypeptide α3 (21 residues), with three repeats of a seven-amino-acid sequence (LETLAKA)(3), forms an amphipathic α-helix and a long fibrous assembly. Here, we investigated the ability of α3-series polypeptides (with 14-42 residues) of various chain lengths to form α-helices and fibrous assemblies. Polypeptide α2 (14 residues), with two same-sequence repeats, did not form an α-helix, but polypeptide α2L (15 residues; α2 with one additional leucine residue on its carboxyl terminal) did form an α-helix and fibrous assembly. Fibrous assembly formation was associated with polypeptides at least as long as polypeptide α2L and with five leucine residues, indicating that the C-terminal leucine has a critical element for stabilization of α-helix and fibril formation. In contrast, polypeptides α5 (35 residues) and α6 (42 residues) aggregated easily, although they formed α-helices. A 15-35-residue chain was required for fibrous assembly formation. Electron microscopy and X-ray fiber diffraction showed that the thinnest fibrous assemblies of polypeptides were about 20 Å and had periodicities coincident with the length of the α-helix in a longitudinal direction. These results indicated that the α-helix structures were orientated along the fibrous axis and assembled into a bundle. Furthermore, the width and length of fibrous assemblies changed with changes in the pH value, resulting in variations in the charged states of the residues. Our results suggest that the formation of fibrous assemblies of amphipathic α-helices is due to the assembly of bundles via the hydrophobic faces of the helices and extension with hydrophobic noncovalent bonds containing a leucine.
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Affiliation(s)
- Toshiaki Takei
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
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20
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Lu X, Liu S, Zhang D, Zhou X, Wang M, Liu Y, Wu J, Du G, Chen J. Enhanced thermal stability and specific activity of Pseudomonas aeruginosa lipoxygenase by fusing with self-assembling amphipathic peptides. Appl Microbiol Biotechnol 2013; 97:9419-27. [DOI: 10.1007/s00253-013-4751-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 01/20/2013] [Accepted: 01/31/2013] [Indexed: 11/24/2022]
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21
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Fusion of an oligopeptide to the N terminus of an alkaline α-amylase from Alkalimonas amylolytica simultaneously improves the enzyme's catalytic efficiency, thermal stability, and resistance to oxidation. Appl Environ Microbiol 2013; 79:3049-58. [PMID: 23455344 DOI: 10.1128/aem.03785-12] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we constructed and expressed six fusion proteins composed of oligopeptides attached to the N terminus of the alkaline α-amylase (AmyK) from Alkalimonas amylolytica. The oligopeptides had various effects on the functional and structural characteristics of AmyK. AmyK-p1, the fusion protein containing peptide 1 (AEAEAKAKAEAEAKAK), exhibited improved specific activity, catalytic efficiency, alkaline stability, thermal stability, and oxidative stability compared with AmyK. Compared with AmyK, the specific activity and catalytic constant (kcat) of AmyK-p1 were increased by 4.1-fold and 3.5-fold, respectively. The following properties were also improved in AmyK-p1 compared with AmyK: kcat/Km increased from 1.8 liter/(g·min) to 9.7 liter/(g·min), stable pH range was extended from 7.0 to 11.0 to 7.0 to 12.0, optimal temperature increased from 50°C to 55°C, and the half-life at 60°C increased by ∼2-fold. Moreover, AmyK-p1 showed improved resistance to oxidation and retained 54% of its activity after incubation with H2O2, compared with 20% activity retained by AmyK. Finally, AmyK-p1 was more compatible than AmyK with the commercial solid detergents tested. The mechanisms responsible for these changes were analyzed by comparing the three-dimensional (3-D) structural models of AmyK and AmyK-p1. The significantly enhanced catalytic efficiency and stability of AmyK-p1 suggests its potential as a detergent ingredient. In addition, the oligopeptide fusion strategy described here may be useful for improving the catalytic efficiency and stability of other industrial enzymes.
