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Tsekrekou M, Giannakou M, Papanikolopoulou K, Skretas G. Protein aggregation and therapeutic strategies in SOD1- and TDP-43- linked ALS. Front Mol Biosci 2024; 11:1383453. [PMID: 38855322 PMCID: PMC11157337 DOI: 10.3389/fmolb.2024.1383453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/02/2024] [Indexed: 06/11/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with severe socio-economic impact. A hallmark of ALS pathology is the presence of aberrant cytoplasmic inclusions composed of misfolded and aggregated proteins, including both wild-type and mutant forms. This review highlights the critical role of misfolded protein species in ALS pathogenesis, particularly focusing on Cu/Zn superoxide dismutase (SOD1) and TAR DNA-binding protein 43 (TDP-43), and emphasizes the urgent need for innovative therapeutic strategies targeting these misfolded proteins directly. Despite significant advancements in understanding ALS mechanisms, the disease remains incurable, with current treatments offering limited clinical benefits. Through a comprehensive analysis, the review focuses on the direct modulation of the misfolded proteins and presents recent discoveries in small molecules and peptides that inhibit SOD1 and TDP-43 aggregation, underscoring their potential as effective treatments to modify disease progression and improve clinical outcomes.
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Affiliation(s)
- Maria Tsekrekou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Maria Giannakou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Katerina Papanikolopoulou
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
- ResQ Biotech, Patras Science Park, Rio, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- ResQ Biotech, Patras Science Park, Rio, Greece
- Institute for Bio-innovation, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
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2
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Jing B, Bi Y, Kong H, Wan W, Wang J, Yu B. Dual-environment-sensitive probe to detect protein aggregation in stressed laryngeal carcinoma cells and tissues. J Mater Chem B 2024; 12:2505-2510. [PMID: 38334693 DOI: 10.1039/d3tb02627b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
The interplay between protein folding and biological activity is crucial, with the integrity of the proteome being paramount to ensuring effective biological function execution. In this study, we report a dual-environment-sensitive probe A1, capable of selectively binding to protein aggregates and dynamically monitoring their formation and degradation. Through in vitro, cellular, and tissue assays, A1 demonstrated specificity in distinguishing aggregated from folded protein states, selectively partitioning into aggregated proteins. Thermal shift assays revealed A1 could monitor the process of protein aggregation upon binding to misfolded proteins and preceding to insoluble aggregate formation. In cellular models, A1 detected stress-induced proteome aggregation in TU212 cells (laryngeal carcinoma cells), revealing a less polar microenvironment within the aggregated proteome. Similarly, tissue samples showed more severe proteome aggregation in cancerous tissues compared to paracancerous tissues. Overall, A1 represents a versatile tool for probing protein aggregation with significant implications for both fundamental research and clinical diagnostics.
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Affiliation(s)
- Biao Jing
- Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yanjie Bi
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
| | - Hui Kong
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
| | - Wang Wan
- Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Jizhe Wang
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
| | - Bo Yu
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
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Chandrasekhar G, Srinivasan E, Nandhini S, Pravallika G, Sanjay G, Rajasekaran R. Computer aided therapeutic tripeptide design, in alleviating the pathogenic proclivities of nocuous α-synuclein fibrils. J Biomol Struct Dyn 2024; 42:483-494. [PMID: 36961221 DOI: 10.1080/07391102.2023.2194003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 03/15/2023] [Indexed: 03/25/2023]
Abstract
Parkinson's disorder (PD) exacerbates neuronal degeneration of motor nerves, thereby effectuating uncoordinated movements and tremors. Aberrant alpha-synuclein (α-syn) is culpable of triggering PD, wherein cytotoxic amyloid aggregates of α-syn get deposited in motor neurons to instigate neuro-degeneration. Amyloid aggregates, typically rich in beta sheets are cardinal targets to mitigate their neurotoxic effects. In this analysis, owing to their interaction specificity, we formulated an efficacious tripeptide out of the aggregation-prone region of α-syn protein. With the help of a proficient computational pipeline, systematic peptide shortening and an adept molecular simulation platform, we formulated a tripeptide, VAV from α-syn structure based hexapeptide KISVRV. Indeed, the VAV tripeptide was able to effectively mitigate the α-syn amyloid fibrils' dynamic rate of beta-sheet formation. Additional trajectory analyses of the VAV- α-syn complex indicated that, upon its dynamic interaction, VAV efficiently altered the distinct pathogenic structural dynamics of α-syn, further advocating its potential in alleviating aberrant α-syn's amyloidogenic proclivities. Consistent findings from various computational analyses have led us to surmise that VAV could potentially re-alter the pathogenic conformational orientation of α-syn, essential to mitigate its cytotoxicity. Hence, VAV tripeptide could be an efficacious therapeutic candidate to efficiently ameliorate aberrant α-syn amyloid mediated neurotoxicity, eventually attenuating the nocuous effects of PD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- G Chandrasekhar
