1
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Golota NC, Michael B, Saliba EP, Linse S, Griffin RG. Structural characterization of E22G Aβ 1-42 fibrils via1H detected MAS NMR. Phys Chem Chem Phys 2024; 26:14664-14674. [PMID: 38715538 PMCID: PMC11110645 DOI: 10.1039/d4cp00553h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
Amyloid fibrils have been implicated in the pathogenesis of several neurodegenerative diseases, the most prevalent example being Alzheimer's disease (AD). Despite the prevalence of AD, relatively little is known about the structure of the associated amyloid fibrils. This has motivated our studies of fibril structures, extended here to the familial Arctic mutant of Aβ1-42, E22G-Aβ1-42. We found E22G-AβM0,1-42 is toxic to Escherichia coli, thus we expressed E22G-Aβ1-42 fused to the self-cleavable tag NPro in the form of its EDDIE mutant. Since the high surface activity of E22G-Aβ1-42 makes it difficult to obtain more than sparse quantities of fibrils, we employed 1H detected magic angle spinning (MAS) nuclear magnetic resonance (NMR) experiments to characterize the protein. The 1H detected 13C-13C methods were first validated by application to fully protonated amyloidogenic nanocrystals of GNNQQNY, and then applied to fibrils of the Arctic mutant of Aβ, E22G-Aβ1-42. The MAS NMR spectra indicate that the biosynthetic samples of E22G-Aβ1-42 fibrils comprise a single conformation with 13C chemical shifts extracted from hCH, hNH, and hCCH spectra that are very similar to those of wild type Aβ1-42 fibrils. These results suggest that E22G-Aβ1-42 fibrils have a structure similar to that of wild type Aβ1-42.
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Affiliation(s)
- Natalie C Golota
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Brian Michael
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Edward P Saliba
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sara Linse
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, SE 22100, Sweden
| | - Robert G Griffin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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2
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Robang A, Roy A, Dodd-o JB, He D, Le JV, McShan AC, Hu Y, Kumar VA, Paravastu AK. Structural Consequences of Introducing Bioactive Domains to Designer β-Sheet Peptide Self-Assemblies. Biomacromolecules 2024; 25:1429-1438. [PMID: 38408372 PMCID: PMC10934295 DOI: 10.1021/acs.biomac.3c00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
We applied solid- and solution-state nuclear magnetic resonance spectroscopy to examine the structure of multidomain peptides composed of self-assembling β-sheet domains linked to bioactive domains. Bioactive domains can be selected to stimulate specific biological responses (e.g., via receptor binding), while the β-sheets provide the desirable nanoscale properties. Although previous work has established the efficacy of multidomain peptides, molecular-level characterization is lacking. The bioactive domains are intended to remain solvent-accessible without being incorporated into the β-sheet structure. We tested for three possible anticipated molecular-level consequences of introducing bioactive domains to β-sheet-forming peptides: (1) the bioactive domain has no effect on the self-assembling peptide structure; (2) the bioactive domain is incorporated into the β-sheet nanofiber; and (3) the bioactive domain interferes with self-assembly such that nanofibers are not formed. The peptides involved in this study incorporated self-assembling domains based on the (SL)6 motif and bioactive domains including a VEGF-A mimic (QK), an IGF-mimic (IGF-1c), and a de novo SARS-CoV-2 binding peptide (SBP3). We observed all three of the anticipated outcomes from our examination of peptides, illustrating the unintended structural effects that could adversely affect the desired biofunctionality and biomaterial properties of the resulting peptide hydrogel. This work is the first attempt to evaluate the structural effects of incorporating bioactive domains into a set of peptides unified by a similar self-assembling peptide domain. These structural insights reveal unmet challenges in the design of highly tunable bioactive self-assembling peptide hydrogels.
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Affiliation(s)
- Alicia
S. Robang
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Abhishek Roy
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Joseph B. Dodd-o
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Dongjing He
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Justin V. Le
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Andrew C. McShan
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Yuhang Hu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Vivek A. Kumar
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
- Department
of Chemicals and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department
of Biology, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Anant K. Paravastu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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3
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Luo M, Pang Y, Li J, Yi L, Wu B, Tian Q, He Y, Wang M, Xia L, He G, Song W, Du Y, Dong Z. miR-429-3p mediates memory decline by targeting MKP-1 to reduce surface GluA1-containing AMPA receptors in a mouse model of Alzheimer's disease. Acta Pharm Sin B 2024; 14:635-652. [PMID: 38322333 PMCID: PMC10840427 DOI: 10.1016/j.apsb.2023.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/24/2023] [Accepted: 10/07/2023] [Indexed: 02/08/2024] Open
Abstract
Alzheimer's disease (AD) is a leading cause of dementia in the elderly. Mitogen-activated protein kinase phosphatase 1 (MKP-1) plays a neuroprotective role in AD. However, the molecular mechanisms underlying the effects of MKP-1 on AD have not been extensively studied. MicroRNAs (miRNAs) regulate gene expression at the post-transcriptional level, thereby repressing mRNA translation. Here, we reported that the microRNA-429-3p (miR-429-3p) was significantly increased in the brain of APP23/PS45 AD model mice and N2AAPP AD model cells. We further found that miR-429-3p could downregulate MKP-1 expression by directly binding to its 3'-untranslated region (3' UTR). Inhibition of miR-429-3p by its antagomir (A-miR-429) restored the expression of MKP-1 to a control level and consequently reduced the amyloidogenic processing of APP and Aβ accumulation. More importantly, intranasal administration of A-miR-429 successfully ameliorated the deficits of hippocampal CA1 long-term potentiation and spatial learning and memory in AD model mice by suppressing extracellular signal-regulated kinase (ERK1/2)-mediated GluA1 hyperphosphorylation at Ser831 site, thereby increasing the surface expression of GluA1-containing α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs). Together, these results demonstrate that inhibiting miR-429-3p to upregulate MKP-1 effectively improves cognitive and synaptic functions in AD model mice, suggesting that miR-429/MKP-1 pathway may be a novel therapeutic target for AD treatment.
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Affiliation(s)
- Man Luo
- Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Yayan Pang
- Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Junjie Li
- Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Lilin Yi
- Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Bin Wu
- Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Qiuyun Tian
- Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Yan He
- Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Maoju Wang
- Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Lei Xia
- Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Guiqiong He
- Department of Anatomy, Basic Medical College, Chongqing Medical University, Chongqing 400016, China
| | - Weihong Song
- Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, Vancouver BC V6T 1Z3, Canada
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Clinical Research Center for Mental Disorders, School of Mental Health and the Affiliated Kangning Hospital, Wenzhou Medical University, Wenzhou 325000, China
| | - Yehong Du
- Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Zhifang Dong
- Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
- Institute for Brain Science and Disease of Chongqing Medical University, Chongqing 400016, China
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4
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Roy A, Dodd-O JB, Robang AS, He D, West O, Siddiqui Z, Aguas ED, Goldberg H, Griffith A, Heffernan C, Hu Y, Paravastu AK, Kumar VA. Self-Assembling Peptides with Insulin-Like Growth Factor Mimicry. ACS APPLIED MATERIALS & INTERFACES 2024; 16:364-375. [PMID: 38145951 DOI: 10.1021/acsami.3c15660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Growth factor (GF) mimicry involves recapitulating the signaling of larger molecules or cells. Although GF mimicry holds considerable promise in tissue engineering and drug design applications, difficulties in targeting the signaling molecule to the site of delivery and dissociation of mimicking peptides from their target receptors continue to limit its clinical application. To address these challenges, we utilized a self-assembling peptide (SAP) platform to generate synthetic insulin-like growth factor (IGF)-signaling, self-assembling GFs. Our peptide hydrogels are biocompatible and bind target IGF receptors in a dose-dependent fashion, activate proangiogenic signaling, and facilitate formation of angiogenic microtubules in vitro. Furthermore, infiltrated hydrogels are stable for weeks to months. We conclude that the enhanced targeting and long-term stability of our SAP/GF mimicry implants may improve the efficacy and safety of future GF mimic therapeutics.
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Affiliation(s)
- Abhishek Roy
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Joseph B Dodd-O
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Alicia S Robang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Dongjing He
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Owen West
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Zain Siddiqui
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Erika Davidoff Aguas
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey 08544, United States
| | - Hannah Goldberg
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Alexandra Griffith
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Corey Heffernan
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Yuhang Hu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Vivek A Kumar
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department of Endodontics, Rutgers School of Dental Medicine, Newark, New Jersey 07103, United States
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5
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Lim S, Cordova DLM, Robang AS, Kuang Y, Ogura KS, Paravastu AK, Arguilla MQ, Ardoña HAM. Thermochromic Behavior of Polydiacetylene Nanomaterials Driven by Charged Peptide Amphiphiles. Biomacromolecules 2023; 24:4051-4063. [PMID: 37552220 PMCID: PMC10498447 DOI: 10.1021/acs.biomac.3c00422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/18/2023] [Indexed: 08/09/2023]
Abstract
The tunability of chromatic phases adapted by chromogenic polymers such as polydiacetylene (PDA) is key to their utility for robust sensing applications. Here, we investigated the influence of charged peptide interactions on the structure-dependent thermochromicity of amphiphilic PDAs. Solid-state NMR and circular dichroism analyses show that our oppositely charged peptide-PDA samples have distinct degrees of structural order, with the coassembled sample being in between the β-sheet-like positive peptide-PDA and the relatively disordered negative peptide-PDA. All solutions exhibit thermochromicity between 20 and 80 °C, whereby the hysteresis of the blue, planar phase is much larger than that of the red, twisted phase. Resonance Raman spectroscopy of films demonstrates that only coassemblies with electrostatic complementarity stabilize coexisting blue and red PDA phases. This work reveals the nature of the structural changes responsible for the thermally responsive chromatic transitions of biomolecule-functionalized polymeric materials and how this process can be directed by sequence-dictated electrostatic interactions.