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22
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23
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24
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Petrlova J, Duong T, Cochran MC, Axelsson A, Mörgelin M, Roberts LM, Lagerstedt JO. The fibrillogenic L178H variant of apolipoprotein A-I forms helical fibrils. J Lipid Res 2011; 53:390-398. [PMID: 22184756 PMCID: PMC3276462 DOI: 10.1194/jlr.m020883] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
A number of amyloidogenic variants of apoA-I have been discovered but most have not
been analyzed. Previously, we showed that the G26R mutation of apoA-I leads to
increased β-strand structure, increased N-terminal protease susceptibility, and
increased fibril formation after several days of incubation. In vivo, this and other
variants mutated in the N-terminal domain (residues 26 to ∼90) lead to renal and
hepatic accumulation. In contrast, several mutations identified within residues 170
to 178 lead to cardiac, laryngeal, and cutaneous protein deposition. Here, we
describe the structural changes in the fibrillogenic variant L178H. Like G26R, the
initial structure of the protein exhibits altered tertiary conformation relative to
wild-type protein along with decreased stability and an altered lipid binding
profile. However, in contrast to G26R, L178H undergoes an increase in helical
structure upon incubation at 37°C with a half time (t1/2) of about 12
days. Upon prolonged incubation, the L178H mutant forms fibrils of a diameter of 10
nm that ranges in length from 30 to 120 nm. These results show that apoA-I, known for
its dynamic properties, has the ability to form multiple fibrillar conformations,
which may play a role in the tissue-specific deposition of the individual
variants.
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Affiliation(s)
- Jitka Petrlova
- Department of Experimental Medical Sciences, Lund University, S-221 84 Lund, Sweden; and
| | - Trang Duong
- Department of Chemistry, California State University Sacramento, Sacramento, CA 95819
| | - Megan C Cochran
- Department of Chemistry, California State University Sacramento, Sacramento, CA 95819
| | - Annika Axelsson
- Department of Experimental Medical Sciences, Lund University, S-221 84 Lund, Sweden; and
| | - Matthias Mörgelin
- Department of Experimental Medical Sciences, and Department of Infection Medicine, Lund University, S-221 84 Lund, Sweden; and
| | - Linda M Roberts
- Department of Chemistry, California State University Sacramento, Sacramento, CA 95819.
| | - Jens O Lagerstedt
- Department of Experimental Medical Sciences, Lund University, S-221 84 Lund, Sweden; and.
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25
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Vácha R, Frenkel D. Relation between molecular shape and the morphology of self-assembling aggregates: a simulation study. Biophys J 2011; 101:1432-9. [PMID: 21943424 DOI: 10.1016/j.bpj.2011.07.046] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 06/29/2011] [Accepted: 07/27/2011] [Indexed: 10/17/2022] Open
Abstract
Proteins can aggregate in a wide variety of structures, both compact and extended. We present simulations of a coarse-grained anisotropic model that reproduce many of the experimentally observed aggregate structures. Conversely, all structures predicted by our model have experimental counterparts (ribbons, multistranded fibrils, and vesicles). The model we use is that of a rodlike particle with an attractive (hydrophobic) stripe on its side. Our Monte Carlo simulations show that aggregate morphologies crucially depend on two parameters. The first one is the width of the attractive stripe and the second one is a presence or absence of attractive interactions at the particle ends. These results provide us with a generic insight into the relation between the shape of protein-protein interaction potential and the morphology of protein aggregates.
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Affiliation(s)
- Robert Vácha
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
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26
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Arsequell G, Rosa M, Mayato C, Dorta RL, Gonzalez-Nunez V, Barreto-Valer K, Marcelo F, Calle LP, Vázquez JT, Rodríguez RE, Jiménez-Barbero J, Valencia G. Synthesis, biological evaluation and structural characterization of novel glycopeptide analogues of nociceptin N/OFQ. Org Biomol Chem 2011; 9:6133-42. [PMID: 21773621 DOI: 10.1039/c1ob05197k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
To examine if the biological activity of the N/OFQ peptide, which is the native ligand of the pain-related and viable drug target NOP receptor, could be modulated by glycosylation and if such effects could be conformationally related, we have synthesized three N/OFQ glycopeptide analogues, namely: [Thr(5)-O-α-D-GalNAc-N/OFQ] (glycopeptide 1), [Ser(10)-O-α-D-GalNAc]-N/OFQ (glycopeptide 2) and [Ser(10)-O-β-D-GlcNAc]-N/OFQ] (glycopeptide 3). They were tested for biological activity in competition binding assays using the zebrafish animal model in which glycopeptide 2 exhibited a slightly improved binding affinity, whereas glycopeptide 1 showed a remarkably reduced binding affinity compared to the parent compound and glycopeptide 3. The structural analysis of these glycopeptides and the parent N/OFQ peptide by NMR and circular dichroism indicated that their aqueous solutions are mainly populated by random coil conformers. However, in membrane mimic environments a certain proportion of the molecules of all these peptides exist as α-helix structures. Interestingly, under these experimental conditions, glycopeptide 1 (glycosylated at Thr-5) exhibited a population of folded hairpin-like geometries. From these facts it is tempting to speculate that nociceptin analogues showing linear helical structures are more complementary and thus interact more efficiently with the native NOP receptor than folded structures, since glycopeptide 1 showed a significantly reduced binding affinity for the NOP receptor.