- Quantitative Biology Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu, India
| | - E Srinivasan
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka, India
| | - S Nandhini
- Quantitative Biology Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu, India
| | - G Pravallika
- Quantitative Biology Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu, India
| | - G Sanjay
- Quantitative Biology Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu, India
| | - R Rajasekaran
- Quantitative Biology Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu, India
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4
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Li X, Rios SE, Nowick JS. Enantiomeric β-sheet peptides from Aβ form homochiral pleated β-sheets rather than heterochiral rippled β-sheets. Chem Sci 2022; 13:7739-7746. [PMID: 35865901 PMCID: PMC9258340 DOI: 10.1039/d2sc02080g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/11/2022] [Indexed: 12/18/2022] Open
Abstract
In 1953, Pauling and Corey postulated “rippled” β-sheets, composed of a mixture of d- and l-peptide strands, as a hypothetical alternative to the now well-established structures of “pleated” β-sheets, which they proposed as a component of all-l-proteins. Growing interest in rippled β-sheets over the past decade has led to the development of mixtures of d- and l-peptides for biomedical applications, and a theory has emerged that mixtures of enantiomeric β-sheet peptides prefer to co-assemble in a heterochiral fashion to form rippled β-sheets. Intrigued by conflicting reports that enantiomeric β-sheet peptides prefer to self-assemble in a homochiral fashion to form pleated β-sheets, we set out address this controversy using two β-sheet peptides derived from Aβ17–23 and Aβ30–36, peptides 1a and 1b. Each of these peptides self-assembles to form tetramers comprising sandwiches of β-sheet dimers in aqueous solution. Through solution-phase NMR spectroscopy, we characterize the different species formed when peptides 1a and 1b are mixed with their respective d-enantiomers, peptides ent-1a and ent-1b. 1H NMR, DOSY, and 1H,15N-HSQC experiments reveal that mixing peptides 1a and ent-1a results in the predominant formation of homochiral tetramers, with a smaller fraction of a new heterochiral tetramer, and mixing peptides 1b and ent-1b does not result in any detectable heterochiral assembly. 15N-edited NOESY reveals that the heterochiral tetramer formed by peptides 1a and ent-1a is composed of two homochiral dimers. Collectively, these NMR studies of Aβ-derived peptides provide compelling evidence that enantiomeric β-sheet peptides prefer to self-assemble in a homochiral fashion in aqueous solution. In aqueous solution, mixtures of l- and d- macrocyclic β-sheet peptides derived from Aβ self-assemble to form homochiral pleated β-sheets but do not co-assemble to form heterochiral rippled β-sheets.![]()
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Affiliation(s)
- Xingyue Li
- Department of Chemistry, University of California Irvine, 4126 Natural Sciences I, Irvine, CA 92697-2025, USA
| | - Stephanie E. Rios
- Department of Chemistry, University of California Irvine, 4126 Natural Sciences I, Irvine, CA 92697-2025, USA
| | - James S. Nowick
- Department of Chemistry, University of California Irvine, 4126 Natural Sciences I, Irvine, CA 92697-2025, USA
- Department of Pharmaceutical Sciences, University of California Irvine, 4126 Natural Sciences I, Irvine, CA 92697-2025, USA
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5
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In Silico Therapeutic Peptide Design Against Pathogenic Domain Swapped Human Cystatin C Dimer. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10191-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Chan KH, Lim J, Jee JE, Aw JH, Lee SS. Peptide-Peptide Co-Assembly: A Design Strategy for Functional Detection of C-peptide, A Biomarker of Diabetic Neuropathy. Int J Mol Sci 2020; 21:ijms21249671. [PMID: 33352955 PMCID: PMC7766332 DOI: 10.3390/ijms21249671] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 12/29/2022] Open
Abstract
Diabetes-related neuropathy is a debilitating condition that may be averted if it can be detected early. One possible way this can be achieved at low cost is to utilise peptides to detect C-peptide, a biomarker of diabetic neuropathy. This depends on peptide-peptide co-assembly, which is currently in a nascent stage of intense study. Instead, we propose a bead-based triple-overlay combinatorial strategy that can preserve inter-residue information during the screening process for a suitable complementary peptide to co-assemble with C-peptide. The screening process commenced with a pentapeptide general library, which revealed histidine to be an essential residue. Further screening with seven tetrapeptide focused libraries led to a table of self-consistent peptide sequences that included tryptophan and lysine at high frequencies. Three complementary nonapeptides (9mer com-peptides), wpkkhfwgq (Trp-D), kwkkhfwgq (Lys-D), and KWKKHFWGQ (Lys-L) (as a negative control) were picked from this table for co-assembly studies with C-peptide. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) and circular dichroism (CD) spectroscopies were utilized to study inter-peptide interactions and changes in secondary structures respectively. ATR-FTIR studies showed that there is indeed inter-peptide interaction between C-peptide and the tryptophan residues of the 9mer com-peptides. CD studies of unaggregated and colloidal C-peptide with the 9mer com-peptides suggest that the extent of co-assembly of C-peptide with Trp-D is greatest, followed by Lys-D and Lys-L. These results are promising and indicate that the presented strategy is viable for designing and evaluating longer complementary peptides, as well as complementary peptides for co-assembly with other polypeptides of interest and importance. We discuss the possibility of designing complementary peptides to inhibit toxic amyloidosis with this approach.
