1
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Ghorbani M, Brooks BR, Klauda JB. Conformational Fluctuations in β2-Microglubulin Using Markov State Modeling and Molecular Dynamics. J Phys Chem B 2023; 127:6887-6895. [PMID: 37527428 DOI: 10.1021/acs.jpcb.3c02473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Conformational dynamics in proteins can give rise to aggregation prone states during folding, and these kinetically stable states could form oligomers and aggregates. In this study, we investigate the intermediate states and near-folded states of β2-microglobulin and their physico-chemical properties using molecular dynamics and Markov state modeling. Analysis of hundreds of microseconds simulation show the importance of the edge strands in the misfolded states that give rise to a high exposure of hydrophobic residues in the core of the protein that could initiate oligomerization and aggregate formation. Our study sheds light on the first step of aggregation of β2m monomers and gave a better picture of the landscape of protein misfolding and aggregation.
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Affiliation(s)
- Mahdi Ghorbani
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, United States
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
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2
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The current state of amyloidosis therapeutics and the potential role of fluorine in their treatment. Biochimie 2022; 202:123-135. [PMID: 35963462 DOI: 10.1016/j.biochi.2022.08.003] [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: 02/16/2022] [Revised: 07/22/2022] [Accepted: 08/04/2022] [Indexed: 11/22/2022]
Abstract
Amyloidosis, commonly known as amyloid-associated diseases, is characterized by improperly folded proteins accumulating in tissues and eventually causing organ damage, which is linked to several disorders ranging from neurodegenerative to peripheral diseases. It has an enormous societal and financial impact on the global health sector. Due to the complexity of protein misfolding and intertwined aggregation, there are no effective disease-modifying medications at present, and the condition is likely mis/non-diagnosed half of the time. Nonetheless, over the last two decades, substantial research into aggregation processes has revealed the possibilities of new intervention approaches. On the other hand, fluorine has been a rising star in therapeutic development for numerous neurodegenerative illnesses and other peripheral diseases. In this study, we revised and emphasized the possible significance of fluorine-modified therapeutic molecules and fluorine-modified nanoparticles (NPs) in the modulation of amyloidogenic proteins, including insulin, amyloid beta peptide (Aβ), prion protein (PrP), transthyretin (TTR) and Huntingtin (htt).
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3
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Mehta D, Singh H, Haridas V, Chaudhuri TK. Molecular Insights into the Inhibition of Dialysis-Related β2m Amyloidosis Orchestrated by a Bispidine Peptidomimetic Analogue. Biochemistry 2022; 61:1473-1484. [PMID: 35749234 DOI: 10.1021/acs.biochem.2c00205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dialysis-related amyloidosis (DRA) is considered an inescapable consequence of renal failure. Upon prolonged hemodialysis, it involves accumulation of toxic β2-microglobulin (β2m) amyloids in bones and joints. Current treatment methods are plagued with high cost, low specificity, and low capacity. Through our in vitro and in cellulo studies, we introduce a peptidomimetic-based approach to help develop future therapeutics against DRA. Our study reports the ability of a nontoxic, core-modified, bispidine peptidomimetic analogue "B(LVI)2" to inhibit acid-induced amyloid fibrillation of β2m (Hβ2m). Using thioflavin-T, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and transmission electron microscopy analysis, we demonstrate that B(LVI)2 delays aggregation lag time of Hβ2m amyloid fibrillation and reduces the yield of Hβ2m amyloid fibrils in a dose-dependent manner. Our findings suggest a B(LVI)2-orchestrated alteration in the route of Hβ2m amyloid fibrillation resulting in the formation of noncytotoxic, morphologically distinct amyloid-like species. Circular dichroism data show gradual sequestration of Hβ2m species in a soluble nonamyloidogenic noncytotoxic conformation in the presence of B(LVI)2. Dynamic light scattering measurements indicate incompetence of Hβ2m species in the presence of B(LVI)2 to undergo amyloid-competent intermolecular associations. Overall, our study reports the antifibrillation property of a novel peptidomimetic with the potential to bring a paradigm shift in therapeutic approaches against DRA.
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Affiliation(s)
- Devanshu Mehta
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Hanuman Singh
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - V Haridas
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Tapan K Chaudhuri
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India
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4
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Dang H, Chen Z, Chen W, Luo X, Liu P, Wang L, Chen J, Tang X, Wang Z, Liang Y. The residues 4 to 6 at the N-terminus in particular modulate fibril propagation of β-microglobulin. Acta Biochim Biophys Sin (Shanghai) 2021; 54:187-198. [PMID: 35130623 PMCID: PMC9909321 DOI: 10.3724/abbs.2021017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The ΔN6 truncation is the main posttranslational modification of β-microglobulin (βM) found in dialysis-related amyloid. Investigation of the interaction of wild-type (WT) βM with N-terminally truncated variants is therefore of medical relevance. However, it is unclear which residues among the six residues at the N-terminus are crucial to the interactions and the modulation of amyloid fibril propagation of βM. We herein analyzed homo- and heterotypic seeding of amyloid fibrils of WT human βM and its N-terminally-truncated variants ΔN1 to ΔN6, lacking up to six residues at the N-terminus. At acidic pH 2.5, we produced amyloid fibrils from recombinant, WT βM and its six truncated variants, and found that ΔN6 βM fibrils exhibit a significantly lower conformational stability than WT βM fibrils. Importantly, under more physiological conditions (pH 6.2), we assembled amyloid fibrils only from recombinant, ΔN4, ΔN5, and ΔN6 βM but not from WT βM and its three truncated variants ΔN1 to ΔN3. Notably, the removal of the six, five or four residues at the N-terminus leads to enhanced fibril formation, and homo- and heterotypic seeding of ΔN6 fibrils strongly promotes amyloid fibril formation of WT βM and its six truncated variants, including at more physiological pH 6.2. Collectively, these results demonstrated that the residues 4 to 6 at the N-terminus particularly modulate amyloid fibril propagation of βM and the interactions of WT βM with N-terminally truncated variants, potentially indicating the direct relevance to the involvement of the protein's aggregation in dialysis-related amyloidosis.
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Affiliation(s)
- Haibin Dang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | - Zhixian Chen
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | - Wang Chen
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | - Xudong Luo
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | | | - Liqiang Wang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | - Jie Chen
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | | | | | - Yi Liang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China,Correspondence address. Tel: +86-27-68754902; E-mail:
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5
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Hofbauer D, Mougiakakos D, Broggini L, Zaiss M, Büttner-Herold M, Bach C, Spriewald B, Neumann F, Bisht S, Nolting J, Zeiser R, Hamarsheh S, Eberhardt M, Vera J, Visentin C, De Luca CMG, Moda F, Haskamp S, Flamann C, Böttcher M, Bitterer K, Völkl S, Mackensen A, Ricagno S, Bruns H. β 2-microglobulin triggers NLRP3 inflammasome activation in tumor-associated macrophages to promote multiple myeloma progression. Immunity 2021; 54:1772-1787.e9. [PMID: 34289378 DOI: 10.1016/j.immuni.2021.07.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/28/2021] [Accepted: 06/30/2021] [Indexed: 12/15/2022]
Abstract
As substantial constituents of the multiple myeloma (MM) microenvironment, pro-inflammatory macrophages have emerged as key promoters of disease progression, bone destruction, and immune impairment. We identify beta-2-microglobulin (β2m) as a driver in initiating inflammation in myeloma-associated macrophages (MAMs). Lysosomal accumulation of phagocytosed β2m promotes β2m amyloid aggregation in MAMs, resulting in lysosomal rupture and ultimately production of active interleukin-1β (IL-1β) and IL-18. This process depends on activation of the NLRP3 inflammasome after β2m accumulation, as macrophages from NLRP3-deficient mice lack efficient β2m-induced IL-1β production. Moreover, depletion or silencing of β2m in MM cells abrogates inflammasome activation in a murine MM model. Finally, we demonstrate that disruption of NLRP3 or IL-18 diminishes tumor growth and osteolytic bone destruction normally promoted by β2m-induced inflammasome signaling. Our results provide mechanistic evidence for β2m's role as an NLRP3 inflammasome activator during MM pathogenesis. Moreover, inhibition of NLRP3 represents a potential therapeutic approach in MM.
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Affiliation(s)
- Daniel Hofbauer
- Department of Internal Medicine 5, University Hospital Erlangen, Erlangen, Germany
| | | | - Luca Broggini
- Department of Biosciences, University of Milan, Milan, Italy; Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, San Donato Milanese, Milano, Italy
| | - Mario Zaiss
- Department of Internal Medicine 3, University Hospital Erlangen, Erlangen, Germany
| | | | - Christian Bach
- Department of Internal Medicine 5, University Hospital Erlangen, Erlangen, Germany
| | - Bernd Spriewald
- Department of Internal Medicine 5, University Hospital Erlangen, Erlangen, Germany
| | - Frank Neumann
- Department of Internal Medicine 1, Saarland University Medical School, Homburg, Germany
| | - Savita Bisht
- Department of Oncology/Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Jens Nolting
- Department of Oncology/Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Robert Zeiser
- Department of Medicine 1, University of Freiburg, Freiburg, Germany
| | | | - Martin Eberhardt
- Department of Dermatology, University Hospital Erlangen, Erlangen, Germany
| | - Julio Vera
- Department of Dermatology, University Hospital Erlangen, Erlangen, Germany
| | | | - Chiara Maria Giulia De Luca
- Divisione di Neurologia 5 - Neuropatologia, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Fabio Moda
- Divisione di Neurologia 5 - Neuropatologia, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Stefan Haskamp
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Cindy Flamann
- Department of Internal Medicine 5, University Hospital Erlangen, Erlangen, Germany
| | - Martin Böttcher
- Department of Internal Medicine 5, University Hospital Erlangen, Erlangen, Germany
| | - Katrin Bitterer
- Department of Internal Medicine 5, University Hospital Erlangen, Erlangen, Germany
| | - Simon Völkl
- Department of Internal Medicine 5, University Hospital Erlangen, Erlangen, Germany
| | - Andreas Mackensen
- Department of Internal Medicine 5, University Hospital Erlangen, Erlangen, Germany
| | - Stefano Ricagno
- Department of Biosciences, University of Milan, Milan, Italy
| | - Heiko Bruns
- Department of Internal Medicine 5, University Hospital Erlangen, Erlangen, Germany.