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Affiliation(s)
- Gemma Arsequell
- Instituto de Química Avanzada de Cataluña (IQAC-CSIC), Barcelona, Spain
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27
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Kushner AM, Guan Z. Modulares Design in natürlichen und biomimetischen elastischen Materialien. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006496] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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28
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Kushner AM, Guan Z. Modular design in natural and biomimetic soft materials. Angew Chem Int Ed Engl 2011; 50:9026-57. [PMID: 21898722 DOI: 10.1002/anie.201006496] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2010] [Indexed: 11/09/2022]
Abstract
Under eons of evolutionary and environmental pressure, biological systems have developed strong and lightweight peptide-based polymeric materials by using the 20 naturally occurring amino acids as principal monomeric units. These materials outperform their man-made counterparts in the following ways: 1) multifunctionality/tunability, 2) adaptability/stimuli-responsiveness, 3) synthesis and processing under ambient and aqueous conditions, and 4) recyclability and biodegradability. The universal design strategy that affords these advanced properties involves "bottom-up" synthesis and modular, hierarchical organization both within and across multiple length-scales. The field of "biomimicry"-elucidating and co-opting nature's basic material design principles and molecular building blocks-is rapidly evolving. This Review describes what has been discovered about the structure and molecular mechanisms of natural polymeric materials, as well as the progress towards synthetic "mimics" of these remarkable systems.
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Affiliation(s)
- Aaron M Kushner
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
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29
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Ardejani MS, Li NX, Orner BP. Stabilization of a protein nanocage through the plugging of a protein-protein interfacial water pocket. Biochemistry 2011; 50:4029-37. [PMID: 21488690 DOI: 10.1021/bi200207w] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The unique structural properties of the ferritin protein cages have provided impetus to focus on the methodical study of these self-assembling nanosystems. Among these proteins, Escherichia coli bacterioferritin (EcBfr), although architecturally very similar to other members of the family, shows structural instability and an incomplete self-assembly behavior by populating two oligomerization states. Through computational analysis and comparison to its homologues, we have found that this protein has a smaller than average dimeric interface on its 2-fold symmetry axis mainly because of the existence of an interfacial water pocket centered around two water-bridged asparagine residues. To investigate the possibility of engineering EcBfr for modified structural stability, we have used a semiempirical computational method to virtually explore the energy differences of the 480 possible mutants at the dimeric interface relative to that of wild-type EcBfr. This computational study also converged on the water-bridged asparagines. Replacing these two asparagines with hydrophobic amino acids resulted in proteins that folded into α-helical monomers and assembled into cages as evidenced by circular dichroism and transmission electron microscopy. Both thermal and chemical denaturation confirmed that, in all cases, these proteins, in agreement with the calculations, possessed increased stability. One of the three mutations shifts the population in favor of the higher-order oligomerization state in solution as evidenced by both size exclusion chromatography and native gel electrophoresis. These results taken together suggest that our low-level design was successful and that it may be possible to apply the strategy of targeting water pockets at protein--protein interfaces to other protein cage and self-assembling systems. More generally, this study further demonstrates the power of jointly employing in silico and in vitro techniques to understand and enhance biostructural energetics.
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Affiliation(s)
- Maziar S Ardejani
- Division of Chemistry and Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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Wu W, Xing L, Zhou B, Lin Z. Active protein aggregates induced by terminally attached self-assembling peptide ELK16 in Escherichia coli. Microb Cell Fact 2011; 10:9. [PMID: 21320350 PMCID: PMC3045283 DOI: 10.1186/1475-2859-10-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 02/15/2011] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND In recent years, it has been gradually realized that bacterial inclusion bodies (IBs) could be biologically active. In particular, several proteins including green fluorescent protein, β-galactosidase, β-lactamase, alkaline phosphatase, D-amino acid oxidase, polyphosphate kinase 3, maltodextrin phosphorylase, and sialic acid aldolase have been successfully produced as active IBs when fused to an appropriate partner such as the foot-and-mouth disease virus capsid protein VP1, or the human β-amyloid peptide Aβ42(F19D). As active IBs may have many attractive advantages in enzyme production and industrial applications, it is of considerable interest to explore them further. RESULTS In this paper, we report that an ionic self-assembling peptide ELK16 (LELELKLK)2 was able to effectively induce the formation of cytoplasmic inclusion bodies in Escherichia coli (E. coli) when attached to the carboxyl termini of four model proteins including lipase A, amadoriase II, β-xylosidase, and green fluorescent protein. These aggregates had a general appearance similar to the usually reported cytoplasmic inclusion bodies (IBs) under transmission electron microscopy or fluorescence confocal microscopy. Except for lipase A-ELK16 fusion, the three other fusion protein aggregates retained comparable specific activities with the native counterparts. Conformational analyses by Fourier transform infrared spectroscopy revealed the existence of newly formed antiparallel beta-sheet structures in these ELK16 peptide-induced inclusion bodies, which is consistent with the reported assembly of the ELK16 peptide. CONCLUSIONS This has been the first report where a terminally attached self-assembling β peptide ELK16 can promote the formation of active inclusion bodies or active protein aggregates in E. coli. It has the potential to render E. coli and other recombinant hosts more efficient as microbial cell factories for protein production. Our observation might also provide hints for protein aggregation-related diseases.