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Affiliation(s)
- Kiat Hwa Chan
- Division of Science, Yale-NUS College, 16 College Avenue West, Singapore 138527, Singapore;
- Correspondence: (K.H.C.); (S.S.L.)
| | - Jaehong Lim
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore; (J.L.); (J.E.J.)
| | - Joo Eun Jee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore; (J.L.); (J.E.J.)
| | - Jia Hui Aw
- Division of Science, Yale-NUS College, 16 College Avenue West, Singapore 138527, Singapore;
| | - Su Seong Lee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore; (J.L.); (J.E.J.)
- Correspondence: (K.H.C.); (S.S.L.)
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7
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Seroski DT, Dong X, Wong KM, Liu R, Shao Q, Paravastu AK, Hall CK, Hudalla GA. Charge guides pathway selection in β-sheet fibrillizing peptide co-assembly. Commun Chem 2020; 3:172. [PMID: 36703436 PMCID: PMC9814569 DOI: 10.1038/s42004-020-00414-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/15/2020] [Indexed: 01/29/2023] Open
Abstract
Peptide co-assembly is attractive for creating biomaterials with new forms and functions. Emergence of these properties depends on the peptide content of the final assembled structure, which is difficult to predict in multicomponent systems. Here using experiments and simulations we show that charge governs content by affecting propensity for self- and co-association in binary CATCH(+/-) peptide systems. Equimolar mixtures of CATCH(2+/2-), CATCH(4+/4-), and CATCH(6+/6-) formed two-component β-sheets. Solid-state NMR suggested the cationic peptide predominated in the final assemblies. The cationic-to-anionic peptide ratio decreased with increasing charge. CATCH(2+) formed β-sheets when alone, whereas the other peptides remained unassembled. Fibrillization rate increased with peptide charge. The zwitterionic CATCH parent peptide, "Q11", assembled slowly and only at decreased simulation temperature. These results demonstrate that increasing charge draws complementary peptides together faster, favoring co-assembly, while like-charged molecules repel. We foresee these insights enabling development of co-assembled peptide biomaterials with defined content and predictable properties.
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Affiliation(s)
- Dillon T Seroski
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Xin Dong
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA
| | - Kong M Wong
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Renjie Liu
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Qing Shao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Carol K Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA
| | - Gregory A Hudalla
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA.
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8
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Wonderly WR, Cristiani TR, Cunha KC, Degen GD, Shea JE, Waite JH. Dueling Backbones: Comparing Peptoid and Peptide Analogues of a Mussel Adhesive Protein. Macromolecules 2020. [DOI: 10.1021/acs.macromol.9b02715] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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9
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Pacheco-Liñán PJ, Martín C, Alonso-Moreno C, Juan A, Hermida-Merino D, Garzón-Ruíz A, Albaladejo J, Van der Auweraer M, Cohen B, Bravo I. The role of water and influence of hydrogen bonding on the self-assembly aggregation induced emission of an anthracene-guanidine-derivative. Chem Commun (Camb) 2020; 56:4102-4105. [PMID: 32163081 DOI: 10.1039/d0cc00990c] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a luminescent anthracene-guanidine derivative that forms rare T-shape dimers, resulting in an excimer with a quantum yield approaching one. Water plays a fundamental role through H-bonding guiding the self-assembly. These results establish a new framework for environmentally friendly aggregation-induced emission luminogens.