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6
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Phyo P, Zhao X, Templeton AC, Xu W, Cheung JK, Su Y. Understanding molecular mechanisms of biologics drug delivery and stability from NMR spectroscopy. Adv Drug Deliv Rev 2021; 174:1-29. [PMID: 33609600 DOI: 10.1016/j.addr.2021.02.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/20/2021] [Accepted: 02/07/2021] [Indexed: 02/06/2023]
Abstract
Protein therapeutics carry inherent limitations of membrane impermeability and structural instability, despite their predominant role in the modern pharmaceutical market. Effective formulations are needed to overcome physiological and physicochemical barriers, respectively, for improving bioavailability and stability. Knowledge of membrane affinity, cellular internalization, encapsulation, and release of drug-loaded carrier vehicles uncover the structural basis for designing and optimizing biopharmaceuticals with enhanced delivery efficiency and therapeutic efficacy. Understanding stabilizing and destabilizing interactions between protein drugs and formulation excipients provide fundamental mechanisms for ensuring the stability and quality of biological products. This article reviews the molecular studies of biologics using solution and solid-state NMR spectroscopy on structural attributes pivotal to drug delivery and stability. In-depth investigation of the structure-function relationship of drug delivery systems based on cell-penetrating peptides, lipid nanoparticles and polymeric colloidal, and biophysical and biochemical stability of peptide, protein, monoclonal antibody, and vaccine, as the integrative efforts on drug product design, will be elaborated.
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Affiliation(s)
- Pyae Phyo
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Xi Zhao
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Allen C Templeton
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Wei Xu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Jason K Cheung
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Yongchao Su
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States.
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7
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Loureiro RJS, Faísca PFN. The Early Phase of β2-Microglobulin Aggregation: Perspectives From Molecular Simulations. Front Mol Biosci 2020; 7:578433. [PMID: 33134317 PMCID: PMC7550760 DOI: 10.3389/fmolb.2020.578433] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/08/2020] [Indexed: 11/24/2022] Open
Abstract
Protein β2-microglobulin is the causing agent of two amyloidosis, dialysis related amyloidosis (DRA), affecting the bones and cartilages of individuals with chronic renal failure undergoing long-term hemodialysis, and a systemic amyloidosis, found in one French family, which impairs visceral organs. The protein’s small size and its biomedical significance attracted the attention of theoretical scientists, and there are now several studies addressing its aggregation mechanism in the context of molecular simulations. Here, we review the early phase of β2-microglobulin aggregation, by focusing on the identification and structural characterization of monomers with the ability to trigger aggregation, and initial small oligomers (dimers, tetramers, hexamers etc.) formed in the so-called nucleation phase. We focus our analysis on results from molecular simulations and integrate our views with those coming from in vitro experiments to provide a broader perspective of this interesting field of research. We also outline directions for future computer simulation studies.
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Affiliation(s)
- Rui J S Loureiro
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal
| | - Patrícia F N Faísca
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal.,Department of Physics, Faculty of Sciences, University of Lisboa, Lisbon, Portugal
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8
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Akizuki S, Kawano K, Iwamoto T, Nakada K, Ohnishi A. Mass spectrometry of urinary β2 microglobulin oligomer in patients with proteinuria. Ther Apher Dial 2020; 25:197-203. [PMID: 32535961 DOI: 10.1111/1744-9987.13547] [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: 03/10/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 11/29/2022]
Abstract
Urinary β2 microglobulin (β2-m) is a marker of renal tubule dysfunction; however, β2-m might become degraded under acidic conditions. To confirm the degradation and consequent deactivation of β2-m under acidic conditions, we used matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) to detect the levels and forms of β2-m in the urine samples of patients with high proteinuria (n = 21) and healthy subjects (n = 6). β2-m was purified in crude form using immunoprecipitation. A signal of 11.74 kDa, corresponding to the molecular weight of β2-m, was detected in all samples. In addition, several high-molecular-weight proteins were detected in a patient as integrals of the intensity at 11.74 kDa. These results indicate that posttranslational modifications of β2-m might be involved in the pathological process of proteinuria. Therefore, MS can be used for monitoring proteinuria and predicting the risk of progression.
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Affiliation(s)
- Setsuko Akizuki
- Department of Laboratory Medicine, The Jikei University Daisan Hospital, Tokyo, Japan.,Central Clinical Laboratory, The Jikei University Daisan Hospital, Tokyo, Japan
| | - Katsumi Kawano
- RI Department, Hachioji Laboratory, SRL, Inc., Tokyo, Japan
| | - Takeo Iwamoto
- Core Research Facilities for Basic Science, Research Center for Medical Science, The Jikei University School of Medicine, Tokyo, Japan
| | - Koji Nakada
- Department of Laboratory Medicine, The Jikei University Daisan Hospital, Tokyo, Japan.,Central Clinical Laboratory, The Jikei University Daisan Hospital, Tokyo, Japan
| | - Akihiro Ohnishi
- Department of Laboratory Medicine, The Jikei University Daisan Hospital, Tokyo, Japan.,Central Clinical Laboratory, The Jikei University Daisan Hospital, Tokyo, Japan
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9
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Hoop CL, Zhu J, Bhattacharya S, Tobita CA, Radford SE, Baum J. Collagen I Weakly Interacts with the β-Sheets of β 2-Microglobulin and Enhances Conformational Exchange To Induce Amyloid Formation. J Am Chem Soc 2020; 142:1321-1331. [PMID: 31875390 PMCID: PMC7135851 DOI: 10.1021/jacs.9b10421] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Amyloidogenesis is
significant in both protein function and pathology.
Amyloid formation of folded, globular proteins is commonly initiated
by partial or complete unfolding. However, how this unfolding event
is triggered for proteins that are otherwise stable in their native
environments is not well understood. The accumulation of the immunoglobulin
protein β2-microglobulin (β2m) into
amyloid plaques in the joints of long-term hemodialysis patients is
the hallmark of dialysis-related amyloidosis (DRA). While β2m does not form amyloid unassisted near neutral pH in vitro, the localization of β2m deposits
to joint spaces suggests a role for the local extracellular matrix
(ECM) proteins, specifically collagens, in promoting amyloid formation.
Indeed, collagen and other ECM components have been observed to facilitate
β2m amyloid formation, but the large size and anisotropy
of the complex, combined with the low affinity of these interactions,
have limited atomic-level elucidation of the amyloid-promoting mechanism(s)
by these molecules. Using solution NMR approaches that uniquely probe
weak interactions in large molecular weight complexes, we are able
to map the binding interfaces on β2m for collagen
I and detect collagen I-induced μs–ms time-scale dynamics
in the β2m backbone. By combining solution NMR relaxation
methods and 15N-dark-state exchange saturation transfer
experiments, we propose a model in which weak, multimodal collagen
I−β2m interactions promote exchange with a
minor population of amyloid-competent species to induce fibrillogenesis.
The results portray the intimate role of the environment in switching
an innocuous protein into an amyloid-competent state, rationalizing
the localization of amyloid deposits in DRA.
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Affiliation(s)
- Cody L Hoop
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | - Jie Zhu
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | | | - Caitlyn A Tobita
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , U.K
| | - Jean Baum
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
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10
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Marcinko TM, Liang C, Savinov S, Chen J, Vachet RW. Structural Heterogeneity in the Preamyloid Oligomers of β-2-Microglobulin. J Mol Biol 2019; 432:396-409. [PMID: 31711963 DOI: 10.1016/j.jmb.2019.10.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/25/2019] [Accepted: 10/30/2019] [Indexed: 11/29/2022]
Abstract
In dialysis patients, the protein β2-microglobulin (β2m) forms amyloid fibrils in a condition known as dialysis-related amyloidosis. To understand the early stages of the amyloid assembly process, we have used native electrospray ionization (ESI) together with ion mobility mass spectrometry (IM-MS) to study soluble preamyloid oligomers. ESI-IM-MS reveals the presence of multiple conformers for the dimer, tetramer, and hexamer that precede the Cu(II)-induced amyloid assembly process, results which are distinct from β2m oligomers formed at low pH. Experimental and computational results indicate that the predominant dimer is a Cu(II)-bound structure with an antiparallel side-by-side configuration. In contrast, tetramers exist in solution in both Cu(II)-bound and Cu(II)-free forms. Selective depletion of Cu(II)-bound species results in two primary conformers-one that is compact and another that is more expanded. Molecular modeling and molecular dynamics simulations identify models for these two tetrameric conformers with unique interactions and interfaces that enthalpically compensate for the loss of Cu(II). Unlike with other amyloid systems in which conformational heterogeneity is often associated with different amyloid morphologies or off-pathway events, conformational heterogeneity in the tetramer seems to be a necessary aspect of Cu(II)-induced amyloid formation by β2m. Moreover, the Cu(II)-free models represent a new advance in our understanding of Cu(II) release in Cu(II)-induced amyloid formation, laying a foundation for further mechanistic studies as well as development of new inhibition strategies.