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Affiliation(s)
- Wei Wu
- Department of Chemical Engineering, Tsinghua University, One Tsinghua Garden Road, Beijing 100084, PR China
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31
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Bromley EHC, Channon KJ. Alpha-helical peptide assemblies giving new function to designed structures. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 103:231-75. [PMID: 21999998 PMCID: PMC7150058 DOI: 10.1016/b978-0-12-415906-8.00001-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
The design of alpha-helical tectons for self-assembly is maturing as a science. We have now reached the point where many different coiled-coil topologies can be reliably produced and validated in synthetic systems and the field is now moving on towards more complex, discrete structures and applications. Similarly the design of infinite or fiber assemblies has also matured, with the creation fibers that have been modified or functionalized in a variety of ways. This chapter discusses the progress made in both of these areas as well as outlining the challenges still to come.
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Robson Marsden H, Kros A. Self-assembly of coiled coils in synthetic biology: inspiration and progress. Angew Chem Int Ed Engl 2010; 49:2988-3005. [PMID: 20474034 DOI: 10.1002/anie.200904943] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Biological self-assembly is very complex and results in highly functional materials. In effect, it takes a bottom-up approach using biomolecular building blocks of precisely defined shape, size, hydrophobicity, and spatial distribution of functionality. Inspired by, and drawing lessons from self-assembly processes in nature, scientists are learning how to control the balance of many small forces to increase the complexity and functionality of self-assembled nanomaterials. The coiled-coil motif, a multipurpose building block commonly found in nature, has great potential in synthetic biology. In this review we examine the roles that the coiled-coil peptide motif plays in self-assembly in nature, and then summarize the advances that this has inspired in the creation of functional units, assemblies, and systems.
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Affiliation(s)
- Hana Robson Marsden
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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Woolfson DN, Mahmoud ZN. More than just bare scaffolds: towards multi-component and decorated fibrous biomaterials. Chem Soc Rev 2010; 39:3464-79. [PMID: 20676443 DOI: 10.1039/c0cs00032a] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We are entering a new phase in biomaterials research in which rational design is being used to produce functionalised materials tailored to specific applications. As is evident from this Themed Issue, there are now a number of distinct types of designed, self-assembling, fibrous biomaterials. Many of these are ripe for development and application for example as scaffolds for 3D cell culture and tissue engineering, and in templating inorganic materials. Whilst a number of groups are making headway towards such applications, there is a general challenge to translate a wealth of excellent basic research into materials with a genuine future in real-life applications. Amongst other contemporary aspects of this evolving research area, a key issue is that of decorating or functionalising what are mostly bare scaffolds. There are a number of hurdles to overcome to achieve effective and controlled labelling of the scaffolds, for instance: maintaining biocompatibility, i.e., by minimising covalent chemistry, or using milder bioconjugation methods; attaining specified levels of decoration, and, in particular, high and stoichiometric labelling; introducing orthogonality, such that two or more functions can be appended to the same scaffold; and, in relevant cases, maintaining the possibility for recombinant peptide/protein production. In this critical review, we present an overview of the different approaches to tackling these challenges largely for self-assembled, peptide-based fibrous systems. We review the field as it stands by placing work within general routes to fibre functionalisation; give worked examples on our own specific system, the SAFs; and explore the potential for future developments in the area. Our feeling is that by tackling the challenges of designing multi-component and functional biomaterials, as a community we stand to learn a great deal about self-assembling biomolecular systems more broadly, as well as, hopefully, delivering new materials that will be truly useful in biotechnology and biomedical applications (107 references).
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Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, UKBS8 1TS.