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Affiliation(s)
- Pedro J Pacheco-Liñán
- Departamento de Química Física, Facultad de Farmacia de Albacete, Universidad de Castilla-La Mancha, Albacete-02071, Spain.
| | - Cristina Martín
- Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium and Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Albacete, Spain
| | - Carlos Alonso-Moreno
- Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Albacete, Spain and Departamento de Inorgánica, Orgánica y Bioquímica, Facultad de Farmacia de Albacete, UCLM, Albacete-02071, Spain
| | - Alberto Juan
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology and TechMed Institute for Health and Biomedical Technologies, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands and Department of Molecular NanoFabrication, MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands
| | - Daniel Hermida-Merino
- Netherlands Organization for Scientific Research, DUBBLE at the ESRF, 71 Avenue des Martyrs, CS40220, 38043 Greno-ble, France
| | - Andrés Garzón-Ruíz
- Departamento de Química Física, Facultad de Farmacia de Albacete, Universidad de Castilla-La Mancha, Albacete-02071, Spain.
| | - José Albaladejo
- Instituto de Investigación en Combustión y Contaminación Atmosférica, Universidad de Castilla-La Mancha, Camino de Moledores s/n, Ciudad Real, 13071, Spain
| | - Mark Van der Auweraer
- Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Boiko Cohen
- Departamento de Química Física, Facultad de Ciencias Ambientales y Bioquímica, and INAMOL, Universidad de Casti-lla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain.
| | - Iván Bravo
- Departamento de Química Física, Facultad de Farmacia de Albacete, Universidad de Castilla-La Mancha, Albacete-02071, Spain. and Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Albacete, Spain
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Lu S, Guo X, Zou M, Zheng Z, Li Y, Li X, Li L, Wang H. Bacteria-Instructed In Situ Aggregation of AuNPs with Enhanced Photoacoustic Signal for Bacterial Infection Bioimaging. Adv Healthc Mater 2020; 9:e1901229. [PMID: 31750997 DOI: 10.1002/adhm.201901229] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/25/2019] [Indexed: 12/19/2022]
Abstract
The emergence of drug-resistant bacteria is becoming the focus of global public health. Early-stage pathogen bioimaging will offer a unique perspective to obtain infection information in patients. A photoacoustic (PA) contrast agent based on functional peptide modified gold nanoparticles (AuNPs@P1) is developed. These nanoparticles can be specifically tailored surface peptides by bacterial overexpressed enzyme inducing in situ aggregation of the gold nanoparticles. In the meantime, the close aggregation based on the hydrogen bonding, π-π stacking, and hydrophobic interaction of the peptide residues on the surface of gold nanoparticles exhibits a typical redshifted and broadened plasmon band. In addition, this active targeting and following in situ stimuli-induced aggregation contribute to increased nanoparticle accumulation in the infected site. Finally, the dynamic aggregation of AuNPs@P1 results in dramatically enhanced photoacoustic signals for bioimaging bacterial infection in vivo with high sensitivity and specificity. It is envisioned that this PA contrast agent may provide a new approach for early detection of bacterial infection in vivo.
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Affiliation(s)
- Shi‐Zhao Lu
- School of Material Science and EngineeringBeijing Institute of Technology No. 5 South Zhongguancun Street, Haidian District Beijing 100081 China
- CAS Center for Excellence in NanoscienceCAS Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyNational Center for Nanoscience and Technology (NCNST)University of Chinese Academy of Sciences No. 11 Beiyitiao, Zhongguancun Beijing 100190 China
| | - Xiao‐Yan Guo
- School of Material Science and EngineeringBeijing Institute of Technology No. 5 South Zhongguancun Street, Haidian District Beijing 100081 China
| | - Mei‐Shuai Zou
- School of Material Science and EngineeringBeijing Institute of Technology No. 5 South Zhongguancun Street, Haidian District Beijing 100081 China
| | - Zi‐Qin Zheng
- School of Material Science and EngineeringBeijing Institute of Technology No. 5 South Zhongguancun Street, Haidian District Beijing 100081 China
- CAS Center for Excellence in NanoscienceCAS Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyNational Center for Nanoscience and Technology (NCNST)University of Chinese Academy of Sciences No. 11 Beiyitiao, Zhongguancun Beijing 100190 China
| | - Yu‐Chuan Li
- School of Material Science and EngineeringBeijing Institute of Technology No. 5 South Zhongguancun Street, Haidian District Beijing 100081 China
| | - Xiao‐Dong Li
- School of Material Science and EngineeringBeijing Institute of Technology No. 5 South Zhongguancun Street, Haidian District Beijing 100081 China
| | - Li‐Li Li
- CAS Center for Excellence in NanoscienceCAS Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyNational Center for Nanoscience and Technology (NCNST)University of Chinese Academy of Sciences No. 11 Beiyitiao, Zhongguancun Beijing 100190 China
| | - Hao Wang
- CAS Center for Excellence in NanoscienceCAS Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyNational Center for Nanoscience and Technology (NCNST)University of Chinese Academy of Sciences No. 11 Beiyitiao, Zhongguancun Beijing 100190 China
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Roy K, Chetia M, Sarkar AK, Chatterjee S. Co-assembly of charge complementary peptides and their applications as organic dye/heavy metal ion (Pb 2+, Hg 2+) absorbents and arsenic( iii/ v) detectors. RSC Adv 2020; 10:42062-42075. [PMID: 35516776 PMCID: PMC9057852 DOI: 10.1039/d0ra08407g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/12/2020] [Indexed: 12/27/2022] Open
Abstract