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Affiliation(s)
- Sujeung Lim
- Department
of Chemical and Biomolecular Engineering, Samueli School of Engineering, University of California, Irvine, California 92697, United States
| | - Dmitri Leo M. Cordova
- Department
of Chemistry, School of Physical Sciences, University of California, Irvine, California 92697, United States
| | - Alicia S. Robang
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yuyao Kuang
- Department
of Chemical and Biomolecular Engineering, Samueli School of Engineering, University of California, Irvine, California 92697, United States
| | - Kaleolani S. Ogura
- Department
of Chemistry, School of Physical Sciences, University of California, Irvine, California 92697, United States
| | - Anant K. Paravastu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Maxx Q. Arguilla
- Department
of Chemistry, School of Physical Sciences, University of California, Irvine, California 92697, United States
| | - Herdeline Ann M. Ardoña
- Department
of Chemical and Biomolecular Engineering, Samueli School of Engineering, University of California, Irvine, California 92697, United States
- Department
of Chemistry, School of Physical Sciences, University of California, Irvine, California 92697, United States
- Department
of Biomedical Engineering, Samueli School of Engineering, University of California, Irvine, California 92697, United States
- Sue
& Bill Gross Stem Cell Research Center, University of California, Irvine, California 92697, United States
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6
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Lends A, Birlirakis N, Cai X, Daskalov A, Shenoy J, Abdul-Shukkoor MB, Berbon M, Ferrage F, Liu Y, Loquet A, Tan KO. Efficient 18.8 T MAS-DNP NMR reveals hidden side chains in amyloid fibrils. JOURNAL OF BIOMOLECULAR NMR 2023:10.1007/s10858-023-00416-5. [PMID: 37289306 DOI: 10.1007/s10858-023-00416-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/02/2023] [Indexed: 06/09/2023]
Abstract
Amyloid fibrils are large and insoluble protein assemblies composed of a rigid core associated with a cross-β arrangement rich in β-sheet structural elements. It has been widely observed in solid-state NMR experiments that semi-rigid protein segments or side chains do not yield easily observable NMR signals at room temperature. The reasons for the missing peaks may be due to the presence of unfavorable dynamics that interfere with NMR experiments, which result in very weak or unobservable NMR signals. Therefore, for amyloid fibrils, semi-rigid and dynamically disordered segments flanking the amyloid core are very challenging to study. Here, we show that high-field dynamic nuclear polarization (DNP), an NMR hyperpolarization technique typically performed at low temperatures, can circumvent this issue because (i) the low-temperature environment (~ 100 K) slows down the protein dynamics to escape unfavorable detection regime, (ii) DNP improves the overall NMR sensitivity including those of flexible side chains, and (iii) efficient cross-effect DNP biradicals (SNAPol-1) optimized for high-field DNP (≥ 18.8 T) are employed to offer high sensitivity and resolution suitable for biomolecular NMR applications. By combining these factors, we have successfully established an impressive enhancement factor of ε ~ 50 on amyloid fibrils using an 18.8 T/ 800 MHz magnet. We have compared the DNP efficiencies of M-TinyPol, NATriPol-3, and SNAPol-1 biradicals on amyloid fibrils. We found that SNAPol-1 (with ε ~ 50) outperformed the other two radicals. The MAS DNP experiments revealed signals of flexible side chains previously inaccessible at conventional room-temperature experiments. These results demonstrate the potential of MAS-DNP NMR as a valuable tool for structural investigations of amyloid fibrils, particularly for side chains and dynamically disordered segments otherwise hidden at room temperature.
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Affiliation(s)
- Alons Lends
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Nicolas Birlirakis
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Xinyi Cai
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Asen Daskalov
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Jayakrishna Shenoy
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Muhammed Bilal Abdul-Shukkoor
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Mélanie Berbon
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Antoine Loquet
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France.
| | - Kong Ooi Tan
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
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7
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Yokoyama K, Thomas J, Ardner W, Kieft M, Neuwirth LS, Liu W. An Approach for In-Situ Detection of Gold Colloid Aggregates Amyloid Formations Within The Hippocampus of The Cohen's Alzheimer's Disease Rat Model By Surface Enhanced Raman Scattering Methods. J Neurosci Methods 2023; 393:109892. [PMID: 37230258 DOI: 10.1016/j.jneumeth.2023.109892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND Amyloid beta (Aβ) peptides, such as Aβ1-40 or Aβ1-42 are regarded as hallmark neuropathological biomarkers associated with Alzheimer's disease (AD). The formation of an aggregates by Aβ1-40 or Aβ1-42-coated gold nano-particles are hypothesized to contain conformation of Aβ oligomers, which could exist only at an initial stage of fibrillogenesis. NEW METHOD The attempt of in-situ detection of externally initiated gold colloid (ca. 80nm diameter) aggregates in the middle section of the hippocampus of the Long Evans Cohen's Alzheimer's disease rat model was conducted through the Surface Enhanced Raman Scattering (SERS) method. RESULTS The SERS spectral features contained modes associated with β-sheet interactions and a significant number of modes that were previously reported in SERS shifts for Alzheimer diseased rodent and human brain tissues; thereby, strongly implying a containment of amyloid fibrils. The spectral patterns were further examined and compared with those collected from in-vitro gold colloid aggregates which were formed from Aβ1-40 - or Aβ1-42 -coated 80nm gold colloid under pH ~4, pH ~7, and pH ~10, and the best matched datasets were found with that of the aggregates of Aβ1-42 -coated 80nm gold colloid at ~pH 4.0. The morphology and physical size of this specific gold colloid aggregate was clearly different from those found in-vitro. COMPARISON WITH EXISTING METHOD(S) The amyloid fibril with a β-sheet conformation identified in previously reported in AD mouse/human brain tissues was involved in a formation of the gold colloid aggregates. However, to our surprise, best explanation for the observed SERS spectral features was possible with those in vitro Aβ1-42 -coated 80nm gold colloid under pH ~4. CONCLUSIONS A formation of gold colloid aggregates was confirmed in the AD rat hippocampal brain section with unique physical morphology compared to those observed in in-vitro Aβ1-42 or Aβ1-40 mediated gold colloid aggregates. It was concluded that a β-sheet conformation identified in previously reported in AD mouse/human brain tissues was in volved in a formation of the gold colloid aggregates.
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Affiliation(s)
- Kazushige Yokoyama
- Department of Chemistry, The State University of New York Geneseo College, Geneseo, NY, USA
| | - Joshua Thomas
- Department of Chemistry, The State University of New York Geneseo College, Geneseo, NY, USA
| | - Windsor Ardner
- Department of Chemistry, The State University of New York Geneseo College, Geneseo, NY, USA
| | - Madison Kieft
- Department of Chemistry, The State University of New York Geneseo College, Geneseo, NY, USA
| | - Lorenz S Neuwirth
- Department of Psychology, The State University of New York Old Westbury, Old Westbury, NY, USA; SUNY Neuroscience Research Institute, The State University of New York Old Westbury, Old Westbury, NY, USA
| | - Wei Liu
- WITec Instruments Corp, Knoxville, TN, USA
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8
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Arunachalam V, Sharma K, Mote KR, Madhu PK. Asynchronising five-fold symmetry sequence for better homonuclear polarisation transfer in magic-angle-spinning solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2023; 124:101858. [PMID: 36796278 DOI: 10.1016/j.ssnmr.2023.101858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Recoupling, decoupling, and multidimensional correlation experiments in magic-angle-spinning (MAS) solid-state NMR can be designed by exploiting the symmetry of internal spin interactions. One such scheme, namely, C521, and its supercycled version SPC521, notated as a five-fold symmetry sequence, is widely used for double-quantum dipole-dipole recoupling. Such schemes are generally rotor synchronised by design. We demonstrate an asynchronous implementation of the SPC521 sequence leading to higher double-quantum homonuclear polarisation transfer efficiency compared to the normal synchronous implementation. Rotor-synchronisation is broken in two different ways: lengthening the duration of one of the pulses, denoted as pulse-width variation (PWV), and mismatching the MAS frequency denoted as MAS variation (MASV). The application of this asynchronous sequence is shown on three different samples, namely, U-13C-alanine and 1,4-13C-labelled ammonium phthalate which include 13Cα-13Cβ, 13Cα-13Co, and 13Co-13Co spin systems, and adenosine 5'- triphosphate disodium salt trihydrate (ATP⋅3H2O). We show that the asynchronous version performs better for spin pairs with small dipole-dipole couplings and large chemical-shift anisotropies, for example, 13Co-13Co. Simulations and experiments are shown to corroborate the results.
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Affiliation(s)
- Vaishali Arunachalam
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad, 500046, India.
| | - Kshama Sharma
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad, 500046, India.
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad, 500046, India.
| | - P K Madhu
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad, 500046, India.
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9
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Aladin V, Sreemantula AK, Biedenbänder T, Marchanka A, Corzilius B. Specific Signal Enhancement on an RNA-Protein Interface by Dynamic Nuclear Polarization. Chemistry 2023; 29:e202203443. [PMID: 36533705 DOI: 10.1002/chem.202203443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/23/2022]
Abstract
Sensitivity and specificity are both crucial for the efficient solid-state NMR structure determination of large biomolecules. We present an approach that features both advantages by site-specific enhancement of NMR spectroscopic signals from the protein-RNA binding site within a ribonucleoprotein (RNP) by dynamic nuclear polarization (DNP). This approach uses modern biochemical techniques for sparse isotope labeling and exploits the molecular dynamics of 13 C-labeled methyl groups exclusively present in the protein. These dynamics drive heteronuclear cross relaxation and thus allow specific hyperpolarization transfer across the biomolecular complex's interface. For the example of the L7Ae protein in complex with a 26mer guide RNA minimal construct from the box C/D complex in archaea, we demonstrate that a single methyl-nucleotide contact is responsible for most of the polarization transfer to the RNA, and that this specific transfer can be used to boost both NMR spectral sensitivity and specificity by DNP.
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Affiliation(s)
- Victoria Aladin
- Institute of Chemistry, University of Rostock, Albert-Einstein-Str. 27, 18059, Rostock, Germany
- Department Life, Light & Matter, University of Rostock, Albert-Einstein-Str. 25, 18059, Rostock, Germany
| | - Arun K Sreemantula
- Institute for Organic Chemistry and, Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Thomas Biedenbänder
- Institute of Chemistry, University of Rostock, Albert-Einstein-Str. 27, 18059, Rostock, Germany
- Department Life, Light & Matter, University of Rostock, Albert-Einstein-Str. 25, 18059, Rostock, Germany
| | - Alexander Marchanka
- Institute for Organic Chemistry and, Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Björn Corzilius
- Institute of Chemistry, University of Rostock, Albert-Einstein-Str. 27, 18059, Rostock, Germany
- Department Life, Light & Matter, University of Rostock, Albert-Einstein-Str. 25, 18059, Rostock, Germany
- Leibniz Institute for Catalysis, Albert-Einstein-Str. 29, 18059, Rostock, Germany
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10
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Islam A, Kikuchi Y, Iimori T. Electroabsorption and Stark Fluorescence Spectroscopies of Thioflavin T. J Phys Chem A 2023; 127:1436-1444. [PMID: 36740807 DOI: 10.1021/acs.jpca.2c07794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Thioflavin T (ThT) is a typical fluorescent marker for detecting the formation of amyloid fibrils, because its fluorescence intensity increases by more than 2 orders of magnitude upon complexation with the fibrils. Strong electrostatic fields on protein surfaces are known to be a significant factor in chemical reactions and biological functions. Therefore, ThT bound to amyloid fibrils must experience strong electric fields. This study employed electroabsorption and Stark fluorescence spectroscopies to clarify the effects of external electric fields on the photophysics of ThT. The absorption spectrum shows two bands ascribed to locally excited (LE) and charge transfer (CT) states. Coupling between the LE and CT states is enhanced in the presence of an external electric field, resulting in fluorescence quenching. The electric field strength of the amyloid fibril surface was inferred from the fluorescence quenching efficiency of ThT.