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Robson Marsden H, Kros A. Selbstorganisation von Coiled-Coils in der synthetischen Biologie: Inspiration und Fortschritt. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200904943] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Woolfson DN. Building fibrous biomaterials from alpha-helical and collagen-like coiled-coil peptides. Biopolymers 2010; 94:118-27. [PMID: 20091877 DOI: 10.1002/bip.21345] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Over the decade and a half, interest has soared in the development of peptide-based biomaterials and their potential applications in biotechnology. This review outlines the advances during this time in the construction of biomaterials based on the alpha-helical coiled-coil and collagen-like peptides. These structures and the resulting designs are distinct from the more commonly used beta-structured peptides, which often lead to hydrogels comprising amyloid-like fibrils. The review covers basic design rules for these helical assemblies, and the various fibrous biomaterials that can be accomplished with them, which include rigid structures with straight, branched, or networked structures, decorated and functionalized systems, and most recently flexible fibers and entangled hydrogel networks. This plethora of alpha-helix-based biomaterials, together with more recent collagen-like assemblies, that are emerging from various laboratories complement those developed using beta-structured peptides, and open exciting new avenues for biomaterials research and potential new application areas.
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Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom.
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36
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Tarafdar PK, Vedantam LV, Kondreddy A, Podile AR, Swamy MJ. Biophysical investigations on the aggregation and thermal unfolding of harpinPss and identification of leucine-zipper-like motifs in harpins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1684-92. [DOI: 10.1016/j.bbapap.2009.07.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 07/11/2009] [Accepted: 07/31/2009] [Indexed: 11/17/2022]
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37
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Pires M, Przybyla D, Chmielewski J. A Metal-Collagen Peptide Framework for Three-Dimensional Cell Culture. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902375] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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38
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Pires M, Przybyla D, Chmielewski J. A Metal-Collagen Peptide Framework for Three-Dimensional Cell Culture. Angew Chem Int Ed Engl 2009; 48:7813-7. [DOI: 10.1002/anie.200902375] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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39
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Getz GS, Wool GD, Reardon CA. Apoprotein A-I mimetic peptides and their potential anti-atherogenic mechanisms of action. Curr Opin Lipidol 2009; 20:171-5. [PMID: 19373084 DOI: 10.1097/mol.0b013e32832ac051] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW Peptides that resemble in physicochemical properties the helices of apoprotein A-I, the major protein of atheroprotective HDL, show promise for the treatment of atherosclerosis-related vascular disease. The properties and promise of these so-called mimetic peptides will be explored in this review. RECENT FINDINGS Both HDL and mimetic peptides are able to scavenge and sequester oxidized lipids and hence protect endothelial cells and arteries from the pro-inflammatory action of oxidized LDL. Active mimetic peptides have an amphipathic alpha-helical secondary structure, whose hydrophobic face is particularly important for its bioactivity. The most frequently employed peptide is 4F. The comparative bioactivity of variants of 4F, particularly tandem helical peptides, has been explored. The recent observation of the very high affinity of bioactive peptides for oxidized fatty acids and phospholipids provides a likely mechanism for the action of these peptides in inhibiting early atherosclerosis formation. It is not clear that these peptides alone are effective in reversing established atherosclerosis, although they may achieve this outcome in synergy with statin therapy. SUMMARY Recent observations of mimetic peptides have pointed to promising therapies for patients with cardiovascular disease. The peptides appear to be well tolerated and effective in promoting the anti-inflammatory properties of HDL.
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Affiliation(s)
- Godfrey S Getz
- Department of Pathology, The University of Chicago, Chicago, Illinois 60637, USA.
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40
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Disorder-to-order conformational transitions in protein structure and its relationship to disease. Mol Cell Biochem 2009; 330:105-20. [PMID: 19357935 DOI: 10.1007/s11010-009-0105-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Accepted: 03/30/2009] [Indexed: 01/22/2023]
Abstract
Function in proteins largely depends on the acquisition of specific structures through folding at physiological time scales. Under both equilibrium and non-equilibrium states, proteins develop partially structured molecules that being intermediates in the process, usually resemble the structure of the fully folded protein. These intermediates, known as molten globules, present the faculty of adopting a large variety of conformations mainly supported by changes in their side chains. Taking into account that the mechanism to obtain a fully packed structure is considered more difficult energetically than forming partially "disordered" folding intermediates, evolution might have conferred upon an important number of proteins the capability to first partially fold and-depending on the presence of specific partner ligands-switch on disorder-to-order transitions to adopt a highly ordered well-folded state and reach the lowest energy conformation possible. Disorder in this context can represent segments of proteins or complete proteins that might exist in the native state. Moreover, because this type of disorder-to-order transition in proteins has been found to be reversible, it has been frequently associated with important signaling events in the cell. Due to the central role of this phenomenon in cell biology, protein misfolding and aberrant disorder-to-order transitions have been at present associated with an important number of diseases.