Learning from nature, molecular self-assembly has been used extensively to generate interesting materials using a bottom up approach. The enthusiasm in this field of research stems from the unique properties of these materials and their diverse applications. The field has not been limited to studying assembly of similar types of molecules but extended to multi component systems via the co-assembly phenomenon. We have designed two charge complementary peptides to study their co-assembly in mechanistic detail in the present work. The cooperative self-assembly is mainly driven by electrostatic interaction that is aided by aromatic interactions, hydrogen bonding interactions and hydrophobic interactions. The hydrogels obtained have been employed in waste water remediation. Both the self-assembled and co-assembled hydrogels are capable of removal of different kinds of organic dyes (cationic, anionic and neutral) and toxic metal ions (Ni2+, Co2+, Pb2+ and Hg2+) individually and as a mixture from water with high efficiency. Additionally, the peptides developed in this study can act as ion sensors and detect arsenic in its most toxic (III/V) oxidation states. Molecular understanding of the assembly process is of fundamental importance in the rational design of such simple, robust yet economically viable materials with versatile and novel applications. Self- and co-assembled gels from charge complementary peptides with waste water remediation applications.![]()
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Affiliation(s)
- Karabi Roy
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Guwahati
- India
| | - Monikha Chetia
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Guwahati
- India
| | - Ankan Kumar Sarkar
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Guwahati
- India
| | - Sunanda Chatterjee
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Guwahati
- India
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12
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Rational design of linear tripeptides against the aggregation of human mutant SOD1 protein causing amyotrophic lateral sclerosis. J Neurol Sci 2019; 405:116425. [PMID: 31422280 DOI: 10.1016/j.jns.2019.116425] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 07/11/2019] [Accepted: 08/09/2019] [Indexed: 12/14/2022]
Abstract
Formation of protein aggregation is considered a hallmark feature of various neurological diseases. Amyotrophic lateral sclerosis is one such devastating neurodegenerative disorder characterized by mutation in Cu/Zn superoxide dismutase protein (SOD1). In our study, we contemplated the most aggregated and pathogenic mutant A4V in a viewpoint of finding a therapeutic regime by inhibiting the formation of the aggregates with the aid of tripeptides since new perspectives in the field of drug design in the current era are being focused on peptide-based drugs. Reports from the experimental study have stipulated that the SOD1 derived peptide, "LSGDHCIIGRTLVVHEKADD" was found to have the inhibitory activity against aggregated SOD1 protein. Moreover, it was determined that the hexapeptide, "LSGDHC" was the key factor in inhibiting the aggregates of SOD1. Accordingly, we utilized the computerized algorithms and programs on determining the binding efficiency and inhibitory activity of hexapeptide on mutant SOD1. Following that, we incorporated a cutting-edge methodology with the use of molecular docking, affinity predictions, alanine scanning, steered molecular dynamics (SMD) and discrete molecular dynamics (DMD) in designing the de novo tripeptides, which could act against the aggregated mutant SOD1 protein. Upon examining the results from the various conformational studies, we identified that CGH had an enhanced binding affinity and inhibitory activity against the aggregated mutant SOD1 protein than other tripeptides and hexapeptide. Thus, our study could be a lead for state-of-the-art design in peptide-based drugs for doctoring the cureless ALS disorder.
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Salveson PJ, Haerianardakani S, Thuy-Boun A, Yoo S, Kreutzer AG, Demeler B, Nowick JS. Repurposing Triphenylmethane Dyes to Bind to Trimers Derived from Aβ. J Am Chem Soc 2018; 140:11745-11754. [PMID: 30125493 DOI: 10.1021/jacs.8b06568] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Soluble oligomers of the β-amyloid peptide, Aβ, are associated with the progression of Alzheimer's disease. Although many small molecules bind to these assemblies, the details of how these molecules interact with Aβ oligomers remain unknown. This paper reports that crystal violet, and other C3 symmetric triphenylmethane dyes, bind to C3 symmetric trimers derived from Aβ17-36. Binding changes the color of the dyes from purple to blue, and causes them to fluoresce red when irradiated with green light. Job plot and analytical ultracentrifugation experiments reveal that two trimers complex with one dye molecule. Studies with several triphenylmethane dyes reveal that three N, N-dialkylamino substituents are required for complexation. Several mutant trimers, in which Phe19, Phe20, and Ile31 were mutated to cyclohexylalanine, valine, and cyclohexylglycine, were prepared to probe the triphenylmethane dye binding site. Size exclusion chromatography, SDS-PAGE, and X-ray crystallographic studies demonstrate that these mutations do not impact the structure or assembly of the triangular trimer. Fluorescence spectroscopy and analytical ultracentrifugation experiments reveal that the dye packs against an aromatic surface formed by the Phe20 side chains and is clasped by the Ile31 side chains. Docking and molecular modeling provide a working model of the complex in which the triphenylmethane dye is sandwiched between two triangular trimers. Collectively, these findings demonstrate that the X-ray crystallographic structures of triangular trimers derived from Aβ can be used to guide the discovery of ligands that bind to soluble oligomers derived from Aβ.