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Affiliation(s)
- Ahatashamul Islam
- Department of Sciences and Informatics, Muroran Institute of Technology, Mizumoto-cho 27-1, Muroran, Hokkaido050-8585, Japan
| | - Yudai Kikuchi
- Department of Sciences and Informatics, Muroran Institute of Technology, Mizumoto-cho 27-1, Muroran, Hokkaido050-8585, Japan
| | - Toshifumi Iimori
- Department of Sciences and Informatics, Muroran Institute of Technology, Mizumoto-cho 27-1, Muroran, Hokkaido050-8585, Japan
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11
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Abstract
Perturbation of cell membranes by amyloid β (Ab) peptide oligomers is one possible mechanism of cytotoxicity in Alzheimer's disease, but the structure of such Ab-membrane complexes is unknown. Here we examine the stability of several putative structures by implicit membrane and all-atom molecular dynamics simulations. The structures include (a) a variety of models proposed by other researchers in the past, (b) a heptameric β barrel determined by grafting the Ab sequence onto α-hemolysin, (c) a similar structure with modified strand orientation and turn location based on an experimental β-hairpin structure, (d) oligomers inserting C-terminal β hairpins into one leaflet of the bilayer, (e) oligomers forming parallel C-terminal β barrels, and (f) a helical hexamer made of C-terminal fragments. The α-hemolysin-grafted structure and its alternately oriented variant are stable in the membrane and form an aqueous pore. In contrast, the C-terminal parallel barrels are not stable, presumably due to excessive hydrophobicity of their inner surface. The helical hexamer also failed to stabilize an aqueous pore for the same reason. The C-terminal hairpin-inserting structures remain stably inserted but, again, do not form an aqueous pore. Our results suggest that only β-barrels inserting a combination of C-terminal and other residues can form stable aqueous pores.
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Affiliation(s)
- Aliasghar Sepehri
- Department of Chemistry, City College of New York, CUNY, 160 Convent Avenue, New York, New York10031, United States
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, CUNY, 160 Convent Avenue, New York, New York10031, United States.,Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, 365 Fifth Avenue, New York, New York10016, United States
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12
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Gupta S, Raskatov JA, Ralston CY. A Hybrid Structural Method for Investigating Low Molecular Weight Oligomeric Structures of Amyloid Beta. Chembiochem 2022; 23:e202200333. [PMID: 35980391 PMCID: PMC9729406 DOI: 10.1002/cbic.202200333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/16/2022] [Indexed: 01/25/2023]
Abstract
Spurred in part by the failure of recent therapeutics targeting amyloid β plaques in Alzheimer's Disease (AD), attention is increasingly turning to the oligomeric forms of this peptide that form early in the aggregation process. However, while numerous amyloid β fibril structures have been characterized, primarily by NMR spectroscopy and cryo-EM, obtaining structural information on the low molecular weight forms of amyloid β that presumably precede and/or seed fibril formation has proved challenging. These transient forms are heterogeneous, and depend heavily on experimental conditions such as buffer, temperature, concentration, and degree of quiescence during measurement. Here, we present the concept for a new approach to delineating structural features of early-stage low molecular weight amyloid β oligomers, using a solvent accessibility assay in conjunction with simultaneous fluorescence measurements.
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Affiliation(s)
- Sayan Gupta
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley CA 94720 (USA)
| | - Jevgenij A. Raskatov
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Physical Science Building 356, 1156 High Street, Santa Cruz, CA 95064 (USA)
| | - Corie Y. Ralston
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley CA 94720 (USA)
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13
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Zhu X, Schrader JM, Irizarry BA, Smith SO, Van Nostrand WE. Impact of Aβ40 and Aβ42 Fibrils on the Transcriptome of Primary Astrocytes and Microglia. Biomedicines 2022; 10:biomedicines10112982. [PMID: 36428550 PMCID: PMC9688026 DOI: 10.3390/biomedicines10112982] [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: 09/29/2022] [Revised: 10/27/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
Fibrillar amyloid β-protein (Aβ) deposits in the brain, which are primarily composed of Aβ40 or Aβ42 peptides, are key pathological features of Alzheimer's disease (AD) and related disorders. Although the underlying mechanisms are still not clear, the Aβ fibrils can trigger a number of cellular responses, including activation of astrocytes and microglia. In addition, fibril structures of the Aβ40 and Aβ42 peptides are known to be polymorphic, which poses a challenge for attributing the contribution of different Aβ sequences and structures to brain pathology. Here, we systematically treated primary astrocytes and microglia with single, well-characterized polymorphs of Aβ40 or Aβ42 fibrils, and performed bulk RNA sequencing to assess cell-specific changes in gene expression. A greater number of genes were up-regulated by Aβ42 fibril-treated glial cells (251 and 2133 genes in astrocyte and microglia, respectively) compared with the Aβ40 fibril-treated glial cells (191 and 251 genes in astrocytes and microglia, respectively). Immunolabeling studies in an AD rat model with parenchymal fibrillar Aβ42 plaques confirmed the expression of PAI-1, MMP9, MMP12, CCL2, and C1r in plaque-associated microglia, and iNOS, GBP2, and C3D in plaque-associated astrocytes, validating markers from the RNA sequence data. In order to better understand these Aβ fibril-induced gene changes, we analyzed gene expression patterns using the Ingenuity pathway analysis program. These analyses further highlighted that Aβ42 fibril treatment up-regulated cellular activation pathways and immune response pathways in glial cells, including IL1β and TNFα in astrocytes, and microglial activation and TGFβ1 in microglia. Further analysis revealed that a number of disease-associated microglial (DAM) genes were surprisingly suppressed in Aβ40 fibril treated microglia. Together, the present findings indicate that Aβ42 fibrils generally show similar, but stronger, stimulating activity of glial cells compared with Aβ40 fibril treatment.
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Affiliation(s)
- Xiaoyue Zhu
- George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, RI 02881, USA
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Joseph M. Schrader
- George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, RI 02881, USA
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Brandon A. Irizarry
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Steven O. Smith
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - William E. Van Nostrand
- George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, RI 02881, USA
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA
- Correspondence: ; Tel.: +1-401-874-2363
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14
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Zhong X, Kumar R, Wang Y, Biverstål H, Ingeborg Jegerschöld C, J B Koeck P, Johansson J, Abelein A, Chen G. Amyloid Fibril Formation of Arctic Amyloid-β 1-42 Peptide is Efficiently Inhibited by the BRICHOS Domain. ACS Chem Biol 2022; 17:2201-2211. [PMID: 35876740 PMCID: PMC9396614 DOI: 10.1021/acschembio.2c00344] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloid-β peptide (Aβ) aggregation is one of the hallmarks of Alzheimer's disease (AD). Mutations in Aβ are associated with early onset familial AD, and the Arctic mutant E22G (Aβarc) is an extremely aggregation-prone variant. Here, we show that BRICHOS, a natural anti-amyloid chaperone domain, from Bri2 efficiently inhibits aggregation of Aβarc by mainly interfering with secondary nucleation. This is qualitatively different from the microscopic inhibition mechanism for the wild-type Aβ, against which Bri2 BRICHOS has a major effect on both secondary nucleation and fibril end elongation. The monomeric Aβ42arc peptide aggregates into amyloid fibrils significantly faster than wild-type Aβ (Aβ42wt), as monitored by thioflavin T (ThT) binding, but the final ThT intensity was strikingly lower for Aβ42arc compared to Aβ42wt fibrils. The Aβ42arc peptide formed large aggregates, single-filament fibrils, and multiple-filament fibrils without obvious twists, while Aβ42wt fibrils displayed a polymorphic pattern with typical twisted fibril architecture. Recombinant human Bri2 BRICHOS binds to the Aβ42arc fibril surface and interferes with the macroscopic fibril arrangement by promoting single-filament fibril formation. This study provides mechanistic insights on how BRICHOS efficiently affects the aggressive Aβ42arc aggregation, resulting in both delayed fibril formation kinetics and altered fibril structure.
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Affiliation(s)
- Xueying Zhong
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, 141 52 Huddinge, Sweden
| | - Rakesh Kumar
- The Department of Biosciences and Nutrition, Karolinska Institutet, 141 52 Huddinge, Sweden
| | - Yu Wang
- The Department of Biosciences and Nutrition, Karolinska Institutet, 141 52 Huddinge, Sweden.,College of Wildlife and Protected Area, Northeast Forestry University, 150040 Harbin, People's Republic of China
| | - Henrik Biverstål
- The Department of Biosciences and Nutrition, Karolinska Institutet, 141 52 Huddinge, Sweden
| | - Caroline Ingeborg Jegerschöld
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, 141 52 Huddinge, Sweden
| | - Philip J B Koeck
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, 141 52 Huddinge, Sweden
| | - Jan Johansson
- The Department of Biosciences and Nutrition, Karolinska Institutet, 141 52 Huddinge, Sweden
| | - Axel Abelein
- The Department of Biosciences and Nutrition, Karolinska Institutet, 141 52 Huddinge, Sweden
| | - Gefei Chen
- The Department of Biosciences and Nutrition, Karolinska Institutet, 141 52 Huddinge, Sweden
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15
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Takamuku M, Sugishita T, Tamaki H, Dong L, So M, Fujiwara T, Matsuki Y. Evolution of α-synuclein conformation ensemble toward amyloid fibril via liquid-liquid phase separation (LLPS) as investigated by dynamic nuclear polarization-enhanced solid-state MAS NMR. Neurochem Int 2022; 157:105345. [DOI: 10.1016/j.neuint.2022.105345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/11/2022] [Accepted: 04/21/2022] [Indexed: 10/18/2022]
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16
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Low KJY, Venkatraman A, Mehta JS, Pervushin K. Molecular mechanisms of amyloid disaggregation. J Adv Res 2022; 36:113-132. [PMID: 35127169 PMCID: PMC8799873 DOI: 10.1016/j.jare.2021.05.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 04/13/2021] [Accepted: 05/16/2021] [Indexed: 12/17/2022] Open
Abstract
Importance of disaggregation mechanism and innate disaggregation in living systems. Different types and mechanism of disaggregation reported in literature. Structural details of the interactions and the disaggregation mechanisms. Amyloid disaggregation in protein aggregation disorders as a potential treatment. Proposed amyloid disaggregation mechanism of an ATP-independent chaperone (L-PGDS).
Introduction Protein aggregation and deposition of uniformly arranged amyloid fibrils in the form of plaques or amorphous aggregates is characteristic of amyloid diseases. The accumulation and deposition of proteins result in toxicity and cause deleterious effects on affected individuals known as amyloidosis. There are about fifty different proteins and peptides involved in amyloidosis including neurodegenerative diseases and diseases affecting vital organs. Despite the strenuous effort to find a suitable treatment option for these amyloid disorders, very few compounds had made it to unsuccessful clinical trials. It has become a compelling challenge to understand and manage amyloidosis with the increased life expectancy and ageing population. Objective While most of the currently available literature and knowledge base focus on the amyloid inhibitory mechanism as a treatment option, it is equally important to organize and understand amyloid disaggregation strategies. Disaggregation strategies are important and crucial as they are present innately functional in many living systems and dissolution of preformed amyloids may provide a direct benefit in many pathological conditions. In this review, we have compiled the known amyloid disaggregation mechanism, interactions, and possibilities of using disaggregases as a treatment option for amyloidosis. Methods We have provided the structural details using protein-ligand docking models to visualize the interaction between these disaggregases with amyloid fibrils and their respective proposed amyloid disaggregation mechanisms. Results After reviewing and comparing the different amyloid disaggregase systems and their proposed mechanisms, we presented two different hypotheses for ATP independent disaggregases using L-PGDS as a model. Conclusion Finally, we have highlighted the importance of understanding the underlying disaggregation mechanisms used by these chaperones and organic compounds before the implementation of these disaggregases as a potential treatment option for amyloidosis.