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Affiliation(s)
- Tyler M Marcinko
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States
| | - Chungwen Liang
- Computational and Modeling Core Facility, Institute for Applied Life Sciences, Amherst, MA 01003, United States
| | - Sergey Savinov
- Computational and Modeling Core Facility, Institute for Applied Life Sciences, Amherst, MA 01003, United States; Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, United States
| | - Jianhen Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States; Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States.
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11
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Narang SS, Shuaib S, Goyal D, Goyal B. In silico-guided identification of potential inhibitors against β2m aggregation in dialysis-related amyloidosis. J Biomol Struct Dyn 2019; 38:3927-3941. [DOI: 10.1080/07391102.2019.1668852] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Simranjeet Singh Narang
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Suniba Shuaib
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry and Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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12
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Karamanos TK, Jackson MP, Calabrese AN, Goodchild SC, Cawood EE, Thompson GS, Kalverda AP, Hewitt EW, Radford SE. Structural mapping of oligomeric intermediates in an amyloid assembly pathway. eLife 2019; 8:46574. [PMID: 31552823 PMCID: PMC6783270 DOI: 10.7554/elife.46574] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 09/24/2019] [Indexed: 01/02/2023] Open
Abstract
Transient oligomers are commonly formed in the early stages of amyloid assembly. Determining the structure(s) of these species and defining their role(s) in assembly is key to devising new routes to control disease. Here, using a combination of chemical kinetics, NMR spectroscopy and other biophysical methods, we identify and structurally characterize the oligomers required for amyloid assembly of the protein ΔN6, a truncation variant of human β2-microglobulin (β2m) found in amyloid deposits in the joints of patients with dialysis-related amyloidosis. The results reveal an assembly pathway which is initiated by the formation of head-to-head non-toxic dimers and hexamers en route to amyloid fibrils. Comparison with inhibitory dimers shows that precise subunit organization determines amyloid assembly, while dynamics in the C-terminal strand hint to the initiation of cross-β structure formation. The results provide a detailed structural view of early amyloid assembly involving structured species that are not cytotoxic.
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Affiliation(s)
- Theodoros K Karamanos
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Matthew P Jackson
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Antonio N Calabrese
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Sophia C Goodchild
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Emma E Cawood
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Gary S Thompson
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Arnout P Kalverda
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Eric W Hewitt
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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13
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Benseny-Cases N, Karamanos TK, Hoop CL, Baum J, Radford SE. Extracellular matrix components modulate different stages in β 2-microglobulin amyloid formation. J Biol Chem 2019; 294:9392-9401. [PMID: 30996004 PMCID: PMC6579475 DOI: 10.1074/jbc.ra119.008300] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/09/2019] [Indexed: 11/26/2022] Open
Abstract
Amyloid deposition of WT human β2-microglobulin (WT-hβ2m) in the joints of long-term hemodialysis patients is the hallmark of dialysis-related amyloidosis. In vitro, WT-hβ2m does not form amyloid fibrils at physiological pH and temperature unless co-solvents or other reagents are added. Therefore, understanding how fibril formation is initiated and maintained in the joint space is important for elucidating WT-hβ2m aggregation and dialysis-related amyloidosis onset. Here, we investigated the roles of collagen I and the commonly administered anticoagulant, low-molecular-weight (LMW) heparin, in the initiation and subsequent aggregation phases of WT-hβ2m in physiologically relevant conditions. Using thioflavin T fluorescence to study the kinetics of amyloid formation, we analyzed how these two agents affect specific stages of WT-hβ2m assembly. Our results revealed that LMW-heparin strongly promotes WT-hβ2m fibrillogenesis during all stages of aggregation. However, collagen I affected WT-hβ2m amyloid formation in contrasting ways: decreasing the lag time of fibril formation in the presence of LMW-heparin and slowing the rate at higher concentrations. We found that in self-seeded reactions, interaction of collagen I with WT-hβ2m amyloid fibrils attenuates surface-mediated growth of WT-hβ2m fibrils, demonstrating a key role of secondary nucleation in WT-hβ2m amyloid formation. Interestingly, collagen I fibrils did not suppress surface-mediated assembly of WT-hβ2m monomers when cross-seeded with fibrils formed from the N-terminally truncated variant ΔN6-hβ2m. Together, these results provide detailed insights into how collagen I and LMW-heparin impact different stages in the aggregation of WT-hβ2m into amyloid, which lead to dramatic effects on the time course of assembly.
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Affiliation(s)
- Núria Benseny-Cases
- From the Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Theodoros K Karamanos
- From the Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Cody L Hoop
- the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
| | - Jean Baum
- the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
| | - Sheena E Radford
- From the Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom and
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14
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Dongmo Foumthuim CJ, Corazza A, Esposito G, Fogolari F. Molecular dynamics simulations of β2-microglobulin interaction with hydrophobic surfaces. MOLECULAR BIOSYSTEMS 2018; 13:2625-2637. [PMID: 29051937 DOI: 10.1039/c7mb00464h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Hydrophobic surfaces are known to adsorb and unfold proteins, a process that has been studied only for a few proteins. Here we address the interaction of β2-microglobulin, a paradigmatic protein for the study of amyloidogenesis, with hydrophobic surfaces. A system with 27 copies of the protein surrounded by a model cubic hydrophobic box is studied by implicit solvent molecular dynamics simulations. Most proteins adsorb on the walls of the box without major distortions in local geometry, whereas free molecules maintain proper structures and fluctuations as observed in explicit solvent molecular dynamics simulations. The major conclusions from the simulations are as follows: (i) the adopted implicit solvent model is adequate to describe protein dynamics and thermodynamics; (ii) adsorption occurs readily and is irreversible on the simulated timescale; (iii) the regions most involved in molecular encounters and stable interactions with the walls are the same as those that are important in protein-protein and protein-nanoparticle interactions; (iv) unfolding following adsorption occurs at regions found to be flexible by both experiments and simulations; (v) thermodynamic analysis suggests a very large contribution from van der Waals interactions, whereas unfavorable electrostatic interactions are not found to contribute much to adsorption energy. Surfaces with different degrees of hydrophobicity may occur in vivo. Our simulations show that adsorption is a fast and irreversible process which is accompanied by partial unfolding. The results and the thermodynamic analysis presented here are consistent with and rationalize previous experimental work.
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15
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Narang SS, Shuaib S, Goyal B. Molecular insights into the inhibitory mechanism of rifamycin SV against β 2 –microglobulin aggregation: A molecular dynamics simulation study. Int J Biol Macromol 2017; 102:1025-1034. [DOI: 10.1016/j.ijbiomac.2017.04.086] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/24/2017] [Accepted: 04/24/2017] [Indexed: 01/30/2023]
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16
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Kiran Kumar E, Prasad DK, Prakash Prabhu N. Concentration dependent switch in the kinetic pathway of lysozyme fibrillation: Spectroscopic and microscopic analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 183:187-194. [PMID: 28448956 DOI: 10.1016/j.saa.2017.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 03/09/2017] [Accepted: 04/14/2017] [Indexed: 06/07/2023]
Abstract
Formation of amyloid fibrils is found to be a general tendency of many proteins. Investigating the kinetic mechanisms and structural features of the intermediates and the final fibrillar state is essential to understand their role in amyloid diseases. Lysozyme, a notable model protein for amyloidogenic studies, readily formed fibrils in vitro at neutral pH in the presence of urea. It, however, showed two different kinetic pathways under varying urea concentrations when probed with thioflavin T (ThT) fluorescence. In 2M urea, lysozyme followed a nucleation-dependent fibril formation pathway which was not altered by varying the protein concentration from 2mg/ml to 8mg/ml. In 4M urea, the protein exhibited concentration dependent change in the mechanism. At lower protein concentrations, lysozyme formed fibrils without any detectable nuclei (nucleation-independent polymerization pathway). When the concentration of the protein was increased above 3mg/ml, the protein followed nucleation-dependent polymerization pathway as observed in the case of 2M urea condition. This was further verified using microscopic images of the fibrils. The kinetic parameters such as lag time, elongation rate, and fibrillation half-time, which were derived from ThT fluorescence changes, showed linear dependency against the initial protein concentration suggested that under the nucleation-dependent pathway conditions, the protein followed primary-nucleation mechanism without any significant secondary nucleation events. The results also suggested that the differences in the initial protein conformation might alter the mechanism of fibrillation; however, at the higher protein concentrations lysozyme shifted to nucleation-dependent pathway.
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Affiliation(s)
- E Kiran Kumar
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Deepak Kumar Prasad
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - N Prakash Prabhu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India.