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Affiliation(s)
- Patrick J Salveson
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
| | - Sepehr Haerianardakani
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
| | - Alexander Thuy-Boun
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
| | - Stan Yoo
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
| | - Adam G Kreutzer
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
| | - Borries Demeler
- Department of Biochemistry , University of Texas Health Science Center , San Antonio , Texas 78229-3900 , United States
| | - James S Nowick
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
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14
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Abstract
Self-assembled peptide nanostructures have been increasingly exploited as functional materials for applications in biomedicine and energy. The emergent properties of these nanomaterials determine the applications for which they can be exploited. It has recently been appreciated that nanomaterials composed of multicomponent coassembled peptides often display unique emergent properties that have the potential to dramatically expand the functional utility of peptide-based materials. This review presents recent efforts in the development of multicomponent peptide assemblies. The discussion includes multicomponent assemblies derived from short low molecular weight peptides, peptide amphiphiles, coiled coil peptides, collagen, and β-sheet peptides. The design, structure, emergent properties, and applications for these multicomponent assemblies are presented in order to illustrate the potential of these formulations as sophisticated next-generation bio-inspired materials.
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Affiliation(s)
- Danielle M Raymond
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216, USA.
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15
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Galzitskaya OV, Selivanova OM. Rosetta Stone for Amyloid Fibrils: The Key Role of Ring-Like Oligomers in Amyloidogenesis. J Alzheimers Dis 2018; 59:785-795. [PMID: 28671122 DOI: 10.3233/jad-170230] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Deeper understanding of processes of protein misfolding, aggregation, formation of oligomers, protofibrils, and fibrils is crucial for the development of future medicine in treatment of amyloid-related diseases. While numerous reports illuminate the field, the above processes are extremely complex, as they depend on many varying parameters, such as the peptide concentration, temperature, pH, presence of metal ions, lipids, and organic solvents. Different mechanisms of amyloid fibril formation have been proposed, but the process of the oligomer-to-fibril transition is the least agreed upon. Our studies of a number of amyloidogenic proteins and peptides (insulin, Aβ peptides, the Bgl2 protein from the yeast cell wall), as well as their amyloidogenic fragments, have allowed us to propose a model of the fibril structure generation. We have found that the main building block of fibrils of any morphology is a ring-like oligomer. The varying models of interaction of ring oligomers with each other revealed in our studies make it possible to explain their polymorphism. Crucially, the amino acid sequence determines the oligomer structure for the given protein/peptide.
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Affiliation(s)
- Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Olga M Selivanova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
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16
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Bhattacharya S, Xu L, Thompson D. Revisiting the earliest signatures of amyloidogenesis: Roadmaps emerging from computational modeling and experiment. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Shayon Bhattacharya
- Department of Physics, Bernal InstituteUniversity of LimerickLimerickIreland
| | - Liang Xu
- Department of Physics, Bernal InstituteUniversity of LimerickLimerickIreland
| | - Damien Thompson
- Department of Physics, Bernal InstituteUniversity of LimerickLimerickIreland
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17
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Selivanova OM, Surin AK, Ryzhykau YL, Glyakina AV, Suvorina MY, Kuklin AI, Rogachevsky VV, Galzitskaya OV. To Be Fibrils or To Be Nanofilms? Oligomers Are Building Blocks for Fibril and Nanofilm Formation of Fragments of Aβ Peptide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:2332-2343. [PMID: 29338255 DOI: 10.1021/acs.langmuir.7b03393] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
To identify the key stages in the amyloid fibril formation we studied the aggregation of amyloidogenic fragments of Aβ peptide, Aβ(16-25), Aβ(31-40), and Aβ(33-42), using the methods of electron microscopy, X-ray analysis, mass spectrometry, and structural modeling. We have found that fragments Aβ(31-40) and Aβ(33-42) form amyloid fibrils in the shape of bundles and ribbons, while fragment Aβ(16-25) forms only nanofilms. We are the first who performed 2D reconstruction of amyloid fibrils by the Markham rotation technique on electron micrographs of negatively stained fragments of Aβ peptide. Combined analysis of the data allows us to speculate that both the fibrils and the films are formed via association of ring-shaped oligomers with the external diameter of about 6 to 7 nm, the internal diameter of 2 to 3 nm, and the height of ∼3 nm. We conclude that such oligomers are the main building blocks in fibrils of any morphology. The interaction of ring oligomers with each other in different ways makes it possible to explain their polymorphism. The new mechanism of polymerization of amyloidogenic proteins and peptides, described here, could stimulate new approaches in the development of future therapeutics for the treatment of amyloid-related diseases.