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17
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Biedenbänder T, Aladin V, Saeidpour S, Corzilius B. Dynamic Nuclear Polarization for Sensitivity Enhancement in Biomolecular Solid-State NMR. Chem Rev 2022; 122:9738-9794. [PMID: 35099939 DOI: 10.1021/acs.chemrev.1c00776] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Solid-state NMR with magic-angle spinning (MAS) is an important method in structural biology. While NMR can provide invaluable information about local geometry on an atomic scale even for large biomolecular assemblies lacking long-range order, it is often limited by low sensitivity due to small nuclear spin polarization in thermal equilibrium. Dynamic nuclear polarization (DNP) has evolved during the last decades to become a powerful method capable of increasing this sensitivity by two to three orders of magnitude, thereby reducing the valuable experimental time from weeks or months to just hours or days; in many cases, this allows experiments that would be otherwise completely unfeasible. In this review, we give an overview of the developments that have opened the field for DNP-enhanced biomolecular solid-state NMR including state-of-the-art applications at fast MAS and high magnetic field. We present DNP mechanisms, polarizing agents, and sample constitution methods suitable for biomolecules. A wide field of biomolecular NMR applications is covered including membrane proteins, amyloid fibrils, large biomolecular assemblies, and biomaterials. Finally, we present perspectives and recent developments that may shape the field of biomolecular DNP in the future.
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Affiliation(s)
- Thomas Biedenbänder
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Victoria Aladin
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Siavash Saeidpour
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Björn Corzilius
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
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18
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Abstract
Structures of amyloid-β fibrils suggest Alzheimer’s disease–modifying strategies.
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Affiliation(s)
- Michael Willem
- Biomedical Center (BMC), Division of Metabolic Biochemistry, Faculty of Medicine, Ludwig Maximilians University Munich, Munich, Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, Ulm, Germany
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19
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Srinivasan E, Chandrasekhar G, Chandrasekar P, Anbarasu K, Vickram AS, Tayubi IA, Rajasekaran R, Karunakaran R. Decoding Conformational Imprint of Convoluted Molecular Interactions Between Prenylflavonoids and Aggregated Amyloid-Beta42 Peptide Causing Alzheimer's Disease. Front Chem 2022; 9:753146. [PMID: 34988060 PMCID: PMC8720757 DOI: 10.3389/fchem.2021.753146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/11/2021] [Indexed: 11/25/2022] Open
Abstract
Protein misfolding occurs due to the loss of native protein structure and adopts an abnormal structure, wherein the misfolded proteins accumulate and form aggregates, which result in the formation of amyloid fibrils that are associated with neurodegenerative diseases. Amyloid beta (Aβ42) aggregation or amyloidosis is contemplated as a unique hallmark characteristic of Alzheimer’s disease (AD). Due to aberrant accrual and aggregation of Aβ42 in extracellular space, the formation of senile plaques is found in AD patients. These senile plaques occur usually in the cognitive and memory region of the brain, enfeebles neurodegeneration, hinders the signaling between synapse, and disrupts neuronal functioning. In recent years, herbal compounds are identified and characterized for their potential as Aβ42 inhibitors. Thus, understanding their structure and molecular mechanics can provide an incredible finding in AD therapeutics. To describe the structure-based molecular studies in the rational designing of drugs against amyloid fibrils, we examined various herbal compounds that belong to prenylflavonoids. The present study characterizes the trends we identified at molecular docking studies and dynamics simulation where we observed stronger binding orientation of bavachalcone, bavachin, and neobavaisoflavone with the amyloid-beta (Aβ42) fibril structure. Hence, we could postulate that these herbal compounds could be potential inhibitors of Aβ42 fibrils; these anti-aggregation agents need to be considered in treating AD.
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Affiliation(s)
- E Srinivasan
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, India.,Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - G Chandrasekhar
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, India
| | - P Chandrasekar
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, India
| | - K Anbarasu
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - A S Vickram
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Iftikhar Aslam Tayubi
- Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - R Rajasekaran
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, India
| | - Rohini Karunakaran
- Unit of Biochemistry, Faculty of Medicine, AIMST University, Bedong, Malaysia
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20
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1H detection and dynamic nuclear polarization-enhanced NMR of Aβ 1-42 fibrils. Proc Natl Acad Sci U S A 2022; 119:2114413119. [PMID: 34969859 PMCID: PMC8740738 DOI: 10.1073/pnas.2114413119] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2021] [Indexed: 12/25/2022] Open
Abstract
Amyloid-β (Aβ) is the subject of intense scrutiny because of its close association with Alzheimer’s disease (AD), which currently afflicts about 50 million people worldwide. The results reported in this manuscript focus on the new possibilities provided by ultrafast magic-angle spinning (MAS) 1H detection and fast-MAS dynamic nuclear polarization (DNP), which have ushered in a new era for NMR-based structural biology, but whose potential has not yet been fully exploited for the structural investigation of complex amyloid assemblies. This work demonstrates the expeditious structural analysis of amyloid fibrils, without requiring preparation of large sample amounts, and sets the stage for future studies of unlabeled AD peptides derived from tissue samples available in limited quantities. Several publications describing high-resolution structures of amyloid-β (Aβ) and other fibrils have demonstrated that magic-angle spinning (MAS) NMR spectroscopy is an ideal tool for studying amyloids at atomic resolution. Nonetheless, MAS NMR suffers from low sensitivity, requiring relatively large amounts of samples and extensive signal acquisition periods, which in turn limits the questions that can be addressed by atomic-level spectroscopic studies. Here, we show that these drawbacks are removed by utilizing two relatively recent additions to the repertoire of MAS NMR experiments—namely, 1H detection and dynamic nuclear polarization (DNP). We show resolved and sensitive two-dimensional (2D) and three-dimensional (3D) correlations obtained on 13C,15N-enriched, and fully protonated samples of M0Aβ1-42 fibrils by high-field 1H-detected NMR at 23.4 T and 18.8 T, and 13C-detected DNP MAS NMR at 18.8 T. These spectra enable nearly complete resonance assignment of the core of M0Aβ1-42 (K16-A42) using submilligram sample quantities, as well as the detection of numerous unambiguous internuclear proximities defining both the structure of the core and the arrangement of the different monomers. An estimate of the sensitivity of the two approaches indicates that the DNP experiments are currently ∼6.5 times more sensitive than 1H detection. These results suggest that 1H detection and DNP may be the spectroscopic approaches of choice for future studies of Aβ and other amyloid systems.
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21
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Lattanzi V, André I, Gasser U, Dubackic M, Olsson U, Linse S. Amyloid β 42 fibril structure based on small-angle scattering. Proc Natl Acad Sci U S A 2021; 118:e2112783118. [PMID: 34815346 PMCID: PMC8640717 DOI: 10.1073/pnas.2112783118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2021] [Indexed: 01/30/2023] Open
Abstract
Amyloid fibrils are associated with a number of neurodegenerative diseases, including fibrils of amyloid β42 peptide (Aβ42) in Alzheimer's disease. These fibrils are a source of toxicity to neuronal cells through surface-catalyzed generation of toxic oligomers. Detailed knowledge of the fibril structure may thus facilitate therapeutic development. We use small-angle scattering to provide information on the fibril cross-section dimension and shape for Aβ42 fibrils prepared in aqueous phosphate buffer at pH = 7.4 and pH 8.0 under quiescent conditions at 37 °C from pure recombinant Aβ42 peptide. Fitting the data using a continuum model reveals an elliptical cross-section and a peptide mass-per-unit length compatible with two filaments of two monomers, four monomers per plane. To provide a more detailed atomistic model, the data were fitted using as a starting state a high-resolution structure of the two-monomer arrangement in filaments from solid-state NMR (Protein Data Bank ID 5kk3). First, a twofold symmetric model including residues 11 to 42 of two monomers in the filament was optimized in terms of twist angle and local packing using Rosetta. A two-filament model was then built and optimized through fitting to the scattering data allowing the two N-termini in each filament to take different conformations, with the same conformation in each of the two filaments. This provides an atomistic model of the fibril with twofold rotation symmetry around the fibril axis. Intriguingly, no polydispersity as regards the number of filaments was observed in our system over separate samples, suggesting that the two-filament arrangement represents a free energy minimum for the Aβ42 fibril.
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Affiliation(s)
- Veronica Lattanzi
- Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden;
- Division of Physical Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Ingemar André
- Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden
| | - Urs Gasser
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Marija Dubackic
- Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden
- Division of Physical Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Ulf Olsson
- Division of Physical Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Sara Linse
- Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden
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22
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Das A. Systematic Search for a Predictor for the Clinical Observables of Alzheimer's Disease. J Phys Chem B 2021; 125:12177-12186. [PMID: 34723517 DOI: 10.1021/acs.jpcb.1c06725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
One of the prevailing life-threatening incurable neurodegenerative diseases that are presently endangering human society as a whole, and hence, baffling the entire spectrum of the scientific and pharmaceutical world, is Alzheimer's disease (AD). AD is a manifestation of self-assembly of both wild-type (sporadic) and mutated (familial) forms of the amyloid-β peptide, a proteolytic product of the amyloid precursor protein, where the self-assembly results in the genesis of pathogenic fibrillar aggregates. Currently prevailing diagnostic and hence therapeutic challenges originate from the unavailability of a specific predictor for clinical observables. The continuous emergence of novel pathogenic mutants with unpredictable phenotypes adds immensely to the nonspecific nature of the problem. The current research reports a simple physical parameter, the binding affinity of a protofilament to its protofibril, which predicts the clinical observables of familial AD with astounding accuracy and more importantly, without any adjustable parameters.
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Affiliation(s)
- Atanu Das
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra 411 008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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23
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Ranjan R, Kayastha AM, Sinha N. Interactions Between Amyloid-β (1-42) and Hydroxyapatite-Cholesterol Spherules Associated with Age-Related Macular Degeneration. Protein J 2021; 40:849-856. [PMID: 34718942 DOI: 10.1007/s10930-021-10026-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2021] [Indexed: 10/19/2022]
Abstract
Drusen deposition on sub-retinal pigment epithelium is the causal factor for age-related macular degeneration for the old-aged individuals. These deposits contain hydroxyapatite-cholesterol spherules on which several proteins and lipids accumulate to cover the retina and choroid, causing blurred vision and blindness. Amyloid-β, the known culprit in Alzheimer's disease, is one among the few major proteins known to occur in these deposits. In the present article, we report preliminary analyses of interactions between amyloid-β and hydroxyapatite-cholesterol composites using Thioflavin-T binding kinetics, solid-state NMR and transmission electron microscopy (TEM). Thioflavin-T fluorescence kinetics shows that amyloid-β (1-42) aggregates only under certain conditions of concentration of cholesterol in the hydroxyapatite-cholesterol composites prepared by two different methods. These results were confirmed by 1D 13C CPMAS solid-state NMR. TEM imaging revealed that there is an exposure of the cholesterol surface in the composites prepared by sonication method. These imaging experiments explain the dependence of aggregation kinetics on the exposure and availability of cholesterol surface in the composites to a certain extent.