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41
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Castillo J, Dimaki M, Svendsen WE. Manipulation of biological samples using micro and nano techniques. Integr Biol (Camb) 2009; 1:30-42. [DOI: 10.1039/b814549k] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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42
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Tsuruta H, Irving TC. Experimental approaches for solution X-ray scattering and fiber diffraction. Curr Opin Struct Biol 2008; 18:601-8. [PMID: 18801437 PMCID: PMC2659704 DOI: 10.1016/j.sbi.2008.08.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Revised: 08/12/2008] [Accepted: 08/31/2008] [Indexed: 01/09/2023]
Abstract
X-ray scattering and diffraction from non-crystalline systems have gained renewed interest in recent years, as focus shifts from the structural chemistry information gained by high-resolution studies to the context of structural physiology at larger length scales. Such techniques permit the study of isolated macromolecules as well as highly organized macromolecular assemblies as a whole under near-physiological conditions. Time-resolved approaches, made possible by advanced synchrotron instrumentation, add a crucial dimension to many of these investigations. This article reviews experimental approaches in non-crystalline X-ray scattering and diffraction that may be used to illuminate important scientific questions such as protein/nucleic acid folding and structure-function relationships in large macromolecular assemblies.
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Affiliation(s)
- H. Tsuruta
- Stanford Synchrotron Radiation Laboratory (SSRL), SLAC, Stanford University, 2575 Sand Hill Rd, MS69, Menlo Park, CA 94025,
| | - T. C. Irving
- Center for Synchrotron Radiation Research and Instrumentation (CSRRI), Department of Biological, Chemical and Physical Sciences, Illinois Institute of Technology, 3101 S. Dearborn, Chicago IL. 60616, USA,
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43
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Dong H, Paramonov SE, Hartgerink JD. Self-assembly of alpha-helical coiled coil nanofibers. J Am Chem Soc 2008; 130:13691-5. [PMID: 18803383 DOI: 10.1021/ja8037323] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The alpha-helical coiled coil is one of the best-studied and most well-understood protein folding motifs. In particular, the coiled coil can be made to self-assemble into a nanofibrous architecture with many potential applications in biomimetic engineering and elsewhere. The key to the assembly of such nanofibers has been the formation of "sticky ended" dimers through careful selection of electrostatically charged amino acids. In this work, we demonstrate for the first time that sticky ended dimers are not a prerequisite for alpha-helical coiled coil nanofiber formation. In contrast, we show that blunt-ended dimers are able to form nanofibers with a uniform diameter of 4 nm while being hundreds of nanometers in length. Furthermore, the length and lateral packing can be controlled through selection of amino acids not involved in the coiled coil interface.
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Affiliation(s)
- He Dong
- Department of Chemistry, Rice University, 6100 Main Street, Mail Stop 60, Houston, Texas 77005, USA
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44
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Gribbon C, Channon KJ, Zhang W, Banwell EF, Bromley EHC, Chaudhuri JB, Oreffo ROC, Woolfson DN. MagicWand: A Single, Designed Peptide That Assembles to Stable, Ordered α-Helical Fibers. Biochemistry 2008; 47:10365-71. [DOI: 10.1021/bi801072s] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Christopher Gribbon
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Kevin J. Channon
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Weijie Zhang
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Eleanor F. Banwell
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Elizabeth H. C. Bromley
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Julian B. Chaudhuri
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Richard O. C. Oreffo
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
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45
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Carnemolla R, Ren X, Biswas TK, Meredith SC, Reardon CA, Wang J, Getz GS. The specific amino acid sequence between helices 7 and 8 influences the binding specificity of human apolipoprotein A-I for high density lipoprotein (HDL) subclasses: a potential for HDL preferential generation. J Biol Chem 2008; 283:15779-88. [PMID: 18385132 PMCID: PMC2414305 DOI: 10.1074/jbc.m710244200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 04/01/2008] [Indexed: 02/02/2023] Open
Abstract
Humans have two major high density lipoprotein (HDL) sub-fractions, HDL(2) and HDL(3), whereas mice have a monodisperse HDL profile. Epidemiological evidence has suggested that HDL(2) is more atheroprotective; however, currently there is no direct experimental evidence to support this postulate. The amino acid sequence of apoA-I is a primary determinant of HDL subclass formation. The majority of the alpha-helical repeats in human apoA-I are proline-punctuated. A notable exception is the boundary between helices 7 and 8, which is located in the transitional segment between the stable N-terminal domain and the C-terminal hydrophobic domain. In this study we ask whether the substitution of a proline-containing sequence (PCS) separating other helices in human apoA-I for the non-proline-containing sequence (NPCS) between helices 7 and 8 (residues 184-190) influences HDL subclass association. The human apoA-I mutant with PCS2 replacing NPCS preferentially bound to HDL(2). In contrast, the mutant where PCS3 replaced NPCS preferentially associated with HDL(3). Thus, the specific amino acid sequence between helices 7 and 8 influences HDL subclass association. The wild-type and mutant proteins exhibited similar physicochemical properties except that the two mutants displayed greater lipid-associated stability versus wild-type human apoA-I. These results focus new attention on the influence of the boundary between helices 7 and 8 on the properties of apoA-I. The expression of these mutants in mice may result in the preferential generation of HDL(2) or HDL(3) and allow us to examine experimentally the anti-atherogenicity of the HDL subclasses.