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17
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Narang SS, Shuaib S, Goyal D, Goyal B. Assessing the effect of D59P mutation in the DE loop region in amyloid aggregation propensity of β2‐microglobulin: A molecular dynamics simulation study. J Cell Biochem 2017; 119:782-792. [DOI: 10.1002/jcb.26241] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 06/27/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Simranjeet S. Narang
- Department of Chemistry School of Basic and Applied Sciences Sri Guru Granth Sahib World University Punjab India
| | - Suniba Shuaib
- Department of Chemistry School of Basic and Applied Sciences Sri Guru Granth Sahib World University Punjab India
| | - Deepti Goyal
- Department of Chemistry School of Basic and Applied Sciences Sri Guru Granth Sahib World University Punjab India
| | - Bhupesh Goyal
- Department of Chemistry School of Basic and Applied Sciences Sri Guru Granth Sahib World University Punjab India
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18
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Young LM, Tu LH, Raleigh DP, Ashcroft AE, Radford SE. Understanding co-polymerization in amyloid formation by direct observation of mixed oligomers. Chem Sci 2017; 8:5030-5040. [PMID: 28970890 PMCID: PMC5613229 DOI: 10.1039/c7sc00620a] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/03/2017] [Indexed: 12/15/2022] Open
Abstract
Although amyloid assembly in vitro is commonly investigated using single protein sequences, fibril formation in vivo can be more heterogeneous, involving co-assembly of proteins of different length, sequence and/or post-translational modifications. Emerging evidence suggests that co-polymerization can alter the rate and/or mechanism of aggregation and can contribute to pathogenicity. Electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is uniquely suited to the study of these heterogeneous ensembles. Here, ESI-IMS-MS combined with analysis of fibrillation rates using thioflavin T (ThT) fluorescence, is used to track the course of aggregation of variants of islet-amyloid polypeptide (IAPP) in isolation and in pairwise mixtures. We identify a sub-population of extended monomers as the key precursors of amyloid assembly, and reveal that the fastest aggregating sequence in peptide mixtures determines the lag time of fibrillation, despite being unable to cross-seed polymerization. The results demonstrate that co-polymerization of IAPP sequences radically alters the rate of amyloid assembly by altering the conformational properties of the mixed oligomers that form.
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Affiliation(s)
- Lydia M Young
- Astbury Centre for Structural Molecular Biology , School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , UK .
| | - Ling-Hsien Tu
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794-3400 , USA
- Genomics Research Center , Academia Sinica , 128 Academia , Taipei 11529 , Taiwan
| | - Daniel P Raleigh
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794-3400 , USA
| | - Alison E Ashcroft
- 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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19
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Proline Residues as Switches in Conformational Changes Leading to Amyloid Fibril Formation. Int J Mol Sci 2017; 18:ijms18030549. [PMID: 28272335 PMCID: PMC5372565 DOI: 10.3390/ijms18030549] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/20/2017] [Accepted: 02/23/2017] [Indexed: 12/15/2022] Open
Abstract
Here we discuss studies of the structure, folding, oligomerization and amyloid fibril formation of several proline mutants of human stefin B, which is a protein inhibitor of lysosomal cysteine cathepsins and a member of the cystatin family. The structurally important prolines in stefin B are responsible for the slow folding phases and facilitate domain swapping (Pro 74) and loop swapping (Pro 79). Moreover, our findings are compared to β2-microglobulin, a protein involved in dialysis-related amyloidosis. The assessment of the contribution of proline residues to the process of amyloid fibril formation may shed new light on the critical molecular events involved in conformational disorders.
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20
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Narang D, Singh A, Mukhopadhyay S. Stepwise unfolding of human β2-microglobulin into a disordered amyloidogenic precursor at low pH. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:65-76. [DOI: 10.1007/s00249-016-1138-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/20/2016] [Accepted: 05/10/2016] [Indexed: 02/08/2023]
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21
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Karamanos TK, Pashley CL, Kalverda AP, Thompson GS, Mayzel M, Orekhov VY, Radford SE. A Population Shift between Sparsely Populated Folding Intermediates Determines Amyloidogenicity. J Am Chem Soc 2016; 138:6271-80. [PMID: 27117876 PMCID: PMC4922733 DOI: 10.1021/jacs.6b02464] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The balance between protein folding and misfolding is a crucial determinant of amyloid assembly. Transient intermediates that are sparsely populated during protein folding have been identified as key players in amyloid aggregation. However, due to their ephemeral nature, structural characterization of these species remains challenging. Here, using the power of nonuniformly sampled NMR methods we investigate the folding pathway of amyloidogenic and nonamyloidogenic variants of β2-microglobulin (β2m) in atomic detail. Despite folding via common intermediate states, we show that the decreased population of the aggregation-prone ITrans state and population of a less stable, more dynamic species ablate amyloid formation by increasing the energy barrier for amyloid assembly. The results show that subtle changes in conformational dynamics can have a dramatic effect in determining whether a protein is amyloidogenic, without perturbation of the mechanism of protein folding.
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Affiliation(s)
- Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, U.K
| | - Clare L Pashley
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, U.K
| | - Arnout P Kalverda
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, U.K
| | - Gary S Thompson
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, U.K
| | - Maxim Mayzel
- The Swedish NMR Centre, University of Gothenburg , Box 465, 40530 Göteborg, Sweden
| | - Vladislav Y Orekhov
- The Swedish NMR Centre, University of Gothenburg , Box 465, 40530 Göteborg, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg , Box 465, 40530 Göteborg, Sweden
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, U.K
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22
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P C, R R. A systematic molecular dynamics approach to the structural characterization of amyloid aggregation propensity of β2-microglobulin mutant D76N. MOLECULAR BIOSYSTEMS 2016; 12:850-9. [DOI: 10.1039/c5mb00759c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Beta-2 microglobulin (β2m) is an amyloidogenic protein belonging to the immunoglobulin superfamily, responsible for the dialysis-related amyloidosis (DRA).
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Affiliation(s)
- Chandrasekaran P
- Bioinformatics Division
- School of Biosciences and Technology
- VIT University
- Vellore 632 014
- India
| | - Rajasekaran R
- Bioinformatics Division
- School of Biosciences and Technology
- VIT University
- Vellore 632 014
- India
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23
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Halabelian L, Relini A, Barbiroli A, Penco A, Bolognesi M, Ricagno S. A covalent homodimer probing early oligomers along amyloid aggregation. Sci Rep 2015; 5:14651. [PMID: 26420657 PMCID: PMC4588566 DOI: 10.1038/srep14651] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/02/2015] [Indexed: 11/20/2022] Open
Abstract
Early oligomers are crucial in amyloid aggregation; however, due to their transient nature they are among the least structurally characterized species. We focused on the amyloidogenic protein beta2-microglobulin (β2m) whose early oligomers are still a matter of debate. An intermolecular interaction between D strands of facing β2m molecules was repeatedly observed, suggesting that such interface may be relevant for β2m dimerization. In this study, by mutating Ser33 to Cys, and assembling the disulphide-stabilized β2m homodimer (DimC33), such DD strand interface was locked. Although the isolated DimC33 display a stability similar to wt β2m under native conditions, it shows enhanced amyloid aggregation propensity. Three distinct crystal structures of DimC33 suggest that dimerization through the DD interface is instrumental for enhancing DimC33 aggregation propensity. Furthermore, the crystal structure of DimC33 in complex with the amyloid-specific dye Thioflavin-T pinpoints a second interface, which likely participates in the first steps of β2m aggregation. The present data provide new insight into β2m early steps of amyloid aggregation.
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Affiliation(s)
- Levon Halabelian
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Annalisa Relini
- Dipartimento di Fisica, Università di Genova, via Dodecaneso 33, 16146 Genova, Italy
| | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, via Celoria 2, 20133 Milan, Italy
| | - Amanda Penco
- Dipartimento di Fisica, Università di Genova, via Dodecaneso 33, 16146 Genova, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.,CIMAINA e Istituto CNR di Biofisica, Milano, Italy
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
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24
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Structural and Thermodynamic Characteristics of Amyloidogenic Intermediates of β-2-Microglobulin. Sci Rep 2015; 5:13631. [PMID: 26348154 PMCID: PMC4562173 DOI: 10.1038/srep13631] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 08/07/2015] [Indexed: 12/27/2022] Open
Abstract
β-2-microglobulin (β2m) self-aggregates to form amyloid fibril in renal patients taking long-term dialysis treatment. Despite the extensive structural and mutation studies carried out so far, the molecular details on the factors that dictate amyloidogenic potential of β2m remain elusive. Here we report molecular dynamics simulations followed by the solvation thermodynamic analyses on the wild-type β2m and D76N, D59P, and W60C mutants at the native (N) and so-called aggregation-prone intermediate (IT) states, which are distinguished by the native cis- and non-native trans-Pro32 backbone conformations. Three major structural and thermodynamic characteristics of the IT-state relative to the N-state in β2m protein are detected that contribute to the increased amyloidogenic potential: (i) the disruption of the edge D-strand, (ii) the increased solvent-exposed hydrophobic interface, and (iii) the increased solvation free energy (less affinity toward solvent water). Mutation effects on these three factors are shown to exhibit a good correlation with the experimentally observed distinct amyloidogenic propensity of the D76N (+), D59P (+), and W60C (−) mutants (+/− for enhanced/decreased). Our analyses thus identify the structural and thermodynamic characteristics of the amyloidogenic intermediates, which will serve to uncover molecular mechanisms and driving forces in β2m amyloid fibril formation.