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Affiliation(s)
- Renuka Ranjan
- Centre of Biomedical Research, SGPGIMS Campus, Raebareily Road, Lucknow, 226014, India.,School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Arvind M Kayastha
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
| | - Neeraj Sinha
- Centre of Biomedical Research, SGPGIMS Campus, Raebareily Road, Lucknow, 226014, India.
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24
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Wickramasinghe A, Xiao Y, Kobayashi N, Wang S, Scherpelz KP, Yamazaki T, Meredith SC, Ishii Y. Sensitivity-Enhanced Solid-State NMR Detection of Structural Differences and Unique Polymorphs in Pico- to Nanomolar Amounts of Brain-Derived and Synthetic 42-Residue Amyloid-β Fibrils. J Am Chem Soc 2021; 143:11462-11472. [PMID: 34308630 PMCID: PMC10279877 DOI: 10.1021/jacs.1c03346] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloid-β (Aβ) fibrils in neuritic plaques are a hallmark of Alzheimer's disease (AD). Since the 42-residue Aβ (Aβ42) fibril is the most pathogenic among different Aβ species, its structural characterization is crucial to our understanding of AD. While several polymorphs have been reported for Aβ40, previous studies of Aβ42 fibrils prepared at neutral pH detected essentially only one structure, with an S-shaped β-sheet arrangement (e.g., Xiao et al. Nat. Struct. Mol. Biol. 2015, 22, 499). Herein, we demonstrate the feasibility of characterizing the structure of trace amounts of brain-derived and synthetic amyloid fibrils by sensitivity-enhanced 1H-detected solid-state NMR (SSNMR) under ultrafast magic angle spinning. By taking advantage of the high sensitivity of this technique, we first demonstrate its applicability for the high-throughput screening of trace amounts of selectively 13C- and 15N-labeled Aβ42 fibril prepared with ∼0.01% patient-derived amyloid (ca. 4 pmol) as a seed. The comparison of 2D 13C/1H SSNMR data revealed marked structural differences between AD-derived Aβ42 (∼40 nmol or ∼200 μg) and synthetic fibrils in less than 10 min, confirming the feasibility of assessing the fibril structure from ∼1 pmol of brain amyloid seed in ∼2.5 h. We also present the first structural characterization of synthetic fully protonated Aβ42 fibril by 1H-detected 3D and 4D SSNMR. With procedures assisted by automated assignments, main-chain resonance assignments were completed for trace amounts (∼42 nmol) of a fully protonated amyloid fibril in the 1H-detection approach. The results suggest that this Aβ42 fibril exhibits a novel fold or polymorph structure.
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Affiliation(s)
- Ayesha Wickramasinghe
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
- NMR Division, RIKEN SPring-8 Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yiling Xiao
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Naohiro Kobayashi
- NMR Division, RIKEN SPring-8 Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Songlin Wang
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Kathryn P. Scherpelz
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Toshio Yamazaki
- NMR Division, RIKEN SPring-8 Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Stephen C. Meredith
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
- Department of Pathology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Yoshitaka Ishii
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
- NMR Division, RIKEN SPring-8 Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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25
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Nam E, Han J, Choi S, Lim MH. Distinct impact of glycation towards the aggregation and toxicity of murine and human amyloid-β. Chem Commun (Camb) 2021; 57:7637-7640. [PMID: 34254069 DOI: 10.1039/d1cc02695j] [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: 11/21/2022]
Abstract
Glycation of human Aβ (hAβ) is implicated to induce the deposition of amyloid aggregates found in the Alzheimer's disease (AD)-affected brain. Murine Aβ (mAβ) differs from hAβ in three different amino acid residues (Gly5, Phe10, and Arg13) and is less likely to form amyloid aggregates. Herein, we report that the advanced glycated end products of mAβ40 over hAβ40 are distinctly generated. The different glycation between the two peptides can govern their aggregation kinetics, structural transition, and cytotoxicity.
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Affiliation(s)
- Eunju Nam
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Jiyeon Han
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Sunhee Choi
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT 05753, USA
| | - Mi Hee Lim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
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26
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Nimerovsky E, Xue K, Movellan K, Andreas L. Heteronuclear and homonuclear radio-frequency-driven recoupling. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:343-353. [PMID: 37904771 PMCID: PMC10539778 DOI: 10.5194/mr-2-343-2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/11/2021] [Indexed: 11/01/2023]
Abstract
The radio-frequency-driven recoupling (RFDR) pulse sequence is used in magic-angle spinning (MAS) NMR to recouple homonuclear dipolar interactions. Here we show simultaneous recoupling of both the heteronuclear and homonuclear dipolar interactions by applying RFDR pulses on two channels. We demonstrate the method, called HETeronuclear RFDR (HET-RFDR), on microcrystalline SH3 samples at 10 and 55.555 kHz MAS. Numerical simulations of both HET-RFDR and standard RFDR sequences allow for better understanding of the influence of offsets and paths of magnetization transfers for both HET-RFDR and RFDR experiments, as well as the crucial role of XY phase cycling.
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Affiliation(s)
- Evgeny Nimerovsky
- Department of NMR-based Structural Biology, Max Planck Institute for
Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Kai Xue
- Department of NMR-based Structural Biology, Max Planck Institute for
Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Kumar Tekwani Movellan
- Department of NMR-based Structural Biology, Max Planck Institute for
Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Loren B. Andreas
- Department of NMR-based Structural Biology, Max Planck Institute for
Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
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27
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Structural details of amyloid β oligomers in complex with human prion protein as revealed by solid-state MAS NMR spectroscopy. J Biol Chem 2021; 296:100499. [PMID: 33667547 PMCID: PMC8042448 DOI: 10.1016/j.jbc.2021.100499] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 02/06/2023] Open
Abstract
Human PrP (huPrP) is a high-affinity receptor for oligomeric amyloid β (Aβ) protein aggregates. Binding of Aβ oligomers to membrane-anchored huPrP has been suggested to trigger neurotoxic cell signaling in Alzheimer’s disease, while an N-terminal soluble fragment of huPrP can sequester Aβ oligomers and reduce their toxicity. Synthetic oligomeric Aβ species are known to be heterogeneous, dynamic, and transient, rendering their structural investigation particularly challenging. Here, using huPrP to preserve Aβ oligomers by coprecipitating them into large heteroassemblies, we investigated the conformations of Aβ(1–42) oligomers and huPrP in the complex by solid-state MAS NMR spectroscopy. The disordered N-terminal region of huPrP becomes immobilized in the complex and therefore visible in dipolar spectra without adopting chemical shifts characteristic of a regular secondary structure. Most of the well-defined C-terminal part of huPrP is part of the rigid complex, and solid-state NMR spectra suggest a loss in regular secondary structure in the two C-terminal α-helices. For Aβ(1–42) oligomers in complex with huPrP, secondary chemical shifts reveal substantial β-strand content. Importantly, not all Aβ(1–42) molecules within the complex have identical conformations. Comparison with the chemical shifts of synthetic Aβ fibrils suggests that the Aβ oligomer preparation represents a heterogeneous mixture of β-strand-rich assemblies, of which some have the potential to evolve and elongate into different fibril polymorphs, reflecting a general propensity of Aβ to adopt variable β-strand-rich conformers. Taken together, our results reveal structural changes in huPrP upon binding to Aβ oligomers that suggest a role of the C terminus of huPrP in cell signaling. Trapping Aβ(1–42) oligomers by binding to huPrP has proved to be a useful tool for studying the structure of these highly heterogeneous β-strand-rich assemblies.
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28
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Brown MR, Radford SE, Hewitt EW. Modulation of β-Amyloid Fibril Formation in Alzheimer's Disease by Microglia and Infection. Front Mol Neurosci 2020; 13:609073. [PMID: 33324164 PMCID: PMC7725705 DOI: 10.3389/fnmol.2020.609073] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/03/2020] [Indexed: 01/06/2023] Open
Abstract
Amyloid plaques are a pathological hallmark of Alzheimer's disease. The major component of these plaques are highly ordered amyloid fibrils formed by amyloid-β (Aβ) peptides. However, whilst Aβ amyloid fibril assembly has been subjected to detailed and extensive analysis in vitro, these studies may not reproduce how Aβ fibrils assemble in the brain. This is because the brain represents a highly complex and dynamic environment, and in Alzheimer's disease multiple cofactors may affect the assembly of Aβ fibrils. Moreover, in vivo amyloid plaque formation will reflect the balance between the assembly of Aβ fibrils and their degradation. This review explores the roles of microglia as cofactors in Aβ aggregation and in the clearance of amyloid deposits. In addition, we discuss how infection may be an additional cofactor in Aβ fibril assembly by virtue of the antimicrobial properties of Aβ peptides. Crucially, by understanding the roles of microglia and infection in Aβ amyloid fibril assembly it may be possible to identify new therapeutic targets for Alzheimer's disease.
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Affiliation(s)
- Madeleine R Brown
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Eric W Hewitt
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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29
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Hu ZW, Au DF, Cruceta L, Vugmeyster L, Qiang W. N-Terminal Modified Aβ Variants Enable Modulations to the Structures and Cytotoxicity Levels of Wild-Type Aβ Fibrils through Cross-Seeding. ACS Chem Neurosci 2020; 11:2058-2065. [PMID: 32603584 DOI: 10.1021/acschemneuro.0c00316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Post-translational modifications (PTMs) of β-amyloid (Aβ) peptides are considered as triggering factors in sporadic Alzheimer's disease. However, studies to show the influence of pre-existing PTM-Aβ fibrils on wild-type Aβ peptides, which directly mimic the triggering scenarios, are rare. Here we show that three types of pathologically relevant PTM-Aβ variants with modifications in a particular segment (from D7 to V12) of the primary sequence lead to distinct impacts on the fibrillization of wild-type Aβ peptides. In general, the triggering effects are observed through cross-seeding between the PTM-Aβ seeds and wild-type peptides, which consequently induce modulations in the resultant wild-type fibril structures and elevations in the fibrillar cytotoxicity levels. Modifications with a similar chemical nature, such as the S8-phosphorylation and Y10-nitration, both of which introduce additional side-chain negative charges, show comparable structural-modulation and cytotoxicity-elevation effects. The results imply the biological influences of PTM-Aβ variants on the formation of amyloid deposits through cross-seeded fibrillization.