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Affiliation(s)
- Ronald Carnemolla
- Department of Pathology and the
Committee of Molecular Metabolism and Nutrition,
The University of Chicago, Chicago, Illinois 60637 and the
Department of Biochemistry and Molecular
Biology, Wayne State University, Detroit, Michigan 48201
| | - Xuefeng Ren
- Department of Pathology and the
Committee of Molecular Metabolism and Nutrition,
The University of Chicago, Chicago, Illinois 60637 and the
Department of Biochemistry and Molecular
Biology, Wayne State University, Detroit, Michigan 48201
| | - Tapan K. Biswas
- Department of Pathology and the
Committee of Molecular Metabolism and Nutrition,
The University of Chicago, Chicago, Illinois 60637 and the
Department of Biochemistry and Molecular
Biology, Wayne State University, Detroit, Michigan 48201
| | - Stephen C. Meredith
- Department of Pathology and the
Committee of Molecular Metabolism and Nutrition,
The University of Chicago, Chicago, Illinois 60637 and the
Department of Biochemistry and Molecular
Biology, Wayne State University, Detroit, Michigan 48201
| | - Catherine A. Reardon
- Department of Pathology and the
Committee of Molecular Metabolism and Nutrition,
The University of Chicago, Chicago, Illinois 60637 and the
Department of Biochemistry and Molecular
Biology, Wayne State University, Detroit, Michigan 48201
| | - Jianjun Wang
- Department of Pathology and the
Committee of Molecular Metabolism and Nutrition,
The University of Chicago, Chicago, Illinois 60637 and the
Department of Biochemistry and Molecular
Biology, Wayne State University, Detroit, Michigan 48201
| | - Godfrey S. Getz
- Department of Pathology and the
Committee of Molecular Metabolism and Nutrition,
The University of Chicago, Chicago, Illinois 60637 and the
Department of Biochemistry and Molecular
Biology, Wayne State University, Detroit, Michigan 48201
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46
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Papapostolou D, Bromley EHC, Bano C, Woolfson DN. Electrostatic control of thickness and stiffness in a designed protein fiber. J Am Chem Soc 2008; 130:5124-30. [PMID: 18361488 DOI: 10.1021/ja0778444] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Attempts to design peptide-based fibers from first principles test our understanding of protein folding and assembly, and potentially provide routes to new biomaterials. Several groups have presented such designs based on alpha-helical and beta-strand building blocks. A key issue is this area now is engineering and controlling fiber morphology and related properties. Previously, we have reported the design and characterization of a self-assembling peptide fiber (SAF) system based on alpha-helical coiled-coil building blocks. With preceding designs, the SAFs are thickened, highly ordered structures in which many coiled coils are tightly bundled. As a result, the fibers behave as rigid rods. Here we report successful attempts to design new fibers that are thinner and more flexible by further programming at the amino-acid sequence level. This was done by introducing extended, or "smeared", electrostatic networks of arginine and glutamate residues to the surfaces of the coiled-coil building blocks. Furthermore, using arginine--rather than lysine--in these networks plays a major role in the fiber assembly, presumably by facilitating multidentate intra and intercoiled-coil salt bridges.