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25
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Bertoletti L, Bisceglia F, Colombo R, Giorgetti S, Raimondi S, Mangione PP, De Lorenzi E. Capillary electrophoresis analysis of different variants of the amyloidogenic protein β2 -microglobulin as a simple tool for misfolding and stability studies. Electrophoresis 2015; 36:2465-72. [PMID: 26084573 DOI: 10.1002/elps.201500148] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/13/2015] [Accepted: 05/21/2015] [Indexed: 11/07/2022]
Abstract
Free solution capillary electrophoresis with UV detection is here used to retrieve information on the conformational changes of wild-type β2 -microglobulin and a series of naturally and artificially created variants known to have different stability and amyloidogenic potential. Under nondenaturing conditions, the resolution of at least two folding conformers at equilibrium is obtained and a third species is detected for the less stable isoforms. Partial denaturation by using chaotropic agents such as acetonitrile or trifluoroethanol reveals that the separated peaks are at equilibrium, as the presence of less structured species is either enhanced or induced at the expenses of the native form. Reproducible CE data allow to obtain an interesting semiquantitative correlation between the peak areas observed and the protein stability. Thermal unfolding over the range 25-42°C is induced inside the capillary for the two pathogenic proteins (wtβ2 -microglobulin and D76N variant): the large differences observed upon small temperature variation draw attention on the robustness of analytical methods when dealing with proteins prone to misfolding and aggregation.
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Affiliation(s)
| | | | | | - Sofia Giorgetti
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Sara Raimondi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - P Patrizia Mangione
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.,Centre for Amyloidosis and Acute Phase Proteins, University College London, London, UK
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26
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Torbeev V, Ebert MO, Dolenc J, Hilvert D. Substitution of proline32 by α-methylproline preorganizes β2-microglobulin for oligomerization but not for aggregation into amyloids. J Am Chem Soc 2015; 137:2524-35. [PMID: 25633201 DOI: 10.1021/ja510109p] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Conversion of soluble folded proteins into insoluble amyloids generally proceeds in three distinct mechanistic stages: (1) initial protein misfolding into aggregation-competent conformers, (2) subsequent formation of oligomeric species and, finally, (3) self-assembly into extended amyloid fibrils. In the work reported herein, we interrogated the amyloidogenesis mechanism of human β2-microglobulin (β2m), which is thought to be triggered by a pivotal cis-trans isomerization of a proline residue at position 32 in the polypeptide, with nonstandard amino acids. Using chemical protein synthesis we prepared a β2m analogue in which Pro32 was replaced by the conformationally constrained amino acid α-methylproline (MePro). The strong propensity of MePro to adopt a trans prolyl bond led to enhanced population of a non-native [trans-MePro32]β2m protein conformer, which readily formed oligomers at neutral pH. In the presence of the antibiotic rifamycin SV, which inhibits amyloid growth of wild-type β2m, [MePro32]β2m was nearly quantitatively converted into different spherical oligomeric species. Self-assembly into amyloid fibrils was not observed in the absence of seeding, however, even at low pH (<3), where wild-type β2m spontaneously forms amyloids. Nevertheless, we found that aggregation-preorganized [MePro32]β2m can act in a prion-like fashion, templating misfolded conformations in a natively folded protein. Overall, these results provide detailed insight into the role of cis-trans isomerization of Pro32 and ensuing structural rearrangements that lead to initial β2m misfolding and aggregation. They corroborate the view that conformational protein dynamics enabled by reversible Pro32 cis-trans interconversion rather than simple population of the trans conformer is critical for both nucleation and subsequent growth of β2m amyloid structures.
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Affiliation(s)
- Vladimir Torbeev
- Laboratory of Organic Chemistry and ‡Laboratory of Physical Chemistry, ETH Zurich , Zurich CH-8093, Switzerland
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27
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Yamada M, Hara S, Yamada T, Katagiri F, Hozumi K, Nomizu M. Double-stranded DNA stereoselectively promotes aggregation of amyloid-like fibrils and generates peptide/DNA matrices. Biopolymers 2014; 102:465-72. [DOI: 10.1002/bip.22571] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 09/22/2014] [Accepted: 09/27/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Masanori Yamada
- Department of Chemistry, Faculty of Science; Okayama University of Science; Ridaicho, Kita-ku Okayama 700-0005 Japan
| | - Sachiko Hara
- Department of Chemistry, Faculty of Science; Okayama University of Science; Ridaicho, Kita-ku Okayama 700-0005 Japan
| | - Tetsuya Yamada
- Research Faculty of Agriculture; Hokkaido University; Sapporo 060-8589 Japan
| | - Fumihiko Katagiri
- School of Pharmacy; Tokyo University of Pharmacy and Life Sciences; Hachioji Tokyo 192-0392 Japan
| | - Kentaro Hozumi
- School of Pharmacy; Tokyo University of Pharmacy and Life Sciences; Hachioji Tokyo 192-0392 Japan
| | - Motoyoshi Nomizu
- School of Pharmacy; Tokyo University of Pharmacy and Life Sciences; Hachioji Tokyo 192-0392 Japan
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28
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Sarell CJ, Karamanos TK, White SJ, Bunka DHJ, Kalverda AP, Thompson GS, Barker AM, Stockley PG, Radford SE. Distinguishing closely related amyloid precursors using an RNA aptamer. J Biol Chem 2014; 289:26859-26871. [PMID: 25100729 PMCID: PMC4175327 DOI: 10.1074/jbc.m114.595066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although amyloid fibrils assembled in vitro commonly involve a single protein, fibrils formed in vivo can contain multiple protein sequences. The amyloidogenic protein human β2-microglobulin (hβ2m) can co-polymerize with its N-terminally truncated variant (ΔN6) in vitro to form hetero-polymeric fibrils that differ from their homo-polymeric counterparts. Discrimination between the different assembly precursors, for example by binding of a biomolecule to one species in a mixture of conformers, offers an opportunity to alter the course of co-assembly and the properties of the fibrils formed. Here, using hβ2m and its amyloidogenic counterpart, ΔΝ6, we describe selection of a 2'F-modified RNA aptamer able to distinguish between these very similar proteins. SELEX with a N30 RNA pool yielded an aptamer (B6) that binds hβ2m with an EC50 of ∼200 nM. NMR spectroscopy was used to assign the (1)H-(15)N HSQC spectrum of the B6-hβ2m complex, revealing that the aptamer binds to the face of hβ2m containing the A, B, E, and D β-strands. In contrast, binding of B6 to ΔN6 is weak and less specific. Kinetic analysis of the effect of B6 on co-polymerization of hβ2m and ΔN6 revealed that the aptamer alters the kinetics of co-polymerization of the two proteins. The results reveal the potential of RNA aptamers as tools for elucidating the mechanisms of co-assembly in amyloid formation and as reagents able to discriminate between very similar protein conformers with different amyloid propensity.
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Affiliation(s)
- Claire J Sarell
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Simon J White
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - David H J Bunka
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Arnout P Kalverda
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Gary S Thompson
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Amy M Barker
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
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Estácio SG, Krobath H, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, Faísca PFN. A simulated intermediate state for folding and aggregation provides insights into ΔN6 β2-microglobulin amyloidogenic behavior. PLoS Comput Biol 2014; 10:e1003606. [PMID: 24809460 PMCID: PMC4014404 DOI: 10.1371/journal.pcbi.1003606] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 03/16/2014] [Indexed: 01/26/2023] Open
Abstract
A major component of ex vivo amyloid plaques of patients with dialysis-related amyloidosis (DRA) is a cleaved variant of β2-microglobulin (ΔN6) lacking the first six N-terminal residues. Here we perform a computational study on ΔN6, which provides clues to understand the amyloidogenicity of the full-length β2-microglobulin. Contrary to the wild-type form, ΔN6 is able to efficiently nucleate fibrillogenesis in vitro at physiological pH. This behavior is enhanced by a mild acidification of the medium such as that occurring in the synovial fluid of DRA patients. Results reported in this work, based on molecular simulations, indicate that deletion of the N-terminal hexapeptide triggers the formation of an intermediate state for folding and aggregation with an unstructured strand A and a native-like core. Strand A plays a pivotal role in aggregation by acting as a sticky hook in dimer assembly. This study further predicts that the detachment of strand A from the core is maximized at pH 6.2 resulting into higher aggregation efficiency. The structural mapping of the dimerization interface suggests that Tyr10, His13, Phe30 and His84 are hot-spot residues in ΔN6 amyloidogenesis. Dialysis-related amyloidosis (DRA) is a conformational disease that affects individuals undergoing long-term haemodialysis. In DRA the progressive accumulation of protein human β2-microglobulin (Hβ2m) in the osteoarticular system, followed by its assembly into amyloid fibrils, eventually leads to tissue erosion and destruction. Disclosing the aggregation mechanism of Hβ2m under physiologically relevant conditions represents a major challenge due to the inability of the protein to efficiently nucleate fibrillogenesis in vitro at physiological pH. On the other hand, ΔN6, a truncated variant of Hβ2m, which is also a major component of ex vivo amyloid deposits extracted from DRA patients, is able to efficiently form amyloid fibrils de novo in physiological conditions. This amyloidogenic behavior is dramatically enhanced in a slightly more acidic pH (6.2) compatible with the mild acidification that occurs in the synovial fluid of DRA patients. In this work, an innovative three-stage methodological approach, relying on an array of molecular simulations, spanning different levels of resolution is used to investigate the initial stage of the de novo aggregation mechanism of ΔN6 in a physiologically relevant pH range. We identify an intermediate state for folding and aggregation, whose potential to dimerize is enhanced at pH 6.2. Our results provide rationalizations for previous experimental observations and new insights into the molecular basis of DRA.