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Affiliation(s)
- Zhi-Wen Hu
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Dan Fai Au
- Department of Chemistry, University of Colorado at Denver, Denver, Colorado 80204, United States
| | - Letticia Cruceta
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Liliya Vugmeyster
- Department of Chemistry, University of Colorado at Denver, Denver, Colorado 80204, United States
| | - Wei Qiang
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
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30
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Strategies for identifying dynamic regions in protein complexes: Flexibility changes accompany methylation in chemotaxis receptor signaling states. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183312. [PMID: 32304758 DOI: 10.1016/j.bbamem.2020.183312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/24/2020] [Accepted: 04/13/2020] [Indexed: 12/11/2022]
Abstract
Bacterial chemoreceptors are organized in arrays composed of helical receptors arranged as trimers of dimers, coupled to a histidine kinase CheA and a coupling protein CheW. Ligand binding to the external domain inhibits the kinase activity, leading to a change in the swimming behavior. Adaptation to an ongoing stimulus involves reversible methylation and demethylation of specific glutamate residues. However, the exact mechanism of signal propagation through the helical receptor to the histidine kinase remains elusive. Dynamics of the receptor cytoplasmic domain is thought to play an important role in the signal transduction, and current models propose inverse dynamic changes in different regions of the receptor. We hypothesize that the adaptational modification (methylation) controls the dynamics by stabilizing a partially ordered domain, which in turn modulates the binding of the kinase, CheA. We investigated the difference in dynamics between the methylated and unmethylated states of the chemoreceptor using solid-state NMR. The unmethylated receptor (CF4E) shows increased flexibility relative to the methylated mimic (CF4Q). Methylation helix 1 (MH1) has been shown to be flexible in the methylated mimic receptor. Our analysis indicates that in addition to MH1, methylation helix 2 also becomes flexible in the unmethylated receptor. In addition, we have demonstrated that both states of the receptor have a rigid region and segments with intermediate timescale dynamics. The strategies used in this study for identifying dynamic regions are applicable to a broad class of proteins and protein complexes with intrinsic disorder and dynamics spanning multiple timescales.
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31
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Wiegand T. A solid-state NMR tool box for the investigation of ATP-fueled protein engines. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 117:1-32. [PMID: 32471533 DOI: 10.1016/j.pnmrs.2020.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 06/11/2023]
Abstract
Motor proteins are involved in a variety of cellular processes. Their main purpose is to convert the chemical energy released during adenosine triphosphate (ATP) hydrolysis into mechanical work. In this review, solid-state Nuclear Magnetic Resonance (NMR) approaches are discussed allowing studies of structures, conformational events and dynamic features of motor proteins during a variety of enzymatic reactions. Solid-state NMR benefits from straightforward sample preparation based on sedimentation of the proteins directly into the Magic-Angle Spinning (MAS) rotor. Protein resonance assignment is the crucial and often time-limiting step in interpreting the wealth of information encoded in the NMR spectra. Herein, potentials, challenges and limitations in resonance assignment for large motor proteins are presented, focussing on both biochemical and spectroscopic approaches. This work highlights NMR tools available to study the action of the motor domain and its coupling to functional processes, as well as to identify protein-nucleotide interactions during events such as DNA replication. Arrested protein states of reaction coordinates such as ATP hydrolysis can be trapped for NMR studies by using stable, non-hydrolysable ATP analogues that mimic the physiological relevant states as accurately as possible. Recent advances in solid-state NMR techniques ranging from Dynamic Nuclear Polarization (DNP), 31P-based heteronuclear correlation experiments, 1H-detected spectra at fast MAS frequencies >100 kHz to paramagnetic NMR are summarized and their applications to the bacterial DnaB helicase from Helicobacter pylori are discussed.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
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32
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Horváth D, Menyhárd DK, Perczel A. Protein Aggregation in a Nutshell: The Splendid Molecular Architecture of the Dreaded Amyloid Fibrils. Curr Protein Pept Sci 2020; 20:1077-1088. [PMID: 31553291 DOI: 10.2174/1389203720666190925102832] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 04/04/2019] [Accepted: 04/07/2019] [Indexed: 11/22/2022]
Abstract
The recent high-resolution structures of amyloid fibrils show that the organization of peptide segments into amyloid aggregate architecture is a general process, though the morphology is more complex and intricate than suspected previously. The amyloid fibrils are often cytotoxic, accumulating as intracellular inclusions or extracellular plaques and have the ability to interfere with cellular physiology causing various cellular malfunctions. At the same time, the highly ordered amyloid structures also present an opportunity for nature to store and protect peptide chains under extreme conditions - something that might be used for designing storage, formulation, and delivery of protein medications or for contriving bio-similar materials of great resistance or structure-ordering capacity. Here we summarize amyloid characteristics; discussing the basic morphologies, sequential requirements and 3D-structure that are required for the understanding of this newly (re)discovered protein structure - a prerequisite for developing either inhibitors or promoters of amyloid-forming processes.
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Affiliation(s)
- Dániel Horváth
- Laboratory of Structural Chemistry & Biology and MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eotvos Lorand University, H-1518, 112, PO Box 32, Budapest, Hungary
| | - Dóra K Menyhárd
- Laboratory of Structural Chemistry & Biology and MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eotvos Lorand University, H-1518, 112, PO Box 32, Budapest, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry & Biology and MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eotvos Lorand University, H-1518, 112, PO Box 32, Budapest, Hungary
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33
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Zhuo XF, Wang J, Zhang J, Jiang LL, Hu HY, Lu JX. Solid-State NMR Reveals the Structural Transformation of the TDP-43 Amyloidogenic Region upon Fibrillation. J Am Chem Soc 2020; 142:3412-3421. [PMID: 32003979 DOI: 10.1021/jacs.9b10736] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
TDP-43 is a primary pathological hallmark protein of amyotrophic lateral sclerosis and frontotemporal lobar degeneration, which may exist in the form of amyloid inclusions in the cells of patients. In addition to serving as a biomarker for these diseases, TDP-43 can also directly trigger neurodegeneration. We previously determined the amyloidogenic core region of TDP-43 (residues 311-360) and showed by solution NMR that this region includes two α-helices [(321-330) and (335-343)] in solution. We suggested that the helix-to-sheet structural transformation initiates TDP-43 aggregation. In the present study, X-ray diffraction shows that TDP-43 (311-360) aggregates adopt a cross-β structure. Thioredoxin (Trx)-fused TDP-43 (311-360) can undergo liquid-liquid phase separation (LLPS) before fibrillation, suggesting that phase separation is an intermediate step before amyloid formation. Solid-state NMR (SSNMR), carried out to elucidate the structural changes of TDP-43 (311-360) at the atomic level, indicates five β-strands of the amyloids formed, with the major two β-strands contributed by the first helical region in the solution structure. The NMR evidence is also in support of the fibril having a parallel in-register conformation, implying a mechanism in which the helix-helix interactions in LLPS are converted into β-strand parallel lateral association upon fibrillation. Our studies have assigned many key interresidue interactions that contribute to the stability of the fibril, including F316 with I318 and Q327 and W334 with A325, A326, A329, and S332. SSNMR with 1H detection reveals a unique close interaction between the indole Nε1-Hε1 of W334 and the side-chain carbonyl of Q343. This interaction could be a very important factor in initiating TDP-43 (311-360) folding/misfolding in LLPS.
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Affiliation(s)
- Xiao-Feng Zhuo
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , People's Republic of China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science , Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai 200031 , People's Republic of China.,University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Jian Wang
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , People's Republic of China
| | - Jing Zhang
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , People's Republic of China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science , Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai 200031 , People's Republic of China.,University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Lei-Lei Jiang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science , Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai 200031 , People's Republic of China
| | - Hong-Yu Hu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science , Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai 200031 , People's Republic of China
| | - Jun-Xia Lu
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , People's Republic of China
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34
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Dobson CM, Knowles TPJ, Vendruscolo M. The Amyloid Phenomenon and Its Significance in Biology and Medicine. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a033878. [PMID: 30936117 DOI: 10.1101/cshperspect.a033878] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The misfolding of proteins is now recognized to be the origin of a large number of medical disorders. One particularly important group of such disorders is associated with the aggregation of misfolded proteins into amyloid structures, and includes conditions ranging from Alzheimer's and Parkinson's diseases to type II diabetes. Such conditions already affect over 500 million people in the world, a number that is rising rapidly, and at present these disorders cannot be effectively treated or prevented. This review provides an overview of this field of science and discusses recent progress in understanding the nature and properties of the amyloid state, the kinetics and mechanism governing its formation, the origins of its links with disease, and the manner in which its formation may be inhibited or suppressed. This latter topic is of particular importance, both to enhance our knowledge of the maintenance of protein homeostasis in living organisms and also to address the development of therapeutic strategies through which to combat the loss of homeostasis and the associated onset and progression of disease.
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Affiliation(s)
- Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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35
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Gallardo R, Ranson NA, Radford SE. Amyloid structures: much more than just a cross-β fold. Curr Opin Struct Biol 2020; 60:7-16. [PMID: 31683043 DOI: 10.1016/j.sbi.2019.09.001] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/04/2019] [Indexed: 01/10/2023]
Abstract
In recent years our understanding of amyloid structure has been revolutionised by innovations in cryo-electron microscopy, electron diffraction and solid-state NMR. These techniques have yielded high-resolution structures of fibrils isolated from patients with neurodegenerative disease, as well as those formed from amyloidogenic proteins in vitro. The results not only show the expected cross-β amyloid structure, but also reveal that the amyloid fold is unexpectedly diverse and complex. Here, we discuss this diversity, highlighting dynamic regions, ligand binding motifs, cavities, non-protein components, and structural polymorphism. Collectively, these variations combine to allow the generic amyloid fold to be realised in three dimensions in different ways, and this diversity may be related to the roles of fibrils in disease.
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Affiliation(s)
- Rodrigo Gallardo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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36
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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: 557] [Impact Index Per Article: 111.4] [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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37
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Malär AA, Smith-Penzel S, Camenisch GM, Wiegand T, Samoson A, Böckmann A, Ernst M, Meier BH. Quantifying proton NMR coherent linewidth in proteins under fast MAS conditions: a second moment approach. Phys Chem Chem Phys 2019; 21:18850-18865. [PMID: 31432055 DOI: 10.1039/c9cp03414e] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Proton detected solid-state NMR under fast magic-angle-spinning (MAS) conditions is currently redefining the applications of solid-state NMR, in particular in structural biology. Understanding the contributions to the spectral linewidth is thereby of paramount importance. When disregarding the sample-dependent inhomogeneous contributions, the NMR proton linewidth is defined by homogeneous broadening, which has incoherent and coherent contributions. Understanding and disentangling these different contributions in multi-spin systems like proteins is still an open issue. The coherent contribution is mainly caused by the dipolar interaction under MAS and is determined by the molecular structure and the proton chemical shifts. Numerical simulation approaches based on numerically exact direct integration of the Liouville-von Neumann equation can give valuable information about the lineshape, but are limited to small spin systems (<12 spins). We present an alternative simulation method for the coherent contributions based on the rapid and partially analytic calculation of the second moments of large spin systems. We first validate the method on a simple system by predicting the 19F linewidth in CaF2 under MAS. We compare simulation results to experimental data for microcrystalline ubiquitin (deuterated 100% back-exchanged at 110 kHz and fully-protonated at 125 kHz). Our results quantitatively explain the observed linewidth per-residue basis for the vast majority of residues.