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Affiliation(s)
- David Papapostolou
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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47
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Wool GD, Reardon CA, Getz GS. Apolipoprotein A-I mimetic peptide helix number and helix linker influence potentially anti-atherogenic properties. J Lipid Res 2008; 49:1268-83. [PMID: 18323574 DOI: 10.1194/jlr.m700552-jlr200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We hypothesize that apolipoprotein A-I (apoA-I) mimetic peptides better mimicking the punctuated alpha-helical repeats of full-length apoA-I are more anti-inflammatory and anti-atherogenic. This study compares a monomeric apoA-I mimetic helix to three different tandem helix peptides in vitro: 4F (18 mer), 4F-proline-4F (37 mer, Pro), 4F-alanine-4F (37 mer, Ala), and 4F-KVEPLRA-4F [the human apoA-I 4/5 interhelical sequence (IHS), 43 mer]. All peptides cleared turbid lipid suspensions, with 4F being most effective. In contrast to lipid clearance, tandem peptides were more effective at remodeling mouse HDL. All four peptides displaced apoA-I and apoE from the HDL, leaving a larger particle containing apoA-II and peptide. Peptide-remodeled HDL particles show no deficit in ABCG1 cholesterol efflux despite the loss of the majority of apoA-I. Tandem peptides show greater ability to efflux cholesterol from lipid-loaded murine macrophages, compared with 4F. Although 4F inhibited oxidation of purified mouse LDL, the Ala tandem peptide increased oxidation. We compared several tandem 4F-based peptides with monomeric 4F in assays that correlated with suggested anti-inflammatory/anti-atherogenic pathways. Tandem 4F-based peptides, which better mimic full-length apoA-I, exceed monomeric 4F in HDL remodeling and cholesterol efflux but not LDL oxidation protection. In addition, apoA-I mimetic peptides may increase reverse cholesterol transport through both ABCA1 as well as ABCG1 pathways.
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Affiliation(s)
- Geoffrey D Wool
- The University of Chicago, Department of Pathology, Chicago, IL, USA
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48
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Gunasekar SK, Haghpanah JS, Montclare JK. Assembly of bioinspired helical protein fibers. POLYM ADVAN TECHNOL 2008. [DOI: 10.1002/pat.1136] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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49
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Abstract
Supramolecular structures arising from a broad range of chemical archetypes are of great technological promise. Defining such structures at the nanoscale is crucial to access principally new types of functional materials for applications in bionanotechnology. In this vein, biomolecular self-assembly has emerged as an efficient approach for building synthetic nanostructures from the bottom up. The approach predominantly employs the spontaneous folding of biopolymers to monodisperse three-dimensional shapes that assemble into hierarchically defined mesoscale composites. An immediate interest here is the extraction of reliable rules that link the chemistry of biopolymers to the mechanisms of their assembly. Once established these can be further harnessed in designing supramolecular objects de novo. Different biopolymer classes compile a rich repertoire of assembly motifs to facilitate the synthesis of otherwise inaccessible nanostructures. Among those are peptide alpha-helices, ubiquitous folding elements of natural protein assemblies. These are particularly appealing candidates for prescriptive supramolecular engineering, as their well-established and conservative design rules give unmatched predictability and rationale. Recent developments of self-assembling systems based on helical peptides, including fibrous systems, nanoscale linkers and reactors will be highlighted herein.
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Affiliation(s)
- M G Ryadnov
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
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Bomhoff G, Sloan K, McLain C, Gogol EP, Fisher MT. The effects of the flavonoid baicalein and osmolytes on the Mg 2+ accelerated aggregation/fibrillation of carboxymethylated bovine 1SS-α-lactalbumin. Arch Biochem Biophys 2006; 453:75-86. [PMID: 16530158 DOI: 10.1016/j.abb.2006.02.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2006] [Accepted: 02/02/2006] [Indexed: 12/01/2022]
Abstract
Many protein conformational diseases arise when proteins form alternative stable conformations, resulting in aggregation and accumulation of the protein as fibrillar deposits, or amyloids. Interestingly, numerous proteins implicated in amyloid protein formation show similar structural and functional properties. Given this similarity, we tested the notion that carboxymethylated bovine alpha-lactalbumin (1SS-alpha-lac) could serve as a general amyloid fibrillation/aggregation model system. Like most amyloid forming systems, Mg2+ ions accelerate 1SS-alpha-lac amyloid fibril formation. While osmolytes such as trimethylamine N-oxide (TMAO), and sucrose enhanced thioflavin T detected aggregation, a mixture of trehalose and TMAO substantially inhibited aggregation. Most importantly however, the flavonoid, baicalein, known to inhibit alpha-synuclein amyloid fibril formation, also inhibits 1SS-alpha-lac amyloid with the same apparent efficacy. These data suggest that the easily obtainable 1SS-alpha-lac protein can serve as a general amyloid model and that some small molecule amyloid inhibitors may function successfully with many different amyloid systems.
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Affiliation(s)
- Greg Bomhoff
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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