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Affiliation(s)
- Olga M Selivanova
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
| | - Alexey K Surin
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
- State Research Center for Applied Microbiology & Biotechnology , Obolensk 142279, Russia
| | - Yury L Ryzhykau
- Moscow Institute of Physics and Technology , Dolgoprudny 141701, Russian Federation
| | - Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
- Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences , Pushchino 142290, Russia
| | - Mariya Yu Suvorina
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
| | - Alexander I Kuklin
- Moscow Institute of Physics and Technology , Dolgoprudny 141701, Russian Federation
- Joint Institute for Nuclear Research , Dubna 141980, Russian Federation
| | - Vadim V Rogachevsky
- Institute of Cell Biophysics, Russian Academy of Sciences , Pushchino 142290, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
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18
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Thomas NC, Bartlett GJ, Woolfson DN, Gellman SH. Toward a Soluble Model System for the Amyloid State. J Am Chem Soc 2017; 139:16434-16437. [PMID: 29116774 PMCID: PMC5939379 DOI: 10.1021/jacs.7b07225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The formation and deposition of amyloids is associated with many diseases. β-Sheet secondary structure is a common feature of amyloids, but the packing of sheets against one another is distinctive relative to soluble proteins. Standard methods that rely on perturbing a polypeptide's sequence and evaluating impact on folding can be problematic for amyloid aggregates because a single sequence can adopt multiple conformations and diverse packing arrangements. We describe initial steps toward a minimum-sized, soluble model system for the amyloid state that supports comparisons among sequence variants. Critical to this goal is development of a new linking strategy to enable intersheet association mediated by side chain interactions, which is characteristic of the amyloid state. The linker design we identified should ultimately support exploration of relationships between sequence and amyloid state stability for specific strand-association modes.
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Affiliation(s)
- Nicole C. Thomas
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Gail J. Bartlett
- School of Chemistry, Cantock’s Close, University of Bristol, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1 TD, UK; BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Derek N. Woolfson
- School of Chemistry, Cantock’s Close, University of Bristol, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1 TD, UK; BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
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19
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Cao Y, Jiang X, Han W. Self-Assembly Pathways of β-Sheet-Rich Amyloid-β(1-40) Dimers: Markov State Model Analysis on Millisecond Hybrid-Resolution Simulations. J Chem Theory Comput 2017; 13:5731-5744. [PMID: 29019683 DOI: 10.1021/acs.jctc.7b00803] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Early oligomerization during amyloid-β (Aβ) aggregation is essential for Aβ neurotoxicity. Understanding how unstructured Aβs assemble into oligomers, especially those rich in β-sheets, is essential but remains challenging as the assembly process is too transient for experimental characterization and too slow for molecular dynamics simulations. So far, atomic simulations are limited only to studies of either oligomer structures or assembly pathways for short Aβ segments. To overcome the computational challenge, we combine in this study a hybrid-resolution model and adaptive sampling techniques to perform over 2.7 ms of simulations of formation of full-length Aβ40 dimers that are the earliest toxic oligomeric species. The Markov state model is further employed to characterize the transition pathways and associated kinetics. Our results show that for two major forms of β-sheet-rich structures reported experimentally, the corresponding assembly mechanisms are markedly different. Hairpin-containing structures are formed by direct binding of soluble Aβ in β-hairpin-like conformations. Formation of parallel, in-register structures resembling fibrils occurs ∼100-fold more slowly and involves a rapid encounter of Aβ in arbitrary conformations followed by a slow structural conversion. The structural conversion proceeds via diverse pathways but always requires transient unfolding of encounter complexes. We find that the transition kinetics could be affected differently by intra-/intermolecular interactions involving individual residues in a conformation-dependent manner. In particular, the interactions involving Aβ's N-terminal part promote the assembly into hairpin-containing structures but delay the formation of fibril-like structures, thus explaining puzzling observations reported previously regarding the roles of this region in the early assembly process.