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Affiliation(s)
- Sílvia G. Estácio
- Centro de Física da Matéria Condensada & Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Heinrich Krobath
- Centro de Física da Matéria Condensada & Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Diogo Vila-Viçosa
- Centro de Química e Bioquímica & Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica & Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Eugene I. Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail: (EIS); (PFNF)
| | - Patrícia F. N. Faísca
- Centro de Física da Matéria Condensada & Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- * E-mail: (EIS); (PFNF)
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30
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Conformer-specific characterization of nonnative protein states using hydrogen exchange and top-down mass spectrometry. Proc Natl Acad Sci U S A 2013; 110:20087-92. [PMID: 24277803 DOI: 10.1073/pnas.1315029110] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Characterization of structure and dynamics of nonnative protein states is important for understanding molecular mechanisms of processes as diverse as folding, binding, aggregation, and enzyme catalysis to name just a few; however, selectively probing local minima within rugged energy landscapes remains a problem. Mass spectrometry (MS) coupled with hydrogen/deuterium exchange (HDX) offers a unique advantage of being able to make a distinction among multiple protein conformers that coexist in solution; however, detailed structural interrogation of such states previously remained out of reach of HDX MS. In this work, we exploited the aforementioned unique feature of HDX MS in combination with the ability of MS to isolate narrow populations of protein ions to characterize individual protein conformers coexisting in solution in equilibrium. Subsequent fragmentation of the protein ions using electron-capture dissociation allowed us to allocate the deuterium distribution along the protein backbone, yielding a backbone-amide protection map for the selected conformer unaffected by contributions from other protein states present in solution. The method was tested with the small regulatory protein ubiquitin (Ub), which is known to form nonnative intermediate states under a variety of mildly denaturing conditions. Protection maps of these intermediate states obtained at residue-level resolution provide clear evidence that they are very similar to the so-called A-state of Ub that is formed in solutions with low pH and high alcohol. Method validation was carried out by comparing the backbone-amide protection map of native Ub with those deduced from high-resolution NMR measurements.
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31
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Sarell CJ, Stockley PG, Radford SE. Assessing the causes and consequences of co-polymerization in amyloid formation. Prion 2013; 7:359-68. [PMID: 24025483 PMCID: PMC4134340 DOI: 10.4161/pri.26415] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
How, and why, different proteins form amyloid fibrils is most often studied in vitro using a single purified protein sequence. However, many amyloid diseases involve co-aggregation of different protein species, including proteins with/without post-translational modifications (e.g., different strains of PrP), proteins of different length (e.g., β₂-microglobulin and ΔN6, Aβ40, and Aβ42), sequence variants (e.g., Aβ and Aβ(ARC)), and proteins from different organisms (e.g., bovine PrP and human PrP). The consequences of co-aggregation of different proteins upon the structure, stability, species transmission and toxicity of the resulting amyloid aggregates is discussed here, including the role of co-aggregation in expanding the repertoire of oligomeric and fibrillar structures and how this can affect their biological and biophysical properties.
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Affiliation(s)
- Claire J Sarell
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology; University of Leeds; Leeds, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology; University of Leeds; Leeds, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology; University of Leeds; Leeds, UK
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32
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Assessing the effect of loop mutations in the folding space of β2-microglobulin with molecular dynamics simulations. Int J Mol Sci 2013; 14:17256-78. [PMID: 23975166 PMCID: PMC3794727 DOI: 10.3390/ijms140917256] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 07/27/2013] [Accepted: 07/30/2013] [Indexed: 12/15/2022] Open
Abstract
We use molecular dynamics simulations of a full atomistic Gō model to explore the impact of selected DE-loop mutations (D59P and W60C) on the folding space of protein human β2-microglobulin (Hβ2m), the causing agent of dialysis-related amyloidosis, a conformational disorder characterized by the deposition of insoluble amyloid fibrils in the osteoarticular system. Our simulations replicate the effect of mutations on the thermal stability that is observed in experiments in vitro. Furthermore, they predict the population of a partially folded state, with 60% of native internal free energy, which is akin to a molten globule. In the intermediate state, the solvent accessible surface area increases up to 40 times relative to the native state in 38% of the hydrophobic core residues, indicating that the identified species has aggregation potential. The intermediate state preserves the disulfide bond established between residue Cys25 and residue Cys80, which helps maintain the integrity of the core region, and is characterized by having two unstructured termini. The movements of the termini dominate the essential modes of the intermediate state, and exhibit the largest displacements in the D59P mutant, which is the most aggregation prone variant. PROPKA predictions of pKa suggest that the population of the intermediate state may be enhanced at acidic pH explaining the larger amyloidogenic potential observed in vitro at low pH for the WT protein and mutant forms.
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33
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Bertoletti L, Regazzoni L, Aldini G, Colombo R, Abballe F, Caccialanza G, De Lorenzi E. Separation and characterisation of beta2-microglobulin folding conformers by ion-exchange liquid chromatography and ion-exchange liquid chromatography–mass spectrometry. Anal Chim Acta 2013; 771:108-14. [DOI: 10.1016/j.aca.2013.01.058] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 01/29/2013] [Accepted: 01/31/2013] [Indexed: 01/07/2023]
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34
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The role of amyloidogenic protein oligomerization in neurodegenerative disease. J Mol Med (Berl) 2013; 91:653-64. [PMID: 23529761 DOI: 10.1007/s00109-013-1025-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 02/20/2013] [Accepted: 03/12/2013] [Indexed: 02/07/2023]
Abstract
A common pathological hallmark in many neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and Huntington's disease, is the formation of fibrillar protein aggregates referred to as amyloids. The amyloidogenic aggregates were long thought to be toxic, but mounting evidence supports the notion that a variety of amyloid aggregate intermediates to fibril formation, termed oligomers, may in fact be the primary culprit leading to neuronal dysfunction and cell death. While amyloid formation is a complex, heterogeneous process, aggregates formed by diverse, diseases-related proteins share many conformational similarities, suggesting common toxic mechanisms among these diseases. Ideally, similar therapeutic strategies may be applicable. This review focuses on the potential role of amyloidogenic oligomers in neurodegenerative disease, highlighting some promising therapeutic strategies.
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35
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Lapidus LJ. Understanding protein aggregation from the view of monomer dynamics. MOLECULAR BIOSYSTEMS 2012; 9:29-35. [PMID: 23104145 DOI: 10.1039/c2mb25334h] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Much work in recent years has been devoted to understanding the complex process of protein aggregation. This review looks at the earliest stages of aggregation, long before the formation of fibrils that are the hallmark of many aggregation-based diseases, and proposes that the first steps are controlled by the reconfiguration dynamics of the monomer. When reconfiguration is much faster or much slower than bimolecular diffusion, then aggregation is slow, but when they are similar, aggregation is fast. The experimental evidence for this model is reviewed and the prospects for small molecule aggregation inhibitors to prevent disease are discussed.
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Affiliation(s)
- Lisa J Lapidus
- Department of Physics and Astronomy and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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36
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Hee CS, Fabian H, Uchanska-Ziegler B, Ziegler A, Loll B. Comparative biophysical characterization of chicken β2-microglobulin. Biophys Chem 2012; 167:26-35. [PMID: 22695053 DOI: 10.1016/j.bpc.2012.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 04/02/2012] [Accepted: 04/05/2012] [Indexed: 01/24/2023]
Abstract
β(2)-microglobulin (β(2)m) is the smallest building block of molecules belonging to the immunoglobulin superfamily. By comparing thermodynamic and structural characteristics of chicken β(2)m with those of other species, we seek to elucidate whether it is possible to pinpoint features that set the avian protein apart from other β(2)m. The thermodynamic assays revealed that chicken β(2)m exhibits a lower melting temperature than human β(2)m, and the H/D exchange behavior observed by infrared spectroscopy indicates a more flexible structure of the former protein. To understand these differences at a molecular level, we determined the structure of free chicken β(2)m by X-ray crystallography to a resolution of 2.0 Å. Our comparisons indicate that certain biophysical characteristics of the chicken protein, particularly its conformational flexibility, diverge considerably from those of the other β(2)m analyzed, although basic structural features have been retained through evolution.
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Affiliation(s)
- Chee-Seng Hee
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität Berlin, Thielallee 73, 14195 Berlin, Germany
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37
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Hodkinson JP, Radford SE, Ashcroft AE. The role of conformational flexibility in β2-microglobulin amyloid fibril formation at neutral pH. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:1783-92. [PMID: 22777780 PMCID: PMC3568905 DOI: 10.1002/rcm.6282] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
RATIONALE Amyloid formation is implicated in a number of human diseases. β(2)-Microglobulin (β(2)m) is the precursor protein in dialysis-related amyloidosis and it has been shown that partial, or more complete, unfolding is key to amyloid fibril formation in this pathology. Here the relationship between conformational flexibility and β(2)m amyloid formation at physiological pH has been investigated. METHODS HDX-ESI-MS was used to study the conformational dynamics of β(2)m. Protein engineering, or the addition of Cu(2+) ions, sodium dodecyl sulphate, trifluoroethanol, heparin, or protein stabilisers, was employed to perturb the conformational dynamics of β(2)m. The fibril-forming propensities of the protein variants and the wild-type protein in the presence of additives, which resulted in >5-fold increase in the EX1 rate of HDX, were investigated further. RESULTS ESI-MS revealed that HDX occurs via a mixed EX1/EX2 mechanism under all conditions. Urea denaturation and tryptophan fluorescence indicated that EX1 exchange occurred from a globally unfolded state in wild-type β(2)m. Although >30-fold increase in the HDX exchange rate was observed both for the protein variants and for the wild-type protein in the presence of specific additives, large increases in exchange rate did not necessarily result in extensive de novo fibril formation. CONCLUSIONS The conformational dynamics measured by the EX1 rate of HDX do not predict the ability of β(2)m to form amyloid fibrils de novo at neutral pH. This suggests that the formation of amyloid fibrils from β(2)m at neutral pH is dependent on the generation of one or more specific aggregation-competent species which facilitate self-assembly.