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Affiliation(s)
- Alexander A Malär
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Susanne Smith-Penzel
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Gian-Marco Camenisch
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Thomas Wiegand
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Ago Samoson
- School of Information Technologies, Tallinn University of Technology, Tallinn, Estonia. and NMR Institute MTÜ, Tallinn, Estonia
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367 Lyon, France.
| | - Matthias Ernst
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
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38
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Jia L, Wang W, Sang J, Wei W, Zhao W, Lu F, Liu F. Amyloidogenicity and Cytotoxicity of a Recombinant C-Terminal His 6-Tagged Aβ 1-42. ACS Chem Neurosci 2019; 10:1251-1262. [PMID: 30537813 DOI: 10.1021/acschemneuro.8b00333] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aggregation of amyloid β peptide (Aβ) is closely associated with the occurrence and development of Alzheimer's disease (AD). Reproducible and detailed studies on the aggregation kinetics and structure of various aggregates have been conducted using recombinant Aβ peptides. While the His6-tag is commonly used in the purification of recombinant proteins due to its great simplicity and affinity, there is little information on the aggregation of His6-tagged Aβ and its corresponding cytotoxicity. Moreover, it is also unclear whether there is an effect of the His6-tag on the amyloidogenicity and cytotoxicity of recombinant Aβ1-42. Herein, a method to express and purify a mutant C-terminally His6-tagged Aβ1-42 (named as Aβ1-42-His6) from Escherichia coli was described. Aβ1-42-His6 aggregated into β-sheet-rich fibrils as shown by thioflavin T fluorescence, atomic force microscopy and circular dichroism spectroscopy. Moreover, the fibrillar recombinant Aβ1-42-His6 showed strong toxicity toward PC12 cells in vitro. Molecular dynamics simulations revealed that the His6-tag contributed little to the secondary structure and intermolecular interactions, including hydrophobic interactions, salt bridges, and hydrogen bonding of the fibrillar pentamer of Aβ1-42. This highlights the biological importance of modification on the molecular structure of Aβ. Thus, the easily purified high-quality Aβ1-42-His6 offers great advantages for screening aggregation inhibitors or in vitro confirmation of rationally designed drugs for the treatment of AD.
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Affiliation(s)
- Longgang Jia
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wenjuan Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jingcheng Sang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wei Wei
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wenping Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Fuping Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Fufeng Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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39
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Abstract
Abstract
Inhibition of amyloid β peptide (Aβ) aggregation is an important goal due to the connection of this process with Alzheimer’s disease. Traditionally, inhibitors were developed with an aim to retard the overall macroscopic aggregation. However, recent advances imply that approaches based on mechanistic insights may be more powerful. In such approaches, the microscopic steps underlying the aggregation process are identified, and it is established which of these step(s) lead to neurotoxicity. Inhibitors are then derived to specifically target steps involved in toxicity. The Aβ aggregation process is composed of at minimum three microscopic steps: primary nucleation of monomers only, secondary nucleation of monomers on fibril surface, and elongation of fibrils by monomer addition. The vast majority of toxic species are generated from the secondary nucleation process: this may be a key process to inhibit in order to limit toxicity. Inhibition of primary nucleation, which delays the emergence of toxic species without affecting their total concentration, may also be effective. Inhibition of elongation may instead increase the toxicity over time. Here we briefly review findings regarding secondary nucleation of Aβ, its dominance over primary nucleation, and attempts to derive inhibitors that specifically target secondary nucleation with an aim to limit toxicity.
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Affiliation(s)
- Sara Linse
- Lund University , Department of Biochemistry and Structural Biology , P.O. Box 124 , 221 00 Lund , Sweden
- Lund University , NanoLund , Lund , Sweden
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40
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Lin Y, Im H, Diem LT, Ham S. Characterizing the structural and thermodynamic properties of Aβ42 and Aβ40. Biochem Biophys Res Commun 2019; 510:442-448. [PMID: 30722990 DOI: 10.1016/j.bbrc.2019.01.124] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 01/28/2019] [Indexed: 01/20/2023]
Abstract
The self-assembly of amyloid-beta (Aβ) proteins in aqueous extracellular environments is implicated in Alzheimer's disease. Among several alloforms of Aβ proteins differing in sequence length, the 42- and 40-residue forms (Aβ42 and Aβ40) are the most abundant ones in the human body. Although the only difference is the additional I41A42 residues in the C-terminus, Aβ42 exhibits more aggregation tendency and stronger neurotoxicity than Aβ40. Here, we investigate the molecular factors that confer more aggregation potential to Aβ42 than to Aβ40 based on molecular dynamics simulations combined with solvation thermodynamic analyses. It is observed that the most salient structural feature of Aβ42 relative to Aβ40 is the more enhanced β-sheet forming tendency, in particular in the C-terminal region. While such a structural characteristic of Aβ42 will certainly serve to facilitate the formation of aggregate species rich in β-sheet structure, we also detect its interesting thermodynamic consequence. Indeed, we find from the decomposition analysis that the C-terminal region substantially increases the solvation free energy (i.e., overall "hydrophobicity") of Aβ42, which is caused by the dehydration of the backbone moieties showing the enhanced tendency of forming the β-structure. Together with the two additional hydrophobic residues (I41A42), this leads to the higher solvation free energy of Aβ42, implying the larger water-mediated attraction toward the self-assembly. Thus, our computational results provide structural and thermodynamic grounds on why Aβ42 has more aggregation propensity than Aβ40 in aqueous environments.
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Affiliation(s)
- Yuxi Lin
- Department of Chemistry, The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro-47-gil 100, Yongsan-ku, Seoul, 04310, South Korea
| | - Haeri Im
- Department of Chemistry, The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro-47-gil 100, Yongsan-ku, Seoul, 04310, South Korea
| | - Le Thi Diem
- Department of Chemistry, The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro-47-gil 100, Yongsan-ku, Seoul, 04310, South Korea
| | - Sihyun Ham
- Department of Chemistry, The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro-47-gil 100, Yongsan-ku, Seoul, 04310, South Korea.
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41
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Lacabanne D, Fogeron ML, Wiegand T, Cadalbert R, Meier BH, Böckmann A. Protein sample preparation for solid-state NMR investigations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 110:20-33. [PMID: 30803692 DOI: 10.1016/j.pnmrs.2019.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 06/09/2023]
Abstract
Preparation of a protein sample for solid-state NMR is in many aspects similar to solution-state NMR approaches, mainly with respect to the need for stable isotope labeling. But the possibility of using solid-state NMR to investigate membrane proteins in (native) lipids adds the important requirement of adapted membrane-reconstitution schemes. Also, dynamic nuclear polarization and paramagnetic NMR in solids need specific schemes using metal ions and radicals. Sample sedimentation has enabled structural investigations of objects inaccessible to other structural techniques, but rotor filling using sedimentation has become increasingly complex with smaller and smaller rotors, as needed for higher and higher magic-angle spinning (MAS) frequencies. Furthermore, solid-state NMR can investigate very large proteins and their complexes without the concomitant increase in line widths, motivating the use of selective labeling and unlabeling strategies, as well as segmental labeling, to decongest spectra. The possibility of investigating sub-milligram amounts of protein today using advanced fast MAS techniques enables alternative protein synthesis schemes such as cell-free expression. Here we review these specific aspects of solid-state NMR sample preparation.
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Affiliation(s)
- Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367 Lyon, France; Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367 Lyon, France
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367 Lyon, France.
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42
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Mason TO, Buell AK. The Kinetics, Thermodynamics and Mechanisms of Short Aromatic Peptide Self-Assembly. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:61-112. [PMID: 31713197 DOI: 10.1007/978-981-13-9791-2_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The self-assembly of short aromatic peptides and peptide derivatives into a variety of different nano- and microstructures (fibrillar gels, crystals, spheres, plates) is a promising route toward the creation of bio-compatible materials with often unexpected and useful properties. Furthermore, such simple self-assembling systems have been proposed as model systems for the self-assembly of longer peptides, a process that can be linked to biological function and malfunction. Much effort has been made in the last 15 years to explore the space of peptide sequences, chemical modifications and solvent conditions in order to maximise the diversity of assembly morphologies and properties. However, quantitative studies of the corresponding mechanisms of, and driving forces for, peptide self-assembly have remained relatively scarce until recently. In this chapter we review the current state of understanding of the thermodynamic driving forces and self-assembly mechanisms of short aromatic peptides into supramolecular structures. We will focus on experimental studies of the assembly process and our perspective will be centered around diphenylalanine (FF), a key motif of the amyloid β sequence and a paradigmatic self-assembly building block. Our main focus is the basic physical chemistry and key structural aspects of such systems, and we will also compare the mechanism of dipeptide aggregation with that of longer peptide sequences into amyloid fibrils, with discussion on how these mechanisms may be revealed through detailed analysis of growth kinetics, thermodynamics and other fundamental properties of the aggregation process.
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Affiliation(s)
- Thomas O Mason
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DTU, Lyngby, Denmark.
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43
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Townsend D, Hughes E, Stewart KL, Griffin JM, Radford SE, Middleton DA. Orientation of a Diagnostic Ligand Bound to Macroscopically Aligned Amyloid-β Fibrils Determined by Solid-State NMR. J Phys Chem Lett 2018; 9:6611-6615. [PMID: 30354142 DOI: 10.1021/acs.jpclett.8b02448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
With amyloid diseases poised to become a major health burden in countries with aging populations, diagnostic molecules that aid the detection of amyloid in vitro and in vivo are of considerable clinical value. Understanding how such ligands recognize their amyloid targets would help to design diagnostics that target specific amyloid types associated with a particular disease, but methods to provide comprehensive information are underdeveloped. Here, solid-state NMR is used to determine the molecular orientation of the amyloid diagnostic 1-fluoro-2,5-bis[( E)-3-carboxy-4-hydroxystyryl]-benzene (FSB) when bound to fibrils of the Alzheimer's amyloid-β polypeptide aligned on a planar substrate. The 19F NMR spectrum of the aligned complex reveals that FSB is oriented approximately parallel with the fibril long axis and bridges four hydrogen-bonded β-sheets. In addition to providing atomic details to aid the design of amyloid-specific diagnostics, this approach will also illuminate the molecular mechanisms of accessory molecules in amyloid disease.
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Affiliation(s)
- David Townsend
- Department of Chemistry , Lancaster University , Lancaster LA1 4YB , United Kingdom
| | - Eleri Hughes
- Department of Chemistry , Lancaster University , Lancaster LA1 4YB , United Kingdom
| | - Katie L Stewart
- Department of Physics , Emory University , Atlanta , Georgia 30322 , United States
| | - John M Griffin
- Materials Science Institute , Lancaster University , Lancaster LA1 4YB , United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology , Faculty of Biological Sciences, University of Leeds , Leeds LS2 9JT , United Kingdom
| | - David A Middleton
- Department of Chemistry , Lancaster University , Lancaster LA1 4YB , United Kingdom
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44
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Buchanan LE, Maj M, Dunkelberger EB, Cheng PN, Nowick JS, Zanni MT. Structural Polymorphs Suggest Competing Pathways for the Formation of Amyloid Fibrils That Diverge from a Common Intermediate Species. Biochemistry 2018; 57:6470-6478. [PMID: 30375231 DOI: 10.1021/acs.biochem.8b00997] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
It is now recognized that many amyloid-forming proteins can associate into multiple fibril structures. Here, we use two-dimensional infrared spectroscopy to study two fibril polymorphs formed by human islet amyloid polypeptide (hIAPP or amylin), which is associated with type 2 diabetes. The polymorphs exhibit different degrees of structural organization near the loop region of hIAPP fibrils. The relative populations of these polymorphs are systematically altered by the presence of macrocyclic peptides which template β-sheet formation at specific sections of the hIAPP sequence. These experiments are consistent with polymorphs that result from competing pathways for fibril formation and that the macrocycles bias hIAPP aggregation toward one pathway or the other. Another macrocyclic peptide that matches the loop region but extends the lag time leaves the relative populations of the polymorphs unaltered, suggesting that the branching point for structural divergence occurs after the lag phase, when the oligomers convert into seeds that template fibril formation. Thus, we conclude that the structures of the polymorphs stem from restricting oligomers along diverging folding pathways, which has implications for drug inhibition, cytotoxicity, and the free energy landscape of hIAPP aggregation.