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Affiliation(s)
- Yang Cao
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, 518055, China
| | - Xuehan Jiang
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, 518055, China
| | - Wei Han
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, 518055, China
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20
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Effects of charge and hydrophobicity on the oligomerization of peptides derived from IAPP. Bioorg Med Chem 2017; 26:1151-1156. [PMID: 29074350 DOI: 10.1016/j.bmc.2017.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/03/2017] [Accepted: 10/04/2017] [Indexed: 01/20/2023]
Abstract
Changes in pH resulting in modifications of charge can dramatically alter the folding and interaction of proteins. This article probes the effects of charge and hydrophobicity on the oligomerization of macrocyclic β-sheet peptides derived from residues 11-17 of IAPP (RLANFLV). Previous studies have shown that a macrocyclic β-sheet peptide containing this IAPP sequence (peptide 1Arg) does not form oligomers in aqueous solution at low millimolar concentrations. Replacing arginine with the uncharged isostere citrulline generates a homologue (peptide 1Cit) that forms a tetramer consisting of a sandwich of hydrogen-bonded dimers. The current study probes the role of charge and hydrophobicity by changing residue 11 to glutamic acid (peptide 1Glu) and leucine (peptide 1Leu). Diffusion-ordered spectroscopy (DOSY) studies show that peptides 1Glu and 1Leu form tetramers in solution. NOESY studies confirm that both peptides form the same sandwich-like tetramer as peptide 1Cit. 1H NMR spectroscopy at various concentrations reveals that peptide 1Leu has the highest propensity to form tetramers. The effects of pH and charge on oligomerization are further probed by incorporating histidine at position 11 (peptide 1His). DOSY studies show that peptide 1His forms a tetramer at high pH. At low pH, peptide 1His forms a new species that has not been previously observed by our research group-a dimer. These studies demonstrate the importance of charge and hydrophobicity in the oligomerization of IAPP-derived peptides.
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21
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Abstract
Aggregation of the islet amyloid polypeptide (IAPP) to form fibrils and oligomers is important in the progression of type 2 diabetes. This article describes X-ray crystallographic and solution-state NMR studies of peptides derived from residues 11-17 of IAPP that assemble to form tetramers. Incorporation of residues 11-17 of IAPP (RLANFLV) into a macrocyclic β-sheet peptide results in a monomeric peptide that does not self-assemble to form oligomers. Mutation of Arg11 to the uncharged isostere citrulline gives peptide homologues that assemble to form tetramers in both the crystal state and in aqueous solution. The tetramers consist of hydrogen-bonded dimers that sandwich together through hydrophobic interactions. The tetramers share several features with structures reported for IAPP fibrils and demonstrate the importance of hydrogen bonding and hydrophobic interactions in the oligomerization of IAPP-derived peptides.
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Affiliation(s)
- Yilin Wang
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025
| | - Adam G. Kreutzer
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025
| | - Nicholas L. Truex
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025
| | - James S. Nowick
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025
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22
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Truex NL, Wang Y, Nowick JS. Assembly of Peptides Derived from β-Sheet Regions of β-Amyloid. J Am Chem Soc 2016; 138:13882-13890. [PMID: 27642651 PMCID: PMC5089065 DOI: 10.1021/jacs.6b06000] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
In
Alzheimer’s disease, aggregation of the β-amyloid
peptide (Aβ) results in the formation of oligomers and fibrils
that are associated with neurodegeneration. Aggregation of Aβ
occurs through interactions between different regions of the peptide.
This paper and the accompanying paper constitute a two-part investigation
of two key regions of Aβ: the central region and the C-terminal
region. These two regions promote aggregation and adopt β-sheet
structure in the fibrils, and may also do so in the oligomers. In
this paper, we study the assembly of macrocyclic β-sheet peptides
that contain residues 17–23 (LVFFAED) from the central region
and residues 30–36 (AIIGLMV) from the C-terminal region. These
peptides assemble to form tetramers. Each tetramer consists of two
hydrogen-bonded dimers that pack through hydrophobic interactions
in a sandwich-like fashion. Incorporation of a single 15N isotopic label into each peptide provides a spectroscopic probe
with which to elucidate the β-sheet assembly and interaction: 1H,15N HSQC studies facilitate the identification
of the monomers and tetramers; 15N-edited NOESY studies
corroborate the pairing of the dimers within the tetramers. In the
following paper, J. Am. Chem. Soc.2016, DOI: 10.1021/jacs.6b06001, we will extend these studies to elucidate the coassembly of the
peptides to form heterotetramers.
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Affiliation(s)
- Nicholas L Truex
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| | - Yilin Wang
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| | - James S Nowick
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
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