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Affiliation(s)
- John P Hodkinson
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT UK
- Correspondence S. E. Radford or A. E. Ashcroft, Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. E-mail: ;
| | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT UK
- Correspondence S. E. Radford or A. E. Ashcroft, Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. E-mail: ;
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38
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Dalal V, Bhattacharya M, Narang D, Sharma PK, Mukhopadhyay S. Nanoscale Fluorescence Imaging of Single Amyloid Fibrils. J Phys Chem Lett 2012; 3:1783-1787. [PMID: 26291859 DOI: 10.1021/jz300687f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Amyloid formation is implicated in a variety of human diseases. It is important to perform high-resolution optical imaging of individual amyloid fibrils to delineate the structural basis of supramolecular protein assembly. However, amyloid fibrils do not lend themselves to the conventional microscopic resolution, which is hindered by the diffraction limit. Here we show super-resolution fluorescence imaging of fluorescently stained amyloid fibrils derived from disease-associated human β2-microglobulin using near-field scanning fluorescence microscopy. Using this technique, we were able to resolve the fibrils that were spatially separated by ∼75 nm. We have also been able to interrogate individual fibrils in a fibril-by-fibril manner by simultaneously monitoring both nanoscale topography and fluorescence brightness along the length of the fibrils. This method holds promise to detect conformational distributions and heterogeneity that are believed to correlate with the supramolecular packing of misfolded proteins within the fibrils in a diverse conformationally enciphered prion strains and amyloid polymorphs.
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Affiliation(s)
- Vijit Dalal
- †Department of Biological Sciences and ‡Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali 140306, India
| | - Mily Bhattacharya
- †Department of Biological Sciences and ‡Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali 140306, India
| | - Dominic Narang
- †Department of Biological Sciences and ‡Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali 140306, India
| | - Pushpender K Sharma
- †Department of Biological Sciences and ‡Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali 140306, India
| | - Samrat Mukhopadhyay
- †Department of Biological Sciences and ‡Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali 140306, India
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39
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Fändrich M. Oligomeric intermediates in amyloid formation: structure determination and mechanisms of toxicity. J Mol Biol 2012; 421:427-40. [PMID: 22248587 DOI: 10.1016/j.jmb.2012.01.006] [Citation(s) in RCA: 281] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 01/03/2012] [Accepted: 01/05/2012] [Indexed: 11/30/2022]
Abstract
Oligomeric intermediates are non-fibrillar polypeptide assemblies that occur during amyloid fibril formation and that are thought to underlie the aetiology of amyloid diseases, such as Alzheimer's disease, Parkinson's disease and Huntington's disease. Focusing primarily on the oligomeric states formed from Alzheimer's disease β-amyloid (Aβ) peptide, this review will make references to other polypeptide systems, highlighting common principles or sequence-specific differences. The covered topics include the structural properties and polymorphism of oligomers, the biophysical mechanism of peptide self-assembly and its role for pathogenicity in amyloid disease. Oligomer-dependent toxicity mechanisms will be explained along with recently emerging possibilities of interference.
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Affiliation(s)
- Marcus Fändrich
- Max-Planck Research Unit for Enzymology of Protein Folding and Martin Luther University Halle-Wittenberg, Weinbergweg 22, 01620 Halle (Saale), Germany.
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40
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McGlinchey RP, Gruschus JM, Nagy A, Lee JC. Probing fibril dissolution of the repeat domain of a functional amyloid, Pmel17, on the microscopic and residue level. Biochemistry 2011; 50:10567-9. [PMID: 22092386 PMCID: PMC3232329 DOI: 10.1021/bi201578h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pmel17 is a human amyloid involved in melanin synthesis. A fragment of Pmel17, the repeat domain (RPT) rich in glutamic acids, forms amyloid only at mildly acidic pH. Unlike pathological amyloids, these fibrils dissolve at neutral pH, supporting a reversible aggregation-disaggregation process. Here, we study RPT dissolution using atomic force microscopy and solution-state nuclear magnetic resonance spectroscopy. Our results reveal asymmetric fibril disassembly proceeding in the absence of intermediates. We suggest that fibril unfolding involves multiple deprotonation events resulting in electrostatic charge repulsion and filament dissolution.
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Affiliation(s)
- Ryan P. McGlinchey
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - James M. Gruschus
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Attila Nagy
- Laboratory of Molecular Physiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jennifer C. Lee
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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41
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Azinas S, Colombo M, Barbiroli A, Santambrogio C, Giorgetti S, Raimondi S, Bonomi F, Grandori R, Bellotti V, Ricagno S, Bolognesi M. D-strand perturbation and amyloid propensity in beta-2 microglobulin. FEBS J 2011; 278:2349-58. [PMID: 21569201 DOI: 10.1111/j.1742-4658.2011.08157.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Proteins hosting main β-sheets adopt specific strategies to avoid intermolecular interactions leading to aggregation and amyloid deposition. Human beta-2 microglobulin (β2m) displays a typical immunoglobulin fold and is known to be amyloidogenic in vivo. Upon severe kidney deficiency, β2m accumulates in the bloodstream, triggering, over the years, pathological deposition of large amyloid aggregates in joints and bones. A β-bulge observed on the edge D β-strand of some β2m crystal structures has been suggested to be crucial in protecting the protein from amyloid aggregation. Conversely, a straight D-strand, observed in different crystal structures of monomeric β2m, could promote amyloid aggregation. More recently, the different conformations observed for the β2m D-strand have been interpreted as the result of intrinsic flexibility, rather than being assigned to a functional protective role against aggregation. To shed light on such contrasting picture, the mutation Asp53→Pro was engineered in β2m, aiming to impair the formation of a regular/straight D-strand. Such a mutant was characterized structurally and biophysically by CD, X-ray crystallography and MS, in addition to an assessment of its amyloid aggregation trends in vitro. The results reported in the present study highlight the conformational plasticity of the edge D-strand, and show that even perturbing the D-strand structure through a Pro residue has only marginal effects on protecting β2m from amyloid aggregation in vitro.
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Affiliation(s)
- Stavros Azinas
- Dipartimento di Scienze Biomolecolari e Biotecnologie and CIMAINA, Università degli Studi di Milano, Milan, Italy
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42
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Buell AK, Dhulesia A, Mossuto MF, Cremades N, Kumita JR, Dumoulin M, Welland ME, Knowles TP, Salvatella X, Dobson CM. Population of nonnative states of lysozyme variants drives amyloid fibril formation. J Am Chem Soc 2011; 133:7737-7743. [PMID: 21528861 PMCID: PMC4982536 DOI: 10.1021/ja109620d] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The propensity of protein molecules to self-assemble into highly ordered, fibrillar aggregates lies at the heart of understanding many disorders ranging from Alzheimer's disease to systemic lysozyme amyloidosis. In this paper we use highly accurate kinetic measurements of amyloid fibril growth in combination with spectroscopic tools to quantify the effect of modifications in solution conditions and in the amino acid sequence of human lysozyme on its propensity to form amyloid fibrils under acidic conditions. We elucidate and quantify the correlation between the rate of amyloid growth and the population of nonnative states, and we show that changes in amyloidogenicity are almost entirely due to alterations in the stability of the native state, while other regions of the global free-energy surface remain largely unmodified. These results provide insight into the complex dynamics of a macromolecule on a multidimensional energy landscape and point the way for a better understanding of amyloid diseases.
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Affiliation(s)
- Alexander K. Buell
- Nanoscience Centre, University of Cambridge, 11 JJ Thomson Avenue, Cambridge CB3 0FF, UK
| | - Anne Dhulesia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Maria F. Mossuto
- Institute for Research in Biomedicine (IRB), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Nunilo Cremades
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Janet R. Kumita
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Mireille Dumoulin
- Centre for Protein Engineering, University of Liège, Sart Tilman, 4000 Liège, Belgium
| | - Mark E. Welland
- Nanoscience Centre, University of Cambridge, 11 JJ Thomson Avenue, Cambridge CB3 0FF, UK
| | - Tuomas P.J. Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB), Baldiri Reixac 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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43
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Gierasch LM. How one bad protein spoils the barrel: structural details of β2-microglobulin amyloidogenicity. Mol Cell 2011; 41:129-31. [PMID: 21255721 DOI: 10.1016/j.molcel.2011.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In this issue, Eichner et al. (2011) describe at atomic resolution the structure of an amyloidogenic state of β(2)-microglobulin and how it may corrupt a soluble counterpart in the pathological scenario that ensues when good proteins go to the "dark side'" and form infectious toxic amyloid.