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Affiliation(s)
- Lauren E Buchanan
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States
| | - Michał Maj
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States
| | - Emily B Dunkelberger
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States
| | - Pin-Nan Cheng
- 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
| | - Martin T Zanni
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States
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45
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Copper Redox Cycling Inhibits Aβ Fibre Formation and Promotes Fibre Fragmentation, while Generating a Dityrosine Aβ Dimer. Sci Rep 2018; 8:16190. [PMID: 30385800 PMCID: PMC6212427 DOI: 10.1038/s41598-018-33935-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 10/04/2018] [Indexed: 12/22/2022] Open
Abstract
Oxidative stress and the formation of plaques which contain amyloid-β (Aβ) peptides are two key hallmarks of Alzheimer’s disease (AD). Dityrosine is found in the plaques of AD patients and Aβ dimers have been linked to neurotoxicity. Here we investigate the formation of Aβ dityrosine dimers promoted by Cu2+/+ Fenton reactions. Using fluorescence measurements and UV absorbance, we show that dityrosine can be formed aerobically when Aβ is incubated with Cu2+ and hydrogen-peroxide, or in a Cu2+ and ascorbate redox mixture. The dityrosine cross-linking can occur for both monomeric and fibrillar forms of Aβ. We show that oxidative modification of Aβ impedes the ability for Aβ monomer to form fibres, as indicated by the amyloid specific dye Thioflavin T (ThT). Transmission electron microscopy (TEM) indicates the limited amyloid assemblies that form have a marked reduction in fibre length for Aβ(1–40). Importantly, the addition of Cu2+ and a reductant to preformed Aβ(1–40) fibers causes their widespread fragmentation, reducing median fibre lengths from 800 nm to 150 nm upon oxidation. The processes of covalent cross-linking of Aβ fibres, dimer formation, and fibre fragmentation within plaques are likely to have a significant impact on Aβ clearance and neurotoxicity.
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46
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Zinke M, Fricke P, Lange S, Zinn‐Justin S, Lange A. Protein-Protein Interfaces Probed by Methyl Labeling and Proton-Detected Solid-State NMR Spectroscopy. Chemphyschem 2018; 19:2457-2460. [PMID: 29917302 PMCID: PMC6220863 DOI: 10.1002/cphc.201800542] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Indexed: 12/18/2022]
Abstract
Proton detection and fast magic-angle spinning have advanced biological solid-state NMR, allowing for the backbone assignment of complex protein assemblies with high sensitivity and resolution. However, so far no method has been proposed to detect intermolecular interfaces in these assemblies by proton detection. Herein, we introduce a concept based on methyl labeling that allows for the assignment of these moieties and for the study of protein-protein interfaces at atomic resolution.
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Affiliation(s)
- Maximilian Zinke
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Pascal Fricke
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Sascha Lange
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Sophie Zinn‐Justin
- Institute for Integrative Biology of the Cell (I2BC) CEA, CNRSUniversité Paris-Sud Université Paris-SaclayGif-sur-Yvette CedexFrance
| | - Adam Lange
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
- Institut für BiologieHumboldt-Universität zu BerlinBerlinGermany
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47
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Przygońska K, Poznański J, Mistarz UH, Rand KD, Dadlez M. Side-chain moieties from the N-terminal region of Aβ are Involved in an oligomer-stabilizing network of interactions. PLoS One 2018; 13:e0201761. [PMID: 30080867 PMCID: PMC6078298 DOI: 10.1371/journal.pone.0201761] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/20/2018] [Indexed: 12/31/2022] Open
Abstract
Oligomeric forms of the Aβ peptide represent the most probable neurotoxic agent in Alzheimer’s disease. The dynamic and heterogeneous character of these oligomers makes their structural characterization by classic methods difficult. Native mass spectrometry, when supported by additional gas phase techniques, like ion mobility separation and hydrogen-deuterium exchange (IM-HDX-MS), enable analysis of different oligomers coexisting in the sample and may provide species-specific structural information for each oligomeric form populated in the gas phase. Here, we have combined these three techniques to obtain insight into the structural properties of oligomers of Aβ1–40 and two variants with scrambled sequences. Gas-phase HDX-MS revealed a sequence-specific engagement of the side-chains of residues located at the N-terminal part of the peptide in a network of oligomer-stabilizing interactions. Oligomer-specific interactions were no longer observed in the case of the fully scrambled sequence. Also, the ability to form alternative structures, observed for WT Aβ peptide, was lost upon scrambling. Our data underscore a role for the N-terminal residues in shaping the equilibria of oligomeric forms. Although the peptide lacking the N-terminal 1–16 residues (p3 peptide) is thought to be benign, the role of the N-terminus has not been sufficiently characterized yet. We speculate that the interaction networks revealed here may be crucial for enabling structural transitions necessary to obtain mature parallel cross-β structures from smaller antiparallel oligomers. We provide a hypothetical molecular model of the trajectory that allows a gradual conversion from antiparallel to parallel oligomers without decomposition of oligomers. Oligomer-defining interactions involving the Aβ peptide N-terminus may be important in production of the neurotoxic forms and thus should not be neglected.
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Affiliation(s)
- Kaja Przygońska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Ulrik H. Mistarz
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Kasper D. Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland
- * E-mail:
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48
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Månsson C, van Cruchten RTP, Weininger U, Yang X, Cukalevski R, Arosio P, Dobson CM, Knowles T, Akke M, Linse S, Emanuelsson C. Conserved S/T Residues of the Human Chaperone DNAJB6 Are Required for Effective Inhibition of Aβ42 Amyloid Fibril Formation. Biochemistry 2018; 57:4891-4902. [DOI: 10.1021/acs.biochem.8b00353] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Cecilia Månsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, 221 00 Lund, Sweden
| | - Remco T. P. van Cruchten
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, 221 00 Lund, Sweden
| | - Ulrich Weininger
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, 221 00 Lund, Sweden
| | - Xiaoting Yang
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, 221 00 Lund, Sweden
| | - Risto Cukalevski
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, 221 00 Lund, Sweden
| | - Paolo Arosio
- Department of Chemistry and Center for Misfolding Diseases, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Christopher M. Dobson
- Department of Chemistry and Center for Misfolding Diseases, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Tuomas Knowles
- Department of Chemistry and Center for Misfolding Diseases, University of Cambridge, Cambridge CB2 1EW, U.K
- Cavendish Laboratory, Department of Physics, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Mikael Akke
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, 221 00 Lund, Sweden
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, 221 00 Lund, Sweden
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, 221 00 Lund, Sweden
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49
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Do TD, Sangwan S, de Almeida NEC, Ilitchev AI, Giammona M, Sawaya MR, Buratto SK, Eisenberg DS, Bowers MT. Distal amyloid β-protein fragments template amyloid assembly. Protein Sci 2018; 27:1181-1190. [PMID: 29349888 DOI: 10.1002/pro.3375] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/16/2018] [Accepted: 01/16/2018] [Indexed: 01/06/2023]
Abstract
Amyloid formation is associated with devastating diseases such as Alzheimer's, Parkinson's and Type-2 diabetes. The large amyloid deposits found in patients suffering from these diseases have remained difficult to probe by structural means. Recent NMR models also predict heterotypic interactions from distinct peptide fragments but limited evidence of heterotypic packed sheets is observed in solution. Here we characterize two segments of the protein amyloid β (Aβ) known to form fibrils in Alzheimer's disease patients. We designed two variants of Aβ(19-24) and Aβ(27-32), IFAEDV (I6V) and NKGAIF (N6F) to lower the aggregation propensity of individual peptides while maintaining the similar interactions between the two segments in their native forms. We found that the variants do not form significant amyloid fibrils individually but a 1:1 mixture forms abundant fibrils. Using ion mobility-mass spectrometry (IM-MS), hetero-oligomers up to decamers were found in the mixture while the individual peptides formed primarily dimers and some tetramers consistent with a strong heterotypic interaction between the two segments. We showed by X-ray crystallography that I6V formed a Class 7 zipper with a weakly packed pair of β-sheets and no segregated dry interface, while N6F formed a more stable Class 1 zipper. In a mixture of equimolar N6F:I6V, I6V forms a more stable zipper than in I6V alone while no N6F or hetero-typic zippers are observed. These data are consistent with a mechanism where N6F catalyzes assembly of I6V into a stable zipper and perhaps into stable, pure I6V fibrils that are observed in AFM measurements.
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Affiliation(s)
- Thanh D Do
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Smriti Sangwan
- Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, University of California, 611 Charles Young Drive East, Los Angeles, California
| | - Natália E C de Almeida
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Alexandre I Ilitchev
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Maxwell Giammona
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Michael R Sawaya
- Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, University of California, 611 Charles Young Drive East, Los Angeles, California
| | - Steven K Buratto
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - David S Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, University of California, 611 Charles Young Drive East, Los Angeles, California
| | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
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50
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Maj M, Lomont JP, Rich KL, Alperstein AM, Zanni MT. Site-specific detection of protein secondary structure using 2D IR dihedral indexing: a proposed assembly mechanism of oligomeric hIAPP. Chem Sci 2018; 9:463-474. [PMID: 29619202 PMCID: PMC5868010 DOI: 10.1039/c7sc03789a] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/02/2017] [Indexed: 12/19/2022] Open
Abstract
Human islet amyloid polypeptide (hIAPP) aggregates into fibrils through oligomers that have been postulated to contain α-helices as well as β-sheets. We employ a site-specific isotope labeling strategy that is capable of detecting changes in dihedral angles when used in conjunction with 2D IR spectroscopy. The method is analogous to the chemical shift index used in NMR spectroscopy for assigning protein secondary structure. We introduce isotope labels at two neighbouring residues, which results in an increased intensity and positive frequency shift if those residues are α-helical versus a negative frequency shift in β-sheets and turns. The 2D IR dihedral index approach is demonstrated for hIAPP in micelles for which the polypeptide structure is known, using pairs of 13C18O isotope labels L12A13 and L16V17, along with single labeled control experiments. Applying the approach to aggregation experiments performed in buffer, we show that about 27-38% of hIAPP peptides adopt an α-helix secondary structure in the monomeric state at L12A13, prior to aggregation, but not at L16V17 residues. At L16V17, the kinetics are described solely by the monomer and fiber conformations, but at L12A13 the kinetics exhibit a third state that is created by an oligomeric intermediate. Control experiments performed with a single isotope label at A13 exhibit two-state kinetics, indicating that a previously unknown change in dihedral angle occurs at L12A13 as hIAPP transitions from the intermediate to fiber structures. We propose a mechanism for aggregation, in which helices seed oligomer formation via structures analogous to leucine rich repeat proteins.
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Affiliation(s)
- Michał Maj
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , USA .
| | - Justin P Lomont
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , USA .
| | - Kacie L Rich
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , USA .
| | - Ariel M Alperstein
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , USA .
| | - Martin T Zanni
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , USA .
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