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Affiliation(s)
- Lila M Gierasch
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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44
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Eichner T, Kalverda AP, Thompson GS, Homans SW, Radford SE. Conformational conversion during amyloid formation at atomic resolution. Mol Cell 2011; 41:161-72. [PMID: 21255727 PMCID: PMC3029554 DOI: 10.1016/j.molcel.2010.11.028] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 10/12/2010] [Accepted: 11/01/2010] [Indexed: 01/19/2023]
Abstract
Numerous studies of amyloid assembly have indicated that partially folded protein species are responsible for initiating aggregation. Despite their importance, the structural and dynamic features of amyloidogenic intermediates and the molecular details of how they cause aggregation remain elusive. Here, we use ΔN6, a truncation variant of the naturally amyloidogenic protein β2-microglobulin (β2m), to determine the solution structure of a nonnative amyloidogenic intermediate at high resolution. The structure of ΔN6 reveals a major repacking of the hydrophobic core to accommodate the nonnative peptidyl-prolyl trans-isomer at Pro32. These structural changes, together with a concomitant pH-dependent enhancement in backbone dynamics on a microsecond-millisecond timescale, give rise to a rare conformer with increased amyloidogenic potential. We further reveal that catalytic amounts of ΔN6 are competent to convert nonamyloidogenic human wild-type β2m (Hβ2m) into a rare amyloidogenic conformation and provide structural evidence for the mechanism by which this conformational conversion occurs.
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Affiliation(s)
- Timo Eichner
- Astbury Centre for Structural Molecular Biology and Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
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45
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Liu C, Sawaya MR, Eisenberg D. β₂-microglobulin forms three-dimensional domain-swapped amyloid fibrils with disulfide linkages. Nat Struct Mol Biol 2011; 18:49-55. [PMID: 21131979 PMCID: PMC3058263 DOI: 10.1038/nsmb.1948] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 09/16/2010] [Indexed: 01/07/2023]
Abstract
β₂-microglobulin (β₂m) is the light chain of the type I major histocompatibility complex. It deposits as amyloid fibrils within joints during long-term hemodialysis treatment. Despite the devastating effects of dialysis-related amyloidosis, full understanding of how fibrils form from soluble β₂m remains elusive. Here we show that β₂m can oligomerize and fibrillize via three-dimensional domain swapping. Isolating a covalently bound, domain-swapped dimer from β₂m oligomers on the pathway to fibrils, we were able to determine its crystal structure. The hinge loop that connects the swapped domain to the core domain includes the fibrillizing segment LSFSKD, whose atomic structure we also determined. The LSFSKD structure reveals a class 5 steric zipper, akin to other amyloid spines. The structures of the dimer and the zipper spine fit well into an atomic model for this fibrillar form of β₂m, which assembles slowly under physiological conditions.
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46
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Debelouchina GT, Platt GW, Bayro MJ, Radford SE, Griffin RG. Intermolecular alignment in β2-microglobulin amyloid fibrils. J Am Chem Soc 2010. [PMID: 21077676 DOI: 10.1021/ja1079871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
The deposition of amyloid-like fibrils, composed primarily of the 99-residue protein β2-microglobulin (β2m), is one of the characteristic symptoms of dialysis-related amyloidosis. Fibrils formed in vitro at low pH and low salt concentration share many properties with the disease related fibrils and have been extensively studied by a number of biochemical and biophysical methods. These fibrils contain a significant β-sheet core and have a complex cryoEM electron density profile. Here, we investigate the intrasheet arrangement of the fibrils by means of (15)N-(13)C MAS NMR correlation spectroscopy. We utilize a fibril sample grown from a 50:50 mixture of (15)N,(12)C- and (14)N,(13)C-labeled β2m monomers, the latter prepared using 2-(13)C glycerol as the carbon source. Together with the use of ZF-TEDOR mixing, this sample allowed us to observe intermolecular (15)N-(13)C backbone-to-backbone contacts with excellent resolution and good sensitivity. The results are consistent with a parallel, in-register arrangement of the protein subunits in the fibrils and suggest that a significant structural reorganization occurs from the native to the fibril state.
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Affiliation(s)
- Galia T Debelouchina
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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47
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Debelouchina GT, Platt GW, Bayro MJ, Radford SE, Griffin RG. Intermolecular alignment in β2-microglobulin amyloid fibrils. J Am Chem Soc 2010; 132:17077-9. [PMID: 21077676 PMCID: PMC2996106 DOI: 10.1021/ja107987f] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2010] [Indexed: 11/29/2022]
Abstract
The deposition of amyloid-like fibrils, composed primarily of the 99-residue protein β2-microglobulin (β2m), is one of the characteristic symptoms of dialysis-related amyloidosis. Fibrils formed in vitro at low pH and low salt concentration share many properties with the disease related fibrils and have been extensively studied by a number of biochemical and biophysical methods. These fibrils contain a significant β-sheet core and have a complex cryoEM electron density profile. Here, we investigate the intrasheet arrangement of the fibrils by means of (15)N-(13)C MAS NMR correlation spectroscopy. We utilize a fibril sample grown from a 50:50 mixture of (15)N,(12)C- and (14)N,(13)C-labeled β2m monomers, the latter prepared using 2-(13)C glycerol as the carbon source. Together with the use of ZF-TEDOR mixing, this sample allowed us to observe intermolecular (15)N-(13)C backbone-to-backbone contacts with excellent resolution and good sensitivity. The results are consistent with a parallel, in-register arrangement of the protein subunits in the fibrils and suggest that a significant structural reorganization occurs from the native to the fibril state.
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Affiliation(s)
- Galia T Debelouchina
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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48
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Santambrogio C, Ricagno S, Colombo M, Barbiroli A, Bonomi F, Bellotti V, Bolognesi M, Grandori R. DE-loop mutations affect beta2 microglobulin stability, oligomerization, and the low-pH unfolded form. Protein Sci 2010; 19:1386-94. [PMID: 20506535 DOI: 10.1002/pro.419] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Beta2 microglobulin (beta2m) is the light chain of class-I major histocompatibility complex (MHC-I). Its accumulation in the blood of patients affected by kidney failure leads to amyloid deposition around skeletal joints and bones, a severe condition known as Dialysis Related Amyloidosis (DRA). In an effort to dissect the structural determinants of beta2m aggregation, several beta2m mutants have been previously studied. Among these, three single-residue mutations in the loop connecting strands D and E (W60G, W60V, D59P) have been shown to affect beta2m amyloidogenic properties, and are here considered. To investigate the biochemical and biophysical properties of wild-type (w.t.) beta2m and the three mutants, we explored thermal unfolding by Trp fluorescence and circular dichroism (CD). The W60G mutant reveals a pronounced increase in conformational stability. Protein oligomerization and reduction kinetics were investigated by electrospray-ionization mass spectrometry (ESI-MS). All the mutations analyzed here reduce the protein propensity to form soluble oligomers, suggesting a role for the DE-loop in intermolecular interactions. A partially folded intermediate, which may be involved in protein aggregation induced by acids, accumulates for all the tested proteins at pH 2.5 under oxidizing conditions. Moreover, the kinetics of disulfide reduction reveals specific differences among the tested mutants. Thus, beta2m DE-loop mutations display long-range effects, affecting stability and structural properties of the native protein and its low-pH intermediate. The evidence presented here hints to a crucial role played by the DE-loop in determining the overall properties of native and partially folded beta2m.
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Affiliation(s)
- Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
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49
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Debelouchina GT, Platt GW, Bayro MJ, Radford SE, Griffin RG. Magic angle spinning NMR analysis of beta2-microglobulin amyloid fibrils in two distinct morphologies. J Am Chem Soc 2010; 132:10414-23. [PMID: 20662519 PMCID: PMC2919207 DOI: 10.1021/ja102775u] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Beta(2)-microglobulin (beta(2)m) is the major structural component of amyloid fibrils deposited in a condition known as dialysis-related amyloidosis. Despite numerous studies that have elucidated important aspects of the fibril formation process in vitro, and a magic angle spinning (MAS) NMR study of the fibrils formed by a small peptide fragment, structural details of beta(2)m fibrils formed by the full-length 99-residue protein are largely unknown. Here, we present a site-specific MAS NMR analysis of fibrils formed by the full-length beta(2)m protein and compare spectra of fibrils prepared under two different conditions. Specifically, long straight (LS) fibrils are formed at pH 2.5, while a very different morphology denoted as worm-like (WL) fibrils is observed in preparations at pH 3.6. High-resolution MAS NMR spectra have allowed us to obtain (13)C and (15)N resonance assignments for 64 residues of beta(2)m in LS fibrils, including part of the highly mobile N-terminus. Approximately 25 residues did not yield observable signals. Chemical shift analysis of the sequentially assigned residues indicates that these fibrils contain an extensive beta-sheet core organized in a non-native manner, with a trans-P32 conformation. In contrast, WL fibrils exhibit more extensive dynamics and appear to have a smaller beta-sheet core than LS fibrils, although both cores seem to share some common elements. Our results suggest that the distinct macroscopic morphological features observed for the two types of fibrils result from variations in structure and dynamics at the molecular level.
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Affiliation(s)
- Galia T. Debelouchina
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Geoffrey W. Platt
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Marvin J. Bayro
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - 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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50
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Ashcroft AE. Mass spectrometry and the amyloid problem--how far can we go in the gas phase? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1087-1096. [PMID: 20363648 DOI: 10.1016/j.jasms.2010.02.026] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Revised: 02/16/2010] [Accepted: 02/19/2010] [Indexed: 05/29/2023]
Abstract
A number of proteins are capable of converting from their soluble, monomeric form into highly-ordered, insoluble aggregates known as amyloid fibrils. In vivo, these fibrils, which accumulate in organs and tissues, are associated with a wide range of amyloid diseases for which there are currently no therapeutic solutions. The molecular details of the pathway from native monomer through oligomeric intermediates to the final amyloid fibril remain a challenging enigma. Over the past few years, mass spectrometry has been applied to investigate the various stages of amyloid fibril formation, and this report summarizes the key steps achieved to date.
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Affiliation(s)
- Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom.
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